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Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that this process critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication through Rtg2 and Rtg3. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. This shows that oxidative stress-induced mitochondrial impairment may be under strict regulatory control. If the results extend to human cells, the results may prove to be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease., Competing Interests: SS, JL, AG, KP, ED, CG, JY, CG, TÄ, PG, LL, MZ, SS, JH, JH, MM, GL, SO, JW No competing interests declared, (© 2022, Stenberg et al.)

Spent alkaline and zinc-carbon batteries contain valuable elements (notably, Zn and Mn), which need to be recovered to keep a circular economy. In this study, the black mass materials from those spent batteries are pyrometallurgically treated via a series of process steps in a pilot-scale KALDO furnace to produce an Mn-Zn product, a ZnO product, and an MnO (manganese monoxide) product, toward applications of Mn-Zn micronutrient fertilizer, zinc metal, and manganese alloy, respectively. After an oxidative roasting step, an Mn-Zn product, containing 43% Mn, 22% Zn, and negligible amounts of toxic elements (notably, Cd, Hg, and Pb), could be produced, being suitable for the micronutrient fertilizer application. After a reductive roasting step, a ZnO product and an MnO product are produced. The attained ZnO product, containing up to 84.6% ZnO, is suitable for zinc metal production when the leaching steps are taken to remove most of the Cl and F in the product. The attained MnO product, containing up to 91.7% MnO, is of premium quality for manganese alloy production, preferably for SiMn alloy production due to its low phosphorus content. The proposed application scenarios could substantially improve the recovery efficiency of those spent batteries., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The rapid horizontal transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. Plasmid-carrying donor strains are constructed in high-throughput. We then mix the resistance plasmid-carrying donors with recipients in a design where only transconjugants can reproduce, measure growth in dense intervals, and extract transmission times as the growth lag. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within Escherichia coli populations, by screening the Keio deletion collection in high replication. We recover all seven known chromosomal gene mutants affecting conjugation as donors and identify many novel mutants, all of which diminish antibiotic resistance transmission. We validate nine of the novel genes' effects in liquid mating assays and complement one of the novel genes' effect on conjugation ( rseA ). The new framework holds great potential for exhaustive disclosing of candidate targets for helper drugs that delay resistance development in patients and societies and improve the longevity of current and future antibiotics. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains. IMPORTANCE The rapid transmission of antibiotic resistance genes on conjugative plasmids between bacterial host cells is a major cause of the accelerating antibiotic resistance crisis. There are currently no experimental platforms for fast and cost-efficient screening of genetic effects on antibiotic resistance transmission by conjugation, which prevents understanding and targeting conjugation. We introduce a novel experimental framework to screen for conjugation-based horizontal transmission of antibiotic resistance between >60,000 pairs of cell populations in parallel. As proof-of-principle, we exhaustively explore chromosomal genes controlling F-plasmid donation within E. coli populations. We recover all previously known and many novel chromosomal gene mutants that affect conjugation efficiency. The new framework holds great potential for rapid screening of compounds that decrease transmission. Further, the platform can easily be adapted to explore interspecies conjugation, plasmid-borne factors, and experimental evolution and be used for rapid construction of strains., (Copyright © 2020 Alalam et al.)

A major rationale for the advocacy of epigenetically mediated adaptive responses is that they facilitate faster adaptation to environmental challenges. This motivated us to develop a theoretical-experimental framework for disclosing the presence of such adaptation-speeding mechanisms in an experimental evolution setting circumventing the need for pursuing costly mutation-accumulation experiments. To this end, we exposed clonal populations of budding yeast to a whole range of stressors. By growth phenotyping, we found that almost complete adaptation to arsenic emerged after a few mitotic cell divisions without involving any phenotypic plasticity. Causative mutations were identified by deep sequencing of the arsenic-adapted populations and reconstructed for validation. Mutation effects on growth phenotypes, and the associated mutational target sizes were quantified and embedded in data-driven individual-based evolutionary population models. We found that the experimentally observed homogeneity of adaptation speed and heterogeneity of molecular solutions could only be accounted for if the mutation rate had been near estimates of the basal mutation rate. The ultrafast adaptation could be fully explained by extensive positive pleiotropy such that all beneficial mutations dramatically enhanced multiple fitness components in concert. As our approach can be exploited across a range of model organisms exposed to a variety of environmental challenges, it may be used for determining the importance of epigenetic adaptation-speeding mechanisms in general., (© 2016 The Authors. Published under the terms of the CC BY 4.0 license.)

Explaining trait differences between individuals is a core and challenging aim of life sciences. Here, we introduce a powerful framework for complete decomposition of trait variation into its underlying genetic causes in diploid model organisms. We sequence and systematically pair the recombinant gametes of two intercrossed natural genomes into an array of diploid hybrids with fully assembled and phased genomes, termed Phased Outbred Lines (POLs). We demonstrate the capacity of this approach by partitioning fitness traits of 6,642 Saccharomyces cerevisiae POLs across many environments, achieving near complete trait heritability and precisely estimating additive (73%), dominance (10%), second (7%) and third (1.7%) order epistasis components. We map quantitative trait loci (QTLs) and find nonadditive QTLs to outnumber (3:1) additive loci, dominant contributions to heterosis to outnumber overdominant, and extensive pleiotropy. The POL framework offers the most complete decomposition of diploid traits to date and can be adapted to most model organisms.

The capacity to map traits over large cohorts of individuals-phenomics-lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker's yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases., (Copyright © 2016 Zackrisson et al.)

Background: Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology., Results: To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis., Conclusions: PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly used to gather this information. One potential caveat is that these measures assume gene flow to be symmetric. However, asymmetric gene flow is common in nature, especially in systems driven by physical processes such as wind or water currents. As information about levels of asymmetric gene flow among populations is essential for the correct interpretation of the distribution of contemporary genetic diversity within species, this should not be overlooked. To obtain information on asymmetric migration patterns from genetic data, complex models based on maximum-likelihood or Bayesian approaches generally need to be employed, often at great computational cost. Here, a new simpler and more efficient approach for understanding gene flow patterns is presented. This approach allows the estimation of directional components of genetic divergence between pairs of populations at low computational effort, using any of the classical or modern measures of genetic differentiation. These directional measures of genetic differentiation can further be used to calculate directional relative migration and to detect asymmetries in gene flow patterns. This can be done in a user-friendly web application called divMigrate-online introduced in this study. Using simulated data sets with known gene flow regimes, we demonstrate that the method is capable of resolving complex migration patterns under a range of study designs.

Protein overexpression based on introduction of multiple gene copies is well established. To improve purification or quantification, proteins are typically fused to peptide tags. In Saccharomyces cerevisiae, this has been hampered by multicopy toxicity of the TAP and GFP cassettes used in the global strain collections. Here, we show that this effect is due to the EF-1α promoter in the HIS3MX marker cassette rather than the tags per se. This promoter is frequently used in heterologous marker cassettes, including HIS3MX, KanMX, NatMX, PatMX and HphMX. Toxicity could be eliminated by promoter replacement or exclusion of the marker cassette. To our knowledge, this is the first report of toxicity caused by introduction of a heterologous promoter alone., (Copyright © 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.)

Variants of lipase were attached to gold nanoparticles (NPs) and their enzymatic activity was studied. The two bioengineered lipase variants have been prepared with biotin groups attached to different residues on the protein outer surface. The biotinylation was evidenced by denaturing polyacrylamide gel electrophoresis and quantified by the ([2-(4'-hydroxyazobenzene)]benzoic acid spectrophotometric test. NPs of 14 +/- 1 nm diameter coated with thiolated-polyethylene glycol ligands containing controlled proportions of biotin moieties have been prepared and characterized by transmission electron microscopy, UV-vis spectroscopy, small angle neutron scattering, and elemental analysis. These biotin-functionalized NPs were conjugated to lipase using streptavidin as a linker molecule. Enzyme activity assays on the lipase-nanoparticle conjugates show that the lipase loading and activity of the NPs can be controlled by varying the percentage of biotin groups in the particle protecting coat. The lipase-NP conjugates prepared using one variant display higher activity than those prepared using the other variant, demonstrating orientation-dependent enzyme activity. Cryogenic transmission electron microscopy was used to visualize the enzymatic activity of lipase-NP on well-defined lipid substrates. It was found that lipase-coated NPs are able to digest the substrates in a different manner in comparison to the free lipase.

A small-angle X-ray scattering (SAXS) set-up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009-0.3 A(-1) for the standard set-up but depends on the sample-to-detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm x 0.37 mm (full width at half-maximum) at the sample position, with a flux of 4 x 10(10) photons s(-1) and lambda = 1.1 A. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead-throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro-fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost-effective SAXS station can be constructed on a multipurpose beamline.

The scattering intensity of polydisperse systems of core-shell and layered hard spheres is considered. The Percus-Yevick solution for the partial structure factors is cast in a form suitable for numerical and analytical treatment. Closed-form, analytical expressions are given for an effective hard-sphere model of the scattering intensity of particles with an internal layered structure and a size polydispersity governed by a Schulz distribution. A similar model for polydisperse hard spheres of core-shell structure but with a monodisperse shell thickness is also presented. The models are tested against small-angle X-ray scattering experiments on a hard-sphere-like microemulsion system.

The self-assembly of the trifluoroacetate salt of the short peptide (ala)6-lys (A6K) in water has been investigated by cryo-transmission electron microscopy and small-angle X-ray scattering. For concentrations below ca. 12%, the peptide does not self-assemble but forms a molecularly dispersed solution. Above this critical concentration, however, A6K self-assembles into several-micrometer-long hollow nanotubes with a monodisperse cross-sectional radius of 26 nm. Because the peptides carry a positive charge, the nanotubes are charge-stabilized. Because of the very large aspect ratio, the tubes form an ordered phase that presumably is nematic.

We report on the mechanism of growth of mesoporous silica (SBA-15, plane group p6m). In situ studies of the formation using ultrasmall angle X-ray scattering (USAXS) and small-angle X-ray scattering (SAXS) covering length scales from 5 to 10,000 A, complemented with UV-vis and transmission electron microscopy (TEM), provide unique data on particle growth coupled with information regarding the progression of the mesostructure formation and the micellar evolution.

A comprehensive experimental study of the dynamics and rheology of concentrated aqueous dispersions of poly(ethylene glycol)-grafted colloidal spheres is reported. The study focuses on good solvent conditions, for which excluded-volume interactions dominate. At high concentrations a glass transition is evident from the nondecaying component of the intensity correlation function measured with three-dimensional dynamic light scattering. Results for the linear viscoelastic and steady shear rheology on approaching the glass transition correlate well with the slowing of the diffusive dynamics; in particular, at, or close to, the concentration where the dynamics becomes nonergodic, the dispersions acquire a low-frequency plateau in the elastic shear modulus as well as a yield stress. The overall behavior of the dispersions conforms to that of hard-sphere dispersions; however, some qualitative differences are observed in the evolution of the dynamics and rheology with increasing concentration near the glass transition.

Small-angle neutron scattering (SANS) measurements are reported on a sterically stabilized, core-shell colloidal system using contrast variation. Aqueous dispersions of polystyrene particles bearing grafted poly(ethylene glycol) (PEG) have been studied over a large range of particle concentrations and two different solvent conditions for the PEG polymer. SANS data are analyzed quantitatively by modeling the particles as core-shell colloids. In a good solvent and under particle contrast conditions, an effective hard-sphere interaction captures excluded-volume interactions up to high concentrations. Contrast variation, through isotopic substitution of both the core and solvent, expedite a detailed study of the PEG layer, both in the dilute limit and as a function of the particle concentration. Upon diminishing the solvent quality, subtle changes in the PEG layer translate into attractions among particles of moderate magnitude.

The effects of temperature changes and polymer addition on the behavior of droplet microemulsions of nonionic surfactant, water, and decane are reported and analyzed within polymer depletion theory. Dilution viscometry and dynamic light scattering were used to confirm that these microemulsions behave essentially as hard-sphere dispersions, providing us with an ideal reference system. Addition of poly(ethylene glycol) (PEG) lowers the emulsification failure boundary, where excess oil is expelled, which can be qualitatively understood by an analysis of the available volume for the polymer. Sufficient addition of PEG causes a fluid-fluid phase separation in qualitative accord with experiments on mixtures of rigid colloidal hard spheres and nonadsorbing polymer. Addition of PEG or raising the temperature causes the collective diffusion coefficient D(C) to decrease. From theory, the initial linear slope of D(C) versus droplet concentration can be used to discriminate between attractions and repulsions. The measured D(C) data for the droplets in the presence of PEG are modeled using the Asakura-Oosawa theory of depletion. Fitting the theory to the measured D(C) data permits for extracting the only unknown parameter, the polymer radius of gyration. Quantitative agreement is found with literature data, demonstrating that polymer depletion occurs in the system and that the Asakura-Oosawa theory provides a faithful description of the phenomenon.