A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets.

Identifying drug targets in tissues and whole blood with thermal-shift profiling.

Monitoring drug-target interactions with methods such as the cellular thermal-shift assay (CETSA) is well established for simple cell systems but remains challenging in vivo. Here we introduce tissue thermal proteome profiling (tissue-TPP), which measures binding of small-molecule drugs to proteins in tissue samples from drug-treated animals by detecting changes in protein thermal stability using quantitative mass spectrometry. We report organ-specific, proteome-wide thermal stability maps and derive target profiles of the non-covalent histone deacetylase inhibitor panobinostat in rat liver, lung, kidney and spleen and of the B-Raf inhibitor vemurafenib in mouse testis.

A profile of adult acute admissions to Lentegeur Psychiatric Hospital, South Africa.

Background: The Western Cape province has the highest documented lifetime prevalence of common mental disorders in South Africa. To ensure the efficient, equitable and effective distribution of current resources, there is a need to determine the profile of patients requiring psychiatric admission.

Aim: To describe patients admitted to the acute adult admissions unit at Lentegeur Hospital.

Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins.

Detecting the targets of drugs and other molecules in intact cellular contexts is a major objective in drug discovery and in biology more broadly. Thermal proteome profiling (TPP) pursues this aim at proteome-wide scale by inferring target engagement from its effects on temperature-dependent protein denaturation. However, a key challenge of TPP is the statistical analysis of the measured melting curves with controlled false discovery rates at high proteome coverage and detection power.

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking.

Systematic analysis of protein turnover in primary cells.

A better understanding of proteostasis in health and disease requires robust methods to determine protein half-lives. Here we improve the precision and accuracy of peptide ion intensity-based quantification, enabling more accurate protein turnover determination in non-dividing cells by dynamic SILAC-based proteomics. This approach allows exact determination of protein half-lives ranging from 10 to >1000 h.

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

We extended thermal proteome profiling to detect transmembrane protein-small molecule interactions in cultured human cells. When we assessed the effects of detergents on ATP-binding profiles, we observed shifts in denaturation temperature for ATP-binding transmembrane proteins. We also observed cellular thermal shifts in pervanadate-induced T cell-receptor signaling, delineating the membrane target CD45 and components of the downstream pathway, and with drugs affecting the transmembrane transporters ATP1A1 and MDR1.

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. We determined the intracellular thermal profiles for up to 7,000 proteins, and by comparing profiles derived from cultured mammalian cells in the presence or absence of a drug we showed that it was possible to identify direct and indirect targets of drugs in living cells in an unbiased manner.

Tracking cancer drugs in living cells by thermal profiling of the proteome.

The thermal stability of proteins can be used to assess ligand binding in living cells. We have generalized this concept by determining the thermal profiles of more than 7000 proteins in human cells by means of mass spectrometry. Monitoring the effects of small-molecule ligands on the profiles delineated more than 50 targets for the kinase inhibitor staurosporine.

Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data.

Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets.

Circulating lysophosphatidylcholines are markers of a metabolically benign nonalcoholic fatty liver.

Objective: Nonalcoholic fatty liver (NAFL) is thought to contribute to insulin resistance and its metabolic complications. However, some individuals with NAFL remain insulin sensitive. Mechanisms involved in the susceptibility to develop insulin resistance in humans with NAFL are largely unknown.

Preanalytical aspects and sample quality assessment in metabolomics studies of human blood.

Background: Metabolomics is a powerful tool that is increasingly used in clinical research. Although excellent sample quality is essential, it can easily be compromised by undetected preanalytical errors. We set out to identify critical preanalytical steps and biomarkers that reflect preanalytical inaccuracies.

Activation of the mitogen-activated protein kinase (MAPK) signalling pathway in the liver of mice is related to plasma glucose levels after acute exercise.

Aims/hypothesis: We aimed to identify, in the liver of mice, signal transduction pathways that show a pronounced regulation by acute exercise. We also aimed to elucidate the role of metabolic stress in this response.

Methods: C57Bl6 mice performed a 60 min run on a treadmill under non-exhaustive conditions.

Laboratory screening for side effects of disease modifying antirheumatic drugs in daily rheumatological practice.

To observe the actual laboratory screening for side effects of disease modifying antirheumatic drugs (DMARDs) in daily rheumatological practice, a retrospective multi-center cohort study was performed on the laboratory tests in DMARD treated rheumatoid arthritis (RA) patients. RA patients were investigated by chart review if they started with a DMARD (cohort 1) or were treated with a DMARD for at least one year (cohort 2). Hematological, hepatic, and renal tests were collected.

[Twenty years of childhood coeliac disease in the Netherlands: more diagnoses and a changed clinical picture].

Objective: To assess the incidence of childhood coeliac disease in the Netherlands and to study the clinical features.

Design: Prospective.

Setting: Leiden University Medical Centre, Leiden, the Netherlands.

The influence of voluntary upper body exercise on the performance of stimulated paralysed human quadriceps.

In this study the influence of voluntary upper body exercise on the performance of stimulated paralysed human quadriceps was investigated in five subjects with spinal cord lesions in the thoracic spine. The experimental setup consisted of computer-controlled stimulation of the quadriceps using electrodes on the surface of the skin, a dynamometer for isometric or isokinetic loading of the lower leg, and a rowing ergometer for upper body exercise. In all subjects, quadriceps fatigue tests were conducted to study the influence of upper body exercise on knee torque during sustained continuous or intermittent stimulation of quadriceps.

Twenty years of childhood coeliac disease in The Netherlands: a rapidly increasing incidence?

Background: The incidence of coeliac disease varies internationally.

Aims: To assess the incidence of childhood coeliac disease in The Netherlands and to study the clinical features and the presence of associated disorders.

Subjects: Identified cases of childhood coeliac disease in The Netherlands in 1993-4 by means of the Dutch Paediatric Surveillance Unit.

Detection of knee unlock during stance by accelerometry.

Detection of knee unlock is a crucial part of finite state artificial reflex control of paraplegic standing supported by functional neuromuscular stimulation (FNS). This paper investigates knee unlock detection schemes using small uniaxial accelerometers mounted on the thigh and shank. Four single and two differential accelerometer configurations were evaluated with respect to knee unlock detection.

Head injuries from bicycle accidents.

This study comprises a total of 159 victims from bicycle accidents treated as inpatients at the Department of Neurosurgery, University of Bonn between January 1987 and June 1995. It was our aim to define the severity and features of bicycle-related head injuries in a defined population. Our results show that 33% of admitted bicycle victims sustained severe head injuries (Glasgow Coma Score 3-8).

Cycle-to-cycle control of swing phase of paraplegic gait induced by surface electrical stimulation.

Parameterised swing phase of gait in paraplegics was obtained using surface electrical stimulation of the hip flexors, hamstrings and quadriceps; the hip flexors were stimulated to obtain a desired hip angle range, the hamstrings to provide foot clearance in the forward swing, and the quadriceps to acquire knee extension at the end of the swing phase. We report on two main aspects; optimisation of the initial stimulation parameters, and parameter adaptation (control). The initial stimulation patterns were experimentally optimised in two paraplegic subjects using a controlled stand device, resulting in an initial satisfactory swinging motion in both subjects.

Lack of reproducibility of a single negative sting challenge response in the assessment of anaphylactic risk in patients with suspected yellow jacket hypersensitivity.

To investigate the reproducibility of a single negative response to sting challenge with a living insect, we rechallenged a group of 61 patients who showed no clinical response to a first sting challenge. All patients had previously had symptoms suggestive of anaphylaxis after a yellow jacket field sting. Thirteen patients (21%) had anaphylactic responses after the second sting challenge, and six of these patients had severe reactions including symptomatic hypotension requiring administration of Adrenalin.

Fatigue of intermittently stimulated paralyzed human quadriceps during imposed cyclical lower leg movements.

In this study the torque output of intermittently stimulated paralyzed human knee extensor muscles during imposed isokinetic cyclical lower leg movements was investigated in four paraplegic subjects. During prolonged (10 min) experiments the influence of knee angular velocity and stimulation parameters on fatigue-induced torque decline was studied. Pulse width and amplitude were set to obtain maximal recruitment.

Modelling the optimal control of cyclical leg movements induced by functional electrical stimulation.

An optimal control strategy for FES-induced cyclical leg movements in paraplegics is proposed. The control of the cyclical movement of a freely swinging leg is considered as an example. Quadriceps and the flexion withdrawal reflex are stimulated in order to generate a cyclical movement, of which the forward swing resembles the swing phase of gait.