Characterizing organic carbon dynamics during biostimulation of a uranium contaminated field site

Uranium contamination of groundwater remains a pressing problem at many former uranium mining and milling operations, such as the Rifle, Integrated Field Research Challenge (IFRC) site. Biostimulation of the subsurface with an organic carbon source such as acetate, followed by the microbially-induced reductive precipitation of uranium has been proposed as an effective remediation strategy. While uranium bioreduction has been studied in several field experiments, the transformation and fate of injected carbon remains poorly understood. This study evaluated the impact of added organic carbon on the long-term biogeochemical attenuation of uranium in the subsurface of a former mill tailings site. Fluorescence and ultraviolet–visible absorbance analyses were used together with dissolved organic carbon (DOC) measurements to track organic carbon dynamics during and post-biostimulation of the 2011 Rifle IFRC experiment. An electron mass balance was performed on well CD01 to account for any unidentified carbon sinks. Measured DOC values increased to 1.76 mM-C during biostimulation, and to 3.18 mM-C post-biostimulation over background DOC values of 0.3–0.4 mM-C. Elevated DOC levels persisted for 90 days after acetate injections ceased. The electron mass balance revealed that assumed electron acceptors would not account for the total amount of acetate consumed. Excitation–emission matrices showed an increase in signals associated with soluble microbial products, during biostimulation, which disappeared post-biostimulation despite an increase in total DOC. Specific ultraviolet absorbance analyses, indicated that DOC present post-biostimulation is less aromatic in nature, compared to background DOC. Our results suggest that microbes convert injected acetate into a form of solid phase organic matter that may be available to sustain iron reduction post-stimulation

XMM-Newton and NuSTAR Observations of the Compact Millisecond Pulsar Binary PSR J1653–0158

We have presented the first joint XMM-Newton and NuSTAR analysis of the millisecond pulsar (MSP) binary PSR J1653−0158. The 75 minute orbital period inferred from optical and gamma-ray observations together with the 1.97 ms pulsation in the gamma-rays indicate that this system is the most compact Black Widow MSP system known to date. The orbital period was not detected in the XMM-Newton and NuSTAR data, probably due to insufficient photon counts obtained in the observations. Fitting the joint X-ray spectrum of PSR J1653−0158 with a power law gives a photon index Γ = 1.71 ± 0.09. The X-ray luminosity of the source in the (0.2–40) keV band is deduced to be 1.18 × 1031 erg s−1, for an adopted distance of 0.84 kpc. We have shown that the broadband X-ray spectrum can be explained by synchrotron radiation from electrons accelerated in the intrabinary shock, and the gamma-rays detected in the Fermi data are curvature radiations from electrons and positrons in the pulsar magnetosphere. Our kinematic analysis of the Tidarren systems PSR J1653–0158 and PSR J1311–3430 indicates that the two Tidarren systems are likely to have originated in the Galactic disk

A web services choreography scenario for interoperating bioinformatics applications

BACKGROUND: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. RESULTS: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). CONCLUSION: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow

A suite of web applications to streamline the interdisciplinary collaboration in secondary data analyses

BACKGROUND: We describe a system of web applications designed to streamline the interdisciplinary collaboration in outcomes research. DESCRIPTION: The outcomes research process can be described as a set of three interrelated phases: design and selection of data sources, analysis, and output. Each of these phases has inherent challenges that can be addressed by a group of five web applications developed by our group. QuestForm allows for the formulation of relevant and well-structured outcomes research questions; Research Manager facilitates the project management and electronic file exchange among researchers; Analysis Charts facilitate the communication of complex statistical techniques to clinicians with varying previous levels of statistical knowledge; Literature Matrices improve the efficiency of literature reviews. An outcomes research question is used to illustrate the use of the system. CONCLUSIONS: The system presents an alternative to streamline the interdisciplinary collaboration of clinicians, statisticians, programmers, and graduate students

Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection

Many new gene copies emerged by gene duplication in hominoids, but little is known with respect to their functional evolution. Glutamate dehydrogenase (GLUD) is an enzyme central to the glutamate and energy metabolism of the cell. In addition to the single, GLUD-encoding gene present in all mammals (GLUD1), humans and apes acquired a second GLUD gene (GLUD2) through retroduplication of GLUD1, which codes for an enzyme with unique, potentially brain-adapted properties. Here we show that whereas the GLUD1 parental protein localizes to mitochondria and the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using evolutionary analysis and resurrected ancestral protein variants, we demonstrate that the enhanced mitochondrial targeting specificity of GLUD2 is due to a single positively selected glutamic acid-to-lysine substitution, which was fixed in the N-terminal mitochondrial targeting sequence (MTS) of GLUD2 soon after the duplication event in the hominoid ancestor ~18–25 million years ago. This MTS substitution arose in parallel with two crucial adaptive amino acid changes in the enzyme and likely contributed to the functional adaptation of GLUD2 to the glutamate metabolism of the hominoid brain and other tissues. We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

Frequency Shift of Carbon-Nanotube-Based Mass Sensor Using Nonlocal Elasticity Theory

The frequency equation of carbon-nanotube-based cantilever sensor with an attached mass is derived analytically using nonlocal elasticity theory. According to the equation, the relationship between the frequency shift of the sensor and the attached mass can be obtained. When the nonlocal effect is not taken into account, the variation of frequency shift with the attached mass on the sensor is compared with the previous study. According to this study, the result shows that the frequency shift of the sensor increases with increasing the attached mass. When the attached mass is small compared with that of the sensor, the nonlocal effect is obvious and increasing nonlocal parameter decreases the frequency shift of the sensor. In addition, when the location of the attached mass is closer to the free end, the frequency shift is more significant and that makes the sensor reveal more sensitive. When the attached mass is small, a high sensitivity is obtained

Bone Mineral Density and Vascular Calcification in Children and Young Adults With CKD 4 to 5 or on Dialysis

Introduction: Older adults with chronic kidney disease (CKD) can have low bone mineral density (BMD) with concurrent vascular calcification. Mineral accrual by the growing skeleton may protect young people with CKD from extraosseous calcification. Our hypothesis was that children and young adults with increasing BMD do not develop vascular calcification. Methods: This was a multicenter longitudinal study in children and young people (5–30 years) with CKD stages 4 to 5 or on dialysis. BMD was assessed by tibial peripheral quantitative computed tomography (pQCT) and lumbar spine dual-energy X-ray absorptiometry (DXA). The following cardiovascular imaging tests were undertaken: cardiac computed tomography for coronary artery calcification (CAC), ultrasound for carotid intima media thickness z-score (cIMTz), pulse wave velocity z-score (PWVz), and carotid distensibility for arterial stiffness. All measures are presented as age-adjusted and sex-adjusted z-scores. Results: One hundred participants (median age 13.82 years) were assessed at baseline and 57 followed up after a median of 1.45 years. Trabecular BMD z-score (TrabBMDz) decreased (P = 0.01), and there was a nonsignificant decrease in cortical BMD z-score (CortBMDz) (P = 0.09). Median cIMTz and PWVz showed nonsignificant increase (P = 0.23 and P = 0.19, respectively). The annualized increase in TrabBMDz (ΔTrabBMDz) was an independent predictor of cIMTz increase (R2 = 0.48, β = 0.40, P = 0.03). Young people who demonstrated statural growth (n = 33) had lower ΔTrabBMDz and also attenuated vascular changes compared with those with static growth (n = 24). Conclusion: This hypothesis-generating study suggests that children and young adults with CKD or on dialysis may develop vascular calcification even as their BMD increases. A presumed buffering capacity of the growing skeleton may offer some protection against extraosseous calcification

Dense transcript profiling in single cells by image correlation decoding

Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression