Lajos Nyarsik's research while affiliated with Max Planck Institute for Molecular Genetics and other places

... The assays have been validated carefully, and results were highly consistent with DNA sequencing. Immobilized LNA probes may also be successfully used in multiplex SNP genotyping assay performed on a microarray platform (32). ...

... The synthesis of Locked Nucleic Acid (LNA) [6] overcame these limitations as LNA modified nucleotides confer low cytotoxicity, high thermostability, resistance to nucleases and stable hybridization abilities with target sequences [7]. Enhanced nucleic acid recognition by LNA-containing oligonucleotides made them desirable for many applications in molecular biology, including genotyping [8] or single nucleotide polymorphism (SNP) analysis [9], hybridization [10,11], decoy and fluorescence polarization [12], expression profiling or microarray [13], allele-specific PCR [14], fluorescent in situ hybridization (FISH) analysis [15], alteration of intron splicing and LNAzymes [16], 5′-nuclease assay [17], real-time PCR [18], siRNA [19], microRNA [20] and antisense [21]. ...

... As proteins are extensively heterogeneous, a simple chip for all types of proteins has not been achieved yet. While DNA is stable, proteins tend to lose their three-dimensional structure and, hence, their functionality and specificity as the conditions fall out of a narrow range (Eickhoff et al. 2002). Though, a variety of proteins and peptide arrays have been developed for the analysis of specific or group of proteins, Surface-Enhanced Laser desorption-ionization (SELDI) Protein ChipR, developed by Ciphergen Biosystems, Inc., involves affinity capture of specific subgroups of proteins based on their biochemical or physical properties which is further analyzed with automated MS (Merchant et al. 2000). ...

... The synthesis of Locked Nucleic Acid (LNA) [6] overcame these limitations as LNA modified nucleotides confer low cytotoxicity, high thermostability, resistance to nucleases and stable hybridization abilities with target sequences [7]. Enhanced nucleic acid recognition by LNA-containing oligonucleotides made them desirable for many applications in molecular biology, including genotyping [8] or single nucleotide polymorphism (SNP) analysis [9], hybridization [10,11], decoy and fluorescence polarization [12], expression profiling or microarray [13], allele-specific PCR [14], fluorescent in situ hybridization (FISH) analysis [15], alteration of intron splicing and LNAzymes [16], 5′-nuclease assay [17], real-time PCR [18], siRNA [19], microRNA [20] and antisense [21]. ...

... MALDI and ESI are highly accurate methods that have been employed for the identification and characterisation of proteins, lipids, sugars and nucleic acids in various biological samples, and as such are ideal for the analysis of bacteria. 124 Whilst some researchers have developed ESI-MS via direct infusion for bacterial classification, 125,126 the vast majority of mass spectrometrybased bacterial identification has been undertaken using MALDI-MS. ...

... The level of expression of all genes of an organism in different types of cells, tissues, developmental stages, or disease processes constitutes essential information for understanding the function of different genes, and to unravel the complex network of biological processes acting in every biological system (Eickhoff et al., 2000). Several challenges pertaining to gene expression studies take account of low abundance, tissue-specific or stage-specific gene expression patterns. ...

... New technologies and the use of automated facilities in the field of protein crystallization have greatly increased the likelihood of obtaining protein crystals. For examples, utilization of sparse matrix screens (Jancarik & Kim, 1991), new screening kits (Cudney et al., 1994;Brzozowski & Walton, 2001;Newman et al., 2005;McPherson & Cudney, 2006;Gorrec, 2009), microfluidics (Hansen et al., 2002;Zheng et al., 2004), automation (Mueller et al., 2001;Santarsiero et al., 2002;Sulzenbacher et al., 2002;Bard et al., 2004;Stock et al., 2005) etc. have contributed a lot in this field. However, the overall success rate remains at approximately 10%, without obvious improvements in the process from purified soluble proteins to structure determination (Kim et al., 2008). ...

... In parallel with new sequencing technologies, scientists have developed high-throughput methods for large-scale genome analyses, such as gene identification, single-nucleotide polymorphism detection and gene expression profiling, in particular cDNA library characterization 17 . To identify and quantify DNA fragments of known sequence in a given sample, DNA microarrays are often used 18,19 . However, this approach suffers from the need to preamplify the target DNA, and resulting data are limited by nonspecific hybridization, adsorption and the need for quantification of fluorescence 18,19 . ...

... Likewise, high yield production (≈2 mg/ml concentration) and purification of a single therapeutic dose of a model protein (superfolder GFP) can be achieved on portable microfluidic bioreactors in which nanoporous membrane were adopted for swift and continuous exchange of small molecules (i.e., nucleotides, inorganic phosphates) and waste products for on-demand, point-of-care applications (Timm, Shankles, Foster, Doktycz, & Retterer, 2016). Similarly, to envision a high-throughput instrument similar to that of protein microarrays, microfluidic devices coupled with CFPS can be adopted for characterization of the expression, immobilization, display, and screening of massive protein libraries in an agile and cost-effective manner (Angenendt et al., 2004). Moreover, "cell mimics" capable of controlling the flux of a natural cell can be replicated by coupling cell-free protein production systems inside nanoporous picolitre volume containers. ...

... Mass spectrometry of purified protein complexes provides an unbiased approach to identifying PPIs, but it is limited to relatively high affinity interactions as well as by sample quantity and purity (Gavin et al., 2011;Frei et al., 2012). Yeast and mammalian two-hybrid systems use libraries that direct fusion protein expression intracellularly and are therefore not readily applicable to extracellular domains (ECDs), which generally do not fold correctly in the cytoplasm (Fiebitz et al., 2008;Rajagopala, 2015). Direct binding assays using immobilized fusion proteins have high sensitivity but require production, purification, and analysis of hundreds or thousands of proteins (Bushell et al., 2008;Ramani et al., 2012;Ö zkan et al., 2013;Tom et al., 2015;Visser et al., 2015;Hsu et al., 2017). ...