bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct Signatures for Mutator Sensitivity of lacZ Reversions and for the Spectrum of lacI/lacO Forward Mutations on the Chromosome of Nondividing Escherichia coli
Authors: Bharatan Shanti M , Reddy Manjula , Gowrishankar J 
Published: April 2021

Abstract
A conditional lethal galE(Ts)-based strategy was employed in Escherichia coli, first to eliminate all growth-associated chromosomal reversions in lacZ or forward mutations in lacI/lacO by incubation at the restrictive temperature and subsequently to recover (as papillae) spontaneous mutations that had arisen in the population of nondividing cells after shift to the permissive temperature. Data from lacZ reversion studies in mutator strains indicated that the products of all genes for mismatch repair (mutHLS, dam, uvrD), of some for oxidative damage repair (mutMT), and of that for polymerase proofreading (dnaQ) are required in dividing cells; some others for oxidative damage repair (mutY, nth nei) are required in both dividing and nondividing cells; and those for alkylation damage repair (ada ogt) are required in nondividing cells. The spectrum of lacI/lacO mutations in nondividing cells was distinguished both by lower frequencies of deletions and IS1 insertions and by the unique occurrence of GC-to-AT transitions at lacO +5. In the second approach to study mutations that had occurred in nondividing cells, lacI/lacO mutants were selected as late-arising papillae from the lawn of a galE+ strain; once again, transitions at lacO +5 were detected among the mutants that had been obtained from populations initially grown on poor carbon sources such as acetate, palmitate, or succinate. Our results indicate that the lacO +5 site is mutable only in nondividing cells, one possible mechanism for which might be that random endogenous alkylation (or oxidative) damage to DNA in these cells is efficiently corrected by the Ada Ogt (or Nth Nei) repair enzymes at most sites but not at lacO +5. Furthermore, the late-arising papillae from the second approach were composed almost exclusively of dominant lacI/lacO mutants. This finding lends support to “instantaneous gratification” models in which a spontaneous lesion, occurring at a random site in DNA of a nondividing cell, is most likely to be fixed as a mutation if it allows the cell to immediately exit the nondividing state.
Reciprocal Translocations in Saccharomyces cerevisiae Formed by Nonhomologous End Joining
Authors: Yu Xin , Gabriel Abram 
Published: April 2021

Abstract
Reciprocal translocations are common in cancer cells, but their creation is poorly understood. We have developed an assay system in Saccharomyces cerevisiae to study reciprocal translocation formation in the absence of homology. We induce two specific double-strand breaks (DSBs) simultaneously on separate chromosomes with HO endonuclease and analyze the subsequent chromosomal rearrangements among surviving cells. Under these conditions, reciprocal translocations via nonhomologous end joining (NHEJ) occur at frequencies of ∼2-7 × 10-5/cell exposed to the DSBs. Yku80p is a component of the cell’s NHEJ machinery. In its absence, reciprocal translocations still occur, but the junctions are associated with deletions and extended overlapping sequences. After induction of a single DSB, translocations and inversions are recovered in wild-type and rad52 strains. In these rearrangements, a nonrandom assortment of sites have fused to the DSB, and their junctions show typical signs of NHEJ. The sites tend to be between open reading frames or within Ty1 LTRs. In some cases the translocation partner is formed by a break at a cryptic HO recognition site. Our results demonstrate that NHEJ-mediated reciprocal translocations can form in S. cerevisiae as a consequence of DSB repair.
Genetic Complexity Underlying Hybrid Male Sterility in Drosophila
Authors: Sawamura Kyoichi , Roote John , Wu Chung-I , Yamamoto Masa-Toshi 
Published: April 2021

Abstract
Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility.
On the Rate and Linearity of Viability Declines in Drosophila Mutation-Accumulation Experiments: Genomic Mutation Rates and Synergistic Epistasis Revisited
Authors: Fry James D 
Published: April 2021

Abstract
High rates of deleterious mutations could severely reduce the fitness of populations, even endangering their persistence; these effects would be mitigated if mutations synergize each others’ effects. An experiment by Mukai in the 1960s gave evidence that in Drosophila melanogaster, viability-depressing mutations occur at the surprisingly high rate of around one per zygote and that the mutations interact synergistically. A later experiment by Ohnishi seemed to support the high mutation rate, but gave no evidence for synergistic epistasis. Both of these studies, however, were flawed by the lack of suitable controls for assessing viability declines of the mutation-accumulation (MA) lines. By comparing homozygous viability of the MA lines to simultaneously estimated heterozygous viability and using estimates of the dominance of mutations in the experiments, I estimate the viability declines relative to an appropriate control. This approach yields two unexpected conclusions. First, in Ohnishi’s experiment as well as in Mukai’s, MA lines showed faster-than-linear declines in viability, indicative of synergistic epistasis. Second, while Mukai’s estimate of the genomic mutation rate is supported, that from Ohnishi’s experiment is an order of magnitude lower. The different results of the experiments most likely resulted from differences in the starting genotypes; even within Mukai’s experiment, a subset of MA lines, which I argue probably resulted from a contamination event, showed much slower viability declines than did the majority of lines. Because different genotypes may show very different mutational behavior, only studies using many founding genotypes can determine the average rate and distribution of effects of mutations relevant to natural populations.
EXO1 Plays a Role in Generating Type I and Type II Survivors in Budding Yeast
Authors: Maringele Laura , Lydall David 
Published: April 2021

Abstract
Telomerase-defective budding yeast cells escape senescence by using homologous recombination to amplify telomeric or subtelomeric structures. Similarly, human cells that enter senescence can use homologous recombination for telomere maintenance, when telomerase cannot be activated. Although recombination proteins required to generate telomerase-independent survivors have been intensively studied, little is known about the nucleases that generate the substrates for recombination. Here we demonstrate that the Exo1 exonuclease is an initiator of the recombination process that allows cells to escape senescence and become immortal in the absence of telomerase. We show that EXO1 is important for generating type I survivors in yku70Δ mre11Δ cells and type II survivors in tlc1Δ cells. Moreover, in tlc1Δ cells, EXO1 seems to contribute to the senescence process itself.
Role of the Nuclease Activity of Saccharomyces cerevisiae Mre11 in Repair of DNA Double-Strand Breaks in Mitotic Cells
Authors: Lewis L Kevin , Storici Francesca , Van Komen Stephen , Calero Shanna , Sung Patrick , Resnick Michael A 
Published: April 2021

Abstract
The Rad50:Mre11:Xrs2 (RMX) complex functions in repair of DNA double-strand breaks (DSBs) by recombination and nonhomologous end-joining (NHEJ) and is also required for telomere stability. The Mre11 subunit exhibits nuclease activities in vitro, but the role of these activities in repair in mitotic cells has not been established. In this study we have performed a comparative study of three mutants (mre11-D16A, -D56N, and -H125N) previously shown to have reduced nuclease activities in vitro. In ends-in and ends-out chromosome recombination assays using defined plasmid and oligonucleotide DNA substrates, mre11-D16A cells were as deficient as mre11 null strains, but defects were small in mre11-D56N and -H125N mutants. mre11-D16A cells, but not the other mutants, also displayed strong sensitivity to ionizing radiation, with residual resistance largely dependent on the presence of the partially redundant nuclease Exo1. mre11-D16A mutants were also most sensitive to the S-phase-dependent clastogens hydroxyurea and methyl methanesulfonate but, as previously observed for D56N and H125N mutants, were not defective in NHEJ. Importantly, the affinity of purified Mre11-D16A protein for Rad50 and Xrs2 was indistinguishable from wild type and the mutant protein formed complexes with equivalent stoichiometry. Although the role of the nuclease activity has been questioned in previous studies, the comparative data presented here suggest that the nuclease function of Mre11 is required for RMX-mediated recombinational repair and telomere stabilization in mitotic cells.
Quantitative Trait Loci Affecting Starvation Resistance in Drosophila melanogaster
Authors: Harbison Susan T , Yamamoto Akihiko H , Fanara Juan J , Norga Koenraad K , Mackay Trudy F C 
Published: April 2021

Abstract
The ability to withstand periods of scarce food resources is an important fitness trait. Starvation resistance is a quantitative trait controlled by multiple interacting genes and exhibits considerable genetic variation in natural populations. This genetic variation could be maintained in the face of strong selection due to a trade-off in resource allocation between reproductive activity and individual survival. Knowledge of the genes affecting starvation tolerance and the subset of genes that affect variation in starvation resistance in natural populations would enable us to evaluate this hypothesis from a quantitative genetic perspective. We screened 933 co-isogenic P-element insertion lines to identify candidate genes affecting starvation tolerance. A total of 383 P-element insertions induced highly significant and often sex-specific mutational variance in starvation resistance. We also used deficiency complementation mapping followed by complementation to mutations to identify 12 genes contributing to variation in starvation resistance between two wild-type strains. The genes we identified are involved in oogenesis, metabolism, and feeding behaviors, indicating a possible link to reproduction and survival. However, we also found genes with cell fate specification and cell proliferation phenotypes, which implies that resource allocation during development and at the cellular level may also influence the phenotypic response to starvation.
Nucleotide Variation in thetinmanandbagpipeHomeobox Genes ofDrosophila melanogaster
Authors: Balakirev Evgeniy S , Ayala Francisco J 
Published: April 2021

AbstractThe tinman (tin) and bagpipe (bap) genes are members of the NK homeobox gene family of Drosophila, so that tin occupies a higher position than bap in the regulatory hierarchy. Little is known about the level and pattern of genetic polymorphism in homeobox genes. We have analyzed nucleotide polymorphism in 27 strains of Drosophila melanogaster and one each of D. simulans and D. sechellia, within two closely linked regions encompassing a partial sequence of tin and the complete sequence of bap. The two genes exhibit different levels and patterns of nucleotide diversity. Two sets of sharply divergent sequence types are detected for tin. The haplotype structure of bap is more complex: about half of the sequences are identical (or virtually so), while the rest are fairly heterogeneous. The level of silent nucleotide variability is 0.0063 for tin but significantly higher, 0.0141, for bap, a level of polymorphism comparable to the most polymorphic structural genes of D. melanogaster. Recombination rate and gene conversion are also higher for bap than for tin. There is strong linkage disequilibrium, with the highest values in the introns of both genes and exon II of bap. The patterns of polymorphism in tin and bap are not compatible with an equilibrium model of selective neutrality. We suggest that negative selection and demographic history are the major factors shaping the pattern of nucleotide polymorphism in the tin and bap genes; moreover, there are clear indications of positive selection in the bap gene.
Evolution ofDMY, a Newly Emergent Male Sex-Determination Gene of Medaka Fish
Authors: Zhang Jianzhi 
Published: April 2021

AbstractThe Japanese medaka fish Oryzias latipes has an XX/XY sex-determination system. The Y-linked sex-determination gene DMY is a duplicate of the autosomal gene DMRT1, which encodes a DM-domain-containing transcriptional factor. DMY appears to have originated recently within Oryzias, allowing a detailed evolutionary study of the initial steps that led to the new gene and new sex-determination system. Here I analyze the publicly available DMRT1 and DMY gene sequences of Oryzias species and report the following findings. First, the synonymous substitution rate in DMY is 1.73 times that in DMRT1, consistent with the male-driven evolution hypothesis. Second, the ratio of the rate of nonsynonymous nucleotide substitution (dN) to that of synonymous substitution (dS) is significantly higher in DMY than in DMRT1. Third, in DMRT1, the dN/dS ratio for the DM domain is lower than that for non-DM regions, as expected from the functional importance of the DM domain. But in DMY, the opposite is observed and the DM domain is likely under positive Darwinian selection. Fourth, only one characteristic amino acid distinguishes all DMY sequences from all DMRT1 sequences, suggesting that a single amino acid change may be largely responsible for the establishment of DMY as the male sex-determination gene in medaka fish.
Spatial and temporal variability in somatic growth in fisheries stock assessment models: evaluating the consequences of misspecification
Authors: Correa Giancarlo M , McGilliard Carey R , Ciannelli Lorenzo , Fuentes Claudio 
Published: April 2021

AbstractDistinct types of fish species experience variation in somatic growth rates over their life span; however, growth has historically been assumed to be invariant across time and space in integrated analysis-based stock assessment. A few previous studies have reported biased and imprecise assessment model outcomes when variability in somatic growth was ignored. In this study, we used a simulation-estimation framework to expand previous analyses and to examine the consequences of ignoring or incorporating spatial and temporal (year- and cohort-specific) variability in somatic growth in stock assessment models. The study included three life history types: small pelagic (e.g. sardine), gadids (e.g. cod), and long-lived (e.g. rockfish). In general, ignoring any type of variability in somatic growth led to biased and imprecise estimates of stock spawning biomass and management quantities. Unequal distribution of fishing mortality across space had large impacts on the performance of estimation models as well. Conversely, accounting for somatic growth variability, either by including an environmental index, estimating annual deviates, or implementing a spatially explicit model, produced unbiased and precise results. This study shows that somatic growth variability might produce large effects in stock assessments when ignored and provides pertinent information for stock assessment best practice guidelines.
An unfitted Eulerian finite element method for the time-dependent Stokes problem on moving domains
Authors: von Wahl Henry , Richter Thomas , Lehrenfeld Christoph 
Published: April 2021

Abstract
We analyse a Eulerian finite element method, combining a Eulerian time-stepping scheme applied to the time-dependent Stokes equations with the CutFEM approach using inf-sup stable Taylor–Hood elements for the spatial discretization. This is based on the method introduced by Lehrenfeld & Olshanskii (2019, A Eulerian finite element method for PDEs in time-dependent domains. ESAIM: M2AN, 53, 585–614) in the context of a scalar convection–diffusion problems on moving domains, and extended to the nonstationary Stokes problem on moving domains by Burman et al. (2019, arXiv:1910.03054 [math.NA]) using stabilized equal-order elements. The analysis includes the geometrical error made by integrating over approximated level set domains in the discrete CutFEM setting. The method is implemented and the theoretical results are illustrated using numerical examples.
Is the German Nuclear strategy lawful under EU law? Article 194(2) TFEU and its limitations
Authors: Rochette Gustavo , Vela Elena 
Published: April 2021

Abstract
Germany streamlined its nuclear phase-out policy following the Fukushima Daishi nuclear accident, planning to decommission all of its nuclear capacity by 2022. As a member of the EU, although Germany is entitled to determine its own energy mix pursuant to Article 194(2) of the TFEU, this policy may conflict with other EU legislation and jurisprudence relevant to the EU energy sector. In particular, in this paper, we argue that the German nuclear phase-out may be contrary to the European Atomic Energy Community Treaty and the primary and secondary EU legislation regarding security of energy supply. We explore how Germany’s commitments under this legislation act as a limitation to its national energy policy autonomy and might entail the unlawfulness of the German nuclear phase-out strategy.
Non-glandular trichomes of sunflower are important in the absorption and translocation of foliar-applied Zn
Authors: Li Cui , Wu Jingtao , Blamey F Pax C , Wang Linlin , Zhou Lina , Paterson David J , van der Ent Antony , Fernández Victoria , Lombi Enzo , Wang Yuheng , Kopittke Peter M 
Published: April 2021

AbstractTrichomes are potentially important for absorption of foliar fertilizers. A study has shown that the non-glandular trichromes (NGTs) of sunflower (Helianthus annuus) accumulated high concentrations of foliar-applied zinc (Zn); however, the mechanisms of Zn accumulation in the NGTs and the fate of this Zn are unclear. Here we investigated how foliar-applied Zn accumulates in the NGTs and the subsequent translocation of this Zn. Time-resolved synchrotron-based X-ray fluorescence microscopy and transcriptional analyses were used to probe the movement of Zn in the NGTs, with the cuticle composition of the NGTs examined using confocal Raman microscopy. The accumulation of Zn in the NGTs is both an initial preferential absorption process and a subsequent translocation process. This preferred absorption is likely because the NGT base has a higher hydrophilicity, whilst the subsequent translocation is due to the presence of plasmodesmata, Zn-chelating ligands, and Zn transporters in the NGTs. Furthermore, the Zn sequestered in the NGTs was eventually translocated out of the trichome once the leaf Zn concentration had decreased, suggesting that the NGTs are also important in maintaining leaf Zn homeostasis. This study demonstrates for the first time that trichomes have a key structural and functional role in the absorption and translocation of foliar-applied Zn.
Overexpression of thioredoxin m in chloroplasts alters carbon and nitrogen partitioning in tobacco
Authors: Ancín María , Larraya Luis , Florez-Sarasa Igor , Bénard Camille , Fernández-San Millán Alicia , Veramendi Jon , Gibon Yves , Fernie Alisdair R , Aranjuelo Iker , Farran Inmaculada 
Published: April 2021

Abstract
In plants, there is a complex interaction between carbon (C) and nitrogen (N) metabolism, and its coordination is fundamental for plant growth and development. Here, we studied the influence of thioredoxin (Trx) m on C and N partitioning using tobacco plants overexpressing Trx m from the chloroplast genome. The transgenic plants showed altered metabolism of C (lower leaf starch and soluble sugar accumulation) and N (with higher amounts of amino acids and soluble protein), which pointed to an activation of N metabolism at the expense of carbohydrates. To further delineate the effect of Trx m overexpression, metabolomic and enzymatic analyses were performed on these plants. These results showed an up-regulation of the glutamine synthetase–glutamate synthase pathway; specifically tobacco plants overexpressing Trx m displayed increased activity and stability of glutamine synthetase. Moreover, higher photorespiration and nitrate accumulation were observed in these plants relative to untransformed control plants, indicating that overexpression of Trx m favors the photorespiratory N cycle rather than primary nitrate assimilation. Taken together, our results reveal the importance of Trx m as a molecular mediator of N metabolism in plant chloroplasts.