Screening of Peptide Libraries against Protective Antigen of Bacillus anthracis in a Disposable Microfluidic Cartridge

Bacterial surface peptide display has gained popularity as a method of affinity reagent generation for a wide variety of applications ranging from drug discovery to pathogen detection. In order to isolate the bacterial clones that express peptides with high affinities to the target molecule, multiple rounds of manual magnetic activated cell sorting (MACS) followed by multiple rounds of fluorescence activated cell sorting (FACS) are conventionally used. Although such manual methods are effective, alternative means of library screening which improve the reproducibility, reduce the cost, reduce cross contamination, and minimize exposure to hazardous target materials are highly desired for practical application. Toward this end, we report the first semi-automated system demonstrating the potential for screening bacterially displayed peptides using disposable microfluidic cartridges. The Micro-Magnetic Separation platform (MMS) is capable of screening a bacterial library containing 3×1010 members in 15 minutes and requires minimal operator training. Using this system, we report the isolation of twenty-four distinct peptide ligands that bind to the protective antigen (PA) of Bacilus anthracis in three rounds of selection. A consensus motif WXCFTC was found using the MMS and was also found in one of the PA binders isolated by the conventional MACS/FACS approach. We compared MMS and MACS rare cell recovery over cell populations ranging from 0.1% to 0.0000001% and found that both magnetic sorting methods could recover cells down to 0.0000001% initial cell population, with the MMS having overall lower standard deviation of cell recovery. We believe the MMS system offers a compelling approach towards highly efficient, semi-automated screening of molecular libraries that is at least equal to manual magnetic sorting methods and produced, for the first time, 15-mer peptide binders to PA protein that exhibit better affinity and specificity than peptides isolated using conventional MACS/FACS

Visualization of proteomics data using R and bioconductor.

Data visualization plays a key role in high-throughput biology. It is an essential tool for data exploration allowing to shed light on data structure and patterns of interest. Visualization is also of paramount importance as a form of communicating data to a broad audience. Here, we provided a short overview of the application of the R software to the visualization of proteomics data. We present a summary of R's plotting systems and how they are used to visualize and understand raw and processed MS-based proteomics data.LG was supported by the European Union 7th Framework Program (PRIME-XS project, grant agreement number 262067) and a BBSRC Strategic Longer and Larger grant (Award BB/L002817/1). LMB was supported by a BBSRC Tools and Resources Development Fund (Award BB/K00137X/1). TN was supported by a ERASMUS Placement scholarship.This is the final published version of the article. It was originally published in Proteomics (PROTEOMICS Special Issue: Proteomics Data Visualisation Volume 15, Issue 8, pages 1375–1389, April 2015. DOI: 10.1002/pmic.201400392). The final version is available at http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400392/abstract

An intrinsically disordered proteins community for ELIXIR.

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders

A proteomics sample metadata representation for multiomics integration and big data analysis

The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.publishedVersio

Present condition and directions of development of Safe Trans Design (STD) system aiding engineering work at auxiliary mine transport planning

W artykule przedstawiono modułowy system wspomagania projektowania transportu kopalnianego STD (Safe Trans Design), opracowany w Instytucie Techniki Górniczej KOMAG, wdrożony i stosowany w Jastrzębskiej Spółce Węglowej S.A. Scharakteryzowano jego poszczególne moduły tematyczne w tym: konfigurator kolejek podwieszonych, moduł obliczeń trakcyjnych oraz moduł analiz kolizyjności 2D. Omówiono kierunki przyszłych prac nad rozwojem systemu.Safe Trans Design (STD) modular system aiding designing of mine transport, which was developed at the KOMAG Institute of Mining Technology, and implemented and used at Jastrzebska Coal Company, JSC, is presented. Its thematic modules, including configurator of suspended monorails, traction calculations module and module for 2D collision analyses, are characterized. Directions of future work on development of the system are discussed

Methods and tools aiding the development of safe technical means for transportation of materials and people

W Laboratorium Metod Wirtualnego Prototypowania ITG KOMAG od szeregu lat prowadzone są prace mające na celu rozwój narzędzi programowych oraz rozwój metod w zakresie wirtualnego prototypowania systemów mechanicznych. W artykule przedstawiono metodę wspomagania projektowania układów pomocniczego transportu kopalnianego oraz metodę służącą do analizy kolizyjności na trasach transportu pomocniczego z użyciem kolejek podwieszonych i spągowych. Zaprezentowano również metody numeryczne stosowane do oceny rozwiązań konstrukcyjnych zawiesi i złączy tras kolejek podwieszonych, ciągników manewrowych oraz kabin operatorów.Work aiming at a development of software tools and methods for virtual prototyping of mechanical systems has been carried out in the Laboratory of Virtual Prototyping Methods at the KOMAG Institute of Mining Technology for many years. Method supporting the designing the auxiliary mine transportation systems and method for analysis of collision possibility on routes of auxiliary transportation by suspended monorails and floor-mounted railways, are presented. Numerical methods used in assessment of design solutions of suspensions and connections of suspended monorails routes, manoeuvring drivetrains and operators' cabins are also given

Numerical analysis of impact load of arch yielding support

Bumping is one of the natural hazards that occur in Polish collieries. It is a common phenomenon but difficult to predict and very often it causes huge losses in mining equipment and roadway structure. Death of miners working underground is most severe result of bumping. To reduce or even to eliminate results of bumping, especially fatal cases, many safety measures have been used. Frame of arch support is one of the measures applied to reduce dangerous results of bumping. Simulation test ofimpact load of arch yielding support was presented in the paper. The simulation of support load was realized in two stages. Static load of frame of yielding arch support was simulated at the first stage. Among others simulation of assembly of arch support components was carried out. Non-linear simulation, including contact phenomena, was conducted for that purpose. First stage of the task was realized in MSC.Marc/Mentat software Structure of yielding arch support was dynamically loaded at the second stage. The forcing corresponded to real dynamic loads that werefound in mine workings. Second stage of the task was realized in MSC.Dytran software The results of simulations carried out at the KOMAG Institute of Mining Technology were compared with the results of tests of arch supports, which were realized at the Central Mining Institute

Some aspects of IR temperature measurements of a disc during experimental investigations of disc brakes

Przedstawiono wybrane wyniki badań hamulca tarczowego na stanowisku laboratoryjnym. W trakcie doświadczeń mierzone były główne parametry procesu hamowania oraz rozkłady temperatury w klocku i na powierzchni tarczy hamulcowej za pomocą kamery termowizyjnej. Zebrane dane pomiarowe stanowią materiał do weryfikacji modeli matematycznych przy numerycznej symulacji działania tego typu hamulców. Głównym tematem tej pracy jest analiza zmian współczynnika emisyjności powierzchni tarczy w warunkach prowadzenia eksperymentów. Znajomość stwierdzonych prawidłowości jest przydatna przy planowaniu i prowadzeniu tego typu badań.Selected results of testing a disc brake on the laboratory stand, Fig. 1, are presented. There were measured the parameters of braking mechanics as well as the temperature distribution in a brake block and on the disc surface. The temperature distribution was determined with use of an infrared camera. The obtained measurement data were used for verification of the mathematical models for numerical simulations of brakes operation. The problems in determination of the disc surface emissivity coefficient and the character of its changeability during experiments at different braking parameters, Figs. 58, were the objectives of the project. The measurements of the emissivity coefficient on the entire disc surface were taken repeatedly, Figs. 2, 3. A correlation between the disc emissivity coefficient and the mechanical parameters of braking was found. Despite the fact that these correlations are qualitative rather than quantitative, they are interesting from the point of view of identification of the braking process as well as of planning such experiments. During the measurements, some interesting practical experience in the field of infrared measurements of temperature of the surface of not high emissivity coefficient was gained. In the project an isothermal protective screen was applied to normalize the radiation impact of the environment on the measurements, Figs 1, 4

Computer aided process of configuration and evaluation of auxiliary mining transport means

W artykule omówiono modułowy system wspomagania projektowania pomocniczego transportu kopalnianego STD (ang. Safe Trans Design) w wersji 2.0, opracowany w Instytucie Techniki Górniczej KOMAG i wdrożony w kopalniach Jastrzębskiej Spółki Węglowej SA. Przedstawiono założenia i strukturę systemu oraz omówiono jego moduły: konfigurator zespołów transportowych, moduł obliczeń trakcyjnych i moduł analizy kolizyjności 2D. System STD stosowany jest w pracach projektowych dotyczących górniczych układów transportowych z wykorzystaniem kolejek podwieszonych i spągowych. Przedstawiono możliwości obliczeń dynamicznych oddziaływania kolejek podwieszonych na trasę jezdną w świetle najnowszych przepisów.The article discusses the STD (Safe Trans Design) modular support system in version 2.0, developed in KOMAG Institute of Mining Technology and implemented in the mines of Jastrzębska Spółka Węglowa SA. The assumptions and structure of the system and its modules have been discussed: the configurator of suspended monorail, the traction calculation module and the 2D collision analysis module. The STD system is used in design works related to mining transport systems with the use of suspended monorails and floor-mounted railways. The possibilities of dynamic calculations of the impact of suspended monorails on the arch road support in the light of the latest regulations are presented