COVID-19 and systemic lupus erythematosus genetics: A balance between autoimmune disease risk and protection against infection

Genome wide association studies show there is a genetic component to severe COVID-19. We find evidence that the genome-wide genetic association signal with severe COVID-19 is correlated with that of systemic lupus erythematosus (SLE), having formally tested this using genetic correlation analysis by LD score regression. To identify the shared associated loci and gain insight into the shared genetic effects, using summary level data we performed meta-analyses, a local genetic correlation analysis and fine-mapping using stepwise regression and functional annotation. This identified multiple loci shared between the two traits, some of which exert opposing effects. The locus with most evidence of shared association is TYK2, a gene critical to the type I interferon pathway, where the local genetic correlation is negative. Another shared locus is CLEC1A, where the direction of effects is aligned, that encodes a lectin involved in cell signaling, and the anti-fungal immune response. Our analyses suggest that several loci with reciprocal effects between the two traits have a role in the defense response pathway, adding to the evidence that SLE risk alleles are protective against infection.     

The action of phospholipase C on ethanolamine plasmalogen (2-acyl-1-alkenylglycerylphosphorylethanolamine)

1. The phospholipase C of Bacillus cereus attacks the ethanolamine plasmalogen of brain to yield a plasmalogenic diglyceride (2-acyl-1-alkenylglycerol). 2. This plasmalogenic diglyceride is analogous to the material obtained by the action of the phospholipase C of Clostridium welchii on the choline plasmalogen of heart.     

Akonni TruTip? and Qiagen? Methods for Extraction of Fetal Circulating DNA - Evaluation by Real-Time and Digital PCR

Due to the low percentage of fetal DNA present in maternal plasma (< 10%) during early gestation, efficient extraction processes are required for successful downstream detection applications in non-invasive prenatal diagnostic testing. In this study, two extraction methods using similar chemistries but different workflows were compared for isolation efficiency and percent fetal DNA recovery. The Akonni Biosystems TruTip technology uses a binding matrix embedded in a pipette tip; the Circulating Nucleic Acids Kit from Qiagen employs a spin column approach. The TruTip method adds an extra step to decrease the recovery of DNA fragments larger than 600 bp from the sample to yield an overall higher percentage of smaller molecular weight DNA, effectively enriching for fetal DNA. In this evaluation, three separate extraction comparison studies were performed - a dilution series of fragmented DNA in plasma, a set of clinical maternal samples, and a blood collection tube time point study of maternal samples. Both extraction methods were found to efficiently extract small fragment DNA from large volumes of plasma. In the amended samples, the TruTip extraction method was ~15% less efficient with overall DNA recovery, but yielded an 87% increase in % fetal DNA relative to the Qiagen method. The average percent increase of fetal DNA of TruTip extracted samples compared to the Qiagen method was 55% for all sets of blinded clinical samples. A study comparing extraction efficiencies from whole blood samples incubated up to 48 hours prior to processing into plasma resulted in more consistent % fetal DNA recoveries using TruTip. The extracted products were tested on two detection platforms, quantitative real-time PCR and droplet digital PCR, and yielded similar results for both extraction methods.     

Effects of storage temperatures and annealing conditions on the structure and properties of potato (Solanum tuberosum) starch

Starches were extracted from freshly harvested potatoes (12 cultivars, grown in Perthshire) and the properties of the starches of six cultivars were compared with starches extracted from the same samples but stored at 5, 25 or 55 degrees C for 7 days before extraction. The amylose (total) content of the freshly extracted starches from tubers stored at 5, 25 or 55 degrees C was on average 27.9+/-2.3, 28.3+/-1.7, 29.2+/-2.2 and 28.8+/-1.5%, respectively, with corresponding phosphorus representing 60+/-16, 64+/-9, 61+/-5 and 63+/-9 mg 100 g(-1). The unit chain distribution by chromatography of the amylopectin molecules from the starches extracted from the different conditions was very similar with an average degree of polymerisation (DP) of 26+/-2 where the two major fractions (F1 and F2) represented 54+/-2 and 19+/-1, respectively. Peak gelatinisation temperatures (Tp) and enthalpies (DeltaH) for the freshly extracted starches and from tubers stored at 5 or 25 degrees C were very similar (63.3+/-1.5 degrees C and 18.6+/-0.8 J g(-1); 63.1+/-1.0 degrees C and 17.7+/-1.5 J g(-1) and; 62.9+/-0.7 degrees C and 18.7+/-1.1 J g(-1), respectively) although starches stored at 55 degrees C were annealed, where Tp represented 71.1+/-1.1 degrees C and DeltaH 18.1+/-1.4 J g(-1). These in situ-annealed starches were comparable in terms of gelatinisation characteristics to annealed freshly extracted starches where on average, T(p) represented 72.7+/-1.0 degrees C and DeltaH 20.8+/-1.0 J g(-1). Annealing of tubers in situ prior to processing might be beneficial with respect to developing new potato-based products.     

Design and synthesis of arylaminoethyl amides as noncovalent inhibitors of cathepsin S. Part 1

A series of Nalpha-acyl-alpha-amino acid-(arylaminoethyl)amides were found to be potent and noncovalent cathepsin S inhibitors. Compound 20 possessed high cathepsin S affinity (Ki=3.3 nM) and showed excellent selectivity over cathepsin K, L, F, and V. Molecular modeling, design, synthesis, and in vitro activity are described.     

Methods for the preparation of protein-oligonucleotide-lipid constructs

A mixture of ionizable cationic lipids, steric barrier lipids, and colipids is used to encapsulate oligonucleotide DNA in lipidic particles called SALP. This material is under development as an adjuvant for vaccines. Previously we have shown that coupling the antigen directly to the surface of SALP can lead to enhanced immunological responses in vivo. Two different methods for preparing ovalbumin-SALP were assessed in this work. Originally the conjugates were prepared by treating SALP containing a maleimide-derivatized lipid with thiolated ovalbumin, a method we refer to as active coupling. This reaction was found to be difficult to control and generally resulted in low coupling efficiencies. The issues relating to this approach were characterized. We have recently developed alternative techniques based on first coupling ovalbumin to a micelle and then incubating the resultant product with SALP, methods we refer to as passive coupling. We have shown that this method allows accurate control of the levels of protein associated SALP and does not suffer from surface saturation effects seen with the active coupling method that places maximum limits on the amount of protein that can be coupled to the SALP surface. The products from the passive coupling protocol are shown to have activity comparable to those derived from the active coupling protocol in investigations of in vivo immune responses.     

Potential impact of grey squirrels Sciurus carolinensis on woodland bird populations in England

Several woodland bird species have declined markedly in abundance in England over the past 40 years, whilst the grey squirrel Sciurus carolinensis, a non-native nest predator, has increased. Given the timing, there has been concern that grey squirrels have driven these declines, although there is little data to support this view. Using novel analytical methods and extensive national bird and grey squirrel monitoring data, we examine whether there is evidence that woodland bird populations in England have been depressed by grey squirrels and whether there is a relationship between nest failure and squirrel numbers. Our results indicate that grey squirrels are very unlikely to have driven observed declines of woodland birds in recent years, although the number of associations, positive as well as negative, between grey squirrels and woodland birds is greater than expected by chance. For this reason, we cannot exclude the possibility that the populations of a small number of bird species, principally increasing species, have been depressed to some degree at sites where a greater number of grey squirrels were present. Of these species, perhaps the most convincing evidence is for Common Blackbird Turdus merula and Eurasian Collared Dove Streptopelia decaocto where nest record data also identified a positive relationship between nest failure at the egg stage and squirrel abundance.     

Heterotachy and tree building: a case study with plastids and eubacteria

The nature of heterotachy at the center of recent controversy over the relative performance of tree-building methods is different from the form of heterotachy that has been inferred in empirical studies. The latter have suggested that proportions of variable sites (p(var)) vary among orthologues and among paralogues. However, the strength of this inference, describing what may be one of the most important evolutionary properties of sequence data, has remained weak. Consequently, other models of sequence evolution have been proposed to explain some long-branch attraction (LBA) problems that could be attributed to differences in p(var). For an empirical case with plastid and eubacterial RNA polymerase sequences, we confirm using capture-recapture estimates and simulations that p(var) can differ among orthologues in anciently diverged evolutionary lineages. We find that parsimony and a least squares distance method that implements an overly simple model of sequence evolution are susceptible to LBA induced by this form of heterotachy. Although homogeneous maximum likelihood inference was found to be robust to model misspecification in our specific example, we caution against assuming that it will always be so.     

Pharmacological profile of the "triple" monoamine neurotransmitter uptake inhibitor, DOV 102,677

1. The molecular and behavioral pharmacology of DOV 102,677 is characterized. 2. This characterization was performed using radioligand binding and neurotransmitter uptake assays targeting the monoamine neurotransmitter receptors. In addition, the effects of DOV 102,677 on extracellular neurotransmitter levels were investigated using in vivo microdialysis. Finally, the effects of DOV 102,677 in the forced swim test, locomotor function, and response to prepulse inhibition was investigated.3. DOV 102,677 is a novel, "triple" uptake inhibitor that suppresses [(3)H]dopamine (DA), [(3)H]norepinephrine (NE) and [(3)H]serotonin (5-HT) uptake by recombinant human transporters with IC(50) values of 129, 103 and 133 nM, respectively. Radioligand binding to the dopamine (DAT), norepinephrine (NET), and serotonin (SERT) transporters is inhibited with k (i) values of 222, 1030, and 740 nM, respectively. DOV 102,677 (20 mg/kg IP) increased extracellular levels of DA and 5-HT in the prefrontal cortex to 320 and 280% above baseline 100 min after administration. DA levels were stably increased for the duration (240 min) of the study, but serotonin levels declined to baseline by 200 min after administration. NE levels increased linearly to a maximum of 348% at 240 min post-dosing. Consistent with these increases in NE levels, the density of beta-adrenoceptors was selectively decreased in the cortex of rats treated with DOV 102,677 (20 mg/kg per day, PO, 35 days). 4. DOV 102,677 dose-dependently reduced the amount of time spent immobile by rats in the forced swim test, a model predictive of antidepressant activity, with a minimum effective dose (MED) of 20 mg/kg and a maximal efficacy comparable to imipramine. This decrease in immobility time did not appear to result from increased motor activity. Further, DOV 102,677 was as effective as methylphenidate in reducing the amplitude of the startle response in juvenile mice, without notably altering motor activity. 5. In summary, DOV 102,677 is an orally active, "balanced" inhibitor of DAT, NET and SERT with therapeutic versatility in treating neuropsychiatric disorders beyond depression.