Increased susceptibility to repeated freeze-thaw cycles in Escherichia coli following long-term evolution in a benign environment

BACKGROUND: In order to study the dynamics of evolutionary change, 12 populations of E. coli B were serially propagated for 20,000 generations in minimal glucose medium at constant 37°C. Correlated changes in various other traits have been previously associated with the improvement in competitive fitness in the selective environment. This study examines whether these evolved lines changed in their ability to tolerate the stresses of prolonged freezing and repeated freeze-thaw cycles during adaptation to a benign environment. RESULTS: All 12 lines that evolved in the benign environment for 20,000 generations are more sensitive to freeze-thaw cycles than their ancestor. The evolved lines have an average mortality rate of 54% per daily cycle, compared to the ancestral rate of 34%. By contrast, there was no significant difference between the evolved lines and their ancestor in mortality during prolonged freezing. There was also some variability among the evolved lines in susceptibility to repeated freeze-thaw cycles. Those lines that had evolved higher competitive fitness in the minimal glucose medium at 37°C also had higher mortality during freeze-thaw cycles. This variability was not associated, however, with differences among lines in DNA repair functionality and mutability. CONCLUSION: The consistency of the evolutionary declines in freeze-thaw tolerance, the correlation between fitness in glucose medium at 37°C and mortality during freeze-thaw cycles, and the absence of greater declines in freeze-thaw survival among the hypermutable lines all indicate a trade-off between performance in minimal glucose medium at 37°C and the capacity to tolerate this stress. Analyses of the mutations that enhance fitness at 37°C may shed light on the physiological basis of this trade-off

Non-uraninite products of microbial U(VI) reduction

A promising remediation approach to mitigate subsurface uranium contamination is the stimulation of indigenous bacteria to reduce mobile U(VI) to sparingly soluble U(IV). The product of microbial uranium reduction is often reported as the mineral uraninite. Here, we show that the end products of uranium reduction by several environmentally relevant bacteria (Gram-positive and Gram-negative) and their spores include a variety of U(IV) species other than uraninite. U(IV) products were prepared in chemically variable media and characterized using transmission electron microscopy (TEM) and X-ray absorption spectroscopy (XAS) to elucidate the factors favoring/inhibiting uraninite formation and to constrain molecular structure/composition of the non-uraninite reduction products. Molecular complexes of U(IV) were found to be bound to biomass, most likely through P-containing ligands. Minor U(IV)-orthophosphates such as ningyoite [CaU(PO4)(2)], U2O(PO4)(2), and U-2(PO4)(P3O10) were observed in addition to uraninite. Although factors controlling the predominance of these species are complex, the presence of various solutes was found to generally inhibit uraninite formation. These results suggest a new paradigm for U(IV) in the subsurface, i.e., that non-uraninite U(IV) products may be found more commonly than anticipated. These findings are relevant for bioremediation strategies and underscore the need for characterizing the stability of non-uraninite U(IV) species in natural settings

Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. The identification of novel associations for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A; and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability to smell the methanethiol produced after eating asparagus (rs4481887, near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and rs11856995, near NR2F2) illustrates the power of the approach

C2 and CFB Genes in Age-Related Maculopathy and Joint Action with CFH and LOC387715 Genes

Background: Age-related maculopathy (ARM) is a common cause of visual impairment in the elderly populations of industrialized countries and significantly affects the quality of life of those suffering from the disease. Variants within two genes, the complement factor H (CFH) and the poorly characterized LOC387715 (ARMS2), are widely recognized as ARM risk factors. CFH is important in regulation of the alternative complement pathway suggesting this pathway is involved in ARM pathogenesis. Two other complement pathway genes, the closely linked complement component receptor (C2) and complement factor B (CFB), were recently shown to harbor variants associated with ARM. Methods/Principal Findings: We investigated two SNPs in C2 and two in CFB in independent case-control and family cohorts of white subjects and found rs547154, an intronic SNP in C2, to be significantly associated with ARM in both our case-control (P-value 0.00007) and family data (P-value 0.00001). Logistic regression analysis suggested that accounting for the effect at this locus significantly (P-value 0.002) improves the fit of a genetic risk model of CFH and LOC387715 effects only. Modeling with the generalized multifactor dimensionality reduction method showed that adding C2 to the two-factor model of CFH and LOC387715 increases the sensitivity (from 63% to 73%). However, the balanced accuracy increases only from 71% to 72%, and the specificity decreases from 80% to 72%. Conclusions/Significance: C2/CFB significantly influences AMD susceptibility and although accounting for effects at this locus does not dramatically increase the overall accuracy of the genetic risk model, the improvement over the CFH-LOC387715 model is statistically significant. © 2008 Jakobsdottir et al

Long-Range Electron Transfer across Cytochrome-Hematite (alpha-Fe2O3) Interfaces

Electrochemical scanning tunneling microscopy was used to assess the distance dependence of electron transfer facilitated by a bacterial multiheme cytochrome to a single crystal iron oxide surface. We measured tunneling current-distance (I-s) profiles across the nanoscale space between Au STM tips and the basal (001) surface of a hematite (alpha-Fe2O3) crystal and compared them to the case in which an intervening small tetraheme cytochrome (STC) from Shewanella oneidensis was covalently linked to the end of the Au tip. Tunneling profiles were collected at constant surface potentials in solutions having a range of ionic strengths. For the case without intervening cytochrome, at short tip-sample separation, the distance dependence of the tunneling current shows a quasi-linear behavior, whereas at longer distances, near-exponential decay is observed. The different regions can be understood first in terms of reduction of interfacial water and ion layers in the electrical double layer associated with the hematite surface, followed by electron tunneling through bulk water. The effective tunneling range and the transition between the two conduction mechanisms are substantially increased when STC is present in the tunneling junction, suggesting that cytochrome molecules provide enhanced tunneling pathways and stronger electronic coupling to the hematite surface. On the basis of these results, cytochrome-mediated electron transfer during bacterial metal reduction may be possible at distances farther than originally speculated. In addition, as multiheme cytochromes and other similar molecules gain attention for their promising role in fuel cells and molecular electronics, we demonstrate that the solution conditions and surface properties of the substrate must be carefully considered