Gloria Torralba

Combinatorial Synthesis of Peptide Arrays onto a Microchip

Arrays promise to advance biology through parallel screening for binding partners. We show the combinatorial in situ synthesis of 40,000 peptide spots per square centimeter on a microchip. Our variant Merrifield synthesis immobilizes activated amino acids as monomers within particles, which are successively attracted by electric fields generated on each pixel electrode of the chip. With all different amino acids addressed, particles are melted at once to initiate coupling. Repetitive coupling cycles should allow for the translation of whole proteomes into arrays of overlapping peptides that could be used for proteome research and antibody profiling.

Combinatorial synthesis of peptide arrays with a laser printer

however, thedecodingofpeptidebindersislaborintensive.Furthermore,problematicpeptides,forexample,hydrophobicpeptidesthatbind nonspecifically to any protein, are also synthesizedduringlibrarypreparationbythesemethods.Arrays do not have these drawbacks. The position of agivenpeptideonanarraycorrespondsdirectlytoitssequence,and problematic peptides can be omitted in subsequentarrays. Peptide arrays were first described by Frank, whosespotsynthesisdominatesthefieldbecauseofitsreliabilityandwideapplicability.

From experimental setup to bioinformatics: An RNAi screening platform to identify host factors involved in HIV-1 replication

RNA interference (RNAi) has emerged as a powerful technique for studying loss‐of‐function phenotypes by specific down‐regulation of gene expression, allowing the investigation of virus‐host interactions by large‐scale high‐throughput RNAi screens. Here we present a robust and sensitive small interfering RNA screening platform consisting of an experimental setup, single‐cell image and statistical analysis as well as bioinformatics. The workflow has been established to elucidate host gene functions exploited by viruses, monitoring both suppression and enhancement of viral replication simultaneously by fluorescence microscopy. The platform comprises a two‐stage procedure in which potential host factors are first identified in a primary screen and afterwards re‐tested in a validation screen to confirm true positive hits. Subsequent bioinformatics allows the identification of cellular genes participating in metabolic pathways and cellular networks utilised by viruses for efficient infection. Our workflow has been used to investigate host factor usage by the human immunodeficiency virus‐1 (HIV‐1), but can also be adapted to other viruses. Importantly, we expect that the description of the platform will guide further screening approaches for virus‐host interactions. The ViroQuant‐CellNetworks RNAi Screening core facility is an integral part of the recently founded BioQuant centre for systems biology at the University of Heidelberg and will provide service to external users in the near future.

High-Precision Combinatorial Deposition of Micro Particle Patterns on a Microelectronic Chip

The behavior of charged bio polymer micro particles when deposited onto a CMOS chip can be analytically modeled in form of the incompressible Navier-Stokes equation and the electrostatic Poisson equation, as we describe in this article. Based on these models, numerical simulations of depositions can be implemented in COMSOL that lead to improvements in the experimental setup, optimizing the size and charge distribution of the micro particles. Adapting the experiments according to the simulation results, we will show the powerful gain in deposition precision, which is essential for a contamination-free deposition and hence high quality combinatorial deposition.

A VLSI for deskewing and fault tolerance in LVDS links

The device presented at this work is a switch implemented in a 0.35 mum CMOS process for compensating the skew which affects parallel data signal transmissions and for providing fault tolerance in large scale scalable systems, for instance used in trigger farms for high energy physics experiments. The SWIFT chip (SWItch for Fault Tolerance) is part of a cluster built around commercially components which has been inspired by the LHCb experiment. The skew is extremely important because it directly affects the sample window available to the receiver logic and either forces to use quality and expensive cables in order to minimize its effects or reduces the maximum signal transmission range or distance. This problem is handled by the deskewing circuitry at the SWIFT chip, which is able to match dynamically the signal transitions at the receiver link by adding an individual delay to each input signal in steps of 100 ps for LVDS signals up to 250 MHz. The deskew module is based on full custom analog delay units plus a digital skew detector block. A 16-bit processor is implemented for processing tasks. The chip compensates dynamically skews of LVDS signals up to 250 MHz in steps of 100 ps and adds fault tolerance to the farm of PCs by allowing the bypassing of a failing compute node to which is attached

Comparison of parallel versus hierarchical systems for data processing in distributed sensor networks

Distributed sensor networks (DSN) often lead to high volumes of data to acquire and the implementation of the data acquisition is highly dependable on the application. In this paper, we define a merit factor (MF), which allows for quantitative comparison of different possible implementations of data acquisition system. Results of the application of this factor to high-energy physics experiments are presented.

Combinatorial Peptide Synthesis on a Microchip

Microchips are used in the combinatorial synthesis of peptide arrays by means of amino acid microparticle deposition. The surface of custom‐built microchips can be equipped with an amino‐modified poly(ethylene glycol)methacrylate (PEGMA) graft polymer coating, which permits high loading of functional groups and resists nonspecific protein adsorption. Specific microparticles that are addressed to the polymer‐coated microchip surface in a well defined pattern release preactivated amino acids upon melting, and thus allow combinatorial synthesis of high‐complexity peptide arrays directly on the chip surface. Currently, arrays with densities of up to 40,000 peptide spots/cm2 can be generated in this way, with a minimum of coupling cycles required for full combinatorial synthesis. Without using any additional blocking agent, specific peptide recognition has been verified by background‐free immunostaining on the chip‐based array. This unit describes microchip surface modification, combinatorial peptide array synthesis on the chip, and a typical immunoassay employing the resulting high‐density peptide arrays. Curr. Protoc. Protein Sci. 57:18.2.1‐18.2.13.

SCI evaluation in multinode environments for computing and data processing applications

The need of high performance low-cost computing systems motivates intense research in the field and some very fine results have been achieved. By clustering cheap personal computers together we place a virtual supercomputer at our disposal. Currently, PC cluster are mainly programmed using message passing programming models. The SCI interconnect technology opens the possibility for shared memory models. In order to profit from all the advantages that SCI offers, an Application Programming Interface for SCI based systems is needed. The SISCI API provides the necessary tools for developing SCI based systems applications like performance tests and other similar utilities. This paper presents an easy application which uses the SCI API functions and was developed to measure the total bandwidth of a cluster. Four PCs with Pentium II and running under Windows NT 4.0 were connected via Dolphins 4-port switch.