538 research outputs found

    Phosphorylation and Methylation of Proteasomal Proteins of the Haloarcheon Haloferax volcanii

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    Proteasomes are composed of 20S core particles (CPs) of α- and β-type subunits that associate with regulatory particle AAA ATPases such as the proteasome-activating nucleotidase (PAN) complexes of archaea. In this study, the roles and additional sites of post-translational modification of proteasomes were investigated using the archaeon Haloferax volcanii as a model. Indicative of phosphorylation, phosphatase-sensitive isoforms of α1 and α2 were detected by 2-DE immunoblot. To map these and other potential sites of post-translational modification, proteasomes were purified and analyzed by tandem mass spectrometry (MS/MS). Using this approach, several phosphosites were mapped including α1 Thr147, α2 Thr13/Ser14 and PAN-A Ser340. Multiple methylation sites were also mapped to α1, thus, revealing a new type of proteasomal modification. Probing the biological role of α1 and PAN-A phosphorylation by site-directed mutagenesis revealed dominant negative phenotypes for cell viability and/or pigmentation for α1 variants including Thr147Ala, Thr158Ala and Ser58Ala. An H. volcanii Rio1p Ser/Thr kinase homolog was purified and shown to catalyze autophosphorylation and phosphotransfer to α1. The α1 variants in Thr and Ser residues that displayed dominant negative phenotypes were significantly reduced in their ability to accept phosphoryl groups from Rio1p, thus, providing an important link between cell physiology and proteasomal phosphorylation

    Estimated Groundwater Withdrawals from Principal Aquifers in the United States, 2015

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    In 2015, about 84,600 million gallons per day (Mgal/d) of groundwater were withdrawn in the United States for various uses including public supply, self-supplied domestic, industrial, mining, thermoelectric power, aquaculture, livestock, and irrigation. Of this total, about 94 percent (79,200 Mgal/d) was withdrawn from principal aquifers, which are defined as regionally extensive aquifers or aquifer systems that have the potential to be used as sources of water of suitable quality and quantity to meet various needs. The remaining 6 percent (5,400 Mgal/d) was withdrawn from other, nonprincipal aquifers in the United States. Sixty-six principal aquifers belonging to 5 major lithologic groups have been identified and delineated in the United States, including Puerto Rico and the U.S. Virgin Islands. Of the water withdrawn from principal aquifers in 2015, 81 percent (63,900 Mgal/d) was from the unconsolidated and semiconsolidated sand and gravel lithologic group, 7.1 percent (5,630 Mgal/d) was from the igneous and metamorphic-rock lithologic group, 6.8 percent (5,360 Mgal/d) was from the carbonate-rock lithologic group, 3.4 percent (2,680 Mgal/d) was from the sandstone lithologic group, and 2.2 percent (1,710 Mgal/d) was from the sandstone and carbonate-rock lithologic group. The most heavily pumped of the 24 principal aquifers and aquifer systems within the unconsolidated and semiconsolidated sand and gravel lithologic group were the High Plains aquifer (12,300 Mgal/d), Mississippi River Valley alluvial aquifer (12,100 Mgal/d), Central Valley aquifer system (11,100 Mgal/d), and Basin and Range basin-fill aquifers (7,390 Mgal/d). Withdrawals for irrigation were 48,100 Mgal/d and accounted for 75 percent of the total withdrawals from this lithologic group. Although unconsolidated sand and gravel aquifers are widely distributed and were used as sources of water in all States except Hawaii and the U.S. Virgin Islands, 56 percent of the total withdrawn from unconsolidated and semiconsolidated sand and gravel aquifers was in just four States: California (15,600 Mgal/d), Arkansas (9,560 Mgal/d), Nebraska (5,570 Mgal/d), and Texas (4,830 Mgal/d). The most heavily pumped of the seven principal aquifers within the igneous and metamorphic-rock lithologic group were the Snake River Plain (2,930 Mgal/d) and Columbia Plateau basaltic-rock aquifers (1,080 Mgal/d), which are located in the northwestern United States and together accounted for 71 percent of the water withdrawn from this lithologic group. Withdrawals for irrigation were 4,190 Mgal/d and accounted for more than 74 percent of the total withdrawals from this lithologic group. Seventy-eight percent of the withdrawals from igneous and metamorphic-rock aquifers were in three States: Idaho (3,230 Mgal/d), Washington (614 Mgal/d), and Oregon (528 Mgal/d). The most heavily pumped of the 15 principal aquifers and aquifer systems within the carbonate-rock lithologic group were the Floridan aquifer system (3,180 Mgal/d) and the Biscayne aquifer (679 Mgal/d), which are in the southeastern United States and together accounted for almost 72 percent of the withdrawals from this lithologic group. Withdrawals for public supply (2,440 Mgal/d) and irrigation (1,610 Mgal/d) together accounted for almost 76 percent of the total withdrawals from this lithologic group. Although water was withdrawn from carbonate-rock aquifers in 35 States, 71 percent of the total withdrawn was in Florida (3,020 Mgal/d) and Georgia (785 Mgal/d). The most heavily pumped of the 15 principal aquifers within the sandstone lithologic group was the Cambrian- Ordovician aquifer system (921 Mgal/d), which is in the north-central United States and accounted for 34 percent of the water withdrawn from this lithologic group. Withdrawals for public supply were 1,030 Mgal/d and accounted for 38 percent of the total withdrawals from this lithologic group. Although sandstone aquifers were used as sources of water in 32 States, 45 percent of the total withdrawn from sandstone aquifers was in five States: Minnesota (321 Mgal/d), Wisconsin (319 Mgal/d), Kansas (193 Mgal/d), Illinois (187 Mgal/d), and Pennsylvania (179 Mgal/d). The most heavily pumped of the five principal aquifers and aquifer systems within the sandstone and carbonate rock lithologic group were the Edwards-Trinity aquifer system (661 Mgal/d) in the south-central United States and the Valley and Ridge aquifers (551 Mgal/d) of the eastern United States, which together accounted for 71 percent of total withdrawals from this lithologic group. Withdrawals from sandstone and carbonate-rock aquifers for public-supply (713 Mgal/d), irrigation (469 Mgal/d), and self-supplied domestic (253 Mgal/d) uses accounted for about 84 percent of the total withdrawals from this lithologic group. Although water was withdrawn from sandstone and carbonate-rock aquifers in 25 States, 65 percent of the total withdrawn was in Texas (651 Mgal/d), Pennsylvania (238 Mgal/d), and Florida (223 Mgal/d)

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

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    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

    Skeletal adaptations in young male mice after 4 weeks aboard the International Space Station

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    Gravity has an important role in both the development and maintenance of bone mass. This is most evident in the rapid and intense bone loss observed in both humans and animals exposed to extended periods of microgravity in spaceflight. Here, cohabitating 9-week-old male C57BL/6 mice resided in spaceflight for ~4 weeks. A skeletal survey of these mice was compared to both habitat matched ground controls to determine the effects of microgravity and baseline samples in order to determine the effects of skeletal maturation on the resulting phenotype. We hypothesized that weight-bearing bones would experience an accelerated loss of bone mass compared to non-weight-bearing bones, and that spaceflight would also inhibit skeletal maturation in male mice. As expected, spaceflight had major negative effects on trabecular bone mass of the following weight-bearing bones: femur, tibia, and vertebrae. Interestingly, as opposed to the bone loss traditionally characterized for most weight-bearing skeletal compartments, the effects of spaceflight on the ribs and sternum resembled a failure to accumulate bone mass. Our study further adds to the insight that gravity has site-specific influences on the skeleton

    A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

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    We have identified a highly conserved RNA motif located upstream of genes encoding molybdate transporters, molybdenum cofactor (Moco) biosynthesis enzymes, and proteins that utilize Moco as a coenzyme. Bioinformatics searches have identified 176 representatives in γ-Proteobacteria, δ-Proteobacteria, Clostridia, Actinobacteria, Deinococcus-Thermus species and DNAs from environmental samples. Using genetic assays, we demonstrate that a Moco RNA in Escherichia coli associated with the Moco biosynthetic operon controls gene expression in response to Moco production. In addition, we provide evidence indicating that this conserved RNA discriminates against closely related analogues of Moco. These results, together with extensive phylogenetic conservation and typical gene control structures near some examples, indicate that representatives of this structured RNA represent a novel class of riboswitches that sense Moco. Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent

    The Marker State Space (MSS) Method for Classifying Clinical Samples

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    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. © 2013 Fallon et al
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