Four-dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing four-dimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio, and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on timsTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer's disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.     

In vivo development of tissue engineered vascular grafts: a fluid-solid-growth model

Biomechanics and Modeling in Mechanobiology - Methods of tissue engineering continue to advance, and multiple clinical trials are underway evaluating tissue engineered vascular grafts (TEVGs)....     

A global analysis of adaptive evolution of operons in cyanobacteria

Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.     

Biomechanical and transcriptional evidence that smooth muscle cell death drives an osteochondrogenic phenotype and severe proximal vascular disease in progeria

Biomechanics and Modeling in Mechanobiology - Hutchinson–Gilford Progeria Syndrome results in rapid aging and severe cardiovascular sequelae that accelerate near end-of-life. We found a...     

Physicochemical properties of bacterial pro-inflammatory lipids influence their interaction with apolipoprotein-derived peptides

Apolipoprotein-derived peptides have emerged as a promising candidate for the treatment of various inflammatory disease conditions. Multiple mechanisms have been proposed to explain the beneficiary effects of these peptides and prominent among them being high-affinity binding of peptides to pro-inflammatory lipids and facilitating their sequestration/metabolism/clearance in the body. Pro-inflammatory lipids differ considerably in their molecular structures, chemical compositions and physicochemical properties. Importance of the properties of the pro-inflammatory lipids in their ability to bind to apolipoprotein-derived peptides is not studied in details. In this study, we have characterized the interaction of synthetic peptides derived from human apolipoprotein E with lipopolysaccharide (LPS) and lipoteichoic acid (LTA), two potent bacterial pro-inflammatory lipids that differ considerably in their molecular structures and chemical compositions. Binding of the peptides to LPS and LTA was monitored by CD spectroscopy. Effect of the peptides on the biological activity of lipids was studied by monitoring the inhibition of LPS- or LTA-induced up-regulation of the inflammatory markers in the human blood cells. Physicochemical properties of lipid aggregates were determined by fluorescence spectroscopy and native PAGE. Our results show that physicochemical properties of LPS and LTA differ considerably and influence their interaction with apolipoprotein-derived peptides.     

Control of scabies in a tribal community using mass screening and treatment with oral ivermectin -A cluster randomized controlled trial in Gadchiroli,India

BackgroundScabies is often endemic in tribal communities and difficult to control. We assessed the efficacy of a community-based intervention using mass screening and treatment with oral ivermectin in controlling scabies.Methods/ FindingsIn this cluster randomised controlled trial, 12 villages were randomly selected from a cluster of 42 tribal villages in Gadchiroli district. In these villages, trained community health workers (CHWs) conducted mass screening for scabies. The diagnosis was confirmed by a physician. Six villages each were randomly allocated to the intervention and usual care arm (control arm). In the intervention arm (population 1184) CHWs provided directly observed oral ivermectin to scabies cases and their household contacts. In the usual care arm (population 1567) scabies cases were referred to the nearest clinic for topical treatment as per the standard practice. The primary outcome was prevalence of scabies two months after the treatment. Secondary outcomes were prevalence of scabies after twelve months of treatment and prevalence of impetigo after two and twelve months of treatment. Outcomes were measured by the team in a similar way as the baseline. The trial was registered with the clinical trial registry of India, number CTRI/2017/01/007704.In the baseline, 2 months and 12 months assessments 92.4%, 96% and 94% of the eligible individuals were screened in intervention villages and 91.4%, 91.3% and 95% in the usual care villages. The prevalence of scabies in the intervention and usual care arm was 8.4% vs 8.1% at the baseline, 2.8% vs 8.8% at two months [adjusted relative risk (ARR) 0.21, 95% CI 0.11–0.38] and 7.3% vs 14.1% (ARR 0.49, 95% CI 0.25–0.98) at twelve months The prevalence of impetigo in the intervention and usual care arm was 1.7% vs 0.6% at baseline, 0.6% vs 1% at two months (ARR 0.55, 95% CI 0.22–1.37) and 0.3% vs 0.7% at 12 months (ARR 0.42, 95% CI 0.06–2.74). Adverse effects due to ivermectin occurred in 12.1% of patients and were mild.ConclusionsMass screening and treatment in the community with oral ivermectin delivered by the CHWs is superior to mass screening followed by usual care involving referral to clinic for topical treatment in controlling scabies in this tribal community in Gadchiroli.     

In Vitro Study on Structural Alteration of Myoglobin by Methylglyoxal

Methylglyoxal (MG), a reactive α-oxoaldehyde, reacts with proteins to form irreversible advanced glycation end products (AGEs) following Maillard-like reaction. MG-induced AGE (MAGE) formation may be significant, particularly in diabetic condition with increased level of MG. Although myoglobin (Mb) is known to react with sugars to form AGEs, its interaction with MG is not known. Here we have studied interaction of Mb with MG. After in vitro reaction between Mb and MG at 25 °C for 7 days, the unchanged Mb and modified Mb (MG-Mb) were separated by ion exchange chromatography. Compared to Mb, MG-Mb exhibited higher electrophoretic mobility in native polyacrylamide gel electrophoresis, increased absorbance around 280 nm and more α-helical content, indicating structural changes of the modified protein. As shown by MALDI-mass spectrometry, MG converted Lys-16 and Lys-133 to carboxyethyllysine in MG-Mb. MAGE thus formed in MG-Mb may be associated with its enhanced mobility in native gel due to neutralization of positive charges and the observed structural changes in comparison with Mb.