Depth-shifting cores incompletely recovered from the upper oceanic crust, IODP Hole 1256D

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 9 (2008): Q08O11, doi:10.1029/2008GC002010.Seafloor drilling operations, especially those in crustal rocks, yield incomplete recovery of drilled sections, and depths of the recovered core pieces are assigned with some uncertainty. Here we present a new depth-shifting method that is simple and rapid, requires little subjective input, and is applicable to any core-log integration problem where sufficient comparable data have been collected in both the open hole and from the recovered core. Over the depth range for which both core and log data have been collected, an automatic algorithm selected the best new depth for each piece. The criteria for determining the best depth were as follows: (1) find new depths for as many pieces as possible, and (2) minimize the difference between core density and log density. In this study, depth-shifting is applied at Integrated Ocean Drilling Program (IODP) Hole 1256D, which is our first opportunity to study a section of intact, in situ upper ocean crust drilled down to gabbro. The new depths significantly improve the agreement between an independent data set and the logging record.Funding for this research was provided by a JOI/USSSP Post-Expedition Award to L.A.G. Mick Spillane of the NOAA Center for Tsunami Research provided tide calculations using OSU TPXO6.2

A Method for Compiling and Executing Expressive Assertions

Programming with assertions constitutes an effective tool to detect and correct programming errors. The ability of executing formal specifications is essential in order to test automatically a program with respect to its assertions. However, formal specifications may describe recursive models which are difficult to identify so current assertion checkers limit, in a considerable way, the expressivity of the assertion language. In this paper, we are interested in showing how transformational synthesis can help to execute “expressive” assertions of the form ∀x(r(x) ⇔ QyR(x, y)) where x is a set of variables to be instantiated at execution time, Q is an existential or universal quantifier and R a quantifier free formula in the language of a particular first-order theory A we call assertion context. The class of assertion contexts is interesting because it presents a balance between expressiveness for writing assertions and existence of effective methods for executing them by means of synthesized (definite) logic programs

Features of 80S mammalian ribosome and its subunits

It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (Pi), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (Kd 30 μM and 1–2 μM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic

Models of hydrothermal circulation within 106 Ma seafloor : constraints on the vigor of fluid circulation and crustal properties, below the Madeira Abyssal Plain

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 6 (2005): Q11001, doi:10.1029/2005GC001013.Heat flow measurements colocated with seismic data across 106 Ma seafloor of the Madeira Abyssal Plain (MAP) reveal variations in seafloor heat flow of ±10–20% that are positively correlated with basement relief buried below thick sediments. Conductive finite element models of sediments and upper basement using reasonable thermal properties are capable of generating the observed positive correlation between basement relief and seafloor heat flow, but with variability of just ±4–8%. Conductive simulations using a high Nusselt number (Nu) proxy for vigorous local convection suggest that Nu = 2–10 within the upper 600–100 m of basement, respectively, is sufficient to achieve a reasonable match to observations. These Nu values are much lower than those inferred on younger ridge flanks where greater thermal homogeneity is achieved in upper basement. Fully coupled simulations suggest that permeability below the MAP is on the order of 10−12–10−10 m2 within the upper 300–600 m of basement. This permeability range is broadly consistent with values determined by single-hole experiments and from modeling studies at other (mostly younger) sites. We infer that the reduction in basement permeability with age that is thought to occur within younger seafloor may slow considerably within older seafloor, helping hydrothermal convection to continue as plates age.Funding in support of this work was provided by the U.S. National Science Foundation (OCE-0001892), the U.S. Science Support Program for IODP (T301A7), and the Institute for Geophysics and Planetary Physics/Los Alamos National Laboratory (1317)

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome

Protein synthesis is catalyzed in the peptidyl transferase center (PTC), located in the large (50S) subunit of the ribosome. No high-resolution structure of the intact ribosome has contained a complete active site including both A- and P-site tRNAs. In addition, although past structures of the 50S subunit have found no ordered proteins at the PTC, biochemical evidence suggests that specific proteins are capable of interacting with the 3′ ends of tRNA ligands. Here we present structures, at 3.6-Å and 3.5-Å resolution respectively, of the 70S ribosome in complex with A- and P-site tRNAs that mimic pre- and post-peptidyl-transfer states. These structures demonstrate that the PTC is very similar between the 50S subunit and the intact ribosome. They also reveal interactions between the ribosomal proteins L16 and L27 and the tRNA substrates, helping to elucidate the role of these proteins in peptidyl transfer

A Bacterial Acetyltransferase Destroys Plant Microtubule Networks and Blocks Secretion

The eukaryotic cytoskeleton is essential for structural support and intracellular transport, and is therefore a common target of animal pathogens. However, no phytopathogenic effector has yet been demonstrated to specifically target the plant cytoskeleton. Here we show that the Pseudomonas syringae type III secreted effector HopZ1a interacts with tubulin and polymerized microtubules. We demonstrate that HopZ1a is an acetyltransferase activated by the eukaryotic co-factor phytic acid. Activated HopZ1a acetylates itself and tubulin. The conserved autoacetylation site of the YopJ / HopZ superfamily, K289, plays a critical role in both the avirulence and virulence function of HopZ1a. Furthermore, HopZ1a requires its acetyltransferase activity to cause a dramatic decrease in Arabidopsis thaliana microtubule networks, disrupt the plant secretory pathway and suppress cell wall-mediated defense. Together, this study supports the hypothesis that HopZ1a promotes virulence through cytoskeletal and secretory disruption

Cleavage of the sarcin–ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding

Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin α-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin–ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interacts with translation factors that hydrolyze GTP, and it is important for their binding to the ribosome, but its precise role is not yet understood. We studied the effect of α-sarcin on defined steps of translation by the bacterial ribosome. α-Sarcin-treated ribosomes showed no defects in mRNA and tRNA binding, peptide-bond formation and sparsomycin-dependent translocation. Cleavage of SRL slightly affected binding of elongation factor Tu ternary complex (EF-Tu•GTP•tRNA) to the ribosome. In contrast, the activity of elongation factor G (EF-G) was strongly impaired in α-sarcin-treated ribosomes. Importantly, cleavage of SRL inhibited EF-G binding, and consequently GTP hydrolysis and mRNA–tRNA translocation. These results suggest that the SRL is more critical in EF-G than ternary complex binding to the ribosome implicating different requirements in this region of the ribosome during protein elongation

Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways

The transition from vegetative growth to reproduction is a major developmental event in plants. To maximise reproductive success, its timing is determined by complex interactions between environmental cues like the photoperiod, temperature and nutrient availability and internal genetic programs. While the photoperiod- and temperature- and gibberellic acid-signalling pathways have been subjected to extensive analysis, little is known about how nutrients regulate floral induction. This is partly because nutrient supply also has large effects on vegetative growth, making it difficult to distinguish primary and secondary influences on flowering. A growth system using glutamine supplementation was established to allow nitrate to be varied without a large effect on amino acid and protein levels, or the rate of growth. Under nitrate-limiting conditions, flowering was more rapid in neutral (12/12) or short (8/16) day conditions in C24, Col-0 and Laer. Low nitrate still accelerated flowering in late-flowering mutants impaired in the photoperiod, temperature, gibberellic acid and autonomous flowering pathways, in the fca co-2 ga1-3 triple mutant and in the ft-7 soc1-1 double mutant, showing that nitrate acts downstream of other known floral induction pathways. Several other abiotic stresses did not trigger flowering in fca co-2 ga1-3, suggesting that nitrate is not acting via general stress pathways. Low nitrate did not further accelerate flowering in long days (16/8) or in 35S::CO lines, and did override the late-flowering phenotype of 35S::FLC lines. We conclude that low nitrate induces flowering via a novel signalling pathway that acts downstream of, but interacts with, the known floral induction pathways