Studies of pseudoachondroplasia chondrocytes and knockdown of the cartilage oligomeric matrix protein

Cartilage oligomeric matrix protein (COMP) is a large, homopentameric, extracellular matrix glycoprotein. Mutations in COMP cause two skeletal dysplasias: pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (EMD1). These dwarfing conditions are caused by retention of misfolded mutant COMP with type IX collagen and matrilin-3 (MATN3) in the rough endoplasmic reticulum (rER) of the chondrocyte. These proteins form a matrix in the rER that continues to expand until it fills the entire cell, eventually causing cell death. Interestingly, loss of COMP in COMP null mice does not affect normal bone development or growth, suggesting that elimination of COMP (wildtype and mutant) expression may prevent PSACH. The hypothesis of these studies was that a hammerhead ribozyme could eliminate or knockdown COMP mRNA expression in PSACH chondrocytes . To test this hypothesis, a human chondrocyte model system that recapitulates the PSACH chondrocyte phenotype was developed by over-expressing mutant (mt-) COMP in normal chondrocytes using a recombinant adenovirus. Chondrocytes over-expressing mt-COMP developed giant rER cisternae containing COMP, type IX collagen and MATN3. Deconvolution microscopy and computer modeling showed that these proteins formed an ordered matrix surrounding a type II pro-collagen core. Additionally, the results show that a hammerhead ribozyme, ribozyme 56 (Ribo56) reduced over-expressed mt-COMP in COS cells and endogenous COMP in normal chondrocytes and mt-COMP in three PSACH chondrocytes cell line (with different mutations) by 40-70%. Altogether, these studies show that the PSACH cellular phenotype can be created in vitro and that the mt-COMP protein burden can be reduced by the presence of a COMP-specific ribozyme. Future studies will focus on designing ribozymes or short interfering RNA (siRNA) technologies that will result in better knockdown of COMP expression as well as the temporal constraints imposed by the PSACH phenotype. ^

The burden of parainfluenza virus infection in patients with hematological malignancy and hematopoietic stem cell transplant (HSCT) recipients in the absence of active immunization and approved therapy: The role of infection control

Background. Community respiratory viruses, mainly RSV and influenza, are significant causes of morbidity and mortality in patients with leukemia and HSCT recipients. The data on impact of PIV infections in these patients is lacking. Methods. We reviewed the records of patients with leukemia and HSCT recipients who developed PIV infection from Oct'02–Nov'07 to determine the outcome of such infections. Results. We identified 200 patients with PIV infections including 80(40%) patients with leukemia and 120 (60%) recipients of HSCT. Median age was 55 y (17-84 y). As compared to HSCT recipients, patients with leukemia had higher APACHE II score (14 vs. 10, p<0.0001); were more likely to have ANC<500 (48% vs. 10%, p<0.0001) and ALC<200 (45% vs. 23.5%, p=0.02). PIV type III was the commonest isolate (172/200, 86%). Most patients 141/200 (70%) had upper respiratory infection (URI), and 59/200 (30%) had pneumonia at presentation. Patients in leukemia group were more likely to require hospitalization due to PIV infection (77% vs. 36% p=0.0001) and were more likely to progress to pneumonia (61% vs. 39%, p=0.002). Fifty five patients received aerosolized ribavirin and/or IVIG. There were no significant differences in the duration of symptoms, length of hospitalization, progression to pneumonia or mortality between the treated verses untreated group. The clinical outcome was unknown in 13 (6%) patients. Complete resolution of symptoms was noted in 91% (171/187) patients and 9% (16/187) patients died. Mortality rate was 17% (16/95) among patients who had PIV pneumonia, with no significant difference between leukemia and HSCT group (16% vs. 17%). The cause of death was acute respiratory failure and/or multi-organ failure in (13, 81%) patients. Conclusions. Patients with leukemia and HSCT could be at high risk for serious PIV infections including PIV pneumonia. Treatment with aerosolized ribavirin and/or IVIG may not have significant effect on the outcome of PIV infection.^

Mechanism of subunit interaction and DNA binding of the heterotrimeric CCAAT binding factor CBF

Many eukaryotic promoters contain a CCAAT element at a site close ($-$80 to $-$120) to the transcription initiation site. CBF (CCAAT Binding Factor), also called NF-Y and CP1, was initially identified as a transcription factor binding to such sites in the promoters of the Type I collagen, albumin and MHC class II genes. CBF is a heteromeric transcription factor and purification and cloning of two of the subunits, CBF-A and CBF-B revealed that it was evolutionarily conserved with striking sequence identities with the yeast polypeptides HAP3 and HAP2, which are components of a CCAAT binding factor in yeast. Recombinant CBF-A and CBF-B however failed to bind to DNA containing CCAAT sequences. Biochemical experiments led to the identification of a third subunit, CBF-C which co-purified with CBF-A and complemented the DNA binding of recombinant CBF-A and CBF-B. We have recently isolated CBF-C cDNAs and have shown that bacterially expressed purified CBF-C binds to CCAAT containing DNA in the presence of recombinant CBF-A and CBF-B. Our experiments also show that a single molecule each of all the three subunits are present in the protein-DNA complex. Interestingly, CBF-C is also evolutionarily conserved and the conserved domain between CBF-C and its yeast homolog HAP5 is sufficient for CBF-C activity. Using GST-pulldown experiments we have demonstrated the existence of protein-protein interaction between CBF-A and CBF-C in the absence of CBF-B and DNA. CBF-B on other hand, requires both CBF-A and CBF-C to form a ternary complex which then binds to DNA. Mutational studies of CBF-A have revealed different domains of the protein which are involved in CBF-C interaction and CBF-B interaction. In addition, CBF-A harbors a domain which is involved in DNA recognition along with CBF-B. Dominant negative analogs of CBF-A have also substantiated our initial observation of assembly of CBF subunits. Our studies define a novel DNA binding structure of heterotrimeric CBF, where the three subunits of CBF follow a particular pathway of assembly of subunits that leads to CBF binding to DNA and activating transcription. ^

Plankton abundance and feeding characteristics of Thysanoessa raschii from Godthabsfjord, Greenland

Despite being a key zooplankton group, knowledge on krill biology from the Arctic is inadequate. The present study examine the functional biology and evaluate the trophic role of krill in the Godthabsfjord (64°N, 51°W) SW Greenland, through a combination of fieldwork and laboratory experiments. Krill biomass was highest in the middle fjord and inner fjord, whereas no krill was found offshore. The dominating species Thysanoessa raschii revealed a type III functional response when fed with the diatom Thalassiosira weissflogii. At food saturation, T. raschii exhibited a daily ration of 1% body C/d. Furthermore, T. raschii was capable of exploiting plankton cells from 5 to 400 µm, covering several trophic levels of the pelagic food web. The calculated grazing impact by T. raschii on the fjord plankton community was negligible. However, the schooling and migratory behaviour of krill will concentrate and elevate the grazing in specific areas of the euphotic zone.

Organic geochemistry, visual composition, atomic ratios, and reflectance at DSDP Site 87-582, 87-583 and 87-584

Geochemical analyses of organic matter were carried out on Quaternary sediments from Sites 582 and 583 (Nankai Trough) and on Pliocene to Miocene sediments from Site 584 (Japan Trench), DSDP Leg 87, to evaluate petroleum-generating potential and to characterize the organic matter. The vitrinite-huminite reflectances of indigenous materials for these sites are less than 0.3% indicating the immature nature of the sediments. The sediments, however, contain remarkable amounts of recycled organic materials. The Quaternary sediments from Sites 582 and 583 contain small amounts of amorphous organic matter (less than 0.75 wt.% organic carbon and 66-90% amorphous debris), which is composed of predominantly recycled, oxidized, and over-matured (or matured) Type III material. The amount of hydrocarbon yield indicates that those sediments have lean-source potential for commercial hydrocarbon generation. The Pliocene to Miocene sediments from Site 584 contain organic matter (0.3-1.09 wt.% organic carbon) of predominantly amorphous debris (68-96%) that originated in two sources, an indigenous Type II material and a recycled, over-matured material. Pyrolysis shows an upward increase in the section of hydrocarbon yield and the same trend is also observed in organic-carbon content. The amount of the yield indicates that the Miocene sediments have lean-to-fair source potential and the Pliocene sediments have fair-to-good source potential.

Geochemistry and pyrolysis at DSDP Hole 77-535

There are substantial differences in the character of organic matter contained in the Pleistocene and Cretaceous sedimentary sequences of DSDP Site 535. The argillaceous Pleistocene section contains type III, gas-prone organic matter whereas the calcareous Cretaceous section is dominated by type II, oil-prone organic matter. A more detailed investigation of the Cretaceous section reveals that the finely laminated limestones of Valanginian to Barremian age are of good to excellent source quality. The indigenous organic matter contained within this organically rich section is thermally immature, not having undergone sufficient thermal diagenesis for the generation and expulsion of hydrocarbons. Within this stratigraphic section, however, staining by mature hydrocarbons was detected. These stains are associated with a fractured interval. These fractures may in turn represent potential migration pathways.

Organic geochemistry of lower Cretaceous sediments at DSDP Hole 77-535

At Site 535, the four lithologic units of Cretaceous age are controlled by two types of sedimentologic facies: (1) the massive light-colored limestones or marly limestones in which the total organic carbon (TOC) content is low and the organic matter more or less oxidized and (2) laminated dark facies in which the TOC content is higher and associated with a well-preserved organic matter of Type II origin. Very little typical Type III organic matter occurs in the whole series from late Berriasian to Aptian and Cenomanian. Fluctuations from oxidizing to reducing environments of deposition are proposed to account for the variations in properties of the Type II organic matter between the different facies. Dark laminated layers are good but immature potential source rocks: petroleum potential is often higher than 2 kg HC/t of rock.

Geochemistry of volcanic rocks of ODP Holes 126-792E and 126-793B

The Izu-Bonin forearc basement volcanic rocks recovered from Holes 792E and 793B show the same phenocrystic assemblage (i.e., plagioclase, two pyroxenes, and Fe-Ti oxides ±olivine), but they differ in the crystallization sequence and their phenocryst chemistry. All the igneous rocks have suffered low-grade hydrothermal alteration caused by interaction with seawater. As a result, only clinopyroxenes, plagioclases, and oxides have preserved their primary igneous compositions. The Neogene olivine-clinopyroxene diabasic intrusion (Unit II) recovered from Hole 793B differs from the basement basaltic andesites because it lacks Cr-spinels and contains abundant titanomagnetites (Usp38.5-46.4) and uncommon FeO-rich (FeO = 29%) spinels. It displays petrological and geochemical similarities to the Izu Arc volcanoes and, thus, can be considered as related to Izu-Bonin Arc magmatic activity. The titanomagnetites (Usp28.5-33) in the calc-alkaline andesitic fragments of the Oligocene volcaniclastic breccia in Hole 793B (Unit VI) represent an early crystallization phase. The Plagioclase phenocrysts enclosed in these rocks show oscillatory zoning and are less Ca-rich (An78.6-67.8) than the plagioclase phenocrysts of the diabase sill and the basement basaltic andesites. Their clinopyroxenes are Fe-rich augites (Fs ? 19.4; FeO = 12%) and thus, differ significantly from the clinopyroxenes of the Hole 793B arc-tholeiitic igneous rocks. The 30-32 Ma porphyritic, two-pyroxene andesites recovered from Hole 792E are very similar to the andesitic clasts of the Neogene breccia recovered in Hole 793B (Unit VI). Both rocks have the same crystallization sequence, and similar chemistry of the Fe-Ti oxides, clinopyroxenes, and plagioclases: that is, Ti-rich (Usp25.5-30.4) magnetites, Fe-rich augites, and intensely oscillatory zoned plagioclases with bytownitic cores (An86-63) and labradorite rims (An73-68). They display a calc-alkaline differentiation trend (Taylor et al., this volume). So, the basement highly porphyritic andesites recovered at Hole 792E, and the Hole 793B andesitic clasts of Unit VI show the same petrological and geochemical characteristics, which are that of calc-alkaline suites. These Oligocene volcanic rocks represent likely the remnants of the Izu-Bonin normal arc magmatic activity, before the forearc rifting and extension. The crystallization sequence in the basaltic andesites recovered from Hole 793B is olivine-orthopyroxene-clinopyroxene-plagioclase-Fe-Ti oxides, indicating a tholeiitic differentiation trend for these volcanic rocks. Type i is an olivine-and Cr-spinel bearing basaltic andesite whereas Type ii is a porphyritic pyroxene-rich basaltic andesite. The porphyritic plagioclase-rich basaltic andesite (Type iii) is similar, in most respects, to Type ii lavas but contains plagioclase phenocrysts. The last, and least common lava is an aphyric to sparsely phyric andesite (Type iv). Cr-spinels, included either in the olivine pseudomorphs of Type i lavas or in the groundmass of Type ii lavas, are Cr-rich and Mg-rich. In contrast, Cr-spinels included in clinopyroxenes and orthopyroxenes (Types i and ii lavas) show lower Cr* and Mg* ratios and higher aluminium contents. Orthopyroxenes from all rock types are Mg-rich enstatites. Clinopyroxenes display endiopsidic to augitic compositions and are TiO2 and Al2O3 depleted. All the crystals exhibit strong zoning patterns, usually normal, although, reverse zoning patterns are not uncommon. The plagioclases show compositions within the range of An90-64. The Fe-Ti oxides of the groundmass are TiO2-poor (Usp16-17). The Hole 793B basaltic andesites show, like the Site 458 bronzites from the Mariana forearc, intermediate features between arc tholeiites and boninites: (1) Cr-spinel in olivine, (2) presence of Mg-rich bronzite, Ca-Mg-rich clinopyroxenes, and Ca-plagioclase phenocrysts, and (3) transitional trace element depletion and epsioln-Nd ratios between arc tholeiites and boninites. Thus, the forearc magmatism of the Izu-Bonin and Mariana arcs, linked to rifting and extension, is represented by a depleted tholeiitic suite that displays boninitic affinities.

Extractable hydrocarbon and carbon isotope geochemistry of Lower Cretaceous sediments of the Exmouth Plateau

The organic geochemical character of rocks selected from Aptian, Valanginian, and Berriasian clay stone and siltstone sequences encountered in Ocean Drilling Program (ODP) Holes 762C and 763C on the Exmouth Plateau was determined by means of a variety of analytical procedures. These sequences represent distal portions of the Mesozoic Barrow delta, in which petroleum source rocks and reservoirs exist on the Australian continent. The organic matter at the ODP sites is thermally immature type III material. Biomarker hydrocarbon compositions are dominated by long-chain, waxy n-alkanes and by C29 steranes, which reflect the land-plant origin of organic matter. Organic carbon d13C values ranged from -26 per mil to -28 per mil, consistent with a C3 land-plant source. Kerogen pyrolysate compositions and hopane isomerization ratios revealed progressively larger contributions of recycled organic matter as the depth of the deltaic sedimentary layers became greater.

Facies and diagenesis of organic matter in sediments at DSDP Leg 87

A series of upper Pliocene to Pleistocene sediment samples from DSDP Sites 582 and 583 (Nankai Trough, active margin off Japan) were investigated by organic geochemical methods including organic carbon determination, Rock- Eval pyrolysis, gas chromatography of extractable hydrocarbons, and kerogen microscopy. The organic carbon content is fairly uniform and moderately low (0.35 to 0.77%) at both sites, although accompanied by high sedimentation rates. The low organic matter concentrations are the result of the combined effect of several factors: low bioproductivity, oxic depositional environment, and dilution with lithogenic material. Organic petrography revealed a mixture of three maceral types: (1) fresh, green fluorescent alginites of aquatic origin probably transported by turbidites from the shelf edge, (2) gelified huminites and paniculate liptinites derived from the erosion of unconsolidated peat, and (3) highly reflecting inertinites derived from continental erosion. By a combination of organic petrography and Rock-Eval pyrolysis results, the organic matter is characterized as mainly type III kerogen with a slight tendency to a mixed type II-III. During Rock-Eval pyrolysis, a mineral matrix effect on the generated hydrocarbons was observed. The organic matter in all sediments has a low level of maturity (below 0.45% Rm) and has not yet reached the onset of thermal hydrocarbon generation according to several geochemical maturation parameters. This low maturity is in contrast to anomalously high extract yields at both sites and large hydrocarbon proportions in the extracts at Site 583. This contrast may be due to early generation of polar compounds and perhaps redistribution of hydrocarbons caused by subduction tectonics. Carbon isotope data of the interstitial hydrocarbon gases indicate their origin from bacterial degradation of organic matter, although only very few bacterially degraded maceral components were detected.

Geochemical characterizations of the Cretaceous formations at DSDP Holes 93-603B and 11-105

Geochemical characterizations of the Cretaceous formations at Site 603 are quite comparable with those at Site 105. In the Blake-Bahama and the Hatteras formations, the petroleum potential is medium (<5 kg HC/t of rock) to very low (<0.5 kg HC/t of rock), and the organic matter is mainly of type III origin, that is, terrestrial. At the top of the Hatteras Formation, there is a condensed series, which chiefly contains organic matter of type II origin, with up to 20 wt.% total organic carbon content in Core 603B-34 and 25 wt.% in Core 105-9. This accumulation corresponds to the Cenomanian/Turonian boundary event. An examination of dinoflagellates in the kerogen concentration assigns dates to the samples studied by organic geochemistry. The Cenomanian and Turonian age of the organic-matter-rich black claystones indicates a low rate of sedimentation, about 1 m/Ma. Furthermore, the occurrence of type II organic matter indicates an anoxic environment with insufficient oxygen renewal to oxidize the sinking hemipelagic organic matter. This organic enrichment is not related to local phenomena but to sedimentation over an extended area, because deposits are well known in various areas with different paleodepths in the North Atlantic.

Geochemistry and kinetic models od Cretaceous samples

The source rock potential of Cretaceous organic rich whole rock samples from deep sea drilling project (DSDP) wells offshore southwestern Africa was investigated using bulk and quantitative pyrolysis techniques. The sample material was taken from organic rich intervals of Aptian, Albian and Turonian aged core samples from DSDP site 364 offshore Angola, DSDP well 530A north of the Walvis Ridge offshore Namibia, and DSDP well 361 offshore South Africa. The analytical program included TOC, Rock-Eval, pyrolysis GC, bulk kinetics and micro-scale sealed vessel pyrolysis (MSSV) experiments. The results were used to determine differences in the source rock petroleum type organofacies, petroleum composition, gas/oil ratio (GOR) and pressure-volume-temperature (PVT) behavior of hydrocarbons generated from these black shales for petroleum system modeling purposes. The investigated Aptian and Albian organic rich shales proved to contain excellent quality marine kerogens. The highest source rock potential was identified in sapropelic shales in DSDP well 364, containing very homogeneous Type II and organic sulfur rich Type IIS kerogen. They generate P-N-A low wax oils and low GOR sulfur rich oils, whereas Type III kerogen rich silty sandstones of DSDP well 361 show a potential for gas/condensate generation. Bulk kinetic experiments on these samples indicate that the organic sulfur contents influence kerogen transformation rates, Type IIS kerogen being the least stable. South of the Walvis Ridge, the Turonian contains predominantly a Type III kerogen. North of the Walvis Ridge, the Turonian black shales contain Type II kerogen and have the potential to generate P-N-A low and high wax oils, the latter with a high GOR at high maturity. Our results provide the first compositional kinetic description of Cretaceous organic rich black shales, and demonstrate the excellent source rock potential, especially of the Aptian-aged source rock, that has been recognized in a number of the South Atlantic offshore basins.

Seawater carbonate chemistry and pteropod Limacina helicina antarctica shell dissolution during experiments, 2012

Anthropogenic ocean acidification is likely to have negative effects on marine calcifying organisms, such as shelled pteropods, by promoting dissolution of aragonite shells. Study of shell dissolution requires an accurate and sensitive method for assessing shell damage. Shell dissolution was induced through incubations in CO2 enriched seawater for between 4 and 14 days. We describe a procedure that allows the level of dissolution to be assessed and classified into three main types: Type I with partial dissolution of the prismatic layer; Type II with exposure of underlying crossed-lamellar layer, and Type III, where crossed-lamellar layer shows signs of dissolution. Levels of dissolution showed a good correspondence to the incubation conditions, with the most severe damage found in specimens held for 14 d in undersaturated condition (Ohm ~ 0.8). This methodology enables the response of small pelagic calcifiers to acidified conditions to be detected at an early stage, thus making pteropods a valuable bioindicator of future ocean acidification.

A bacterial cysteine protease effector protein interferes with photosynthesis to suppress plant innate immune responses

The bacterial pathogen Pseudomonas syringae pv tomato DC3000 suppresses plant innate immunity with effector proteins injected by a type III secretion system (T3SS). The cysteine protease effector HopN1, which reduces the ability of DC3000 to elicit programmed cell death in non-host tobacco, was found to also suppress the production of defence-associated reactive oxygen species (ROS) and callose when delivered by Pseudomonas fluorescens heterologously expressing a P. syringae T3SS. Purified His 6 -tagged HopN1 was used to identify tomato PsbQ, a member of the oxygen evolving complex of photosystem II (PSII), as an interacting protein. HopN1 localized to chloroplasts and both degraded PsbQ and inhibited PSII activity in chloroplast preparations, whereas a HopN1 D299A non-catalytic mutant lost these abilities. Gene silencing of NtPsbQ in tobacco compromised ROS production and programmed cell death.

Theory of intermittency applied to classical pathological cases

The classical theory of intermittency developed for return maps assumes uniform density of points reinjected from the chaotic to laminar region. Though it works fine in some model systems, there exist a number of so-called pathological cases characterized by a significant deviation of main characteristics from the values predicted on the basis of the uniform distribution. Recently, we reported on how the reinjection probability density (RPD) can be generalized. Here, we extend this methodology and apply it to different dynamical systems exhibiting anomalous type-II and type-III intermittencies. Estimation of the universal RPD is based on fitting a linear function to experimental data and requires no a priori knowledge on the dynamical model behind. We provide special fitting procedure that enables robust estimation of the RPD from relatively short data sets (dozens of points). Thus, the method is applicable for a wide variety of data sets including numerical simulations and real-life experiments. Estimated RPD enables analytic evaluation of the length of the laminar phase of intermittent behaviors. We show that the method copes well with dynamical systems exhibiting significantly different statistics reported in the literature. We also derive and classify characteristic relations between the mean laminar length and main controlling parameter in perfect agreement with data provided by numerical simulations