Tracking down protein-protein interaction via FRET-system using site-specific thiol-labeling

A novel Cys-specific bioorthogonalized linker was synthesized and applied in combination with bioorthogonally applicable fluorescent markers to track down protein–protein (p38-MK2) interactions by FRET.</p

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

Background: Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. Methods: Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. Results: We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. Conclusions: IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data. © 2017 The Author(s)

Short communication: Upper critical temperature-humidity index for dairy calves based on physiological stress variables

In this study, upper critical values of the temperature-humidity index (THI) were determined in Holstein bull calves (n = 16) based on noninvasive physiological parameters. Meteorological and animal-based data were recorded for a 4-d period following a 24-h habituation. The estimated upper critical THI values based on the assessment of respiratory rate, rectal temperature, ear temperature, heart rate, and salivary cortisol concentrations were 82.4, 88.1, 83.0, 78.3, and 88.8, respectively. We inferred that welfare of young calves may be compromised above a THI of 78 and that calves experience significant heat stress above a THI of 88. Based on the present findings, upper critical THI should be considered to minimize the duration of impaired welfare during summer heat stress episodes. Key words: upper critical temperature-humidity index, heat stress, dairy calve

Epistasis, aneuploidy, and functional mutations underlie evolution of resistance to induced microtubule depolymerization

Cells with blocked microtubule polymerization are delayed in mitosis, but eventually manage to proliferate despite substantial chromosome missegregation. While several studies have analyzed the first cell division after microtubule depolymerization, we have asked how cells cope long-term with microtubule impairment. We allowed 24 clonal populations of yeast cells with beta-tubulin mutations preventing proper microtubule polymerization, to evolve for ˜150 generations. At the end of the laboratory evolution experiment, cells had regained the ability to form microtubules and were less sensitive to microtubule-depolymerizing drugs. Whole-genome sequencing identified recurrently mutated genes, in particular for tubulins and kinesins, as well as pervasive duplication of chromosome VIII. Recreating these mutations and chromosome VIII disomy prior to evolution confirmed that they allow cells to compensate for the original mutation in beta-tubulin. Most of the identified mutations did not abolish function, but rather restored microtubule functionality. Analysis of the temporal order of resistance development in independent populations repeatedly revealed the same series of events: disomy of chromosome VIII followed by a single additional adaptive mutation in either tubulins or kinesins. Since tubulins are highly conserved among eukaryotes, our results have implications for understanding resistance to microtubule-targeting drugs widely used in cancer therapy. © 2021 IFOM – the FIRC Institute of Molecular Oncolog

High hydrostatic pressure: Can we trust published data?

Abstract. There are numerous new technologies whose implementation in food industry is hampered by the fact that people hesitate to invest in expensive systems which they cannot be sure will work or at least are questionable in terms of a given product. Until recently, preservation by HHP, high hydrostatic pressure, was such a technology, and still is today in some branches of the food industry. Investigations were conducted to answer the question of whether the literature, the laboratory, and the industrial (or at least pilot plant) measurements and results agree with one another. We compared the literature data with two HHP systems which were significantly different in terms of treatment capacity, but their efficiency in killing microbes was studied under the same treatment parameters. Our results show that in nearly all cases only minimal differences exist between the data in the literature and the measurements taken on the two appliances

High hydrostatic pressure: Can we trust published data?

There are numerous new technologies whose implementation in food industry is hampered by the fact that people hesitate to invest in expensive systems which they cannot be sure will work or at least are questionable in terms of a given product. Until recently, preservation by HHP, high hydrostatic pressure, was such a technology, and still is today in some branches of the food industry. Investigations were conducted to answer the question of whether the literature, the laboratory, and the industrial (or at least pilot plant) measurements and results agree with one another. We compared the literature data with two HHP systems which were significantly different in terms of treatment capacity, but their efficiency in killing microbes was studied under the same treatment parameters. Our results show that in nearly all cases only minimal differences exist between the data in the literature and the measurements taken on the two appliances