Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis.

Adaptive evolution of clonally dividing cells and microbes is the ultimate cause of cancer and infectious diseases. The possibility of constraining the adaptation of cell populations, by inhibiting proteins enhancing the evolvability, has therefore attracted interest. However, our current understanding of how genes influence adaptation kinetics is limited, partly because accurately measuring adaptation for many cell populations is challenging. We used a high-throughput adaptive laboratory evolution platform to track the adaptation of >18,000 cell populations corresponding to single-gene deletion strains in the haploid yeast deletion collection. We report that the preadaptation fitness of gene knockouts near-perfectly (R2= 0.91) predicts their adaptation to arsenic, leaving at the most a marginal role for dedicated evolvability gene functions. We tracked the adaptation of another >23,000 gene knockout populations to a diverse range of selection pressures and generalized the almost perfect (R2=0.72-0.98) capacity of preadaptation fitness to predict adaptation. We also reconstructed mutations in FPS1, ASK10, and ARR3, which together account for almost all arsenic adaptation in wild-type cells, in gene deletions covering a broad fitness range and show that the predictability of arsenic adaptation can be understood as a by global epistasis, where excluding arsenic is more beneficial to arsenic unfit cells. The paucity of genes with a meaningful evolvability effect on adaptation diminishes the prospects of developing adjuvant drugs aiming to slow antimicrobial and chemotherapy resistance.

Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation.

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.

Domestication reprogrammed the budding yeast life cycle.

Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.

Aborting meiosis allows recombination in sterile diploid yeast hybrids.

Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.

Metallophobic Coatings to Enable Shape Reconfigurable Liquid Metal Inside 3D Printed Plastics.

Liquid metals adhere to most surfaces despite their high surface tension due to the presence of a native gallium oxide layer. The ability to change the shape of functional fluids within a three-dimensional (3D) printed part with respect to time is a type of four-dimensional printing, yet surface adhesion limits the ability to pump liquid metals in and out of cavities and channels without leaving residue. Rough surfaces prevent adhesion, but most methods to roughen surfaces are difficult or impossible to apply on the interior of parts. Here, we show that silica particles suspended in an appropriate solvent can be injected inside cavities to coat the walls. This technique creates a transparent, nanoscopically rough (10-100 nm scale) coating that prevents adhesion of liquid metals on various 3D printed plastics and commercial polymers. Liquid metals roll and even bounce off treated surfaces (the latter occurs even when dropped from heights as high as 70 cm). Moreover, the coating can be removed locally by laser ablation to create selective wetting regions for metal patterning on the exterior of plastics. To demonstrate the utility of the coating, liquid metals were dynamically actuated inside a 3D printed channel or chamber without pinning the oxide, thereby demonstrating electrical circuits that can be reconfigured repeatably.

A yeast living ancestor reveals the origin of genomic introgressions.

Genome introgressions drive evolution across the animal1, plant2 and fungal3 kingdoms. Introgressions initiate from archaic admixtures followed by repeated backcrossing to one parental species. However, how introgressions arise in reproductively isolated species, such as yeast4, has remained unclear. Here we identify a clonal descendant of the ancestral yeast hybrid that founded the extant Saccharomyces cerevisiae Alpechin lineage5, which carries abundant Saccharomyces paradoxus introgressions. We show that this clonal descendant, hereafter defined as a 'living ancestor', retained the ancestral genome structure of the first-generation hybrid with contiguous S. cerevisiae and S. paradoxus subgenomes. The ancestral first-generation hybrid underwent catastrophic genomic instability through more than a hundred mitotic recombination events, mainly manifesting as homozygous genome blocks generated by loss of heterozygosity. These homozygous sequence blocks rescue hybrid fertility by restoring meiotic recombination and are the direct origins of the introgressions present in the Alpechin lineage. We suggest a plausible route for introgression evolution through the reconstruction of extinct stages and propose that genome instability allows hybrids to overcome reproductive isolation and enables introgressions to emerge.

Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging.

Aging varies among individuals due to both genetics and environment, but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct quantitative trait loci (QTLs) that control chronological life span (CLS) in calorie-rich and calorie-restricted environments and under rapamycin exposure. Calorie restriction and rapamycin extended life span in virtually all genotypes but through different genetic variants. We tracked the two major QTLs to the cell wall glycoprotein genes FLO11 and HPF1 We found that massive expansion of intragenic tandem repeats within the N-terminal domain of HPF1 was sufficient to cause pronounced life span shortening. Life span impairment by HPF1 was buffered by rapamycin but not by calorie restriction. The HPF1 repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing their exposure to surrounding oxygen. The higher oxygenation altered methionine, lipid, and purine metabolism, and inhibited quiescence, which explains the life span shortening. We conclude that fast-evolving intragenic repeat expansions can fundamentally change the relationship between cells and their environment with profound effects on cellular lifestyle and longevity.

Low-Temperature Side Contact to Carbon Nanotube Transistors: Resistance Distributions Down to 10 nm Contact Length.

Carbon nanotube field-effect transistors (CNFETs) promise to improve the energy efficiency, speed, and transistor density of very large scale integration circuits owing to the intrinsic thin channel body and excellent charge transport properties of carbon nanotubes. Low-temperature fabrication (e.g., <400 °C) is a key enabler for the monolithic three-dimensional (3D) integration of CNFET digital logic into a device technology platform that overcomes memory bandwidth bottlenecks for data-abundant applications such as big-data analytics and machine learning. However, high contact resistance for short CNFET contacts has been a major roadblock to establishing CNFETs as a viable technology because the contact resistance, in series with the channel resistance, reduces the on-state current of CNFETs. Additionally, the variation in contact resistance remains unstudied for short contacts and will further degrade the energy efficiency and speed of CNFET circuits. In this work, we investigate by experiments the contact resistance and statistical variation of room-temperature fabricated CNFET contacts down to 10 nm contact lengths. These CNFET contacts are ∼15 nm shorter than the state-of-the-art Si CMOS "7 nm node" contact length, allowing for multiple generations of future scaling of the transistor-contacted gate pitch. For the 10 nm contacts, we report contact resistance values down to 6.5 kΩ per source/drain contact for a single carbon nanotube (CNT) with a median contact resistance of 18.2 kΩ. The 10 nm contacts reduce the CNFET current by as little as 13% at VDS = 0.7 V compared with the best reported 200 nm contacts to date, corroborated by results in this work. Our analysis of RC from 232 single-CNT CNFETs between the long-contact (e.g., 200 nm) and short-contact (e.g., 10 nm) regimes quantifies the resistance variation and projects the impact on CNFET current variability versus the number of CNT in the transistor. The resistance distribution reveals contact-length-dependent RC variations become significant below 20 nm contact length. However, a larger source of CNFET resistance variation is apparent at all contact lengths used in this work. To further investigate the origins of this contact-length-independent resistance variation, we analyze the variation of RC in arrays of identical CNFETs along a single CNT of constant diameter and observe the random occurrence of high  RC, even on correlated CNFETs.

Shared Molecular Targets Confer Resistance over Short and Long Evolutionary Timescales.

Pre-existing and de novo genetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the evolutionary dynamics in drug-treated yeast populations with different levels of pre-existing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of pre-existing variation alone boosts the adaptation by 64.1% and 51.5% in hydroxyurea and rapamycin, respectively. The causative pre-existing and de novo variants were selected on shared targets: RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. Interestingly, the pre-existing and de novo TOR variants map to different functional domains and act via distinct mechanisms. The pre-existing TOR variants from two domesticated strains exhibited opposite rapamycin resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how pre-existing and de novo variants interactively drive adaptation and deepens our understanding of clonally evolving populations.

Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

InAs nanowire MOSFETs in three-transistor configurations: single balanced RF down-conversion mixers.

Integration of III-V semiconductors on Si substrates allows for the realization of high-performance, low power III-V electronics on the Si-platform. In this work, we demonstrate the implementation of single balanced down-conversion mixer circuits, fabricated using vertically aligned InAs nanowire devices on Si. A thin, highly doped InAs buffer layer has been introduced to reduce the access resistance and serve as a bottom electrode. Low-frequency voltage conversion gain is measured up to 7 dB for a supply voltage of 1.5V. Operation of these mixers extends into the GHz regime with a -3 dB cut-off frequency of 2 GHz, limited by the optical lithography system used. The circuit dc power consumption is measured at 3.9 mW.

Hard X-ray detection using a single 100 nm diameter nanowire.

Submicron sized sensors could allow higher resolution in X-ray imaging and diffraction measurements, which are ubiquitous for materials science and medicine. We present electrical measurements of a single 100 nm diameter InP nanowire transistor exposed to hard X-rays. The X-ray induced conductance is over 5 orders of magnitude larger than expected from reported data for X-ray absorption and carrier lifetimes. Time-resolved measurements show very long characteristic lifetimes on the order of seconds, tentatively attributed to long-lived traps, which give a strong amplification effect. As a proof of concept, we use the nanowire to directly image an X-ray nanofocus with submicron resolution.

Comparative sequence analysis and mutagenesis of ethylene forming enzyme (EFE) 2-oxoglutarate/Fe(II)-dependent dioxygenase homologs.

BACKGROUND: Ethylene is one of the most used chemical monomers derived from non-renewable sources and we are investigating the possibility of producing it in yeast via the ethylene forming enzyme (EFE) from Pseudomonas syringae. To enable engineering strategies to improve the enzyme, it is necessary to identify the regions and amino acid residues involved in ethylene formation. RESULTS: We identified the open reading frame for the EFE homolog in Penicillium digitatum and also showed its capability of mediating ethylene production in yeast. The sequence of the EFE homologs from P.digitatum and P. syringae was compared to that of the non-functional EFE-homolog from Penicillium chrysogenum and ten amino acids were found to correlate with ethylene production. Several of these amino acid residues were found to be important for ethylene production via point mutations in P. syringae EFE. The EFE homolog from P. chrysogenum was engineered at 10 amino acid residues to mimic the P. syringae EFE, but this did not confer ethylene producing capability.Furthermore, we predicted the structure of EFE by homology to known structures of 2-oxoglutarate/Fe(II) dependent dioxygenases. Three of the amino acids correlating with ethylene production are located in the predicted 2-oxoglutarate binding domain. A protein domain specific for the EFE-class was shown to be essential for activity. Based on the structure and alanine substitutions, it is likely that amino acids (H189, D191 and H268) are responsible for binding the Fe(II) ligand. CONCLUSION: We provide further insight into the structure and function of the ethylene forming (EFE) - subclass of 2-oxoglutarate/Fe(II) dependent dioxygenases. We conclude that residues in addition to the 10 identified positions implicated in ethylene production by sequence comparison, are important for determining ethylene formation. We also demonstrate the use of an alternative EFE gene. The data from this study will provide the basis for directed protein engineering to enhance the ethylene production capability and properties of EFE.

Ethylene production in relation to nitrogen metabolism in Saccharomyces cerevisiae.

We have previously shown that ethylene production in Saccharomyces cerevisiae expressing the ethylene-forming enzyme (EFE) from Pseudomonas syringae is strongly influenced by variations in the mode of cultivation as well as the choice of nitrogen source. Here, we have studied the influence of nitrogen metabolism on the production of ethylene further. Using ammonium, glutamate, glutamate/arginine, and arginine as nitrogen sources, it was found that glutamate (with or without arginine) correlates with a high ethylene production, most likely linked to an observed increase in 2-oxoglutarate levels. Arginine as a sole nitrogen source caused a reduced ethylene production. A reduction of arginine levels, accomplished using an arginine auxotrophic ARG4-deletion strain in the presence of limiting amounts of arginine or through CAR1 overexpression, did however not correlate with an increased ethylene production. As expected, arginine was necessary for ethylene production as ethylene production in the ARG4-deletion strain ceased at the time when arginine was depleted. In conclusion, our data suggest that high levels of 2-oxoglutarate and a limited amount of arginine are required for successful ethylene production in yeast.

Why Bariatric surgery should be given high priority: an argument from law and morality.

In recent years, bariatric surgery has become an increasingly popular treatment of obesity. The amount of resources spent on this kind of surgery has led to a heated debate among health care professionals and the general public, as each procedure costs at minimum $14,500 and thousands of patients undergo surgery every year. So far, no substantial argument for or against giving this treatment a high priority has, however, been presented. In this article, I argue that regardless which moral perspective we consider--greatest need, utility or personal responsibility--the conclusion is that we should give bariatric surgery a high priority when allocating scarce resources in health care.

Differential tolerance to cyanobacterial exposure between geographically distinct populations of Perca fluviatilis.

Toxic cyanobacterial blooms are an important problem worldwide. Cyanobacteria may negatively impact young-of-the-year (YOY) fish directly (toxin production, turbidity, decrease in water quality) or indirectly (trophic toxin transfer, changes in prey species composition). Here we test whether there are any differences in cyanobacterial tolerance between four geographically distinct populations of European perch (Perca fluviatilis). We show that P. fluviatilis may develop tolerance against cyanobacteria demonstrated by the ability of individuals from a marine site (exposed to annual cyanobacterial blooms) to increase their detoxification more than individuals from an oligotrophic site (rarely exposed to cyanobacteria). Our results also revealed significant interaction effects between genotypes within a population and response to cyanobacterial exposure in terms of absolute growth and detoxification activity. This genotype by treatment interaction may result in local adaptations to cyanobacterial exposure in P. fluviatilis. Hence, the sensitivity against cyanobacterial exposure may differ between within species populations increasing the importance of local management of fish populations.

The right perspective on responsibility for ill health.

There is a growing trend in policy making of holding people responsible for their lifestyle-based diseases. This has sparked a heated debate on whether people are responsible for these illnesses, which has now come to an impasse. In this paper, I present a psychological model that explains why different views on people's responsibility for their health exist and how we can reach a resolution of the disagreement. My conclusion is that policymakers should not perceive people as responsible while health care personnel should take the opposing view.

Effects of the filamentous cyanobacterium Nodularia on fitness and feeding behavior of young-of-the-year (YOY) Eurasian perch (Perca fluviatilis).

This study reveals that both cyanobacterial toxicity and turbidity have the potential to reduce the growth and energy storage of young-of-the-year (YOY) perch and thereby influence survival rates. During the 1990's a reduction in recruitment of YOY perch (Perca fluviatilis) occurred along the Swedish East coast. Concurrently, large blooms of filamentous cyanobacteria have increased in the Baltic Proper and in coastal waters. This study examined whether extended exposure to toxic and non-toxic filamentous cyanobacterium Nodularia affect YOY perch growth and feeding behavior under simulated bloom conditions (30 days at 50 µg Chl a L(-1)). Specific growth rate (SGR), the somatic condition index (SCI) and the lipid content of YOY perch (10-12 weeks old) were significantly lower in perch exposed to Nodularia compared to fed controls (no Nodularia). YOY perch exposed to non-toxic Nodularia displayed a higher attack rate than perch living in Nodularia free controls in 2 out of 3 trials. Reductions in growth and energy storage, mediated by cyanobacteria, increase the risk of starvation and predation and could locally influence recruitment of YOY perch.