A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes

Quantitative nucleolar proteomics reveals nuclear re-organization during stress- induced senescence in mouse fibroblast

<p>Abstract</p> <p>Background</p> <p>Nucleolus is the most prominent mammalian organelle within the nucleus which is also the site for ribosomal biogenesis. There have been many reports indicating the involvement of nucleolus in the process of aging. Several proteins related to aging have been shown to localize in the nucleolus, which suggests the role of this organelle in senescence.</p> <p>Results</p> <p>In this study, we used quantitative mass spectrometry to map the flux of proteins into and out of the nucleolus during the induction of senescence in cultured mammalian cells. Changes in the abundance of 344 nucleolar proteins in sodium butyrate-induced senescence in NIH3T3 cells were studied by SILAC (stable isotope labeling by amino acids in cell culture)-based mass spectrometry. Biochemically, we have validated the proteomic results and confirmed that B23 (nucleophosmin) protein was down-regulated, while poly (ADP-ribose) polymerase (PARP) and nuclear DNA helicase II (NDH II/DHX9/RHA) were up-regulated in the nucleolus upon treatment with sodium butyrate. Accumulation of chromatin in the nucleolus was also observed, by both proteomics and microscopy, in sodium butyrate-treated cells. Similar observations were found in other models of senescence, namely, in mitoxantrone- (MTX) treated cells and primary fibroblasts from the Lamin A knockout mice.</p> <p>Conclusion</p> <p>Our data indicate an extensive nuclear organization during senescence and suggest that the redistribution of B23 protein and chromatin can be used as an important marker for senescence.</p

South China Sea Rifted Margin Testing hypotheses for lithosphere thinning during continental breakup: Drilling at the South China Sea rifted margin

International Ocean Discovery Program Expedition 368 is the second of two consecutive cruises that form the South China Sea Rifted Margin program. Expeditions 367 and 368 share the common key objectives of testing scientific hypotheses of breakup of the northern South China Sea (SCS) margin and comparing its rifting style and history to other nonvolcanic or magma-poor rifted margins. Four primary sites were selected for the overall program: one in the outer margin high (OMH) and three seaward of the OMH on distinct, margin-parallel basement ridges. These three ridges are informally labeled A, B, and C. They are located within the continent-ocean transition (COT) zone ranging from the OMH to the interpreted steady-state oceanic crust (Ridge C) of the SCS. The main scientific objectives include 1. Determining the nature of the basement within crustal units across the COT of the SCS that are critical to constrain style of rifting, 2. Constraining the time interval from initial crustal extension and plate rupture to the initial generation of igneous ocean crust, 3. Constraining vertical crustal movements during breakup, and 4. Examining the nature of igneous activity from rifting to seafloor spreading. In addition, the sediment cores from the drill sites targeting primarily tectonic and basement objectives will provide information on the Cenozoic regional environmental development of the Southeast Asia margin. Expedition 368 was planned to drill at two primary sites (U1501 and U1503) at the OMH and Ridge C, respectively. However, based on drilling results from Expedition 367, Expedition 368 chose to insert an alternate site on Ridge A (Site U1502). In total, the expedition completed operations at four sites (U1501, U1502, U1504, and U1505). Site U1503, however, was not completed beyond casing to 990 m because of mechanical problems with the drilling equipment that limited the expedition from 25 May 2017 to the end of the expedition to operate with a drill string not longer than 3400 m. New alternate Site U1504 proposed during Expedition 367 met this condition. Site U1505 also met the operational constraints of the 3400 m drill string (total) and was an alternate site for the already drilled Site U1501. At Site U1501, we cored to 697.1 m in 9.4 days, with 78.5% recovery. We also drilled ahead for 433.5 m in Hole U1501D and then logged downhole data from 78.3 to 399.3 m. In 19.3 days at Site U1502, we penetrated 1679.0 m, set 723.7 m of casing and cored a total of 576.3 m with 53.5% recovery, and collected downhole log data from 785.3 to 875.3 m and seismic data through the 10¾ inch casing. At Site U1503, we penetrated 995.1 m, setting 991.5 m of 10¾ inch casing, but no cores were taken. At Site U1504, we took 40 rotary core barrel (RCB) cores over two holes. The cored interval between both holes was 277.3 m with 26.8% recovery. An 88.2 m interval was drilled in Hole U1504B. At Site U1505, we cored 668.0 m with 101.1% recovery. Logging data was collected from 80.1 to 341.2 m. Operations at this site covered 6.1 days. Except for Site U1505, we drilled to acoustic basement, which prior to the expedition, except for Site U1501, had been interpreted to be crystalline basement. A total of 6.65 days were lost due to mechanical breakdown or waiting on spare supplies for repair of drilling equipment. At Site U1501 on the OMH, coring ~45 m into the acoustic basement sampled highly lithified sandstone to conglomerate of presumed Mesozoic age overlain by siliciclastic Eocene pre- to synrift sediments of Oligocene age and topped by primarily carbonaceous postrift sediments of early Miocene to Pleistocene age. Site U1502 on Ridge A was cased to 723.7 m. At this site, we recovered 180 m of hydrothermally altered brecciated basalts comprising sheet and pillow lavas below deep-marine sediments of Oligocene to late Miocene age. Coring was not performed within the upper 380 m (~Pliocene-Pleistocene) at Site U1502. At Site U1503 on Ridge C, 991.5 m of casing was installed in preparation for the planned deep drilling to ~1800 m, but no coring was performed due to mechanical failures, and the site was abandoned without further activity. Coring at Site U1504 on the OMH ~45 km east of Site U1501 recovered metamorphic schist to gneiss (greenschist facies) below late Eocene (?) carbonate rocks (partly reef debris) and early Miocene to Pleistocene sediments. At Site U1505, we cored to 480.15 m through Pleistocene to late Oligocene mainly carbonaceous ooze followed at depth by early Oligocene to late Eocene siliciclastic sediments. Efforts were made at every drill site to correlate the core with the seismic data and seismic stratigraphic unconformities interpreted within the Eocene to Plio-Pleistocene sedimentary sequence prior to drilling. The predrilling interpretation of ages of these unconformities was in general confirmed by drilling results. As a result of the constraints on the length of drill string that could be deployed during the later part of Expedition 368, the secondary expedition objectives addressing the environmental history of the SCS and Southeast Asia received more focus than planned because these sites are located in shallower water depths and required less penetration depth. This forced change in emphasis, however, was without fatal consequences for the primary tectonic objectives. The two expeditions together provided solid evidence for a process of breakup that included vigorous synrift magmatism as opposed to the often-favored interpretation of the SCS margin as a magma-starved margin

Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains

Cyclic nucleotide-binding (CNB) domains allosterically regulate the activity of proteins with diverse functions, but the mechanisms that enable the cyclic nucleotide-binding signal to regulate distant domains are not well understood. Here we use optical tweezers and molecular dynamics to dissect changes in folding energy landscape associated with cAMP-binding signals transduced between the two CNB domains of protein kinase A (PKA). We find that the response of the energy landscape upon cAMP binding is domain specific, resulting in unique but mutually coordinated tasks: one CNB domain initiates cAMP binding and cooperativity, whereas the other triggers inter-domain interactions that promote the active conformation. Inter-domain interactions occur in a stepwise manner, beginning in intermediate-liganded states between apo and cAMP-bound domains. Moreover, we identify a cAMP-responsive switch, the N3A motif, whose conformation and stability depend on cAMP occupancy. This switch serves as a signaling hub, amplifying cAMP-binding signals during PKA activation

Higher-Order Beliefs in Simple Trading Models

We examine the role of higher order beliefs in asset markets where coordination between a buyer and seller can lead to gains to trade. The scenarios are modeled such that trader’s strategies do not only depend upon their beliefs of underlying economic phenomena, but also upon the others’ beliefs regarding the beliefs of themselves. Under certain parameters the breakdown of coordination is predicted–even when both traders are certain the underlying phenomena dictates trade is advantageous. We demonstrate the equilibrium predictions can be constructed via a small number of iterated thought exercises. The experimental design allows us to control for various behavioral phenomena and examine subjects’ decisions across different accounting regimes as to tease out strategic uncertainty due solely to information asymmetry. In this setting we find evidence supporting higher order beliefs. An implication is that the lack of uniformity leads to lack of common knowledge of the beliefs of others, which in turn leads to the spreading of inefficient outcomes

Surface Interactions And Degradation Of A Fluoroquinolone Antibiotic In The Dark In Aqueous Tio2 Suspensions

Fluoroquinolone Antibiotics (fqs) Are Important Drugs Used In Human And Veterinary Medicine. Their Detection In Natural Waters And Waste Water Treatment Plants, Along With Increased Resistance To Fqs Among Some Bacteria, Have Generated An Increased Interest In The Fate Of These Drugs In The Environment. Partitioning Of Fqs Between An Aqueous Solution And Attendant Substrates Depends, In Part, On The Surface Reactivity Of The Adsorbent, Commonly A Function Of Particle Size, Surface Charge, And Functional Groups. This Study Investigated The Surface Interactions Between The Fq Drug Ofloxacin (ofl) And Titanium Oxide (tio2), A Common Catalyst And Widely-observed Constituent In Many Consumer Products. Raman And Fluorescence Spectroscopic Techniques, As Well As Lc/ms, Were Used To Determine The Ofl Moieties Present On Tio2 Surfaces And In Attendant Solutions. Raman Spectra Indicate That The C=o (ketone) Group Of The Quinolone Core, The Nh+ Of The Piperazinyl Ring, And Ch3 Of Benzoxazine Core Are The Most Active In Sorption Onto The Tio2 Surface. Raman Spectra Also Show That The Sorbed Benzoxazine-quinolone Core And Piperazinyl Moieties Are Readily Desorbed From The Surface By Re-suspending Samples In Water. Importantly, We Found That Ofl Could Be Degraded By Reacting With Tio2 Even In The Dark. Complementary Lc/ms Analysis Of The Attendant Supernatants Indicates The Presence Of De-piperazinylated And De-carboxylated Ofl Breakdown Products In Supernatant Solutions. Together, Both Raman And Lc/ms Analyses Indicate That Tio2 Breaks The Compound Into Piperazinyl And Carboxylate Groups Which Attach To The Surface, Whereas Decarboxylated And Hydroxylated Quinolone Moieties Remain In Solution. The Present Study Thus Identifies The Sorption Mechanisms And Breakdown Products Of Ofl During Dark Reactions With Tio2, Which Is Critically Important For Understanding The Fate And Transport Of Ofl As It Enters The Soil And Aquatic Environment. (c) 2015 Elsevier B.v. All Rights Reserved

Temporal patterns of <it>broad </it>isoform expression during the development of neuronal lineages in <it>Drosophila</it>

<p>Abstract</p> <p>Background</p> <p>During the development of the central nervous system (CNS) of <it>Drosophila</it>, neuronal stem cells, the neuroblasts (NBs), first generate a set of highly diverse neurons, the primary neurons that mature to control larval behavior, and then more homogeneous sets of neurons that show delayed maturation and are primarily used in the adult. These latter, 'secondary' neurons show a complex pattern of expression of <it>broad</it>, which encodes a transcription factor usually associated with metamorphosis, where it acts as a key regulator in the transitions from larva and pupa.</p> <p>Results</p> <p>The Broad-Z3 (Br-Z3) isoform appears transiently in most central neurons during embryogenesis, but persists in a subset of these cells through most of larval growth. Some of the latter are embryonic-born secondary neurons, whose development is arrested until the start of metamorphosis. However, the vast bulk of the secondary neurons are generated during larval growth and bromodeoxyuridine incorporation shows that they begin expressing Br-Z3 about 7 hours after their birth, approximately the time that they have finished outgrowth to their initial targets. By the start of metamorphosis, the oldest secondary neurons have turned off Br-Z3 expression, while the remainder, with the exception of the very youngest, maintain Br-Z3 while they are interacting with potential partners in preparation for neurite elaboration. That Br-Z3 may be involved in early sprouting is suggested by ectopically expressing this isoform in remodeling primary neurons, which do not normally express Br-Z3. These cells now sprout into ectopic locations. The expression of Br-Z3 is transient and seen in all interneurons, but two other isoforms, Br-Z4 and Br-Z1, show a more selective expression. Analysis of MARCM clones shows that the Br-Z4 isoform is expressed by neurons in virtually all lineages, but only in those cells born during a window during the transition from the second to the third larval instar. Br-Z4 expression is then maintained in this temporal cohort of cells into the adult.</p> <p>Conclusion</p> <p>These data show the potential for diverse functions of Broad within the developing CNS. The Br-Z3 isoform appears in all interneurons, but not motoneurons, when they first begin to interact with potential targets. Its function during this early sorting phase needs to be defined. Two other Broad isoforms, by contrast, are stably expressed in cohorts of neurons in all lineages and are the first examples of persisting molecular 'time-stamps' for <it>Drosophila </it>postembryonic neurons.</p