Biology subjects

Braslavsky, I.

Publications and source records attributed to Braslavsky, I..

4 recordsLinked to original sources

bioRxiv2023

Highly conserved, positively charged tandem repeats mediate multimerization of ice nucleation proteins

In nature, frost can form at a few degrees below 0 {degrees}C. However, this process requires the assembly of tens of thousands of ice-like water molecules that align together to initiate freezing at these relatively high temperatures. Water ordering on this scale is mediated by the ice nucleation proteins of common environmental bacteria like Pseudomonas syringae and P. borealis. However, individually, these 100-kDa proteins are too small to organize enough water molecules for frost formation, and it is not known how giant, megadalton-sized multimers, which are crucial for ice nucleation at high sub-zero temperatures, form. The ability of multimers to self-assemble was suggested when the transfer of an ice nucleation protein gene into Escherichia coli led to efficient ice nucleation. Here we demonstrate that a positively-charged sub-domain at the C-terminal end of the central beta-solenoid of the ice nucleation protein is crucial for multimerization. Truncation, relocation, or change of the charge of this subdomain caused a catastrophic loss of ice nucleation ability. Cryo-electron tomography of the recombinant E. coli showed that the ice nucleation protein multimers form fibres that are [~] 5 nm across and up to 200 nm long. A model of these fibres as an overlapping series of antiparallel dimers can account for all their known properties and suggests a route to making cell-free ice nucleators for biotechnological applications.

biochemistry↗

bioRxiv2020

Kinetics and Fidelity of Psychrophilic DNA Polymerases

The discovery of extremophiles helped enable the development of groundbreaking technology such as polymerase chain reaction. Temperature variation is often an essential step of these technology platforms, but the effect of temperature on the error rate of polymerases from different origins is under-explored. Here, we applied high-throughput sequencing to profile the error rates of DNA polymerases from psychrophilic, mesophilic, and thermophilic origins with single-molecule resolution. We found that reaction temperature substantially increases substitution and deletion error rates of psychrophilic and mesophilic DNA polymerases. Our motif analysis shows that the substitution error profiles cluster according to phylogenetic similarity of polymerases, not reaction temperature, thus suggesting that reaction temperature increases global error rate of polymerases independent of sequence context. Intriguingly, we also found that the DNA polymerase I of a psychrophilic bacteria exhibits higher polymerization activity than its mesophilic ortholog across all temperature ranges, including down to -19{degrees}C which is well below the freezing temperature of water. Our results provide a useful reference for how reaction temperature, a crucial parameter of biochemistry, can affect DNA polymerase fidelity in organisms adapted to a wide range of thermal environments.

biochemistry↗

bioRxiv2017

On a non-trivial application of Algebraic Topology to Molecular Biology

Brouwers fixed point theorem, a fundamental theorem in algebraic topology proved more than a hundred years ago, states that given any continuous map from a closed, simply connected set into itself, there is a point that is mapped unto itself. Here we point out the connection between a one-dimensional application of Brouwers fixed point theorem and a mechanism proposed to explain how extension of single-stranded DNA substrates by recombinases of the RecA superfamily facilitates significantly the search for homologous sequences on long chromosomes.

molecular biology↗

bioRxiv2017

Matrix-corrected mass spectrometry enables sensitive detection of food allergens and reveals widespread soy contamination of processed foods

The frequent use of precautionary food allergen labeling statements such as \"may contain\" poses challenges to allergic individuals who rely on such labeling to determine whether a food is safe to consume. We developed a multiplexed liquid chromatography-mass spectrometry assay targeting 14 common allergens in order to survey how frequently these precautionary statements indicate allergen contamination and to assess whether variations in precautionary phrasing affect the likelihood of allergen contamination. A survey of 84 foods revealed how scheduled multiple reaction monitoring (MRM) transition interference derived from complex and heterogeneous sample matrices hinders sensitive analyte detection. As a solution, we developed MAtrix-Dependent Interference Correction (MADIC), an approach to sensitively detect trace peptide quantities through interference identification and stringent peptide quality control criteria. Applying this method, we find frequent contamination of soy in breads and corn flour, and observe additional instances of food contamination with tree nuts, wheat, milk, and egg. In some of these cases, the food had no precautionary labeling for the offending allergen. We also find that only 10% of warning labels are indicative of contamination, and that products with \"same facility\" precautionary labeling are not necessarily less likely to contain trace amounts of allergens than products labeled \"may contain.\"

immunology↗