Efficacy of a Mer and Flt3 tyrosine kinase small molecule inhibitor, UNC1666, in acute myeloid leukemia

PubMed Central

Lee-Sherick, Alisa B.; Zhang, Weihe; Menachof, Kelly K.; Hill, Amanda A.; Rinella, Sean; Kirkpatrick, Gregory; Page, Lauren S.; Stashko, Michael A.; Jordan, Craig T.; Wei, Qi; Liu, Jing; Zhang, Dehui; DeRyckere, Deborah; Wang, Xiaodong; Frye, Stephen; Earp, H. Shelton; Graham, Douglas K.

2015-01-01

Mer and Flt3 receptor tyrosine kinases have been implicated as therapeutic targets in acute myeloid leukemia (AML). In this manuscript we describe UNC1666, a novel ATP-competitive small molecule tyrosine kinase inhibitor, which potently diminishes Mer and Flt3 phosphorylation in AML. Treatment with UNC1666 mediated biochemical and functional effects in AML cell lines expressing Mer or Flt3 internal tandem duplication (ITD), including decreased phosphorylation of Mer, Flt3 and downstream effectors Stat, Akt and Erk, induction of apoptosis in up to 98% of cells, and reduction of colony formation by greater than 90%, compared to treatment with vehicle. These effects were dose-dependent, with inhibition of downstream signaling and functional effects correlating with the degree of Mer or Flt3 kinase inhibition. Treatment of primary AML patient samples expressing Mer and/or Flt3-ITD with UNC1666 also inhibited Mer and Flt3 intracellular signaling, induced apoptosis, and inhibited colony formation. In summary, UNC1666 is a novel potent small molecule tyrosine kinase inhibitor that decreases oncogenic signaling and myeloblast survival, thereby validating dual Mer/Flt3 inhibition as an attractive treatment strategy for AML. PMID:25762638

Taking aim at Mer and Axl receptor tyrosine kinases as novel therapeutic targets in solid tumors

PubMed Central

Linger, Rachel M.A.; Keating, Amy K.; Earp, H. Shelton

2010-01-01

Importance of the field Axl and/or Mer expression correlates with poor prognosis in several cancers. Until recently, the specific role of these receptor tyrosine kinases (RTKs) in the development and progression of cancer remained unexplained. Studies demonstrating that Axl and Mer contribute to mechanisms of cell survival, migration, invasion, metastasis, and chemosensitivity justify further investigation of Axl and Mer as novel therapeutic targets in cancer. Areas covered in this review Axl and Mer signaling pathways in cancer cells are summarized and evidence validating these RTKs as therapeutic targets in glioblastoma multiforme, non-small cell lung cancer, and breast cancer is examined. A comprehensive discussion of Axl and/or Mer inhibitors in development is also provided. What the reader will gain Potential toxicities associated with Axl or Mer inhibition are addressed. We hypothesize that the probable action of Mer and Axl inhibitors on cells within the tumor microenvironment will provide a unique therapeutic opportunity to target both tumor cells and the stromal components which facilitate disease progression. Take home message Axl and Mer mediate multiple oncogenic phenotypes and activation of these RTKs constitutes a mechanism of chemoresistance in a variety of solid tumors. Targeted inhibition of these RTKs may be effective as anti-tumor and/or anti-metastatic therapy, particularly if combined with standard cytotoxic therapies. PMID:20809868

MER Telemetry Processor

NASA Technical Reports Server (NTRS)

Lee, Hyun H.

2012-01-01

MERTELEMPROC processes telemetered data in data product format and generates Experiment Data Records (EDRs) for many instruments (HAZCAM, NAVCAM, PANCAM, microscopic imager, Moessbauer spectrometer, APXS, RAT, and EDLCAM) on the Mars Exploration Rover (MER). If the data is compressed, then MERTELEMPROC decompresses the data with an appropriate decompression algorithm. There are two compression algorithms (ICER and LOCO) used in MER. This program fulfills a MER specific need to generate Level 1 products within a 60-second time requirement. EDRs generated by this program are used by merinverter, marscahv, marsrad, and marsjplstereo to generate higher-level products for the mission operations. MERTELEPROC was the first GDS program to process the data product. Metadata of the data product is in XML format. The software allows user-configurable input parameters, per-product processing (not streambased processing), and fail-over is allowed if the leading image header is corrupted. It is used within the MER automated pipeline. MERTELEMPROC is part of the OPGS (Operational Product Generation Subsystem) automated pipeline, which analyzes images returned by in situ spacecraft and creates level 1 products to assist in operations, science, and outreach.

Environmental Conditions Constrain the Distribution and Diversity of Archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

USGS Publications Warehouse

Wang, Y.; Boyd, E.; Crane, S.; Lu-Irving, P.; Krabbenhoft, D.; King, S.; Dighton, J.; Geesey, G.; Barkay, T.

2011-01-01

The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient. ?? 2011 Springer Science+Business Media, LLC.

Environmental conditions constrain the distribution and diversity of archaeal merA in Yellowstone National Park, Wyoming, U.S.A.

PubMed

Wang, Yanping; Boyd, Eric; Crane, Sharron; Lu-Irving, Patricia; Krabbenhoft, David; King, Susan; Dighton, John; Geesey, Gill; Barkay, Tamar

2011-11-01

The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of merA. The recovery of novel and deeply rooted MerA lineages from these habitats supports previous evidence that indicates merA originated in a thermophilic environment. Generalized linear models indicate that the distribution of putative archaeal merA lineages was constrained by a combination of pH, dissolved organic carbon, dissolved total mercury and sulfide. The models failed to identify statistically well supported trends for the distribution of putative bacterial merA lineages as a function of these or other measured environmental variables, suggesting that these lineages were either influenced by environmental parameters not considered in the present study, or the bacterial primer sets were designed to target too broad of a class of genes which may have responded differently to environmental stimuli. The widespread occurrence of merA in the geothermal environments implies a prominent role for Hg detoxification in these environments. Moreover, the differences in the distribution of the merA genes amplified with the four merA primer sets suggests that the organisms putatively engaged in this activity have evolved to occupy different ecological niches within the geothermal gradient.

A camel-derived MERS-CoV with a variant spike protein cleavage site and distinct fusion activation properties

PubMed Central

Millet, Jean Kaoru; Goldstein, Monty E; Labitt, Rachael N; Hsu, Hung-Lun; Daniel, Susan; Whittaker, Gary R

2016-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) continues to circulate in both humans and camels, and the origin and evolution of the virus remain unclear. Here we characterize the spike protein of a camel-derived MERS-CoV (NRCE-HKU205) identified in 2013, early in the MERS outbreak. NRCE-HKU205 spike protein has a variant cleavage motif with regard to the S2′ fusion activation site—notably, a novel substitution of isoleucine for the otherwise invariant serine at the critical P1′ cleavage site position. The substitutions resulted in a loss of furin-mediated cleavage, as shown by fluorogenic peptide cleavage and western blot assays. Cell–cell fusion and pseudotyped virus infectivity assays demonstrated that the S2′ substitutions decreased spike-mediated fusion and viral entry. However, cathepsin and trypsin-like protease activation were retained, albeit with much reduced efficiency compared with the prototypical EMC/2012 human strain. We show that NRCE-HKU205 has more limited fusion activation properties possibly resulting in more restricted viral tropism and may represent an intermediate in the complex pattern of MERS-CoV ecology and evolution. PMID:27999426

Extensive Viable Middle East Respiratory Syndrome (MERS) Coronavirus Contamination in Air and Surrounding Environment in MERS Isolation Wards.

PubMed

Kim, Sung-Han; Chang, So Young; Sung, Minki; Park, Ji Hoon; Bin Kim, Hong; Lee, Heeyoung; Choi, Jae-Phil; Choi, Won Suk; Min, Ji-Young

2016-08-01

The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) outside the Middle East occurred in South Korea in 2015 and resulted in 186 laboratory-confirmed infections, including 36 (19%) deaths. Some hospitals were considered epicenters of infection and voluntarily shut down most of their operations after nearly half of all transmissions occurred in hospital settings. However, the ways that MERS-CoV is transmitted in healthcare settings are not well defined. We explored the possible contribution of contaminated hospital air and surfaces to MERS transmission by collecting air and swabbing environmental surfaces in 2 hospitals treating MERS-CoV patients. The samples were tested by viral culture with reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescence assay (IFA) using MERS-CoV Spike antibody, and electron microscopy (EM). The presence of MERS-CoV was confirmed by RT-PCR of viral cultures of 4 of 7 air samples from 2 patients' rooms, 1 patient's restroom, and 1 common corridor. In addition, MERS-CoV was detected in 15 of 68 surface swabs by viral cultures. IFA on the cultures of the air and swab samples revealed the presence of MERS-CoV. EM images also revealed intact particles of MERS-CoV in viral cultures of the air and swab samples. These data provide experimental evidence for extensive viable MERS-CoV contamination of the air and surrounding materials in MERS outbreak units. Thus, our findings call for epidemiologic investigation of the possible scenarios for contact and airborne transmission, and raise concern regarding the adequacy of current infection control procedures. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Middle East Respiratory Syndrome (MERS)

MedlinePlus

Middle East Respiratory Syndrome Coronavirus; MERS-CoV; Novel coronavirus; nCoV ... for Disease Control and Prevention website. Middle East Respiratory Syndrome (MERS): Frequently asked questions and answers. www. ...

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation.In vitroreplication attenuation also extends toin vivomodels, allowing use of dORF3-5 as a live attenuated vaccine platform.more » Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. IMPORTANCEThe initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants.« less

Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen

PubMed Central

Pallesen, Jesper; Wang, Nianshuang; Corbett, Kizzmekia S.; Wrapp, Daniel; Kirchdoerfer, Robert N.; Turner, Hannah L.; Cottrell, Christopher A.; Becker, Michelle M.; Wang, Lingshu; Shi, Wei; Kong, Wing-Pui; Andres, Erica L.; Kettenbach, Arminja N.; Denison, Mark R.; Chappell, James D.; Graham, Barney S.; Ward, Andrew B.

2017-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. PMID:28807998

The MER/CIP Portal for Ground Operations

NASA Technical Reports Server (NTRS)

Chan, Louise; Desai, Sanjay; DOrtenzio, Matthew; Filman, Robtert E.; Heher, Dennis M.; Hubbard, Kim; Johan, Sandra; Keely, Leslie; Magapu, Vish; Mak, Ronald

2003-01-01

We developed the Mars Exploration Rover/Collaborative Information Portal (MER/CIP) to facilitate MER operations. MER/CIP provides a centralized, one-stop delivery platform integrating science and engineering data from several distributed heterogeneous data sources. Key issues for MER/CIP include: 1) Scheduling and schedule reminders; 2) Tracking the status of daily predicted outputs; 3) Finding and analyzing data products; 4) Collaboration; 5) Announcements; 6) Personalization.

Middle East Respiratory Syndrome (MERS)

MedlinePlus

... Controls Cancel Submit Search The CDC Middle East Respiratory Syndrome (MERS) Note: Javascript is disabled or is ... Recommend on Facebook Tweet Share Compartir Middle East Respiratory Syndrome (MERS) is viral respiratory illness that was ...

KAnalyze: a fast versatile pipelined k-mer toolkit.

PubMed

Audano, Peter; Vannberg, Fredrik

2014-07-15

Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/. © The Author 2014. Published by Oxford University Press.

Effective inhibition of MERS-CoV infection by resveratrol.

PubMed

Lin, Shih-Chao; Ho, Chi-Tang; Chuo, Wen-Ho; Li, Shiming; Wang, Tony T; Lin, Chi-Chen

2017-02-13

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is an emerging viral pathogen that causes severe morbidity and mortality. Up to date, there is no approved or licensed vaccine or antiviral medicines can be used to treat MERS-CoV-infected patients. Here, we analyzed the antiviral activities of resveratrol, a natural compound found in grape seeds and skin and in red wine, against MERS-CoV infection. We performed MTT and neutral red uptake assays to assess the survival rates of MERS-infected Vero E6 cells. In addition, quantitative PCR, western blotting, and immunofluorescent assays determined the intracellular viral RNA and protein expression. For viral productivity, we utilized plaque assays to confirm the antiviral properties of resveratrol against MERS-CoV. Resveratrol significantly inhibited MERS-CoV infection and prolonged cellular survival after virus infection. We also found that the expression of nucleocapsid (N) protein essential for MERS-CoV replication was decreased after resveratrol treatment. Furthermore, resveratrol down-regulated the apoptosis induced by MERS-CoV in vitro. By consecutive administration of resveratrol, we were able to reduce the concentration of resveratrol while achieving inhibitory effectiveness against MERS-CoV. In this study, we first demonstrated that resveratrol is a potent anti-MERS agent in vitro. We perceive that resveratrol can be a potential antiviral agent against MERS-CoV infection in the near future.

Molecular interaction study of commercial cyclic peptides and MERS-COV papain-like protease as novel drug candidate for MERS-COV

NASA Astrophysics Data System (ADS)

Nasution, M. A. F.; Azzuhdi, M. G.; Tambunan, U. S. F.

2017-07-01

Middle-east respiratory syndrome coronavirus (MERS-CoV) has become the current outbreak, MERS-CoV infection results in illness at the respiratory system, digestive, and even lead to death with an average mortality caused by MERS-CoV infection reaches 50 %. Until now, there is not any effective vaccine or drug to ward off MERS-CoV infection. Papain-like protease (PLpro) is responsible for cleavage of a nonstructural protein that is essential for viral maturation. Inhibition of PLpro with a ligand will block the cleavage process of nonstructural protein, thus reduce the infection of MERS-CoV. Through of bioinformatics study with molecular docking and binding interaction analysis of commercial cyclic peptides, aldosterone secretion inhibiting factor (1-35) (bovine) was obtained as an inhibitor for PLpro. Thus, aldosterone secretion inhibiting factor (1-35) (bovine) has a potential as a novel candidate drug for treating MERS-CoV.

The mechanism of neutral red-mediated microbial electrosynthesis in Escherichia coli: menaquinone reduction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrington, Timothy D.; Tran, Vi N.; Mohamed, Abdelrhman

The aim of this work was to elucidate the mechanism of mediated microbial electrosynthesis via neutral red from an electrode to fermenting Escherichia coli cultures in a bioelectrochemical system. Chemical reduction of NAD+ by reduced neutral red did not occur as predicted. Instead, neutral red was shown to reduce the menaquinone pool in the inner bacterial membrane. The reduced menaquinone pool altered fermentative metabolite production via the arcB redox-sensing cascade in the absence of terminal electron acceptors. When the acceptors DMSO, fumarate, or nitrate were provided, as many as 19% of the electrons trapped in the reduced acceptors were derivedmore » from the electrode. These results demonstrate the mechanism of neutral red-mediated microbial electrosynthesis during fermentation as well as how neutral red enables microbial electrosynthesis of reduced terminal electron acceptors.« less

Microbially Mediated Glass Alteration in the Geological Record: Textural clues for Microbial Functions.

NASA Astrophysics Data System (ADS)

Staudigel, H.; Furnes, H.; McLoughlin, N.; Banerjee, N.

2007-12-01

Fe and Mn oxidizing microbes interact with their environment through the microbially mediated formation of Fe/Mn oxides and through the corrosion textures they may leave behind in the solids they colonize and from which they extract nutrients. Understanding the geo-biology of Fe and Mn oxidation may focus on the study of the microbes themselves, the mineral products, its biocorrosion features and the relationships between these types of observations. We have reviewed our own data on glass bio-corrosion and in particular the wider literature on microbial mineral tunneling to develop a two stage biocorrosion model for volcanic glass that offers feedback for our understanding of the mechanisms and the dynamics of microbial dissolution. Traces of microbially mediated dissolution of volcanic glass are commonly observed in volcanic glass found in submarine volcanoes on the seafloor, and in uplifted submarine volcanoes of almost any geological age back to the origin of life. Two main bioalteration textures care observed, granular and tubular. Based on a comparison of these features in particular with tunneling by ectomycorrhizal fungi, we propose two distinct types of biocorrosion that affects glass: (1) Granular alteration textures, made up of colonies of microbe-sized, near spherical mineral - filled cavities that form irregular clusters ranging to a tens of micron thick bands at the glas surfaces. These granular textures are interpreted as the result of microbial colonization. accompanied by dissolution of the glass in their contact surface, deposition of authigenic minerals and the formation of a biofilm, that eventually seals the glass from easy access by seawater for hydration, or from microbes accessing Fe (II) in the glass. (2) The most spectacular bioalteration feature, repesented by the formation of tubes cannot be easily formed by the former mechanism because near spherical, individual microbes are likely not to produce the directionality that is required to

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

KAnalyze: a fast versatile pipelined K-mer toolkit

PubMed Central

Audano, Peter; Vannberg, Fredrik

2014-01-01

Motivation: Converting nucleotide sequences into short overlapping fragments of uniform length, k-mers, is a common step in many bioinformatics applications. While existing software packages count k-mers, few are optimized for speed, offer an application programming interface (API), a graphical interface or contain features that make it extensible and maintainable. We designed KAnalyze to compete with the fastest k-mer counters, to produce reliable output and to support future development efforts through well-architected, documented and testable code. Currently, KAnalyze can output k-mer counts in a sorted tab-delimited file or stream k-mers as they are read. KAnalyze can process large datasets with 2 GB of memory. This project is implemented in Java 7, and the command line interface (CLI) is designed to integrate into pipelines written in any language. Results: As a k-mer counter, KAnalyze outperforms Jellyfish, DSK and a pipeline built on Perl and Linux utilities. Through extensive unit and system testing, we have verified that KAnalyze produces the correct k-mer counts over multiple datasets and k-mer sizes. Availability and implementation: KAnalyze is available on SourceForge: https://sourceforge.net/projects/kanalyze/ Contact: fredrik.vannberg@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24642064

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

PubMed Central

Rabaey, Korneel; Boon, Nico; Siciliano, Steven D.; Verhaege, Marc; Verstraete, Willy

2004-01-01

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components. PMID:15345423

From SARS to MERS: evidence and speculation.

PubMed

Gao, Hainv; Yao, Hangping; Yang, Shigui; Li, Lanjuan

2016-12-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel zoonotic pathogen. In 2012, the infectious outbreak caused by MERS-CoV in Saudi Arabia has spread to more than 1600 patients in 26 countries, resulting in over 600 deaths.Without a travel history, few clinical and radiological features can reliably differentiate MERS from SARS. But in real world, comparing with SARS, MERS presents more vaguely defined epidemiology, more severe symptoms, and higher case fatality rate. In this review, we summarize the recent findings in the field of MERS-CoV, especially its molecular virology, interspecies mechanisms, clinical features, antiviral therapies, and the further investigation into this disease. As a newly emerging virus, many questions are not fully answered, including the exact mode of transmission chain, geographical distribution, and animal origins. Furthermore, a new protocol needs to be launched to rapidly evaluate the effects of unproven antiviral drugs and vaccine to fasten the clinical application of new drugs.

MERS transmission and risk factors: a systematic review.

PubMed

Park, Ji-Eun; Jung, Soyoung; Kim, Aeran; Park, Ji-Eun

2018-05-02

Since Middle East respiratory syndrome (MERS) infection was first reported in 2012, many studies have analysed its transmissibility and severity. However, the methodology and results of these studies have varied, and there has been no systematic review of MERS. This study reviews the characteristics and associated risk factors of MERS. We searched international (PubMed, ScienceDirect, Cochrane) and Korean databases (DBpia, KISS) for English- or Korean-language articles using the terms "MERS" and "Middle East respiratory syndrome". Only human studies with > 20 participants were analysed to exclude studies with low representation. Epidemiologic studies with information on transmissibility and severity of MERS as well as studies containing MERS risk factors were included. A total of 59 studies were included. Most studies from Saudi Arabia reported higher mortality (22-69.2%) than those from South Korea (20.4%). While the R 0 value in Saudi Arabia was < 1 in all but one study, in South Korea, the R 0 value was 2.5-8.09 in the early stage and decreased to < 1 in the later stage. The incubation period was 4.5-5.2 days in Saudi Arabia and 6-7.8 days in South Korea. Duration from onset was 4-10 days to confirmation, 2.9-5.3 days to hospitalization, 11-17 days to death, and 14-20 days to discharge. Older age and concomitant disease were the most common factors related to MERS infection, severity, and mortality. The transmissibility and severity of MERS differed by outbreak region and patient characteristics. Further studies assessing the risk of MERS should consider these factors.

Phagocytosis of microparticles by alveolar macrophages during acute lung injury requires MerTK.

PubMed

Mohning, Michael P; Thomas, Stacey M; Barthel, Lea; Mould, Kara J; McCubbrey, Alexandria L; Frasch, S Courtney; Bratton, Donna L; Henson, Peter M; Janssen, William J

2018-01-01

Microparticles are a newly recognized class of mediators in the pathophysiology of lung inflammation and injury, but little is known about the factors that regulate their accumulation and clearance. The primary objective of our study was to determine whether alveolar macrophages engulf microparticles and to elucidate the mechanisms by which this occurs. Alveolar microparticles were quantified in bronchoalveolar fluid of mice with lung injury induced by LPS and hydrochloric acid. Microparticle numbers were greatest at the peak of inflammation and declined as inflammation resolved. Isolated, fluorescently labeled particles were placed in culture with macrophages to evaluate ingestion in the presence of endocytosis inhibitors. Ingestion was blocked with cytochalasin D and wortmannin, consistent with a phagocytic process. In separate experiments, mice were treated intratracheally with labeled microparticles, and their uptake was assessed though microscopy and flow cytometry. Resident alveolar macrophages, not recruited macrophages, were the primary cell-ingesting microparticles in the alveolus during lung injury. In vitro, microparticles promoted inflammatory signaling in LPS primed epithelial cells, signifying the importance of microparticle clearance in resolving lung injury. Microparticles were found to have phosphatidylserine exposed on their surfaces. Accordingly, we measured expression of phosphatidylserine receptors on macrophages and found high expression of MerTK and Axl in the resident macrophage population. Endocytosis of microparticles was markedly reduced in MerTK-deficient macrophages in vitro and in vivo. In conclusion, microparticles are released during acute lung injury and peak in number at the height of inflammation. Resident alveolar macrophages efficiently clear these microparticles through MerTK-mediated phagocytosis.

Microbial communities mediating algal detritus turnover under anaerobic conditions

PubMed Central

Morrison, Jessica M.; Murphy, Chelsea L.; Baker, Kristina; Zamor, Richard M.; Nikolai, Steve J.; Wilder, Shawn; Elshahed, Mostafa S.

2017-01-01

Background Algae encompass a wide array of photosynthetic organisms that are ubiquitously distributed in aquatic and terrestrial habitats. Algal species often bloom in aquatic ecosystems, providing a significant autochthonous carbon input to the deeper anoxic layers in stratified water bodies. In addition, various algal species have been touted as promising candidates for anaerobic biogas production from biomass. Surprisingly, in spite of its ecological and economic relevance, the microbial community involved in algal detritus turnover under anaerobic conditions remains largely unexplored. Results Here, we characterized the microbial communities mediating the degradation of Chlorella vulgaris (Chlorophyta), Chara sp. strain IWP1 (Charophyceae), and kelp Ascophyllum nodosum (phylum Phaeophyceae), using sediments from an anaerobic spring (Zodlteone spring, OK; ZDT), sludge from a secondary digester in a local wastewater treatment plant (Stillwater, OK; WWT), and deeper anoxic layers from a seasonally stratified lake (Grand Lake O’ the Cherokees, OK; GL) as inoculum sources. Within all enrichments, the majority of algal biomass was metabolized within 13–16 weeks, and the process was accompanied by an increase in cell numbers and a decrease in community diversity. Community surveys based on the V4 region of the 16S rRNA gene identified different lineages belonging to the phyla Bacteroidetes, Proteobacteria (alpha, delta, gamma, and epsilon classes), Spirochaetes, and Firmicutes that were selectively abundant under various substrate and inoculum conditions. Within all kelp enrichments, the microbial communities structures at the conclusion of the experiment were highly similar regardless of the enrichment source, and were dominated by the genus Clostridium, or family Veillonellaceae within the Firmicutes. In all other enrichments the final microbial community was dependent on the inoculum source, rather than the type of algae utilized as substrate. Lineages enriched

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

PubMed Central

Mohammad-Noori, Morteza; Beer, Michael A.

2014-01-01

Abstract Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem. PMID:25033408

Enhanced regulatory sequence prediction using gapped k-mer features.

PubMed

Ghandi, Mahmoud; Lee, Dongwon; Mohammad-Noori, Morteza; Beer, Michael A

2014-07-01

Oligomers of length k, or k-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features, the probability of observing any specific k-mer becomes very small, and k-mer counts approach a binary variable, with most k-mers absent and a few present once. Thus, any statistical learning approach using k-mers as features becomes susceptible to noisy training set k-mer frequencies once k becomes large. To address this problem, we introduce alternative feature sets using gapped k-mers, a new classifier, gkm-SVM, and a general method for robust estimation of k-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.

Deciphering MERS-CoV Evolution in Dromedary Camels.

PubMed

Du, Lin; Han, Guan-Zhu

2016-02-01

The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) poses a potential threat to global public health. Many aspects of the evolution and transmission of MERS-CoV in its animal reservoir remain unclear. A recent study provides new insights into the evolution and transmission of MERS-CoV in dromedary camels. Copyright © 2015 Elsevier Ltd. All rights reserved.

Effect of long-term fertilization on humic redox mediators in multiple microbial redox reactions.

PubMed

Guo, Peng; Zhang, Chunfang; Wang, Yi; Yu, Xinwei; Zhang, Zhichao; Zhang, Dongdong

2018-03-01

This study investigated the effects of different long-term fertilizations on humic substances (HSs), humic acids (HAs) and humins, functioning as redox mediators for various microbial redox biotransformations, including 2,2',4,4',5,5'- hexachlorobiphenyl (PCB 153 ) dechlorination, dissimilatory iron reduction, and nitrate reduction, and their electron-mediating natures. The redox activity of HSs for various microbial redox metabolisms was substantially enhanced by long-term application of organic fertilizer (pig manure). As a redox mediator, only humin extracted from soils with organic fertilizer amendment (OF-HM) maintained microbial PCB 153 dechlorination activity (1.03 μM PCB 153 removal), and corresponding HA (OF-HA) most effectively enhanced iron reduction and nitrate reduction by Shewanella putrefaciens. Electrochemical analysis confirmed the enhancement of their electron transfer capacity and redox properties. Fourier transform infrared analysis showed that C=C and C=O bonds, and carboxylic or phenolic groups in HSs might be the redox functional groups affected by fertilization. This research enhances our understanding of the influence of anthropogenic fertility on the biogeochemical cycling of elements and in situ remediation ability in agroecosystems through microorganisms' metabolisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Rapid and Specific Assay for the Detection of MERS-CoV

PubMed Central

Huang, Pei; Wang, Hualei; Cao, Zengguo; Jin, Hongli; Chi, Hang; Zhao, Jincun; Yu, Beibei; Yan, Feihu; Hu, Xingxing; Wu, Fangfang; Jiao, Cuicui; Hou, Pengfei; Xu, Shengnan; Zhao, Yongkun; Feng, Na; Wang, Jianzhong; Sun, Weiyang; Wang, Tiecheng; Gao, Yuwei; Yang, Songtao; Xia, Xianzhu

2018-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel human coronavirus that can cause human respiratory disease. The development of a detection method for this virus that can lead to rapid and accurate diagnosis would be significant. In this study, we established a nucleic acid visualization technique that combines the reverse transcription loop-mediated isothermal amplification technique and a vertical flow visualization strip (RT-LAMP-VF) to detect the N gene of MERS-CoV. The RT-LAMP-VF assay was performed in a constant temperature water bath for 30 min, and the result was visible by the naked eye within 5 min. The RT-LAMP-VF assay was capable of detecting 2 × 101 copies/μl of synthesized RNA transcript and 1 × 101 copies/μl of MERS-CoV RNA. The method exhibits no cross-reactivities with multiple CoVs including SARS-related (SARSr)-CoV, HKU4, HKU1, OC43 and 229E, and thus exhibits high specificity. Compared to the real-time RT-PCR (rRT-PCR) method recommended by the World Health Organization (WHO), the RT-LAMP-VF assay is easy to handle, does not require expensive equipment and can rapidly complete detection within 35 min. PMID:29896174

Human Centered Design and Development for NASA's MerBoard

NASA Technical Reports Server (NTRS)

Trimble, Jay

2003-01-01

This viewgraph presentation provides an overview of the design and development process for NASA's MerBoard. These devices are large interactive display screens which can be shown on the user's computer, which will allow scientists in many locations to interpret and evaluate mission data in real-time. These tools are scheduled to be used during the 2003 Mars Exploration Rover (MER) expeditions. Topics covered include: mission overview, Mer Human Centered Computers, FIDO 2001 observations and MerBoard prototypes.

The microbially mediated soil organic carbon loss under degenerative succession in an alpine meadow.

PubMed

Zhang, Yuguang; Liu, Xiao; Cong, Jing; Lu, Hui; Sheng, Yuyu; Wang, Xiulei; Li, Diqiang; Liu, Xueduan; Yin, Huaqun; Zhou, Jizhong; Deng, Ye

2017-07-01

Land-cover change has long been recognized as having marked effect on the amount of soil organic carbon (SOC). However, the microbially mediated processes and mechanisms on SOC are still unclear. In this study, the soil samples in a degenerative succession from alpine meadow to alpine steppe meadow in the Qinghai-Tibetan Plateau were analysed using high-throughput technologies, including Illumina sequencing and geochip functional gene arrays. The soil microbial community structure and diversity were significantly (p < .05) different between alpine meadow and alpine steppe meadow; the microbial ɑ-diversity in alpine steppe meadow was significantly (p < .01) higher than in alpine meadow. Molecular ecological network analysis indicated that the microbial community structure in alpine steppe meadow was more complex and tighter than in the alpine meadow. The relative abundance of soil microbial labile carbon degradation genes (e.g., pectin and hemicellulose) was significantly higher in alpine steppe meadow than in alpine meadow, but the relative abundance of soil recalcitrant carbon degradation genes (e.g., chitin and lignin) showed the opposite tendency. The Biolog Ecoplate experiment showed that microbially mediated soil carbon utilization was more active in alpine steppe meadow than in alpine meadow. Consequently, more soil labile carbon might be decomposed in alpine steppe meadow than in alpine meadow. Therefore, the degenerative succession of alpine meadow because of climate change or anthropogenic activities would most likely decrease SOC and nutrients medicated by changing soil microbial community structure and their functional potentials for carbon decomposition. © 2017 John Wiley & Sons Ltd.

THE NEAR-EQUILIBRIUM OF MICROBIALLY MEDIATED REDOX COUPLES IN REDUCING GROUNDWATER ENVIRONMENTS

EPA Science Inventory

Redox couples are commonly held to be in disequilibrium among each other in most natural waters. To evaluate this view for microbially mediated, reducing, groundwater environments, monitoring data were examined for several couples under conditions ranging from nitrate-detectable...

Evidence of mercury trapping in biofilm-EPS and mer operon-based volatilization of inorganic mercury in a marine bacterium Bacillus cereus BW-201B.

PubMed

Dash, Hirak R; Basu, Subham; Das, Surajit

2017-04-01

Biofilm-forming mercury-resistant marine bacterium Bacillus cereus BW-201B has been explored to evident that the bacterial biofilm-EPS (exopolymers) trap inorganic mercury but subsequently release EPS-bound mercury for induction of mer operon-mediated volatilization of inorganic mercury. The isolate was able to tolerate 50 ppm of mercury and forms biofilm in presence of mercury. mer operon-mediated volatilization was confirmed, and -SH was found to be the key functional group of bacterial EPS responsible for mercury binding. Biofilm-EPS-bound mercury was found to be internalized to the bacterial system as confirmed by reversible conformational change of -SH group and increased expression level of merA gene in a timescale experiment. Biofilm-EPS trapped Hg after 24 h of incubation, and by 96 h, the volatilization process reaches to its optimum confirming the internalization of EPS-bound mercury to the bacterial cells. Biofilm disintegration at the same time corroborates the results.

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

DOE PAGES

Menachery, Vineet D.; Schafer, Alexandra; Burnum-Johnson, Kristin E.; ...

2018-01-16

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways in order to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems based approach, we examined differential regulation of IFNγ dependent genes following infection with highly pathogenic viruses including influenza (H5N1-VN1203, H1N1-CA04) and coronaviruses (SARS-CoV, MERS-CoV). Categorizing by function, we observed down regulation of genes associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down regulation of antigenmore » presentation genes and was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation rather than histone modification plays a crucial role in MERS-CoV mediated antagonism of antigen presentation genes; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Altogether, the results indicate a common approach utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.« less

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menachery, Vineet D.; Schäfer, Alexandra; Burnum-Johnson, Kristin E.

Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways in order to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems based approach, we examined differential regulation of IFNγ dependent genes following infection with highly pathogenic viruses including influenza (H5N1-VN1203, H1N1-CA04) and coronaviruses (SARS-CoV, MERS-CoV). Categorizing by function, we observed down regulation of genes associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down regulation of antigenmore » presentation genes and was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation rather than histone modification plays a crucial role in MERS-CoV mediated antagonism of antigen presentation genes; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common approach utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.« less

MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

PubMed Central

Menachery, Vineet D.; Mitchell, Hugh D.; Cockrell, Adam S.; Gralinski, Lisa E.; Yount, Boyd L.; Graham, Rachel L.; McAnarney, Eileen T.; Douglas, Madeline G.; Scobey, Trevor; Beall, Anne; Dinnon, Kenneth; Kocher, Jacob F.; Hale, Andrew E.; Stratton, Kelly G.; Waters, Katrina M.

2017-01-01

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. PMID:28830941

New method for characterizing electron mediators in microbial systems using a thin-layer twin-working electrode cell.

PubMed

Hassan, Md Mahamudul; Cheng, Ka Yu; Ho, Goen; Cord-Ruwisch, Ralf

2017-01-15

Microbial biofilms are significant ecosystems where the existence of redox gradients drive electron transfer often via soluble electron mediators. This study describes the use of two interfacing working electrodes (WEs) to simulate redox gradients within close proximity (250µm) for the detection and quantification of electron mediators. By using a common counter and reference electrode, the potentials of the two WEs were independently controlled to maintain a suitable "voltage window", which enabled simultaneous oxidation and reduction of electron mediators as evidenced by the concurrent anodic and cathodic currents, respectively. To validate the method, the electrochemical properties of different mediators (hexacyanoferrate, HCF, riboflavin, RF) were characterized by stepwise shifting the "voltage window" (ranging between 25 and 200mV) within a range of potentials after steady equilibrium current of both WEs was established. The resulting differences in electrical currents between the two WEs were recorded across a defined potential spectrum (between -1V and +0.5V vs. Ag/AgCl). Results indicated that the technique enabled identification (by the distinct peak locations at the potential scale) and quantification (by the peak of current) of the mediators for individual species as well as in an aqueous mixture. It enabled a precise determination of mid-potentials of the externally added mediators (HCF, RF) and mediators produced by pyocyanin-producing Pseudomonas aeruginosa (WACC 91) culture. The twin working electrode described is particularly suitable for studying mediator-dependent microbial electron transfer processes or simulating redox gradients as they exist in microbial biofilms. Copyright © 2016 Elsevier B.V. All rights reserved.

SARS and MERS: recent insights into emerging coronaviruses.

PubMed

de Wit, Emmie; van Doremalen, Neeltje; Falzarano, Darryl; Munster, Vincent J

2016-08-01

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 marked the second introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The continuing introductions of MERS-CoV from dromedary camels, the subsequent travel-related viral spread, the unprecedented nosocomial outbreaks and the high case-fatality rates highlight the need for prophylactic and therapeutic measures. Scientific advancements since the 2002-2003 severe acute respiratory syndrome coronavirus (SARS-CoV) pandemic allowed for rapid progress in our understanding of the epidemiology and pathogenesis of MERS-CoV and the development of therapeutics. In this Review, we detail our present understanding of the transmission and pathogenesis of SARS-CoV and MERS-CoV, and discuss the current state of development of measures to combat emerging coronaviruses.

Deterministic and stochastic models for middle east respiratory syndrome (MERS)

NASA Astrophysics Data System (ADS)

Suryani, Dessy Rizki; Zevika, Mona; Nuraini, Nuning

2018-03-01

World Health Organization (WHO) data stated that since September 2012, there were 1,733 cases of Middle East Respiratory Syndrome (MERS) with 628 death cases that occurred in 27 countries. MERS was first identified in Saudi Arabia in 2012 and the largest cases of MERS outside Saudi Arabia occurred in South Korea in 2015. MERS is a disease that attacks the respiratory system caused by infection of MERS-CoV. MERS-CoV transmission occurs directly through direct contact between infected individual with non-infected individual or indirectly through contaminated object by the free virus. Suspected, MERS can spread quickly because of the free virus in environment. Mathematical modeling is used to illustrate the transmission of MERS disease using deterministic model and stochastic model. Deterministic model is used to investigate the temporal dynamic from the system to analyze the steady state condition. Stochastic model approach using Continuous Time Markov Chain (CTMC) is used to predict the future states by using random variables. From the models that were built, the threshold value for deterministic models and stochastic models obtained in the same form and the probability of disease extinction can be computed by stochastic model. Simulations for both models using several of different parameters are shown, and the probability of disease extinction will be compared with several initial conditions.

Rapid detection of MERS coronavirus-like viruses in bats: pote1ntial for tracking MERS coronavirus transmission and animal origin.

PubMed

Woo, Patrick C Y; Lau, Susanna K P; Chen, Yixin; Wong, Emily Y M; Chan, Kwok-Hung; Chen, Honglin; Zhang, Libiao; Xia, Ningshao; Yuen, Kwok-Yung

2018-03-07

Recently, we developed a monoclonal antibody-based rapid nucleocapsid protein detection assay for diagnosis of MERS coronavirus (MERS-CoV) in humans and dromedary camels. In this study, we examined the usefulness of this assay to detect other lineage C betacoronaviruses closely related to MERS-CoV in bats. The rapid MERS-CoV nucleocapsid protein detection assay was tested positive in 24 (88.9%) of 27 Tylonycteris bat CoV HKU4 (Ty-BatCoV-HKU4) RNA-positive alimentary samples of Tylonycteris pachypus and 4 (19.0%) of 21 Pipistrellus bat CoV HKU5 (Pi-BatCoV-HKU5) RNA-positive alimentary samples of Pipistrellus abramus. There was significantly more Ty-BatCoV-HKU4 RNA-positive alimentary samples than Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive by the rapid MERS-CoV nucleocapsid protein detection assay (P < 0.001 by Chi-square test). The rapid assay was tested negative in all 51 alimentary samples RNA-positive for alphacoronaviruses (Rhinolophus bat CoV HKU2, Myotis bat CoV HKU6, Miniopterus bat CoV HKU8 and Hipposideros batCoV HKU10) and 32 alimentary samples positive for lineage B (SARS-related Rhinolophus bat CoV HKU3) and lineage D (Rousettus bat CoV HKU9) betacoronaviruses. No significant difference was observed between the viral loads of Ty-BatCoV-HKU4/Pi-BatCoV-HKU5 RNA-positive alimentary samples that were tested positive and negative by the rapid test (Mann-Witney U test). The rapid MERS-CoV nucleocapsid protein detection assay is able to rapidly detect lineage C betacoronaviruses in bats. It detected significantly more Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5 because MERS-CoV is more closely related to Ty-BatCoV-HKU4 than Pi-BatCoV-HKU5. This assay will facilitate rapid on-site mass screening of animal samples for ancestors of MERS-CoV and tracking transmission in the related bat species.

Microbially mediated mineral carbonation

NASA Astrophysics Data System (ADS)

Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2010-12-01

Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

Intratracheal exposure of common marmosets to MERS-CoV Jordan-n3/2012 or MERS-CoV EMC/2012 isolates does not result in lethal disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov; Via, Laura E.; Kumar, Mia R.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) continues to be a threat to human health in the Middle East. Development of countermeasures is ongoing; however, an animal model that faithfully recapitulates human disease has yet to be defined. A recent study indicated that inoculation of common marmosets resulted in inconsistent lethality. Based on these data we sought to compare two isolates of MERS-CoV. We followed disease progression in common marmosets after intratracheal exposure with: MERS-CoV-EMC/2012, MERS-CoV-Jordan-n3/2012, media, or inactivated virus. Our data suggest that common marmosets developed a mild to moderate non-lethal respiratory disease, which was quantifiable by computed tomography (CT),more » with limited other clinical signs. Based on CT data, clinical data, and virological data, MERS-CoV inoculation of common marmosets results in mild to moderate clinical signs of disease that are likely due to manipulations of the marmoset rather than as a result of robust viral replication. - Highlights: • Common marmosets infected with MERS-EMC and MERS-JOR did not develop lethal disease. • Infected subjects developed transient signs of clinical disease. • CT indicated few differences between the infected and control groups. • Marmosets do not faithfully replicate human MERS pathogenesis.« less

Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

DOE Office of Scientific and Technical Information (OSTI.GOV)

Firestone, Mary

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbonmore » decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.« less

Potential for Mercury Reduction by Microbes in the High Arctic▿

PubMed Central

Poulain, Alexandre J.; Ní Chadhain, Sinéad M.; Ariya, Parisa A.; Amyot, Marc; Garcia, Edenise; Campbell, Peter G. C.; Zylstra, Gerben J.; Barkay, Tamar

2007-01-01

The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions. PMID:17293515

Understanding M-ligand bonding and mer-/fac-isomerism in tris(8-hydroxyquinolinate) metallic complexes.

PubMed

Lima, Carlos F R A C; Taveira, Ricardo J S; Costa, José C S; Fernandes, Ana M; Melo, André; Silva, Artur M S; Santos, Luís M N B F

2016-06-28

Tris(8-hydroxyquinolinate) metallic complexes, Mq3, are one of the most important classes of organic semiconductor materials. Herein, the nature of the chemical bond in Mq3 complexes and its implications on their molecular properties were investigated by a combined experimental and computational approach. Various Mq3 complexes, resulting from the alteration of the metal and substitution of the 8-hydroxyquinoline ligand in different positions, were prepared. The mer-/fac-isomerism in Mq3 was explored by FTIR and NMR spectroscopy, evidencing that, irrespective of the substituent, mer- and fac-are the most stable molecular configurations of Al(iii) and In(iii) complexes, respectively. The relative M-ligand bond dissociation energies were evaluated experimentally by electrospray ionization tandem mass spectrometry (ESI-MS-MS), showing a non-monotonous variation along the group (Al > In > Ga). The results reveal a strong covalent character in M-ligand bonding, which allows for through-ligand electron delocalization, and explain the preferred molecular structures of Mq3 complexes as resulting from the interplay between bonding and steric factors. The mer-isomer reduces intraligand repulsions, being preferred for smaller metals, while the fac-isomer is favoured for larger metals where stronger covalent M-ligand bonds can be formed due to more extensive through-ligand conjugation mediated by metal "d" orbitals.

A mouse model for MERS coronavirus-induced acute respiratory distress syndrome.

PubMed

Cockrell, Adam S; Yount, Boyd L; Scobey, Trevor; Jensen, Kara; Douglas, Madeline; Beall, Anne; Tang, Xian-Chun; Marasco, Wayne A; Heise, Mark T; Baric, Ralph S

2016-11-28

Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel virus that emerged in 2012, causing acute respiratory distress syndrome (ARDS), severe pneumonia-like symptoms and multi-organ failure, with a case fatality rate of ∼36%. Limited clinical studies indicate that humans infected with MERS-CoV exhibit pathology consistent with the late stages of ARDS, which is reminiscent of the disease observed in patients infected with severe acute respiratory syndrome coronavirus. Models of MERS-CoV-induced severe respiratory disease have been difficult to achieve, and small-animal models traditionally used to investigate viral pathogenesis (mouse, hamster, guinea-pig and ferret) are naturally resistant to MERS-CoV. Therefore, we used CRISPR-Cas9 gene editing to modify the mouse genome to encode two amino acids (positions 288 and 330) that match the human sequence in the dipeptidyl peptidase 4 receptor, making mice susceptible to MERS-CoV infection and replication. Serial MERS-CoV passage in these engineered mice was then used to generate a mouse-adapted virus that replicated efficiently within the lungs and evoked symptoms indicative of severe ARDS, including decreased survival, extreme weight loss, decreased pulmonary function, pulmonary haemorrhage and pathological signs indicative of end-stage lung disease. Importantly, therapeutic countermeasures comprising MERS-CoV neutralizing antibody treatment or a MERS-CoV spike protein vaccine protected the engineered mice against MERS-CoV-induced ARDS.

Overexpression of a bacterial mercury transporter MerT in Arabidopsis enhances mercury tolerance.

PubMed

Xu, Sheng; Sun, Bin; Wang, Rong; He, Jia; Xia, Bing; Xue, Yong; Wang, Ren

2017-08-19

The phytoremediation by using of green plants in the removal of environmental pollutant is an environment friendly, green technology that is cost effective and energetically inexpensive. By using Agrobacterium-mediated gene transfer, we generated transgenic Arabidopsis plants ectopically expressing mercuric transport protein gene (merT) from Pseudomonas alcaligenes. Compared with wild-type (WT) plants, overexpressing PamerT in Arabidopsis enhanced the tolerance to HgCl 2 . Further results showed that the enhanced total activities or corresponding transcripts of antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POD) were observed in transgenic Arabidopsis under HgCl 2 stress. These results were confirmed by the alleviation of oxidative damage, as indicated by the decrease of thiobarbituric acid reactive substances (TBARS) contents and reactive oxygen species (ROS) accumulation. In addition, localization analysis of PaMerT in Arabidopsis protoplast showed that it is likely to be associated with vacuole. In all, PamerT increased mercury (Hg) tolerance in transgenic Arabidopsis, and decreased production of Hg-induced ROS, thereby protecting plants from oxidative damage. The present study has provided further evidence that bacterial MerT plays an important role in the plant tolerance to HgCl 2 and in reducing the production of ROS induced by HgCl 2 . Copyright © 2017 Elsevier Inc. All rights reserved.

Cultivation of Hard-To-Culture Subsurface Mercury-Resistant Bacteria and Discovery of New merA Gene Sequences▿

PubMed Central

Rasmussen, L. D.; Zawadsky, C.; Binnerup, S. J.; Øregaard, G.; Sørensen, S. J.; Kroer, N.

2008-01-01

Mercury-resistant bacteria may be important players in mercury biogeochemistry. To assess the potential for mercury reduction by two subsurface microbial communities, resistant subpopulations and their merA genes were characterized by a combined molecular and cultivation-dependent approach. The cultivation method simulated natural conditions by using polycarbonate membranes as a growth support and a nonsterile soil slurry as a culture medium. Resistant bacteria were pregrown to microcolony-forming units (mCFU) before being plated on standard medium. Compared to direct plating, culturability was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25 different 16S rRNA gene sequences were observed, including Alpha-, Beta-, and Gammaproteobacteria; Actinobacteria; Firmicutes; and Bacteroidetes. The diversity of isolates obtained by direct plating included eight different 16S rRNA gene sequences (Alpha- and Betaproteobacteria and Actinobacteria). Partial sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One of the sequences did not result in a match in the BLAST search. The results illustrate the power of integrating advanced cultivation methodology with molecular techniques for the characterization of the diversity of mercury-resistant populations and assessing the potential for mercury reduction in contaminated environments. PMID:18441111

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

Treesearch

Aimee T. Classen; Steven T. Overby; Stephen C. Hart; George W. Koch; Thomas G. Whitham

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality of an ecosystem or indirectly by shifting the composition of microbial communities that mediate nutrient processes. We examined the effects of tree susceptibility and resistance to herbivory on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore...

Evaluation of candidate vaccine approaches for MERS-CoV

DOE PAGES

Wang, Lingshu; Shi, Wei; Joyce, M. Gordon; ...

2015-07-28

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanismsmore » were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.« less

Evaluation of candidate vaccine approaches for MERS-CoV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Lingshu; Shi, Wei; Joyce, M. Gordon

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV vaccine development. Efforts focused solely on the receptor-binding domain (RBD) of the viral Spike (S) glycoprotein may not optimize neutralizing antibody (NAb) responses. Here we show that immunogens based on full-length S DNA and S1 subunit protein elicit robust serum-neutralizing activity against several MERS-CoV strains in mice and non-human primates. Serological analysis and isolation of murine monoclonal antibodies revealed that immunization elicits NAbs to RBD and, non-RBD portions of S1 and S2 subunit. Multiple neutralization mechanismsmore » were demonstrated by solving the atomic structure of a NAb-RBD complex, through sequencing of neutralization escape viruses and by constructing MERS-CoV S variants for serological assays. Immunization of rhesus macaques confers protection against MERS-CoV-induced radiographic pneumonia, as assessed using computerized tomography, supporting this strategy as a promising approach for MERS-CoV vaccine development.« less

MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard A.; Panyala, Ajay R.; Glass, Kevin A.

MerCat is a parallel, highly scalable and modular property software package for robust analysis of features in next-generation sequencing data. MerCat inputs include assembled contigs and raw sequence reads from any platform resulting in feature abundance counts tables. MerCat allows for direct analysis of data properties without reference sequence database dependency commonly used by search tools such as BLAST and/or DIAMOND for compositional analysis of whole community shotgun sequencing (e.g. metagenomes and metatranscriptomes).

Mars Exploration Rover (MER) aeroshell

NASA Image and Video Library

2003-01-31

In the Payload Hazardous Servicing Facility, workers prepare the Mars Exploration Rover (MER) aeroshell for transfer to a rotation stand. Set to launch in 2003, the MER Mission will consist of two identical rovers designed to cover roughly 110 yards (100 meters) each Martian day. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. The rovers will be identical to each other, but will land at different regions of Mars. The first rover has a launch window opening May 30, and the second rover a window opening June 25, 2003.

Turtle: identifying frequent k-mers with cache-efficient algorithms.

PubMed

Roy, Rajat Shuvro; Bhattacharya, Debashish; Schliep, Alexander

2014-07-15

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k-mers and not in the, typically much larger, total number of k-mers in the read library. We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times. The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Novel chimeric virus-like particles vaccine displaying MERS-CoV receptor-binding domain induce specific humoral and cellular immune response in mice.

PubMed

Wang, Chong; Zheng, Xuexing; Gai, Weiwei; Wong, Gary; Wang, Hualei; Jin, Hongli; Feng, Na; Zhao, Yongkun; Zhang, Weijiao; Li, Nan; Zhao, Guoxing; Li, Junfu; Yan, Jinghua; Gao, Yuwei; Hu, Guixue; Yang, Songtao; Xia, Xianzhu

2017-04-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has continued spreading since its emergence in 2012 with a mortality rate of 35.6%, and is a potential pandemic threat. Prophylactics and therapies are urgently needed to address this public health problem. We report here the efficacy of a vaccine consisting of chimeric virus-like particles (VLP) expressing the receptor binding domain (RBD) of MERS-CoV. In this study, a fusion of the canine parvovirus (CPV) VP2 structural protein gene with the RBD of MERS-CoV can self-assemble into chimeric, spherical VLP (sVLP). sVLP retained certain parvovirus characteristics, such as the ability to agglutinate pig erythrocytes, and structural morphology similar to CPV virions. Immunization with sVLP induced RBD-specific humoral and cellular immune responses in mice. sVLP-specific antisera from these animals were able to prevent pseudotyped MERS-CoV entry into susceptible cells, with neutralizing antibody titers reaching 1: 320. IFN-γ, IL-4 and IL-2 secreting cells induced by the RBD were detected in the splenocytes of vaccinated mice by ELISpot. Furthermore, mice inoculated with sVLP or an adjuvanted sVLP vaccine elicited T-helper 1 (Th1) and T-helper 2 (Th2) cell-mediated immunity. Our study demonstrates that sVLP displaying the RBD of MERS-CoV are promising prophylactic candidates against MERS-CoV in a potential outbreak situation. Copyright © 2017 Elsevier B.V. All rights reserved.

Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

NASA Astrophysics Data System (ADS)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system

Analyzing MER Uplink Reports

NASA Technical Reports Server (NTRS)

Savin, Stephen C.

2005-01-01

The MER project includes two rovers working simultaneously on opposite sides of Mars each receiving commands only once a day. Creating this uplink is critical, since a failed uplink means a lost day and a waste of money. Examining the process of creating this uplink, I tracked the use of the system developed for requesting observations as well as the development, from stage to stage, in forming an activity plan. I found the system for requesting observations was commonly misused, if used at all. There are half a dozen reports to document the creation of the uplink plan and often there are discrepancies among them. Despite this, the uplink process worked very well and MER has been one of the most successful missions for NASA in recent memory. Still it is clear there is room for improvement.

Middle East respiratory syndrome coronavirus (MERS-CoV): animal to human interaction

PubMed Central

Omrani, Ali S.; Al-Tawfiq, Jaffar A.

2015-01-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a novel enzootic betacoronavirus that was first described in September 2012. The clinical spectrum of MERS-CoV infection in humans ranges from an asymptomatic or mild respiratory illness to severe pneumonia and multi-organ failure; overall mortality is around 35.7%. Bats harbour several betacoronaviruses that are closely related to MERS-CoV but more research is needed to establish the relationship between bats and MERS-CoV. The seroprevalence of MERS-CoV antibodies is very high in dromedary camels in Eastern Africa and the Arabian Peninsula. MERS-CoV RNA and viable virus have been isolated from dromedary camels, including some with respiratory symptoms. Furthermore, near-identical strains of MERS-CoV have been isolated from epidemiologically linked humans and camels, confirming inter-transmission, most probably from camels to humans. Though inter-human spread within health care settings is responsible for the majority of reported MERS-CoV cases, the virus is incapable at present of causing sustained human-to-human transmission. Clusters can be readily controlled with implementation of appropriate infection control procedures. Phylogenetic and sequencing data strongly suggest that MERS-CoV originated from bat ancestors after undergoing a recombination event in the spike protein, possibly in dromedary camels in Africa, before its exportation to the Arabian Peninsula along the camel trading routes. MERS-CoV serosurveys are needed to investigate possible unrecognized human infections in Africa. Amongst the important measures to control MERS-CoV spread are strict regulation of camel movement, regular herd screening and isolation of infected camels, use of personal protective equipment by camel handlers and enforcing rules banning all consumption of unpasteurized camel milk and urine. PMID:26924345

Potential MER Landing Site in Melas Chasma

NASA Technical Reports Server (NTRS)

Weitz, C. M.; Parker, Timothy J.; Anderson, F. Scott

2001-01-01

We have selected one area in Valles Marineris as a potential landing site for the Mars Exploration Rover (MER) mission. After 30 years of analyses, the formation of the Valles Marineris system of troughs and its associated deposits still remains an enigma. Understanding all aspects of the Valles Marineris would significantly contribute to deciphering the internal and external history of Mars. A landing site within Melas Chasma could provide insight into both the formation of Valles Marineris and the composition and origin of the interior layered deposits (ILDs). The ILDs have been proposed as: (1) sedimentary deposits formed in lakes mass wasted material from the walls; (3) remnants of the wall rock; (4) carbonate deposits; (5) aeolian deposits; and (6) volcanic. More recently, Malin and Edgett suggest that the fine-scale, rhythmic layering seen in the interior deposits, as well as other layered deposits in craters, supports a sedimentary origin. Because an understanding of the formation of Valles Marineris and its interior deposits is so important to deciphering the history of Mars, we have proposed a landing site for the MER mission on an exposure of interior deposits in western Melas Chasma. Either MER-A and MER-B could land at this same location.

Phytoremediation using microbially mediated metal accumulation in Sorghum bicolor.

PubMed

Phieler, René; Merten, Dirk; Roth, Martin; Büchel, Georg; Kothe, Erika

2015-12-01

Reclaiming land that has been anthropogenically contaminated with multiple heavy metal elements, e.g., during mining operations, is a growing challenge worldwide. The use of phytoremediation has been discussed with varying success. Here, we show that a careful examination of options of microbial determination of plant performance is a key element in providing a multielement remediation option for such landscapes. We used both (a) mycorrhiza with Rhizophagus irregularis and (b) bacterial amendments with Streptomyces acidiscabies E13 and Streptomyces tendae F4 to mediate plant-promoting and metal-accumulating properties to Sorghum bicolor. In pot experiments, the effects on plant growth and metal uptake were scored, and in a field trial at a former uranium leaching heap site near Ronneburg, Germany, we could show the efficacy under field conditions. Different metals could be extracted at the same time, with varying microbial inoculation and soil amendment scenarios possible when a certain metal is the focus of interest. Especially, manganese was extracted at very high levels which might be useful even for phytomining approaches.

Replication and shedding of MERS-CoV in Jamaican fruit bats (Artibeus jamaicensis)

PubMed Central

Munster, Vincent J.; Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Miazgowicz, Kerri L.; Milne-Price, Shauna; Bushmaker, Trenton; Rosenke, Rebecca; Scott, Dana; Hawkinson, Ann; de Wit, Emmie; Schountz, Tony; Bowen, Richard A.

2016-01-01

The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) highlights the zoonotic potential of Betacoronaviruses. Investigations into the origin of MERS-CoV have focused on two potential reservoirs: bats and camels. Here, we investigated the role of bats as a potential reservoir for MERS-CoV. In vitro, the MERS-CoV spike glycoprotein interacted with Jamaican fruit bat (Artibeus jamaicensis) dipeptidyl peptidase 4 (DPP4) receptor and MERS-CoV replicated efficiently in Jamaican fruit bat cells, suggesting there is no restriction at the receptor or cellular level for MERS-CoV. To shed light on the intrinsic host-virus relationship, we inoculated 10 Jamaican fruit bats with MERS-CoV. Although all bats showed evidence of infection, none of the bats showed clinical signs of disease. Virus shedding was detected in the respiratory and intestinal tract for up to 9 days. MERS-CoV replicated transiently in the respiratory and, to a lesser extent, the intestinal tracts and internal organs; with limited histopathological changes observed only in the lungs. Analysis of the innate gene expression in the lungs showed a moderate, transient induction of expression. Our results indicate that MERS-CoV maintains the ability to replicate in bats without clinical signs of disease, supporting the general hypothesis of bats as ancestral reservoirs for MERS-CoV. PMID:26899616

3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012.

PubMed

Johnson, Reed F; Bagci, Ulas; Keith, Lauren; Tang, Xianchun; Mollura, Daniel J; Zeitlin, Larry; Qin, Jing; Huzella, Louis; Bartos, Christopher J; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H; Paulty, Michael H; Velasco, Jesus; Whaley, Kevin J; Johnson, Joshua C; Pettitt, James; Ork, Britini L; Solomon, Jeffrey; Oberlander, Nicholas; Zhu, Quan; Sun, Jiusong; Holbrook, Michael R; Olinger, Gene G; Baric, Ralph S; Hensley, Lisa E; Jahrling, Peter B; Marasco, Wayne A

2016-03-01

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10(6) PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a human anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. Published by Elsevier Inc.

A Novel Role of MerC in Methylmercury Transport and Phytoremediation of Methylmercury Contamination.

PubMed

Sone, Yuka; Uraguchi, Shimpei; Takanezawa, Yasukazu; Nakamura, Ryosuke; Pan-Hou, Hidemitsu; Kiyono, Masako

2017-01-01

MerC, encoded by merC in the transposon Tn21 mer operon, is a heavy metal transporter with potential applications for phytoremediation of heavy metals such as mercuric ion and cadmium. In this study, we demonstrate that MerC also acts as a transporter for methylmercury. When MerC was expressed in Escherichia coli XL1-Blue, cells became hypersensitive to CH 3 Hg(I) and the uptake of CH 3 Hg(I) by these cells was higher than that by cells of the isogenic strain. Moreover, transgenic Arabidopsis plants expressing bacterial MerC or MerC fused to plant soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) accumulated CH 3 Hg(I) effectively and their growth was comparable to the wild-type plants. These results demonstrate that when the bacterium-derived merC gene is ectopically introduced in genetically modified plants, MerC expression in the transgenic plants promotes the transport and sequestration of methylmercury. Thus, our results show that the expression of merC in Arabidopsis results in transgenic plants that could be used for the phytoremediation and elimination of toxic methylmercury from the environment.

Influence of coral and algal exudates on microbially mediated reef metabolism.

PubMed

Haas, Andreas F; Nelson, Craig E; Rohwer, Forest; Wegley-Kelly, Linda; Quistad, Steven D; Carlson, Craig A; Leichter, James J; Hatay, Mark; Smith, Jennifer E

2013-01-01

producers were always estimated to be net autotrophic. However, estimates of microbial consumption of DOC at the reef scale surpassed the DOC exudation rates suggesting net consumption of DOC at the reef-scale. In situ mesocosm experiments using custom-made benthic chambers placed over different types of benthic communities exhibited identical trends to those found in incubation experiments. Here we provide the first comprehensive dataset examining direct primary producer-induced, and indirect microbially mediated alterations of elemental cycling in both benthic and planktonic reef environments over diurnal cycles. Our results highlight the variability of the influence of different benthic primary producers on microbial metabolism in reef ecosystems and the potential implications for energy transfer to higher trophic levels during shifts from coral to algal dominance on reefs.

Nutrient Limitation of Microbial Mediated Decomposition and Arctic Soil Chronology

NASA Astrophysics Data System (ADS)

Melle, C. J.; Darrouzet-Nardi, A.; Wallenstein, M. D.

2012-12-01

effective soil age. My research is focused on addressing the questions of the extent of microbial N limitation in arctic tundra soils, the potential for co-limitation of labile C despite a high SOC environment, and the dependence, if any, nutrient limitation may have on the effective age of the soil. I have addressed these questions by conducting a laboratory soil incubation of factorial design with treatments of amended glucose, amended ammonium nitrate, and a control consisting of an addition of an equivalent volume of deionized water. Moist acid tundra soils possessing similar soil properties from two arctic sites of close proximity yet with varying deglaciation chronologies were utilized in my study. Soil properties of C-mineralization via respiration, microbial biomass, and nitrogen content in the forms of ammonium, nitrate, and total free amino acids and microbial extra-cellular enzyme production were assayed to determine the microbial response to the experimental treatments. Through the results of this work, I hope to better our understanding of biogeochemical cycling within arctic tundra ecosystems and the response to climate change by contributing to existing knowledge of nutrient limitation on microbial mediated decomposition of SOC in the arctic and how this may differ in soils of varying effective age.

KMC 2: fast and resource-frugal k-mer counting.

PubMed

Deorowicz, Sebastian; Kokot, Marek; Grabowski, Szymon; Debudaj-Grabysz, Agnieszka

2015-05-15

Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory. We present a novel method for k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM. Our disk-based method bears some resemblance to MSPKmerCounter, yet replacing the original minimizers with signatures (a carefully selected subset of all minimizers) and using (k, x)-mers allows to significantly reduce the I/O and a highly parallel overall architecture allows to achieve unprecedented processing speeds. For example, KMC 2 counts the 28-mers of a human reads collection with 44-fold coverage (106 GB of compressed size) in about 20 min, on a 6-core Intel i7 PC with an solid-state disk. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Reed F., E-mail: johnsonreed@mail.nih.gov; Bagci, Ulas; Center for Research in Computer Vision

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the causative agent of a severe, lethal respiratory disease occurring across several countries in the Middle East. To date there have been over 1600 laboratory confirmed cases of MERS-CoV in 26 countries with a case fatality rate of 36%. Given the endemic region, it is possible that MERS-CoV could spread during the annual Hajj pilgrimage, necessitating countermeasure development. In this report, we describe the clinical and radiographic changes of rhesus monkeys following infection with 5×10{sup 6} PFU MERS-CoV Jordan-n3/2012. Two groups of NHPs were treated with either a humanmore » anti-MERS monoclonal antibody 3B11-N or E410-N, an anti-HIV antibody. MERS-CoV Jordan-n3/2012 infection resulted in quantifiable changes by computed tomography, but limited other clinical signs of disease. 3B11-N treated subjects developed significantly reduced lung pathology when compared to infected, untreated subjects, indicating that this antibody may be a suitable MERS-CoV treatment. - Highlights: • MERS-CoV Jordan-n3/2012 challenge of rhesus monkeys results in a mild disease. • CT can be used to monitor disease progression to aid models of human disease. • Treatment with the human monoclonal antibody 3B11-N resulted in decreased disease.« less

Development of Animal Models Against Emerging Coronaviruses: From SARS to MERS coronavirus

PubMed Central

Sutton, Troy C; Subbarao, Kanta

2016-01-01

Two novel coronaviruses have emerged to cause severe disease in humans. While bats may be the primary reservoir for both viruses, SARS coronavirus (SARS-CoV) likely crossed into humans from civets in China, and MERS coronavirus (MERS-CoV) has been transmitted from camels in the Middle East. Unlike SARS-CoV that resolved within a year, continued introductions of MERS-CoV present an on-going public health threat. Animal models are needed to evaluate countermeasures against emerging viruses. With SARS-CoV, several animal species were permissive to infection. In contrast, most laboratory animals are refractory or only semi-permissive to infection with MERS-CoV. This host-range restriction is largely determined by sequence heterogeneity in the MERS-CoV receptor. We describe animal models developed to study coronaviruses, with a focus on host-range restriction at the level of the viral receptor and discuss approaches to consider in developing a model to evaluate countermeasures against MERS-CoV. PMID:25791336

Engineered Single-Chain, Antiparallel, Coiled Coil Mimics the MerR Metal Binding Site

PubMed Central

Song, Lingyun; Caguiat, Jonathan; Li, Zhongrui; Shokes, Jacob; Scott, Robert A.; Olliff, Lynda; Summers, Anne O.

2004-01-01

The repressor-activator MerR that controls transcription of the mercury resistance (mer) operon is unusual for its high sensitivity and specificity for Hg(II) in in vivo and in vitro transcriptional assays. The metal-recognition domain of MerR resides at the homodimer interface in a novel antiparallel arrangement of α-helix 5 that forms a coiled-coil motif. To facilitate the study of this novel metal binding motif, we assembled this antiparallel coiled coil into a single chain by directly fusing two copies of the 48-residue α-helix 5 of MerR. The resulting 107-residue polypeptide, called the metal binding domain (MBD), and wild-type MerR were overproduced and purified, and their metal-binding properties were determined in vivo and in vitro. In vitro MBD bound ca. 1.0 equivalent of Hg(II) per pair of binding sites, just as MerR does, and it showed only a slightly lower affinity for Hg(II) than did MerR. Extended X-ray absorption fine structure data showed that MBD has essentially the same Hg(II) coordination environment as MerR. In vivo, cells overexpressing MBD accumulated 70 to 100% more 203Hg(II) than cells bearing the vector alone, without deleterious effects on cell growth. Both MerR and MBD variously bound other thiophilic metal ions, including Cd(II), Zn(II), Pb(II), and As(III), in vitro and in vivo. We conclude that (i) it is possible to simulate in a single polypeptide chain the in vitro and in vivo metal-binding ability of dimeric, full-length MerR and (ii) MerR's specificity in transcriptional activation does not reside solely in the metal-binding step. PMID:14996817

Transmission characteristics of MERS and SARS in the healthcare setting: a comparative study.

PubMed

Chowell, Gerardo; Abdirizak, Fatima; Lee, Sunmi; Lee, Jonggul; Jung, Eunok; Nishiura, Hiroshi; Viboud, Cécile

2015-09-03

The Middle East respiratory syndrome (MERS) coronavirus has caused recurrent outbreaks in the Arabian Peninsula since 2012. Although MERS has low overall human-to-human transmission potential, there is occasional amplification in the healthcare setting, a pattern reminiscent of the dynamics of the severe acute respiratory syndrome (SARS) outbreaks in 2003. Here we provide a head-to-head comparison of exposure patterns and transmission dynamics of large hospital clusters of MERS and SARS, including the most recent South Korean outbreak of MERS in 2015. To assess the unexpected nature of the recent South Korean nosocomial outbreak of MERS and estimate the probability of future large hospital clusters, we compared exposure and transmission patterns for previously reported hospital clusters of MERS and SARS, based on individual-level data and transmission tree information. We carried out simulations of nosocomial outbreaks of MERS and SARS using branching process models rooted in transmission tree data, and inferred the probability and characteristics of large outbreaks. A significant fraction of MERS cases were linked to the healthcare setting, ranging from 43.5 % for the nosocomial outbreak in Jeddah, Saudi Arabia, in 2014 to 100 % for both the outbreak in Al-Hasa, Saudi Arabia, in 2013 and the outbreak in South Korea in 2015. Both MERS and SARS nosocomial outbreaks are characterized by early nosocomial super-spreading events, with the reproduction number dropping below 1 within three to five disease generations. There was a systematic difference in the exposure patterns of MERS and SARS: a majority of MERS cases occurred among patients who sought care in the same facilities as the index case, whereas there was a greater concentration of SARS cases among healthcare workers throughout the outbreak. Exposure patterns differed slightly by disease generation, however, especially for SARS. Moreover, the distributions of secondary cases per single primary case varied

Mouse-adapted MERS coronavirus causes lethal lung disease in human DPP4 knockin mice.

PubMed

Li, Kun; Wohlford-Lenane, Christine L; Channappanavar, Rudragouda; Park, Jung-Eun; Earnest, James T; Bair, Thomas B; Bates, Amber M; Brogden, Kim A; Flaherty, Heather A; Gallagher, Tom; Meyerholz, David K; Perlman, Stanley; McCray, Paul B

2017-04-11

The Middle East respiratory syndrome (MERS) emerged in Saudi Arabia in 2012, caused by a zoonotically transmitted coronavirus (CoV). Over 1,900 cases have been reported to date, with ∼36% fatality rate. Lack of autopsies from MERS cases has hindered understanding of MERS-CoV pathogenesis. A small animal model that develops progressive pulmonary manifestations when infected with MERS-CoV would advance the field. As mice are restricted to infection at the level of DPP4, the MERS-CoV receptor, we generated mice with humanized exons 10-12 of the mouse Dpp4 locus. Upon inoculation with MERS-CoV, human DPP4 knockin (KI) mice supported virus replication in the lungs, but developed no illness. After 30 serial passages through the lungs of KI mice, a mouse-adapted virus emerged (MERS MA ) that grew in lungs to over 100 times higher titers than the starting virus. A plaque-purified MERS MA clone caused weight loss and fatal infection. Virus antigen was observed in airway epithelia, pneumocytes, and macrophages. Pathologic findings included diffuse alveolar damage with pulmonary edema and hyaline membrane formation associated with accumulation of activated inflammatory monocyte-macrophages and neutrophils in the lungs. Relative to the parental MERS-CoV, MERS MA viruses contained 13-22 mutations, including several within the spike (S) glycoprotein gene. S-protein mutations sensitized viruses to entry-activating serine proteases and conferred more rapid entry kinetics. Recombinant MERS MA bearing mutant S proteins were more virulent than the parental virus in hDPP4 KI mice. The hDPP4 KI mouse and the MERS MA provide tools to investigate disease causes and develop new therapies.

Increase methylmercury accumulation in Arabidopsis thaliana expressing bacterial broad-spectrum mercury transporter MerE

PubMed Central

2013-01-01

The bacterial merE gene derived from the Tn21 mer operon encodes a broad-spectrum mercury transporter that governs the transport of methylmercury and mercuric ions across bacterial cytoplasmic membranes, and this gene is a potential molecular tool for improving the efficiency of methylmercury phytoremediation. A transgenic Arabidopsis engineered to express MerE was constructed and the impact of expression of MerE on methylmercury accumulation was evaluated. The subcellular localization of transiently expressed GFP-tagged MerE was examined in Arabidopsis suspension-cultured cells. The GFP-MerE was found to localize to the plasma membrane and cytosol. The transgenic Arabidopsis expressing MerE accumulated significantly more methymercury and mercuric ions into plants than the wild-type Arabidopsis did. The transgenic plants expressing MerE was significantly more resistant to mercuric ions, but only showed more resistant to methylmercury compared with the wild type Arabidopsis. These results demonstrated that expression of the bacterial mercury transporter MerE promoted the transport and accumulation of methylmercury in transgenic Arabidopsis, which may be a useful method for improving plants to facilitate the phytoremediation of methylmercury pollution. PMID:24004544

MERS in the U.S.

MedlinePlus

... traveler departed Riyadh, Saudi Arabia and traveled by plane to London, England, then to Chicago, Illinois. The ... MERS. On May 1, the patient traveled by plane from Jeddah, Saudi Arabia to London, England; to ...

PEDF and PEDF-derived peptide 44mer inhibit oxygen-glucose deprivation-induced oxidative stress through upregulating PPARγ via PEDF-R in H9c2 cells.

PubMed

Zhuang, Wei; Zhang, Hao; Pan, Jiajun; Li, Zhimin; Wei, Tengteng; Cui, Huazhu; Liu, Zhiwei; Guan, Qiuhua; Dong, Hongyan; Zhang, Zhongming

2016-04-08

Pigment epithelial-derived factor (PEDF) is a glycoprotein with broad biological activities including inhibiting oxygen-glucose deprivation(OGD)-induced cardiomyocytes apoptosis through its anti-oxidative properties. PEDF derived peptide-44mer shows similar cytoprotective effect to PEDF. However, the molecular mechanisms mediating cardiomyocytes apoptosis have not been fully established. Here we found that PEDF and 44mer decreased the content of ROS. This content was abolished by either PEDF-R small interfering RNA (siRNA) or PPARγ antagonist. The level of Lysophosphatidic acid (LPA) and phospholipase A2 (PLA2) was observed as drawn from the ELISA assays. PEDF and 44mer sequentially induced PPARγ expression was observed both in qPCR and Western blot assays. The level of LPA and PLA2 and PPARγ expression increased by PEDF and 44mer was significantly attenuated by PEDF-R siRNA. However, PEDF and 44mer inhibited the H9c2 cells and cultured neonatal rat myocardial cells apoptosis rate. On the other hand, TUNEL assay and cleavage of procaspase-3 showed that PEDF-R siRNA or PPARγ antagonist increased the apoptosis again. We conclude that under OGD condition, PEDF and 44mer reduce H9c2 cells apoptosis and inhibit OGD-induced oxidative stress via its receptor PEDF-R and the PPARγ signaling pathway. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbial DNA records historical delivery of anthropogenic mercury

PubMed Central

Poulain, Alexandre J; Aris-Brosou, Stéphane; Blais, Jules M; Brazeau, Michelle; Keller, Wendel (Bill); Paterson, Andrew M

2015-01-01

Mercury (Hg) is an anthropogenic pollutant that is toxic to wildlife and humans, but the response of remote ecosystems to globally distributed Hg is elusive. Here, we use DNA extracted from a dated sediment core to infer the response of microbes to historical Hg delivery. We observe a significant association between the mercuric reductase gene (merA) phylogeny and the timing of Hg deposition. Using relaxed molecular clock models, we show a significant increase in the scaled effective population size of the merA gene beginning ~200 years ago, coinciding with the Industrial Revolution and a coincident strong signal for positive selection acting on residues in the terminal region of the mercuric reductase. This rapid evolutionary response of microbes to changes in the delivery of anthropogenic Hg indicates that microbial genomes record ecosystem response to pollutant deposition in remote regions. PMID:26057844

WATER ON MARS: EVIDENCE FROM MER MISSION RESULTS

NASA Technical Reports Server (NTRS)

Landis, Geoffrey A.

2006-01-01

The Mars Exploration Rover (MER) mission landed two rovers on Mars, equipped with a highly-capable suite of science instruments. The Spirit rover landed on the inside Gusev Crater on January 5, 2004, and the Opportunity rover three weeks later on Meridiani Planum. This paper summarizes some of the findings from the MER rovers related to the NASA science strategy of investigating past and present water on Mars.

Development of animal models against emerging coronaviruses: From SARS to MERS coronavirus.

PubMed

Sutton, Troy C; Subbarao, Kanta

2015-05-01

Two novel coronaviruses have emerged to cause severe disease in humans. While bats may be the primary reservoir for both viruses, SARS coronavirus (SARS-CoV) likely crossed into humans from civets in China, and MERS coronavirus (MERS-CoV) has been transmitted from camels in the Middle East. Unlike SARS-CoV that resolved within a year, continued introductions of MERS-CoV present an on-going public health threat. Animal models are needed to evaluate countermeasures against emerging viruses. With SARS-CoV, several animal species were permissive to infection. In contrast, most laboratory animals are refractory or only semi-permissive to infection with MERS-CoV. This host-range restriction is largely determined by sequence heterogeneity in the MERS-CoV receptor. We describe animal models developed to study coronaviruses, with a focus on host-range restriction at the level of the viral receptor and discuss approaches to consider in developing a model to evaluate countermeasures against MERS-CoV. Copyright © 2015. Published by Elsevier Inc.

Recapitulating phylogenies using k-mers: from trees to networks.

PubMed

Bernard, Guillaume; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k -mers (subsequences at fixed length k ). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel's idea of ontogeny, we argue that genome phylogenies can be inferred using k -mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.

Unraveling the drivers of MERS-CoV transmission

PubMed Central

Cauchemez, Simon; Nouvellet, Pierre; Cori, Anne; Jombart, Thibaut; Clapham, Hannah; Moore, Sean; Mills, Harriet Linden; Salje, Henrik; Collins, Caitlin; Rodriquez-Barraquer, Isabel; Riley, Steven; Truelove, Shaun; Algarni, Homoud; Alhakeem, Rafat; AlHarbi, Khalid; Turkistani, Abdulhafiz; Aguas, Ricardo J.; Cummings, Derek A. T.; Van Kerkhove, Maria D.; Donnelly, Christl A.; Lessler, Justin; Fraser, Christophe; Al-Barrak, Ali; Ferguson, Neil M.

2016-01-01

With more than 1,700 laboratory-confirmed infections, Middle East respiratory syndrome coronavirus (MERS-CoV) remains a significant threat for public health. However, the lack of detailed data on modes of transmission from the animal reservoir and between humans means that the drivers of MERS-CoV epidemics remain poorly characterized. Here, we develop a statistical framework to provide a comprehensive analysis of the transmission patterns underlying the 681 MERS-CoV cases detected in the Kingdom of Saudi Arabia (KSA) between January 2013 and July 2014. We assess how infections from the animal reservoir, the different levels of mixing, and heterogeneities in transmission have contributed to the buildup of MERS-CoV epidemics in KSA. We estimate that 12% [95% credible interval (CI): 9%, 15%] of cases were infected from the reservoir, the rest via human-to-human transmission in clusters (60%; CI: 57%, 63%), within (23%; CI: 20%, 27%), or between (5%; CI: 2%, 8%) regions. The reproduction number at the start of a cluster was 0.45 (CI: 0.33, 0.58) on average, but with large SD (0.53; CI: 0.35, 0.78). It was >1 in 12% (CI: 6%, 18%) of clusters but fell by approximately one-half (47% CI: 34%, 63%) its original value after 10 cases on average. The ongoing exposure of humans to MERS-CoV from the reservoir is of major concern, given the continued risk of substantial outbreaks in health care systems. The approach we present allows the study of infectious disease transmission when data linking cases to each other remain limited and uncertain. PMID:27457935

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

Prophylaxis With a Middle East Respiratory Syndrome Coronavirus (MERS-CoV)–Specific Human Monoclonal Antibody Protects Rabbits From MERS-CoV Infection

PubMed Central

Houser, Katherine V.; Gretebeck, Lisa; Ying, Tianlei; Wang, Yanping; Vogel, Leatrice; Lamirande, Elaine W.; Bock, Kevin W.; Moore, Ian N.; Dimitrov, Dimiter S.; Subbarao, Kanta

2016-01-01

With >1600 documented human infections with Middle East respiratory syndrome coronavirus (MERS-CoV) and a case fatality rate of approximately 36%, medical countermeasures are needed to prevent and limit the disease. We examined the in vivo efficacy of the human monoclonal antibody m336, which has high neutralizing activity against MERS-CoV in vitro. m336 was administered to rabbits intravenously or intranasally before infection with MERS-CoV. Prophylaxis with m336 resulted in a reduction of pulmonary viral RNA titers by 40–9000-fold, compared with an irrelevant control antibody with little to no inflammation or viral antigen detected. This protection in rabbits supports further clinical development of m336. PMID:26941283

Analysis of mercuric reductase (merA) gene diversity in an anaerobic mercury-contaminated sediment enrichment.

PubMed

Ní Chadhain, Sinéad M; Schaefer, Jeffra K; Crane, Sharron; Zylstra, Gerben J; Barkay, Tamar

2006-10-01

The reduction of ionic mercury to elemental mercury by the mercuric reductase (MerA) enzyme plays an important role in the biogeochemical cycling of mercury in contaminated environments by partitioning mercury to the atmosphere. This activity, common in aerobic environments, has rarely been examined in anoxic sediments where production of highly toxic methylmercury occurs. Novel degenerate PCR primers were developed which span the known diversity of merA genes in Gram-negative bacteria and amplify a 285 bp fragment at the 3' end of merA. These primers were used to create a clone library and to analyse merA diversity in an anaerobic sediment enrichment collected from a mercury-contaminated site in the Meadowlands, New Jersey. A total of 174 sequences were analysed, representing 71 merA phylotypes and four novel MerA clades. This first examination of merA diversity in anoxic environments suggests an untapped resource for novel merA sequences.

Antibodies against MERS coronavirus in dromedary camels, United Arab Emirates, 2003 and 2013.

PubMed

Meyer, Benjamin; Müller, Marcel A; Corman, Victor M; Reusken, Chantal B E M; Ritz, Daniel; Godeke, Gert-Jan; Lattwein, Erik; Kallies, Stephan; Siemens, Artem; van Beek, Janko; Drexler, Jan F; Muth, Doreen; Bosch, Berend-Jan; Wernery, Ulrich; Koopmans, Marion P G; Wernery, Renate; Drosten, Christian

2014-04-01

Middle East respiratory syndrome coronavirus (MERS-CoV) has caused an ongoing outbreak of severe acute respiratory tract infection in humans in the Arabian Peninsula since 2012. Dromedary camels have been implicated as possible viral reservoirs. We used serologic assays to analyze 651 dromedary camel serum samples from the United Arab Emirates; 151 of 651 samples were obtained in 2003, well before onset of the current epidemic, and 500 serum samples were obtained in 2013. Recombinant spike protein-specific immunofluorescence and virus neutralization tests enabled clear discrimination between MERS-CoV and bovine CoV infections. Most (632/651, 97.1%) camels had antibodies against MERS-CoV. This result included all 151 serum samples obtained in 2003. Most (389/651, 59.8%) serum samples had MERS-CoV-neutralizing antibody titers >1,280. Dromedary camels from the United Arab Emirates were infected at high rates with MERS-CoV or a closely related, probably conspecific, virus long before the first human MERS cases.

Mapping Potential Amplification and Transmission Hotspots for MERS-CoV, Kenya.

PubMed

Gikonyo, Stephen; Kimani, Tabitha; Matere, Joseph; Kimutai, Joshua; Kiambi, Stella G; Bitek, Austine O; Juma Ngeiywa, K J Z; Makonnen, Yilma J; Tripodi, Astrid; Morzaria, Subhash; Lubroth, Juan; Rugalema, Gabriel; Fasina, Folorunso Oludayo

2018-03-16

Dromedary camels have been implicated consistently as the source of Middle East respiratory syndrome coronavirus (MERS-CoV) human infections and attention to prevent and control it has focused on camels. To understanding the epidemiological role of camels in the transmission of MERS-CoV, we utilized an iterative empirical process in Geographic Information System (GIS) to identify and qualify potential hotspots for maintenance and circulation of MERS-CoV, and produced risk-based surveillance sites in Kenya. Data on camel population and distribution were used to develop camel density map, while camel farming system was defined using multi-factorial criteria including the agro-ecological zones (AEZs), production and marketing practices. Primary and secondary MERS-CoV seroprevalence data from specific sites were analyzed, and location-based prevalence matching with camel densities was conducted. High-risk convergence points (migration zones, trade routes, camel markets, slaughter slabs) were profiled and frequent cross-border camel movement mapped. Results showed that high camel-dense areas and interaction (markets and migration zones) were potential hotspot for transmission and spread. Cross-border contacts occurred with in-migrated herds at hotspot locations. AEZ differential did not influence risk distribution and plausible risk factors for spatial MERS-CoV hotspots were camel densities, previous cases of MERS-CoV, high seroprevalence and points of camel convergences. Although Kenyan camels are predisposed to MERS-CoV, no shedding is documented to date. These potential hotspots, determined using anthropogenic, system and trade characterizations should guide selection of sampling/surveillance sites, high-risk locations, critical areas for interventions and policy development in Kenya, as well as instigate further virological examination of camels.

Monoclonal Antibody Shows Promise as Potential Therapeutic for MERS | Poster

Cancer.gov

A monoclonal antibody has proven effective in preventing Middle Eastern Respiratory Syndrome (MERS) in lab animals, suggesting further development as a potential intervention for the deadly disease in humans, according to new research. MERS is a newly emerged coronavirus first detected in humans in 2012. Most cases have occurred in the Middle East, but the disease has appeared elsewhere. In all, MERS has infected more than 1,700 individuals and killed more than 600, according to the World Health Organization. No vaccines or antiviral therapies currently exist. Several candidate vaccines are being developed, and some have been tested in animal models, a prerequisite to human clinical trials.

Demonstration of Mer-Cure Technology for Enhanced Mercury Control

DOE Office of Scientific and Technical Information (OSTI.GOV)

John Marion; Dave O'Neill; Kevin Taugher

2008-06-01

Alstom Power Inc. has completed a DOE/NETL-sponsored program (under DOE Cooperative Agreement No. De-FC26-07NT42776) to demonstrate Mer-Cure{trademark}, one of Alstom's mercury control technologies for coal-fired boilers. The Mer-Cure{trademark}system utilizes a small amount of Mer-Clean{trademark} sorbent that is injected into the flue gas stream for oxidation and adsorption of gaseous mercury. Mer-Clean{trademark} sorbents are carbon-based and prepared with chemical additives that promote oxidation and capture of mercury. The Mer-Cure{trademark} system is unique in that the sorbent is injected into an environment where the mercury capture kinetics is accelerated. The full-scale demonstration program originally included test campaigns at two host sites: LCRA's 480-MW{sub e} Fayette Unit No.3 and Reliant Energy's 190-MW{sub e} Shawville Unit No.3. The only demonstration tests actually done were the short-term tests at LCRA due to budget constraints. This report gives a summary of the demonstration testing at Fayette Unit No.3. The goals for this Mercury Round 3 program, established by DOE/NETL under the original solicitation, were to reduce the uncontrolled mercury emissions by 90% at a cost significantly less than 50% of the previous target ofmore » $$60,000/lb mercury removed. The results indicated that Mer-Cure{trademark} technology could achieve mercury removal of 90% based on uncontrolled stack emissions. The estimated costs for 90% mercury control, at a sorbent cost of $$0.75 to $2.00/lb respectively, were $13,400 to $18,700/lb Hg removed. In summary, the results from demonstration testing show that the goals established by DOE/NETL were met during this test program. The goal of 90% mercury reduction was achieved. Estimated mercury removal costs were 69-78% lower than the benchmark of $60,000/lb mercury removed, significantly less than 50% of the baseline removal cost.« less

MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity.

PubMed

Chu, Daniel K W; Hui, Kenrie P Y; Perera, Ranawaka A P M; Miguel, Eve; Niemeyer, Daniela; Zhao, Jincun; Channappanavar, Rudragouda; Dudas, Gytis; Oladipo, Jamiu O; Traoré, Amadou; Fassi-Fihri, Ouafaa; Ali, Abraham; Demissié, Getnet F; Muth, Doreen; Chan, Michael C W; Nicholls, John M; Meyerholz, David K; Kuranga, Sulyman A; Mamo, Gezahegne; Zhou, Ziqi; So, Ray T Y; Hemida, Maged G; Webby, Richard J; Roger, Francois; Rambaut, Andrew; Poon, Leo L M; Perlman, Stanley; Drosten, Christian; Chevalier, Veronique; Peiris, Malik

2018-03-20

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa as well as in the Arabian Peninsula, zoonotic disease appears confined to the Arabian Peninsula. MERS-CoVs from Africa have hitherto been poorly studied. We genetically and phenotypically characterized MERS-CoV from dromedaries sampled in Morocco, Burkina Faso, Nigeria, and Ethiopia. Viruses from Africa (clade C) are phylogenetically distinct from contemporary viruses from the Arabian Peninsula (clades A and B) but remain antigenically similar in microneutralization tests. Viruses from West (Nigeria, Burkina Faso) and North (Morocco) Africa form a subclade, C1, that shares clade-defining genetic signatures including deletions in the accessory gene ORF4b Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung. BF785 replicated to lower titer in lungs of human DPP4-transduced mice. A reverse genetics-derived recombinant MERS-CoV (EMC) lacking ORF4b elicited higher type I and III IFN responses than the isogenic EMC virus in Calu-3 cells. However, ORF4b deletions may not be the major determinant of the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to zoonotic potential. There is an urgent need for studies of MERS-CoV at the animal-human interface. Copyright © 2018 the Author(s). Published by PNAS.

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

Humic acids enhance the microbially mediated release of sedimentary ferrous iron.

PubMed

Chang, Chun-Han; Wei, Chia-Cheng; Lin, Li-Hung; Tu, Tzu-Hsuan; Liao, Vivian Hsiu-Chuan

2016-03-01

Iron (Fe) is an essential element for many organisms, but high concentrations of iron can be toxic. The complex relation between iron, arsenic (As), bacteria, and organic matter in sediments and groundwater is still an issue of environmental concern. The present study addresses the effects of humic acids and microorganisms on the mobilization of iron in sediments from an arsenic-affected area, and the microbial diversity was analyzed. The results showed that the addition of 50, 100, and 500 mg/L humic acids enhanced ferrous iron (Fe(II)) release in a time-dependent and dose-dependent fashion under anaerobic conditions. A significant increase in the soluble Fe(II) concentrations occurred in the aqueous phases of the samples during the first 2 weeks, and aqueous Fe(II) reached its maximum concentrations after 8 weeks at the following Fe(II) concentrations: 28.95 ± 1.16 mg/L (original non-sterilized sediments), 32.50 ± 0.71 mg/L (50 mg/L humic acid-amended, non-sterilized sediments), 37.50 ± 1.85 mg/L (100 mg/L humic acid-amended, non-sterilized sediments), and 39.00 ± 0.43 mg/L (500 mg/L humic acid-amended, non-sterilized sediments). These results suggest that humic acids can further enhance the microbially mediated release of sedimentary iron under anaerobic conditions. By contrast, very insignificant amounts of iron release were observed from sterilized sediments (the abiotic controls), even with the supplementation of humic acids under anaerobic incubation. In addition, the As(III) release was increased from 50 ± 10 μg/L (original non-sterilized sediments) to 110 ± 45 μg/L (100 mg/L humic acid-amended, non-sterilized sediments) after 8 weeks of anaerobic incubation. Furthermore, a microbial community analysis indicated that the predominant class was changed from Alphaproteobacteria to Deltaproteobacteria, and clearly increased populations of Geobacter sp., Paludibacter sp., and Methylophaga sp. were found after adding humic acids

Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond.

PubMed

Lu, Guangwen; Wang, Qihui; Gao, George F

2015-08-01

Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that crossed the species barriers to infect humans. The mechanism of viral interspecies transmission is an important scientific question to be addressed. These coronaviruses contain a surface-located spike (S) protein that initiates infection by mediating receptor-recognition and membrane fusion and is therefore a key factor in host specificity. In addition, the S protein needs to be cleaved by host proteases before executing fusion, making these proteases a second determinant of coronavirus interspecies infection. Here, we summarize the progress made in the past decade in understanding the cross-species transmission of SARS-CoV and MERS-CoV by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming. Copyright © 2015 Elsevier Ltd. All rights reserved.

Debate on MERS-CoV respiratory precautions: surgical mask or N95 respirators?

PubMed Central

Chung, Jasmine Shimin; Ling, Moi Lin; Seto, Wing Hong; Ang, Brenda Sze Peng; Tambyah, Paul Anantharajah

2014-01-01

Since the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in mid-2012, there has been controversy over the respiratory precaution recommendations in different guidelines from various international bodies. Our understanding of MERS-CoV is still evolving. Current recommendations on infection control practices are heavily influenced by the lessons learnt from severe acute respiratory syndrome. A debate on respiratory precautions for MERS-CoV was organised by Infection Control Association (Singapore) and the Society of Infectious Disease (Singapore). We herein discuss and present the evidence for surgical masks for the protection of healthcare workers from MERS-CoV. PMID:25017402

Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process.

PubMed

Zhu, Weihuang; Shi, Mengran; Yu, Dan; Liu, Chongxuan; Huang, Tinglin; Wu, Fengchang

2016-03-29

The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into "redox mediator-iron oxide" interaction in the presence of DIRB. Two pre-incubation reaction systems of the "strain S12- goethite" and the "strain S12-AQS" were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for "Quinone-Iron" interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among "quinone-DIRB- goethite" under biotic/abiotic driven.

Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) in adults-a case report and literature review.

PubMed

Yuan, Junliang; Yang, Shuna; Wang, Shuangkun; Qin, Wei; Yang, Lei; Hu, Wenli

2017-05-25

Mild encephalitis/encephalopathy with reversible splenial lesion (MERS) is a rare clinico-radiological entity characterized by the magnetic resonance imaging (MRI) finding of a reversible lesion in the corpus callosum, sometimes involved the symmetrical white matters. Many cases of child-onset MERS with various causes have been reported. However, adult-onset MERS is relatively rare. The clinical characteristics and pathophysiologiccal mechanisms of adult-onset MERS are not well understood. We reviewed the literature on adult-onset MERS in order to describe the characteristics of MERS in adults and to provide experiences for clinician. We reported a case of adult-onset MERS with acute urinary retension and performed literature search from PubMed and web of science databases to identify other adult-onset MERS reports from Januarary 2004 to March 2016. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed on selection process. And then we summarized the clinico-radiological features of adult-onset MERS. Twenty-nine adult-onset MERS cases were reviewed from available literature including the case we have. 86.2% of the cases (25/29) were reported in Asia, especially in Japan. Ages varied between 18 and 59 years old with a 12:17 female-to-male ratio. The major cause was infection by virus or bacteria. Fever and headache were the most common clinical manifestation, and acute urinary retention was observed in 6 patients. All patients recovered completely within a month. Adult-onset MERS is an entity with a broad clinico-radiological spectrum because of the various diseases and conditions. There are similar characteristics between MERS in adults and children, also some differences.

Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter.

PubMed

Mohamed Hashim, Ezzeddin Kamil; Abdullah, Rosni

2015-12-21

Empirical analysis on k-mer DNA has been proven as an effective tool in finding unique patterns in DNA sequences which can lead to the discovery of potential sequence motifs. In an extensive study of empirical k-mer DNA on hundreds of organisms, the researchers found unique multi-modal k-mer spectra occur in the genomes of organisms from the tetrapod clade only which includes all mammals. The multi-modality is caused by the formation of the two lowest modes where k-mers under them are referred as the rare k-mers. The suppression of the two lowest modes (or the rare k-mers) can be attributed to the CG dinucleotide inclusions in them. Apart from that, the rare k-mers are selectively distributed in certain genomic features of CpG Island (CGI), promoter, 5' UTR, and exon. We correlated the rare k-mers with hundreds of annotated features using several bioinformatic tools, performed further intrinsic rare k-mer analyses within the correlated features, and modeled the elucidated rare k-mer clustering feature into a classifier to predict the correlated CGI and promoter features. Our correlation results show that rare k-mers are highly associated with several annotated features of CGI, promoter, 5' UTR, and open chromatin regions. Our intrinsic results show that rare k-mers have several unique topological, compositional, and clustering properties in CGI and promoter features. Finally, the performances of our RWC (rare-word clustering) method in predicting the CGI and promoter features are ranked among the top three, in eight of the CGI and promoter evaluations, among eight of the benchmarked datasets. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Monoclonal Antibody Shows Promise as Potential Therapeutic for MERS | Poster

Cancer.gov

A monoclonal antibody has proven effective in preventing Middle Eastern Respiratory Syndrome (MERS) in lab animals, suggesting further development as a potential intervention for the deadly disease in humans, according to new research. MERS is a newly emerged coronavirus first detected in humans in 2012. Most cases have occurred in the Middle East, but the disease has appeared

KMC 3: counting and manipulating k-mer statistics.

PubMed

Kokot, Marek; Dlugosz, Maciej; Deorowicz, Sebastian

2017-09-01

Counting all k -mers in a given dataset is a standard procedure in many bioinformatics applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm together with KMC tools for manipulating k -mer databases. Usefulness of the tools is shown on a few real problems. Program is freely available at http://sun.aei.polsl.pl/REFRESH/kmc . sebastian.deorowicz@polsl.pl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Activated Microglia Desialylate and Phagocytose Cells via Neuraminidase, Galectin-3, and Mer Tyrosine Kinase

PubMed Central

Nomura, Koji; Vilalta, Anna; Allendorf, David H.; Hornik, Tamara C.

2017-01-01

Activated microglia can phagocytose dying, stressed, or excess neurons and synapses via the phagocytic receptor Mer tyrosine kinase (MerTK). Galectin-3 (Gal-3) can cross-link surface glycoproteins by binding galactose residues that are normally hidden below terminal sialic acid residues. Gal-3 was recently reported to opsonize cells via activating MerTK. We found that LPS-activated BV-2 microglia rapidly released Gal-3, which was blocked by calcineurin inhibitors. Gal-3 bound to MerTK on microglia and to stressed PC12 (neuron-like) cells, and it increased microglial phagocytosis of PC12 cells or primary neurons, which was blocked by inhibition of MerTK. LPS-activated microglia exhibited a sialidase activity that desialylated PC12 cells and could be inhibited by Tamiflu, a neuraminidase (sialidase) inhibitor. Sialidase treatment of PC12 cells enabled Gal-3 to bind and opsonize the live cells for phagocytosis by microglia. LPS-induced microglial phagocytosis of PC12 was prevented by small interfering RNA knockdown of Gal-3 in microglia, lactose inhibition of Gal-3 binding, inhibition of neuraminidase with Tamiflu, or inhibition of MerTK by UNC569. LPS-induced phagocytosis of primary neurons by primary microglia was also blocked by inhibition of MerTK. We conclude that activated microglia release Gal-3 and a neuraminidase that desialylates microglial and PC12 surfaces, enabling Gal-3 binding to PC12 cells and their phagocytosis via MerTK. Thus, Gal-3 acts as an opsonin of desialylated surfaces, and inflammatory loss of neurons or synapses may potentially be blocked by inhibiting neuraminidases, Gal-3, or MerTK. PMID:28500071

MERS, SARS and other coronaviruses as causes of pneumonia.

PubMed

Yin, Yudong; Wunderink, Richard G

2018-02-01

Human coronaviruses (HCoVs) have been considered to be relatively harmless respiratory pathogens in the past. However, after the outbreak of the severe acute respiratory syndrome (SARS) and emergence of the Middle East respiratory syndrome (MERS), HCoVs have received worldwide attention as important pathogens in respiratory tract infection. This review focuses on the epidemiology, pathogenesis and clinical characteristics among SARS-coronaviruses (CoV), MERS-CoV and other HCoV infections. © 2017 Asian Pacific Society of Respirology.

Differential mercury volatilization by tobacco organs expressing a modified bacterial merA gene.

PubMed

He, Y K; Sun, J G; Feng, X Z; Czakó, M; Márton, L

2001-09-01

Mercury pollution is a major environmental problem accompanying industrial activities. Most of the mercury released ends up and retained in the soil as complexes of the toxic ionic mercury (Hg2+), which then can be converted by microbes into the even more toxic methylmercury which tends to bioaccumulate. Mercury detoxification of the soil can also occur by microbes converting the ionic mercury into the least toxic metallic mercury (Hg0) form, which then evaporates. The remediation potential of transgenic plants carrying the MerA gene from E. coli encoding mercuric ion reductase could be evaluated. A modified version of the gene, optimized for plant codon preferences (merApe9, Rugh et al. 1996), was introduced into tobacco by Agrobacterium-mediated leaf disk transformation. Transgenic seeds were resistant to HgCl2 at 50 microM, and some of them (10-20% ) could germinate on media containing as much as 350 microM HgCl2, while the control plants were fully inhibited or died on 50 microM HgCl2. The rate of elemental mercury evolution from Hg2+ (added as HgCl2) was 5-8 times higher for transgenic plants than the control. Mercury volatilization by isolated organs standardized for fresh weight was higher (up to 5 times) in the roots than in shoots or the leaves. The data suggest that it is the root system of the transgenic plants that volatilizes most of the reduced mercury (Hg0). It also suggests that much of the mercury need not enter the vascular system to be transported to the leaves for volatilization. Transgenic plants with the merApe9 gene may be used to mercury detoxification for environmental improvement in mercury-contaminated regions more efficiently than it had been predicted based on data on volatilization of whole plants via the upper parts only (Rugh et al. 1996).

MERS-CoV infection: Mind the public knowledge gap.

PubMed

Bawazir, Amen; Al-Mazroo, Eman; Jradi, Hoda; Ahmed, Anwar; Badri, Motasim

In August 2015, the Corona outbreak caused by Middle East respiratory syndrome coronavirus (MERS-CoV) was the 9th episode since June 2012 in Saudi Arabia. Little is known about the public awareness toward the nature or prevention of the disease. The aim of this work was to assess the knowledge of the adult population in Riyadh toward the MERS-CoV. In this cross-sectional survey, a self-administrated questionnaire was distributed to randomly selected participants visiting malls in Riyadh. The questionnaire contained measurable epidemiological and clinical MERS-CoV knowledge level variables and relevant source of information. The study included 676 participants. Mean age was 32.5 (±SD 8.6) years and 353 (47.8%) were males. Almost all participants heard about the corona disease and causative agent. The study showed a fair overall knowledge (66.0%), less knowledge on epidemiological features of the disease (58.3%), and good knowledge (90.7%) on the clinical manifestation of the MERS-CoV. Internet was the major (89.0%) source of disease information, and other sources including health care providers, SMS, television, magazines and books were low rated (all <25%). In a multivariate logistic regression analysis age ≤30 years (Odds Ratio (OR)=1.647, 95%CI 1.048-2.584, P=0.030), male gender (OR=1.536, 95%CI 1.105-2.134, P=0.01), and no tertiary education (OR=1.957, 95%CI 1.264-3.030, P=0.003) were independent significant predictors of poor epidemiological knowledge. This study concludes that there was inadequate epidemiological knowledge received by the public and the reliance mostly on the clinical manifestations to recognizing the MERS-CoV disease. Comprehensive public health education programs is important to increase awareness of simple epidemiological determinants of the disease is warranted. Copyright © 2017. Published by Elsevier Ltd.

Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

PubMed

LeBouder, Emmanuel; Rey-Nores, Julia E; Raby, Anne-Catherine; Affolter, Michael; Vidal, Karine; Thornton, Catherine A; Labéta, Mario O

2006-03-15

The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

Characteristics and kinetic analysis of AQS transformation and microbial goethite reduction: Insight into “redox mediator-microbe-iron oxide” interaction process

DOE PAGES

Zhu, Weihuang; Shi, Mengran; Yu, Dan; ...

2016-03-29

Here, the characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into “redox mediator-iron oxide” interaction in the presence of DIRB. Two pre-incubation reaction systems of the “strain S12-goethite” and the “strain S12-AQS” were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of themore » redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for “Quinone-Iron” interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among “quinone-DIRB- goethite” under biotic/abiotic driven.« less

Investigating the Effects of Mass Media Exposure on the Uptake of Preventive Measures by Hong Kong Residents during the 2015 MERS Outbreak: The Mediating Role of Interpersonal Communication and the Perception of Concern.

PubMed

Ludolph, Ramona; Schulz, Peter J; Chen, Ling

2018-01-01

In 2015, South Korea experienced the largest outbreak to date of the Middle East Respiratory Syndrome (MERS-CoV) outside the Middle East. Fears related to a potential spread of the disease led to an increased alert level as well as heightened media coverage in the neighboring Hong Kong. A cross-sectional survey (N = 533) among residents of Hong Kong was conducted to assess the relationships between the effects of outbreak-related mass media coverage, interpersonal communication, the perceived level of concern in one's close environment, and the uptake of preventive measures. A serial multiple mediator model finds that interpersonal communication and higher perceived concern indirectly influence the effects of media coverage on the engagement in preventive actions. These results expand previous research on the mediating role of interpersonal communication and support assumptions about a modified two-step flow of communication in the context of a public health emergency.

Challenges presented by MERS corona virus, and SARS corona virus to global health.

PubMed

Al-Hazmi, Ali

2016-07-01

Numerous viral infections have arisen and affected global healthcare facilities. Millions of people are at severe risk of acquiring several evolving viral infections through several factors. In the present article we have described about risk factors, chance of infection, and prevention methods of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and severe acute respiratory syndrome (SARS-CoV), human coronaviruses (CoVs) frequently cause a normal cold which is mild and self-restricting. Zoonotic transmission of CoVs such as the newly discovered MERS-CoV and SARS-CoV, may be associated with severe lower respiratory tract infection. The present review provides the recent clinical and pathological information on MERS and SARS. The task is to transform these discoveries about MERS and SARS pathogenesis and to develop intervention methods that will eventually allow the effective control of these recently arising severe viral infections. Global health sector has learnt many lessons through the recent outbreak of MERS and SARS, but the need for identifying new antiviral treatment was not learned. In the present article we have reviewed the literature on the several facets like transmission, precautions and effectiveness of treatments used in patients with MERS-CoV and SARS infections.

Using pseudoalignment and base quality to accurately quantify microbial community composition

PubMed Central

Novembre, John

2018-01-01

Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies. PMID:29659582

Worry experienced during the 2015 Middle East Respiratory Syndrome (MERS) pandemic in Korea

PubMed Central

Ro, Jun-Soo; Lee, Jin-Seok; Kang, Sung-Chan; Jung, Hye-Min

2017-01-01

Background Korea failed in its risk communication during the early stage of the Middle East Respiratory Syndrome (MERS) outbreak; consequently, it faced difficulties in managing MERS, while disease-related worry increased. Disease-related worry can help disease prevention and management, but can also have a detrimental effect. This study measured the overall level of disease-related worry during the MERS outbreak period in Korea and the influencing factors and levels of disease-related worry during key outbreak periods. Methods The cross-sectional survey included 1,000 adults who resided in Korea. An ordinal logistic regression was performed for the overall level of MERS-related worry, and influencing factors of worry were analyzed. A reliability test was performed on the levels of MERS-related worry during key outbreak periods. Results The overall level of MERS-related worry was 2.44. Multivariate analysis revealed that women and respondents w very poor subjective health status had higher levels of worry. Respondents with very high stress in daily life had higher levels of worry than those who reported having little stress. The reliability test results on MERS-related worry scores during key outbreak periods showed consistent scores during each period. Conclusion Level of worry increased in cases having higher perceived susceptibility and greater trust in informal information, while initial stage of outbreak was closely associated with that at later stages. These findings suggest the importance of managing the level of worry by providing timely and accurate disease-related information during the initial stage of disease outbreak. PMID:28273131

[Competition between redox mediator and oxygen in the microbial fuel cell].

PubMed

Alferov, S V; Vozchikova, S V; Arlyapov, V A; Alferov, V A; Reshetilov, A N

2017-01-01

The maximal rates and effective constants of 2,6-dichlorphenolindophenol and oxygen reduction by bacterim Gluconobacter oxydans in bacterial fuel cells under different conditions were evaluated. In an open-circuit mode, the rate of 2,6-dichlorphenolindophenol reduction coupled with ethanol oxidation under oxygen and nirogen atmospheres were 1.0 and 1.1 μM s–1 g–1, respectively. In closed-circuit mode, these values were 0.4 and 0.44 μM s–1 g–1, respectively. The initial rate of mediator reduction with the use of membrane fractions of bacteria in oxygen and nitrogen atmospheres in open-circuit mode were 6.3 and 6.9 μM s–1 g–1, whereas these values in closed-circuit mode comprised 2.2 and 2.4 μM s–1 g–1, respectively. The oxygen reduction rates in the presence and absence of 2,6-dichlorphenolindophenol were 0.31 and 0.32 μM s–1 g–1, respectively. The data obtained in this work demonstrated independent electron transfer from bacterial redox centers to the mediator and the absence of competition between the redox mediator and oxygen. The results can make it possible to reduce costs of microbial fuel cells based on activity of acetic acid bacteria G. oxydans.

The role microbial sulfate reduction in the direct mediation of sedimentary authigenic carbonate precipitation

NASA Astrophysics Data System (ADS)

Turchyn, A. V.; Walker, K.; Sun, X.

2016-12-01

The majority of modern deep marine sediments are bathed in water that is undersaturated with respect to calcium carbonate. However, within marine sediments changing chemical conditions, driven largely by the microbial oxidation of organic carbon in the absence of oxygen, lead to supersaturated conditions and drive calcium carbonate precipitation. This sedimentary calcium carbonate is often called `authigenic carbonate', and is found in the form of cements and disseminated crystals within the marine sedimentary pile. As this precipitation of this calcium carbonate is microbially mediated, identifying authigenic carbonate within the geological record and understanding what information its geochemical and/or isotopic signature may hold is key for understanding its importance and what information it may contain past life. However, the modern controls on authigenic carbonate precipitation remain enigmatic because the myriad of microbially mediated reactions occurring within sediments both directly and indirectly impact the proton balance. In this submission we present data from 25 ocean sediment cores spanning the globe where we explore the deviation from the stoichiometrically predicted relationships among alkalinity, calcium and sulfate concentrations. In theory for every mol of organic carbon reduced by sulfate, two mol of alkalinity is produced, and to precipitate subsurface calcium carbonate one mol of calcium is used to consume two mol of alkalinity. We use this data with a model to explore changes in carbonate saturation state with depth below the seafloor. Alkalinity changes in the subsurface are poorly correlated with changes in calcium concentrations, however calcium concentrations are directly and tightly coupled to changes in sulfate concentrations in all studied sites. This suggests a direct role for sulfate reducing bacteria in the precipitation of subsurface carbonate cements.

Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes.

PubMed

Lin, Min-Han; Moses, David C; Hsieh, Chih-Hua; Cheng, Shu-Chun; Chen, Yau-Hung; Sun, Chiao-Yin; Chou, Chi-Yuan

2018-02-01

Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in southern China in late 2002 and caused a global outbreak with a fatality rate around 10% in 2003. Ten years later, a second highly pathogenic human CoV, MERS-CoV, emerged in the Middle East and has spread to other countries in Europe, North Africa, North America and Asia. As of November 2017, MERS-CoV had infected at least 2102 people with a fatality rate of about 35% globally, and hence there is an urgent need to identify antiviral drugs that are active against MERS-CoV. Here we show that a clinically available alcohol-aversive drug, disulfiram, can inhibit the papain-like proteases (PL pro s) of MERS-CoV and SARS-CoV. Our findings suggest that disulfiram acts as an allosteric inhibitor of MERS-CoV PL pro but as a competitive (or mixed) inhibitor of SARS-CoV PL pro . The phenomenon of slow-binding inhibition and the irrecoverability of enzyme activity after removing unbound disulfiram indicate covalent inactivation of SARS-CoV PL pro by disulfiram, while synergistic inhibition of MERS-CoV PL pro by disulfiram and 6-thioguanine or mycophenolic acid implies the potential for combination treatments using these three clinically available drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

Far-UVC light: A new tool to control the spread of airborne-mediated microbial diseases.

PubMed

Welch, David; Buonanno, Manuela; Grilj, Veljko; Shuryak, Igor; Crickmore, Connor; Bigelow, Alan W; Randers-Pehrson, Gerhard; Johnson, Gary W; Brenner, David J

2018-02-09

Airborne-mediated microbial diseases such as influenza and tuberculosis represent major public health challenges. A direct approach to prevent airborne transmission is inactivation of airborne pathogens, and the airborne antimicrobial potential of UVC ultraviolet light has long been established; however, its widespread use in public settings is limited because conventional UVC light sources are both carcinogenic and cataractogenic. By contrast, we have previously shown that far-UVC light (207-222 nm) efficiently inactivates bacteria without harm to exposed mammalian skin. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. We show for the first time that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm 2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Continuous very low dose-rate far-UVC light in indoor public locations is a promising, safe and inexpensive tool to reduce the spread of airborne-mediated microbial diseases.

The Ballerina Experiment on the Rømer Mission

NASA Astrophysics Data System (ADS)

Brandt, Soren

The Rømer mission has recently been approved as the next mission within the Danish Small Satellite Program. The scientific payload will consist of two separate experiments, the MONS and the Ballerina payloads. The primary objective of Ballerina is to provide accurate, real-time positions relayed to ground for ~ 70 Gamma Ray Bursts (GRBs) per year, and to study the temporal and spectral evolution of the early GRB X-ray afterglow. As an additional goal, Ballerina will detect and study bright X-ray transients, in particular X-ray novae and micro-quasar systems. R{\\o}mer is currently scheduled for launch in late 2003.

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

PubMed Central

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Boosting mediated electron transfer in bioelectrochemical systems with tailored defined microbial cocultures.

PubMed

Schmitz, Simone; Rosenbaum, Miriam A

2018-05-19

Bioelectrochemical systems (BES) hold great promise for sustainable energy generation via a microbial catalyst from organic matter, for example, from wastewater. To improve current generation in BES, understanding the underlying microbiology of the electrode community is essential. Electron mediator producing microorganism like Pseudomonas aeruginosa play an essential role in efficient electricity generation in BES. These microbes enable even nonelectroactive microorganism like Enterobacter aerogenes to contribute to current production. Together they form a synergistic coculture, where both contribute to community welfare. To use microbial co-operation in BES, the physical and chemical environments provided in the natural habitats of the coculture play a crucial role. Here, we show that synergistic effects in defined cocultures of P. aeruginosa and E. aerogenes can be strongly enhanced toward high current production by adapting process parameters, like pH, temperature, oxygen demand, and substrate requirements. Especially, oxygen was identified as a major factor influencing coculture behavior and optimization of its supply could enhance electric current production over 400%. Furthermore, operating the coculture in fed-batch mode enabled us to obtain very high current densities and to harvest electrical energy for 1 month. In this optimized condition, the coulombic efficiency of the process was boosted to 20%, which is outstanding for mediator-based electron transfer. This study lays the foundation for a rationally designed utilization of cocultures in BES for bioenergy generation from specific wastewaters or for bioprocess sensing and for benefiting from their synergistic effects under controlled bioprocess condition. © 2018 Wiley Periodicals, Inc.

Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.

PubMed

Almutairy, Meznah; Torng, Eric

2018-01-01

Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method.

Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches

PubMed Central

Torng, Eric

2018-01-01

Bioinformatics applications and pipelines increasingly use k-mer indexes to search for similar sequences. The major problem with k-mer indexes is that they require lots of memory. Sampling is often used to reduce index size and query time. Most applications use one of two major types of sampling: fixed sampling and minimizer sampling. It is well known that fixed sampling will produce a smaller index, typically by roughly a factor of two, whereas it is generally assumed that minimizer sampling will produce faster query times since query k-mers can also be sampled. However, no direct comparison of fixed and minimizer sampling has been performed to verify these assumptions. We systematically compare fixed and minimizer sampling using the human genome as our database. We use the resulting k-mer indexes for fixed sampling and minimizer sampling to find all maximal exact matches between our database, the human genome, and three separate query sets, the mouse genome, the chimp genome, and an NGS data set. We reach the following conclusions. First, using larger k-mers reduces query time for both fixed sampling and minimizer sampling at a cost of requiring more space. If we use the same k-mer size for both methods, fixed sampling requires typically half as much space whereas minimizer sampling processes queries only slightly faster. If we are allowed to use any k-mer size for each method, then we can choose a k-mer size such that fixed sampling both uses less space and processes queries faster than minimizer sampling. The reason is that although minimizer sampling is able to sample query k-mers, the number of shared k-mer occurrences that must be processed is much larger for minimizer sampling than fixed sampling. In conclusion, we argue that for any application where each shared k-mer occurrence must be processed, fixed sampling is the right sampling method. PMID:29389989

Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.

PubMed

Alnazawi, Mohamed; Altaher, Abdallah; Kandeel, Mahmoud

2017-01-01

Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

PubMed

Pan, Tony; Flick, Patrick; Jain, Chirag; Liu, Yongchao; Aluru, Srinivas

2017-10-09

Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's k-mer counter performs similarly or better than the best existing k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1% of the k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first k-mer indexing library for distributed memory environments, and the first extensible library for general k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.

Simrank: Rapid and sensitive general-purpose k-mer search tool

PubMed Central

2011-01-01

Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity. PMID:21524302

Nordic Winter and Cold: Their Correspondence with Tomas Tranströmer's Poetry

ERIC Educational Resources Information Center

Hosian, Mohammad Akbar

2015-01-01

The Nobel Prize winning poet Tomas Tranströmer was born and bred in Sweden, a remarkably Scandinavian country. Topographically, Scandinavian countries are locations of extreme cold and snowing. This distinguishing climatic condition has had a dominant influence and impact on almost all Scandinavian art and literature, including Tomas Tranströmer's…

Phenetic Comparison of Prokaryotic Genomes Using k-mers

PubMed Central

Déraspe, Maxime; Raymond, Frédéric; Boisvert, Sébastien; Culley, Alexander; Roy, Paul H.; Laviolette, François; Corbeil, Jacques

2017-01-01

Abstract Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets. PMID:28957508

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture.

PubMed

Qin, Yuan; Druzhinina, Irina S; Pan, Xueyu; Yuan, Zhilin

2016-11-15

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Large supramolecular structures of 33-mer gliadin peptide activate toll-like receptors in macrophages.

PubMed

Herrera, María Georgina; Pizzuto, Malvina; Lonez, Caroline; Rott, Karsten; Hütten, Andreas; Sewald, Norbert; Ruysschaert, Jean-Marie; Dodero, Veronica Isabel

2018-04-22

Gliadin, an immunogenic protein present in wheat, is not fully degraded by humans and after the normal gastric and pancreatic digestion, the immunodominant 33-mer gliadin peptide remains unprocessed. The 33-mer gliadin peptide is found in human faeces and urine, proving not only its proteolytic resistance in vivo but more importantly its transport through the entire human body. Here, we demonstrate that 33-mer supramolecular structures larger than 220 nm induce the overexpression of nuclear factor kappa B (NF-κB) via a specific Toll-like Receptor (TLR) 2 and (TLR) 4 dependent pathway and the secretion of pro-inflammatory cytokines such as IP-10/CXCL10 and TNF-α. Using helium ion microscopy, we elucidated the initial stages of oligomerisation of 33-mer gliadin peptide, showing that rod-like oligomers are nucleation sites for protofilament formation. The relevance of the 33-mer supramolecular structures in the early stages of the disease is paving new perspectives in the understanding of gluten-related disorders. Copyright © 2018. Published by Elsevier Inc.

Public response to MERS-CoV in the Middle East: iPhone survey in six countries.

PubMed

Alqahtani, Amani S; Rashid, Harunor; Basyouni, Mada H; Alhawassi, Tariq M; BinDhim, Nasser F

Gulf Cooperation Council (GCC) countries bear the heaviest brunt of MERS-CoV. This study aims to compare public awareness and practice around MERS-CoV across GCC countries. A cross-sectional survey was conducted using the Gulf Indicators (GI) smartphone app among people in the six GCC countries, namely Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Bahrain, and Oman. A total of 1812 participants recruited. All were aware of MERS-CoV, yet the perception and practice around MERS-CoV varied widely between countries. Over two thirds were either "not concerned" or "slightly concerned" about contracting MERS-CoV; believing that they were under Allah's (God's) protection (40%) was the most cited reason. While 79% were aware that the disease can transmit through droplet from infected person, only 12% stated that MERS-CoV transmits via camels; people in Saudi Arabia were better aware of the transmission. Nevertheless, only 22% of respondents believed that camels are the zoonotic reservoir of MERS-CoV. Those who were concerned about contracting MERS-CoV (aOR: 1.6, 95% CI: 1.2-2.1, p<0.01) and those who thought MERS-CoV to be a severe disease only for those with high-risk conditions (aOR: 1.5, 95% CI: 1.1-2.1, p<0.01) were more likely to believe that camels are the zoonotic source. However, residents of KSA (aOR: 0.03, 95% CI: 0.01-0.07, p<0.01), UAE (aOR: 0.01, 95% CI: 0.004-0.02, p<0.01) and Kuwait (aOR: 0.03, 95% CI: 0.01-0.07, p<0.01) were less likely to believe that camels are the main zoonotic source compared to respondents from the other countries. Hygienic measures were more commonly adopted than avoidance of camels or their raw products, yet there was a discrepancy between the countries. This study highlights that despite being aware of the ongoing MERS-CoV epidemic; many people lack accurate understanding about MERS-CoV transmission, prevention, and are not fully compliant with preventive measures. Copyright © 2017 The Authors. Published by Elsevier Ltd

28-mer Fragment Derived from Enterocin CRL35 Displays an Unexpected Bactericidal Effect on Listeria Cells.

PubMed

Masias, Emilse; Sanches, Paulo R S; Dupuy, Fernando G; Acuna, Leonardo; Bellomio, Augusto; Cilli, Eduardo; Saavedra, Lucila; Minahk, Carlos

2015-01-01

Two shorter peptides derived from enterocin CRL35, a 43-mer bacteriocin, were synthesized i.e. the N-terminal fragment spanning from residues 1 to 15, and a 28-mer fragment that represents the C-terminal of enterocin CRL35, the residues 16 to 43. The separate peptides showed no activity when combined. On one hand, the 28-mer peptide displayed an unpredicted antimicrobial activity. On the other, 15- mer peptide had no consistent anti-Listeria effect. The dissociation constants calculated from experimental data indicated that all peptides could bind at similar extent to the sensitive cells. However, transmembrane electrical potential was not dissipated to the same level by the different peptides; whereas the full-length and the C-terminal 28-mer fragment induced almost full dissipation, 15-mer fragment produced only a slow and incomplete effect. Furthermore, a different interaction of each peptide with membranes was demonstrated based on studies carried out with liposomes, which led us to conclude that activity was related to structure rather than to net positive charges. These results open up the possibility of designing new peptides based on the 28-mer fragment with enhanced activity, which would represent a promising approach for combating Listeria and other pathogens.

Determining geographical spread pattern of MERS-CoV by distance method using Kimura model

NASA Astrophysics Data System (ADS)

Amiroch, Siti; Rohmatullah, Arif

2017-03-01

MERS-CoV or generally called as Middle East Respiratory Syndrome Coronavirus, a respiratory disease syndrome caused by a corona virus that attacks the respiratory tract ranging from mild to severe acute indication of fever, cough and shortness of breath. The cases happened relate to the countries in the Arabian Peninsula (Middle East) and there were 356 deaths have been reported due to the spread of the epidemic MERS. The data used in the case of MERS are the data DNA sequences taken from Genbank, the online database of the United States that stores the results of molecular biological experiments from all over the world (http://www.ncbi.nlm.nih.gov). In this case, bioinformatics plays an important role of reading sequences of DNA and genetic information by using the main device in the form of software that is supported by the availability of the Internet, while the analysis there in made and proven with mathematical methods. In similar research conducted by molecular biologists and physicians, the process of DNA sequencing is done with software that is already available like BLAST. In order to determine the MERS geographical distribution patterns in the Arabian Peninsula is done with program Clustal W, Bayesian, Phylip, etc. In this study, the writer use the Matlab simulation for all processes starting sequence alignment, counting the number of transitions and transversion substitutions for each sequence and its location up to the process of forming a phylogenetic tree that figures out the pattern of spread of the epidemic MERS. Mathematical analysis performed on a decline in the formula is to find Kimura evolutionary models and the process of forming a phylogenetic tree (the pattern of the epidemic MERS distribution) with neighbor joining algorithm. Finally it was obtained the pattern of geographical spread with 6 groups epidemic of MERS which ultimately turns out that all the MERS viruses that were spread in the Arabian Peninsula everything are almost the same as

Building predictive models for MERS-CoV infections using data mining techniques.

PubMed

Al-Turaiki, Isra; Alshahrani, Mona; Almutairi, Tahani

Recently, the outbreak of MERS-CoV infections caused worldwide attention to Saudi Arabia. The novel virus belongs to the coronaviruses family, which is responsible for causing mild to moderate colds. The control and command center of Saudi Ministry of Health issues a daily report on MERS-CoV infection cases. The infection with MERS-CoV can lead to fatal complications, however little information is known about this novel virus. In this paper, we apply two data mining techniques in order to better understand the stability and the possibility of recovery from MERS-CoV infections. The Naive Bayes classifier and J48 decision tree algorithm were used to build our models. The dataset used consists of 1082 records of cases reported between 2013 and 2015. In order to build our prediction models, we split the dataset into two groups. The first group combined recovery and death records. A new attribute was created to indicate the record type, such that the dataset can be used to predict the recovery from MERS-CoV. The second group contained the new case records to be used to predict the stability of the infection based on the current status attribute. The resulting recovery models indicate that healthcare workers are more likely to survive. This could be due to the vaccinations that healthcare workers are required to get on regular basis. As for the stability models using J48, two attributes were found to be important for predicting stability: symptomatic and age. Old patients are at high risk of developing MERS-CoV complications. Finally, the performance of all the models was evaluated using three measures: accuracy, precision, and recall. In general, the accuracy of the models is between 53.6% and 71.58%. We believe that the performance of the prediction models can be enhanced with the use of more patient data. As future work, we plan to directly contact hospitals in Riyadh in order to collect more information related to patients with MERS-CoV infections. Copyright © 2016

Effects of Human Recombinant PEDF Protein and PEDF-Derived Peptide 34-mer on Choroidal Neovascularization

PubMed Central

Amaral, Juan

2010-01-01

Purpose. Pigment epithelium-derived factor (PEDF) is a serpin with antiangiogenic properties. Previously, the authors showed that PEDF injected into the subconjunctiva reaches the choroid. Here, they examined the effects of PEDF polypeptide fragments on vessel sprouting and on choroidal neovascularization (CNV) after subconjunctival administration. Methods. Recombinant human PEDF (rhuPEDF) was cleaved at its serpin-exposed loop by limited chymotrypsin proteolysis. Synthetic PEDF peptides 34-mer (Asp44-Asn77) and 44-mer (Val78-Thr121) were used. Ex vivo chick aortic vessel sprouting assays were performed. CNV was induced in rats by laser injury of Bruch's membrane. Daily subconjunctival injections (0.01–10 pmol/d protein) were performed for 5 days starting at day of injury or at the seventh day after injury. New vessel volumes were quantified using optical sections of choroid/RPE flat-mounts labeled with isolectin-Ib4. PEDF distribution was evaluated by immunofluorescence of choroid/RPE/retina cross-sections. Results. Full-length rhuPEDF, cleaved rhuPEDF, or peptide 34-mer exhibited ex vivo antiangiogenic activity, but peptide 44-mer was inefficient. PEDF immunostaining around CNV lesions diminished after laser injury. Subconjunctival administration of rhuPEDF or 34-mer at 0.1 pmol/d decreased CNV lesion volumes by 52% and 47%, respectively, whereas those of 44-mer were similar to vehicle injections. Doses of 0.1 and 1 pmol/d rhuPEDF decreased fully developed CNV complex volumes by 45% and 50%, respectively, compared with vehicle injections. Conclusions. A functional region for the inhibition of vessel sprouting and CNV resides within the 34-mer region of PEDF. Furthermore, subconjunctival administration of optimal range dosages of rhuPEDF or 34-mer can suppress and regress rat CNV lesions, demonstrating that these agents reach the choroid/RPE complex as functionally active molecules. PMID:19850839

Sparse evidence of MERS-CoV infection among animal workers living in Southern Saudi Arabia during 2012

PubMed Central

Memish, Ziad A; Alsahly, Ahmad; Masri, Malak al; Heil, Gary L; Anderson, Benjamin D; Peiris, Malik; Khan, Salah Uddin; Gray, Gregory C

2015-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging viral pathogen that primarily causes respiratory illness. We conducted a seroprevalence study of banked human serum samples collected in 2012 from Southern Saudi Arabia. Sera from 300 animal workers (17% with daily camel exposure) and 50 non-animal-exposed controls were examined for serological evidence of MERS-CoV infection by a pseudoparticle MERS-CoV spike protein neutralization assay. None of the sera reproducibly neutralized the MERS-CoV-pseudotyped lentiviral vector. These data suggest that serological evidence of zoonotic transmission of MERS-CoV was not common among animal workers in Southern Saudi Arabia during July 2012. PMID:25470665

Mercuric ion reduction and resistance in transgenic Arabidopsis thaliana plants expressing a modified bacterial merA gene.

PubMed Central

Rugh, C L; Wilde, H D; Stack, N M; Thompson, D M; Summers, A O; Meagher, R B

1996-01-01

With global heavy metal contamination increasing, plants that can process heavy metals might provide efficient and ecologically sound approaches to sequestration and removal. Mercuric ion reductase, MerA, converts toxic Hg2+ to the less toxic, relatively inert metallic mercury (Hg0) The bacterial merA sequence is rich in CpG dinucleotides and has a highly skewed codon usage, both of which are particularly unfavorable to efficient expression in plants. We constructed a mutagenized merA sequence, merApe9, modifying the flanking region and 9% of the coding region and placing this sequence under control of plant regulatory elements. Transgenic Arabidopsis thaliana seeds expressing merApe9 germinated, and these seedlings grew, flowered, and set seed on medium containing HgCl2 concentrations of 25-100 microM (5-20 ppm), levels toxic to several controls. Transgenic merApe9 seedlings evolved considerable amounts of Hg0 relative to control plants. The rate of mercury evolution and the level of resistance were proportional to the steady-state mRNA level, confirming that resistance was due to expression of the MerApe9 enzyme. Plants and bacteria expressing merApe9 were also resistant to toxic levels of Au3+. These and other data suggest that there are potentially viable molecular genetic approaches to the phytoremediation of metal ion pollution. Images Fig. 2 Fig. 3 Fig. 4 PMID:8622910

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems

PubMed Central

Venkidusamy, Krishnaveni; Hari, Ananda Rao; Megharaj, Mallavarapu

2018-01-01

Exoelectrogenic biofilms capable of extracellular electron transfer are important in advanced technologies such as those used in microbial electrochemical remediation systems (MERS) Few bacterial strains have been, nevertheless, obtained from MERS exoelectrogenic biofilms and characterized for bioremediation potential. Here we report the identification of one such bacterial strain, Citrobacter sp. KVM11, a petrophilic, iron reducing bacterial strain isolated from hydrocarbon fed MERS, producing anodic currents in microbial electrochemical systems. Fe(III) reduction of 90.01 ± 0.43% was observed during 5 weeks of incubation with Fe(III) supplemented liquid cultures. Biodegradation screening assays showed that the hydrocarbon degradation had been carried out by metabolically active cells accompanied by growth. The characteristic feature of diazo dye decolorization was used as a simple criterion for evaluating the electrochemical activity in the candidate microbe. The electrochemical activities of the strain KVM11 were characterized in a single chamber fuel cell and three electrode electrochemical cells. The inoculation of strain KVM11 amended with acetate and citrate as the sole carbon and energy sources has resulted in an increase in anodic currents (maximum current density) of 212 ± 3 and 359 ± mA/m2 with respective coulombic efficiencies of 19.5 and 34.9% in a single chamber fuel cells. Cyclic voltammetry studies showed that anaerobically grown cells of strain KVM11 are electrochemically active whereas aerobically grown cells lacked the electrochemical activity. Electrobioremediation potential of the strain KVM11 was investigated in hydrocarbonoclastic and dye detoxification conditions using MERS. About 89.60% of 400 mg l-1 azo dye was removed during the first 24 h of operation and it reached below detection limits by the end of the batch operation (60 h). Current generation and biodegradation capabilities of strain KVM11 were examined using an initial

Petrophilic, Fe(III) Reducing Exoelectrogen Citrobacter sp. KVM11, Isolated From Hydrocarbon Fed Microbial Electrochemical Remediation Systems.

PubMed

Venkidusamy, Krishnaveni; Hari, Ananda Rao; Megharaj, Mallavarapu

2018-01-01

Exoelectrogenic biofilms capable of extracellular electron transfer are important in advanced technologies such as those used in microbial electrochemical remediation systems (MERS) Few bacterial strains have been, nevertheless, obtained from MERS exoelectrogenic biofilms and characterized for bioremediation potential. Here we report the identification of one such bacterial strain, Citrobacter sp. KVM11, a petrophilic, iron reducing bacterial strain isolated from hydrocarbon fed MERS, producing anodic currents in microbial electrochemical systems. Fe(III) reduction of 90.01 ± 0.43% was observed during 5 weeks of incubation with Fe(III) supplemented liquid cultures. Biodegradation screening assays showed that the hydrocarbon degradation had been carried out by metabolically active cells accompanied by growth. The characteristic feature of diazo dye decolorization was used as a simple criterion for evaluating the electrochemical activity in the candidate microbe. The electrochemical activities of the strain KVM11 were characterized in a single chamber fuel cell and three electrode electrochemical cells. The inoculation of strain KVM11 amended with acetate and citrate as the sole carbon and energy sources has resulted in an increase in anodic currents (maximum current density) of 212 ± 3 and 359 ± mA/m 2 with respective coulombic efficiencies of 19.5 and 34.9% in a single chamber fuel cells. Cyclic voltammetry studies showed that anaerobically grown cells of strain KVM11 are electrochemically active whereas aerobically grown cells lacked the electrochemical activity. Electrobioremediation potential of the strain KVM11 was investigated in hydrocarbonoclastic and dye detoxification conditions using MERS. About 89.60% of 400 mg l -1 azo dye was removed during the first 24 h of operation and it reached below detection limits by the end of the batch operation (60 h). Current generation and biodegradation capabilities of strain KVM11 were examined using an initial

The effect of multiple external representations (MERs) worksheets toward complex system reasoning achievement

NASA Astrophysics Data System (ADS)

Sumarno; Ibrahim, M.; Supardi, Z. A. I.

2018-03-01

The application of a systems approach to assessing biological systems provides hope for a coherent understanding of cell dynamics patterns and their relationship to plant life. This action required the reasoning about complex systems. In other sides, there were a lot of researchers who provided the proof about the instructional successions. They involved the multiple external representations which improved the biological learning. The researcher conducted an investigation using one shoot case study design which involved 30 students in proving that the MERs worksheets could affect the student's achievement of reasoning about complex system. The data had been collected based on test of reasoning about complex system and student's identification result who worked through MERs. The result showed that only partially students could achieve reasoning about system complex, but their MERs skill could support their reasoning ability of complex system. This study could bring a new hope to develop the MERs worksheet as a tool to facilitate the reasoning about complex system.

Feasibility of Using Convalescent Plasma Immunotherapy for MERS-CoV Infection, Saudi Arabia.

PubMed

Arabi, Yaseen M; Hajeer, Ali H; Luke, Thomas; Raviprakash, Kanakatte; Balkhy, Hanan; Johani, Sameera; Al-Dawood, Abdulaziz; Al-Qahtani, Saad; Al-Omari, Awad; Al-Hameed, Fahad; Hayden, Frederick G; Fowler, Robert; Bouchama, Abderrezak; Shindo, Nahoko; Al-Khairy, Khalid; Carson, Gail; Taha, Yusri; Sadat, Musharaf; Alahmadi, Mashail

2016-09-01

We explored the feasibility of collecting convalescent plasma for passive immunotherapy of Middle East respiratory syndrome coronavirus (MERS-CoV) infection by using ELISA to screen serum samples from 443 potential plasma donors: 196 patients with suspected or laboratory-confirmed MERS-CoV infection, 230 healthcare workers, and 17 household contacts exposed to MERS-CoV. ELISA-reactive samples were further tested by indirect fluorescent antibody and microneutralization assays. Of the 443 tested samples, 12 (2.7%) had a reactive ELISA result, and 9 of the 12 had reactive indirect fluorescent antibody and microneutralization assay titers. Undertaking clinical trials of convalescent plasma for passive immunotherapy of MERS-CoV infection may be feasible, but such trials would be challenging because of the small pool of potential donors with sufficiently high antibody titers. Alternative strategies to identify convalescent plasma donors with adequate antibody titers should be explored, including the sampling of serum from patients with more severe disease and sampling at earlier points during illness.

Nucleation and Growth Kinetics from LaMer Burst Data.

PubMed

Chu, Daniel B K; Owen, Jonathan S; Peters, Baron

2017-10-12

In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics. Finally, we show how the nucleation kinetics determine the particle size distribution. We suggest that measured particle size distributions might therefore provide ways to test theoretical models of homogeneous nucleation kinetics.

The impact of multichannel microelectrode recording (MER) in deep brain stimulation of the basal ganglia.

PubMed

Kinfe, Thomas M; Vesper, Jan

2013-01-01

Deep brain stimulation (DBS) of the basal ganglia (Ncl. subthalamicus, Ncl. ventralis intermedius thalami, globus pallidus internus) has become an evidence-based and well-established treatment option in otherwise refractory movement disorders. The Ncl. subthalamicus (STN) is the target of choice in Parkinson's disease.However, a considerable discussion is currently ongoing with regard to the necessity for micro-electrode recording (MER) in DBS surgery.The present review provides an overview on deep brain stimulation and (MER) of the STN in patients with Parkinson's disease. Detailed description is given concerning the multichannel MER systems nowadays available for DBS of the basal ganglia, especially of the STN, as a useful tool for target refinement. Furthermore, an overview is given of the historical aspects, spatial mapping of the STN by MER, and its impact for accuracy and precision in current functional stereotactic neurosurgery.The pros concerning target refinement by MER means on the one hand, and cons including increased bleeding risk, increased operation time, local or general anesthesia, and single versus multichannel microelectrode recording are discussed in detail. Finally, the authors favor the use of MER with intraoperative testing combined with imaging to achieve a more precise electrode placement, aiming to ameliorate clinical outcome in therapy-resistant movement disorders.

Conserved antigenic sites between MERS-CoV and Bat-coronavirus are revealed through sequence analysis.

PubMed

Sharmin, Refat; Islam, Abul B M M K

2016-01-01

MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the degree of conserved antigenic sites among them. It is of importance to elucidate the shared antigenic-sites and extent of conservation between them to understand the evolutionary dynamics of MERS-CoV. Multiple sequence alignment of the spike (S), membrane (M), enveloped (E) and nucleocapsid (N) proteins was employed to identify the sequence conservation among MERS and Bat (HKU4, HKU5) coronaviruses. We used various in silico tools to predict the conserved antigenic sites. We found that MERS-CoV shared 30 % of its S protein antigenic sites with HKU4 and 70 % with HKU5 bat-CoV. Whereas 100 % of its E, M and N protein's antigenic sites are found to be conserved with those in HKU4 and HKU5. This sharing suggests that in case of pathogenicity MERS-CoV is more closely related to HKU5 bat-CoV than HKU4 bat-CoV. The conserved epitopes indicates their evolutionary relationship and ancestry of pathogenicity.

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding

PubMed Central

Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

2017-01-01

Abstract Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k-mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k-mer co-occurrence information with recent advances in deep learning. Results: We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k-mer embedding. We first split DNA sequences into k-mers and pre-train k-mer embedding vectors based on the co-occurrence matrix of k-mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k-mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. Availability and implementation: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm. Contact: tingchen@tsinghua.edu.cn or ruijiang

Managing PV Power on Mars - MER Rovers

NASA Technical Reports Server (NTRS)

Stella, Paul M.; Chin, Keith; Wood, Eric; Herman, Jennifer; Ewell, Richard

2009-01-01

The MER Rovers have recently completed over 5 years of operation! This is a remarkable demonstration of the capabilities of PV power on the Martian surface. The extended mission required the development of an efficient process to predict the power available to the rovers on a day-to-day basis. The performance of the MER solar arrays is quite unlike that of any other Space array and perhaps more akin to Terrestrial PV operation, although even severe by that comparison. The impact of unpredictable factors, such as atmospheric conditions and dust accumulation (and removal) on the panels limits the accurate prediction of array power to short time spans. Based on the above, it is clear that long term power predictions are not sufficiently accurate to allow for detailed long term planning. Instead, the power assessment is essentially a daily activity, effectively resetting the boundary points for the overall predictive power model. A typical analysis begins with the importing of the telemetry from each rover's previous day's power subsystem activities. This includes the array power generated, battery state-of-charge, rover power loads, and rover orientation, all as functions of time. The predicted performance for that day is compared to the actual performance to identify the extent of any differences. The model is then corrected for these changes. Details of JPL's MER power analysis procedure are presented, including the description of steps needed to provide the final prediction for the mission planners. A dust cleaning event of the solar array is also highlighted to illustrate the impact of Martian weather on solar array performance

Dromedary camels and the transmission of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

PubMed Central

Hemida, Maged G; Elmoslemany, Ahmed; Al-Hizab, Fahad; Alnaeem, Abdulmohsen; Almathen, Faisal; Faye, Bernard; Chu, Daniel KW; Perera, Ranawaka A; Peiris, Malik

2015-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is an existential threat to global public health. The virus has been repeatedly detected in dromedary camels (Camelus dromedarius). Adult animals in many countries in the Middle East as well as in North and East Africa showed high (>90%) sero-prevalence to the virus. MERS-CoV isolated from dromedaries is genetically and phenotypically similar to viruses from humans. We summarise current understanding of the ecology of MERS-CoV in animals and transmission at the animal-human interface. We review aspects of husbandry, animal movements and trade and the use and consumption of camel dairy and meat products in the Middle East that may be relevant to the epidemiology of MERS. We also highlight the gaps in understanding the transmission of this virus in animals and from animals to humans. PMID:26256102

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

Cell Surface Display of MerR on Saccharomyces cerevisiae for Biosorption of Mercury.

PubMed

Wei, Qinguo; Yan, Jiakuo; Chen, Yao; Zhang, Lei; Wu, Xiaoyang; Shang, Shuai; Ma, Shisheng; Xia, Tian; Xue, Shuyu; Zhang, Honghai

2018-01-01

The metalloregulatory protein MerR which plays important roles in mer operon system exhibits high affinity and selectivity toward mercury (II) (Hg 2+ ). In order to improve the adsorption ability of Saccharomyces cerevisiae for Hg 2+ , MerR was displayed on the surface of S. cerevisiae for the first time with an α-agglutinin-based display system in this study. The merR gene was synthesized after being optimized and added restriction endonuclease sites EcoR I and Mlu I. The display of MerR was indirectly confirmed by the enhanced adsorption ability of S. cerevisiae for Hg 2+ and colony PCR. The hydride generation atomic absorption spectrometry was applied to measure the Hg 2+ content in water. The engineered yeast strain not only showed higher tolerance to Hg, but also their adsorption ability was much higher than that of origin and control strains. The engineered yeast could adsorb Hg 2+ under a wide range of pH levels, and it could also adsorb Hg 2+ effectively with Cd 2+ and Cu 2+ coexistence. Furthermore, the engineered yeast strain could adsorb ultra-trace Hg 2+ effectively. The results above showed that the surface-engineered yeast strain could adsorb Hg 2+ under complex environmental conditions and could be used for the biosorption and bioremediation of environmental Hg contaminants.

Influence of anisotropy on percolation and jamming of linear k-mers on square lattice with defects

NASA Astrophysics Data System (ADS)

Tarasevich, Yu Yu; Laptev, V. V.; Burmistrov, A. S.; Shinyaeva, T. S.

2015-09-01

By means of the Monte Carlo simulation, we study the layers produced by the random sequential adsorption of the linear rigid objects (k-mers also known as rigid or stiff rods, sticks, needles) onto the square lattice with defects in the presence of an external field. The value of k varies from 2 to 32. The point defects randomly and uniformly placed on the substrate hinder adsorption of the elongated objects. The external field affects isotropic deposition of the particles, consequently the deposited layers are anisotropic. We study the influence of the defect concentration, the length of the objects, and the external field on the percolation threshold and the jamming concentration. Our main findings are (i) the critical defect concentration at which the percolation never occurs even at jammed state decreases for short k-mers (k < 16) and increases for long k-mers (k > 16) as anisotropy increases, (ii) the corresponding critical k-mer concentration decreases with anisotropy growth, (iii) the jamming concentration decreases drastically with growth of k-mer length for any anisotropy, (iv) for short k-mers, the percolation threshold is almost insensitive to the defect concentration for any anisotropy.

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya

PubMed Central

Deem, Sharon L.; Fèvre, Eric M.; Kinnaird, Margaret; Browne, A. Springer; Muloi, Dishon; Godeke, Gert-Jan; Koopmans, Marion; Reusken, Chantal B.

2015-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary camels, representing nine herds in Laikipia County, showed a high seroprevalence (46.9%) to MERS-CoV antibodies. Between herd differences were present (14.3%– 82.9%), but was not related to management type or herd isolation. Further research should focus on identifying similarity between MERS-CoV viral isolates in Kenya and clinical isolates from the Middle East and elsewhere. PMID:26473733

Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County, Kenya.

PubMed

Deem, Sharon L; Fèvre, Eric M; Kinnaird, Margaret; Browne, A Springer; Muloi, Dishon; Godeke, Gert-Jan; Koopmans, Marion; Reusken, Chantal B

2015-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary camels, representing nine herds in Laikipia County, showed a high seroprevalence (46.9%) to MERS-CoV antibodies. Between herd differences were present (14.3%- 82.9%), but was not related to management type or herd isolation. Further research should focus on identifying similarity between MERS-CoV viral isolates in Kenya and clinical isolates from the Middle East and elsewhere.

Histopathology of Middle East respiratory syndrome coronovirus (MERS-CoV) infection - clinicopathological and ultrastructural study.

PubMed

Alsaad, Khaled O; Hajeer, Ali H; Al Balwi, Mohammed; Al Moaiqel, Mohammed; Al Oudah, Nourah; Al Ajlan, Abdulaziz; AlJohani, Sameera; Alsolamy, Sami; Gmati, Giamal E; Balkhy, Hanan; Al-Jahdali, Hamdan H; Baharoon, Salim A; Arabi, Yaseen M

2018-02-01

The pathogenesis, viral localization and histopathological features of Middle East respiratory syndrome - coronavirus (MERS-CoV) in humans are not described sufficiently. The aims of this study were to explore and define the spectrum of histological and ultrastructural pathological changes affecting various organs in a patient with MERS-CoV infection and represent a base of MERS-CoV histopathology. We analysed the post-mortem histopathological findings and investigated localisation of viral particles in the pulmonary and extrapulmonary tissue by transmission electron microscopic examination in a 33-year-old male patient of T cell lymphoma, who acquired MERS-CoV infection. Tissue needle biopsies were obtained from brain, heart, lung, liver, kidney and skeletal muscle. All samples were collected within 45 min from death to reduce tissue decomposition and artefact. Histopathological examination showed necrotising pneumonia, pulmonary diffuse alveolar damage, acute kidney injury, portal and lobular hepatitis and myositis with muscle atrophic changes. The brain and heart were histologically unremarkable. Ultrastructurally, viral particles were localised in the pneumocytes, pulmonary macrophages, renal proximal tubular epithelial cells and macrophages infiltrating the skeletal muscles. The results highlight the pulmonary and extrapulmonary pathological changes of MERS-CoV infection and provide the first evidence of the viral presence in human renal tissue, which suggests tissue trophism for MERS-CoV in kidney. © 2017 John Wiley & Sons Ltd.

Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

NASA Astrophysics Data System (ADS)

Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

2016-09-01

The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between -35 and -10 elements.

Microbially mediated barite dissolution in anoxic brines

USGS Publications Warehouse

Ouyang, Bingjie; Akob, Denise M.; Dunlap, Darren S.; Renock, Devon

2017-01-01

Fluids injected into shale formations during hydraulic fracturing of black shale return with extraordinarily high total-dissolved-solids (TDS) and high concentrations of barium (Ba) and radium (Ra). Barite, BaSO4, has been implicated as a possible source of Ba as well as a problematic mineral scale that forms on internal well surfaces, often in close association with radiobarite, (Ba,Ra)SO4. The dissolution of barite by abiotic processes is well quantified. However, the identification of microbial communities in flowback and produced water necessitates the need to understand barite dissolution in the presence of bacteria. Therefore, we evaluated the rates and mechanisms of abiotic and microbially-mediated barite dissolution under anoxic and hypersaline conditions in the laboratory. Barite dissolution experiments were conducted with bacterial enrichment cultures established from produced water from Marcellus Shale wells located in northcentral Pennsylvania. These cultures were dominated by anaerobic halophilic bacteria from the genus Halanaerobium. Dissolved Ba was determined by ICP-OES and barite surfaces were investigated by SEM and AFM. Our results reveal that: 1) higher amounts of barium (up to ∼5 × ) are released from barite in the presence of Halanaerobium cultures compared to brine controls after 30 days of reaction, 2) etch pits that develop on the barite (001) surface in the presence of Halanaerobium exhibit a morphology that is distinct from those that form during control experiments without bacteria, 3) etch pits that develop in the presence of Halanaerobium exhibit a morphology that is similar to the morphology of etch pits formed in the presence of strong organic chelators, EDTA and DTPA, and 4) experiments using dialysis membranes to separate barite from bacteria suggest that direct contact between the two is not required in order to promote dissolution. These results suggest that Halanaerobium increase the rate of barite dissolution in anoxic and

Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding.

PubMed

Min, Xu; Zeng, Wanwen; Chen, Ning; Chen, Ting; Jiang, Rui

2017-07-15

Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning. We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k -mer embedding. We first split DNA sequences into k -mers and pre-train k -mer embedding vectors based on the co-occurrence matrix of k -mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k -mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility. The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm . tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cn. Supplementary materials are available at

The receptor tyrosine kinase MerTK activates phospholipase C γ2 during recognition of apoptotic thymocytes by murine macrophages

PubMed Central

Todt, Jill C.; Hu, Bin; Curtis, Jeffrey L.

2008-01-01

Apoptotic leukocytes must be cleared efficiently by macrophages (Mø). Apoptotic cell phagocytosis by Mø requires the receptor tyrosine kinase (RTK) MerTK (also known as c-Mer and Tyro12), the phosphatidylserine receptor (PS-R), and the classical protein kinase C (PKC) isoform βII, which translocates to Mø membrane and cytoskeletal fractions in a PS-R-dependent fashion. How these molecules cooperate to induce phagocytosis is unknown. Because the phosphatidylinositol-specific phospholipase (PI-PLC) PLC γ2 is downstream of RTKs in some cell types and can activate classical PKCs, we hypothesized that MerTK signals via PLC γ2. To test this hypothesis, we examined the interaction of MerTK and PLC γ2 in resident murine PMø and in the murine Mø cell line J774A.1 (J774) following exposure to apoptotic thymocytes. We found that, as with PMø, J774 phagocytosis of apoptotic thymocytes was inhibited by antibody against MerTK. Western blotting and immunoprecipitation showed that exposure to apoptotic cells produced three time-dependent changes in PMø and J774: (1) tyrosine phosphorylation of MerTK; (2) association of PLC γ2 with MerTK; and (3) tyrosine phosphorylation of PLC γ2. Phosphorylation of PLC γ2 and its association with MerTK was also induced by cross-linking MerTK using antibody. A PI-PLC appears to be required for phagocytosis of apoptotic cells because the PI-PLC inhibitor Et-18-OCH3 and the PLC inhibitor U73122, but not the inactive control U73343, blocked phagocytosis without impairing adhesion. On apoptotic cell adhesion to Mø, MerTK signals at least in part via PLC γ2. PMID:14704368

Structural Analysis of the Hg(II)-Regulatory Protein Tn501 MerR from Pseudomonas aeruginosa

PubMed Central

Wang, Dan; Huang, Shanqing; Liu, Pingying; Liu, Xichun; He, Yafeng; Chen, Weizhong; Hu, Qingyuan; Wei, Tianbiao; Gan, Jianhua; Ma, Jing; Chen, Hao

2016-01-01

The metalloprotein MerR is a mercury(II)-dependent transcriptional repressor-activator that responds to mercury(II) with extraordinary sensitivity and selectivity. It’s widely distributed in both Gram-negative and Gram-positive bacteria but with barely detectable sequence identities between the two sources. To provide structural basis for the considerable biochemical and biophysical experiments previously performed on Tn501 and Tn21 MerR from Gram-negative bacteria, we analyzed the crystal structure of mercury(II)-bound Tn501 MerR. The structure in the metal-binding domain provides Tn501 MerR with a high affinity for mercury(II) and the ability to distinguish mercury(II) from other metals with its unique planar trigonal coordination geometry, which is adopted by both Gram-negative and Gram-positive bacteria. The mercury(II) coordination state in the C-terminal metal-binding domain is transmitted through the allosteric network across the dimer interface to the N-terminal DNA-binding domain. Together with the previous mutagenesis analyses, the present data indicate that the residues in the allosteric pathway have a central role in maintaining the functions of Tn501 MerR. In addition, the complex structure exhibits significant differences in tertiary and quaternary structural arrangements compared to those of Bacillus MerR from Gram-positive bacteria, which probably enable them to function with specific promoter DNA with different spacers between −35 and −10 elements. PMID:27641146

Comparison of microbial taxonomic and functional shift pattern along contamination gradient.

PubMed

Ren, Youhua; Niu, Jiaojiao; Huang, Wenkun; Peng, Deliang; Xiao, Yunhua; Zhang, Xian; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-06-14

The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.

Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeremy Semrau; Sung-Woo Lee; Jeongdae Im

2010-09-30

The overall objective of this project, 'Strategies to Optimize Microbially-Mediated Mitigation of Greenhouse Gas Emissions from Landfill Cover Soils' was to develop effective, efficient, and economic methodologies by which microbial production of nitrous oxide can be minimized while also maximizing microbial consumption of methane in landfill cover soils. A combination of laboratory and field site experiments found that the addition of nitrogen and phenylacetylene stimulated in situ methane oxidation while minimizing nitrous oxide production. Molecular analyses also indicated that methane-oxidizing bacteria may play a significant role in not only removing methane, but in nitrous oxide production as well, although themore » contribution of ammonia-oxidizing archaea to nitrous oxide production can not be excluded at this time. Future efforts to control both methane and nitrous oxide emissions from landfills as well as from other environments (e.g., agricultural soils) should consider these issues. Finally, a methanotrophic biofiltration system was designed and modeled for the promotion of methanotrophic activity in local methane 'hotspots' such as landfills. Model results as well as economic analyses of these biofilters indicate that the use of methanotrophic biofilters for controlling methane emissions is technically feasible, and provided either the costs of biofilter construction and operation are reduced or the value of CO{sub 2} credits is increased, can also be economically attractive.« less

Identifying Monoclonal Antibodies that Potently Inhibit MERS-CoV | Center for Cancer Research

Cancer.gov

The Middle East respiratory syndrome coronavirus (MERS-CoV), first isolated in September 2012, infects cells lining the human airway, causing severe flu-like symptoms that, in some cases, lead to death. As of July 2, 2014, 824 confirmed cases of MERS-CoV infection, including at least 286 related deaths, have been reported to the World Health Organization. While there are

Identifying Monoclonal Antibodies that Potently Inhibit MERS-CoV | Center for Cancer Research

Cancer.gov

The Middle East respiratory syndrome coronavirus (MERS-CoV), first isolated in September 2012, infects cells lining the human airway, causing severe flu-like symptoms that, in some cases, lead to death. As of July 2, 2014, 824 confirmed cases of MERS-CoV infection, including at least 286 related deaths, have been reported to the World Health Organization. While there are currently no effective therapies against the virus, monoclonal antibodies (MAbs) may be a promising candidate. Having previously developed MAbs against other viruses, including the related severe acute respiratory syndrome coronavirus or SARS-CoV, Dimiter Dimitrov, Ph.D., of CCR’s Laboratory of Experimental Immunology (LEI), and his colleagues decided to pan a library of antigen binding fragments (Fab) for activity against MERS-CoV.

An assessment of the level of concern among hospital-based health-care workers regarding MERS outbreaks in Saudi Arabia.

PubMed

Abolfotouh, Mostafa A; AlQarni, Ali A; Al-Ghamdi, Suliman M; Salam, Mahmoud; Al-Assiri, Mohammed H; Balkhy, Hanan H

2017-01-03

Middle East Respiratory Syndrome (MERS) is caused by MERS coronavirus (MERS-CoV). More than 80% of reported cases have occurred in Saudi Arabia, with a mortality exceeding 50%. Health-care workers (HCWs) are at risk of acquiring and transmitting this virus, so the concerns of HCWs in Saudi Arabia regarding MERS were evaluated. An anonymous, self-administered, previously validated questionnaire was given to 1031 HCWs at three tertiary hospitals in Saudi Arabia from October to December, 2014. Concerns regarding the disease, its severity and governmental efforts to contain it, as well as disease outcomes were assessed using 31 concern statements in five distinct domains. A total concern score was calculated for each HCW. Multiple regression analyses were used to identify predictors of high concern scores. The average age of participants was 37.1 ± 9.0 years, 65.8% were married and 59.1% were nurses. The majority of respondents (70.4%) felt at risk of contracting a MERS-CoV infection at work, 69.1% felt threatened if a colleague contracted MERS-CoV, 60.9% felt obliged to care for patients infected with MERS-CoV and 87.8% did not feel safe at work using standard precautions. In addition, 87.7% believed that the government should isolate patients with MERS in specialized hospitals, 73.7% agreed with travel restriction to and from areas affected by MERS and 65.3% agreed with avoiding inviting expatriates from such areas. After adjustment for covariates, high concern scores were significantly associated with being a Saudi national (p < 0.001), a non-physician (p < 0.001) and working in the central region (p < 0.001). The majority of respondents reported concern regarding MERS-CoV infection from exposure at work. The overall level of concern may be influenced by previous experience of MERS outbreaks and related cultural issues. The concerns of HCWs may affect their overall effectiveness in an outbreak and should be addressed by incorporating management

Biological Effects of c-Mer Receptor Tyrosine Kinase in Hematopoietic Cells Depend on the Grb2 Binding Site in the Receptor and Activation of NF-κB

PubMed Central

Georgescu, Maria-Magdalena; Kirsch, Kathrin H.; Shishido, Tomoyuki; Zong, Chen; Hanafusa, Hidesaburo

1999-01-01

The c-Mer receptor tyrosine kinase (RTK) is most closely related to chicken c-Eyk and belongs to the Axl RTK subfamily. Although not detected in normal lymphocytes, c-Mer is expressed in B- and T-cell leukemia cell lines, suggesting an association with lymphoid malignancies. To gain an understanding of the role of this receptor in lymphoid cells, we expressed in murine interleukin-3 (IL-3)-dependent Ba/F3 pro-B-lymphocyte cells a constitutively active receptor, CDMer, formed from the CD8 extracellular domain and the c-Mer intracellular domain. Cells transfected with a plasmid encoding the CDMer receptor became IL-3 independent. When tyrosine (Y)-to-phenylalanine (F) mutations were introduced into c-Mer, only the Y867 change significantly reduced the IL-3-independent cell proliferation. The Y867 residue in the CDMer receptor mediated the binding of Grb2, which recruited the p85 phosphatidylinositol 3-kinase (PI 3-kinase). Despite the difference in promotion of proliferation, both the CDMer and mutant F867 receptors activated Erk in transfected cells. On the other hand, we found that both transcriptional activation of NF-κB and activation of PI 3-kinase were significantly suppressed with the F867 mutant receptor, suggesting that the activation of antiapoptotic pathways is the major mechanism for the observed phenotypic difference. Consistent with this notion, apoptosis induced by IL-3 withdrawal was strongly prevented by CDMer but not by the F867 mutant receptor. PMID:9891051

Planning Mars Memory: Learning from the MER Mission

NASA Technical Reports Server (NTRS)

Charlotte, Linde

2004-01-01

This viewgraph presentation discusses ways in which the lessons learned from a mission can be systematically remembered, retained, and applied by individuals and by an organization as a whole. The presentation cites lessons learned from the Mars Exploration Rover (MER) Mission as examples.

The Role of an Aggrecan 32mer Fragment in Post-Traumatic Osteoarthritis

DTIC Science & Technology

2017-10-01

Award Number: W81XWH-16-1-0706 TITLE: The Role of an Aggrecan 32mer Fragment in Post -Traumatic Osteoarthritis PRINCIPAL INVESTIGATOR: Professor...TITLE AND SUBTITLE The Role of an Aggrecan 32mer Fragment in Post - Traumatic Osteoarthritis 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-16-1-0706 5c...reduction in knee hyperalgesia, but not mechanical allodynia, in mice at 8 weeks post -surgery. This trend was not statistically significant, however, we are

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji-Won

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component comprising at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes duringmore » consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.« less

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOEpatents

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

Impact of defects on percolation in random sequential adsorption of linear k-mers on square lattices.

PubMed

Tarasevich, Yuri Yu; Laptev, Valeri V; Vygornitskii, Nikolai V; Lebovka, Nikolai I

2015-01-01

The effect of defects on the percolation of linear k-mers (particles occupying k adjacent sites) on a square lattice is studied by means of Monte Carlo simulation. The k-mers are deposited using a random sequential adsorption mechanism. Two models L(d) and K(d) are analyzed. In the L(d) model it is assumed that the initial square lattice is nonideal and some fraction of sites d is occupied by nonconducting point defects (impurities). In the K(d) model the initial square lattice is perfect. However, it is assumed that some fraction of the sites in the k-mers d consists of defects, i.e., is nonconducting. The length of the k-mers k varies from 2 to 256. Periodic boundary conditions are applied to the square lattice. The dependences of the percolation threshold concentration of the conducting sites p(c) vs the concentration of defects d are analyzed for different values of k. Above some critical concentration of defects d(m), percolation is blocked in both models, even at the jamming concentration of k-mers. For long k-mers, the values of d(m) are well fitted by the functions d(m)∝k(m)(-α)-k(-α) (α=1.28±0.01 and k(m)=5900±500) and d(m)∝log(10)(k(m)/k) (k(m)=4700±1000) for the L(d) and K(d) models, respectively. Thus, our estimation indicates that the percolation of k-mers on a square lattice is impossible even for a lattice without any defects if k⪆6×10(3).

Successful recovery of MERS CoV pneumonia in a patient with acquired immunodeficiency syndrome: a case report.

PubMed

Shalhoub, Sarah; AlZahrani, Abdulwahab; Simhairi, Raed; Mushtaq, Adnan

2015-01-01

Middle East Respiratory Syndrome Coronavirus (MERS CoV) may cause severe pneumonia with significant morbidity and mortality, particularly in patients with multiple comorbid condition. MERS CoV pneumonia has not been previously reported in patients with Human Immunodeficiency Virus (HIV). Herein, we report a case of MERS CoV pneumonia with a successful outcome in a patient recently diagnosed with HIV. Copyright © 2014 Elsevier B.V. All rights reserved.

Disk-based k-mer counting on a PC

PubMed Central

2013-01-01

Background The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. Results We propose a simple, yet efficient, parallel disk-based algorithm for counting k-mers. Experiments show that it usually offers the fastest solution to the considered problem, while demanding a relatively small amount of memory. In particular, it is capable of counting the statistics for short-read human genome data, in input gzipped FASTQ file, in less than 40 minutes on a PC with 16 GB of RAM and 6 CPU cores, and for long-read human genome data in less than 70 minutes. On a more powerful machine, using 32 GB of RAM and 32 CPU cores, the tasks are accomplished in less than half the time. No other algorithm for most tested settings of this problem and mammalian-size data can accomplish this task in comparable time. Our solution also belongs to memory-frugal ones; most competitive algorithms cannot efficiently work on a PC with 16 GB of memory for such massive data. Conclusions By making use of cheap disk space and exploiting CPU and I/O parallelism we propose a very competitive k-mer counting procedure, called KMC. Our results suggest that judicious resource management may allow to solve at least some bioinformatics problems with massive data on a commodity personal computer. PMID:23679007

Value, Market Preferences and Trade of Beche-De-Mer from Pacific Island Sea Cucumbers

PubMed Central

Purcell, Steven W.

2014-01-01

Market preferences of natural resources contribute to shape their exploitation and production. Beche-de-mer, the product after gutting, cooking, salting and drying sea cucumbers, is exported worldwide to Asian dried seafood markets. A better understanding of the trade, value and market preferences of Pacific island beche-de-mer could identify critical postharvest processing techniques and management strategies for fisheries and aquaculture. Data were collected on export prices and trade of beche-de-mer from Kiribati, Fiji, Tonga and New Caledonia, and the selling prices, respective sizes and organoleptic properties of the products in stores in China. Export prices varied considerably within and among the four countries and low-value species were the most exported by volume. Most of the beche-de-mer from the four Pacific islands is exported to Hong Kong, where quality products are sold and others are distributed to mainland China. Prices of the beche-de-mer in Chinese stores varied up to ten-fold and were mostly influenced by species, body size and, to a lesser extent, physical damage to the products. Market prices across species (averaging US$15–385 kg−1) appear to have mostly increased six- to twelve-fold over the past decade. The data allude that fisheries for Holothuria scabra, H. lessoni, H. fuscogilva, H. whitmaei and Thelenota ananas should be most carefully managed because they were the highest-value species and under greatest demand. The relationships between size of beche-de-mer and sale price were species specific and highly varied. This study also highlights the need for better regulations and/or enforcement of minimum size limits in sea cucumber fisheries, which can help to maximise economic benefits of wild stocks. PMID:24736374

Value, market preferences and trade of Beche-de-mer from Pacific Island sea cucumbers.

PubMed

Purcell, Steven W

2014-01-01

Market preferences of natural resources contribute to shape their exploitation and production. Beche-de-mer, the product after gutting, cooking, salting and drying sea cucumbers, is exported worldwide to Asian dried seafood markets. A better understanding of the trade, value and market preferences of Pacific island beche-de-mer could identify critical postharvest processing techniques and management strategies for fisheries and aquaculture. Data were collected on export prices and trade of beche-de-mer from Kiribati, Fiji, Tonga and New Caledonia, and the selling prices, respective sizes and organoleptic properties of the products in stores in China. Export prices varied considerably within and among the four countries and low-value species were the most exported by volume. Most of the beche-de-mer from the four Pacific islands is exported to Hong Kong, where quality products are sold and others are distributed to mainland China. Prices of the beche-de-mer in Chinese stores varied up to ten-fold and were mostly influenced by species, body size and, to a lesser extent, physical damage to the products. Market prices across species (averaging US$15-385 kg-1) appear to have mostly increased six- to twelve-fold over the past decade. The data allude that fisheries for Holothuria scabra, H. lessoni, H. fuscogilva, H. whitmaei and Thelenota ananas should be most carefully managed because they were the highest-value species and under greatest demand. The relationships between size of beche-de-mer and sale price were species specific and highly varied. This study also highlights the need for better regulations and/or enforcement of minimum size limits in sea cucumber fisheries, which can help to maximise economic benefits of wild stocks.

Healthcare Workers Emotions, Perceived Stressors and Coping Strategies During a MERS-CoV Outbreak.

PubMed

Khalid, Imran; Khalid, Tabindeh J; Qabajah, Mohammed R; Barnard, Aletta G; Qushmaq, Ismael A

2016-03-01

Healthcare workers (HCWs) are at high risk of contracting Middle East respiratory syndrome coronavirus (MERS-CoV) during an epidemic. We explored the emotions, perceived stressors, and coping strategies of healthcare workers who worked during a MERS-CoV outbreak in our hospital. A cross-sectional descriptive survey design. A tertiary care hospital. HCWs (150) who worked in high risk areas during the April-May 2014 MERS-CoV outbreak that occurred in Jeddah, Saudi Arabia. We developed and administered a "MERS-CoV staff questionnaire" to study participants. The questionnaire consisted of 5 sections with 72 questions. The sections evaluated hospital staffs emotions, perceived stressors, factors that reduced their stress, coping strategies, and motivators to work during future outbreaks. Responses were scored on a scale from 0-3. The varying levels of stress or effectiveness of measures were reported as mean and standard deviation, as appropriate. Completed questionnaires were returned by 117 (78%) of the participants. The results had many unique elements. HCWs ethical obligation to their profession pushed them to continue with their jobs. The main sentiments centered upon fear of personal safety and well-being of colleagues and family. Positive attitudes in the workplace, clinical improvement of infected colleagues, and stoppage of disease transmission among HCWs after adopting strict protective measures alleviated their fear and drove them through the epidemic. They appreciated recognition of their efforts by hospital management and expected similar acknowledgment, infection control guidance, and equipment would entice them to work during future epidemics. The MERS-CoV outbreak was a distressing time for our staff. Hospitals can enhance HCWs experiences during any future MERS-CoV outbreak by focusing on the above mentioned aspects. © 2016 Marshfield Clinic.

Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition

PubMed Central

Freedman, Zachary; Zak, Donald R.; Xue, Kai; He, Zhili; Zhou, Jizhong

2013-01-01

Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems. PMID:23220961

Replication and Shedding of MERS-CoV in Upper Respiratory Tract of Inoculated Dromedary Camels

PubMed Central

Adney, Danielle R.; van Doremalen, Neeltje; Brown, Vienna R.; Bushmaker, Trenton; Scott, Dana; de Wit, Emmie; Munster, Vincent J.

2014-01-01

In 2012, a novel coronavirus associated with severe respiratory disease in humans emerged in the Middle East. Epidemiologic investigations identified dromedary camels as the likely source of zoonotic transmission of Middle East respiratory syndrome coronavirus (MERS-CoV). Here we provide experimental support for camels as a reservoir for MERS-CoV. We inoculated 3 adult camels with a human isolate of MERS-CoV and a transient, primarily upper respiratory tract infection developed in each of the 3 animals. Clinical signs of the MERS-CoV infection were benign, but each of the camels shed large quantities of virus from the upper respiratory tract. We detected infectious virus in nasal secretions through 7 days postinoculation, and viral RNA up to 35 days postinoculation. The pattern of shedding and propensity for the upper respiratory tract infection in dromedary camels may help explain the lack of systemic illness among naturally infected camels and the means of efficient camel-to-camel and camel-to-human transmission. PMID:25418529

T-cell immunity of SARS-CoV: Implications for vaccine development against MERS-CoV.

PubMed

Liu, William J; Zhao, Min; Liu, Kefang; Xu, Kun; Wong, Gary; Tan, Wenjie; Gao, George F

2017-01-01

Over 12 years have elapsed since severe acute respiratory syndrome (SARS) triggered the first global alert for coronavirus infections. Virus transmission in humans was quickly halted by public health measures and human infections of SARS coronavirus (SARS-CoV) have not been observed since. However, other coronaviruses still pose a continuous threat to human health, as exemplified by the recent emergence of Middle East respiratory syndrome (MERS) in humans. The work on SARS-CoV widens our knowledge on the epidemiology, pathophysiology and immunology of coronaviruses and may shed light on MERS coronavirus (MERS-CoV). It has been confirmed that T-cell immunity plays an important role in recovery from SARS-CoV infection. Herein, we summarize T-cell immunological studies of SARS-CoV and discuss the potential cross-reactivity of the SARS-CoV-specific immunity against MERS-CoV, which may provide useful recommendations for the development of broad-spectrum vaccines against coronavirus infections. Copyright © 2016 Elsevier B.V. All rights reserved.

EDs on heightened alert for MERS-CoV as first cases reach the US.

PubMed

2014-07-01

The first cases of Middle East Respiratory Syndrome coronavirus (MERS-CoV) have turned up in the United States. First, in late April, a patient tested positive for the virus at a hospital in Munster, IN, and then shortly thereafter, a second patient tested positive at a hospital in Orlando, FL. While both patients have since recovered from the virus and been released, the cases have raised awareness of the infectious threat of MERS-CoV, and they have put EDs and other frontline providers on heightened alert for patients with severe respiratory symptoms and other risk factors. While MERS-CoV is not yet as contagious as seasonal influenza or the severe acute respiratory syndrome (SARS) that started in China and then swept around the globe in 2003, it is more deadly. The World Health Organization reports that roughly one-quarter of 514 people who have tested positive for the virus have died. Experts note that health care workers make up a large percentage of the documented cases of MERS-CoV, and they point out that most human-to-human transmissions of the virus occur in the hospital setting. Public health officials urge emergency personnel to pay strict attention to infection control practices, and to query patients who present with fever and respiratory distress about recent travel to the Arabian Peninsula and/or close contact with a person who has a confirmed or probable case of MERS-CoV.

21 CFR 177.1040 - Acrylonitrile/styrene copoly-mer.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Acrylonitrile/styrene copoly-mer. 177.1040 Section 177.1040 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... Internal Standard Method”; “Infrared Spectrophotometric Determination of Polymer Extracted from Barex 210...

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

DOE PAGES

Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou; ...

2016-04-29

Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marlow, Jeffery; Skennerton, Connor T.; Li, Zhou

Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to

Biomineralization of U(VI) phosphate promoted by microbially-mediated phytate hydrolysis in contaminated soils

NASA Astrophysics Data System (ADS)

Salome, Kathleen R.; Beazley, Melanie J.; Webb, Samuel M.; Sobecky, Patricia A.; Taillefert, Martial

2017-01-01

The bioreduction of uranium may immobilize a significant fraction of this toxic contaminant in reduced environments at circumneutral pH. In oxic and low pH environments, however, the low solubility of U(VI)-phosphate minerals also makes them good candidates for the immobilization of U(VI) in the solid phase. As inorganic phosphate is generally scarce in soils, the biomineralization of U(VI)-phosphate minerals via microbially-mediated organophosphate hydrolysis may represent the main immobilization process of uranium in these environments. In this study, contaminated sediments were incubated aerobically in two pH conditions to examine whether phytate, a naturally-occurring and abundant organophosphate in soils, could represent a potential phosphorous source to promote U(VI)-phosphate biomineralization by natural microbial communities. While phytate hydrolysis was not evident at pH 7.0, nearly complete hydrolysis was observed both with and without electron donor at pH 5.5, suggesting indigenous microorganisms express acidic phytases in these sediments. While the rate of hydrolysis of phytate generally increased in the presence of uranium, the net rate of inorganic phosphate production in solution was decreased and inositol phosphate intermediates were generated in contrast to similar incubations conducted without uranium. These findings suggest uranium stress enhanced the phytate-metabolism of the microbial community, while simultaneously inhibiting phosphatase production and/or activity by the indigenous population. Finally, phytate hydrolysis drastically decreased uranium solubility, likely due to formation of ternary sorption complexes, U(VI)-phytate precipitates, and U(VI)-phosphate minerals. Overall, the results of this study provide evidence for the ability of natural microbial communities to liberate phosphate from phytate in acidic sediments, possibly as a detoxification mechanism, and demonstrate the potential utility of phytate-promoted uranium

Prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels in Abu Dhabi Emirate, United Arab Emirates.

PubMed

Yusof, Mohammed F; Eltahir, Yassir M; Serhan, Wissam S; Hashem, Farouk M; Elsayed, Elsaeid A; Marzoug, Bahaaeldin A; Abdelazim, Assem Si; Bensalah, Oum Keltoum A; Al Muhairi, Salama S

2015-06-01

High seroprevalence of Middle East respiratory syndrome corona virus (MERS-CoV) in dromedary camels has been previously reported in United Arab Emirates (UAE). However, the molecular detection of the virus has never been reported before in UAE. Of the 7,803 nasal swabs tested in the epidemiological survey, MERS-CoV nucleic acid was detected by real-time PCR in a total of 126 (1.6 %) camels. Positive camels were detected at the borders with Saudi Arabia and Oman and in camels' slaughter houses. MERS-CoV partial sequences obtained from UAE camels were clustering with human- and camel-derived MERS-CoV sequences in the same geographic area. Results provide further evidence of MERS-CoV zoonosis.

TAM receptors Tyro3 and Mer as novel targets in colorectal cancer.

PubMed

Schmitz, Robin; Valls, Aida Freire; Yerbes, Rosario; von Richter, Sophie; Kahlert, Christoph; Loges, Sonja; Weitz, Jürgen; Schneider, Martin; Ruiz de Almodovar, Carmen; Ulrich, Alexis; Schmidt, Thomas

2016-08-30

CRC remains the third most common cancer worldwide with a high 5-year mortality rate in advanced cases. Combined with chemotherapy, targeted therapy is an additional treatment option. However as CRC still escapes targeted therapy the vigorous search for new targets is warranted to increase patients´ overall survival. In this study we describe a new role for Gas6/protein S-TAM receptor interaction in CRC. Gas6, expressed by tumor-infiltrating M2-like macrophages, enhances malignant properties of tumor cells including proliferation, invasion and colony formation. Upon chemotherapy macrophages increase Gas6 synthesis, which significantly attenuates the cytotoxic effect of 5-FU chemotherapy on tumor cells. The anti-coagulant protein S has similar effects as Gas6.In CRC patient samples Tyro3 was overexpressed within the tumor. In-vitro inhibition of Tyro3 and Mer reduces tumor cell proliferation and sensitizes tumor cells to chemotherapy. Moreover high expression of Tyro3 and Mer in tumor tissue significantly shortens CRC patients´ survival. Various in vitro models were used to investigate the role of Gas6 and its TAM receptors in human CRC cells, by stimulation (rhGas6) and knockdown (siRNA) of Axl, Tyro3 and Mer. In terms of a translational research, we additionally performed an expression analysis in human CRC tissue and analyzed the medical record of these patients. Tyro3 and Mer represent novel therapeutic targets in CRC and warrant further preclinical and clinical investigation in the future.

Inferences of Strength of Soil Deposits along MER Rover Traverses

NASA Astrophysics Data System (ADS)

Richter, L.; Schmitz, N.; Weiss, S.; Mer/Athena Team

As the two MER Mars Exploration Rovers ,Spirit' and ,Opportunity' traverse terrains within Gusev crater and at Meridiani Planum, respectively, they leave behind wheel tracks that are routinely imaged by the different sets of cameras as part of the Athena instrument suite. Stereo observations of these tracks reveal wheel sinkage depths which are diagnostic of the strength of the soil-like deposits crossed by the vehicles, and observations of track morphology at different imaging scales - including that of the Microscopic Imager - allow estimations of soil grain size distributions. This presentation will discuss results of systematic analyses of MER-A and -B wheel track observations with regard to solutions for soil bearing strength and soil shear strength. Data are analyzed in the context of wheel-soil theory calibrated to the shape of the MER wheel and by consulting comparisons with terrestrial soils. Results are applicable to the top ˜20-30 cm of the soil deposits, the depth primarily affected by the stress distribution under the wheels. The large number of wheel track observations per distance travelled enables investigations of variations of soil physical properties as a function of spatial scale, type of surface feature encountered, and local topography. Exploiting relationships between soil strength and degree of soil consolidation known from lunar regolith and dry terrestrial soils allows one to relate inferred soil strengths to bulk density. This provides a means to ground-truth radar Fresnel reflection coefficients obtained for the landing sites from Earth-based observations. Moreover, bulk density is correlated with soil dielectric constant, a parameter of direct relevance also for Mars-orbiting radars. The obtained estimates for soil bulk density are also used to determine local thermal conductivity of near-surface materials, based on correlations between the two quantities, and to subsequently estimate thermal inertia. This represents an independent

The MER Mossbauer Spectrometers: 40 Months of Operation on the Martian Surface

NASA Technical Reports Server (NTRS)

Fleischer, Iris; Rodionov, D.; Schroeder, C.; Morris, R.; Yen, A.; Ming, D.; McCoy, T.; Mittlefehldt, D.; Gellert, R.; Cohen, B.;

Science Activity Planner for the MER Mission

NASA Technical Reports Server (NTRS)

Norris, Jeffrey S.; Crockett, Thomas M.; Fox, Jason M.; Joswig, Joseph C.; Powell, Mark W.; Shams, Khawaja S.; Torres, Recaredo J.; Wallick, Michael N.; Mittman, David S.

2008-01-01

The Maestro Science Activity Planner is a computer program that assists human users in planning operations of the Mars Explorer Rover (MER) mission and visualizing scientific data returned from the MER rovers. Relative to its predecessors, this program is more powerful and easier to use. This program is built on the Java Eclipse open-source platform around a Web-browser-based user-interface paradigm to provide an intuitive user interface to Mars rovers and landers. This program affords a combination of advanced display and simulation capabilities. For example, a map view of terrain can be generated from images acquired by the High Resolution Imaging Science Explorer instrument aboard the Mars Reconnaissance Orbiter spacecraft and overlaid with images from a navigation camera (more precisely, a stereoscopic pair of cameras) aboard a rover, and an interactive, annotated rover traverse path can be incorporated into the overlay. It is also possible to construct an overhead perspective mosaic image of terrain from navigation-camera images. This program can be adapted to similar use on other outer-space missions and is potentially adaptable to numerous terrestrial applications involving analysis of data, operations of robots, and planning of such operations for acquisition of scientific data.

KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation.

PubMed

Wang, Dapeng; Xu, Jiayue; Yu, Jun

2015-09-16

The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data.

Estimating Potential Incidence of MERS-CoV Associated with Hajj Pilgrims to Saudi Arabia, 2014

PubMed Central

Lessler, Justin; Rodriguez-Barraquer, Isabel; Cummings, Derek A.T.; Garske, Tini; Van Kerkhove, Maria; Mills, Harriet; Truelove, Shaun; Hakeem, Rafat; Albarrak, Ali; Ferguson, Neil M.; Aguas, Ricardo; Algarni, Homud; AlHarbi, Khalid; Cauchemez, Simon; Clapham, Hannah; Collins, Caitlin; Cori, Anne; Donnelly, Christl; Fraser, Christophe; Jombart, Thibaut; Moore, Sean M.; Nouvellet, Pierre; Riley, Steven; Salje, Henrik; Turkistani, Abdulhafiz

2014-01-01

Between March and June 2014 the Kingdom of Saudi Arabia (KSA) had a large outbreak of MERS-CoV, renewing fears of a major outbreak during the Hajj this October. Using KSA Ministry of Health data, the MERS-CoV Scenario and Modeling Working Group forecast incidence under three scenarios. In the expected incidence scenario, we estimate 6.2 (95% Prediction Interval [PI]: 1–17) pilgrims will develop MERS-CoV symptoms during the Hajj, and 4.0 (95% PI: 0–12) foreign pilgrims will be infected but return home before developing symptoms. In the most pessimistic scenario, 47.6 (95% PI: 32–66) cases will develop symptoms during the Hajj, and 29.0 (95% PI: 17–43) will be infected but return home asymptomatic. Large numbers of MERS-CoV cases are unlikely to occur during the 2014 Hajj even under pessimistic assumptions, but careful monitoring is still needed to detect possible mass infection events and minimize introductions into other countries.   PMID:25685624

Up-Regulation of Soluble Axl and Mer Receptor Tyrosine Kinases Negatively Correlates with Gas6 in Established Multiple Sclerosis Lesions

PubMed Central

Weinger, Jason G.; Omari, Kakuri M.; Marsden, Kurt; Raine, Cedric S.; Shafit-Zagardo, Bridget

2009-01-01

Multiple sclerosis is a disease that is characterized by inflammation, demyelination, and axonal damage; it ultimately forms gliotic scars and lesions that severely compromise the function of the central nervous system. Evidence has shown previously that altered growth factor receptor signaling contributes to lesion formation, impedes recovery, and plays a role in disease progression. Growth arrest-specific protein 6 (Gas6), the ligand for the TAM receptor tyrosine kinase family, consisting of Tyro3, Axl, and Mer, is important for cell growth, survival, and clearance of debris. In this study, we show that levels of membrane-bound Mer (205 kd), soluble Mer (∼150 kd), and soluble Axl (80 kd) were all significantly elevated in homogenates from established multiple sclerosis lesions comprised of both chronic active and chronic silent lesions. Whereas in normal tissue Gas6 positively correlated with soluble Axl and Mer, there was a negative correlation between Gas6 and soluble Axl and Mer in established multiple sclerosis lesions. In addition, increased levels of soluble Axl and Mer were associated with increased levels of mature ADAM17, mature ADAM10, and Furin, proteins that are associated with Axl and Mer solubilization. Soluble Axl and Mer are both known to act as decoy receptors and block Gas6 binding to membrane-bound receptors. These data suggest that in multiple sclerosis lesions, dysregulation of protective Gas6 receptor signaling may prolong lesion activity. PMID:19541935

Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, J.; Wu, L.; Gentry, T.

2006-04-05

To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approximately 2000 unique and group-specific probes with <85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50 C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appearedmore » to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ({approx}1.3{sup o} 10{sup 7} cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r{sup 2} = 0.95-0.99). Application of this microarray to naphthalene-amended enrichments and soil microcosms demonstrated that composition of the microflora varied depending on incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in enrichments, the genes involved in naphthalene degradation from Gram-negative microorganisms such as Ralstonia, Comamonas, and Burkholderia were most abundant in the soil microcosms (as well as those for polyaromatic hydrocarbon and nitrotoluene degradation). Although naphthalene degradation is widely known and studied in Pseudomonas, Pseudomonas genes were not detected in either system. Real-time PCR analysis of 4 representative genes was consistent with microarray-based quantification (r{sup 2} = 0.95). Currently, we are also applying this microarray to the study of

Protection of rat liver against hepatic ischemia-reperfusion injury by a novel selenocysteine-containing 7-mer peptide

PubMed Central

Jiang, Qianqian; Pan, Yu; Cheng, Yupeng; Li, Huiling; Li, Hui

2016-01-01

Hepatic ischemia-reperfusion (I-R) injury causes acute organ damage or dysfunction, and remains a problem for liver transplantation. In the I-R phase, the generation of reactive oxygen species aggravates the injury. In the current study, a novel selenocysteine-containing 7-mer peptide (H-Arg-Sec-Gly-Arg-Asn-Ala-Gln-OH) was constructed to imitate the active site of an antioxidant enzyme, glutathione peroxidase (GPX). The 7-mer peptide which has a lower molecular weight, and improved water-solubility, higher stability and improved cell membrane permeability compared with other GPX mimics. Its GPX activity reached 13 U/µmol, which was 13 times that of ebselen (a representative GPX mimic). The effect of this GPX mimic on I-R injury of the liver was assessed in rats. The 7-mer peptide significantly inhibited the increase in serum hepatic amino-transferases, tissue malondialdehyde, nitric oxide contents, myeloperoxidase activity and decrease of GPX activity compared with I-R tissue. Following treatment with the 7-mer peptide, the expression of B-cell CLL/lymphoma-2 (Bcl-2) was significantly upregulated at the mRNA and protein level compared with the I-R group, as determined by reverse transcription-polymerase chain reaction and immunohistochemistry, respectively. By contrast, Bcl-2 associated X protein (Bax) was downregulated by the 7-mer peptide compared the I-R group. Histological and ultrastructural changes of the rat liver tissue were also compared among the experimental groups. The results of the current study suggest that the 7-mer peptide protected the liver against hepatic I-R injury via suppression of oxygen-derived free radicals and regulation of Bcl-2 and Bax expression, which are involved in the apoptosis of liver cells. The findings of the present study will further the investigation of the 7-mer peptide as an effective therapeutic agent in hepatic I-R injury. PMID:27431272

Electrical conductivity of a monolayer produced by random sequential adsorption of linear k -mers onto a square lattice

NASA Astrophysics Data System (ADS)

Tarasevich, Yuri Yu.; Goltseva, Valeria A.; Laptev, Valeri V.; Lebovka, Nikolai I.

2016-10-01

The electrical conductivity of a monolayer produced by the random sequential adsorption (RSA) of linear k -mers (particles occupying k adjacent adsorption sites) onto a square lattice was studied by means of computer simulation. Overlapping with predeposited k -mers and detachment from the surface were forbidden. The RSA process continued until the saturation jamming limit, pj. The isotropic (equiprobable orientations of k -mers along x and y axes) and anisotropic (all k -mers aligned along the y axis) depositions for two different models—of an insulating substrate and conducting k -mers (C model) and of a conducting substrate and insulating k -mers (I model)—were examined. The Frank-Lobb algorithm was applied to calculate the electrical conductivity in both the x and y directions for different lengths (k =1 - 128) and concentrations (p =0 - pj) of the k -mers. The "intrinsic electrical conductivity" and concentration dependence of the relative electrical conductivity Σ (p ) (Σ =σ /σm for the C model and Σ =σm/σ for the I model, where σm is the electrical conductivity of substrate) in different directions were analyzed. At large values of k the Σ (p ) curves became very similar and they almost coincided at k =128 . Moreover, for both models the greater the length of the k -mers the smoother the functions Σx y(p ) ,Σx(p ) and Σy(p ) . For the more practically important C model, the other interesting findings are (i) for large values of k (k =64 ,128 ), the values of Σx y and Σy increase rapidly with the initial increase of p from 0 to 0.1; (ii) for k ≥16 , all the Σx y(p ) and Σx(p ) curves intersect with each other at the same isoconductivity points; (iii) for anisotropic deposition, the percolation concentrations are the same in the x and y directions, whereas, at the percolation point the greater the length of the k -mers the larger the anisotropy of the electrical conductivity, i.e., the ratio σy/σx (>1 ).

Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen.

PubMed

Bannai, Hiroshi; Nemoto, Manabu; Tsujimura, Koji; Yamanaka, Takashi; Maeda, Ken; Kondo, Takashi

2016-02-01

To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA.

Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein

PubMed Central

Millet, Jean Kaoru; Whittaker, Gary R.

2014-01-01

Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly identified betacoronavirus causing high morbidity and mortality in humans. The coronavirus spike (S) protein is the main determinant of viral entry, and although it was previously shown that MERS-CoV S can be activated by various proteases, the details of the mechanisms of proteolytic activation of fusion are still incompletely characterized. Here, we have uncovered distinctive characteristics of MERS-CoV S. We identify, by bioinformatics and peptide cleavage assays, two cleavage sites for furin, a ubiquitously expressed protease, which are located at the S1/S2 interface and at the S2′ position of the S protein. We show that although the S1/S2 site is proteolytically processed by furin during protein biosynthesis, the S2′ site is cleaved upon viral entry. MERS-CoV pseudovirion infection was shown to be enhanced by elevated levels of furin expression, and entry could be decreased by furin siRNA silencing. Enhanced furin activity appeared to partially override the low pH-dependent nature of MERS-CoV entry. Inhibition of furin activity was shown to decrease MERS-CoV S-mediated entry, as well as infection by the virus. Overall, we show that MERS-CoV has evolved an unusual two-step furin activation for fusion, suggestive of a role during the process of emergence into the human population. The ability of MERS-CoV to use furin in this manner, along with other proteases, may explain the polytropic nature of the virus. PMID:25288733

Multi-Agent Modeling and Simulation Approach for Design and Analysis of MER Mission Operations

NASA Technical Reports Server (NTRS)

Seah, Chin; Sierhuis, Maarten; Clancey, William J.

2005-01-01

A space mission operations system is a complex network of human organizations, information and deep-space network systems and spacecraft hardware. As in other organizations, one of the problems in mission operations is managing the relationship of the mission information systems related to how people actually work (practices). Brahms, a multi-agent modeling and simulation tool, was used to model and simulate NASA's Mars Exploration Rover (MER) mission work practice. The objective was to investigate the value of work practice modeling for mission operations design. From spring 2002 until winter 2003, a Brahms modeler participated in mission systems design sessions and operations testing for the MER mission held at Jet Propulsion Laboratory (JPL). He observed how designers interacted with the Brahms tool. This paper discussed mission system designers' reactions to the simulation output during model validation and the presentation of generated work procedures. This project spurred JPL's interest in the Brahms model, but it was never included as part of the formal mission design process. We discuss why this occurred. Subsequently, we used the MER model to develop a future mission operations concept. Team members were reluctant to use the MER model, even though it appeared to be highly relevant to their effort. We describe some of the tool issues we encountered.

Improvement of an enzyme-linked immunosorbent assay for equine herpesvirus type 4 by using a synthetic-peptide 24-mer repeat sequence of glycoprotein G as an antigen

PubMed Central

BANNAI, Hiroshi; NEMOTO, Manabu; TSUJIMURA, Koji; YAMANAKA, Takashi; MAEDA, Ken; KONDO, Takashi

2015-01-01

To increase the sensitivity of an enzyme-linked immunosorbent assay (ELISA) for equine herpesvirus type 4 (EHV-4) that uses a 12-mer peptide of glycoprotein G (gG4-12-mer: MKNNPIYSEGSL) [4], we used a longer peptide consisting of a 24-mer repeat sequence (gG4-24-mer: MKNNPIYSEGSLMLNVQHDDSIHT) as an antigen. Sera of horses experimentally infected with EHV-4 reacted much more strongly to the gG4-24-mer peptide than to the gG4-12-mer peptide. We used peptide ELISAs to test paired sera from horses naturally infected with EHV-4 (n=40). gG4-24-mer ELISA detected 37 positive samples (92.5%), whereas gG4-12-mer ELISA detected only 28 (70.0%). gG4-24-mer ELISA was much more sensitive than gG4-12-mer ELISA. PMID:26424485

Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV.

PubMed

Lee, Hyun; Lei, Hao; Santarsiero, Bernard D; Gatuz, Joseph L; Cao, Shuyi; Rice, Amy J; Patel, Kavankumar; Szypulinski, Michael Z; Ojeda, Isabel; Ghosh, Arun K; Johnson, Michael E

2015-06-19

The Middle East Respiratory Syndrome coronavirus (MERS-CoV) papain-like protease (PLpro) blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it has been proven to play a crucial role in SARS-CoV PLpro inhibitor binding. Four SARS-CoV PLpro lead inhibitors were tested against MERS-CoV PLpro, none of which were effective against MERS-CoV PLpro. Structure and sequence alignments revealed that two residues, Y269 and Q270, responsible for inhibitor binding to SARS-CoV PLpro, were replaced by T274 and A275 in MERS-CoV PLpro, making critical binding interactions difficult to form for similar types of inhibitors. High-throughput screening (HTS) of 25 000 compounds against both PLpro enzymes identified a small fragment-like noncovalent dual inhibitor. Mode of inhibition studies by enzyme kinetics and competition surface plasmon resonance (SPR) analyses suggested that this compound acts as a competitive inhibitor with an IC50 of 6 μM against MERS-CoV PLpro, indicating that it binds to the active site, whereas it acts as an allosteric inhibitor against SARS-CoV PLpro with an IC50 of 11 μM. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpro may differ from that of SARS-CoV PLpro. In addition, inhibitory activity of this compound was selective for SARS-CoV and MERS-CoV PLpro enzymes over two human homologues, the ubiquitin C-terminal hydrolases 1 and 3 (hUCH-L1 and hUCH-L3).

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

PubMed Central

Sievers, Aaron; Bosiek, Katharina; Bisch, Marc; Dreessen, Chris; Riedel, Jascha; Froß, Patrick; Hausmann, Michael; Hildenbrand, Georg

2017-01-01

In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used. The results were analyzed by including positional information based on visualizations as genomic maps and by applying basic vector correlation methods. This analysis was concentrated on small word lengths (1 ≤ k ≤ 4) on relatively small viral genomes of Papillomaviridae and Herpesviridae, while also checking its usability for larger sequences, namely human chromosome 2 and the homologous chromosomes (2A, 2B) of a chimpanzee. Using this alignment-free analysis, several regions with specific characteristics in Papillomaviridae and Herpesviridae formerly identified by independent, mostly alignment-based methods, were confirmed. Correlations between the k-mer content and several genes in these genomes have been found, showing similarities between classified and unclassified viruses, which may be potentially useful for further taxonomic research. Furthermore, unknown k-mer correlations in the genomes of Human Herpesviruses (HHVs), which are probably of major biological function, are found and described. Using the chromosomes of a chimpanzee and human that are currently known, identities between the species on every analyzed chromosome were reproduced. This demonstrates the feasibility of our approach for large data sets of complex genomes. Based on these results, we suggest k-mer analysis with positional resolution as a method for closing a gap between the effectiveness of alignment-based methods (like NCBI BLAST) and the high pace of

Risk of global spread of Middle East respiratory syndrome coronavirus (MERS-CoV) via the air transport network.

PubMed

Gardner, Lauren M; Chughtai, Abrar A; MacIntyre, C Raina

2016-06-01

Middle East respiratory syndrome coronavirus (MERS-CoV) emerged from the Kingdom of Saudi Arabia (KSA) in 2012 and has since spread to 26 countries. All cases reported so far have either been in the Middle East or linked to the region through passenger air travel, with the largest outbreak outside KSA occurring in South Korea. Further international spread is likely due to the high travel volumes of global travel, as well as the occurrence of large annual mass gathering such as the Haj and Umrah pilgrimages that take place in the region. In this study, a transport network modelling framework was used to quantify the risk of MERS-CoV spreading internationally via air travellers. All regions connected to MERS-CoV affected countries via air travel are considered, and the countries at highest risk of travel-related importations of MERS-CoV were identified, ranked and compared with actual spread of MERS cases. The model identifies all countries that have previously reported a travel acquired case to be in the top 50 at-risk countries. India, Pakistan and Bangladesh are the highest risk countries which have yet to report a case, and should be prepared for the possibility of (pilgrims and general) travellers returning infected with MERS-CoV. In addition, the UK, Egypt, Turkey and the USA are at risk of more cases. We have demonstrated a risk-analysis approach, using travel patterns, to prioritize countries at highest risk for MERS-CoV importations. In order to prevent global outbreaks such as the one seen in South Korea, it is critical for high-risk countries to be prepared and have appropriate screening and triage protocols in place to identify travel-related cases of MERS-CoV. The results from the model can be used by countries to prioritize their airport and hospital screening and triage protocols. © International Society of Travel Medicine, 2016. All rights reserved. Published by Oxford University Press. For permissions, please e-mail: journals.permissions@oup.com.

Applying Reactive Barrier Technology to Enhance Microbially-mediated Denitrification during Managed Aquifer Recharge

NASA Astrophysics Data System (ADS)

Beganskas, S.; Weir, W. B.; Harmon, R. E.; Gorski, G.; Fisher, A. T.; Saltikov, C.; Young, K. S.; Runneals, D.; Teo, E. K.; Stoneburner, B.; Hernandez, J.

2015-12-01

We are running field experiments to observe and quantify microbially-mediated water quality improvement via denitrification during infiltration in the shallow subsurface. Nitrate is a pervasive groundwater contaminant, and nitrate removal through denitrification can occur during infiltration in natural and anthropogenic systems, including during managed aquifer recharge (MAR). The rate of denitrification can vary depending on factors such as infiltration rate; previous work suggests that denitrification rates can increase monotonically with infiltration rates until reaching a critical threshold. We are performing controlled field tests of variables that affect denitrification rate, including sampling to link water chemistry changes to microbial ecology and activity. This study explores how microbial activity and denitrification rates respond to different infiltration rates and the presence or absence of a reactive material (wood chips, a carbon source). We are conducting four two-week-long tests, each under different conditions. For each test, we measure bulk infiltration rate (the sum of lateral and vertical infiltration), vertical infiltration rate using heat as a tracer, and water level. We collect surface and subsurface water samples daily, and we collect soil samples at the start and end of each test. For each water sample, we are measuring NO3-, NO2-, NH3, DOC, and N and O isotopes in nitrate. Soil samples will be tested for grain size, total C/N, and the presence of microbiological genes associated with denitrification. These results will expand our knowledge of the conditions under which denitrification occurs by implicating specific microorganisms and physical infiltration parameters. Our design has the potential for additional experimentation with variables that impact water chemistry during infiltration. This study has broad applications for designing MAR systems that effectively improve water supply and water quality.

NCI Researchers Discover Exceptionally Potent Antibodies with Potential for Prophylaxis and Therapy of MERS-Coronavirus Infections | Poster

Cancer.gov

By Andrea Frydl, Contributing Writer In a recent article published in the Journal of Virology, Tianlei Ying, Ph.D., Dimiter Dimitrov, Ph.D., and their colleagues in the Laboratory of Experimental Immunology (LEI), Cancer and Inflammation Program, NCI Center for Cancer Research, reported the identification of three human monoclonal antibodies (m336, m337, and m338) that target the part of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) that is responsible for binding to its receptor. These antibodies are exceptionally potent inhibitors of MERS-CoV infection and also provide a basis for creating a future MERS-CoV vaccine.

KENNEDY SPACE CENTER, FLA. - An overhead crane lifts the Mars Exploration Rover 2 (MER-2) entry vehicle from its stand to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - An overhead crane lifts the Mars Exploration Rover 2 (MER-2) entry vehicle from its stand to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - With help from workers, the overhead crane lowers the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - With help from workers, the overhead crane lowers the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - An overhead crane moves the Mars Exploration Rover 2 (MER-2) entry vehicle across the Payload Hazardous Servicing Facility toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - An overhead crane moves the Mars Exploration Rover 2 (MER-2) entry vehicle across the Payload Hazardous Servicing Facility toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - Workers in the Payload Hazardous Servicing Facility help guide the Mars Exploration Rover 2 (MER-2) entry vehicle toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - Workers in the Payload Hazardous Servicing Facility help guide the Mars Exploration Rover 2 (MER-2) entry vehicle toward a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - The overhead crane settles the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - The overhead crane settles the Mars Exploration Rover 2 (MER-2) entry vehicle onto a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors

PubMed Central

Almatouq, Abdullah; Babatunde, Akintunde O.

2016-01-01

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, −550 ± 10 mV and 50 mL/min respectively, for COD, pHcathode, ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m2 power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value. PMID:27043584

Concurrent Phosphorus Recovery and Energy Generation in Mediator-Less Dual Chamber Microbial Fuel Cells: Mechanisms and Influencing Factors.

PubMed

Almatouq, Abdullah; Babatunde, Akintunde O

2016-03-29

This study investigated the mechanism and key factors influencing concurrent phosphorus (P) recovery and energy generation in microbial fuel cells (MFC) during wastewater treatment. Using a mediator-less dual chamber microbial fuel cell operated for 120 days; P was shown to precipitate as struvite when ammonium and magnesium chloride solutions were added to the cathode chamber. Monitoring data for chemical oxygen demand (COD), pH, oxidation reduction potential (ORP) and aeration flow rate showed that a maximum 38% P recovery was achieved; and this corresponds to 1.5 g/L, pH > 8, -550 ± 10 mV and 50 mL/min respectively, for COD, pH(cathode), ORP and cathode aeration flow rate. More importantly, COD and aeration flow rate were shown to be the key influencing factors for the P recovery and energy generation. Results further show that the maximum P recovery corresponds to 72 mW/m² power density. However, the energy generated at maximum P recovery was not the optimum; this shows that whilst P recovery and energy generation can be concurrently achieved in a microbial fuel cell, neither can be at the optimal value.

Genome-reconstruction for eukaryotes from complex natural microbial communities.

PubMed

West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

2018-04-01

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

Characterization of novel monoclonal antibodies against the MERS-coronavirus spike protein and their application in species-independent antibody detection by competitive ELISA.

PubMed

Fukushi, Shuetsu; Fukuma, Aiko; Kurosu, Takeshi; Watanabe, Shumpei; Shimojima, Masayuki; Shirato, Kazuya; Iwata-Yoshikawa, Naoko; Nagata, Noriyo; Ohnishi, Kazuo; Ato, Manabu; Melaku, Simenew Keskes; Sentsui, Hiroshi; Saijo, Masayuki

2018-01-01

Since discovering the Middle East respiratory syndrome coronavirus (MERS-CoV) as a causative agent of severe respiratory illness in the Middle East in 2012, serological testing has been conducted to assess antibody responses in patients and to investigate the zoonotic reservoir of the virus. Although the virus neutralization test is the gold standard assay for MERS diagnosis and for investigating the zoonotic reservoir, it uses live virus and so must be performed in high containment laboratories. Competitive ELISA (cELISA), in which a labeled monoclonal antibody (MAb) competes with test serum antibodies for target epitopes, may be a suitable alternative because it detects antibodies in a species-independent manner. In this study, novel MAbs against the spike protein of MERS-CoV were produced and characterized. One of these MAbs was used to develop a cELISA. The cELISA detected MERS-CoV-specific antibodies in sera from MERS-CoV-infected rats and rabbits immunized with the spike protein of MERS-CoV. The MAb-based cELISA was validated using sera from Ethiopian dromedary camels. Relative to the neutralization test, the cELISA detected MERS-CoV-specific antibodies in 66 Ethiopian dromedary camels with a sensitivity and specificity of 98% and 100%, respectively. The cELISA and neutralization test results correlated well (Pearson's correlation coefficients=0.71-0.76, depending on the cELISA serum dilution). This cELISA may be useful for MERS epidemiological investigations on MERS-CoV infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermally induced defluorination during a mer to fac transformation of a blue-green phosphorescent cyclometalated iridium(III) complex.

PubMed

Zheng, Yonghao; Batsanov, Andrei S; Edkins, Robert M; Beeby, Andrew; Bryce, Martin R

2012-01-02

The new homoleptic tris-cyclometalated [Ir(C^N)(3)] complexes mer-8, fac-8, and fac-9 incorporating γ-carboline ligands are reported. Reaction of 3-(2,4-difluorophenyl)-5-(2-ethylhexyl)-pyrido[4,3-b]indole 6 with iridium(III) chloride under standard cyclometalating conditions gave the homoleptic complex mer-8 in 63% yield. The X-ray crystal structure of mer-8 is described. The Ir-C and Ir-N bonds show the expected bond length alternations for the differing trans influence of phenyl and pyridyl ligands. mer-8 quantitatively isomerized to fac-8 upon irradiation with UV light. However, heating mer-8 at 290 °C in glycerol led to an unusual regioselective loss of one fluorine atom from each of the ligands, yielding fac-9 in 58% yield. fac-8 is thermally very stable: no decomposition was observed when fac-8 was heated in glycerol at 290 °C for 48 h. The γ-carboline system of fac-8 enhances thermal stability compared to the pyridyl analogue fac-Ir(46dfppy)(3)10, which decomposes extensively upon being heated in glycerol at 290 °C for 2 h. Complexes mer-8, fac-8, and fac-9 are emitters of blue-green light (λ(max)(em) = 477, 476, and 494 nm, respectively). The triplet lifetimes for fac-8 and fac-9 are ~4.5 μs at room temperature; solution Φ(PL) values are 0.31 and 0.22, respectively.

Characterization of MER Landing Sites Using MOC and MOLA

NASA Technical Reports Server (NTRS)

Anderson, F. S.; Parker, T. J.

2002-01-01

The MOC images for MER are compared with MOLA data to characterize and locate each image. MOLA profiles show that Hematite remains benign, Melas and Isidis are rougher, and Athabasca and Gusev have regions of significant small scale topography. Additional information is contained in the original extended abstract.

Electricity generation in microbial fuel cells using neutral red as an electronophore

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, D.H.; Zeikus, J.G.

2000-04-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. Inmore » microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator was 10-fold more than the amount produced when thionin was the electron mediator. The amount of electrical energy generated and the amount of current produced from glucose in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge was used in the fuel cell, stable and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Their results are discussed in relation to factors that may improve the relatively low electrical efficiencies obtained with microbial fuel cells.« less

Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update.

PubMed

Aly, Mahmoud; Elrobh, Mohamed; Alzayer, Maha; Aljuhani, Sameera; Balkhy, Hanan

2017-01-01

The emergence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections has become a global issue of dire concerns. MERS-CoV infections have been identified in many countries all over the world whereas high level occurrences have been documented in the Middle East and Korea. MERS-CoV is mainly spreading across the geographical region of the Middle East, especially in the Arabian Peninsula, while some imported sporadic cases were reported from the Europe, North America, Africa, and lately Asia. The prevalence of MERS-CoV infections across the Gulf Corporation Council (GCC) countries still remains unclear. Therefore, the objective of the current study was to report the prevalence of MERS-CoV in the GCC countries and to also elucidate on its demographics in the Arabian Peninsula. To date, the World Health Organization (WHO) has reported 1,797 laboratory-confirmed cases of MERS-CoV infection since June 2012, involving 687 deaths in 27 different countries worldwide. Within a time span of 4 years from June 2012 to July 2016, we collect samples form MERS-CoV infected individuals from National Guard Hospital, Riyadh, and Ministry of health Saudi Arabia and other GCC countries. Our data comprise a total of 1550 cases (67.1% male and 32.9% female). The age-specific prevalence and distribution of MERS-CoV was as follow: <20 yrs (36 cases: 3.28%), 20-39 yrs (331 cases: 30.15%), 40-59 yrs (314 cases: 28.60%), and the highest-risk elderly group aged ≥60 yrs (417 cases: 37.98%). The case distribution among GCC countries was as follows: Saudi Arabia (1441 cases: 93%), Kuwait (4 cases: 0.3%), Bahrain (1 case: 0.1%), Oman (8 cases: 0.5%), Qatar (16 cases: 1.0%), and United Arab Emirates (80 cases: 5.2%). Thus, MERS-CoV was found to be more prevalent in Saudi Arabia especially in Riyadh, where 756 cases (52.4%) were the worst hit area of the country identified, followed by the western region Makkah where 298 cases (20.6%) were recorded. This prevalence update

Interaction of SARS and MERS Coronaviruses with the Antiviral Interferon Response.

PubMed

Kindler, E; Thiel, V; Weber, F

2016-01-01

Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) are the most severe coronavirus (CoV)-associated diseases in humans. The causative agents, SARS-CoV and MERS-CoV, are of zoonotic origin but may be transmitted to humans, causing severe and often fatal respiratory disease in their new host. The two coronaviruses are thought to encode an unusually large number of factors that allow them to thrive and replicate in the presence of efficient host defense mechanisms, especially the antiviral interferon system. Here, we review the recent progress in our understanding of the strategies that highly pathogenic coronaviruses employ to escape, dampen, or block the antiviral interferon response in human cells. © 2016 Elsevier Inc. All rights reserved.

MERS-CoV at the Animal–Human Interface: Inputs on Exposure Pathways from an Expert-Opinion Elicitation

PubMed Central

Funk, Anna L.; Goutard, Flavie Luce; Miguel, Eve; Bourgarel, Mathieu; Chevalier, Veronique; Faye, Bernard; Peiris, J. S. Malik; Van Kerkhove, Maria D.; Roger, Francois Louis

2016-01-01

Nearly 4 years after the first report of the emergence of Middle-East respiratory syndrome Coronavirus (MERS-CoV) and nearly 1800 human cases later, the ecology of MERS-CoV, its epidemiology, and more than risk factors of MERS-CoV transmission between camels are poorly understood. Knowledge about the pathways and mechanisms of transmission from animals to humans is limited; as of yet, transmission risks have not been quantified. Moreover the divergent sanitary situations and exposures to animals among populations in the Arabian Peninsula, where human primary cases appear to dominate, vs. other regions in the Middle East and Africa, with no reported human clinical cases and where the virus has been detected only in dromedaries, represents huge scientific and health challenges. Here, we have used expert-opinion elicitation in order to obtain ideas on relative importance of MERS-CoV risk factors and estimates of transmission risks from various types of contact between humans and dromedaries. Fourteen experts with diverse and extensive experience in MERS-CoV relevant fields were enrolled and completed an online questionnaire that examined pathways based on several scenarios, e.g., camels–camels, camels–human, bats/other species to camels/humans, and the role of diverse biological substances (milk, urine, etc.) and potential fomites. Experts believed that dromedary camels play the largest role in MERS-CoV infection of other dromedaries; however, they also indicated a significant influence of the season (i.e. calving or weaning periods) on transmission risk. All experts thought that MERS-CoV-infected dromedaries and asymptomatic humans play the most important role in infection of humans, with bats and other species presenting a possible, but yet undefined, risk. Direct and indirect contact of humans with dromedary camels were identified as the most risky types of contact, when compared to consumption of various camel products, with estimated “most likely�

Gold nanoparticles produced in situ mediate bioelectricity and hydrogen production in a microbial fuel cell by quantized capacitance charging.

PubMed

Kalathil, Shafeer; Lee, Jintae; Cho, Moo Hwan

2013-02-01

Oppan quantized style: By adding a gold precursor at its cathode, a microbial fuel cell (MFC) is demonstrated to form gold nanoparticles that can be used to simultaneously produce bioelectricity and hydrogen. By exploiting the quantized capacitance charging effect, the gold nanoparticles mediate the production of hydrogen without requiring an external power supply, while the MFC produces a stable power density. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

PubMed Central

Boyd, Eric S.; Barkay, Tamar

2012-01-01

Mercuric mercury (Hg[II]) is a highly toxic and mobile element that is likely to have had a pronounced and adverse effect on biology since Earth’s oxygenation ∼2.4 billion years ago due to its high affinity for protein sulfhydryl groups, which upon binding destabilize protein structure and decrease enzyme activity, resulting in a decreased organismal fitness. The central enzyme in the microbial mercury detoxification system is the mercuric reductase (MerA) protein, which catalyzes the reduction of Hg(II) to volatile Hg(0). In addition to MerA, mer operons encode for proteins involved in regulation, Hg binding, and organomercury degradation. Mer-mediated approaches have had broad applications in the bioremediation of mercury-contaminated environments and industrial waste streams. Here, we examine the composition of 272 individual mer operons and quantitatively map the distribution of mer-encoded functions on both taxonomic SSU rRNA gene and MerA phylogenies. The results indicate an origin and early evolution of MerA among thermophilic bacteria and an overall increase in the complexity of mer operons through evolutionary time, suggesting continual gene recruitment and evolution leading to an improved efficiency and functional potential of the Mer detoxification system. Consistent with a positive relationship between the evolutionary history and topology of MerA and SSU rRNA gene phylogenies (Mantel R = 0.81, p < 0.01), the distribution of the majority of mer functions, when mapped on these phylograms, indicates an overall tendency to inherit mer-encoded functions through vertical descent. However, individual mer functions display evidence of a variable degree of vertical inheritance, with several genes exhibiting strong evidence for acquisition via lateral gene transfer and/or gene loss. Collectively, these data suggest that (i) mer has evolved from a simple system in geothermal environments to a widely distributed and more complex and efficient

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong

KENNEDY SPACE CENTER, FLA. - In the foreground, three solid rocket boosters (SRBs) suspended in the launch tower flank the Delta II rocket (in the background) that will launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-15

KENNEDY SPACE CENTER, FLA. - In the foreground, three solid rocket boosters (SRBs) suspended in the launch tower flank the Delta II rocket (in the background) that will launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

First confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the United States, updated information on the epidemiology of MERS-CoV infection, and guidance for the public, clinicians, and public health authorities - May 2014.

PubMed

Bialek, Stephanie R; Allen, Donna; Alvarado-Ramy, Francisco; Arthur, Ray; Balajee, Arunmozhi; Bell, David; Best, Susan; Blackmore, Carina; Breakwell, Lucy; Cannons, Andrew; Brown, Clive; Cetron, Martin; Chea, Nora; Chommanard, Christina; Cohen, Nicole; Conover, Craig; Crespo, Antonio; Creviston, Jeanean; Curns, Aaron T; Dahl, Rebecca; Dearth, Stephanie; DeMaria, Alfred; Echols, Fred; Erdman, Dean D; Feikin, Daniel; Frias, Mabel; Gerber, Susan I; Gulati, Reena; Hale, Christa; Haynes, Lia M; Heberlein-Larson, Lea; Holton, Kelly; Ijaz, Kashef; Kapoor, Minal; Kohl, Katrin; Kuhar, David T; Kumar, Alan M; Kundich, Marianne; Lippold, Susan; Liu, Lixia; Lovchik, Judith C; Madoff, Larry; Martell, Sandra; Matthews, Sarah; Moore, Jessica; Murray, Linda R; Onofrey, Shauna; Pallansch, Mark A; Pesik, Nicki; Pham, Huong; Pillai, Satish; Pontones, Pam; Pringle, Kimberly; Pritchard, Scott; Rasmussen, Sonja; Richards, Shawn; Sandoval, Michelle; Schneider, Eileen; Schuchat, Anne; Sheedy, Kristine; Sherin, Kevin; Swerdlow, David L; Tappero, Jordan W; Vernon, Michael O; Watkins, Sharon; Watson, John

2014-05-16

Since mid-March 2014, the frequency with which cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection have been reported has increased, with the majority of recent cases reported from Saudi Arabia and United Arab Emirates (UAE). In addition, the frequency with which travel-associated MERS cases have been reported and the number of countries that have reported them to the World Health Organization (WHO) have also increased. The first case of MERS in the United States, identified in a traveler recently returned from Saudi Arabia, was reported to CDC by the Indiana State Department of Health on May 1, 2014, and confirmed by CDC on May 2. A second imported case of MERS in the United States, identified in a traveler from Saudi Arabia having no connection with the first case, was reported to CDC by the Florida Department of Health on May 11, 2014. The purpose of this report is to alert clinicians, health officials, and others to increase awareness of the need to consider MERS-CoV infection in persons who have recently traveled from countries in or near the Arabian Peninsula. This report summarizes recent epidemiologic information, provides preliminary descriptions of the cases reported from Indiana and Florida, and updates CDC guidance about patient evaluation, home care and isolation, specimen collection, and travel as of May 13, 2014.

Changes in Microbial (Bacteria and Archaea) Plankton Community Structure after Artificial Dispersal in Grazer-Free Microcosms

PubMed Central

Karayanni, Hera; Meziti, Alexandra; Spatharis, Sofie; Genitsaris, Savvas; Courties, Claude; Kormas, Konstantinos A.

2017-01-01

Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions. PMID:28587211

Adaptive evolution influences the infectious dose of MERS-CoV necessary to achieve severe respiratory disease.

PubMed

Douglas, Madeline G; Kocher, Jacob F; Scobey, Trevor; Baric, Ralph S; Cockrell, Adam S

2018-04-01

We recently established a mouse model (288-330 +/+ ) that developed acute respiratory disease resembling human pathology following infection with a high dose (5 × 10 6 PFU) of mouse-adapted MERS-CoV (icMERSma1). Although this high dose conferred fatal respiratory disease in mice, achieving similar pathology at lower viral doses may more closely reflect naturally acquired infections. Through continued adaptive evolution of icMERSma1 we generated a novel mouse-adapted MERS-CoV (maM35c4) capable of achieving severe respiratory disease at doses between 10 3 and 10 5 PFU. Novel mutations were identified in the maM35c4 genome that may be responsible for eliciting etiologies of acute respiratory distress syndrome at 10-1000 fold lower viral doses. Importantly, comparative genetics of the two mouse-adapted MERS strains allowed us to identify specific mutations that remained fixed through an additional 20 cycles of adaptive evolution. Our data indicate that the extent of MERS-CoV adaptation determines the minimal infectious dose required to achieve severe respiratory disease. Copyright © 2017 Elsevier Inc. All rights reserved.

Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus.

PubMed

Maslow, Joel N

2017-12-02

The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed.

Thermophysical properties of the MER and Beagle II landing site regions on Mars

NASA Astrophysics Data System (ADS)

Jakosky, Bruce M.; Hynek, Brian M.; Pelkey, Shannon M.; Mellon, Michael T.; Martínez-Alonso, Sara; Putzig, Nathaniel E.; Murphy, Nate; Christensen, Philip R.

2006-08-01

We analyzed remote-sensing observations of the Isidis Basin, Gusev Crater, and Meridiani Planum landing sites for Beagle II, MER-A Spirit, and MER-B Opportunity spacecraft, respectively. We emphasized the thermophysical properties using daytime and nighttime radiance measurements from the Mars Global Surveyor (MGS) Thermal Emission Spectrometer and Mars Odyssey Thermal Emission Imaging System (THEMIS) and thermal inertias derived from nighttime data sets. THEMIS visible images, MGS Mars Orbiter Camera (MOC) narrow-angle images, and MGS Mars Orbiter Laser Altimeter (MOLA) data are incorporated as well. Additionally, the remote-sensing data were compared with ground-truth at the MER sites. The Isidis Basin surface layer has been shaped by aeolian processes and erosion by slope winds coming off of the southern highlands and funneling through notches between massifs. In the Gusev region, surface materials of contrasting thermophysical properties have been interpreted as rocks or bedrock, duricrust, and dust deposits; these are consistent with a complex geological history dominated by volcanic and aeolian processes. At Meridiani Planum the many layers having different thermophysical and erosional properties suggest periodic deposition of differing sedimentological facies possibly related to clast size, grain orientation and packing, or mineralogy.

High-Resolution Topomapping of Mars: Life After MER Site Selection

NASA Technical Reports Server (NTRS)

Kirk, R. L.; Howington-Kraus, E.; Hare, T. M.; Soricone, R.; Ross, K.; Weller, L.; Rosiek, M.; Redding, B.; Galuszka, D.; Haldemann, A. F. C.

2004-01-01

In this abstract we describe our ongoing use of high-resolution images from the Mars Global Surveyor Mars Orbiter Camera Narrow-Angle subsystem (MGS MOC-NA) to derive quantitative topographic and slope data for the martian surface at 3 - 10-m resolution. Our efforts over the past several years focused on assessment of candidate landing sites for the Mars Exploration Rovers (MER) and culminated in the selection of sites in Gusev crater and Meridiani Planum as safe as well as scientifically compelling. As of this writing, MER-A (Spirit) has landed safely in Gusev and we are performing a limited amount of additional mapping near the landing point to support localization of the lander and rover operations planning. The primary focus of our work, however, has been extending our techniques to sample a variety of geologic terrains planetwide to support both a variety of geoscientific studies and planning and data analysis for missions such as Mars Express, Mars Reconnaissance Orbiter, and Phoenix.

Mild encephalopathy/encephalitis with a reversible splenial lesion (MERS): A report of five neonatal cases.

PubMed

Sun, Dan; Chen, Wen-Hong; Baralc, Suraj; Wang, Juan; Liu, Zhi-Sheng; Xia, Yuan-Peng; Chen, Lei

2017-06-01

Mild encephalopathy/encephalitis with a reversible splenial (MERS) lesion is a clinic-radiological entity. The clinical features of MERS in neonates are still not systemically reported. This paper presents five cases of MERS, and the up-to-date reviews of previously reported cases were collected and analyzed in the literature. Here we describe five cases clinically diagnosed with MERS. All of them were neonates and the average age was about 4 days. They were admitted for the common neurological symptoms such as hyperspasmia, poor reactivity and delirium. Auxiliary examinations during hospitalization also exhibited features in common. In this report, we reached following conclusions. Firstly, magnetic resonance imaging revealed solitary or comprehensive lesions in the splenium of corpus callosum, some of them extending to almost the whole corpus callosum. The lesions showed low intensity signal on T1-weighted images, homogeneously hyperintense signal on T2-weighted images, fluid-attenuated inversion recovery and diffusion-weighted images, and exhibited an obvious reduced diffusion on apparent diffusion coefficient map. Moreover, the lesions in the magnetic resonance imaging disappeared very quickly even prior to the clinical recovery. Secondly, all the cases depicted here suffered electrolyte disturbances especially hyponatremia which could be easily corrected. Lastly, all of the cases recovered quickly over one week to one month and majority of them exhibited signs of infections and normal electroencephalography.

Electricity Generation in Microbial Fuel Cells Using Neutral Red as an Electronophore

PubMed Central

Park, Doo Hyun; Zeikus, J. Gregory

2000-01-01

Neutral red (NR) was utilized as an electron mediator in microbial fuel cells consuming glucose to study both its efficiency during electricity generation and its role in altering anaerobic growth and metabolism of Escherichia coli and Actinobacillus succinogenes. A study of chemical fuel cells in which NADH, NR, and ferricyanide were the electron donor, the electronophore, and the electron acceptor, respectively, showed that electrical current produced from NADH was proportional to the concentration of NADH. Fourfold more current was produced from NADH in chemical fuel cells when NR was the electron mediator than when thionin was the electron mediator. In microbial fuel cells in which E. coli resting cells were used the amount of current produced from glucose when NR was the electron mediator (3.5 mA) was 10-fold more than the amount produced when thionin was the electron mediator (0.4 mA). The amount of electrical energy generated (expressed in joules per mole of substrate) and the amount of current produced from glucose (expressed in milliamperes) in NR-mediated microbial fuel cells containing either E. coli or A. succinogenes were about 10- and 2-fold greater, respectively, when resting cells were used than when growing cells were used. Cell growth was inhibited substantially when these microbial fuel cells were making current, and more oxidized end products were formed under these conditions. When sewage sludge (i.e., a mixed culture of anaerobic bacteria) was used in the fuel cell, stable (for 120 h) and equivalent levels of current were obtained with glucose, as observed in the pure-culture experiments. These results suggest that NR is better than other electron mediators used in microbial fuel cells and that sludge production can be decreased while electricity is produced in fuel cells. Our results are discussed in relation to factors that may improve the relatively low electrical efficiencies (1.2 kJ/mol) obtained with microbial fuel cells. PMID:10742202

Meter-scale slopes of candidate MER landing sites from point photoclinometry

USGS Publications Warehouse

Beyer, R.A.; McEwen, A.S.; Kirk, R.L.

2003-01-01

Photoclinometry was used to analyze the small-scale roughness of areas that fall within the proposed Mars Exploration Rover (MER) 2003 landing ellipses. The landing ellipses presented in this study were those in Athabasca Valles, Elysium Planitia, Eos Chasma, Gusev Crater, Isidis Planitia, Melas Chasma, and Meridiani Planum. We were able to constrain surface slopes on length scales comparable to the image resolution (1.5 to 12 m/pixel). The MER 2003 mission has various engineering constraints that each candidate landing ellipse must satisfy. These constraints indicate that the statistical slope values at 5 m baselines are an important criterion. We used our technique to constrain maximum surface slopes across large swaths of each image, and built up slope statistics for the images in each landing ellipse. We are confident that all MER 2003 landing site ellipses in this study, with the exception of the Melas Chasma ellipse, are within the small-scale roughness constraints. Our results have provided input into the landing hazard assessment process. In addition to evaluating the safety of the landing sites, our mapping of small-scale roughnesses can also be used to better define and map morphologic units. The morphology of a surface is characterized by the slope distribution and magnitude of slopes. In looking at how slopes are distributed, we can better define landforms and determine the boundaries of morphologic units. Copyright 2003 by the American Geophysical Union.

Proteomic Characterization of Central Pacific Oxygen Minimum Zone Microbial Communities

NASA Astrophysics Data System (ADS)

Saunders, J. K.; McIlvin, M. M.; Moran, D.; Held, N.; Futrelle, J.; Webb, E.; Santoro, A.; Dupont, C.; Saito, M.

2018-05-01

Microbial proteomic profiles are excellent for surveying vast expanses of pelagic ecosystems for links between microbial communities and the biogeochemical cycles they mediate. Data from the ProteOMZ expedition supports the utility of this method.

Geology of the MER 2003 "Elysium" candidate landing site in southeastern Utopia Planitia, Mars

USGS Publications Warehouse

Tanaka, K.L.; Carr, M.H.; Skinner, J.A.; Gilmore, M.S.; Hare, T.M.

2003-01-01

The NASA Mars Exploration Rover (MER) Project has been considering a landing-site ellipse designated EP78B2 in southeastern Utopia Planitia, southwest of Elysium Mons. The site appears to be relatively safe for a MER landing site because of its predicted low wind velocities in mesoscale atmospheric circulation models and its low surface roughness at various scales as indicated by topographic and imaging data sets. Previously, the site's surface rocks have been interpreted to be marine sediments or lava flows. In addition, we suggest that Late Noachian to Early Hesperian collapse and mass wasting of Noachian highland rocks contributed to the deposition of detritus in the area of the ellipse. Furthermore, we document partial Late Hesperian to Early Amazonian resurfacing of the ellipse by flows and vents that may be of mud or silicate volcanic origin. A rover investigation of the Utopia landing site using the MER Athena instrument package might address some fundamental aspects of Martian geologic evolution, such as climate change, hydrologic evolution, and magmatic and tectonic history. Copyright 2003 by the American Geophysical Union.

Vaccines for emerging infectious diseases: Lessons from MERS coronavirus and Zika virus

PubMed Central

Maslow, Joel N.

2017-01-01

ABSTRACT The past decade and a half has been characterized by numerous emerging infectious diseases. With each new threat, there has been a call for rapid vaccine development. Pathogens such as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and the Zika virus represent either new viral entities or viruses emergent in new geographic locales and characterized by novel complications. Both serve as paradigms for the global spread that can accompany new pathogens. In this paper, we review the epidemiology and pathogenesis of MERS-CoV and Zika virus with respect to vaccine development. The challenges in vaccine development and the approach to clinical trial design to test vaccine candidates for disease entities with a changing epidemiology are discussed. PMID:28846484

Development of Fluorescent Reverse Transcription Loop-mediated Isothermal Amplification (RT-LAMP) using Quenching Probes for the Detection of the Middle East Respiratory Syndrome Coronavirus.

PubMed

Shirato, Kazuya; Semba, Shohei; El-Kafrawy, Sherif A; Hassan, Ahmed M; Tolah, Ahmed M; Takayama, Ikuyo; Kageyama, Tsutomu; Notomi, Tsugunori; Kamitani, Wataru; Matsuyama, Shutoku; Azhar, Esam Ibraheem

2018-05-12

Clinical detection of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in patients is achieved using genetic diagnostic methods, such as real-time RT-PCR assay. Previously, we developed a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay for the detection of MERS-CoV [Virol J. 2014. 11:139]. Generally, amplification of RT-LAMP is monitored by the turbidity induced by precipitation of magnesium pyrophosphate with newly synthesized DNA. However, this mechanism cannot completely exclude the possibility of unexpected reactions. Therefore, in this study, fluorescent RT-LAMP assays using quenching probes (QProbes) were developed specifically to monitor only primer-derived signals. Two primer sets (targeting nucleocapsid and ORF1a sequences) were constructed to confirm MERS cases by RT-LAMP assay only. Our data indicate that both primer sets were capable of detecting MERS-CoV RNA to the same level as existing genetic diagnostic methods, and that both were highly specific with no cross-reactivity observed with other respiratory viruses. These primer sets were highly efficient in amplifying target sequences derived from different MERS-CoV strains, including camel MERS-CoV. In addition, the detection efficacy of QProbe RT-LAMP was comparable to that of real-time RT-PCR assay using clinical specimens from patients in Saudi Arabia. Altogether, these results indicate that QProbe RT-LAMP assays described here can be used as powerful diagnostic tools for rapid detection and surveillance of MERS-CoV infections. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Characterization of Martian Rock Shape for MER Airbag Drop Tests

NASA Astrophysics Data System (ADS)

Dimaggio, E. N.; Schroeder, R.; Castle, N.; Golombek, M.

2002-12-01

Rock distributions for the final platforms used in airbag drop tests are currently being designed for the Mars Exploration Rovers (MER) scheduled to launch in 2003. Like Mars Pathfinder (MPF), launched in 1996, MER will use a series of airbags to cushion its landing on the surface of Mars. Previous MER airbag drop tests have shown that sharp, angular (triangular) rocks >20 cm high may be hazardous. To aid in defining the rock distributions for the final airbag tests, images from the Viking Landers 1 and 2 and MPF were used to identify rocks that are >20 cm high, and characterize them as triangular, square or round. Approximately 33% of all rocks analyzed are triangular. Of the rocks analyzed that are ~20-60 cm high, ~14% are triangular. Most of these triangular rocks are small, ~20-30 cm high. Rock distributions of previous airbag platforms were similarly classified and show a greater percentage of triangular and square rocks that are ~20-60 cm high than at the landing sites. The burial of a rock (perched, partially buried or buried) was also considered because perched rocks may pose less of a threat to the airbags than those buried because perched rocks can be dislodged and roll during impact. Approximately 19% of all rocks analyzed, and ~19% of rocks that are ~20-60 cm high, are triangular and partially buried or buried. These data suggest that the platform rock distributions appropriately represented the risks to the airbags associated with triangular rocks. A similar percentage of >20 cm high triangular rocks will be added to the drop test platforms to represent landing site rock distributions.

Stimulation of Microbially Mediated Arsenic Release in Bangladesh Aquifers by Young Carbon Indicated by Radiocarbon Analysis of Sedimentary Bacterial Lipids.

PubMed

Whaley-Martin, K J; Mailloux, B J; van Geen, A; Bostick, B C; Silvern, R F; Kim, C; Ahmed, K M; Choudhury, I; Slater, G F

2016-07-19

The sources of reduced carbon driving the microbially mediated release of arsenic to shallow groundwater in Bangladesh remain poorly understood. Using radiocarbon analysis of phospholipid fatty acids (PLFAs) and potential carbon pools, the abundance and carbon sources of the active, sediment-associated, in situ bacterial communities inhabiting shallow aquifers (<30 m) at two sites in Araihazar, Bangladesh, were investigated. At both sites, sedimentary organic carbon (SOC) Δ(14)C signatures of -631 ± 54‰ (n = 12) were significantly depleted relative to dissolved inorganic carbon (DIC) of +24 ± 30‰ and dissolved organic carbon (DOC) of -230 ± 100‰. Sediment-associated PLFA Δ(14)C signatures (n = 10) at Site F (-167‰ to +20‰) and Site B (-163‰ to +21‰) were highly consistent and indicated utilization of carbon sources younger than the SOC, likely from the DOC pool. Sediment-associated PLFA Δ(14)C signatures were consistent with previously determined Δ(14)C signatures of microbial DNA sampled from groundwater at Site F indicating that the carbon source for these two components of the subsurface microbial community is consistent and is temporally stable over the two years between studies. These results demonstrate that the utilization of relatively young carbon sources by the subsurface microbial community occurs at sites with varying hydrology. Further they indicate that these young carbon sources drive the metabolism of the more abundant sediment-associated microbial communities that are presumably more capable of Fe reduction and associated release of As. This implies that an introduction of younger carbon to as of yet unaffected sediments (such as those comprising the deeper Pleistocene aquifer) could stimulate microbial communities and result in arsenic release.

KENNEDY SPACE CENTER, FLA. - The fairing for the Mars Exploration Rover 2 (MER-2/MER-A) arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - The fairing for the Mars Exploration Rover 2 (MER-2/MER-A) arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - An overhead crane is in place to lift the Mars Exploration Rover 2 (MER-2) entry vehicle to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - An overhead crane is in place to lift the Mars Exploration Rover 2 (MER-2) entry vehicle to move it to a spin table for a dry-spin test. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch for MER-2 (MER-A) is scheduled for June 5.

Characterization of mediators of microbial virulence and innate immunity using the Caenorhabditis elegans host-pathogen model.

PubMed

Alegado, Rosanna A; Campbell, Marianne C; Chen, Will C; Slutz, Sandra S; Tan, Man-Wah

2003-07-01

The soil-borne nematode, Caenorhabditis elegans, is emerging as a versatile model in which to study host-pathogen interactions. The worm model has shown to be particularly effective in elucidating both microbial and animal genes involved in toxin-mediated killing. In addition, recent work on worm infection by a variety of bacterial pathogens has shown that a number of virulence regulatory genes mediate worm susceptibility. Many of these regulatory genes, including the PhoP/Q two-component regulators in Salmonella and LasR in Pseudomonas aeruginosa, have also been implicated in mammalian models suggesting that findings in the worm model will be relevant to other systems. In keeping with this concept, experiments aimed at identifying host innate immunity genes have also implicated pathways that have been suggested to play a role in plants and animals, such as the p38 MAP kinase pathway. Despite rapid forward progress using this model, much work remains to be done including the design of more sensitive methods to find effector molecules and further characterization of the exact interaction between invading pathogens and C. elegans' cellular components.

Exploring Gusev with MER A

NASA Astrophysics Data System (ADS)

Grin, E. A.; Cabrol, N. A.; Des Marais, D.; Farmer, J.; Greeley, R.; Carr, M.; Kramer, M.; Moore, J.; Sutter, B.; Fike, D.; Kuzmin, R.; Grant, F.; Barlow, N.; Newsom, H.; Tanaka, K.; Urquhart, M.; de Goursac, O.; Grisby, B.

2002-12-01

Gusev will be an outstanding candidate to achieve the 2003 MER mission goals. The crater has collected sediments from a diversity of parent rocks in the vast Maadim Vallis watershed over a period of three billion years. Because of the interaction between Gusev and Maadim, it has been proposed that a significant volume of the sedimentary material in the crater is of aqueous origin. Mars Odyssey has shown that the hydrogen abundance in the Gusev region is higher than average at corresponding latitudes. This observation could be consistent with a past long lived aqueous activity. The presence of aqueous material is central to the MER mission because it can provide clues about the past water history, climate changes, and the potential habitability of Mars. However, while Gusev is recognized as a primary site because of its past fluvio lacustrine activity, the geological diversity and history of its immediate surroundings makes it exceptional and provides the foundation for an exciting exploration leading to key discoveries. In addition to aqueous, many other processes can have contributed to the material in the crater basin: volcanic, Apollinaris patera is only 200 km away, aeolian, glacial, and global airfall processes. How to identify the signature of each process? What was their succession in time? Do we see the evolution from perennial to more episodic lakes? Do we see interaction between volcanic, glacial, aeolian and lacustrine processes? What was the recurrence of dry episodes? What type of measurements can provide a definitive answer for each of these questions in the 600 m traverse range that the rover will accomplish? What diversity can we also expect in this range? Finally, the uniqueness and potential of Gusev does not reside only in this exceptional diversity. As there is evidence for long lived lake episodes, Gusev also offers the unique possibility to study for the first time the results of the in situ formation of aqueous sediments and minerals in their

KENNEDY SPACE CENTER, FLA. - Workers on the launch tower of Complex 17-A, Cape Canaveral Air Force Station, stand by while a solid rocket booster (SRB) is lifted to vertical. It is one of nine that will help launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-15

KENNEDY SPACE CENTER, FLA. - Workers on the launch tower of Complex 17-A, Cape Canaveral Air Force Station, stand by while a solid rocket booster (SRB) is lifted to vertical. It is one of nine that will help launch Mars Exploration Rover 2 (MER-2). NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

Translating MAPGEN to ASPEN for MER

NASA Technical Reports Server (NTRS)

Rabideau, Gregg R.; Knight, Russell L.; Lenda, Matthew; Maldague, Pierre F.

2013-01-01

This software translates MAPGEN (Europa and APGEN) domains to ASPEN, and the resulting domain can be used to perform planning for the Mars Exploration Rover (MER). In other words, this is a conversion of two distinct planning languages (both declarative and procedural) to a third (declarative) planning language in order to solve the problem of faithful translation from mixed-domain representations into the ASPEN Modeling Language. The MAPGEN planning system is an example of a hybrid procedural/declarative system where the advantages of each are leveraged to produce an effective planner/scheduler for MER tactical planning. The adaptation of the planning system (ASPEN) was investigated, and, with some translation, much of the procedural knowledge encoding is amenable to declarative knowledge encoding. The approach was to compose translators from the core languages used for adapting MAGPEN, which consists of Europa and APGEN. Europa is a constraint- based planner/scheduler where domains are encoded using a declarative model. APGEN is also constraint-based, in that it tracks constraints on resources and states and other variables. Domains are encoded in both constraints and code snippets that execute according to a forward sweep through the plan. Europa and APGEN communicate to each other using proxy activities in APGEN that represent constraints and/or tokens in Europa. The composition of a translator from Europa to ASPEN was fairly straightforward, as ASPEN is also a declarative planning system, and the specific uses of Europa for the MER domain matched ASPEN s native encoding fairly closely. On the other hand, translating from APGEN to ASPEN was considerably more involved. On the surface, the types of activities and resources one encodes in APGEN appear to match oneto- one to the activities, state variables, and resources in ASPEN. But, when looking into the definitions of how resources are profiled and activities are expanded, one sees code snippets that access

Seasonality in ocean microbial communities.

PubMed

Giovannoni, Stephen J; Vergin, Kevin L

2012-02-10

Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

Follow-up chest radiographic findings in patients with MERS-CoV after recovery

PubMed Central

Das, Karuna M; Lee, Edward Y; Singh, Rajvir; Enani, Mushira A; Al Dossari, Khalid; Van Gorkom, Klaus; Larsson, Sven G; Langer, Ruth D

2017-01-01

Purpose: To evaluate the follow-up chest radiographic findings in patients with Middle East respiratory syndrome coronavirus (MERS-CoV) who were discharged from the hospital following improved clinical symptoms. Materials and Methods: Thirty-six consecutive patients (9 men, 27 women; age range 21–73 years, mean ± SD 42.5 ± 14.5 years) with confirmed MERS-CoV underwent follow-up chest radiographs after recovery from MERS-CoV. The 36 chest radiographs were obtained at 32 to 230 days with a median follow-up of 43 days. The reviewers systemically evaluated the follow-up chest radiographs from 36 patients for lung parenchymal, airway, pleural, hilar and mediastinal abnormalities. Lung parenchyma and airways were assessed for consolidation, ground-glass opacity (GGO), nodular opacity and reticular opacity (i.e., fibrosis). Follow-up chest radiographs were also evaluated for pleural thickening, pleural effusion, pneumothorax and lymphadenopathy. Patients were categorized into two groups: group 1 (no evidence of lung fibrosis) and group 2 (chest radiographic evidence of lung fibrosis) for comparative analysis. Patient demographics, length of ventilations days, number of intensive care unit (ICU) admission days, chest radiographic score, chest radiographic deterioration pattern (Types 1-4) and peak lactate dehydrogenase level were compared between the two groups using the student t-test, Mann-Whitney U test and Fisher's exact test. Results: Follow-up chest radiographs were normal in 23 out of 36 (64%) patients. Among the patients with abnormal chest radiographs (13/36, 36%), the following were found: lung fibrosis in 12 (33%) patients GGO in 2 (5.5%) patients, and pleural thickening in 2 (5.5%) patients. Patients with lung fibrosis had significantly greater number of ICU admission days (19 ± 8.7 days; P value = 0.001), older age (50.6 ± 12.6 years; P value = 0.02), higher chest radiographic scores [10 (0-15.3); P value = 0.04] and higher peak lactate dehydrogenase

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

PubMed

Mapleson, Daniel; Garcia Accinelli, Gonzalo; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo J

2017-02-15

De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . bernardo.clavijo@earlham.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Microbial mitigation-exacerbation continuum: a novel framework for microbiome effects on hosts in the face of stress.

PubMed

David, Aaron S; Thapa-Magar, Khum B; Afkhami, Michelle E

2018-03-01

A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the Mitigation-Exacerbation Continuum as a novel framework to conceptualize microbial mediation of stress. We (1) use this continuum to quantify microbial mediation of stress for six plant species and (2) test the association between these continuum values and natural species' abundance. We factorially manipulated a common stress (allelopathy) and the presence of soil microbes to quantify microbial effects in benign and stressed environments for two critical early life-history metrics, seed germination and seedling biomass. Although we found evidence of both mitigation and exacerbation among the six species, exacerbation was more common. Across species, the degree of microbial-mediated effects on germination explained >80% of the variation of natural field abundances. Our results suggest a critical role of soil microbes in mediating plant stress responses, and a potential microbial mechanism underlying species abundance. © 2018 by the Ecological Society of America.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

PubMed Central

Momeni, Babak; Xie, Li; Shou, Wenying

2017-01-01

Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. DOI: http://dx.doi.org/10.7554/eLife.25051.001 PMID:28350295

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments.

PubMed

Wang, Yanping; Wiatrowski, Heather A; John, Ria; Lin, Chu-Ching; Young, Lily Y; Kerkhof, Lee J; Yee, Nathan; Barkay, Tamar

2013-02-01

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.

Geology of a Proposed MER Landing Site in Western Melas Chasma

NASA Technical Reports Server (NTRS)

Weitz, C. M.; Parker, T. J.; Anderson, F. S.; Grant, J. A.

2002-01-01

A proposed landing site for the Mars Exploration Rover (MER) has been identified in western Melas Chasma. The landing ellipse contains a blocky, bright deposit which we propose formed as a landslide, perhaps beneath a former lake. Additional information is contained in the original extended abstract.

Overview of preparedness and response for Middle East respiratory syndrome coronavirus (MERS-CoV) in Oman.

PubMed

Al-Abaidani, I S; Al-Maani, A S; Al-Kindi, H S; Al-Jardani, A K; Abdel-Hady, D M; Zayed, B E; Al-Harthy, K S; Al-Shaqsi, K H; Al-Abri, S S

2014-12-01

Several countries in the Middle East and around 22 countries worldwide have reported cases of human infection with the Middle East respiratory syndrome coronavirus (MERS-CoV). The exceptionally high fatality rate resulting from MERS-CoV infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. Within the framework of the national acute respiratory illness surveillance, the Ministry of Health in the Sultanate of Oman has announced two confirmed cases of MERS-CoV to date. The aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. The absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in Oman. Copyright © 2014. Published by Elsevier Ltd.

Enhanced inflammation in New Zealand white rabbits when MERS-CoV reinfection occurs in the absence of neutralizing antibody

PubMed Central

Houser, Katherine V.; Gretebeck, Lisa; Vogel, Leatrice; Sutton, Troy; Orandle, Marlene; Moore, Ian N.

2017-01-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that was first detected in humans in 2012 as a cause of severe acute respiratory disease. As of July 28, 2017, there have been 2,040 confirmed cases with 712 reported deaths. While many infections have been fatal, there have also been a large number of mild or asymptomatic cases discovered through monitoring and contact tracing. New Zealand white rabbits are a possible model for asymptomatic infection with MERS-CoV. In order to discover more about non-lethal infections and to learn whether a single infection with MERS-CoV would protect against reinfection, we inoculated rabbits with MERS-CoV and monitored the antibody and inflammatory response. Following intranasal infection, rabbits developed a transient dose-dependent pulmonary infection with moderately high levels of viral RNA, viral antigen, and perivascular inflammation in multiple lung lobes that was not associated with clinical signs. The rabbits developed antibodies against viral proteins that lacked neutralizing activity and the animals were not protected from reinfection. In fact, reinfection resulted in enhanced pulmonary inflammation, without an associated increase in viral RNA titers. Interestingly, passive transfer of serum from previously infected rabbits to naïve rabbits was associated with enhanced inflammation upon infection. We further found this inflammation was accompanied by increased recruitment of complement proteins compared to primary infection. However, reinfection elicited neutralizing antibodies that protected rabbits from subsequent viral challenge. Our data from the rabbit model suggests that people exposed to MERS-CoV who fail to develop a neutralizing antibody response, or persons whose neutralizing antibody titers have waned, may be at risk for severe lung disease on re-exposure to MERS-CoV. PMID:28817732

The Synechocystis PCC6803 MerA-like enzyme operates in the reduction of both mercury and uranium under the control of the glutaredoxin 1 enzyme.

PubMed

Marteyn, Benoit; Sakr, Samer; Farci, Sandrine; Bedhomme, Mariette; Chardonnet, Solenne; Decottignies, Paulette; Lemaire, Stéphane D; Cassier-Chauvat, Corinne; Chauvat, Franck

2013-09-01

In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX(2)C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes.

The Synechocystis PCC6803 MerA-Like Enzyme Operates in the Reduction of Both Mercury and Uranium under the Control of the Glutaredoxin 1 Enzyme

PubMed Central

Marteyn, Benoit; Sakr, Samer; Farci, Sandrine; Bedhomme, Mariette; Chardonnet, Solenne; Decottignies, Paulette; Lemaire, Stéphane D.; Cassier-Chauvat, Corinne

2013-01-01

In a continuing effort to analyze the selectivity/redundancy of the three glutaredoxin (Grx) enzymes of the model cyanobacterium Synechocystis PCC6803, we have characterized an enzyme system that plays a crucial role in protection against two toxic metal pollutants, mercury and uranium. The present data show that Grx1 (Slr1562 in CyanoBase) selectively interacts with the presumptive mercuric reductase protein (Slr1849). This MerA enzyme plays a crucial role in cell defense against both mercuric and uranyl ions, in catalyzing their NADPH-driven reduction. Like MerA, Grx1 operates in cell protection against both mercury and uranium. The Grx1-MerA interaction requires cysteine 86 (C86) of Grx1 and C78 of MerA, which is critical for its reductase activity. MerA can be inhibited by glutathionylation and subsequently reactivated by Grx1, likely through deglutathionylation. The two Grx1 residues C31, which belongs to the redox active site (CX2C), and C86, which operates in MerA interactions, are both required for reactivation of MerA. These novel findings emphasize the role of glutaredoxins in tolerance to metal stress as well as the evolutionary conservation of the glutathionylation process, so far described mostly for eukaryotes. PMID:23852862

Association between Australian Hajj Pilgrims' awareness of MERS-CoV, and their compliance with preventive measures and exposure to camels.

PubMed

Alqahtani, Amani S; Wiley, Kerrie E; Mushta, Sami M; Yamazaki, Kaoruko; BinDhim, Nasser F; Heywood, Anita E; Booy, Robert; Rashid, Harunor

2016-05-01

Through a prospective cohort study the relationship between travellers' awareness of MERS-CoV, and compliance with preventive measures and exposure to camels was evaluated among Australian Hajj pilgrims who attended Hajj in 2015. Only 28% of Australian Hajj pilgrims were aware of MERS-CoV in Saudi Arabia. Those who were aware of MERS-CoV were more likely to receive recommended vaccines [odds ratio (OR) 3.1, 95% confidence interval (CI): 1.5-5.9, P < 0.01], but there was no significant difference in avoiding camels or their raw products during Hajj between those who were aware of MERS-CoV and those who were not (OR 1.2, 95% CI: 0.3-5.2, P = 0.7). Hajj pilgrims' awareness is reflected in some of their practices but not in all. © International Society of Travel Medicine, 2016. All rights reserved. Published by Oxford University Press. For permissions, please e-mail: journals.permissions@oup.com.

From Prime to Extended Mission: Evolution of the MER Tactical Uplink Process

NASA Technical Reports Server (NTRS)

Mishkin, Andrew H.; Laubach, Sharon

2006-01-01

To support a 90-day surface mission for two robotic rovers, the Mars Exploration Rover mission designed and implemented an intensive tactical operations process, enabling daily commanding of each rover. Using a combination of new processes, custom software tools, a Mars-time staffing schedule, and seven-day-a-week operations, the MER team was able to compress the traditional weeks-long command-turnaround for a deep space robotic mission to about 18 hours. However, the pace of this process was never intended to be continued indefinitely. Even before the end of the three-month prime mission, MER operations began evolving towards greater sustainability. A combination of continued software tool development, increasing team experience, and availability of reusable sequences first reduced the mean process duration to approximately 11 hours. The number of workshifts required to perform the process dropped, and the team returned to a modified 'Earth-time' schedule. Additional process and tool adaptation eventually provided the option of planning multiple Martian days of activity within a single workshift, making 5-day-a-week operations possible. The vast majority of the science team returned to their home institutions, continuing to participate fully in the tactical operations process remotely. MER has continued to operate for over two Earth-years as many of its key personnel have moved on to other projects, the operations team and budget have shrunk, and the rovers have begun to exhibit symptoms of aging.

Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

PubMed Central

Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

2017-01-01

Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI: http://dx.doi.org/10.7554/eLife.21900.001 PMID:28051769

The Merli-Missiroli-Pozzi Two-Slit Electron-Interference Experiment.

PubMed

Rosa, Rodolfo

In 2002 readers of Physics World voted Young's double-slit experiment with single electrons as "the most beautiful experiment in physics" of all time. Pier Giorgio Merli, Gian Franco Missiroli, and Giulio Pozzi carried out this experiment in a collaboration between the Italian Research Council and the University of Bologna almost three decades earlier. I examine their experiment, place it in historical context, and discuss its philosophical implications.

Estimation of basic reproduction number of the Middle East respiratory syndrome coronavirus (MERS-CoV) during the outbreak in South Korea, 2015.

PubMed

Chang, Hyuk-Jun

2017-06-13

In South Korea, an outbreak of Middle East respiratory syndrome (MERS) occurred in 2015. It was the second largest MERS outbreak. As a result of the outbreak in South Korea, 186 infections were reported, and 36 patients died. At least 16,693 people were isolated with suspicious symptoms. This paper estimates the basic reproduction number of the MERS coronavirus (CoV), using data on the spread of MERS in South Korea. The basic reproduction number of an epidemic is defined as the average number of secondary cases that an infected subject produces over its infectious period in a susceptible and uninfected population. To estimate the basic reproduction number of the MERS-CoV, we employ data from the 2015 South Korea MERS outbreak and the susceptible-infected-removed (SIR) model, a mathematical model that uses a set of ordinary differential equations (ODEs). We fit the model to the epidemic data of the South Korea outbreak minimizing the sum of the squared errors to identify model parameters. Also we derive the basic reproductive number as the terms of the parameters of the SIR model. Then we determine the basic reproduction number of the MERS-CoV in South Korea in 2015 as 8.0977. It is worth comparing with the basic reproductive number of the 2014 Ebola outbreak in West Africa including Guinea, Sierra Leone, and Liberia, which had values of 1.5-2.5. There was no intervention to control the infection in the early phase of the outbreak, thus the data used here provide the best conditions to evaluate the epidemic characteristics of MERS, such as the basic reproduction number. An evaluation of basic reproduction number using epidemic data could be problematic if there are stochastic fluctuations in the early phase of the outbreak, or if the report is not accurate and there is bias in the data. Such problems are not relevant to this study because the data used here were precisely reported and verified by Korea Hospital Association.

Probing the mer- to fac-isomerization of tris-cyclometallated homo- and heteroleptic (C,N)3 iridium(III) complexes.

PubMed

McDonald, Aidan R; Lutz, Martin; von Chrzanowski, Lars S; van Klink, Gerard P M; Spek, Anthony L; van Koten, Gerard

2008-08-04

We have developed techniques which allow for covalent tethering, via a "hetero" cyclometallating ligand, of heteroleptic tris-cyclometallated iridium(III) complexes to polymeric supports (for application in light-emitting diode technologies). This involved the selective synthesis and thorough characterization of heteroleptic [Ir(C,N) 2(C',N')] tris-cyclometallated iridium(III) complexes. Furthermore, the synthesis and characterization of heteroleptic [Ir(C,N) 2OR] complexes is presented. Under standard thermal conditions for the synthesis of the facial ( fac) isomer of tris-cyclometallated complexes, it was not possible to synthesize pure heteroleptic complexes of the form [Ir(C,N) 2(C',N')]. Instead, a mixture of homo- and heteroleptic complexes was acquired. It was found that a stepwise procedure involving the synthesis of a pure meridonial ( mer) isomer followed by photochemical isomerization of this mer to the fac isomer was necessary to synthesize pure fac-[Ir(C,N) 2(C',N')] complexes. Under thermal isomerization conditions, the conversion of mer-[Ir(C,N) 2(C',N')] to fac-[Ir(C,N) 2(C',N')] was also not a clean reaction, with again a mixture of homo- and heteroleptic complexes acquired. An investigation into the thermal mer to fac isomerization of both homo- and heteroleptic tris-cyclometallated complexes is presented. It was found that the process is an alcohol-catalyzed reaction with the formation of an iridium alkoxide [Ir(C,N) 2OR] intermediate in the isomerization process. This catalyzed reaction can be carried out between 50 and 100 degrees C, the first such example of low-temperature mer-fac thermal isomerization. We have synthesized analogous complexes and have shown that they do indeed react so as to give fac-tris-cyclometallated products. A detailed explanation of the intermediates (and all of their stereoisomers, in particular when systems of the generic formula [M(a,b) 2(a',b')] are synthesized) formed in the mer to fac isomerization process is

Periodontitis: from microbial immune subversion to systemic inflammation

PubMed Central

Hajishengallis, George

2014-01-01

Periodontitis is a dysbiotic inflammatory disease with an adverse impact on systemic health. Recent studies have provided insights into the emergence and persistence of dysbiotic oral microbial communities, which can mediate inflammatory pathology at local as well as distant sites. This Review discusses mechanisms of microbial immune subversion that tip the balance from homeostasis to disease in oral or extraoral sites. PMID:25534621

Microbial reduction of iodate

USGS Publications Warehouse

Councell, T.B.; Landa, E.R.; Lovley, D.R.

1997-01-01

The different oxidation species of iodine have markedly different sorption properties. Hence, changes in iodine redox states can greatly affect the mobility of iodine in the environment. Although a major microbial role has been suggested in the past to account for these redox changes, little has been done to elucidate the responsible microorganisms or the mechanisms involved. In the work presented here, direct microbial reduction of iodate was demonstrated with anaerobic cell suspensions of the sulfate reducing bacterium Desulfovibrio desulfuricans which reduced 96% of an initial 100 ??M iodate to iodide at pH 7 in 30 mM NaHCO3 buffer, whereas anaerobic cell suspensions of the dissimilatory Fe(III)-reducing bacterium Shewanella putrefaciens were unable to reduce iodate in 30 mM NaHCO3 buffer (pH 7). Both D. desulfuricans and S. putrefaciens were able to reduce iodate at pH 7 in 10 mM HEPES buffer. Both soluble ferrous iron and sulfide, as well as iron monosulfide (FeS) were shown to abiologically reduce iodate to iodide. These results indicate that ferric iron and/or sulfate reducing bacteria are capable of mediating both direct, enzymatic, as well as abiotic reduction of iodate in natural anaerobic environments. These microbially mediated reactions may be important factors in the fate and transport of 129I in natural systems.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minjing; Gao, Yuqian; Qian, Wei-Jun

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different frommore » that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.« less

Microbial mercury methylation in Antarctic sea ice.

PubMed

Gionfriddo, Caitlin M; Tate, Michael T; Wick, Ryan R; Schultz, Mark B; Zemla, Adam; Thelen, Michael P; Schofield, Robyn; Krabbenhoft, David P; Holt, Kathryn E; Moreau, John W

2016-08-01

Atmospheric deposition of mercury onto sea ice and circumpolar sea water provides mercury for microbial methylation, and contributes to the bioaccumulation of the potent neurotoxin methylmercury in the marine food web. Little is known about the abiotic and biotic controls on microbial mercury methylation in polar marine systems. However, mercury methylation is known to occur alongside photochemical and microbial mercury reduction and subsequent volatilization. Here, we combine mercury speciation measurements of total and methylated mercury with metagenomic analysis of whole-community microbial DNA from Antarctic snow, brine, sea ice and sea water to elucidate potential microbially mediated mercury methylation and volatilization pathways in polar marine environments. Our results identify the marine microaerophilic bacterium Nitrospina as a potential mercury methylator within sea ice. Anaerobic bacteria known to methylate mercury were notably absent from sea-ice metagenomes. We propose that Antarctic sea ice can harbour a microbial source of methylmercury in the Southern Ocean.

Selective DNA-Mediated Assembly of Gold Nanoparticles on Electroded Substrates

DTIC Science & Technology

2008-06-01

might use the Watson - Crick base-pairing of DNA as a means for ultrahigh-precision engineering is well- known.5,6 The idea is to use the highly specific...Selective DNA -Mediated Assembly of Gold Nanoparticles on Electroded Substrates K. E. Sapsford,†,‡,∇ D. Park,§ E. R. Goldman,‡ E. E. Foos,| S. A...electrodes via DNA hybridization. Protocols are demonstrated for maximizing selectivity and coverage using 15mers as the active binding agents. Detailed

The Effects of the Mars Exploration Rovers (MER) Work Schedule Regime on Locomotor Activity Circadian Rhythms, Sleep and Fatigue

NASA Technical Reports Server (NTRS)

DeRoshia, Charles W.; Colletti, Laura C.; Mallis, Melissa M.

2008-01-01

This study assessed human adaptation to a Mars sol by evaluating sleep metrics obtained by actigraphy and subjective responses in 22 participants, and circadian rhythmicity in locomotor activity in 9 participants assigned to Mars Exploration Rover (MER) operational work schedules (24.65 hour days) at the Jet Propulsion Laboratory in 2004. During MER operations, increased work shift durations and reduced sleep durations and time in bed were associated with the appearance of pronounced 12-hr (circasemidian) rhythms with reduced activity levels. Sleep duration, workload, and circadian rhythm stability have important implications for adaptability and maintenance of operational performance not only of MER operations personnel but also in space crews exposed to a Mars sol of 24.65 hours during future Mars missions.

T-cell-mediated immune response to respiratory coronaviruses

PubMed Central

Channappanavar, Rudragouda; Zhao, Jincun; Perlman, Stanley

2014-01-01

Emerging respiratory coronaviruses such as the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome coronavirus (MERS-CoV) pose potential biological threats to humans. SARS and MERS are manifested as severe atypical pneumonia associated with high morbidity and mortality in humans. The majority of studies carried out in SARS-CoV-infected humans and animals attribute a dysregulated/exuberant innate response as a leading contributor to SARS-CoV-mediated pathology. A decade after the 2002–2003 SARS epidemic, we do not have any approved preventive or therapeutic agents available in case of re-emergence of SARS-CoV or other related viruses. A strong neutralizing antibody response generated against the spike (S) glycoprotein of SARS-CoV is completely protective in the susceptible host. However, neutralizing antibody titers and the memory B cell response are short-lived in SARS-recovered patients and the antibody will target primary homologous strain. Interestingly, the acute phase of SARS in humans is associated with a severe reduction in the number of T cells in the blood. Surprisingly, only a limited number of studies have explored the role of the T cell-mediated adaptive immune response in respiratory coronavirus pathogenesis. In this review, we discuss the role of anti-virus CD4 and CD8 T cells during respiratory coronavirus infections with a special emphasis on emerging coronaviruses. PMID:24845462

MAPGEN : mixed initiative planning and scheduling for the Mars '03 MER mission

NASA Technical Reports Server (NTRS)

Ai-Chang, Mitchell; Bresina, John; Charest, Len; Jonsson, Ari; Hsu, Jennifer; Kanefsky, Bob; Maldague, Pierre; Morris, Paul; Rajan, Kanna; Yglesias, Jeffrey

2003-01-01

The Mars Exploration Rovers Mars '03 mission is one of NASA's most ambitious science missions to date. The rovers will be launched in the summer of 2003 with each rover carrying instruments to conduct remote and in-situ observation to elucidate the planet's past climate, water activity, and habitability. Science is the primary driver of MER and, as a consequence, making best use of the scientific instruments, within the available resources, is a crucial aspect of the mission. To address this critically, the MER project has selected MAPGEN (Mixed-Initiative Activity Plan GENerator) as an activity planning tool. MAPGEN combines two exiting systems, each with a strong heritage: APGEN the Activity Planning tool from the Jet Propulsion Laboratory and the Europs Planning/Scheduling system from NASA Ames Research Center. This paper discusses the issues arising from combining these tools in the context of this mission.

Sulfur-Mediated Electron Shuttling Sustains Microbial Long-Distance Extracellular Electron Transfer with the Aid of Metallic Iron Sulfides.

PubMed

Kondo, Katsuhito; Okamoto, Akihiro; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-07-07

In addition to serving as an energy source for microbial growth, iron sulfides are proposed to act as naturally occurring electrical wires that mediate long-distance extracellular electron transfer (EET) and bridge spatially discrete redox environments. These hypothetical EET reactions stand on the abilities of microbes to use the interfacial electrochemistry of metallic/semiconductive iron sulfides to maintain metabolisms; however, the mechanisms of these phenomena remain unexplored. To obtain insight into EET to iron sulfides, we monitored EET at the interface between Shewanella oneidensis MR-1 cells and biomineralized iron sulfides in an electrochemical cell. Respiratory current steeply increased with the concomitant formation of poorly crystalline mackinawite (FeS) minerals, indicating that S. oneidensis has the ability to exploit extracellularly formed metallic FeS for long-distance EET. Deletion of major proteins of the metal-reduction (Mtr) pathway (OmcA, MtrC, CymA, and PilD) caused only subtle effects on the EET efficiency, a finding that sharply contrasts the majority of studies that report that the Mtr pathway is indispensable for the reduction of metal oxides and electrodes. The gene expression analyses of polysulfide and thiosulfate reductase suggest the existence of a sulfur-mediated electron-shuttling mechanism by which HS(-) ions and water-soluble polysulfides (HS(n)(-), where n ≥ 2) generated in the periplasmic space deliver electrons from cellular metabolic processes to cell surface-associated FeS. The finding of this Mtr-independent pathway indicates that polysulfide reductases complement the function of outer-membrane cytochromes in EET reactions and, thus, significantly expand the number of microbial species potentially capable of long-distance EET in sulfur-rich anoxic environments.

Microbial interactions in building of communities

PubMed Central

Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

2012-01-01

SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

KENNEDY SPACE CENTER, FLA. - At right is the Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, that will launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-15

KENNEDY SPACE CENTER, FLA. - At right is the Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, that will launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2) is installed around the Mars Exploration Rover 2 (MER-2). MER-2 is one of NASA's twin Mars Exploration Rovers designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-2 is scheduled to launch no earlier than June 8 as MER-A, with two launch opportunities each day during the launch period that closes on June 19.

NASA Image and Video Library

2003-05-31

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2) is installed around the Mars Exploration Rover 2 (MER-2). MER-2 is one of NASA's twin Mars Exploration Rovers designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can't yet go. MER-2 is scheduled to launch no earlier than June 8 as MER-A, with two launch opportunities each day during the launch period that closes on June 19.

Effect of salt concentration and mediators in salt bridge microbial fuel cell for electricity generation from synthetic wastewater.

PubMed

Sevda, Surajbhan; Sreekrishnan, T R

2012-01-01

The aim of this study was to investigate the feasibility of using agar salt bridges for proton transport in Microbial Fuel Cells (MFC). It also tries to elucidate and effect of mediators on electricity production from wastewaters through experimentation using a simulated wastewater. In order to offset the very high cost of proton exchange membrane, salt bridges have been used in dual chamber MFCs. When the concentration of salt was varied in agar salt bridges from 1% to 10%, the volumetric power density changed from 1.71 to 84.99 mW/m(3) with a concomitant variation in power density from 0.32 to 16.02 mW/m(2). The maximum power density was observed at 5% salt concentration with 10% agar, which was accompanied by 88.41% COD reduction. In the case of methylene blue (0.01 mM) as the electron mediator, the voltage and current generation were 0.551 V and 0.47 mA, respectively. A maximum open circuit voltage of 0.718 V was seen at 0.08 mM methylene blue concentration, whereas maximum power densities of 17.59 mW/m(2) and 89.22 mW/m(3) were obtained. Different concentrations of neutral red were also tried out as mediators. A maximum open circuit voltage of 0.730 V was seen at 0.01 mM neutral red, corresponding to a power density of 12.02 mW/m(2) (volumetric power density of 60.97 mW/m(3)). Biofilm formation on the electrode surface was not observed in the presence of mediators, but was present in the absence of mediators. The results clearly demonstrated the feasibility to use agar salt bridge for proton transport and role of mediators in MFCs to generate electricity.

MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection

PubMed Central

Kubinak, Jason L.; Stephens, W. Zac; Soto, Ray; Petersen, Charisse; Chiaro, Tyson; Gogokhia, Lasha; Bell, Rickesha; Ajami, Nadim J.; Petrosino, Joseph F.; Morrison, Linda; Potts, Wayne K.; Jensen, Peter E.; O'Connell, Ryan M.; Round, June L.

2015-01-01

The presentation of protein antigens on the cell surface by major histocompatibility complex (MHC) molecules coordinates vertebrate adaptive immune responses, thereby mediating susceptibility to a variety of autoimmune and infectious diseases. The composition of symbiotic microbial communities (the microbiota) is influenced by host immunity and can have a profound impact on host physiology. Here we use an MHC congenic mouse model to test the hypothesis that genetic variation at MHC genes among individuals mediates susceptibility to disease by controlling microbiota composition. We find that MHC genotype significantly influences antibody responses against commensals in the gut, and that these responses are correlated with the establishment of unique microbial communities. Transplantation experiments in germfree mice indicate that MHC-mediated differences in microbiota composition are sufficient to explain susceptibility to enteric infection. Our findings indicate that MHC polymorphisms contribute to defining an individual's unique microbial fingerprint that influences health. PMID:26494419

The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015.

PubMed

Lee, Ji Yeon; Kim, You-Jin; Chung, Eun Hee; Kim, Dae-Won; Jeong, Ina; Kim, Yeonjae; Yun, Mi-Ran; Kim, Sung Soon; Kim, Gayeon; Joh, Joon-Sung

2017-07-14

In 2015, the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside the Middle East occurred in South Korea. We summarized the epidemiological, clinical, and laboratory findings of the first Korean case of MERS-CoV and analyzed whole-genome sequences of MERS-CoV derived from the patient. A 68-year-old man developed fever and myalgia 7 days after returning to Korea, following a 10-day trip to the Middle East. Before diagnosis, he visited 4 hospitals, potentially resulting in secondary transmission to 28 patients. On admission to the National Medical Center (day 9, post-onset of clinical illness), he presented with drowsiness, hypoxia, and multiple patchy infiltrations on the chest radiograph. He was intubated (day 12) because of progressive acute respiratory distress syndrome (ARDS) and INF-α2a and ribavirin treatment was commenced. The treatment course was prolonged by superimposed ventilator associated pneumonia. MERS-CoV PCR results converted to negative from day 47 and the patient was discharged (day 137), following rehabilitation therapy. The complete genome sequence obtained from a sputum sample (taken on day 11) showed the highest sequence similarity (99.59%) with the virus from an outbreak in Riyadh, Saudi Arabia, in February 2015. The first case of MERS-CoV infection had high transmissibility and was associated with a severe clinical course. The patient made a successful recovery after early treatment with antiviral agents and adequate supportive care. This first case in South Korea became a super-spreader because of improper infection control measures, rather than variations of the virus.

KENNEDY SPACE CENTER, FLA. - After arriving at Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off its transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - After arriving at Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off its transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) reaches the top of the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) reaches the top of the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off the transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted off the transporter. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, a crane is in place to lift the fairing for the Mars Exploration Rover 2 (MER-2/MER-A). The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, a crane is in place to lift the fairing for the Mars Exploration Rover 2 (MER-2/MER-A). The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is moved inside the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5..

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is moved inside the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5..

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Treesearch

Jennifer M. Fraterrigo; Teri C. Balser; Monica g. Turner

2006-01-01

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid...

Anaerobic Mercury Methylation and Demethylation by Geobacter bemidjiensis Bem

DOE PAGES

Lu, Xia; Liu, Yurong; Johs, Alexander; ...

2016-03-28

Two competing processes controlling the net production and bioaccumulation of neurotoxic methylmercury (MeHg) in natural ecosystems are microbial methylation and demethylation. Though mercury (Hg) methylation by anaerobic microorganisms and demethylation by aerobic Hg-resistant bacteria have both been extensively studied, little attention has been given to MeHg degradation by anaerobic bacteria, particularly the iron-reducing bacterium Geobacter bemidjensis Bem. Here we report, for the first time, that the strain G. bemidjensis Bem can methylate inorganic Hg and degrade MeHg concurrently under anoxic conditions. Our results suggest that G. bemidjensis cells utilize a reductive demethylation pathway to degrade MeHg, with elemental Hg(0) asmore » the major reaction product, possibly due to the presence of homologs encoding both organo-mercurial lyase (MerB) and mercuric reductase (MerA) in this organism. In addition, the cells can mediate multiple reactions including Hg/MeHg sorption, Hg reduction and oxidation, resulting in both time and concentration dependent Hg species transformations. Moderate concentrations (10 500 M) of Hg-binding ligands such as cysteine enhance Hg(II) methylation but inhibit MeHg degradation. These findings indicate a cycle of methylation and demethylation among anaerobic bacteria and suggest that mer-mediated demethylation may play a role in the net balance of MeHg production in anoxic water and sediments.« less

MICROBIAL ENZYME ACTIVITY FOR CHARACTERIZING NUTRIENT LOADING TO GREAT LAKES COASTAL WETLANDS

EPA Science Inventory

Energy and material flows in aquatic ecosystems are mediated by microbial carbon and nutrient cycling. Extracellular enzymes produced by the microbial community aid in the degradation of organic matter and the resultant acquisition of limiting nutrients. Organic carbon sequestrat...

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa

PubMed Central

Bosire, Erick M.; Blank, Lars M.

2016-01-01

ABSTRACT Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa. We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm−2 with ∼150 μg ml−1 phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. IMPORTANCE Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an

MER5101, a novel Aβ1-15:DT conjugate vaccine, generates a robust anti-Aβ antibody response and attenuates Aβ pathology and cognitive deficits in APPswe/PS1ΔE9 transgenic mice.

PubMed

Liu, Bin; Frost, Jeffrey L; Sun, Jing; Fu, Hongjun; Grimes, Stephen; Blackburn, Peter; Lemere, Cynthia A

2013-04-17

Active amyloid-β (Aβ) immunotherapy is under investigation to prevent or treat early Alzheimer's disease (AD). In 2002, a Phase II clinical trial (AN1792) was halted due to meningoencephalitis in ∼6% of the AD patients, possibly caused by a T-cell-mediated immunological response. Thus, generating a vaccine that safely generates high anti-Aβ antibody levels in the elderly is required. In this study, MER5101, a novel conjugate of Aβ1-15 peptide (a B-cell epitope fragment) conjugated to an immunogenic carrier protein, diphtheria toxoid (DT), and formulated in a nanoparticular emulsion-based adjuvant, was administered to 10-month-old APPswe/PS1ΔE9 transgenic (Tg) and wild-type (Wt) mice. High anti-Aβ antibody levels were observed in both vaccinated APPswe/PS1ΔE9 Tg and Wt mice. Antibody isotypes were mainly IgG1 and IgG2b, suggesting a Th2-biased response. Restimulation of splenocytes with the Aβ1-15:DT conjugate resulted in a strong proliferative response, whereas proliferation was absent after restimulation with Aβ1-15 or Aβ1-40/42 peptides, indicating a cellular immune response against DT while avoiding an Aβ-specific T-cell response. Moreover, significant reductions in cerebral Aβ plaque burden, accompanied by attenuated microglial activation and increased synaptic density, were observed in MER5101-vaccinated APPswe/PS1ΔE9 Tg mice compared with Tg adjuvant controls. Last, MER5101-immunized APPswe/PS1ΔE9 Tg mice showed improvement of cognitive deficits in both contextual fear conditioning and the Morris water maze. Our novel, highly immunogenic Aβ conjugate vaccine, MER5101, shows promise for improving Aβ vaccine safety and efficacy and therefore, may be useful for preventing and/or treating early AD.

Diflerent formulations of microbial respiratory losses and microbial efficiency have pronounced short and long term consequences for soil C dynamics and soil respiration

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Billings, S. A.

2016-12-01

Much of the variability in projections of Earth's future C balance derives from uncertainty in how to formulate and parameterize models of biologically mediated transformations of soil organic C (SOC). Over the past decade, models of belowground decomposition have incorporated more realism, namely microbial biomass and exoenzyme pools, but it remains unclear whether microbially mediated decomposition is accurately formulated. Different models and different assumptions about how microbial efficiency, defined in terms of respiratory losses, varies with temperature exert great influence on SOC and CO2 flux projections for the future. Here, we incorporate a physiologically realistic formulation of CO2 loss from microbes, distinct from extant formulations and logically consistent with microbial C uptake and losses, into belowground dynamics and contrast its projections for SOC pools and CO2 flux from soils to those from the phenomenological formulations of efficiency in current models. We quantitatively describe how short and long term SOC dynamics are influenced by different mathematical formulations of efficiency, and that our lack of knowledge regarding loss rates from SOC and microbial biomass pools, specific respiration rate and maximum substrate uptake rate severely constrains our ability to confidently parameterize microbial SOC modules in Earth System Models. Both steady-state SOC and microbial biomass C pools, as well as transient responses to perturbations, can differ substantially depending on how microbial efficiency is derived. In particular, the discrepancy between SOC stocks for different formulations of efficiency varies from negligible to more than two orders of magnitude, depending on the relative values of respiratory versus non-respiratory losses from microbial biomass. Mass-specific respiration and proportional loss rates from soil microbes emerge as key determinants of the consequences of different formulations of efficiency for C flux in soils.

The Ames MER microscopic imager toolkit

USGS Publications Warehouse

Sargent, R.; Deans, Matthew; Kunz, C.; Sims, M.; Herkenhoff, K.

2005-01-01

12The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a ??3mm depth of field and a 31??31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser.This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission. ?? 2005 IEEE.

The Ames MER Microscopic Imager Toolkit

NASA Technical Reports Server (NTRS)

Sargent, Randy; Deans, Matthew; Kunz, Clayton; Sims, Michael; Herkenhoff, Ken

2005-01-01

The Mars Exploration Rovers, Spirit and Opportunity, have spent several successful months on Mars, returning gigabytes of images and spectral data to scientists on Earth. One of the instruments on the MER rovers, the Athena Microscopic Imager (MI), is a fixed focus, megapixel camera providing a plus or minus mm depth of field and a 3lx31mm field of view at a working distance of 63 mm from the lens to the object being imaged. In order to maximize the science return from this instrument, we developed the Ames MI Toolkit and supported its use during the primary mission. The MI Toolkit is a set of programs that operate on collections of MI images, with the goal of making the data more understandable to the scientists on the ground. Because of the limited depth of field of the camera, and the often highly variable topography of the terrain being imaged, MI images of a given rock are often taken as a stack, with the Instrument Deployment Device (IDD) moving along a computed normal vector, pausing every few millimeters for the MI to acquire an image. The MI Toolkit provides image registration and focal section merging, which combine these images to form a single, maximally in-focus image, while compensating for changes in lighting as well as parallax due to the motion of the camera. The MI Toolkit also provides a 3-D reconstruction of the surface being imaged using stereo and can embed 2-D MI images as texture maps into 3-D meshes produced by other imagers on board the rover to provide context. The 2-D images and 3-D meshes output from the Toolkit are easily viewed by scientists using other mission tools, such as Viz or the MI Browser. This paper describes the MI Toolkit in detail, as well as our experience using it with scientists at JPL during the primary MER mission.

Anticorrosive Microbial Polysaccharides: Structure-Function Relationships

USDA-ARS?s Scientific Manuscript database

Water-soluble microbial polysaccharides are often implicated in biofilm formation and are believed to mediate cell-cell aggregation and adhesion to surfaces. Generally, biofilm formation is considered harmful or undesirable, as it leads to increased drag, plugging of pores, dimished heat transfer, ...

The response of soil carbon storage and microbially mediated carbon turnover to simulated climatic disturbance in a northern peatland forest. Revisiting the concept of soil organic matter recalcitrance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kostka, Joel

the chemical evolution of peat, with large shifts in microbial populations occurring in the biogeochemical hotspot, the mesotelm, where the highest rates of decomposition were detected. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens dominated in the deeper catotelm. Evidence pointed to the availability of phosphorus as well as nitrogen limiting the microbially-mediated turnover of organic carbon at MEF. Prior to initiation of the experimental treatments, our study provided key baseline data for the SPRUCE site on the vertical stratification of peat decomposition, key enzymatic pathways, and microbial taxa containing these pathways. The sensitivity of soil carbon turnover to climate change is strongly linked to recalcitrant carbon stocks and the temperature sensitivity of decomposition is thought to increase with increasing molecular complexity of carbon substrates. This project delivered results on how climate change perturbations impact the microbially-mediated turnover of recalcitrant organic matter in peatland forest soils, both under controlled conditions in the laboratory and at the ecosystem-scale in the field. This project revisited the concept of “recalcitrance” in the regulation of soil carbon turnover using a combination of natural abundance radiocarbon and optical spectroscopic measurements on bulk DOM, and high resolution molecular characterization of DOM. The project elucidated how organic matter reactivity and decomposition will respond to climate change in a both a qualitative (organic matter lability) and quantitiative (increased rates) manner. An Aromaticity Index was developed to represent a more direct and accurate parameter for modeling of DOM reactivity in peatlands. The abundance and community composition of soil

The effects of downwelling radiance on MER surface spectra: the evil that atmospheres do

NASA Astrophysics Data System (ADS)

Wolff, M.; Ghosh, A.; Arvidson, R.; Christensen, P.; Guinness, E.; Ruff, S.; Seelos, F.; Smith, M.; Athena Science

2004-11-01

While it may not be surprising to some that downwelling radiation in the martian atmosphere may contribute a non-negligible fraction of the radiance for a given surface scene, others remain shocked and surprised (and often dismayed) to discover this fact; particularly with regard to mini-TES observations. Naturally, the relative amplitude of this sky ``contamination'' is often a complicated function of meteorological conditions, viewing geometry, surface properties, and (for the IR) surface temperature. Ideally, one would use a specialized observations to mimic the actual hemispherical-directional nature of the problem. Despite repeated attempts to obtain Pancam complete sky observations and mini-TES sky octants, such observations are not available in the MER observational database. As a result, one is left with the less-enviable, though certainly more computationally intensive, task of connecting point observations (radiance and derived meteorological parameters) to a hemispherical integral of downwelling radiance. Naturally, one must turn to a radiative transfer analysis, despite oft-repeated attempts to assert otherwise. In our presentation, we offer insight into the conditions under which one must worry about atmospheric removal, as well as semi-empirical approaches (based upon said radiative transfer efforts) for producing the correction factors from the available MER atmospheric observations. This work is proudly supported by the MER program through NASA/JPL Contract No. 1242889 (MJW), as well as the contracts for the co-authors.

Rapid and Effective Virucidal Activity of Povidone-Iodine Products Against Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and Modified Vaccinia Virus Ankara (MVA).

PubMed

Eggers, Maren; Eickmann, Markus; Zorn, Juergen

2015-12-01

Since the first case of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infection was reported in 2012, the virus has infected more than 1300 individuals in 26 countries, and caused more than 480 deaths. Human-to-human transmission requires close contact, and has typically occurred in the healthcare setting. Improved global awareness, together with improved hygiene practices in healthcare facilities, has been highlighted as key strategies in controlling the spread of MERS-CoV. This study tested the in vitro efficacy of three formulations of povidone iodine (PVP-I: 4% PVP-I skin cleanser, 7.5% PVP-I surgical scrub, and 1% PVP-I gargle/mouthwash) against a reference virus (Modified vaccinia virus Ankara, MVA) and MERS-CoV. According to EN14476, a standard suspension test was used to assess virucidal activity against MVA and large volume plating was used for MERS-CoV. All products were tested under clean (0.3 g/L bovine serum albumin, BSA) and dirty conditions (3.0 g/L BSA + 3.0 mL/L erythrocytes), with application times of 15, 30, and 60 s for MVA, and 15 s for MERS-CoV. The products were tested undiluted, 1:10 and 1:100 diluted against MVA, and undiluted against MERS-CoV. A reduction in virus titer of ≥4 log10 (corresponding to an inactivation of ≥99.99%) was regarded as evidence of virucidal activity. This was achieved versus MVA and MERS-CoV, under both clean and dirty conditions, within 15 s of application of each undiluted PVP-I product. These data indicate that PVP-I-based hand wash products for potentially contaminated skin, and PVP-I gargle/mouthwash for reduction of viral load in the oral cavity and the oropharynx, may help to support hygiene measures to prevent transmission of MERS-CoV. Mundipharma Research GmbH & Co.

Computational modeling of the bat HKU4 coronavirus 3CLpro inhibitors as a tool for the development of antivirals against the emerging Middle East respiratory syndrome (MERS) coronavirus.

PubMed

Abuhammad, Areej; Al-Aqtash, Rua'a A; Anson, Brandon J; Mesecar, Andrew D; Taha, Mutasem O

2017-11-01

The Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging virus that poses a major challenge to clinical management. The 3C-like protease (3CL pro ) is essential for viral replication and thus represents a potential target for antiviral drug development. Presently, very few data are available on MERS-CoV 3CL pro inhibition by small molecules. We conducted extensive exploration of the pharmacophoric space of a recently identified set of peptidomimetic inhibitors of the bat HKU4-CoV 3CL pro . HKU4-CoV 3CL pro shares high sequence identity (81%) with the MERS-CoV enzyme and thus represents a potential surrogate model for anti-MERS drug discovery. We used 2 well-established methods: Quantitative structure-activity relationship (QSAR)-guided modeling and docking-based comparative intermolecular contacts analysis. The established pharmacophore models highlight structural features needed for ligand recognition and revealed important binding-pocket regions involved in 3CL pro -ligand interactions. The best models were used as 3D queries to screen the National Cancer Institute database for novel nonpeptidomimetic 3CL pro inhibitors. The identified hits were tested for HKU4-CoV and MERS-CoV 3CL pro inhibition. Two hits, which share the phenylsulfonamide fragment, showed moderate inhibitory activity against the MERS-CoV 3CL pro and represent a potential starting point for the development of novel anti-MERS agents. To the best of our knowledge, this is the first pharmacophore modeling study supported by in vitro validation on the MERS-CoV 3CL pro . MERS-CoV is an emerging virus that is closely related to the bat HKU4-CoV. 3CL pro is a potential drug target for coronavirus infection. HKU4-CoV 3CL pro is a useful surrogate model for the identification of MERS-CoV 3CL pro enzyme inhibitors. dbCICA is a very robust modeling method for hit identification. The phenylsulfonamide scaffold represents a potential starting point for MERS coronavirus 3CL pro inhibitors

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

NASA Astrophysics Data System (ADS)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

Structural and Biochemical Characterization of a Copper-Binding Mutant of the Organomercurial Lyase MerB: Insight into the Key Role of the Active Site Aspartic Acid in Hg-Carbon Bond Cleavage and Metal Binding Specificity.

PubMed

Wahba, Haytham M; Lecoq, Lauriane; Stevenson, Michael; Mansour, Ahmed; Cappadocia, Laurent; Lafrance-Vanasse, Julien; Wilkinson, Kevin J; Sygusch, Jurgen; Wilcox, Dean E; Omichinski, James G

2016-02-23

In bacterial resistance to mercury, the organomercurial lyase (MerB) plays a key role in the detoxification pathway through its ability to cleave Hg-carbon bonds. Two cysteines (C96 and C159; Escherichia coli MerB numbering) and an aspartic acid (D99) have been identified as the key catalytic residues, and these three residues are conserved in all but four known MerB variants, where the aspartic acid is replaced with a serine. To understand the role of the active site serine, we characterized the structure and metal binding properties of an E. coli MerB mutant with a serine substituted for D99 (MerB D99S) as well as one of the native MerB variants containing a serine residue in the active site (Bacillus megaterium MerB2). Surprisingly, the MerB D99S protein copurified with a bound metal that was determined to be Cu(II) from UV-vis absorption, inductively coupled plasma mass spectrometry, nuclear magnetic resonance, and electron paramagnetic resonance studies. X-ray structural studies revealed that the Cu(II) is bound to the active site cysteine residues of MerB D99S, but that it is displaced following the addition of either an organomercurial substrate or an ionic mercury product. In contrast, the B. megaterium MerB2 protein does not copurify with copper, but the structure of the B. megaterium MerB2-Hg complex is highly similar to the structure of the MerB D99S-Hg complexes. These results demonstrate that the active site aspartic acid is crucial for both the enzymatic activity and metal binding specificity of MerB proteins and suggest a possible functional relationship between MerB and its only known structural homologue, the copper-binding protein NosL.

Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

PubMed Central

Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

2009-01-01

Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

KENNEDY SPACE CENTER, FLA. - The Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, is having solid rocket boosters (SRBs) installed that will help launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-15

KENNEDY SPACE CENTER, FLA. - The Delta II rocket on Launch Complex 17-A, Cape Canaveral Air Force Station, is having solid rocket boosters (SRBs) installed that will help launch Mars Exploration Rover 2 (MER-2) on June 5. In the center are three more solid rocket boosters that will be added to the Delta, which will carry nine in all. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch as MER-A. MER-1 (MER-B) will launch June 25.

Biodegradation and surfactant-mediated biodegradation of diesel fuel by 218 microbial consortia are not correlated to cell surface hydrophobicity.

PubMed

Owsianiak, Mikołaj; Szulc, Alicja; Chrzanowski, Łukasz; Cyplik, Paweł; Bogacki, Mariusz; Olejnik-Schmidt, Agnieszka K; Heipieper, Hermann J

2009-09-01

In this study, we elucidated the role of cell surface hydrophobicity (microbial adhesion to hydrocarbons method, MATH) and the effect of anionic rhamnolipids and nonionic Triton X-100 surfactants on biodegradation of diesel fuel employing 218 microbial consortia isolated from petroleum-contaminated soils. Applied enrichment procedure with floating diesel fuel as a sole carbon source in liquid cultures resulted in consortia of varying biodegradation potential and diametrically different cell surface properties, suggesting that cell surface hydrophobicity is a conserved parameter. Surprisingly, no correlations between cell surface hydrophobicity and biodegradation of diesel fuel were found. Nevertheless, both surfactants altered cell surface hydrophobicity of the consortia in similar manner: increased for the hydrophilic and decreased for the hydrophobic cultures. In addition to this, the surfactants exhibited similar influence on diesel fuel biodegradation: Increase was observed for initially slow-degrading cultures and the opposite for fast degraders. This indicates that in the surfactant-mediated biodegradation, effectiveness of surfactants depends on the specification of microorganisms and not on the type of surfactant. In contrary to what was previously reported for pure strains, cell surface hydrophobicity, as determined by MATH, is not a good descriptor of biodegrading potential for mixed cultures.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification†

PubMed Central

Wu, Liyou; Liu, Xueduan; Schadt, Christopher W.; Zhou, Jizhong

2006-01-01

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. PMID:16820490

Strain- and Substrate-Dependent Redox Mediator and Electricity Production by Pseudomonas aeruginosa.

PubMed

Bosire, Erick M; Blank, Lars M; Rosenbaum, Miriam A

2016-08-15

Pseudomonas aeruginosa is an important, thriving member of microbial communities of microbial bioelectrochemical systems (BES) through the production of versatile phenazine redox mediators. Pure culture experiments with a model strain revealed synergistic interactions of P. aeruginosa with fermenting microorganisms whereby the synergism was mediated through the shared fermentation product 2,3-butanediol. Our work here shows that the behavior and efficiency of P. aeruginosa in mediated current production is strongly dependent on the strain of P. aeruginosa We compared levels of phenazine production by the previously investigated model strain P. aeruginosa PA14, the alternative model strain P. aeruginosa PAO1, and the BES isolate Pseudomonas sp. strain KRP1 with glucose and the fermentation products 2,3-butanediol and ethanol as carbon substrates. We found significant differences in substrate-dependent phenazine production and resulting anodic current generation for the three strains, with the BES isolate KRP1 being overall the best current producer and showing the highest electrochemical activity with glucose as a substrate (19 μA cm(-2) with ∼150 μg ml(-1) phenazine carboxylic acid as a redox mediator). Surprisingly, P. aeruginosa PAO1 showed very low phenazine production and electrochemical activity under all tested conditions. Microbial fuel cells and other microbial bioelectrochemical systems hold great promise for environmental technologies such as wastewater treatment and bioremediation. While there is much emphasis on the development of materials and devices to realize such systems, the investigation and a deeper understanding of the underlying microbiology and ecology are lagging behind. Physiological investigations focus on microorganisms exhibiting direct electron transfer in pure culture systems. Meanwhile, mediated electron transfer with natural redox compounds produced by, for example, Pseudomonas aeruginosa might enable an entire microbial

Comparing K-mer based methods for improved classification of 16S sequences.

PubMed

Vinje, Hilde; Liland, Kristian Hovde; Almøy, Trygve; Snipen, Lars

2015-07-01

The need for precise and stable taxonomic classification is highly relevant in modern microbiology. Parallel to the explosion in the amount of sequence data accessible, there has also been a shift in focus for classification methods. Previously, alignment-based methods were the most applicable tools. Now, methods based on counting K-mers by sliding windows are the most interesting classification approach with respect to both speed and accuracy. Here, we present a systematic comparison on five different K-mer based classification methods for the 16S rRNA gene. The methods differ from each other both in data usage and modelling strategies. We have based our study on the commonly known and well-used naïve Bayes classifier from the RDP project, and four other methods were implemented and tested on two different data sets, on full-length sequences as well as fragments of typical read-length. The difference in classification error obtained by the methods seemed to be small, but they were stable and for both data sets tested. The Preprocessed nearest-neighbour (PLSNN) method performed best for full-length 16S rRNA sequences, significantly better than the naïve Bayes RDP method. On fragmented sequences the naïve Bayes Multinomial method performed best, significantly better than all other methods. For both data sets explored, and on both full-length and fragmented sequences, all the five methods reached an error-plateau. We conclude that no K-mer based method is universally best for classifying both full-length sequences and fragments (reads). All methods approach an error plateau indicating improved training data is needed to improve classification from here. Classification errors occur most frequent for genera with few sequences present. For improving the taxonomy and testing new classification methods, the need for a better and more universal and robust training data set is crucial.

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

PubMed Central

Kingsford, Carl

2017-01-01

With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap detection, sparse suffix arrays for creating smaller indexes, and Bloom filters for speeding up sequence search. Here, we propose an alternative paradigm that can lead to substantial further improvement in these and other tasks. For integers k and L > k, we say that a set of k-mers is a universal hitting set (UHS) if every possible L-long sequence must contain a k-mer from the set. We develop a heuristic called DOCKS to find a compact UHS, which works in two phases: The first phase is solved optimally, and for the second we propose several efficient heuristics, trading set size for speed and memory. The use of heuristics is motivated by showing the NP-hardness of a closely related problem. We show that DOCKS works well in practice and produces UHSs that are very close to a theoretical lower bound. We present results for various values of k and L and by applying them to real genomes show that UHSs indeed improve over minimizers. In particular, DOCKS uses less than 30% of the 10-mers needed to span the human genome compared to minimizers. The software and computed UHSs are freely available at github.com/Shamir-Lab/DOCKS/ and acgt.cs.tau.ac.il/docks/, respectively. PMID:28968408

Searching for animal models and potential target species for emerging pathogens: Experience gained from Middle East respiratory syndrome (MERS) coronavirus.

PubMed

Vergara-Alert, Júlia; Vidal, Enric; Bensaid, Albert; Segalés, Joaquim

2017-06-01

Emerging and re-emerging pathogens represent a substantial threat to public health, as demonstrated with numerous outbreaks over the past years, including the 2013-2016 outbreak of Ebola virus in western Africa. Coronaviruses are also a threat for humans, as evidenced in 2002/2003 with infection by the severe acute respiratory syndrome coronavirus (SARS-CoV), which caused more than 8000 human infections with 10% fatality rate in 37 countries. Ten years later, a novel human coronavirus (Middle East respiratory syndrome coronavirus, MERS-CoV), associated with severe pneumonia, arose in the Kingdom of Saudi Arabia. Until December 2016, MERS has accounted for more than 1800 cases and 35% fatality rate. Finding an animal model of disease is key to develop vaccines or antivirals against such emerging pathogens and to understand its pathogenesis. Knowledge of the potential role of domestic livestock and other animal species in the transmission of pathogens is of importance to understand the epidemiology of the disease. Little is known about MERS-CoV animal host range. In this paper, experimental data on potential hosts for MERS-CoV is reviewed. Advantages and limitations of different animal models are evaluated in relation to viral pathogenesis and transmission studies. Finally, the relevance of potential new target species is discussed.

Application of State Analysis and Goal-based Operations to a MER Mission Scenario

NASA Technical Reports Server (NTRS)

Morris, John Richard; Ingham, Michel D.; Mishkin, Andrew H.; Rasmussen, Robert D.; Starbird, Thomas W.

2006-01-01

State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the system behavior in terms of state variables and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper first describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.

Application of State Analysis and Goal-Based Operations to a MER Mission Scenario

NASA Technical Reports Server (NTRS)

Morris, J. Richard; Ingham, Michel D.; Mishkin, Andrew H.; Rasmussen, Robert D.; Starbird, Thomas W.

2006-01-01

State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the behavior of states and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.

Early microbial contact, the breast milk microbiome and child health.

PubMed

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

Treatment outcomes for patients with Middle Eastern Respiratory Syndrome Coronavirus (MERS CoV) infection at a coronavirus referral center in the Kingdom of Saudi Arabia.

PubMed

Al Ghamdi, Mohammed; Alghamdi, Khalid M; Ghandoora, Yasmeen; Alzahrani, Ameera; Salah, Fatmah; Alsulami, Abdulmoatani; Bawayan, Mayada F; Vaidya, Dhananjay; Perl, Trish M; Sood, Geeta

2016-04-21

Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV) is a poorly understood disease with no known treatments. We describe the clinical features and treatment outcomes of patients with laboratory confirmed MERS-CoV at a regional referral center in the Kingdom of Saudi Arabia. In 2014, a retrospective chart review was performed on patients with a laboratory confirmed diagnosis of MERS-CoV to determine clinical and treatment characteristics associated with death. Confounding was evaluated and a multivariate logistic regression was performed to assess the independent effect of treatments administered. Fifty-one patients had an overall mortality of 37 %. Most patients were male (78 %) with a mean age of 54 years. Almost a quarter of the patients were healthcare workers (23.5 %) and 41 % had a known exposure to another person with MERS-CoV. Survival was associated with male gender, working as a healthcare worker, history of hypertension, vomiting on admission, elevated respiratory rate, abnormal lung exam, elevated alanine transaminase (ALT), clearance of MERS-CoV on repeat PCR polymerase chain reaction (PCR) testing, and mycophenolate mofetil treatment. Survival was reduced in the presence of coronary artery disease, hypotension, hypoxemia, CXR (chest X-ray) abnormalities, leukocytosis, creatinine >1 · 5 mg/dL, thrombocytopenia, anemia, and renal failure. In a multivariate analysis of treatments administered, severity of illness was the greatest predictor of reduced survival. Care for patients with MERS-CoV remains a challenge. In this retrospective cohort, interferon beta and mycophenolate mofetil treatment were predictors of increased survival in the univariate analysis. Severity of illness was the greatest predictor of reduced survival in the multivariate analysis. Larger randomized trials are needed to better evaluate the efficacy of these treatment regimens for MERS-CoV.

Cross-sectional surveillance of Middle East respiratory syndrome coronavirus (MERS-CoV) in dromedary camels and other mammals in Egypt, August 2015 to January 2016

PubMed Central

Ali, Mohamed; El-Shesheny, Rabeh; Kandeil, Ahmed; Shehata, Mahmoud; Elsokary, Basma; Gomaa, Mokhtar; Hassan, Naglaa; El Sayed, Ahmed; El-Taweel, Ahmed; Sobhy, Heba; Oludayo, Fasina Folorunso; Dauphin, Gwenaelle; El Masry, Ihab; Wolde, Abebe Wossene; Daszak, Peter; Miller, Maureen; VonDobschuetz, Sophie; Gardner, Emma; Morzaria, Subhash; Lubroth, Juan; Makonnen, Yilma Jobre

2017-01-01

A cross-sectional study was conducted in Egypt to determine the prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) in imported and resident camels and bats, as well as to assess possible transmission of the virus to domestic ruminants and equines. A total of 1,031 sera, 1,078 nasal swabs, 13 rectal swabs, and 38 milk samples were collected from 1,078 camels in different types of sites. In addition, 145 domestic animals and 109 bats were sampled. Overall, of 1,031 serologically-tested camels, 871 (84.5%) had MERS-CoV neutralising antibodies. Seroprevalence was significantly higher in imported (614/692; 88.7%) than resident camels (257/339; 5.8%) (p < 0.05). Camels from Sudan (543/594; 91.4%) had a higher seroprevalence than those from East Africa (71/98; 72.4%) (p < 0.05). Sampling site and age were also associated with MERS-CoV seroprevalence (p < 0.05). All tested samples from domestic animals and bats were negative for MERS-CoV antibodies except one sheep sample which showed a 1:640 titre. Of 1,078 camels, 41 (3.8%) were positive for MERS-CoV genetic material. Sequences obtained were not found to cluster with clade A or B MERS-CoV sequences and were genetically diverse. The presence of neutralising antibodies in one sheep apparently in contact with seropositive camels calls for further studies on domestic animals in contact with camels. PMID:28333616

Nutrient Addition Leads to a Weaker CO2 Sink and Higher CH4 Emissions through Vegetation-Microclimate Feedbacks at Mer Bleue Bog, Canada

NASA Astrophysics Data System (ADS)

Bubier, J. L.; Arnkil, S.; Humphreys, E.; Juutinen, S.; Larmola, T.; Moore, T. R.

2015-12-01

Atmospheric nitrogen (N) deposition has led to nutrient enrichment in wetlands globally, affecting plant community composition, carbon (C) cycling, and microbial dynamics. Nutrient-limited boreal bogs are long-term sinks of carbon dioxide (CO2), but sources of methane (CH4), an important greenhouse gas. We fertilized Mer Bleue Bog, a Sphagnum moss and evergreen shrub-dominated ombrotrophic bog near Ottawa, Ontario, for 10-15 years with N as NO3 and NH4 at 5, 10 and 20 times ambient N deposition (0.6-0.8 g N m-2 y-1), with and without phosphorus (P) and potassium (K). Treatments were applied to triplicate plots (3 x 3 m) from May - August 2000-2015 and control plots received distilled water. We measured net ecosystem CO2 exchange (NEE), ecosystem photosynthesis and respiration, and CH4 flux with climate-controlled chambers; leaf-level CO2 exchange and biochemistry; substrate-induced respiration, CH4 production and consumption potentials with laboratory incubations; plant species composition and abundance; and microclimate (peat temperature, moisture, light interception). After 15 years, we have found that NEE has decreased, and CH4 emissions have increased, in the highest nutrient treatments owing to changes in vegetation, microtopography, and peat characteristics. Vegetation changes include a loss of Sphagnum moss and introduction of new deciduous species. Simulated atmospheric N deposition has not benefitted the photosynthetic apparatus of the dominant evergreen shrubs, but resulted in higher foliar respiration, contributing to a weaker ecosystem CO2 sink. Loss of moss has led to wetter near-surface substrate, higher rates of decomposition and CH4 emission, and a shift in microbial communities. Thus, elevated atmospheric deposition of nutrients may endanger C storage in peatlands through a complex suite of feedbacks and interactions among vegetation, microclimate, and microbial communities.

Stepwise self-assembly of C60 mediated by atomic scale moiré magnifiers

NASA Astrophysics Data System (ADS)

Gruznev, D. V.; Matetskiy, A. V.; Bondarenko, L. V.; Utas, O. A.; Zotov, A. V.; Saranin, A. A.; Chou, J. P.; Wei, C. M.; Lai, M. Y.; Wang, Y. L.

2013-04-01

Self-assembly of atoms or molecules on a crystal surface is considered one of the most promising methods to create molecular devices. Here we report a stepwise self-assembly of C60 molecules into islands with unusual shapes and preferred sizes on a gold-indium-covered Si(111) surface. Specifically, 19-mer islands prefer a non-compact boomerang shape, whereas hexagonal 37-mer islands exhibit extraordinarily enhanced stability and abundance. The stepwise self-assembly is mediated by the moiré interference between an island with its underlying lattice, which essentially maps out the adsorption-energy landscape of a C60 on different positions of the surface with a lateral magnification factor and dictates the probability for the subsequent attachment of C60 to an island’s periphery. Our discovery suggests a new method for exploiting the moiré interference to dynamically assist the self-assembly of particles and provides an unexplored tactic of engineering atomic scale moiré magnifiers to facilitate the growth of monodispersed mesoscopic structures.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the first half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is raised to a vertical position for its lift up the launch tower. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) nears the top of the launch tower. The fairing will be installed around the payload for protection during launch on a Delta II rocket. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) nears the top of the launch tower. The fairing will be installed around the payload for protection during launch on a Delta II rocket. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

Metabolic interactions and dynamics in microbial communities

NASA Astrophysics Data System (ADS)

Segre', Daniel

Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

Using Mars and the Mer Mission to Teach Science: A Curriculum Designed for Teachers and Their Students

NASA Astrophysics Data System (ADS)

Aubele, J. C.; Stanley, J.; Grochowski, A.; Jones, K.; Aragon, J.

2006-12-01

Learning opportunities can be exceptionally successful when linked to national, newsworthy events. Planetary missions are particularly exciting in engaging teachers, and their students, because they combine the human "stories" of scientists and engineers with cutting-edge technology and new science. Planetary suface missions, such as the Mars Exploration Rover (MER) mission, return beautiful and human-scale images that can virtually transport the viewer to another world. The MER mission allows children and adults to participate in the exploration of one of our nearest neighbors in space. New discoveries in the natural history of Mars have been used as the basis of a new integrated curriculum created by Museum and class-room educators designed to serve informal (family learning) and formal (classroom) audiences. The curriculum uses Mars and the MER mission as a "hook" to teach a wide range of topics that relate to all of the sciences, mathematics, social studies (history and exploration), science and society, career readiness, language and literacy, and visual arts. The curriculum, entitled "Making Tracks on Mars: Teacher Resource and Activity Guide," includes the following key features that have contributed to its success and usefulness: (1) basic information about Mars, Mars missions, and the MER mission providing teachers with the knowledge they may lack; (2) activities that follow a standardized format and include necessary information, pre-lesson preparation and post-lesson closure and extensions, and all information and/or images needed; (3) activities that cross the curriculum and can be used to address many different standards; (4) relevant state and national standards listed for each activity; (5) annotated MER image file and PowerPoint presentation for easy classroom use; (6) lists of additional Mars-related resources; (7) emphasis on local connections to the mission to enable teachers and students to feel personally connected; (8) elementary through high

Extracellular Electron Uptake: Among Autotrophs and Mediated by Surfaces.

PubMed

Tremblay, Pier-Luc; Angenent, Largus T; Zhang, Tian

2017-04-01

Autotrophic microbes can acquire electrons from solid donors such as steel, other microbial cells, or electrodes. Based on this feature, bioprocesses are being developed for the microbial electrosynthesis (MES) of useful products from the greenhouse gas CO 2 . Extracellular electron-transfer mechanisms involved in the acquisition of electrons from metals by electrical microbially influenced corrosion (EMIC), from other living cells by interspecies electron transfer (IET), or from an electrode during MES rely on: (i) mediators such as H 2 ; (ii) physical contact through electron-transfer proteins; or (iii) mediator-generating enzymes detached from cells. This review explores the interactions of autotrophs with solid electron donors and their importance in nature and for biosustainable technologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

PubMed Central

LeProust, Emily M.; Peck, Bill J.; Spirin, Konstantin; McCuen, Heather Brummel; Moore, Bridget; Namsaraev, Eugeni; Caruthers, Marvin H.

2010-01-01

We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology). PMID:20308161

Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion.

PubMed

Pulsipher, Katherine W; Villegas, Jose A; Roose, Benjamin W; Hicks, Tacey L; Yoon, Jennifer; Saven, Jeffery G; Dmochowski, Ivan J

2017-07-18

Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation. These data suggest that salt solutions or charged AuNPs can shield unfavorable electrostatic interactions at AfFtn dimer-dimer interfaces, but specific "hot-spot" residues controlling assembly have not been identified. To investigate this further, we computationally designed three AfFtn mutants (E65R, D138K, and A127R) that introduce a single positive charge at sites along the dimer-dimer interface. These proteins exhibited different assembly kinetics and thermodynamics, which were ranked in order of increasing 24mer propensity: A127R < wild type < D138K ≪ E65R. E65R assembled into the 24mer across a wide range of ionic strengths (0-800 mM NaCl), and the dissociation temperature for the 24mer was 98 °C. X-ray crystal structure analysis of the E65R mutant identified a more compact, closed-pore cage geometry. A127R and D138K mutants exhibited wild-type ability to encapsulate and stabilize 5 nm AuNPs, whereas E65R did not encapsulate AuNPs at the same high yields. This work illustrates designed protein cages with distinct assembly and encapsulation properties.

Delta II Heavy MER-B Prelaunch

NASA Image and Video Library

2003-07-07

On Launch Complex 17-B, Cape Canaveral Air Force Station, the Delta II Heavy launch vehicle carrying the rover "Opportunity" for the second Mars Exploration Rover mission is poised for launch after rollback of the Mobile Service Tower. Opportunity will reach Mars on Jan. 25, 2004. Together the two MER rovers, Spirit (launched June 10) and Opportunity, seek to determine the history of climate and water at two sites on Mars where conditions may once have been favorable to life. The rovers are identical. They will navigate themselves around obstacles as they drive across the Martian surface, traveling up to about 130 feet each Martian day. Each rover carries five scientific instruments including a panoramic camera and microscope, plus a rock abrasion tool that will grind away the outer surfaces of rocks to expose their interiors for examination. Each rover’s prime mission is planned to last three months on Mars.

mer and fac isomerism in tris chelate diimine metal complexes.

PubMed

Dabb, Serin L; Fletcher, Nicholas C

2015-03-14

In this perspective, we highlight the issue of meridional (mer) and facial (fac) orientation of asymmetrical diimines in tris-chelate transition metal complexes. Diimine ligands have long been the workhorse of coordination chemistry, and whilst there are now good strategies to isolate materials where the inherent metal centered chirality is under almost complete control, and systematic methodologies to isolate heteroleptic complexes, the conceptually simple geometrical isomerism has not been widely investigated. In systems where the two donor atoms are significantly different in terms of the σ-donor and π-accepting ability, the fac isomer is likely to be the thermodynamic product. For the diimine complexes with two trigonal planar nitrogen atoms there is much more subtlety to the system, and external factors such as the solvent, lattice packing and the various steric considerations play a delicate role in determining the observed and isolable product. In this article we discuss the possibilities to control the isomeric ratio in labile systems, consider the opportunities to separate inert complexes and discuss the observed differences in their spectroscopic properties. Finally we report on the ligand orientation in supramolecular systems where facial coordination leads to simple regular structures such as helicates and tetrahedra, but the ability of the ligand system to adopt a mer orientation enables self-assembled structures of considerable beauty and complexity.

Microbial Fe biomineralization in mafic and ultramafic rocks

NASA Astrophysics Data System (ADS)

Templeton, A. S.; Mayhew, L.; McCollom, T.; Trainor, T.

2011-12-01

Fluid-filled microfractures within mafic and ultramafic rocks, such as basalt and peridotite, may be one of the most ubiquitous microbial habitats on the modern and ancient earth. In seafloor and subseafloor systems, one of the dominant energy sources is the oxidation of Fe by numerous potential oxidants under aerobic to anaerobic conditions. In particular, the oxidation of Fe may be directly catalyzed by microbial organisms, or result in the production of molecular hydrogen which can then fuel diverse lithotrophic metabolisms. However, it remains challenging to identify the dominant metabolic activities and unravel the microscale biogeochemical processes occuring within such rock-hosted systems. We are investigating the mechanisms of solid-state Fe-oxidation and biomineralization in basalt, olivine, pyroxenes and basalts, in the presence and absence of microbial organisms that can thrive across the full stability range of water. In this talk we will present synchrotron-based x-ray scattering and spectroscopic analyses of Fe speciation within secondary minerals formed during microbially-mediated vs. abiotic water-rock interactions. Determining the valence state and mineralogy of Fe-bearing phases is critical for determining the water-rock reaction pathways and identifying potential biominerals that may form; therefore, we will highlight new approaches for identifying key Fe transformations within complex geological media. In addition, many of our experimental studies involve the growth of lithotrophic biofilms on well-characterized mineral surfaces in order to determine the chemistry of the microbe-mineral interface during progressive electron-transfer reactions. By coupling x-ray spectroscopy, x-ray diffraction, and electron-microscopy measurements, we will also contrast the evolution of mineral surfaces that undergo microbially-mediated oxidative alteration against minerals surfaces that produce H2 to sustain anaerobic microbial communities.

Evaluation of Kefir as a New Anodic Biocatalyst Consortium for Microbial Fuel Cell.

PubMed

Silveira, Gustavo; Schneedorf, José Maurício

2018-02-21

Kefir, a combined consortium of bacteria and yeast encapsulated by a polymeric matrix of exopolysaccharides, was used as anodic biocatalyst in a two-chamber microbial fuel cell (MFC). Fermentation was followed during 72 h and polarization curves were obtained from linear sweep voltammetry. The effect of methylene blue as charge-transfer mediator in the kefir metabolism was evaluated. UV/Vis spectrophotometry and cyclic voltammetry were applied to evaluate the redox state of the mediator and to characterize the electrochemical activity, whereas current interruption was used for internal resistance determination. Aiming to establish a relationship between the microbial development inside the anodic chamber with the generated power in the MFC, total titratable acidity, pH, viscosity, carbohydrate assimilation, and microbial counting were assayed. The kefir-based MFC demonstrated a maximum power density of 54 mW m -2 after 24 h fermentation, revealing the potential use of kefir as a biocatalyst for microbial fuel cells.

Electrochemical performance and microbial community profiles in microbial fuel cells in relation to electron transfer mechanisms.

PubMed

Uria, Naroa; Ferrera, Isabel; Mas, Jordi

2017-10-18

Microbial fuel cells (MFCs) operating with complex microbial communities have been extensively reported in the past, and are commonly used in applications such as wastewater treatment, bioremediation or in-situ powering of environmental sensors. However, our knowledge on how the composition of the microbial community and the different types of electron transfer to the anode affect the performance of these bioelectrochemical systems is far from complete. To fill this gap of knowledge, we designed a set of three MFCs with different constrains limiting direct and mediated electron transfer to the anode. The results obtained indicate that MFCs with a naked anode on which a biofilm was allowed unrestricted development (MFC-A) had the most diverse archaeal and bacterial community, and offered the best performance. In this MFC both, direct and mediated electron transfer, occurred simultaneously, but direct electron transfer was the predominant mechanism. Microbial fuel cells in which the anode was enclosed in a dialysis membrane and biofilm was not allowed to develop (MFC-D), had a much lower power output (about 60% lower), and a prevalence of dissolved redox species that acted as putative electron shuttles. In the anolyte of this MFC, Arcobacter and Methanosaeta were the prevalent bacteria and archaea respectively. In the third MFC, in which the anode had been covered by a cation selective nafion membrane (MFC-N), power output decreased a further 5% (95% less than MFC-A). In this MFC, conventional organic electron shuttles could not operate and the low power output obtained was presumably attributed to fermentation end-products produced by some of the organisms present in the anolyte, probably Pseudomonas or Methanosaeta. Electron transfer mechanisms have an impact on the development of different microbial communities and in turn on MFC performance. Although a stable current was achieved in all cases, direct electron transfer MFC showed the best performance concluding

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

An Overview of Electron Acceptors in Microbial Fuel Cells

PubMed Central

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at the cathode as electron acceptors through reduction. Some contaminants can also function as electron mediators at the anode or cathode. While previous studies have done a thorough assessment of electron donors, cathodic electron acceptors and mediators have not been as well described. Oxygen is widely used as an electron acceptor due to its high oxidation potential and ready availability. Recent studies, however, have begun to assess the use of different electron acceptors because of the (1) diversity of redox potential, (2) needs of alternative and more efficient cathode reaction, and (3) expanding of MFC based technologies in different areas. The aim of this review was to evaluate the performance and applicability of various electron acceptors and mediators used in MFCs. This review also evaluated the corresponding performance, advantages and disadvantages, and future potential applications of select electron acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators. PMID:28469607

MicroRNA categorization using sequence motifs and k-mers.

PubMed

Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

2017-03-14

Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.

Tuning in and catching on? Examining the relationship between pandemic communication and awareness and knowledge of MERS in the USA.

PubMed

Lin, Leesa; McCloud, Rachel F; Bigman, Cabral A; Viswanath, Kasisomayajula

2017-06-01

Large-scale influenza outbreaks over the last decade, such as SARS and H1N1, have brought to global attention the importance of emergency risk communication and prompted the international community to develop communication responses. Since pandemic outbreaks are relatively infrequent, there is a dearth of evidence addressing the following questions: (i) Have the resources invested in strategic and routine communication for past pandemic outbreaks yielded public health preparedness benefits? (ii) Have past efforts sensitized people to pay attention to new pandemic threats? The Middle East Respiratory Syndrome (MERS) that was followed closely by major media outlets in the USA provides an opportunity to examine the relationship between exposure to public communication about epidemics and public awareness and knowledge about new risks. In December, 2013, we surveyed a nationally representative sample of 627 American adults and examined the associations between people's awareness to prior pandemics and their awareness of and knowledge about MERS. Awareness of prior pandemics was significantly associated with awareness and knowledge of MERS. The most common sources from which people first heard about MERS were also identified. Communication inequalities were observed between racial/ethnic and socioeconomic positions, suggesting a need for more effective pandemic communication. © The Author 2016. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial limitation in a changing world: A stoichiometric approach for predicting microbial resource limitation and fluxes

NASA Astrophysics Data System (ADS)

Midgley, M.; Phillips, R.

2014-12-01

Microbes mediate fluxes of carbon (C), nitrogen (N), and phosphorus (P) in soils depending on ratios of available C, N, and P relative to microbial demand. Hence, characterizing microbial C and nutrient limitation in soils is critical for predicting how ecosystems will respond to human alterations of climate and nutrient availability. Here, we take a stoichiometric approach to assessing microbial C, N, and P limitation by using threshold element ratios (TERs). TERs enable shifting resource limitation to be assessed by matching C, N and P ratios from microbial biomass, extracellular enzyme activities, and soil nutrient concentrations. We assessed microbial nutrient limitation in temperate forests dominated by trees that associate with one of two mycorrhizal symbionts: arbsucular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. We found that both ECM and AM microbial communities were co-limited by C and N, supporting conventional wisdom that microbes are C-limited and temperate forests are N-limited. However, AM microbial communities were relatively more C-limited than ECM communities (P=0.001). In response to chronic field N fertilization, both AM and ECM communities became relatively more P-limited (P=0.011), but they remained N- and C-limited overall. Thus, realistic levels of N deposition may not dampen microbial N limitation. Reflecting differences in relative limitation, N mineralization rates were higher in AM soils than in ECM soils (P=0.004) while C mineralization rates were higher in ECM soils than in AM soils (P=0.023). There were no significant differences in P flux between AM and ECM soils or detectable mineralization responses to N addition, indicating that mineralization rates are closely tied to C and nutrient limitation. Overall, we found that 1) microbial resource limitation can be detected without resource addition; and 2) TERs and ratios of labile resources are viable tools for predicting mineralization responses to resource additions.

MIMOS II on MER One Year of Mossbauer Spectroscopy on the Surface of Mars: From Jarosite at Meridiani Planum to Goethite at Gusev Crater

NASA Technical Reports Server (NTRS)

Klingelhoefer, G.; Rodionov, D. S.; Morris, R. V.; Schroeder, C.; deSouza, P. A.; Ming, D. W.; Yen, A. S.; Bernhardt, B.; Renz, F.; Fleischer, I.

2005-01-01

The miniaturized Mossbauer (MB) spectrometer MIMOS II [1] is part of the Athena payload of NASA s twin Mars Exploration Rovers "Spirit" (MER-A) and "Opportunity" (MER-B). It determines the Fe-bearing mineralogy of Martian soils and rocks at the Rovers respective landing sites, Gusev crater and Meridiani Planum. Both spectrometers performed successfully during first year of operation. Total integration time is about 49 days for MERA (79 samples) and 34 days for MER-B (85 samples). For curiosity it might be interesting to mention that the total odometry of the oscillating part of the MB drive exceeds 35 km for both rovers.

Construction and performance evaluation of mediator-less microbial fuel cell using carbon nanotubes as an anode material.

PubMed

Roh, Sung-Hee; Kim, Sun-Il

2012-05-01

A microbial fuel cell (MFC) is a device that converts chemical energy to electrical energy using the catalytic reaction of microorganisms. We investigated the performance of mediator-less MFC with carbon nanotubes (CNTs)/graphite felt composite electrodes. The addition of CNTs to a graphite felt electrode increases the specific surface area of the electrode and enhances the charge transfer capability so as to cause considerable improvement of the electrochemical activity for the anode reaction in a MFC. The performance of the MFC using CNTs/graphite felt electrode has been compared against a plain graphite felt electrode based MFC. A CNTs/graphite felt electrode showed as high as 15% increase in the power density (252 mW/m2) compared to graphite felt electrode (214 mW/m2). The CNTs/graphite felt anode therefore offers good prospects for application in MFCs.

Structural and Biochemical Characterization of Organotin and Organolead Compounds Binding to the Organomercurial Lyase MerB Provide New Insights into Its Mechanism of Carbon–Metal Bond Cleavage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wahba, Haytham M.; Stevenson, Michael J.; Mansour, Ahmed

2017-01-03

The organomercurial lyase MerB has the unique ability to cleave carbon–Hg bonds, and structural studies indicate that three residues in the active site (C96, D99, and C159 in E. coli MerB) play important roles in the carbon–Hg bond cleavage. However, the role of each residue in carbon–metal bond cleavage has not been well-defined. To do so, we have structurally and biophysically characterized the interaction of MerB with a series of organotin and organolead compounds. Studies with two known inhibitors of MerB, dimethyltin (DMT) and triethyltin (TET), reveal that they inhibit by different mechanisms. In both cases the initial binding ismore » to D99, but DMT subsequently binds to C96, which induces a conformation change in the active site. In contrast, diethyltin (DET) is a substrate for MerB and the SnIV product remains bound in the active site in a coordination similar to that of HgII following cleavage of organomercurial compounds. The results with analogous organolead compounds are similar in that trimethyllead (TML) is not cleaved and binds only to D99, whereas diethyllead (DEL) is a substrate and the PbIV product remains bound in the active site. Binding and cleavage is an exothermic reaction, while binding to D99 has negligible net heat flow. These results show that initial binding of organometallic compounds to MerB occurs at D99 followed, in some cases, by cleavage and loss of the organic moieties and binding of the metal ion product to C96, D99, and C159. The N-terminus of MerA is able to extract the bound PbVI but not the bound SnIV. These results suggest that MerB could be utilized for bioremediation applications, but certain organolead and organotin compounds may present an obstacle by inhibiting the enzyme.« less

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion.

PubMed

Peterson, Robyn A; Gueniche, Audrey; Adam de Beaumais, Ségolène; Breton, Lionel; Dalko-Csiba, Maria; Packer, Nicolle H

2016-03-01

There is increasing evidence that secretory fluids such as tears, saliva and milk play an important role in protecting the human body from infection via a washing mechanism involving glycan-mediated adhesion of potential pathogens to secretory glycoproteins. Interaction of sweat with bacteria is well established as the cause of sweat-associated malodor. However, the role of sweat glycoproteins in microbial attachment has received little, if any, research interest in the past. In this review, we demonstrate how recent published studies involving high-throughput proteomic analysis have inadvertently, and fortuitously, exposed an abundance of glycoproteins in sweat, many of which have also been identified in other secretory fluids. We bring together research demonstrating microbial adhesion to these secretory glycoproteins in tears, saliva and milk and suggest a similar role of the sweat glycoproteins in mediating microbial attachment to sweat and/or skin. The contribution of glycan-mediated microbial adhesion to sweat glycoproteins, and the associated impact on sweat derived malodor and pathogenic skin infections are unchartered new research areas that we are beginning to explore. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

NIPTmer: rapid k-mer-based software package for detection of fetal aneuploidies.

PubMed

Sauk, Martin; Žilina, Olga; Kurg, Ants; Ustav, Eva-Liina; Peters, Maire; Paluoja, Priit; Roost, Anne Mari; Teder, Hindrek; Palta, Priit; Brison, Nathalie; Vermeesch, Joris R; Krjutškov, Kaarel; Salumets, Andres; Kaplinski, Lauris

2018-04-04

Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/ .

Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015

PubMed Central

Miguel, Eve; Chevalier, Véronique; Ayelet, Gelagay; Ben Bencheikh, Med Nadir; Boussini, Hiver; Chu, Daniel KW; El Berbri, Ikhlass; Fassi-Fihri, Ouaffa; Faye, Bernard; Fekadu, Getnet; Grosbois, Vladimir; Ng, Bryan CY; Perera, Ranawaka APM; So, TY; Traore, Amadou; Roger, François; Peiris, Malik

2017-01-01

Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February–March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2–28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7–20.4) and Morocco (up to 7.6%; 95% CI: 1.9–26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100–100 and 99.4%; 95% CI: 95.4–99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2–89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005). PMID:28382915

Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015.

PubMed

Miguel, Eve; Chevalier, Véronique; Ayelet, Gelagay; Ben Bencheikh, Med Nadir; Boussini, Hiver; Chu, Daniel Kw; El Berbri, Ikhlass; Fassi-Fihri, Ouaffa; Faye, Bernard; Fekadu, Getnet; Grosbois, Vladimir; Ng, Bryan Cy; Perera, Ranawaka Apm; So, T Y; Traore, Amadou; Roger, François; Peiris, Malik

2017-03-30

Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February-March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2-28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7-20.4) and Morocco (up to 7.6%; 95% CI: 1.9-26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100-100 and 99.4%; 95% CI: 95.4-99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2-89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005). This article is copyright of The Authors, 2017.

Microbial certification of the MER spacecraft

NASA Technical Reports Server (NTRS)

Schubert, W. W.; Arakelian, T.; Barengoltz, J. B.; Chough, N. G.; Chung, S. Y.; Law, J.; Kirschner, L.; Koukol, R. C.; Newlin, L. E.; Morales, F.

2003-01-01

We conclude in this paper that a combination of Dry Heat Microbrial Reduction and control measures during complex mechanical assembly processes can result in a total spore bioburden that meets requirements.

Junctional and allele-specific residues are critical for MERS-CoV neutralization by an exceptionally potent germline-like antibody

DOE PAGES

Ying, Tianlei; Prabakaran, Ponraj; Du, Lanying; ...

2015-09-15

The MERS-CoV is an emerging virus, which already infected more than 1,300 humans with high (~36%) mortality. Here, we show that m336, an exceptionally potent human anti-MERS-CoV antibody, is almost germline with only one somatic mutation in the heavy chain. The structure of Fab m336 in complex with the MERS-CoV receptor-binding domain reveals that its IGHV1-69-derived heavy chain provides more than 85% binding surface and that its epitope almost completely overlaps with the receptor-binding site. Analysis of antibodies from 69 healthy humans suggests an important role of the V(D)J recombination-generated junctional and allele-specific residues for achieving high affinity of bindingmore » at such low levels of somatic hypermutation. Our results also have important implications for development of vaccine immunogens based on the newly identified m336 epitope as well as for elucidation of mechanisms of neutralization by m336-like antibodies and their elicitation in vivo.« less

Strength and Deformability of Light-toned Layered Deposits Observed by MER Opportunity: Eagle to Erebus Craters

NASA Astrophysics Data System (ADS)

Okubo, C. H.; Schultz, R. A.; Nahm, A. L.

2007-07-01

The strength and deformability of light-toned layered deposits are estimated based on measurements of porosity from Microscopic Imager data acquired by MER Opportunity during its traverse from Eagle Crater to Erebus Crater.

Comparison of incubation period distribution of human infections with MERS-CoV in South Korea and Saudi Arabia.

PubMed

Virlogeux, Victor; Fang, Vicky J; Park, Minah; Wu, Joseph T; Cowling, Benjamin J

2016-10-24

The incubation period is an important epidemiologic distribution, it is often incorporated in case definitions, used to determine appropriate quarantine periods, and is an input to mathematical modeling studies. Middle East Respiratory Syndrome coronavirus (MERS) is an emerging infectious disease in the Arabian Peninsula. There was a large outbreak of MERS in South Korea in 2015. We examined the incubation period distribution of MERS coronavirus infection for cases in South Korea and in Saudi Arabia. Using parametric and nonparametric methods, we estimated a mean incubation period of 6.9 days (95% credibility interval: 6.3-7.5) for cases in South Korea and 5.0 days (95% credibility interval: 4.0-6.6) among cases in Saudi Arabia. In a log-linear regression model, the mean incubation period was 1.42 times longer (95% credibility interval: 1.18-1.71) among cases in South Korea compared to Saudi Arabia. The variation that we identified in the incubation period distribution between locations could be associated with differences in ascertainment or reporting of exposure dates and illness onset dates, differences in the source or mode of infection, or environmental differences.

NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

Cancer.gov

Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an

The Role of Social Work for Foreign Residents in an Epidemic: The MERS Crisis in the Republic of Korea.

PubMed

Park, Hong-Jae; Lee, Bong Joo

2016-01-01

This article explores the experiences of foreign residents during the period of the Middle East Respiratory Syndrome (MERS) outbreak in (South) Korea and discusses from a social work perspective the implications of their experiences and their needs. Data were obtained from interviews with 22 foreigners who either live and work or study in Korea. The data were then interpreted using a thematic analysis approach in a multilingual research context. The findings from the study show that foreign residents experienced a wide range of social and psychoemotional difficulties during the MERS health threat. Implications for social work practice in an epidemic emergency are presented.

Eicosanoid-mediated immunity in insects

USDA-ARS?s Scientific Manuscript database

Eicosanoid is a collective term for oxygenated metabolites of C20 polyunsaturated fatty acids. As seen in mammals, eicosanoids play crucial roles in mediating various physiological processes, including immune responses, in insects. Upon microbial pathogen infection, non-self recognition signals are ...

Microbial ecology of hot desert edaphic systems.

PubMed

Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

2015-03-01

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Representation of Dormant and Active Microbial Dynamics for Ecosystem Modeling

NASA Astrophysics Data System (ADS)

Wang, G.; Mayes, M. A.; Gu, L.; Schadt, C. W.

2013-12-01

Experimental observations and modeling efforts have shown that dormancy is likely a common strategy for microorganisms to contend with environmental stress. We review the state-of-the-art in modeling approaches for microbial dormancy and discuss the rationales of these models. We proved that the physiological state index model is not appropriate for describing transformation between active and dormant states. Based on the generally accepted assumptions summarized from ten existing models, we postulated a new synthetic microbial physiology component within the Microbial-ENzyme-mediated Decomposition (MEND) model. Both the steady state active fraction (rss) and substrate saturation level (Øss) positively depend on two physiological indices: α and β. The index α = mR /(μG+ mR), where μG and mR represent the maximum specific growth and maintenance rates, respectively, for active microbes. β denotes the ratio of dormant to active maintenance rate. The rss equals to Øss only under the condition of β→0, and they are identical to α. When substrate availability is the only limiting factor, the maximum rss is ca. 0.5 with α≤0.5 and β ≤0.01. This threshold value (0.5) of rss (not dynamic r) can explain the low active microbial fractions observed in undisturbed soils. The applications of the improved model to a 14C-labeled glucose induced respiration dataset and a batch experimental dataset show satisfactory model performance. We found that the exponential growth respiration rates can only be used to determine μG and initial active microbial biomass (Ba0), thus we suggest using respiration data representing both exponential growth and non-accelerating phases to robustly determine other important parameters such as initial total live microbial biomass (B0), initial active fraction (r0), μG, α, and the half-saturation constant (Ks). Similar improved representations of microbial physiology should be incorporated into existing ecosystem models in order to

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and Mars Exploration Rover 2 (MER-A) are ready for the third launch attempt after weather concerns postponed earlier attempts. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and Mars Exploration Rover 2 (MER-A) are ready for the third launch attempt after weather concerns postponed earlier attempts. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - A solid rocket booster arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-14

KENNEDY SPACE CENTER, FLA. - A solid rocket booster arrives at Launch Complex 17-A, Cape Canaveral Air Force Station. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE PAGES

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; ...

2017-09-28

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

NASA Astrophysics Data System (ADS)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan; Zhou, Xiaolu; Wang, Meng; Zhang, Kerou; Wang, Gangsheng

2017-10-01

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195 Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated by Xu et al. (2014). We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and mineral-associated organic carbon (MOC). However, our work represents the first step toward a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Kefeng; Peng, Changhui; Zhu, Qiuan

Microbial physiology plays a critical role in the biogeochemical cycles of the Earth system. However, most traditional soil carbon models are lacking in terms of the representation of key microbial processes that control the soil carbon response to global climate change. In this study, the improved process-based model TRIPLEX-GHG was developed by coupling it with the new MEND (Microbial-ENzyme-mediated Decomposition) model to estimate total global soil organic carbon (SOC) and global soil microbial carbon. The new model (TRIPLEX-MICROBE) shows considerable improvement over the previous version (TRIPLEX-GHG) in simulating SOC. We estimated the global soil carbon stock to be approximately 1195more » Pg C, with 348 Pg C located in the high northern latitudes, which is in good agreement with the well-regarded Harmonized World Soil Database (HWSD) and the Northern Circumpolar Soil Carbon Database (NCSCD). We also estimated the global soil microbial carbon to be 21 Pg C, similar to the 23 Pg C estimated. We found that the microbial carbon quantity in the latitudinal direction showed reversions at approximately 30°N, near the equator and at 25°S. A sensitivity analysis suggested that the tundra ecosystem exhibited the highest sensitivity to a 1°C increase or decrease in temperature in terms of dissolved organic carbon (DOC), microbial biomass carbon (MBC) and mineral-associated organic carbon (MOC). Furthermore, our work represents the first step towards a new generation of ecosystem process models capable of integrating key microbial processes into soil carbon cycles.« less

Avoiding student infection during a Middle East respiratory syndrome (MERS) outbreak: a single medical school experience.

PubMed

Park, Seung Won; Jang, Hye Won; Choe, Yon Ho; Lee, Kyung Soo; Ahn, Yong Chan; Chung, Myung Jin; Lee, Kyu-Sung; Lee, Kyunghoon; Han, Taehee

2016-06-01

In outbreaks of infectious disease, medical students are easily overlooked in the management of healthcare personnel protection although they serve in clinical clerkships in hospitals. In the early summer of 2015, Middle East respiratory syndrome (MERS) struck South Korea, and students of Sungkyunkwan University School of Medicine (SKKUSOM) were at risk of contracting the disease. The purpose of this report is to share SKKUSOM's experience against the MERS outbreak and provide suggestions for medical schools to consider in the face of similar challenges. Through a process of reflection-on-action, we examined SKKUSOM's efforts to avoid student infection during the MERS outbreak and derived a few practical guidelines that medical schools can adopt to ensure student safety in outbreaks of infectious disease. The school leadership conducted ongoing risk assessment and developed contingency plans to balance student safety and continuity in medical education. They rearranged the clerkships to another hospital and offered distant lectures and tutorials. Five suggestions are extracted for medical schools to consider in infection outbreaks: instant cessation of clinical clerkships; rational decision making on a school closure; use of information technology; constant communication with hospitals; and open communication with faculty, staff, and students. Medical schools need to take the initiative and actively seek countermeasures against student infection. It is essential that medical schools keep constant communication with their index hospitals and the involved personnel. In order to assure student learning, medical schools may consider offering distant education with online technology.

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

PubMed

Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

2017-02-15

Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities. Ocean sediments represent one of Earth's largest and most poorly studied biomes. These habitats are characterized by complex microbial communities where competition for space and nutrients can be intense. This study addressed the hypothesis that secondary metabolites produced by the sediment-inhabiting actinomycete Salinispora arenicola affect community composition and thus mediate interactions among competing microbes. Next-generation amplicon sequencing of mesocosm experiments revealed complex communities that shifted following exposure to S

Incorporating the soil environment and microbial community into plant competition theory

PubMed Central

Ke, Po-Ju; Miki, Takeshi

2015-01-01

Plants affect microbial communities and abiotic properties of nearby soils, which in turn influence plant growth and interspecific interaction, forming a plant-soil feedback (PSF). PSF is a key determinant influencing plant population dynamics, community structure, and ecosystem functions. Despite accumulating evidence for the importance of PSF and development of specific PSF models, different models are not yet fully integrated. Here, we review the theoretical progress in understanding PSF. When first proposed, PSF was integrated with various mathematical frameworks to discuss its influence on plant competition. Recent theoretical models have advanced PSF research at different levels of ecological organizations by considering multiple species, applying spatially explicit simulations to examine how local-scale predictions apply to larger scales, and assessing the effect of PSF on plant temporal dynamics over the course of succession. We then review two foundational models for microbial- and litter-mediated PSF. We present a theoretical framework to illustrate that although the two models are typically presented separately, their behavior can be understood together by invasibility analysis. We conclude with suggestions for future directions in PSF theoretical studies, which include specifically addressing microbial diversity to integrate litter- and microbial-mediated PSF, and apply PSF to general coexistence theory through a trait-based approach. PMID:26500621

Through the eye of the needle: a review of isotope approaches to quantify microbial processes mediating soil carbon balance.

PubMed

Paterson, Eric; Midwood, Andrew J; Millard, Peter

2009-01-01

For soils in carbon balance, losses of soil carbon from biological activity are balanced by organic inputs from vegetation. Perturbations, such as climate or land use change, have the potential to disrupt this balance and alter soil-atmosphere carbon exchanges. As the quantification of soil organic matter stocks is an insensitive means of detecting changes, certainly over short timescales, there is a need to apply methods that facilitate a quantitative understanding of the biological processes underlying soil carbon balance. We outline the processes by which plant carbon enters the soil and critically evaluate isotopic methods to quantify them. Then, we consider the balancing CO(2) flux from soil and detail the importance of partitioning the sources of this flux into those from recent plant assimilate and those from native soil organic matter. Finally, we consider the interactions between the inputs of carbon to soil and the losses from soil mediated by biological activity. We emphasize the key functional role of the microbiota in the concurrent processing of carbon from recent plant inputs and native soil organic matter. We conclude that quantitative isotope labelling and partitioning methods, coupled to those for the quantification of microbial community substrate use, offer the potential to resolve the functioning of the microbial control point of soil carbon balance in unprecedented detail.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection from Oman to Thailand, June 2015

PubMed Central

Plipat, Tanarak; Buathong, Rome; Wacharapluesadee, Supaporn; Siriarayapon, Potjaman; Pittayawonganon, Chakrarat; Sangsajja, Chariya; Kaewpom, Thongchai; Petcharat, Sininat; Ponpinit, Teerada; Jumpasri, Jaruphan; Joyjinda, Yutthana; Rodpan, Apaporn; Ghai, Siriporn; Jittmittraphap, Akanitt; Khongwichit, Sarawut; Smith, Duncan R; Corman, Victor M; Drosten, Christian; Hemachudha, Thiravat

2017-01-01

Thailand reported the first Middle East respiratory syndrome (MERS) case on 18 June 2015 (day 4) in an Omani patient with heart condition who was diagnosed with pneumonia on hospital admission on 15 June 2015 (day 1). Two false negative RT-PCR on upper respiratory tract samples on days 2 and 3 led to a 48-hour diagnosis delay and a decision to transfer the patient out of the negative pressure unit (NPU). Subsequent examination of sputum later on day 3 confirmed MERS coronavirus (MERS-CoV) infection. The patient was immediately moved back into the NPU and then transferred to Bamrasnaradura Infectious Disease Institute. Over 170 contacts were traced; 48 were quarantined and 122 self-monitored for symptoms. High-risk close contacts exhibiting no symptoms, and whose laboratory testing on the 12th day after exposure was negative, were released on the 14th day. The Omani Ministry of Health (MOH) was immediately notified using the International Health Regulation (IHR) mechanism. Outbreak investigation was conducted in Oman, and was both published on the World Health Organization (WHO) intranet and shared with Thailand’s IHR focal point. The key to successful infection control, with no secondary transmission, were the collaborative efforts among hospitals, laboratories and MOHs of both countries. PMID:28840828

Evaluation of nine popular de novo assemblers in microbial genome assembly.

PubMed

Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher

2017-12-01

Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

MER : from landing to six wheels on Mars ... twice

NASA Technical Reports Server (NTRS)

Krajewski, Joel; Burke, Kevin; Lewicki, Chris; Limonadi, Daniel; Trebi-Ollennu, Ashitey; Voorhees, Chris

2005-01-01

Application of the Pathfinder landing system design to enclose the much larger Mars Exploration Rover required a variety of Rover deployments to achieve the surface driving configuration. The project schedule demanded that software design, engineering model test, and flight hardware build to be accomplished in parallel. This challenge was met through (a) bounding unknown environments against which to design and test, (b) early mechanical prototype testing, (c) constraining the scope of on-board autonomy to survival-critical deployments, (d) executing a balance of nominal and off-nominal test cases, (e) developing off-nominal event mitigation techniques before landing, (f) flexible replanning in response to surprises during operations. Here is discussed several specific events encountered during initial MER surface operations.

Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers.

PubMed

Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlogl, Udo; Al-Nazawi, Mohamed

2018-08-01

Structural studies related to Middle East Respiratory Syndrome Coronavirus (MERS CoV) infection process are so limited. In this study, molecular dynamics (MD) simulations were carried out to unravel changes in the MERS CoV heptad repeat domains (HRs) and factors affecting fusion state HR stability. Results indicated that HR trimer is more rapidly stabilized, having stable system energy and lower root mean square deviations (RMSDs). While trimers were the predominant active form of CoVs HRs, monomers were also discovered in both of viral and cellular membranes. In order to find the differences between S2 monomer and trimer molecular dynamics, S2 monomer was modelled and subjected to MD simulation. In contrast to S2 trimer, S2 monomer was unstable, having high RMSDs with major drifts above 8 Å. Fluctuation of HR residue positions revealed major changes in the C-terminal of HR2 and the linker coil between HR1 and HR2 in both monomer and trimer. Hydrophobic residues at the a and d positions of HR helices stabilize the whole system, with minimal changes in RMSD. The global distance test and contact area difference scores support instability of MERS CoV S2 monomer. Analysis of HR1-HR2 inter-residue contacts and interaction energy revealed three energy scales along HR helices. Two strong interaction energies were identified at the start of the HR2 helix and at the C-terminal of HR2. The identified critical residues by MD simulation and residues at the a and d positions of HR helix were strong stabilizers of HR recognition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications.

PubMed

Kim, K H; Tandi, T E; Choi, J W; Moon, J M; Kim, M S

2017-02-01

Since the first case of Middle East respiratory syndrome coronavirus (MERS-CoV) in South Korea was reported on 20 th May 2015, there have been 186 confirmed cases, 38 deaths and 16,752 suspected cases. Previously published research on South Korea's MERS outbreak was limited to the early stages, when few data were available. Now that the outbreak has ended, albeit unofficially, a more comprehensive review is appropriate. Data were obtained through the MERS portal by the Ministry for Health and Welfare (MOHW) and Korea Centres for Disease Control and Prevention, press releases by MOHW, and reports by the MERS Policy Committee of the Korean Medical Association. Cases were analysed for general characteristics, exposure source, timeline and infection generation. Sex, age and underlying diseases were analysed for the 38 deaths. Beginning with the index case that infected 28 others, an in-depth analysis was conducted. The average age was 55 years, which was a little higher than the global average of 50 years. As in most other countries, more men than women were affected. The case fatality rate was 19.9%, which was lower than the global rate of 38.7% and the rate in Saudi Arabia (36.5%). In total, 184 patients were infected nosocomially and there were no community-acquired infections. The main underlying diseases were respiratory diseases, cancer and hypertension. The main contributors to the outbreak were late diagnosis, quarantine failure of 'super spreaders', familial care-giving and visiting, non-disclosure by patients, poor communication by the South Korean Government, inadequate hospital infection management, and 'doctor shopping'. The outbreak was entirely nosocomial, and was largely attributable to infection management and policy failures, rather than biomedical factors. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

Yeast surface display of dehydrogenases in microbial fuel-cells.

PubMed

Gal, Idan; Schlesinger, Orr; Amir, Liron; Alfonta, Lital

2016-12-01

Two dehydrogenases, cellobiose dehydrogenase from Corynascus thermophilus and pyranose dehydrogenase from Agaricus meleagris, were displayed for the first time on the surface of Saccharomyces cerevisiae using the yeast surface display system. Surface displayed dehydrogenases were used in a microbial fuel cell and generated high power outputs. Surface displayed cellobiose dehydrogenase has demonstrated a midpoint potential of -28mV (vs. Ag/AgCl) at pH=6.5 and was used in a mediator-less anode compartment of a microbial fuel cell producing a power output of 3.3μWcm(-2) using lactose as fuel. Surface-displayed pyranose dehydrogenase was used in a microbial fuel cell and generated high power outputs using different substrates, the highest power output that was achieved was 3.9μWcm(-2) using d-xylose. These results demonstrate that surface displayed cellobiose dehydrogenase and pyranose dehydrogenase may successfully be used in microbial bioelectrochemical systems. Copyright © 2016 Elsevier B.V. All rights reserved.

Novel approaches to microbial enhancement of oil recovery.

PubMed

Kryachko, Yuriy

2018-01-20

Microbially enhanced oil recovery (MEOR) was shown to be feasible in a number of laboratory experiments and field trials. However, it has not been widely used in the oil industry because necessary conditions cannot always be easily established in an oil reservoir. Novel approaches to MEOR, which are based on newly discovered biosurfactant-mediated MEOR-mechanisms, are discussed in this review. Particularly, the possibility of combining MEOR with chemical enhancement of oil recovery in heterogeneous oil reservoirs, which involves rock surface wettability shifts and emulsion inversions, is discussed. In wider (centimeter/millimeter-scale) rock pores, the activity of (bio)surfactants and microbial cells attached to oil may allow releasing trapped oil blobs through oil-in-water emulsification. After no more oil can be emulsified, the addition of alkali or surfactants, which turn rock surface oil-wet, may help release oil droplets trapped in narrow (micrometer-scale) pores through coalescence of the droplets and water-in-oil emulsification. Experiments demonstrating the possibility of (bio)surfactant-mediated enhancement of immiscible gas-driven oil recovery are also reviewed. Interestingly, very low (bio)surfactant concentrations were shown to be needed for enhancement of immiscible gas-driven oil recovery. Some possible side effects of MEOR, such as unintended bioplugging and microbially influenced corrosion (MIC), are discussed as well. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Delta II Heavy MER-B - MST Rollback

NASA Image and Video Library

2003-07-07

The Mobile Service Tower is ready to be rolled back at Launch Complex 17-B, Cape Canaveral Air Force Station, to launch the Delta II Heavy launch vehicle carrying the rover "Opportunity" on the second Mars Exploration Rover mission. Opportunity will reach Mars on Jan. 25, 2004. Together the two MER rovers, Spirit (launched June 10) and Opportunity, seek to determine the history of climate and water at two sites on Mars where conditions may once have been favorable to life. The rovers are identical. They will navigate themselves around obstacles as they drive across the Martian surface, traveling up to about 130 feet each Martian day. Each rover carries five scientific instruments including a panoramic camera and microscope, plus a rock abrasion tool that will grind away the outer surfaces of rocks to expose their interiors for examination. Each rover’s prime mission is planned to last three months on Mars.

Microbial shaping of wrinkle structures in siliciclastic deposits

NASA Astrophysics Data System (ADS)

Bosak, T.; Mariotti, G.; Pruss, S. B.; Perron, J.; O'Grady, M.

2013-12-01

Wrinkle structures are millimeter- to centimeter-scale elongated or reticulate sedimentary structures that resemble symmetric ripples. Sharp-crested and flat-topped wrinkle structures up to 1 cm wide occur on numerous bedding planes in the Neoproterozoic and Cambrian, as well as in some Archean and Phanerozoic siliciclastic deposits. Because similar, but unlithified structures occur in some modern, microbially-colonized sands, wrinkle structures are typically interpreted as microbially induced sedimentary structures. However, it is unclear if physical processes, such as the motion of suspended sand grains, can produce similar features in sand even before microbial colonization. We introduced mat fragments to the surface of silica sand in wave tanks and generated sharp-crested, flat-topped and pitted wrinkle structures. The abrasion of the sandy surface by rolling, low density, millimeter-size fragments of microbial mats produces wrinkle structures at extremely weak orbital velocities that cannot move sand grains in the absence of light particles. Wrinkle structures form in a few hours and can become colonized by microbial mats within weeks. Thus, wrinkle structures are patterns formed by microbially mediated sand motion at low orbital velocities in the absence of bioturbation. Once formed, wrinkle structures can be colonized and stabilized by microbial mats, but the shape of these mats does not dictate the shape of wrinkle structures. These experiments bolster the interpretation of wrinkle structures as morphological signatures of organic particles and early life in Archean and Proterozoic siliciclastic deposits.

MICROBIAL TRANSFORMATION RATE CONSTANTS OF STRUCTURALLY DIVERSE MAN-MADE CHEMICALS

EPA Science Inventory

To assist in estimating microbially mediated transformation rates of man-made chemicals from their chemical structures, all second order rate constants that have been measured under conditions that make the values comparable have been extracted from the literature and combined wi...

Polyphyletic origin of MERS coronaviruses and isolation of a novel clade A strain from dromedary camels in the United Arab Emirates

PubMed Central

Lau, Susanna K P; Wernery, Renate; Wong, Emily Y M; Joseph, Sunitha; Tsang, Alan K L; Patteril, Nissy Annie Georgy; Elizabeth, Shyna K; Chan, Kwok-Hung; Muhammed, Rubeena; Kinne, Jöerg; Yuen, Kwok-Yung; Wernery, Ulrich; Woo, Patrick C Y

2016-01-01

Little is known regarding the molecular epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) circulating in dromedaries outside Saudi Arabia. To address this knowledge gap, we sequenced 10 complete genomes of MERS-CoVs isolated from 2 live and 8 dead dromedaries from different regions in the United Arab Emirates (UAE). Phylogenetic analysis revealed one novel clade A strain, the first detected in the UAE, and nine clade B strains. Strain D998/15 had a distinct phylogenetic position within clade A, being more closely related to the dromedary isolate NRCE-HKU205 from Egypt than to the human isolates EMC/2012 and Jordan-N3/2012. A comparison of predicted protein sequences also demonstrated the existence of two clade A lineages with unique amino acid substitutions, A1 (EMC/2012 and Jordan-N3/2012) and A2 (D998/15 and NRCE-HKU205), circulating in humans and camels, respectively. The nine clade B isolates belong to three distinct lineages: B1, B3 and B5. Two B3 strains, D1271/15 and D1189.1/15, showed evidence of recombination between lineages B4 and B5 in ORF1ab. Molecular clock analysis dated the time of the most recent common ancestor (tMRCA) of clade A to March 2011 and that of clade B to November 2011. Our data support a polyphyletic origin of MERS-CoV in dromedaries and the co-circulation of diverse MERS-CoVs including recombinant strains in the UAE. PMID:27999424

Microbial fuel cell (MFC) power performance improvement through enhanced microbial electrogenicity.

PubMed

Li, Ming; Zhou, Minghua; Tian, Xiaoyu; Tan, Chaolin; McDaniel, Cameron T; Hassett, Daniel J; Gu, Tingyue

Within the past 5 years, tremendous advances have been made to maximize the performance of microbial fuel cells (MFCs) for both "clean" bioenergy production and bioremediation. Most research efforts have focused on parameters including (i) optimizing reactor configuration, (ii) electrode construction, (iii) addition of redox-active, electron donating mediators, (iv) biofilm acclimation and feed nutrient adjustment, as well as (v) other parameters that contribute to enhanced MFC performance. To date, tremendous advances have been made, but further improvements are needed for MFCs to be economically practical. In this review, the diversity of electrogenic microorganisms and microbial community changes in mixed cultures are discussed. More importantly, different approaches including chemical/genetic modifications and gene regulation of exoelectrogens, synthetic biology approaches and bacterial community cooperation are reviewed. Advances in recent years in metagenomics and microbiomes have allowed researchers to improve bacterial electrogenicity of robust biofilms in MFCs using novel, unconventional approaches. Taken together, this review provides some important and timely information to researchers who are examining additional means to enhance power production of MFCs. Copyright © 2018 Elsevier Inc. All rights reserved.

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE PAGES

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; ...

2016-02-08

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

Imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection from Oman to Thailand, June 2015.

PubMed

Plipat, Tanarak; Buathong, Rome; Wacharapluesadee, Supaporn; Siriarayapon, Potjaman; Pittayawonganon, Chakrarat; Sangsajja, Chariya; Kaewpom, Thongchai; Petcharat, Sininat; Ponpinit, Teerada; Jumpasri, Jaruphan; Joyjinda, Yutthana; Rodpan, Apaporn; Ghai, Siriporn; Jittmittraphap, Akanitt; Khongwichit, Sarawut; Smith, Duncan R; Corman, Victor M; Drosten, Christian; Hemachudha, Thiravat

2017-08-17

Thailand reported the first Middle East respiratory syndrome (MERS) case on 18 June 2015 (day 4) in an Omani patient with heart condition who was diagnosed with pneumonia on hospital admission on 15 June 2015 (day 1). Two false negative RT-PCR on upper respiratory tract samples on days 2 and 3 led to a 48-hour diagnosis delay and a decision to transfer the patient out of the negative pressure unit (NPU). Subsequent examination of sputum later on day 3 confirmed MERS coronavirus (MERS-CoV) infection. The patient was immediately moved back into the NPU and then transferred to Bamrasnaradura Infectious Disease Institute. Over 170 contacts were traced; 48 were quarantined and 122 self-monitored for symptoms. High-risk close contacts exhibiting no symptoms, and whose laboratory testing on the 12th day after exposure was negative, were released on the 14th day. The Omani Ministry of Health (MOH) was immediately notified using the International Health Regulation (IHR) mechanism. Outbreak investigation was conducted in Oman, and was both published on the World Health Organization (WHO) intranet and shared with Thailand's IHR focal point. The key to successful infection control, with no secondary transmission, were the collaborative efforts among hospitals, laboratories and MOHs of both countries. This article is copyright of The Authors, 2017.

Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors.

PubMed

Kumar, Vathan; Tan, Kian-Pin; Wang, Ying-Ming; Lin, Sheng-Wei; Liang, Po-Huang

2016-07-01

Severe acute respiratory syndrome (SARS) led to a life-threatening form of atypical pneumonia in late 2002. Following that, Middle East Respiratory Syndrome (MERS-CoV) has recently emerged, killing about 36% of patients infected globally, mainly in Saudi Arabia and South Korea. Based on a scaffold we reported for inhibiting neuraminidase (NA), we synthesized the analogues and identified compounds with low micromolar inhibitory activity against 3CL(pro) of SARS-CoV and MERS-CoV. Docking studies show that a carboxylate present at either R(1) or R(4) destabilizes the oxyanion hole in the 3CL(pro). Interestingly, 3f, 3g and 3m could inhibit both NA and 3CL(pro) and serve as a starting point to develop broad-spectrum antiviral agents. Copyright © 2016 Elsevier Ltd. All rights reserved.

Public Health Network Structure and Collaboration Effectiveness during the 2015 MERS Outbreak in South Korea: An Institutional Collective Action Framework

PubMed Central

Andrew, Simon A.

2017-01-01

Following the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea, this research aims to examine the structural effect of public health network explaining collaboration effectiveness, which is defined as joint efforts to improve quality of service provision, cost savings, and coordination. We tested the bonding and bridging effects on collaboration effectiveness during the MERS outbreak response by utilizing an institutional collective action framework. The analysis results of 114 organizations responding during the crisis show a significant association between the bonding effect and the effectiveness of collaboration, as well as a positive association between risk communication in disseminating public health information and the effectiveness of collaboration. PMID:28914780

An overview of field-specific designs of microbial EOR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robertson, E.P.; Bala, G.A.; Fox, S.L.

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery processmore » for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.« less

Microbial diversity in restored wetlands of San Francisco Bay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils,more » we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.« less

Concepts and tools for predictive modeling of microbial dynamics.

PubMed

Bernaerts, Kristel; Dens, Els; Vereecken, Karen; Geeraerd, Annemie H; Standaert, Arnout R; Devlieghere, Frank; Debevere, Johan; Van Impe, Jan F

2004-09-01

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Extracellular Saccharide-Mediated Reduction of Au3+ to Gold Nanoparticles: New Insights for Heavy Metals Biomineralization on Microbial Surfaces.

PubMed

Kang, Fuxing; Qu, Xiaolei; Alvarez, Pedro J J; Zhu, Dongqiang

2017-03-07

Biomineralization is a critical process controlling the biogeochemical cycling, fate, and potential environmental impacts of heavy metals. Despite the indispensability of extracellular polymeric substances (EPS) to microbial life and their ubiquity in soil and aquatic environments, the role played by EPS in the transformation and biomineralization of heavy metals is not well understood. Here, we used gold ion (Au 3+ ) as a model heavy metal ion to quantitatively assess the role of EPS in biomineralization and discern the responsible functional groups. Integrated spectroscopic analyses showed that Au 3+ was readily reduced to zerovalent gold nanoparticles (AuNPs, 2-15 nm in size) in aqueous suspension of Escherichia coli or dissolved EPS extracted from microbes. The majority of AuNPs (95.2%) was formed outside Escherichia coli cells, and the removal of EPS attached to cells pronouncedly suppressed Au 3+ reduction, reflecting the predominance of the extracellular matrix in Au 3+ reduction. XPS, UV-vis, and FTIR analyses corroborated that Au 3+ reduction was mediated by the hemiacetal groups (aldehyde equivalents) of reducing saccharides of EPS. Consistently, the kinetics of AuNP formation obeyed pseudo-second-order reaction kinetics with respect to the concentrations of Au 3+ and the hemiacetal groups in EPS, with minimal dependency on the source of microbial EPS. Our findings indicate a previously overlooked, universally significant contribution of EPS to the reduction, mineralization, and potential detoxification of metal species with high oxidation state.

Etude de la performance des radars hautes-frequences CODAR et WERA pour la mesure des courants marins en presence partielle de glace de mer

NASA Astrophysics Data System (ADS)

Kamli, Emna

Les radars hautes-frequences (RHF) mesurent les courants marins de surface avec une portee pouvant atteindre 200 kilometres et une resolution de l'ordre du kilometre. Cette etude a pour but de caracteriser la performance des RHF, en terme de couverture spatiale, pour la mesure des courants de surface en presence partielle de glace de mer. Pour ce faire, les mesures des courants de deux radars de type CODAR sur la rive sud de l'estuaire maritime du Saint-Laurent, et d'un radar de type WERA sur la rive nord, prises pendant l'hiver 2013, ont ete utilisees. Dans un premier temps, l'aire moyenne journaliere de la zone ou les courants sont mesures par chaque radar a ete comparee a l'energie des vagues de Bragg calculee a partir des donnees brutes d'acceleration fournies par une bouee mouillee dans la zone couverte par les radars. La couverture des CODARs est dependante de la densite d'energie de Bragg, alors que la couverture du WERA y est pratiquement insensible. Un modele de fetch appele GENER a ete force par la vitesse du vent predite par le modele GEM d'Environnement Canada pour estimer la hauteur significative ainsi que la periode modale des vagues. A partir de ces parametres, la densite d'energie des vagues de Bragg a ete evaluee pendant l'hiver a l'aide du spectre theorique de Bretschneider. Ces resultats permettent d'etablir la couverture normale de chaque radar en absence de glace de mer. La concentration de glace de mer, predite par le systeme canadien operationnel de prevision glace-ocean, a ete moyennee sur les differents fetchs du vent selon la direction moyenne journaliere des vagues predites par GENER. Dans un deuxieme temps, la relation entre le ratio des couvertures journalieres obtenues pendant l'hiver 2013 et des couvertures normales de chaque radar d'une part, et la concentration moyenne journaliere de glace de mer d'autre part, a ete etablie. Le ratio des couvertures decroit avec l'augmentation de la concentration de glace de mer pour les deux types

Microbial community assembly and metabolic function during mammalian corpse decomposition

USGS Publications Warehouse

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

KENNEDY SPACE CENTER, FLA. - Leaving smoke and steam behind, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - Leaving smoke and steam behind, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - Amid billows of smoke and steam, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - Amid billows of smoke and steam, the Delta II rocket with its Mars Exploration Rover (MER-A) payload lifts off the pad on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - A third solid rocket booster (SRB) is lifted up the launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station. They are three of nine SRBs that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-14

KENNEDY SPACE CENTER, FLA. - A third solid rocket booster (SRB) is lifted up the launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station. They are three of nine SRBs that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, workers complete raising a solid rocket booster to a vertical position. It will be lifted up the launch tower and mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-14

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, workers complete raising a solid rocket booster to a vertical position. It will be lifted up the launch tower and mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the outside of the launch tower. Visible on another side is the Delta II rocket that will carry the payload into space. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

NASA Image and Video Library

2003-04-30

KENNEDY SPACE CENTER, FLA. - At Launch Complex 17-A, Cape Canaveral Air Force Station, the second half of the fairing for the Mars Exploration Rover 2 (MER-2/MER-A) is lifted up the outside of the launch tower. Visible on another side is the Delta II rocket that will carry the payload into space. The fairing will be installed around the payload for protection during launch. The MER Mission consists of two identical rovers designed to cover roughly 110 yards each Martian day over various terrain. Each rover will carry five scientific instruments that will allow it to search for evidence of liquid water that may have been present in the planet's past. Identical to each other, the rovers will land at different regions of Mars. Launch date for MER-A is scheduled for June 5.

Molecular mechanisms of CRISPR-mediated microbial immunity.

PubMed

Gasiunas, Giedrius; Sinkunas, Tomas; Siksnys, Virginijus

2014-02-01

Bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. Thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. Not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. Phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. The antagonistic interaction between bacteria and rapidly diversifying viruses promotes the evolution and dissemination of bacteriophage-resistance mechanisms in bacteria. Recently, an adaptive microbial immune system, named clustered regularly interspaced short palindromic repeats (CRISPR) and which provides acquired immunity against viruses and plasmids, has been identified. Unlike the restriction–modification anti-phage barrier that subjects to cleavage any foreign DNA lacking a protective methyl-tag in the target site, the CRISPR–Cas systems are invader-specific, adaptive, and heritable. In this review, we focus on the molecular mechanisms of interference/immunity provided by different CRISPR–Cas systems.

NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

Cancer.gov

Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an enzyme known as the 3C-like protease (3CLpro), which, if blocked, can prevent the virus from replicating...

Flow-through Column Experiments and Modeling of Microbially Mediated Cr(VI) Reduction at Hanford 100H

NASA Astrophysics Data System (ADS)

Yang, L.; Molins, S.; Beller, H. R.; Brodie, E. L.; Steefel, C.; Nico, P. S.; Han, R.

2010-12-01

Microbially mediated Cr(VI) reduction at the Hanford 100H area was investigated by flow-through column experiments. Three separate experiments were conducted to promote microbial activities associated with denitrification, iron and sulfate reduction, respectively. Replicate columns packed with natural sediments from the site under anaerobic environment were injected with 5mM Lactate as the electron donor and 5 μM Cr(VI) in all experiments. Sulfate and nitrate solutions were added to act as the main electron acceptors in the respective experiments, while iron columns relied on the indigenous sediment iron (and manganese) oxides as electron acceptors. Column effluent solutions were analyzed by IC and ICP-MS to monitor the microbial consumption/conversion of lactate and the associated Cr(VI) reduction. Biogeochemical reactive transport modeling was performed to gain further insights into the reaction mechanisms and Cr(VI) bioreduction rates. All experimental columns showed a reduction of the injected Cr(VI). Columns under denitrifying conditions showed the least Cr(VI) reduction at early stages (<60 days) compared to columns run under other experimental conditions, but became more active over time, and ultimately showed the most consistent Cr(VI) reduction. A strong correlation between denitrification and Cr(VI) reduction processes was observed and was in agreement with the results obtained in batch experiments with a denitrifying bacterium isolated from the Hanford site. The accumulation of nitrite does not appear to have an adverse effect on Cr(VI) reduction rates. Reactive transport simulations indicated that biomass growth completely depleted influent ammonium, and called for an additional source of N to account for the measured reduction rates. Iron columns were the least active with undetectable consumption of the injected lactate, slowest cell growth, and the smallest change in Cr(VI) concentrations during the course of the experiment. In contrast, columns

Microbial imprint on soil-atmosphere H2, COS, and CO2 fluxes

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Commane, R.; Munger, J. W.; Wofsy, S. C.; Prinn, R. G.

2013-12-01

Microorganisms drive large trace gas fluxes between soil and atmosphere, but the signal can be difficult to detect and quantify in the presence of stronger exchange processes in an ecosystem. Partitioning methods are often needed to estimate trace gas budgets and to develop process-based models to explore the sensitivity of microbe-mediated fluxes. In this study, we test the performance of trace gases with predominantly microbe-mediated soil fluxes as a metric of the soil microbial uptake activity of other trace gases. Using simultaneous, collocated measurements at Harvard Forest, we consider three trace gases with microbe-mediated soil fluxes of various importance relative to their other (mainly plant-mediated) ecosystem fluxes: molecular hydrogen (H2), carbonyl sulfide (COS), and carbon dioxide (CO2). These gases probe different aspects of the soil trace-gas microbiology. Soil H2 uptake is a redox reaction driving the energy metabolism of a portion of the microbial community, while soil CO2 respiration is a partial proxy for the overall soil microbial metabolism. In comparison, very little is understood about the microbiological and environmental drivers of soil COS uptake and emissions. In this study, we find that H2, COS, and CO2 soil uptake rates are often correlated, but the relative soil uptake between gases is not constant, and is influenced by seasonality and local environmental conditions. We also consider how differences in the microbial communities and pathways involved in the soil fluxes may explain differences in the observations. Our results are important for informing previous studies using tracer approaches. For example, H2 has been used to estimate COS soil uptake, which must be accounted for to use COS as a carbon cycle tracer. Furthermore, the global distribution of H2 deposition velocity has been inferred from net primary productivity (CO2). Given that insufficient measurement frequency and spatial distribution exists to partition global net

Screening sourdough samples for gliadin-degrading activity revealed Lactobacillus casei strains able to individually metabolize the coeliac-disease-related 33-mer peptide.

PubMed

Alvarez-Sieiro, Patricia; Redruello, Begoña; Ladero, Victor; Martín, Maria Cruz; Fernández, María; Alvarez, Miguel A

2016-05-01

A selective culture medium containing acid-hydrolyzed gliadins as the sole nitrogen source was used in the search for sourdough-indigenous lactic acid bacteria (LAB) with gliadin-metabolizing activity. Twenty gliadin-degrading LAB strains were isolated from 10 sourdoughs made in different ways and from different geographical regions. Fifteen of the 20 isolated strains were identified as Lactobacillus casei, a species usually reported as subdominant in sourdough populations. The other 5 gliadin-degrading strains belonged to the more commonly encountered sourdough species Leuconostoc mesenteroides and Lactobacillus plantarum. All these strains were shown to be safe in terms of their resistance to antimicrobial agents. When individually incubated with the α2-gliadin-derived immunotoxic 33-mer peptide (97.5 ppm), half of the L. casei strains metabolized at least 50% of it within 24 h. One strain metabolized 82% of the 33-mer peptide within 8 h and made it fully disappear within 12 h. These results reveal for the first time the presence in sourdough of proteolytic L. casei strains with the capacity to individually metabolize the coeliac-disease-related 33-mer peptide.

Alisporivir inhibits MERS- and SARS-coronavirus replication in cell culture, but not SARS-coronavirus infection in a mouse model.

PubMed

de Wilde, Adriaan H; Falzarano, Darryl; Zevenhoven-Dobbe, Jessika C; Beugeling, Corrine; Fett, Craig; Martellaro, Cynthia; Posthuma, Clara C; Feldmann, Heinz; Perlman, Stanley; Snijder, Eric J

2017-01-15

Currently, there is no registered treatment for infections with emerging zoonotic coronaviruses like SARS- and MERS-coronavirus. We here report that in cultured cells low-micromolar concentrations of alisporivir, a non-immunosuppressive cyclosporin A-analog, inhibit the replication of four different coronaviruses, including MERS- and SARS-coronavirus. Ribavirin was found to further potentiate the antiviral effect of alisporivir in these cell culture-based infection models, but this combination treatment was unable to improve the outcome of SARS-CoV infection in a mouse model. Nevertheless, our data provide a basis to further explore the potential of Cyp inhibitors as host-directed, broad-spectrum inhibitors of coronavirus replication. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Possible Evidence for Iron Sulfates, Iron Sulfides, and Elemental Sulfur at Gusev Crater, Mars, from Mer, Crism, and Analog Data

NASA Technical Reports Server (NTRS)

Morris, R. V.; Ming, D. W.; Yen, A.; Arvidson, R. E.; Gruener, J.; Humm, D.; Klingelhoefer, G.; Murchie, S.; Schroeder, C.; Seelos, F., IV;

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Effect of microbially mediated iron mineral transformation on temporal variation of arsenic in the Pleistocene aquifers of the central Yangtze River basin.

PubMed

Deng, Yamin; Zheng, Tianliang; Wang, Yanxin; Liu, Lun; Jiang, Hongchen; Ma, Teng

2018-04-01

Significant seasonal variation of groundwater arsenic (As) concentrations in shallow aquifers of the Jianghan Plain, central Yangtze River Basin has been reported recently, but the underlying mechanisms remain not well understood. To elaborate biogeochemical processes responsible for the observed As concentration variation, 42-day incubation experiments were done using sediment samples collected respectively from the depth of 26, 36 and 60m of the As-affected aquifer which were labeled respectively as JH26, JH36, JH60. Where JH denotes Jianghan Plain, and the number indicates the depth of the sediment sample. The results indicated that As could be mobilized from the sediments of 26m and 36m depth under the stimulation of exogenous organic carbon, with the maximum As release amount of 1.60 and 1.03mgkg -1 , respectively, while the sediments at 60m depth did not show As mobilization. The microbially mediated reductive dissolution of amorphous iron oxides and reduction of As(V) to As(III) could account for the observed As mobilization. The 16S rRNA high-throughput sequencing results indicated that the variation of microbial community correlated with the released As concentration (R=0.7, P<0.05) and the iron-reducing bacteria, including Pseudomonas, Clostridium and Geobacter, were the main drivers for the As mobilization from the sediments at 26m and 36m depth. The increase of arsC gene abundance (up to 1.4×10 5 copies g -1 ) during As release suggested that As reduction was mediated by the resistant reduction mechanism. By contrast, in the 60m sediments where the Fe and As release was absent, the iron-reducing bacteria accounted for a very minor proportion and sulfate-reducing bacteria were predominant in the microbial community. In addition, after 30days of incubation, the released As in the 26m sediments was immobilized via co-precipitation with or adsorption onto the Fe-sulfide mineral newly-formed by the bacterial sulfate reduction. These results are consistent

Microbial enzyme activities of peatland soils in south central Alaska lowlands

EPA Science Inventory

Microbial enzyme activities related to carbon and nutrient acquisition were measured on Alaskan peatland soils as indicators of nutrient limitation and biochemical sustainability. Peat decomposition is mediated by microorganisms and enzymes that in turn are limited by various ph...

Photochemistry of Iron and Ruthenium Carbonyl Complexes: Evidence for Light-Induced Loss of Carbon Monoxide and Reductive Elimination of Triethylsilane from cis-mer-HM(SiEt3)(CO)3(PPh3).

DTIC Science & Technology

1983-05-21

JEOL FX9OQ Fourier transform or Bruker 250 or 270 MHz Fourier transform spectrometer. Irradiations. Photochemical reactions were carried out using a...Ph 3 ) 3nd -t-Etin V,- a 313 nm quantum yield of -0.6. The process is photochemically everse if the cis-mer-HM(SiPh 3 )(CO) 3 (PPh 3) is irradiated...process is photochemically reversed if the cis-mer-HM(SiPh 3 )(CO)3 (PPh 3 ) is irradiated in t.e presence of excess Et3SiH. Irradiation of cis-mer-HM

Microbial response to space environment, part B

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Chassay, C. E.; Ellis, W. L.; Foster, B. G.; Volz, P. A.; Spizizen, J.; Buecker, H.; Wrenn, R. T.; Simmonds, R. C.; Long, R. A.

1972-01-01

The performance of the microbial response to space environment experiment is considered excellent by all investigators. For most microbial systems, only preliminary survival data are available at this time. None of the available data indicate space flight-mediated changes in cell viability or recovery. One quite important observation has been made at this early date, however. The eggs produced after mice had been infected with N. dubius larvae demonstrated a significant decrease in hatchability when compared to identical ground controls. Except for the fact that the Apollo 16 flight larvae had been on board the command module, treatment of the flown larvae and ground control larvae was the same; neither had been exposed to UV irradiation. The significance and implications of this finding are currently being studied.

GAS6/Mer axis regulates the homing and survival of the E2A/PBX1 positive B-cell precursor acute lymphoblastic leukemia in the bone marrow niche

PubMed Central

Shiozawa, Yusuke; Pedersen, Elisabeth A.; Taichman, Russell S.

2009-01-01

Despite improvements in current combinational chemotherapy regimens, the prognosis of the (1;19)(q23;p13) translocation (E2A/PBX1) positive B-cell precursor acute lymphoblastic leukemia (ALL) is poor in pediatric leukemia patients. In this study, we examined the roles of GAS6/Mer axis in the interactions between E2A/PBX1 positive B-cell precursor ALL cells and the osteoblastic niche in the bone marrow. The data show that primary human osteoblasts secrete GAS6 in response to the Mer-over-expressed E2A/PBX1 positive ALL cells through MAPK signaling pathway and that leukemia cells migrate toward GAS6 using pathways activated by Mer. Importantly, GAS6 supports the survival and prevents apoptosis from chemotherapy of E2A/PBX1 positive ALL cells by inducing dormancy. Together, these data suggest that GAS6/Mer axis regulates the homing and survival of the E2A/PBX1 positive B-cell precursor ALL in the bone marrow niche. PMID:19922767

Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community

PubMed Central

Zhang, Dayi; Berry, James P; Zhu, Di; Wang, Yun; Chen, Yin; Jiang, Bo; Huang, Shi; Langford, Harry; Li, Guanghe; Davison, Paul A; Xu, Jian; Aries, Eric; Huang, Wei E

2015-01-01

Although uncultured microorganisms have important roles in ecosystems, their ecophysiology in situ remains elusive owing to the difficulty of obtaining live cells from their natural habitats. In this study, we employed a novel magnetic nanoparticle-mediated isolation (MMI) method to recover metabolically active cells of a group of previously uncultured phenol degraders, Burkholderiales spp., from coking plant wastewater biosludge; five other culturable phenol degraders—Rhodococcus sp., Chryseobacterium sp. and three different Pseudomonas spp.—were also isolated from the same biosludge using traditional methods. The kinetics of phenol degradation by MMI-recovered cells (MRCs) was similar to that of the original sludge. Stable isotope probing (SIP) and pyrosequencing of the 16S rRNA from the ‘heavy' DNA (13C-DNA) fractions indicated that Burkholderiales spp. were the key phenol degraders in situ in the biosludge, consistent with the results of MRCs. Single-cell Raman micro-spectroscopy was applied to probe individual bacteria in the MRCs obtained from the SIP experiment and showed that 79% of them were fully 13C-labelled. Biolog assays on the MRCs revealed the impact of various carbon and nitrogen substrates on the efficiency of phenol degradation in the wastewater treatment plant biosludge. Specifically, hydroxylamine, a metabolite of ammonia oxidisation, but not nitrite, nitrate or ammonia, inhibited phenol degradation in the biosludge. Our results provided a novel insight into the occasional abrupt failure events that occur in the wastewater treatment plant. This study demonstrated that MMI is a powerful tool to recover live and functional cells in situ from a complex microbial community to enable further characterisation of their physiology. PMID:25191996

Microbial community assembly and metabolic function during mammalian corpse decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in lowmore » abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.« less

Identification of Electrode Respiring, Hydrocarbonoclastic Bacterial Strain Stenotrophomonas maltophilia MK2 Highlights the Untapped Potential for Environmental Bioremediation

PubMed Central

Venkidusamy, Krishnaveni; Megharaj, Mallavarapu

2016-01-01

Electrode respiring bacteria (ERB) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (MERS) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. Very few ERB have been isolated from MERS, those exhibited a bioremediation potential toward organic contaminants. Here we report once such bacterial strain, Stenotrophomonas maltophilia MK2, a facultative anaerobic bacterium isolated from a hydrocarbon fed MERS, showed a potent hydrocarbonoclastic behavior under aerobic and anaerobic environments. Distinct properties of the strain MK2 were anaerobic fermentation of the amino acids, electrode respiration, anaerobic nitrate reduction and the ability to metabolize n-alkane components (C8–C36) of petroleum hydrocarbons (PH) including the biomarkers, pristine and phytane. The characteristic of diazoic dye decolorization was used as a criterion for pre-screening the possible electrochemically active microbial candidates. Bioelectricity generation with concomitant dye decolorization in MERS showed that the strain is electrochemically active. In acetate fed microbial fuel cells (MFCs), maximum current density of 273 ± 8 mA/m2 (1000 Ω) was produced (power density 113 ± 7 mW/m2) by strain MK2 with a coulombic efficiency of 34.8%. Further, the presence of possible alkane hydroxylase genes (alkB and rubA) in the strain MK2 indicated that the genes involved in hydrocarbon degradation are of diverse origin. Such observations demonstrated the potential of facultative hydrocarbon degradation in contaminated environments. Identification of such a novel petrochemical hydrocarbon degrading ERB is likely to offer a new route to the sustainable bioremedial process of source zone contamination with simultaneous energy generation through MERS. PMID:28018304

AIDS, Avian flu, SARS, MERS, Ebola, Zika… what next?

PubMed

Reperant, Leslie A; Osterhaus, Albert D M E

2017-08-16

Emerging infections have threatened humanity since times immemorial. The dramatic anthropogenic, behavioral and social changes that have affected humanity and the environment in the past century have accelerated the intrusion of novel pathogens into the global human population, sometimes with devastating consequences. The AIDS and influenza pandemics have claimed and will continue to claim millions of lives. The recent SARS and Ebola epidemics have threatened populations across borders. The emergence of MERS may well be warning signals of a nascent pandemic threat, while the potential for geographical spread of vector-borne diseases, such as Zika, but also Dengue and Chikungunya is unprecedented. Novel technologies and innovative approaches have multiplied to address and improve response preparedness towards the increasing yet unpredictable threat posed by emerging pathogens. Copyright © 2017. Published by Elsevier Ltd.

Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2′-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate

PubMed Central

Shiba, Yoshinobu; Masuda, Hirofumi; Watanabe, Naoki; Ego, Takeshi; Takagaki, Kazuchika; Ishiyama, Kouichi; Ohgi, Tadaaki; Yano, Junichi

2007-01-01

A long RNA oligomer, a 110mer with the sequence of a precursor-microRNA candidate, has been chemically synthesized in a single synthesizer run by means of standard automated phosphoramidite chemistry. The synthetic method involved the use of 2-cyanoethoxymethyl (CEM), a 2′-hydroxyl protecting group recently developed in our laboratory. We improved the methodology, introducing better coupling and capping conditions. The overall isolated yield of highly pure 110mer was 5.5%. Such a yield on a 1-μmol scale corresponds to 1 mg of product and emphasizes the practicality of the CEM method for synthesizing oligomers of more than 100 nt in sufficient quantity for biological research. We confirmed the identity of the 110mer by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, as well as HPLC, electrophoretic methods, and RNase-digestion experiments. The 110mer also showed sense-selective specific gene-silencing activity. As far as we know, this is the longest chemically synthesized RNA oligomer reported to date. Furthermore, the identity of the 110mer was confirmed by both physicochemical and biological methods. PMID:17459888

When Information from Public Health Officials is Untrustworthy: The Use of Online News, Interpersonal Networks, and Social Media during the MERS Outbreak in South Korea.

PubMed

Jang, Kyungeun; Baek, Young Min

2018-03-20

Public health officials (PHOs) are responsible for providing trustworthy information during a public health crisis; however, there is little research on how the public behaves when their expectations for such information are violated. Drawing on media dependency theory and source credibility research as our primary theoretical framework, we tested how credibility of information from PHOs is associated with people's reliance on a particular communication channel in the context of the 2015 Middle East Respiratory Syndrome (MERS) outbreak in South Korea. Using nationally representative data (N = 1036) collected during the MERS outbreak, we found that less credible information from PHOs led to more frequent use of online news, interpersonal networks, and social media for acquiring MERS-related information. However, credibility of information from PHOs was not associated with the use of television news or print newspapers. The theoretical and practical implications of our results on communication channels usage are discussed.

MER Surface Phase; Blurring the Line Between Fault Protection and What is Supposed to Happen

NASA Technical Reports Server (NTRS)

Reeves, Glenn E.

2008-01-01

An assessment on the limitations of communication with MER rovers and how such constraints drove the system design, flight software and fault protection architecture, blurring the line between traditional fault protection and expected nominal behavior, and requiring the most novel autonomous and semi-autonomous elements of the vehicle software including communication, surface mobility, attitude knowledge acquisition, fault protection, and the activity arbitration service.

Microbial Life Driving Low-Temperature Basalt Alteration in the Subsurface: Decoupling Abiotic Processes from Biologically-Mediated Rock Alteration

NASA Astrophysics Data System (ADS)

Moore, R.; Lecoeuvre, A.; Stephant, S.; Dupraz, S.; Ranchou-Peyruse, M.; Ranchou-Peyruse, A.; Gérard, E.; Ménez, B.

2017-12-01

Microorganisms are involved with specific rock alteration processes in the deep subsurface. It is a challenge to link any contribution microbial life may have on rock alteration with specific functions or phyla because many alteration features and secondary minerals produced by metabolic processes can also produce abiotically. Here, two flow-through experiments were designed to mimic the circulation of a CO2-rich fluid through crystalline basalt. In order to identify microbially-mediated alteration and be able to link it with specific metabolisms represented in the subsurface, a relatively fresh crystalline basalt substrate was subsampled, sterilized and used as the substrate for both experiments. In one experiment, the substrate was left sterile, and in the other it was inoculated with an enrichment culture derived from the same aquifer as the rock substrate. Initial results show that the inoculum contained Proteobacteria and Firmicutes, which have diverse metabolic potentials. Fluid and rock analyses before, during, and after the experiments show that mineralogy, fluid chemistry, and dissolution processes differ between the sterile and inoculated systems. In the inoculated experiment iron-rich orthopyroxenes were preferentially dissolved while in the sterile system clinopyroxenes and plagioclases both exhibited a higher degree of dissolution. Additionally, the patterns of CO2 consumption and production over the duration of both experiments is different. This suggest that in a low-temperature basalt system with microorganisms CO2 is either consumed to produce biomass, or that carbonates are produced and then subsequently preserved. This suite of results combined with molecular ecology analyses can be used to conclude that in low-temperature basalts microorganisms play an intrinsic role in rock alteration.

A predictive wheel-soil interaction model for planetary rovers validated in testbeds and against MER Mars rover performance data

NASA Astrophysics Data System (ADS)

Richter, L.; Ellery, A.; Gao, Y.; Michaud, S.; Schmitz, N.; Weiss, S.

Successful designs of vehicles intended for operations on planetary objects outside the Earth demand, just as for terrestrial off-the-road vehicles, a careful assessment of the terrain relevant for the vehicle mission and predictions of the mobility performance to allow rational trade-off's to be made for the choice of the locomotion concept and sizing. Principal issues driving the chassis design for rovers are the stress-strain properties of the planetary surface soil, the distribution of rocks in the terrain representing potential obstacles to movement, and the gravity level on the celestial object in question. Thus far, planetary rovers have been successfully designed and operated for missions to the Earth's moon and to the planet Mars, including NASA's Mars Exploration Rovers (MER's) `Spirit' and `Opportunity' being in operation on Mars since their landings in January 2004. Here we report on the development of a wheel-soil interaction model with application to wheel sizes and wheel loads relevant to current and near-term robotic planetary rovers, i.e. wheel diameters being between about 200 and 500 mm and vertical quasistatic wheel loads in operation of roughly 100 to 200 N. Such a model clearly is indispensable for sizings of future rovers to analyse the aspect of rover mobility concerned with motion across soils. This work is presently funded by the European Space Agency (ESA) as part of the `Rover Chassis Evaluation Tools' (RCET) effort which has developed a set of S/W-implemented models for predictive mobility analysis of rovers in terms of movement on soils and across obstacles, coupled with dedicated testbeds to validate the wheel-soil models. In this paper, we outline the details of the wheel-soil modelling performed within the RCET work and present comparisons of predictions of wheel performance (motion resistance, torque vs. slip and drawbar pull vs. slip) for specific test cases with the corresponding measurements performed in the RCET single wheel

Extraintestinal manifestations of celiac disease: 33-mer gliadin binding to glutamate receptor GRINA as a new explanation.

PubMed

Garcia-Quintanilla, Albert; Miranzo-Navarro, Domingo

2016-05-01

We propose a biochemical mechanism for celiac disease and non-celiac gluten sensitivity that may rationalize many of the extradigestive disorders not explained by the current immunogenetic model. Our hypothesis is based on the homology between the 33-mer gliadin peptide and a component of the NMDA glutamate receptor ion channel - the human GRINA protein - using BLASTP software. Based on this homology the 33-mer may act as a natural antagonist interfering with the normal interactions of GRINA and its partners. The theory is supported by numerous independent data from the literature, and provides a mechanistic link with otherwise unrelated disorders, such as cleft lip and palate, thyroid dysfunction, restless legs syndrome, depression, ataxia, hearing loss, fibromyalgia, dermatitis herpetiformis, schizophrenia, toxoplasmosis, anemia, osteopenia, Fabry disease, Barret's adenocarcinoma, neuroblastoma, urinary incontinence, recurrent miscarriage, cardiac anomalies, reduced risk of breast cancer, stiff person syndrome, etc. The hypothesis also anticipates better animal models, and has the potential to open new avenues of research. © 2016 WILEY Periodicals, Inc.

Microbial Herd Protection Mediated by Antagonistic Interaction in Polymicrobial Communities

PubMed Central

Wong, Megan J. Q.; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian

2016-01-01

ABSTRACT In host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist, despite significant antagonistic interactions between species, are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through the delivery of toxic effectors. It is well established that intraspecies protection is conferred by immunity proteins that neutralize effector toxicities. In contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS-active antagonistic bacterial species, Aeromonas hydrophila and Vibrio cholerae, to demonstrate that interspecies protection is dependent on effectors. A. hydrophila and V. cholerae do not share conserved immunity genes but could coexist equally in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the competing wild-type strain. Time-lapse microscopic analyses showed that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interactions inside each cluster and restricting the interactions to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulated our experimental observations. These results provide mechanistic insights regarding the general role of microbial weapons in determining the structures of complex multispecies communities. IMPORTANCE Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in

Microbial herd protection mediated by antagonistic interaction in polymicrobial communities.

PubMed

Wong, Megan; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian; Dong, Tao G

2016-09-16

In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities. By contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS active antagonistic bacteria, Aeromonas hydrophila (AH) and Vibrio cholerae (VC), to demonstrate that interspecies protection is dependent on effectors. AH and VC do not share conserved immunity genes but could equally co-exist in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the other competing wild type. Time-lapse microscopy analyses show that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interaction inside each cluster and restricting it to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulate our experimental observation. These results provide mechanistic insights for the general role of microbial weapons in determining the structures of complex multispecies communities. Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and exchange of genetic materials

Microbial community composition affects soil fungistasis.

PubMed

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

2003-02-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

Microbial Community Composition Affects Soil Fungistasis†

PubMed Central

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J. A.; Kowalchuk, George A.; van Veen, Johannes A.

2003-01-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis. PMID:12571002

Diversification of the celiac disease α-gliadin complex in wheat: a 33-mer peptide with six overlapping epitopes, evolved following polyploidization.

PubMed

Ozuna, Carmen V; Iehisa, Julio C M; Giménez, María J; Alvarez, Juan B; Sousa, Carolina; Barro, Francisco

2015-06-01

The gluten proteins from wheat, barley and rye are responsible both for celiac disease (CD) and for non-celiac gluten sensitivity, two pathologies affecting up to 6-8% of the human population worldwide. The wheat α-gliadin proteins contain three major CD immunogenic peptides: p31-43, which induces the innate immune response; the 33-mer, formed by six overlapping copies of three highly stimulatory epitopes; and an additional DQ2.5-glia-α3 epitope which partially overlaps with the 33-mer. Next-generation sequencing (NGS) and Sanger sequencing of α-gliadin genes from diploid and polyploid wheat provided six types of α-gliadins (named 1-6) with strong differences in their frequencies in diploid and polyploid wheat, and in the presence and abundance of these CD immunogenic peptides. Immunogenic variants of the p31-43 peptide were found in most of the α-gliadins. Variants of the DQ2.5-glia-α3 epitope were associated with specific types of α-gliadins. Remarkably, only type 1 α-gliadins contained 33-mer epitopes. Moreover, the full immunodominant 33-mer fragment was only present in hexaploid wheat at low abundance, probably as the result of allohexaploidization events from subtype 1.2 α-gliadins found only in Aegilops tauschii, the D-genome donor of hexaploid wheat. Type 3 α-gliadins seem to be the ancestral type as they are found in most of the α-gliadin-expressing Triticeae species. These findings are important for reducing the incidence of CD by the breeding/selection of wheat varieties with low stimulatory capacity of T cells. Moreover, advanced genome-editing techniques (TALENs, CRISPR) will be easier to implement on the small group of α-gliadins containing only immunogenic peptides. © 2015 Society for Experimental Biology and John Wiley & Sons Ltd.

Patterns of Human Respiratory Viruses and Lack of MERS-Coronavirus in Patients with Acute Upper Respiratory Tract Infections in Southwestern Province of Saudi Arabia

PubMed Central

Alshrari, Ahmed S.; Badroon, Nassrin A.; Hassan, Ahmed M.; Alsubhi, Tagreed L.; Ejeeli, Saleh

2017-01-01

We undertook enhanced surveillance of those presenting with respiratory symptoms at five healthcare centers by testing all symptomatic outpatients between November 2013 and January 2014 (winter time). Nasal swabs were collected from 182 patients and screened for MERS-CoV as well as other respiratory viruses using RT-PCR and multiplex microarray. A total of 75 (41.2%) of these patients had positive viral infection. MERS-CoV was not detected in any of the samples. Human rhinovirus (hRV) was the most detected pathogen (40.9%) followed by non-MERS-CoV human coronaviruses (19.3%), influenza (Flu) viruses (15.9%), and human respiratory syncytial virus (hRSV) (13.6%). Viruses differed markedly depending on age in which hRV, Flu A, and hCoV-OC43 were more prevalent in adults and RSV, hCoV-HKU1, and hCoV-NL63 were mostly restricted to children under the age of 15. Moreover, coinfection was not uncommon in this study, in which 17.3% of the infected patients had dual infections due to several combinations of viruses. Dual infections decreased with age and completely disappeared in people older than 45 years. Our study confirms that MERS-CoV is not common in the southwestern region of Saudi Arabia and shows high diversity and prevalence of other common respiratory viruses. This study also highlights the importance and contribution of enhanced surveillance systems for better infection control. PMID:28348590

Live microbial cells adsorb Mg2+ more effectively than lifeless organic matter

NASA Astrophysics Data System (ADS)

Qiu, Xuan; Yao, Yanchen; Wang, Hongmei; Duan, Yong

2018-03-01

The Mg2+ content is essential in determining different Mg-CaCO3 minerals. It has been demonstrated that both microbes and the organic matter secreted by microbes are capable of allocating Mg2+ and Ca2+ during the formation of Mg-CaCO3, yet detailed scenarios remain unclear. To investigate the mechanism that microbes and microbial organic matter potentially use to mediate the allocation of Mg2+ and Ca2+ in inoculating systems, microbial mats and four marine bacterial strains ( Synechococcus elongatus, Staphylococcus sp., Bacillus sp., and Desulfovibrio vulgaris) were incubated in artificial seawater media with Mg/Ca ratios ranging from 0.5 to 10.0. At the end of the incubation, the morphology of the microbial mats and the elements adsorbed on them were analyzed using scanning electronic microscopy (SEM) and energy diffraction spectra (EDS), respectively. The content of Mg2+ and Ca2+ adsorbed by the extracellular polysaccharide substances (EPS) and cells of the bacterial strains were analyzed with atomic adsorption spectroscopy (AAS). The functional groups on the surface of the cells and EPS of S. elongatus were estimated using automatic potentiometric titration combined with a chemical equilibrium model. The results show that live microbial mats generally adsorb larger amounts of Mg2+ than Ca2+, while this rarely is the case for autoclaved microbial mats. A similar phenomenon was also observed for the bacterial strains. The living cells adsorb more Mg2+ than Ca2+, yet a reversed trend was observed for EPS. The functional group analysis indicates that the cell surface of S. elongatus contains more basic functional groups (87.24%), while the EPS has more acidic and neutral functional groups (83.08%). These features may be responsible for the different adsorption behavior of Mg2+ and Ca2+ by microbial cells and EPS. Our work confirms the differential Mg2+ and Ca2+ mediation by microbial cells and EPS, which may provide insight into the processes that microbes use to

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that

mer, fac, and Bidentate Coordination of an Alkyl-POP Ligand in the Chemistry of Nonclassical Osmium Hydrides.

PubMed

Esteruelas, Miguel A; García-Yebra, Cristina; Martín, Jaime; Oñate, Enrique

2017-01-03

Nonclassical and classical osmium polyhydrides containing the diphosphine 9,9-dimethyl-4,5-bis(diisopropylphosphino)xanthene (xant(P i Pr 2 ) 2 ), coordinated in κ 3 -mer, κ 3 -fac, and κ 2 -P,P fashions, have been isolated during the cyclic formation of H 2 by means of the sequential addition of H + and H - or H - and H + to the classical trihydride OsH 3 Cl{xant(P i Pr 2 ) 2 } (1). This complex adds H + to form the compressed dihydride dihydrogen complex [OsCl(H···H)(η 2 -H 2 ){xant(P i Pr 2 ) 2 }] + (2). Under argon, cation 2 loses H 2 and the resulting unsaturated fragment dimerizes to give [(Os(H···H){xant(P i Pr 2 ) 2 }) 2 (μ-Cl) 2 ] 2+ (3). During the transformation the phosphine changes its coordination mode from mer to fac. The benzofuran counterpart of 1, OsH 3 Cl{dbf(P i Pr 2 ) 2 } (4; dbf(P i Pr 2 ) 2 = 4,6-bis(diisopropylphosphino)dibenzofuran), also adds H + to afford the benzofuran counterpart of 2, [OsCl(H···H)(η 2 -H 2 ){xant(P i Pr 2 ) 2 }] + (5), which in contrast to the latter is stable and does not dimerize. Acetonitrile breaks the chloride bridge of 3 to form the dihydrogen [OsCl(η 2 -H 2 )(CH 3 CN){xant(P i Pr 2 ) 2 }] + (6), regenerating the mer coordination of the diphosphine. The hydride ion also breaks the chloride bridge of 3. The addition of KH to 3 leads to 1, closing a cycle for the formation of H 2 . Complex 1 reacts with a second hydride ion to give OsH 4 {xant(P i Pr 2 ) 2 } (7) as consequence of the displacement of the chloride. Similarly to the latter, the oxygen atom of the mer-coordinated diphosphine of 7 has a tendency to be displaced by the hydride ion. Thus, the addition of KH to 7 yields [OsH 5 {xant(P i Pr 2 ) 2 }] - (8), containing a κ 2 -P,P-diphosphine. Complex 8 is easily protonated to afford OsH 6 {xant(P i Pr 2 ) 2 } (9), which releases H 2 to regenerate 7, closing a second cycle for the formation of molecular hydrogen.

Microbial community assembly and metabolic function during mammalian corpse decomposition.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-08

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. Copyright © 2016, American Association for the Advancement of Science.

Electricity generation from acetate and glucose by sedimentary bacterium attached to electrode in microbial-anode fuel cells

NASA Astrophysics Data System (ADS)

Zhang, Enren; Xu, Wei; Diao, Guowang; Shuang, Chendong

Microbial-anode fuel cells (MAFCs) with high electron recovery (>50%) from acetate and glucose have been constructed in this study. By inoculating fresh sedimentary microorganisms into anaerobic anode compartments, a stable current (∼0.42 mA for acetate-fed MAFCs; ∼0.35 mA for glucose-fed MAFCs) is generated from the oxidation of the added organic matter until its concentration decreases to a low level. SEM micrographs indicate that thick biofilms of microbial communities (coccoid cells with a diameter of ∼0.5 μm in acetate-fed MAFCs; rod-shaped cells with a length of 2.0-4.0 μm and a width of 0.5-0.7 μm in glucose-fed MAFCs) completely cover the anode electrodes. These anodophillic biofilms are thought to be responsible for the current generation, and make these microbial-anode fuel cells exhibit good performance even when the growth medium is replaced by a salt buffer without any growth factor. In comparison with those microbial fuel cells that require the addition of artificial electron transfer-mediating compounds, the findings in this study imply a potential way to develop excellent mediator-less MAFCs for electricity generation from organic matter by using substrate-induced anodophillic microbial species.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-09

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower begins to roll back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - The launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station, clears the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-09

KENNEDY SPACE CENTER, FLA. - The launch tower on Launch Complex 17-A, Cape Canaveral Air Force Station, clears the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are in the clear after tower rollback in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-09

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are in the clear after tower rollback in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload leaps off the launch pad into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower (right) and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower (right) and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are viewed as the launch tower overhead rolls back. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are viewed as the launch tower overhead rolls back. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload are free of the tower and ready for launch. This will be the third launch attempt in as many days after weather concerns postponed the launches June 8 and June 9. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload breaks forth from the smoke and steam into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - The Delta II rocket with its Mars Exploration Rover (MER-A) payload breaks forth from the smoke and steam into the blue sky to begin its journey to Mars. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload waits for rollback of the launch tower in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-09

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload waits for rollback of the launch tower in preparation for a second attempt at launch. The first attempt on June 8, 2003, was scrubbed due to bad weather in the vicinity. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower rolls back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts, June 8 and June 9, were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, the launch tower rolls back from the Boeing Delta II rocket and its Mars Exploration Rover (MER-A) payload in preparation for another launch attempt. The first two attempts, June 8 and June 9, were postponed due to weather concerns. MER-A is the first of two rovers being launched to Mars. When the two rovers arrive at Mars in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - Blue sky and sun give a dramatic backdrop for the launch of the Delta II rocket with its Mars Exploration Rover (MER-A) payload. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

NASA Image and Video Library

2003-06-10

KENNEDY SPACE CENTER, FLA. - Blue sky and sun give a dramatic backdrop for the launch of the Delta II rocket with its Mars Exploration Rover (MER-A) payload. Liftoff occurred on time at 1:58 p.m. EDT from Launch Complex 17-A, Cape Canaveral Air Force Station. MER-A, known as "Spirit," is the first of two rovers being launched to Mars. When the two rovers arrive at the red planet in 2004, they will bounce to airbag-cushioned landings at sites offering a balance of favorable conditions for safe landings and interesting science. The rovers see sharper images, can explore farther and examine rocks better than anything that has ever landed on Mars. The designated site for the MER-A mission is Gusev Crater, which appears to have been a crater lake. The second rover, MER-B, is scheduled to launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is raised off the transporter. When vertical, it will be lifted up the launch tower and mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-14

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is raised off the transporter. When vertical, it will be lifted up the launch tower and mated to the Delta rocket (in the background) to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is moved into position to raise to vertical and lift up the launch tower. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

NASA Image and Video Library

2003-05-14

KENNEDY SPACE CENTER, FLA. - On Launch Complex 17-A, Cape Canaveral Air Force Station, a solid rocket booster is moved into position to raise to vertical and lift up the launch tower. It is one of nine that will be mated to the Delta rocket to launch Mars Exploration Rover 2. NASA’s twin Mars Exploration Rovers are designed to study the history of water on Mars. These robotic geologists are equipped with a robotic arm, a drilling tool, three spectrometers, and four pairs of cameras that allow them to have a human-like, 3D view of the terrain. Each rover could travel as far as 100 meters in one day to act as Mars scientists' eyes and hands, exploring an environment where humans can’t yet go. MER-2 is scheduled to launch June 5 as MER-A. MER-1 (MER-B) will launch June 25.

Non-genomic oestrogen receptor signal in B lymphocytes: An approach towards therapeutic interventions for infection, autoimmunity and cancer.

PubMed

Seto, Karsen; Hoang, Minh; Santos, Thaddeus; Bandyopadhyay, Mausumi; Kindy, Mark S; Dasgupta, Subhajit

2016-07-01

The non-genomic membrane bound oestrogen receptor (mER) regulates intracellular signals through receptor-ligand interactions. The mER, along with G-protein coupled oestrogen receptor GPR 30 (GPER), induces diverse cell signalling pathways in murine lymphocytes. The mER isoform ER-alpha46 has recently been demonstrated in human B and T lymphocytes as an analogue receptor for chemokine CCL18, the signalling events of which are not clearly understood. Ligand-induced mER and GPER signalling events are shared with BCR, CD19 mediated intracellular signalling through phospholipase C, PIP2/IP3/PI3 mediated activation of Akt, MAP kinase, and mTOR. Oestrogen has the ability to induce CD40-mediated activation of B cells. The complete signalling pathways of mER, GPR30 and their interaction with other signals are targeted areas for novel drug development in B cells during infection, autoimmunity and cancer. Therefore, an in depth investigation is critical for determining shared signal outputs during B cell activation. Here, we focus on the mode of action of membrane bound ER in B cells as therapeutic checkpoints. Copyright © 2016 Elsevier Ltd. All rights reserved.

Recognition of dengue virus protein using epitope-mediated molecularly imprinted film.

PubMed

Tai, Dar-Fu; Lin, Chung-Yin; Wu, Tzong-Zeng; Chen, Li-Kuang

2005-08-15

Molecularly imprinted film was fabricated in the presence of a pentadecapeptide onto a quartz crystal microbalance (QCM) chip. This 15-mer peptide has been known as the linear epitope of the dengue virus NS1 protein. Imprinting resulted in an increased polymer affinity toward the corresponding templates but also to the virus protein. Direct detection of the dengue virus protein was achieved quantitatively. The QCM chip response to the NS1 protein was obtained using epitope-mediated imprinting demonstrating a comparable frequency shift in chips immobilized with monoclonal antibodies. The binding effect was further enhanced and confirmed using a monoclonal antibody to form a sandwich with the MIP-NS1 protein complex on the chip. No pretreatment was required.

Microbial dormancy improves development and experimental validation of ecosystem model

DOE PAGES

Wang, Gangsheng; Jagadamma, Sindhu; Mayes, Melanie; ...

2014-07-11

Climate feedbacks from soils can result from environmental change followed by response of plant and microbial communities, and/or associated changes in nutrient cycling. Explicit consideration of microbial life history traits and functions may be necessary to predict climate feedbacks due to changes in the physiology and community composition of microbes and their associated effect on carbon cycling. Here, we enhanced the Microbial-Enzyme-mediated Decomposition (MEND) model by incorporating microbial dormancy and the ability to track multiple isotopes of carbon. We tested two versions of MEND, i.e., MEND with dormancy and MEND without dormancy, against long-term (270 d) lab incubations of fourmore » soils with isotopically-labeled substrates. MEND without dormancy adequately fitted multiple observations (total and 14C respiration, and dissolved organic carbon), but at the cost of significantly underestimating the total microbial biomass. The MEND with dormancy improved estimates of microbial biomass by 20 71% over the MEND without dormancy. We observed large differences for two fitted model parameters, the specific maintenance and growth rates for active microbes, depending on whether dormancy was considered. Together our model extrapolations of the incubation study show that long-term soil incubations with observations in multiple carbon pools are necessary to estimate both decomposition and microbial parameters. These efforts should provide essential support to future field- and global-scale simulations and enable more confident predictions of feedbacks between environmental change and carbon cycling.« less

Nitrogen cycle in microbial mats: completely unknown?