Apolipoprotein A-V is a potential target for treating coronary artery disease: evidence from genetic and metabolomic analyses

Triglyceride (TG)-lowering LPL variants in combination with genetic LDL-C-lowering variants are associated with reduced risk of coronary artery disease (CAD). Genetic variation in the APOA5 gene encoding apolipoprotein A-V also strongly affects TG levels, but the potential clinical impact and underlying mechanisms are yet to be resolved. Here, we aimed to study the effects of APOA5 genetic variation on CAD risk and plasma lipoproteins through factorial genetic association analyses. Using data from 309,780 European-ancestry participants from the UK Biobank, we evaluated the effects of lower TG levels as a result of genetic variation in APOA5 and/or LPL on CAD risk with or without a background of reduced LDL-C. Next, we compared lower TG levels via APOA5 and LPL variation with over 100 lipoprotein measurements in a combined sample from the Netherlands Epidemiology of Obesity study (N = 4,838) and the Oxford Biobank (N = 6,999). We found that lower TG levels due to combined APOA5 and LPL variation and genetically-influenced lower LDL-C levels afforded the largest reduction in CAD risk (odds ratio: 0.78 (0.73–0.82)). Compared to patients with genetically-influenced lower TG via LPL, genetically-influenced lower TG via APOA5 had similar and independent, but notably larger, effects on the lipoprotein profile. Our results suggest that lower TG levels as a result of APOA5 variation have strong beneficial effects on CAD risk and the lipoprotein profile, which suggest apo A-V may be a potential novel therapeutic target for CAD prevention.     

Leaching losses of nitrogen from a clay soil under grass and cereal crops in Finland

Summary A 16-plot experimental field was established in 1975 on a clay soil in Jokioinen, Finland. The water discharge through tile drains was measured and its ammonium and nitrate N contents determined for each plot separately. The surface runoff was also measured and analysed. The annual runoff and the N leached from the surface of moderately fertilized (100 kg/ha/y N) cereal plots varied during 1976–1982 from 21 to 301 mm and from 2 to 7 kg/ha, respectively. The discharge of water and leaching of N through subdrains varied from 65 to 225 mm and from 1 to 38 kg/ha, respectively. The highest leaching was probably caused by a previous fallow. The annual N uptake by the crop varied between 41 and 122 kg/ha.Of the fertilizer-N used for cereals, 20% of that applied in the autumn was lost, but only 1 to 4 per cent was lost when applied in the spring. There was much less N leaching from ley than from barley plots, although the former was given twice as much N. The rate of N fertilization had only a very slight effect on N leaching from both ley and barley plots.The results were compared with those obtained in lysimeters filled with clay, silt, sand and peat soils. No definite conclusions can be drawn because the lysimeter experimental data are only for the first year.     

Molecular Modelling of The Mechanism of Action of Organic Clay-Swelling Inhibitors

Abstract

It is well known that the sodium smectite class of clays swells macroscopically in contact with water, whereas under normal conditions the potassium form does not. In recent work using molecular simulation methods, we have provided a quantitative explanation both for the swelling behaviour of sodium smectite clays and the lack of swelling of potassium smectites [1]. In the present paper, we apply similar modelling methods to study the mechanism of inhibition of clay-swelling by a range of organic molecules.

Experimentally, it is known that polyalkylene glycols (polyethers) of intermediate to high relative molecular mass are effective inhibitors of smectite clay swelling. We use a range of atomistic simulation techniques, including Monte Carlo and molecular dynamics, to investigate the interactions between a selection of these compounds, water, and a model smectite clay mineral. These interactions occur by means of organised intercalation of water and organic molecules within the galleries between individual clay layers.

The atomic interaction potentials deployed in this work are not as highly optimised as those used in our clay-cation-water work [1]. Nevertheless, our simulations yield trends and results that are in qualitative and sometimes semi-quantitative agreement with experimental findings on similiar (but not identical) systems. The internal energy of adsorption of simple polyethers per unit mass on the model clay is not significantly different from that for water adsorption; our Monte Carlo studies indicate that entropy is the driving force for the sorption of the simpler organic molecules inside the clay layers: a single long chain polyethylene glycol can displace a large number of water molecules, each of whose translational entropy is greatly enhanced when outside the clay. Hydrophobically modified polyalkylene glycols also enjoy significant van der Waals interactions within the layers which they form within the clay galleries.

In conjunction with experimental studies, our work furnishes valuable insights into the relative effectiveness of the compounds considered and reveals the generic features that high performance clay-swelling inhibitors should possess. For optimal inhibitory activity, these compounds should be reasonably long chain linear organic molecules with localised hydrophobic and hydrophilic regions along the chain. On intercalation of these molecules within the clay layers, the hydrophobic regions provide an effective seal against ingress of water, while the hydrophilic ones enhance the binding of the sodium cations to the clay surface, preventing their hydration and the ensuing clay swelling.     

Inhibition of co-operative enzymes by substrate-analogues: Possible implications for the physiological significance of negative co-operativity illustrated by phenylalanine metabolism in higher plants

The “Hill” equation for co-operative binding-systems has been extended to describe the effect of substrate-analogue on the binding of substrate to an oligomeric protein. It is demonstrated that the more negatively co-operative the binding-system, the more sensitive is the binding of substrate to inhibition by increases in the relative concentration of substrate-analogue. It is proposed that the physiological significance of negative co-operativity for enzymes may be complementary to the physiological significance of positive co-operativity. The effect of negative co-operativity is to make substrate binding more sensitive to inhibition by relative increases in the concentration of substrate-analogue (e.g. for many enzymes product of the reaction) at the expense of decreased sensitivity of substrate binding to relative changes in substrate concentration compared to a system with equivalent, independent substrate binding sites. In contrast, the effect of positive co-operativity is to make the enzyme more sensitive to relative changes in substrate concentration at the expense of decreased sensitivity to inhibition by relative increases in product concentration, compared to an enzyme without co-operative binding.     

Removal of Prymnesium parvum (Haptophyceae) and its toxins using clay minerals

Laboratory experiments were conducted to examine the ability of several clay minerals from Sweden to remove the fish-killing microalga, Prymnesium parvum Carter, from suspension. In their commercial form (i.e. after incineration at 400 °C), seawater slurries (salinity = 26) of the three minerals tested were generally ineffective at removing P. parvum from culture within a range of 0.01 to 0.50 g/L, and after 2.5 h of flocculation and settling. Dry bentonite (SWE1) displayed the highest removal efficiency (RE) at 17.5%, with 0.50 g/L. Illite (SWE3) averaged only 7.5% RE between 0.10 to 0.50 g/L, while kaolinite (SWE2) kept the cells suspended instead of removing them. Brief mixing of the clay-cell suspension after SWE1 addition improved RE by a factor of 2.5 (i.e. 49% at 0.50 g/L), relative to no mixing. The addition of polyaluminum chloride (PAC, at 5 ppm) to 0.50 g/L SWE1 also improved RE to 50% relative to SWE1 alone, but only minor improvements in RE were seen with SWE2 and SWE2 combined with PAC. In further experiments, P. parvum grown in NP-replete conditions were removed in greater numbers than cells in N- or P-limited cultures, at 0.10–0.25 g/L of SWE1 and 5 ppm PAC. With 0.50 g/L, RE converged at 40% for all three culture conditions. The toxin concentration of NP-replete cultures decreased from 24.2 to 9.2 μg/mL (60% toxin RE) with 0.10–0.50 g/L SWE1 treatment and 5 ppm PAC. A strong correlation was found between cell and toxin RE (r²=0.995). For N-limited cultures, toxin RE ranged between 21 and 87% with the same clay/PAC concentrations, although the correlation between cell and toxin removal was more moderate (r²=0.746) than for NP-replete conditions. Interestingly, the toxin concentration within the clay-cell pellet increased dramatically after treatment, suggesting that clay addition may stimulate toxin production in N-stressed cells. For P-limited cultures, toxin concentration also decreased following clay/PAC treatment (i.e. 36% toxin RE), but toxin removal was poorly correlated to cell removal (r²=0.462). To determine whether incineration affected SWE1’s removal ability, a sample of its wet, unprocessed form was tested. The RE of wet bentonite (SWE4) was slightly better than that of SWE1 (31% versus 17%, respectively, at 0.50 g/L), but when 5 ppm PAC was added, RE increased from 10 to 64% with 0.05 g/L of SWE4, and increased further to 77% with 0.50 g/L. There were no significant differences in RE among NP-replete, N-limited and P-limited cultures using PAC-treated SWE4. Finally, RE varied with P. parvum concentration, reaching a maximum level at the lowest cell concentration (1×10³ cells/mL): 100% RE with 0.10 and 0.50 g/L SWE4 + 5 ppm PAC. RE dropped as cell concentration increased to 1×10⁴ and 5×10⁴ cells/mL, but rose again when concentration increased to 1×10⁵ cells/mL, the concentration used routinely for the removal experiments above. Based on these results, SWE4 with PAC was the most effective mineral sample against P. parvum. Overall, these studies demonstrated that clay flocculation can be effective at removing P. parvum and its toxins only under certain treatment conditions with respect to cell concentration, clay type and concentration, and physiological status.     

An unusual megaspore of uncertain systematic affinity from Lower Cretaceous deposits in south-east England and its biostratigraphic and palaeoenvironmental significance

An unusual megaspore has been recorded from beds within the Weald Clay Group of south-east England. Described as Clockhousea capelensis gen. et sp. nov., it is characterised by having a thick outer layer of exine consisting of closely packed columnar to clavate elements with constricted bases attached to a perforated inner layer and a sculpture that ranges from having the appearance of a negative reticulum through closely spaced verrucae to a mixture of verrucate and essentially baculate elements, all of which are surface manifestations and extensions of the underlying structure. These characters do not readily indicate a systematic relationship with any known heterosporous plant genus or family. The localised occurrence and relative abundance of the spores in a few beds suggest that some of the parent plants grew close to water bodies where they were deposited and preserved. Their recovery from sediments of late Hauterivian–early Barremian age indicates that the species has potential as a biostratigraphic marker in the upper Wealden succession of southern England and perhaps elsewhere.     

Rare, threatened and alien species in the gastropod communities in the clay pit ponds in relation to the environmental factors (The Ciechanowska Upland, Central Poland)

The objectives of the present survey were to formulate a zoocenological analysis of the gastropod communities in clay pit ponds, as well as to determine the relationships between the gastropods and their environments, and to evaluate the water habitats in terms of their ecological-conservation value. The physical and chemical parameters of water, gastropod species and macrophytes occurring in the ponds indicate mesotrophic conditions. Principal Component Analysis (PCA) reveals a correlation between gastropod density and nitrates, a correlation between gastropod density and alkalinity, and additionally shows a correlation between gastropod density and chlorides. The pond surface area, nitrates, chlorides concentrate, alkalinity, and substratum have all affected these gastropod communities. The occurrence of the first permanent population of Ferrissia clessiniana (Jickeli, 1882) was recorded in Poland. Valvata naticina Menke 1845 has become a critically rare species (CR) due to the pollution of water environments. Five other species, e.g. Anisus vorticulus (Troschel, 1834) and Planorbis carinatus O.F. Müller, 1774 are recorded on the Polish Red List of Species. The clay pit ponds of the Ciechanowska Upland, because of their distinctive environmental features, provide a refuge where a number of rare, threatened and alien gastropod species live.     

Steneosaurus edwardsi (Thalattosuchia: Teleosauridae), the largest known crocodylomorph of the Middle Jurassic

Teleosaurids were a clade of marine crocodylomorphs that were globally distributed during the Jurassic Period. They evolved a wide range of body sizes, from small (～2–3 m) to very large (> 9 m). Until now, the largest known Middle Jurassic teleosaurid was ‘Steneosaurus’ obtusidens, from the Oxford Clay Formation of the UK. Here, we re‐examine a very large Oxford Clay specimen (ilium, ischium, and femur) that had been tentatively attributed to ‘S.’ obtusidens. Based on comparative anatomical study with the ‘S.’ obtusidens holotype and referred specimens of Steneosaurus edwardsi and Steneosaurus leedsi, we conclude that this very large individual actually pertains to S. edwardsi. Based on comparisons with the Machimosaurus mosae neotype (which has a complete femur and skeleton), we estimate a total length in excess of 7 m for this large S. edwardsi individual, making it the largest known Middle Jurassic teleosaurid. Therefore, along with the closely related genus Machimosaurus, this clade of large‐bodied Middle–Late Jurassic teleosaurids were the largest species during the first 100 million years of crocodylomorph evolution. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, ●● , ●●–●●.     

Metal ion-biomolecule interactions. II. Methylmercuration of the deprotonated amino groups in adenine,guanine, and cytosine derivatives,and its relationship to amino group acidity

Proton nmr spectroscopic evidence is presented for methylmercury(II) binding to the deprotonated amino groups in adenosine, 9-methyladenine, guanosine, 1-methylguanosine, and cytidine under basic conditions. Except for the guanosine case, ¹H nmr spectra of the products from aqueous or ethanolic 1:1 mixtures of substrate and MeHgOH are consistent with methylmercuration of the deprotonated amino groups. Guanosine undergoes initial binding of MeHg to N₁, and a second equivalent of MeHgOH is necessary to effect amino binding. The nmr spectra of the complexed adenine derivatives suggest that different geometrical isomers exist in (CD₃)₂SO solution, reflecting the partial double bond character of the C₆N bond in these systems. Using a correlation relating the magnitude of the ¹⁹⁹Hg-¹H coupling constant (J) for MeHg-ligand complexes with the ligand pK_a (J = ?3.88 pK_a + 248.5, extending over 13 pK units, based on a variety of N and O donor ligands), estimates (± 0.3 pK unit) of the pK_as of the amino groups of the above substrates have been made. In this way, pK_a values of 15.5 (cytidine), 17.0 (adenosine and 9-methyladenine), 15.1 (guanosine), and 14.9 (1-methylguanosine) are obtained. In the cases where comparisons with literature pK_a data can be made, good agreement is found.     

Genome assembly using Nanopore-guided long and error-free DNA reads

Background

Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing. However, existing long-read technologies still have several limitations that complicate their use for most research laboratories, as well as in large and/or complex genome projects. In 2014, Oxford Nanopore released the MinION® device, a small and low-cost single-molecule nanopore sequencer, which offers the possibility of sequencing long DNA fragments.

Results

The assembly of long reads generated using the Oxford Nanopore MinION® instrument is challenging as existing assemblers were not implemented to deal with long reads exhibiting close to 30% of errors. Here, we presented a hybrid approach developed to take advantage of data generated using MinION® device. We sequenced a well-known bacterium, Acinetobacter baylyi ADP1 and applied our method to obtain a highly contiguous (one single contig) and accurate genome assembly even in repetitive regions, in contrast to an Illumina-only assembly. Our hybrid strategy was able to generate NaS (Nanopore Synthetic-long) reads up to 60 kb that aligned entirely and with no error to the reference genome and that spanned highly conserved repetitive regions. The average accuracy of NaS reads reached 99.99% without losing the initial size of the input MinION® reads.

Conclusions

We described NaS tool, a hybrid approach allowing the sequencing of microbial genomes using the MinION® device. Our method, based ideally on 20x and 50x of NaS and Illumina reads respectively, provides an efficient and cost-effective way of sequencing microbial or small eukaryotic genomes in a very short time even in small facilities. Moreover, we demonstrated that although the Oxford Nanopore technology is a relatively new sequencing technology, currently with a high error rate, it is already useful in the generation of high-quality genome assemblies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1519-z) contains supplementary material, which is available to authorized users.