The ins and outs of metal homeostasis by the root nodule actinobacterium Frankia

Background: Frankia are actinobacteria that form a symbiotic nitrogen-fixing association with actinorhizal plants, and play a significant role in actinorhizal plant colonization of metal contaminated areas. Many Frankia strains are known to be resistant to several toxic metals and metalloids including Pb2+, Al+3, SeO2, Cu2+, AsO4, and Zn2+. With the availability of eight Frankia genome databases, comparative genomics approaches employing phylogeny, amino acid composition analysis, and synteny were used to identify metal homeostasis mechanisms in eight Frankia strains. Characterized genes from the literature and a meta-analysis of 18 heavy metal gene microarray studies were used for comparison. Results: Unlike most bacteria, Frankia utilize all of the essential trace elements (Ni, Co, Cu, Se, Mo, B, Zn, Fe, and Mn) and have a comparatively high percentage of metalloproteins, particularly in the more metal resistant strains. Cation diffusion facilitators, being one of the few known metal resistance mechanisms found in the Frankia genomes, were strong candidates for general divalent metal resistance in all of the Frankia strains. Gene duplication and amino acid substitutions that enhanced the metal affinity of CopA and CopCD proteins may be responsible for the copper resistance found in some Frankia strains. CopA and a new potential metal transporter, DUF347, may be involved in the particularly high lead tolerance in Frankia. Selenite resistance involved an alternate sulfur importer (CysPUWA) that prevents sulfur starvation, and reductases to produce elemental selenium. The pattern of arsenate, but not arsenite, resistance was achieved by Frankia using the novel arsenite exporter (AqpS) previously identified in the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Based on the presence of multiple tellurite resistance factors, a new metal resistance (tellurite) was identified and confirmed in Frankia. Conclusions: Each strain had a unique combination of metal import, binding, modification, and export genes that explain differences in patterns of metal resistance between strains. Frankia has achieved similar levels of metal and metalloid resistance as bacteria from highly metal-contaminated sites. From a bioremediation standpoint, it is important to understand mechanisms that allow the endosymbiont to survive and infect actinorhizal plants in metal contaminated soils

Coupling bioturbation activity to metal (Fe and Mn) profiles in situ

This work was supported by a University of Aberdeen 6th century scholarship (awarded to L. T.), CEFAS Lowestoft (DP204), NERC NFSD support (08/02) and a SAMS research bursary (awarded to L. T)Peer reviewedPublisher PD

Simultaneous determination of in situ vertical transitions of color, pore-water metals, and visualization of infaunal activity in marine sediments

The vertical color transition from brown to gray-green in marine sediments is linked to the Fe redox boundary and is commonly used as a proxy for biogeochemical state. We combine time-lapse sediment profile imaging with diffusive gradient thin (DGT) gels to obtain simultaneous in situ measurements of sediment color profiles, pore-water Fe and Mn profiles, and qualitative estimates of faunal activity at the Oyster Ground and North Dogger (North Sea). Analysis of Fe and Mn profiles using generalized additive modeling reveals that high variability between profiles within the sites makes it difficult to determine any intersite differences in trace metal behavior. At the Oyster Ground, the depth of sediment color transition (4.78 +/- 0.76 cm) was not significantly different from the Fe redox boundary (7.67 +/- 4.04 cm). At the North Dogger, there was a significant discrepancy between the depth of the sediment color transition (2.86 +/- 0.78 cm) and the Fe redox boundary (10.17 +/- 1.04 cm), which most likely results from high sulfate reduction rates at the North Dogger, leading to complexation of reduced iron to a form not available to the DGT technique. The differences in the coupling of sediment color and the Fe redox boundary between stations is likely to be related to variations in recent infaunal bioturbation activity, rather than variations in sediment source or fundamental differences in bulk sediment chemistry. Our results highlight the importance of the infaunal community in mediating Fe and Mn cycles, which are key pathways in the degradation of organic matter, and suggest that descriptions of bulk chemistry alone may be insufficient to understand the dynamics of biogeochemical cycling

Culture Clash: The Medical Encounter as a Source of Health Disparities

In 2002, the Institute of Medicine (IOM) issued its landmark report entitled Unequal Treatment: Confronting Racial and Ethnic Disparities in Health Care. The report identified three potential sources of healthcare disparities for minority and other underserved communities - patient-level factors, healthcare system-level factors, and care process-level factors. Care process-level factors included issues such as bias, stereotyping, prejudice and clinical uncertainty on the part of healthcare providers. Recommendations to address these factors included a call for additional research, interventions to enhance patient-provider communication, and integration of cross-cultural education into the training of all current and future health professionals. In this presentation, I will briefly review models of health disparities and the role of provider beliefs in these disparities. I will describe various forms of bias (e.g., stereotypes, prejudice,implicit, explicit) and patient-level outcomes of experiencing bias. I will discuss the current research into provider bias and its limitations. Finally, I will discuss the relationship of cultural competence to bias. Specifically, I will propose a model for Culturally Competent Communication and how the use of the model for assessing and training provider behavior could serve as a framework for addressing provider bias as a cause of health disparities

Review of the spatial and temporal distribution by life stage for 19 North Sea fish species

Considering the increase in human activity in the North Sea, particularly cargo shipping and the rapidly expanding construction and operation of oil platforms and wind farms, as well as the continued use of the area for military purposes, fisheries and sand extraction, there is a growing concern about the potentially harmful impacts of such anthropogenic activities on marine life. Particular concerns have been raised about the effect of loud impulse sounds and high noise levels, which may affect marine animal life in different ways: habitat use, such as feeding and migration, and reproduction patterns may be disturbed. In the extreme case animals may suffer from sub-lethal or lethal physical damage such as hearing loss and disrupted swim ladders. Knowledge of the spatial distribution and seasonal patterns in the presence of different life stages of marine species is therefore critical for assessing to what extent the dispersion of marine life overlaps with the distribution of human activities and for estimating how potentially harmful impacts can be mitigated both spatially and temporally. The aim of this desk study is consequently to provide a concise overview of existing information on seasonal patterns in the dispersion of fish species in the North Sea, in particular by highlighting the knowledge gaps

Applications of the Quantum Algorithm for st-Connectivity

We present quantum algorithms for various problems related to graph connectivity. We give simple and query-optimal algorithms for cycle detection and odd-length cycle detection (bipartiteness) using a reduction to st-connectivity. Furthermore, we show that our algorithm for cycle detection has improved performance under the promise of large circuit rank or a small number of edges. We also provide algorithms for detecting even-length cycles and for estimating the circuit rank of a graph. All of our algorithms have logarithmic space complexity

A Local Search Algorithm for the Min-Sum Submodular Cover Problem

We consider the problem of solving the Min-Sum Submodular Cover problem using local search. The Min-Sum Submodular Cover problem generalizes the NP-complete Min-Sum Set Cover problem, replacing the input set cover instance with a monotone submodular set function. A simple greedy algorithm achieves an approximation factor of 4, which is tight unless P=NP [Streeter and Golovin, NeurIPS, 2008]. We complement the greedy algorithm with analysis of a local search algorithm. Building on work of Munagala et al. [ICDT, 2005], we show that, using simple initialization, a straightforward local search algorithm achieves a $(4+\epsilon)$-approximate solution in time $O(n^3\log(n/\epsilon))$, provided that the monotone submodular set function is also second-order supermodular. Second-order supermodularity has been shown to hold for a number of submodular functions of practical interest, including functions associated with set cover, matching, and facility location. We present experiments on two special cases of Min-Sum Submodular Cover and find that the local search algorithm can outperform the greedy algorithm on small data sets

Robust and Space-Efficient Dual Adversary Quantum Query Algorithms

The general adversary dual is a powerful tool in quantum computing because it gives a query-optimal bounded-error quantum algorithm for deciding any Boolean function. Unfortunately, the algorithm uses linear qubits in the worst case, and only works if the constraints of the general adversary dual are exactly satisfied. The challenge of improving the algorithm is that it is brittle to arbitrarily small errors since it relies on a reflection over a span of vectors. We overcome this challenge and build a robust dual adversary algorithm that can handle approximately satisfied constraints. As one application of our robust algorithm, we prove that for any Boolean function with polynomially many 1-valued inputs (or in fact a slightly weaker condition) there is a query-optimal algorithm that uses logarithmic qubits. As another application, we prove that numerically derived, approximate solutions to the general adversary dual give a bounded-error quantum algorithm under certain conditions. Further, we show that these conditions empirically hold with reasonable iterations for Boolean functions with small domains. We also develop several tools that may be of independent interest, including a robust approximate spectral gap lemma, a method to compress a general adversary dual solution using the Johnson-Lindenstrauss lemma, and open-source code to find solutions to the general adversary dual