AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.

Parkour LIMS: high-quality sample preparation in next generation sequencing.

MOTIVATION: This paper presents Parkour, a software package for sample processing and quality management of next generation sequencing data and samples. RESULTS: Starting with user requests, Parkour allows tracking and assessing samples based on predefined quality criteria through different stages of the sample preparation workflow. Ideally suited for academic core laboratories, the software aims to maximize efficiency and reduce turnaround time by intelligent sample grouping and a clear assignment of staff to work units. Tools for automated invoicing, interactive statistics on facility usage and simple report generation minimize administrative tasks. Provided as a web application, Parkour is a convenient tool for both deep sequencing service users and laboratory personal. A set of web APIs allow coordinated information sharing with local and remote bioinformaticians. The flexible structure allows workflow customization and simple addition of new features as well as the expansion to other domains. AVAILABILITY AND IMPLEMENTATION: The code and documentation are available at https://github.com/maxplanck-ie/parkour. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Primary thrombocythemia and pregnancy: treatment and outcome in fifteen cases.

Pregnancy in patients with primary thrombocythemia (PT) is reported to be often complicated by recurrent abortion and fetal growth retardation. Fifteen pregnancies in nine patients with PT are reported. Nine pregnancies had a good outcome, with the birth of a healthy infant. There were two spontaneous abortions and three intrauterine deaths. One pregnancy was electively terminated after extensive thrombosis in the splanchnic district requiring surgical entero-resection. In five pregnancies the mother received no treatment; in ten pregnancies acetylsalicylic acid (ASA) was prescribed to the mother as soon as she was found pregnant, subcutaneous heparin was added from the middle trimester in seven cases. In patients treated with ASA and subcutaneous heparin pregnancies had a good outcome. Administration of ASA and heparin during pregnancy appears to improve the outcome in patients with PT and can prevent severe maternal complications, but requires close monitoring.

Availability of synthetic salmon calcitonin in tissue fluid after a single intravenous dose.

To obtain further information about the availability of salmon calcitonin in the biophase compartment that surrounds the receptor site, salmon calcitonin concentrations in plasma and skin blister fluid (SBF) after a single i.v. dose of 100 IU synthetic salmon calcitonin were compared in 15 healthy volunteers. Serial blood and SBF samples were collected before and up to 8 h after administration and calcitonin was determined by a specific RIA. The maximum concentration in plasma was 225 pg.ml-1 (in the first sample at 15 min), whereas in SBF the mean peak of 84 pg.ml-1 was reached after about 30 min. The distribution of salmon calcitonin into SBF, defined as the ratio of the AUCs in SBF and plasma, was 1.5. The kinetic profiles of salmon calcitonin in plasma and interstitial fluid were different. Calcitonin in plasma peaked and then levelled out, while in SBF it persisted longer than in plasma. This is the first report of the distribution of salmon calcitonin into blister fluid.

Plasmid-to-chromosome gene transfer in Haemophilus influenza during growth.

A low level of recombination between homologous regions of plasmids and the host chromosome occurred during cell growth. The plasmids contained antibiotic resistance markers on the homologous regions which were only expressed when they were integrated into the chromosome. Such recombination took place in Rec+ rec-2 mutants but not in rec-1 mutants.