Conserved active site cysteine residue of archaeal THI4 homolog is essential for thiamine biosynthesis in Haloferax volcanii

Background: Thiamine (vitamin B1) is synthesized de novo by certain yeast, fungi, plants, protozoans, bacteria and archaea. The pathway of thiamine biosynthesis by archaea is poorly understood, particularly the route of sulfur relay to form the thiazole ring. Archaea harbor structural homologs of both the bacterial (ThiS-ThiF) and eukaryotic (THI4) proteins that mobilize sulfur to thiazole ring precursors by distinct mechanisms. Results: Based on comparative genome analysis, halophilic archaea are predicted to synthesize the pyrimidine moiety of thiamine by the bacterial pathway, initially suggesting that also a bacterial ThiS-ThiF type mechanism for synthesis of the thiazole ring is used in which the sulfur carrier ThiS is first activated by ThiF-catalyzed adenylation. The only ThiF homolog of Haloferax volcanii (UbaA) was deleted but this had no effect on growth in the absence of thiamine. Usage of the eukaryotic THI4-type sulfur relay was initially considered less likely for thiamine biosynthesis in archaea, since the active-site cysteine residue of yeast THI4p that donates the sulfur to the thiazole ring by a suicide mechanism is replaced by a histidine residue in many archaeal THI4 homologs and these are described as D-ribose-1,5-bisphosphate isomerases. The THI4 homolog of the halophilic archaea, including Hfx. volcanii (HVO_0665, HvThi4) was found to differ from that of methanogens and thermococci by having a cysteine residue (Cys165) corresponding to the conserved active site cysteine of yeast THI4p (Cys205). Deletion of HVO_0665 generated a thiamine auxotroph that was trans-complemented by a wild-type copy of HVO_0665, but not the modified gene encoding an HvThi4 C165A variant. Conclusions: Based on our results, we conclude that the archaeon Hfx. volcanii uses a yeast THI4-type mechanism for sulfur relay to form the thiazole ring of thiamine. We extend this finding to a relatively large group of archaea, including haloarchaea, ammonium oxidizing archaea, and some methanogen and Pyrococcus species, by observing that these organisms code for THI4 homologs that have a conserved active site cysteine residue which is likely used in thiamine biosynthesis. Thus, archaeal members of IPR002922 THI4 family that have a conserved cysteine active site should be reexamined for a function in thiamine biosynthesis

Soret Effect Study on High-Pressure CO2-Water Solutions Using UV-Raman Spectroscopy and a Concentric-Tube Optical Cell

Spatially resolved deep-UV Raman spectroscopy was applied to solutions of CO2 and H2O (or D2O), which were subject to a temperature gradient in a thermally regulated high-pressure concentric-tube Raman cell in an attempt to measure a Soret effect in the vicinity of the critical point of CO2. Although Raman spectra of solutions of CO2 dissolved in D2O at 10 MPa and temperatures near the critical point of CO2 had adequate signal-to-noise and spatial resolution to observe a Soret effect with a Soret coefficient with magnitude of |ST| > 0.03, no evidence for an effect of this size was obtained for applied temperature gradients up to 19oC. The presence of 1 M NaCl did not make a difference. In contrast, the concentration of CO2 dissolved in H2O was shown to vary significantly across the temperature gradient when excess CO2 was present, but the results could be explained simply by the variation in CO2 solubility over the temperature range and not to kinetic factors. For mixtures of D2O dissolved in scCO2 at 10 MPa and temperatures close to the critical point of CO2, the Raman peaks for H2O were too weak to measure with confidence even at the limit of D2O solubility

Glycogene Expression Alterations Associated with Pancreatic Cancer Epithelial-Mesenchymal Transition in Complementary Model Systems

The ability to selectively detect and target cancer cells that have undergone an epithelial-mesenchymal transition (EMT) may lead to improved methods to treat cancers such as pancreatic cancer. The remodeling of cellular glycosylation previously has been associated with cell differentiation and may represent a valuable class of molecular targets for EMT.As a first step toward investigating the nature of glycosylation alterations in EMT, we characterized the expression of glycan-related genes in three in-vitro model systems that each represented a complementary aspect of pancreatic cancer EMT. These models included: 1) TGFβ-induced EMT, which provided a look at the active transition between states; 2) a panel of 22 pancreatic cancer cell lines, which represented terminal differentiation states of either epithelial-like or mesenchymal-like; and 3) actively-migrating and stationary cells, which provided a look at the mechanism of migration. We analyzed expression data from a list of 587 genes involved in glycosylation (biosynthesis, sugar transport, glycan-binding, etc.) or EMT. Glycogenes were altered at a higher prevalence than all other genes in the first two models (p<0.05 and <0.005, respectively) but not in the migration model. Several functional themes were shared between the induced-EMT model and the cell line panel, including alterations to matrix components and proteoglycans, the sulfation of glycosaminoglycans; mannose receptor family members; initiation of O-glycosylation; and certain forms of sialylation. Protein-level changes were confirmed by Western blot for the mannose receptor MRC2 and the O-glycosylation enzyme GALNT3, and cell-surface sulfation changes were confirmed using Alcian Blue staining.Alterations to glycogenes are a major component of cancer EMT and are characterized by changes to matrix components, the sulfation of GAGs, mannose receptors, O-glycosylation, and specific sialylated structures. These results provide leads for targeting aggressive and drug resistant forms of pancreatic cancer cells

Directive 02-14: Tax Obligations of Persons Purchasing Cigarettes in Interstate Commerce for which the Massachusetts Cigarette Excise Has Not Been Paid

The development of accurate clinical biomarkers has been challenging in part due to the diversity between patients and diseases. One approach to account for the diversity is to use multiple markers to classify patients, based on the concept that each individual marker contributes information from its respective subclass of patients. Here we present a new strategy for developing biomarker panels that accounts for completely distinct patient subclasses. Marker State Space (MSS) defines "marker states" based on all possible patterns of high and low values among a panel of markers. Each marker state is defined as either a case state or a control state, and a sample is classified as case or control based on the state it occupies. MSS was used to define multi-marker panels that were robust in cross validation and training-set/test-set analyses and that yielded similar classification accuracy to several other classification algorithms. A three-marker panel for discriminating pancreatic cancer patients from control subjects revealed subclasses of patients based on distinct marker states. MSS provides a straightforward approach for modeling highly divergent subclasses of patients, which may be adaptable for diverse applications.</p

The European Plate Observing System and the Arctic

The European Plate Observing System (EPOS) aims to integrate existing infrastructures in the solid earth sciences into a single infrastructure, enabling earth scientists across Europe to combine, model, and interpret multidisciplinary datasets at different time and length scales. In particular, a primary objective is to integrate existing research infrastructures within the fields of seismology, geodesy, geophysics, geology, rock physics, and volcanology at a pan-European level. The added value of such integration is not visible through individual analyses of data from each research infrastructure; it needs to be understood in a long-term perspective that includes the time when changes implied by current scientific research results are fully realized and their societal impacts have become clear. EPOS is now entering its implementation phase following a four-year preparatory phase during which 18 member countries in Europe contributed more than 250 research infrastructures to the building of this pan-European vision. The Arctic covers a significant portion of the European plate and therefore plays an important part in research on the solid earth in Europe. However, the work environment in the Arctic is challenging. First, most of the European Plate boundary in the Arctic is offshore, and hence, sub-sea networks must be built for solid earth observation. Second, ice covers the Arctic Ocean where the European Plate boundary crosses through the Gakkel Ridge, so innovative technologies are needed to monitor solid earth deformation. Therefore, research collaboration with other disciplines such as physical oceanography, marine acoustics, and geo-biology is necessary. The establishment of efficient research infrastructures suitable for these challenging conditions is essential both to reduce costs and to stimulate multidisciplinary research.Le système European Plate Observing System (EPOS) vise l’intégration des infrastructures actuelles en sciences de la croûte terrestre afin de ne former qu’une seule infrastructure pour que les spécialistes des sciences de la Terre des quatre coins de l’Europe puissent combiner, modéliser et interpréter des ensembles de données multidisciplinaires moyennant diverses échelles de temps et de longueur. Un des principaux objectifs consiste plus particulièrement à intégrer les infrastructures de recherche existantes se rapportant aux domaines de la sismologie, de la géodésie, de la géophysique, de la géologie, de la physique des roches et de la volcanologie à l’échelle paneuropéenne. La valeur ajoutée de cette intégration n’est pas visible au moyen des analyses individuelles des données émanant de chaque infrastructure de recherche. Elle doit plutôt être considérée à la lumière d’une perspective à long terme, lorsque les changements qu’impliquent les résultats de recherche scientifique actuels auront été entièrement réalisés et que les incidences sur la société seront claires. Le système EPOS est en train d’amorcer sa phase de mise en oeuvre. Cette phase succède à la phase préparatoire de quatre ans pendant laquelle 18 pays membres de l’Europe ont soumis plus de 250 infrastructures de recherche en vue de l’édification de cette vision paneuropéenne. L’Arctique couvre une grande partie de la plaque européenne et par conséquent, il joue un rôle important dans les travaux de recherche portant sur la croûte terrestre en Europe. Cependant, le milieu de travail de l’Arctique n’est pas sans défis. Premièrement, la majorité de la limite de la plaque européenne se trouvant dans l’Arctique est située au large, ce qui signifie que des réseaux marins doivent être aménagés pour permettre l’observation de la croûte terrestre. Deuxièmement, de la glace recouvre l’océan Arctique, là où la limite de la plaque européenne traverse la dorsale de Gakkel, ce qui signifie qu’il faut recourir à des technologies innovatrices pour surveiller la déformation de la croûte terrestre. C’est pourquoi les travaux de recherche doivent nécessairement se faire en collaboration avec d’autres disciplines comme l’océanographie physique, l’acoustique marine et la géobiologie. L’établissement d’infrastructures de recherche efficaces capables de faire face à ces conditions rigoureuses s’avère essentiel, tant pour réduire les coûts que pour stimuler la recherche multidisciplinaire

Development and Validation Protocol for an Instrument to Measure Household Water Insecurity Across Cultures and Ecologies the Household Water InSecurity Experiences (HWISE) Scale

Introduction A wide range of water-related problems contribute to the global burden of disease. Despite the many plausible consequences for health and well-being, there is no validated tool to measure individual- or household-level water insecurity equivalently across varying cultural and ecological settings. Accordingly, we are developing the Household Water Insecurity Experiences (HWISE) Scale to measure household-level water insecurity in multiple contexts. Methods and analysis After domain specification and item development, items were assessed for both content and face validity. Retained items are being asked in surveys in 28 sites globally in which waterrelated problems have been reported (eg, shortages, excess water and issues with quality), with a target of at least 250 participants from each site. Scale development will draw on analytic methods from both classical test and item response theories and include item reduction and factor structure identification. Scale evaluation will entail assessments of reliability, and predictive, convergent, and discriminant validity, as well as the assessment of differentiation between known groups. Ethics and dissemination Study activities received necessary ethical approvals from institutional review bodies relevant to each site. We anticipate that the final HWISE Scale will be completed by late 2018 and made available through open-access publication. Associated findings will be disseminated to public health professionals, scientists, practitioners and policymakers through peer-reviewed journals, scientific presentations and meetings with various stakeholders. Measures to quantify household food insecurity have transformed policy, research and humanitarian aid efforts globally, and we expect that an analogous measure for household water insecurity will be similarly impactful

Projected WIMP sensitivity of the LUX-ZEPLIN dark matter experiment

LUX-ZEPLIN (LZ) is a next-generation dark matter direct detection experiment that will operate 4850 feet underground at the Sanford Underground Research Facility (SURF) in Lead, South Dakota, USA. Using a two-phase xenon detector with an active mass of 7 tonnes, LZ will search primarily for low-energy interactions with weakly interacting massive particles (WIMPs), which are hypothesized to make up the dark matter in our galactic halo. In this paper, the projected WIMP sensitivity of LZ is presented based on the latest background estimates and simulations of the detector. For a 1000 live day run using a 5.6-tonne fiducial mass, LZ is projected to exclude at 90% confidence level spin-independent WIMP-nucleon cross sections above 1.4×10-48 cm2 for a 40 GeV/c2 mass WIMP. Additionally, a 5σ discovery potential is projected, reaching cross sections below the exclusion limits of recent experiments. For spin-dependent WIMP-neutron(-proton) scattering, a sensitivity of 2.3×10-43 cm2 (7.1×10-42 cm2) for a 40 GeV/c2 mass WIMP is expected. With underground installation well underway, LZ is on track for commissioning at SURF in 2020

Energy partition of seismic coda waves in layered media: theory and application to Pinyon Flats Observatory

We have studied the partition of shear, compressional and kinetic energies in the coda of ten earthquakes recorded on a dense array, located at Pinyon Flats Observatory (PFO), California. We observe a clear stabilization of the shear to compressional ($W^s/W^p$) energy ratio in the coda, with an average value of about 2.8. The ratio between the vertical and horizontal kinetic energies ($V^2/H^2$) can be measured from 5 to 25Hz and shows an abrupt transitionfrom 0.1 in the 5-10Hz band, to about 0.8 in the 15-25Hz band. These measured values are in sharp contrast with the theoretical prediction for equipartitioned elastic waves in a homogeneous half-space. To explain these observations, we have developed a theory of equipartition in a layered elastic half-space. Using a rigorous spectral decomposition of the elastic wave equation, we define equipartition as a white noise distributed over the complete set of eigenfunctions. The theory predicts that close to the resonance frequency of a low-velocity layer, the ratio between shear and compressional energies strongly decreases. Using a detailed model of the subsurface at PFO, this conterintuitive result is found to be in good qualitative and quantitative agreement with the observations