The concurrent emergence and causes of double volcanic hotspot tracks on the Pacific plate.

Mantle plumes are buoyant upwellings of hot rock that transport heat from Earth's core to its surface, generating anomalous regions of volcanism that are not directly associated with plate tectonic processes. The best-studied example is the Hawaiian-Emperor chain, but the emergence of two sub-parallel volcanic tracks along this chain, Loa and Kea, and the systematic geochemical differences between them have remained unexplained. Here we argue that the emergence of these tracks coincides with the appearance of other double volcanic tracks on the Pacific plate and a recent azimuthal change in the motion of the plate. We propose a three-part model that explains the evolution of Hawaiian double-track volcanism: first, mantle flow beneath the rapidly moving Pacific plate strongly tilts the Hawaiian plume and leads to lateral separation between high- and low-pressure melt source regions; second, the recent azimuthal change in Pacific plate motion exposes high- and low-pressure melt products as geographically distinct volcanoes, explaining the simultaneous emergence of double-track volcanism across the Pacific; and finally, secondary pyroxenite, which is formed as eclogite melt reacts with peridotite, dominates the low-pressure melt region beneath Loa-track volcanism, yielding the systematic geochemical differences observed between Loa- and Kea-type lavas. Our results imply that the formation of double-track volcanism is transitory and can be used to identify and place temporal bounds on plate-motion changes.

Lithospheric controls on magma composition along Earth's longest continental hotspot track.

Hotspots are anomalous regions of volcanism at Earth's surface that show no obvious association with tectonic plate boundaries. Classic examples include the Hawaiian-Emperor chain and the Yellowstone-Snake River Plain province. The majority are believed to form as Earth's tectonic plates move over long-lived mantle plumes: buoyant upwellings that bring hot material from Earth's deep mantle to its surface. It has long been recognized that lithospheric thickness limits the rise height of plumes and, thereby, their minimum melting pressure. It should, therefore, have a controlling influence on the geochemistry of plume-related magmas, although unambiguous evidence of this has, so far, been lacking. Here we integrate observational constraints from surface geology, geochronology, plate-motion reconstructions, geochemistry and seismology to ascertain plume melting depths beneath Earth's longest continental hotspot track, a 2,000-kilometre-long track in eastern Australia that displays a record of volcanic activity between 33 and 9 million years ago, which we call the Cosgrove track. Our analyses highlight a strong correlation between lithospheric thickness and magma composition along this track, with: (1) standard basaltic compositions in regions where lithospheric thickness is less than 110 kilometres; (2) volcanic gaps in regions where lithospheric thickness exceeds 150 kilometres; and (3) low-volume, leucitite-bearing volcanism in regions of intermediate lithospheric thickness. Trace-element concentrations from samples along this track support the notion that these compositional variations result from different degrees of partial melting, which is controlled by the thickness of overlying lithosphere. Our results place the first observational constraints on the sub-continental melting depth of mantle plumes and provide direct evidence that lithospheric thickness has a dominant influence on the volume and chemical composition of plume-derived magmas.

Assessment of dietary ratios of red clover and corn silages on milk production and milk quality in dairy cows.

Twenty-four multiparous Holstein-Friesian dairy cows were used in a replicated 3×3 Latin square changeover design experiment to test the effects of changing from corn (Zea mays) silage to red clover (Trifolium pratense) silage in graded proportions on feed intakes, milk production, and whole-body N and P partitioning. Three dietary treatments with ad libitum access to 1 of 3 forage mixtures plus a standard allowance of 4kg/d dairy concentrates were offered. The 3 treatment forage mixtures were, on a dry matter (DM) basis: (1) R10: 90% corn silage and 10% red clover silage, (2) R50: 50% corn silage and 50% red clover silage, and (3) R90: 10% corn silage and 90% red clover silage. In each of 3 experimental periods, there were 21d for adaptation to diets, and 7d for measurements. Diet crude protein intakes increased, and starch intakes decreased, as the silage mixture changed from 90% corn to 90% red clover, although the highest forage DM intakes and milk yields were achieved on diet R50. Although milk fat yields were unaffected by diet, milk protein yields were highest with the R 0250 diet. Whole-body partitioning of N was measured in a subset of cows (n=9), and both the daily amount and proportion of N consumed that was excreted in feces and urine increased as the proportion of red clover silage in the diet increased. However, the apparent efficiency of utilization of feed N for milk protein production decreased from 0.33g/g for diet R10 to 0.25g/g for diet R90. The urinary excretion of purine derivatives (sum of allantoin and uric acid) tended to increase, suggesting greater flow of microbial protein from the rumen, as the proportion of red clover silage in the diet increased, and urinary creatinine excretion was affected by diet. Fecal shedding of E. coli was not affected by dietary treatment. In conclusion, even though microbial protein flow may have been greatest from the R 0450 diet, optimum feed intakes and milk yields were achieved on a diet that contained a 1:1 DM mixture of corn and red clover silages.

Protein evolution. On the ancestry of barrels.

Most proteins consist of several domains linked together in a single polypeptide chain, and many of these proteins have evolved by gene duplication and fusion. Miles and Davies discuss the study by Lang et al., who show that this type of protein evolution may also occur in b/a barrel proteins, a common single-domain protein fold. Other single domain proteins may have arisen from similar evolutionary mechanisms.

Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily.

The transforming growth factors-beta (TGF-beta 1 through -beta 5) are a family of homodimeric cytokines that regulate proliferation and function in many cell types. Family members have 66 to 80% sequence identity and nine strictly conserved cysteines. A crystal structure of a member of this family, TGF-beta 2, has been determined at 2.1 angstrom (A) resolution and refined to an R factor of 0.172. The monomer lacks a well-defined hydrophobic core and displays an unusual elongated nonglobular fold with dimensions of approximately 60 A by 20 A by 15 A. Eight cysteines form four intrachain disulfide bonds, which are clustered in a core region forming a network complementary to the network of hydrogen bonds. The dimer is stabilized by the ninth cysteine, which forms an interchain disulfide bond, and by two identical hydrophobic interfaces. Sequence profile analysis of other members of the TGF-beta superfamily, including the activins, inhibins, and several developmental factors, imply that they also adopt the TGF-beta fold.

Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.

Genomic evolution has been profoundly influenced by DNA transposition, a process whereby defined DNA segments move freely about the genome. Transposition is mediated by transposases, and similar events are catalyzed by retroviral integrases such as human immunodeficiency virus-1 (HIV-1) integrase. Understanding how these proteins interact with DNA is central to understanding the molecular basis of transposition. We report the three-dimensional structure of prokaryotic Tn5 transposase complexed with Tn5 transposon end DNA determined to 2.3 angstrom resolution. The molecular assembly is dimeric, where each double-stranded DNA molecule is bound by both protein subunits, orienting the transposon ends into the active sites. This structure provides a molecular framework for understanding many aspects of transposition, including the binding of transposon end DNA by one subunit and cleavage by a second, cleavage of two strands of DNA by a single active site via a hairpin intermediate, and strand transfer into target DNA.

Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases.

HIV integrase is the enzyme responsible for inserting the viral DNA into the host chromosome; it is essential for HIV replication. The crystal structure of the catalytically active core domain (residues 50 to 212) of HIV-1 integrase was determined at 2.5 A resolution. The central feature of the structure is a five-stranded beta sheet flanked by helical regions. The overall topology reveals that this domain of integrase belongs to a superfamily of polynucleotidyl transferases that includes ribonuclease H and the Holliday junction resolvase RuvC. The active site region is identified by the position of two of the conserved carboxylate residues essential for catalysis, which are located at similar positions in ribonuclease H. In the crystal, two molecules form a dimer with a extensive solvent-inaccessible interface of 1300 A2 per monomer.

Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement.

Joint refinement of macromolecules against crystallographic and nuclear magnetic resonance (NMR) observations is presented as a way of combining experimental information from the two methods. The model of interleukin-1 beta derived by the joint x-ray and NMR refinement is shown to be consistent with the experimental observations of both methods and to have crystallographic R value and geometrical parameters that are of the same quality as or better than those of models obtained by conventional crystallographic studies. The few NMR observations that are violated by the model serve as an indicator for genuine differences between the crystal and solution structures. The joint x-ray-NMR refinement can resolve structural ambiguities encountered in studies of multidomain proteins, in which low- to medium-resolution diffraction data can be complemented by higher resolution NMR data obtained for the individual domains.

Assessment of dietary ratios of red clover and grass silages on milk production and milk quality in dairy cows.

Twenty-four multiparous Holstein-Friesian dairy cows were used in a replicated 4 x 4 Latin square changeover design experiment to test the effects of changing from ryegrass (Lolium perenne) silage to red clover (Trifolium pratense) silage in graded proportions on feed intakes, milk production, milk organoleptic qualities, and whole-body nitrogen partitioning. Four dietary treatments, comprising ad libitum access to 1 of 4 forage mixtures plus a standard allowance of 4 kg/d dairy concentrates, were offered. The 4 forage mixtures were, on a dry matter (DM) basis: 1) 100% grass silage, 2) 66% grass silage: 34% red clover silage, 3) 34% grass silage: 66% red clover silage, and 4) 100% red clover silage. In each of 4 experimental periods, there were 21 d for adaptation to diets and 7 d for measurements. There was an increase in both DM intakes and milk yields as the proportion of red clover in the diet increased. However, the increase in milk yield was not as great as the increase in DM intake, so that the efficiency of milk production, in terms of yield (kg) of milk per kg of DM intake, decreased. The concentrations of protein, milk fat, and the shorter chain saturated fatty acids decreased, whereas C18 polyunsaturated fatty acids (PUFA) and long-chain PUFA (C20+) increased as the proportion of red clover in the diet increased. There was little effect of dietary treatment on the organoleptic qualities of milk as assessed by taste panel analysis. There were no effects on the aroma of milk, on aftertaste, or overall liking of the milk. Milk was thicker and creamier in color when cows were fed grass silage compared with red clover silage. The flavor of milk was largely unaffected by dietary treatment. In conclusion, increasing the proportion of red clover in the diet of dairy cows increased feed intakes and milk yields, decreased the concentration of fat and protein in milk, increased PUFA for healthiness, and had little effect on milk organoleptic characteristics.

Remission of histiocytic ulcerative colitis in Boxer dogs correlates with eradication of invasive intramucosal Escherichia coli.

BACKGROUND: Historically, histiocytic ulcerative (HUC) (or granulomatous) colitis of Boxer dogs was considered an idiopathic immune-mediated disease with a poor prognosis. Recent reports of dramatic responses to enrofloxacin and the discovery of invasive Escherichia coli within the colonic mucosa of affected Boxer dogs support an infectious etiology. HYPOTHESIS: Invasive E. coli is associated with colonic inflammation in Boxer dogs with HUC, and eradication of intramucosal E. coli correlates with clinical and histologic remission. ANIMALS: Seven Boxer dogs with HUC. METHODS: Prospective case series. Colonic biopsies were obtained at initial evaluation in 7 dogs, and in 5 dogs after treatment with enrofloxacin. Biopsies were evaluated by standardized histopathology, and fluorescence in situ hybridization (FISH) with probes to eubacteria and E. coli. RESULTS: Intramucosal E. coli was present in colonic biopsies of 7/7 Boxers with HUC. Clinical response was noted in all dogs within 2 weeks of enrofloxacin (7 + or - 3.06 mg/kg q24 h, for 9.5 + or - 3.98 weeks) and was sustained in 6 dogs (median disease-free interval to date of 47 months, range 17-62). FISH was negative for E. coli in 4/5 dogs after enrofloxacin. E. coli resistant to enrofloxacin were present in the FISH-positive dog that relapsed. CONCLUSIONS AND CLINICAL RELEVANCE: The correlation between clinical remission and the eradication of mucosally invasive E. coli during treatment with enrofloxacin supports the causal involvement of E. coli in the development of HUC in susceptible Boxer dogs. A poor response to enrofloxacin treatment might be due to colonization with enrofloxacin-resistant E. coli.

Hypokalaemic paresis, hypertension, alkalosis and adrenal-dependent hyperadrenocorticism in a dog.

Generalised paresis, severe hypokalaemia and kaliuresis, metabolic alkalosis and hypertension, characteristic of mineralocorticoid excess, were identified in a dog with hyperadrenocorticism due to a functional adrenocortical carcinoma. Aldosterone concentration was decreased and deoxycorticosterone concentration increased in the presence of hypokalaemia. These metabolic abnormalities resolved with resection of the carcinoma. Mineralocorticoid excess in dogs with hyperadrenocorticism is generally considered to be of little clinical significance but resulted in the acute presentation of this patient. The possible pathogenesis of mineralocorticoid excess in this case of canine hyperadrenocorticism is discussed.

Retroviral integrases and their cousins.

The recently determined structures of the catalytic domains of HIV integrase, avian sarcoma virus integrase and the Mu transposase are strikingly similar to each other and also exhibit significant similarity to several nucleases. All these enzymes of cut polynucleotides, leaving 3'OH and 5'PO4 groups. The integrase and transposase also possess a strand-transfer activity that splices DNA. The structural similarities among members of this superfamily of polynucleotidyl transferases suggest that they share a similar mechanism of catalysis.

Epithelial cyst of the cardiac papillary muscle: case report and review of the literature.

BACKGROUND: Reports of endodermal heterotopia (previously known as inclusion cysts) in cardiac atria are rare and there is only a single previous case report of endodermal heterotopia in a cardiac papillary muscle. AIM AND METHODS: A cyst in a cardiac papillary muscle was identified during the autopsy of an 87-year-old man who had died from an unrelated myocardial infarction. The cyst was examined histologically and mucin staining and immunostaining were carried out. RESULTS: We report a unilocular cyst in a cardiac papillary muscle, which is lined by low cuboidal, pseudostratified and occasionally ciliated respiratory-type epithelium, surrounded by a layer of smooth muscle. The immunohistochemical features (MNF116+, cytokeratin (CK)7+, CK8+, CK18+, CK19+, epithelial membrane antigen positive, scattered cells positive for neuroendocrine markers) suggest that this is an endodermal heterotopia. Immunostaining of positive thyroid transcription factor-1 provides evidence for bronchogenic differentiation. DISCUSSION: The differential diagnoses of cystic structures in cardiac papillary muscle and the origin and importance of endodermal heterotopias are discussed.

Crystal structure of the NAD complex of human deoxyhypusine synthase: an enzyme with a ball-and-chain mechanism for blocking the active site.

BACKGROUND: Eukaryotic initiation factor 5A (elF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalysed by the enzyme deoxyhypusine synthase (DHS). The modified version of elF-5A, and DHS, are required for eukaryotic cell proliferation. Knowledge of the three-dimensional structure of this key enzyme should permit the design of specific inhibitors that may be useful as anti-proliferative agents. RESULTS: The crystal structure of human DHS with bound NAD cofactor has been determined and refined at 2.2 A resolution. The enzyme is a tetramer of four identical subunits arranged with 222 symmetry; each subunit contains a nucleotide-binding (or Rossmann) fold. The tetramer comprises two tightly associated dimers and contains four active sites, two in each dimer interface. The catalytic portion of each active site is located in one subunit while the NAD-binding site is located in the other. The entrance to the active-site cavity is blocked by a two-turn alpha helix, part of a third subunit, to which it is joined by an extended loop. CONCLUSIONS: The active site of DHS is a cavity buried below the surface of the enzyme at the interface between two subunits. In the conformation observed here, the substrate-binding site is inaccessible and we propose that the reaction steps carried out by the enzyme must be accompanied by significant conformational changes, the least of which would be the displacement of the two-turn alpha helix.

The first step in sugar transport: crystal structure of the amino terminal domain of enzyme I of the E. coli PEP: sugar phosphotransferase system and a model of the phosphotransfer complex with HPr.

BACKGROUND: The bacterial phosphoenolpyruvate (PEP): sugar phosphotransferase system (PTS) transports exogenous hexose sugars through the membrane and tightly couples transport with phosphoryl transfer from PEP to the sugar via several phosphoprotein intermediates. The phosphate group is first transferred to enzyme I, second to the histidine-containing phosphocarrier protein HPr, and then to one of a number of sugar-specific enzymes II. The structures of several HPrs and enzymes IIA are known. Here we report the structure of the N-terminal half of enzyme I from Escherichia coli (EIN). RESULTS: The crystal structure of EIN (MW approximately 30 kDa) has been determined and refined at 2.5 A resolution. It has two distinct structural subdomains; one contains four alpha helices arranged as two hairpins in a claw-like conformation. The other consists of a beta sandwich containing a three-stranded antiparallel beta sheet and a four-stranded parallel beta sheet, together with three short alpha helices. Plausible models of complexes between EIN and HPr can be made without assuming major structural changes in either protein. CONCLUSIONS: The alpha/beta subdomain of EIN is topologically similar to the phosphohistidine domain of the enzyme pyruvate phosphate dikinase, which is phosphorylated by PEP on a histidyl residue but does not interact with HPr. It is therefore likely that features of this subdomain are important in the autophosphorylation of enzyme I. The helical subdomain of EIN is not found in pyruvate phosphate dikinase; this subdomain is therefore more likely to be involved in phosphoryl transfer to HPr.

Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 A.

The crystal structure of the Fab of McPC603, a phosphocholine-binding mouse myeloma protein, has been refined at 2.7 A resolution by a combination of restrained least-squares refinement and molecular modeling. The overall structure remains as previously reported, with an elbow bend angle between the variable and constant modules of 133 degrees. Some adjustments have been made in the structure of the loops as a result of the refinement. The hypervariable loops are all visible in the electron density map with the exception of three residues in the first hypervariable loop of the light chain. A sulfate ion occupies the site of binding of the phosphate moiety of phosphocholine.

Isolation of chloroform-resistant mutants of filamentous phage: localization in models of phage structure.

Interaction of fd or M13 filamentous phage with a chloroform/water interface induces morphological change, contracting the filaments sequentially into shortened rods (I-forms), and then into spheroidal particles (S-forms). To further investigate this phage contraction, 34 and 26 chloroform-resistant isolates of fd and M13, respectively, were selected after chloroform treatment of wild-type phages at pH 8. 2 and 4 degrees C. DNA sequencing of gene VIII of the 34 fd isolates revealed five different mutants: these were D5H, M28L, V31L, I37T, and S50T. All 26 M13 isolates were I37T. These mutants exhibited variable sensitivity to chloroform, but all contracted much more slowly than wild-type phage during treatment at 4 degrees C. They all contracted like wild-type phage at 37 degrees C. Site-directed mutagenesis showed that the indicated single mutations carried the chloroform resistance. In structural models of the phage, the D5H locus is on the outside and the S50T locus is on the inside. The M28L and I37T loci are buried in a mostly hydrophobic region in the middle. Although these four mutants are spread out radially, they are localized in the axial direction into a thin disk in the model. The last mutant locus, V31L, is out of this disk, but this locus is proximal to the M28L and I37T loci and also in contact with the surface via a deep hydrophobic hole or depression. These five mutants, their locations, and their variable affects on contraction suggest that chloroform-induced contraction involves a specific mechanism rather than a generalized solvent-induced denaturation and that the critical structural changes occur in a localized level in the phage. These results add weight to suggestions that the sequential contraction of filaments-->I-forms-->S-forms mimic corresponding steps in phage penetration, and, in the reverse order, for phage assembly.