Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein.

The worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the repeated emergence of variants of concern. For the Omicron variant, sub-lineages BA.1 and BA.2, respectively, contain 33 and 29 nonsynonymous and indel spike protein mutations. These amino acid substitutions and indels are implicated in increased transmissibility and enhanced immune evasion. By reverting individual spike mutations of BA.1 or BA.2, we characterize the molecular effects of the Omicron spike mutations on expression, ACE2 receptor affinity, and neutralizing antibody recognition. We identified key mutations enabling escape from neutralizing antibodies at a variety of epitopes. Stabilizing mutations in the N-terminal and S2 domains of the spike protein can compensate for destabilizing mutations in the receptor binding domain, enabling the record number of mutations in Omicron. Our results provide a comprehensive account of the mutational effects in the Omicron spike protein and illustrate previously uncharacterized mechanisms of host evasion.

One hundred years of pyloric stenosis in the Royal Hospital for Sick Children Edinburgh.

AIM: Pyloric stenosis was first reported in 1717 and was treatable from the start of the 1900s. Our hospital opened in 1860. In this study we report the historical account of the management of pyloric stenosis in Edinburgh from 1910 to 2013. METHOD: Historic discharge summaries, theatre records, and distinguished surgeons' operation and lecture notes dating back to 1910 with regard to pyloric stenosis were identified and reviewed. We present this history and compare our contemporary data. RESULTS: In February 1911, Harold Styles performed a pyloromyotomy, but did not report it at the time. However, the record of this operation and date were later published by Mason Brown in 1956. For the period 1926-1936, we report the management of 7 patients, of which only 3 survived. For the period 1947-1956, 515 patients were treated, with a mortality rate of 4.08%. Our current series for 1999-2012 has a mortality rate of zero and complication rate of 5.3%. CONCLUSIONS: During the period 1910 to present day in Edinburgh, pyloric stenosis has gone from being medically managed with bad outcomes to a condition with 100% survival. The only surgical advance has been the development of the Rammstedt pyloromyotomy. Of interest we document that a pyloromyotomy was performed here in February 1910. The improved outcome is mainly due to better understanding of the physiological disturbance in pyloric stenosis and advances in anaesthetics and microbiology.

Recent progress in synthetic and biological studies of GPI anchors and GPI-anchored proteins.

Covalent attachment of glycosylphosphatidylinositols (GPIs) to the protein C-terminus is one of the most common posttranslational modifications in eukaryotic cells. In addition to anchoring surface proteins to the cell membrane, GPIs also have many other important biological functions, determined by their unique structure and property. This account has reviewed the recent progress made in disclosing GPI and GPI-anchored protein biosynthesis, in the chemical and chemoenzymatic synthesis of GPIs and GPI-anchored proteins, and in understanding the conformation, organization, and distribution of GPIs in the lipid membrane.

Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

Chemotrapping-atomic fluorescence spectrometric method as a field method for volatile arsenic in natural gas.

Volatile arsenic compounds in natural gas, existing in the form of trimethylarsine (TMAs), have been determined using gas cryo-trapping gas chromatography coupled to inductively coupled plasma-mass spectrometry (CT-GC-ICP-MS). The results from a number of different gas wells revealed a huge concentration spread ranging from below the detection limit of 0.2 up to 1800 microg/m(3) TMAs (as As) in the gas. Due to the toxicity and corrosive nature of these arsines, they need near real time monitoring via a method that can easily be implemented on site, i.e. during gas exploitation. Here, we introduce a novel method which utilises silver nitrate impregnated silica gel tubes for quantitative chemotrapping of trimethylarsine (TMAs) from a natural gas matrix. Subsequent elution with hot nitric acid followed by online photo-oxidation hydride generation atomic fluorescence spectrometry (HG-AFS) is used for the determination of TMAs gas standards in nitrogen and natural gas samples, respectively. The chemotrapping method was validated using CT-GC-ICP-MS as a reference method. The recovery of arsenic from nitrogen or natural gas matrix ranged from 85 to 113% for a range of 20 to 2000 ng As. Trapping efficiency was >98%, from the methods LOD of 20 ng to 4.8 microg (absolute amount As) with sample sizes of 0.02 and 2 L gas. Method performance was established by comparing the results obtained for eight natural gas samples containing between 1 and 140 microg As/m(3) with those achieved by the reference method (CT-GC-ICP-MS).