Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants.

Proteogenomics integrates genomic and proteomic data to elucidate cellular processes by identifying variant peptides, including single amino acid variants (SAAVs). In this study, we assessed the capability of data-independent acquisition mass spectrometry (DIA-MS) to identify SAAV peptides in HeLa cells using various search engine pipelines. We developed a customised sequence database (DB) incorporating SAAV sequences from the HeLa genome and conducted searches using DIA-NN, Spectronaut, and Fragpipe-MSFragger.

Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme.

In recent years, a plethora of different data-independent acquisition methods have been developed for proteomics to cover a wide range of requirements. Current deep proteome profiling methods rely on fractionations, elaborate chromatography, and mass spectrometry setups or display suboptimal quantitative precision. We set out to develop an easy-to-use one shot DIA method that achieves high quantitative precision and high proteome coverage.

Detection of Known and Novel Small Proteins in Using a Combination of Bottom-Up and Digest-Free Proteomics and Proteogenomics.

Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen .

Adaptation and Resistance: How Copes with the Bisphenol A Substitute Bisphenol F.

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome.

Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.

Background: The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.

A chronic hypoxic response in photoreceptors alters the vitreous proteome in mice.

Reduced oxygenation of the outer retina in the aging eye may activate a chronic hypoxic response in RPE and photoreceptor cells and is considered as a risk factor for the development of age-related macular degeneration (AMD). In mice, a chronically active hypoxic response in the retinal pigment epithelium (RPE) or photoreceptors leads to age-dependent retinal degeneration. To identify proteins that may serve as accessible markers for a chronic hypoxic insult to photoreceptors, we used proteomics to determine the protein composition of the vitreous humor in genetically engineered mice that lack the von Hippel-Lindau tumor suppressor (Vhl) specifically in rods (rod) or cones (all-cone).

The Proteomic Landscape in the Vitreous of Patients With Age-Related and Diabetic Retinal Disease.

Purpose: In contrast to neovascular AMD (nAMD), no treatment option exists for dry AMD. Hence, the identification of specific biomarkers is required to facilitate diagnosis and therapy of dry AMD.

Methods: The proteome of 34 vitreous humor samples (dry AMD: n = 6; nAMD: n = 10; proliferative diabetic retinopathy [PDR]: n = 9; epiretinal membrane [ERM]: n = 9) was analyzed by liquid chromatography coupled mass spectrometry.

Hif1a inactivation rescues photoreceptor degeneration induced by a chronic hypoxia-like stress.

Reduced choroidal blood flow and tissue changes in the ageing human eye impair oxygen delivery to photoreceptors and the retinal pigment epithelium. As a consequence, mild but chronic hypoxia may develop and disturb cell metabolism, function and ultimately survival, potentially contributing to retinal pathologies such as age-related macular degeneration (AMD). Here, we show that several hypoxia-inducible genes were expressed at higher levels in the aged human retina suggesting increased activity of hypoxia-inducible transcription factors (HIFs) during the physiological ageing process.

Targeting Hif1a rescues cone degeneration and prevents subretinal neovascularization in a model of chronic hypoxia.

Background: Degeneration of cone photoreceptors leads to loss of vision in patients suffering from age-related macular degeneration (AMD) and other cone dystrophies. Evidence, such as choroidal ischemia and decreased choroidal blood flow, implicates reduced tissue oxygenation in AMD pathology and suggests a role of the cellular response to hypoxia in disease onset and progression. Such a chronic hypoxic situation may promote several cellular responses including stabilization of hypoxia-inducible factors (HIFs).

Elovl4 5-bp deletion does not accelerate cone photoreceptor degeneration in an all-cone mouse.

Mutations in the elongation of very long chain fatty acid 4 (ELOVL4) gene cause Stargardt macular dystrophy 3 (STGD3), a rare, juvenile-onset, autosomal dominant form of macular degeneration. Although several mouse models have already been generated to investigate the link between the three identified disease-causing mutations in the ELOVL4 gene, none of these models recapitulates the early-onset cone photoreceptor cell death observed in the macula of STGD3 patients. To address this specifically, we investigated the effect of mutant ELOVL4 in a mouse model with an all-cone retina.

Correction to: Plasma levels of hypoxia-regulated factors in patients with age-related macular degeneration.

The original publication of this paper contains mistakes due to incorrect order of first and last names.

Plasma levels of hypoxia-regulated factors in patients with age-related macular degeneration.

Purpose: Various hypoxia-related proteins are differentially expressed in the retina and secreted to the vitreous and/or aqueous humor of patients affected by dry or neovascular age-related macular degeneration (nAMD). To determine whether these conditions alter concentrations of cytokines also in the systemic circulation, we measured plasma levels of six hypoxia-related proteins.

Methods: Plasma was prepared from EDTA blood that was collected from patients affected by dry AMD (n = 5), nAMD (n = 11), proliferative diabetic retinopathy (PDR; n = 9), and patients with an epiretinal membrane (ERM; n = 11).

Digoxin-induced retinal degeneration depends on rhodopsin.

Na,K-ATPases are energy consuming ion pumps that are required for maintaining ion homeostasis in most cells. In the retina, Na,K-ATPases are especially important to sustain the dark current in photoreceptor cells needed for rapid hyperpolarization of rods and cones in light. Cardiac glycosides like digoxin inhibit the activity of Na,K-ATPases by targeting their catalytic alpha subunits.

Cystatin F is a biomarker of prion pathogenesis in mice.

Misfolding of the cellular prion protein (PrPC) into the scrapie prion protein (PrPSc) results in progressive, fatal, transmissible neurodegenerative conditions termed prion diseases. Experimental and epidemiological evidence point toward a protracted, clinically silent phase in prion diseases, yet there is no diagnostic test capable of identifying asymptomatic individuals incubating prions. In an effort to identify early biomarkers of prion diseases, we have compared global transcriptional profiles in brains from pre-symptomatic prion-infected mice and controls.

Hypoxic preconditioning protects photoreceptors against light damage independently of hypoxia inducible transcription factors in rods.

Hypoxic preconditioning protects photoreceptors against light-induced degeneration preserving retinal morphology and function. Although hypoxia inducible transcription factors 1 and 2 (HIF1, HIF2) are the main regulators of the hypoxic response, photoreceptor protection does not depend on HIF1 in rods. Here we used rod-specific Hif2a single and Hif1a;Hif2a double knockout mice to investigate the potential involvement of HIF2 in rods for protection after hypoxic preconditioning.

Comprehensive analysis of heterotrimeric G-protein complex diversity and their interactions with GPCRs in solution.

Agonist binding to G-protein-coupled receptors (GPCRs) triggers signal transduction cascades involving heterotrimeric G proteins as key players. A major obstacle for drug design is the limited knowledge of conformational changes upon agonist binding, the details of interaction with the different G proteins, and the transmission to movements within the G protein. Although a variety of different GPCR/G protein complex structures would be needed, the transient nature of this complex and the intrinsic instability against dissociation make this endeavor very challenging.

Preclinical efficacy and safety of an anti-IL-1β vaccine for the treatment of type 2 diabetes.

Neutralization of the inflammatory cytokine interleukin-1β (IL-1β) is a promising new strategy to prevent the β-cell destruction, which leads to type 2 diabetes. Here, we describe the preclinical development of a therapeutic vaccine against IL-1β consisting of a detoxified version of IL-1β chemically cross-linked to virus-like particles of the bacteriophage Qβ. The vaccine was well tolerated and induced robust antibody responses in mice, which neutralized the biological activity of IL-1β, as shown both in cellular assays and in challenge experiments in vivo.

Experimental validation of a simple approximation to determine the linewidth of a laser from its frequency noise spectrum.

Laser frequency fluctuations can be characterized either comprehensively by the frequency noise spectrum or in a simple but incomplete manner by the laser linewidth. A formal relation exists to calculate the linewidth from the frequency noise spectrum, but it is laborious to apply in practice. We recently proposed a much simpler geometrical approximation applicable to any arbitrary frequency noise spectrum.

Frequency discriminators for the characterization of narrow-spectrum heterodyne beat signals: application to the measurement of a sub-hertz carrier-envelope-offset beat in an optical frequency comb.

We describe a radio-frequency (RF) discriminator, or frequency-to-voltage converter, based on a voltage-controlled oscillator phase-locked to the signal under test, which has been developed to analyze the frequency noise properties of an RF signal, e.g., a heterodyne optical beat signal between two lasers or between a laser and an optical frequency comb.

Fully stabilized optical frequency comb with sub-radian CEO phase noise from a SESAM-modelocked 1.5-µm solid-state laser.

We report the first full stabilization of an optical frequency comb generated from a femtosecond diode-pumped solid-state laser (DPSSL) operating in the 1.5-μm spectral region. The stability of the comb is characterized in free-running and in phase-locked operation by measuring the noise properties of the carrier-envelope offset (CEO) beat, of the repetition rate, and of a comb line at 1558 nm.

Excitations of a superfluid in a three-dimensional optical lattice.

We prepare a Bose-Einstein condensed gas in a three-dimensional optical lattice and study the excitation spectrum of the superfluid phase for different interaction strengths. We probe the response of the system by modulating the depth of the optical lattice along one axis. The interactions can be controlled independently by varying the tunnel coupling along the other two lattice axes.

Transition from a strongly interacting 1d superfluid to a Mott insulator.

We study 1D trapped Bose gases in the strongly interacting regime. The systems are created in an optical lattice and are subject to a longitudinal periodic potential. Bragg spectroscopy enables us to investigate the excitation spectrum in different regimes.