bluuebunny/crossref_metadata_2025 huggingface dataset:
The Roles of REV3 and RAD57 in Double-Strand-Break-Repair-Induced Mutagenesis of Saccharomyces cerevisiae
Authors: Rattray Alison J , Shafer Brenda K , McGill Carolyn B , Strathern Jeffrey N
Published: April 2021

The DNA synthesis associated with recombinational repair of chromosomal double-strand breaks (DSBs) has a lower fidelity than normal replicative DNA synthesis. Here, we use an inverted-repeat substrate to monitor the fidelity of repair of a site-specific DSB. DSB induction made by the HO endonuclease stimulates recombination >5000-fold and is associated with a >1000-fold increase in mutagenesis of an adjacent gene. We demonstrate that most break-repair-induced mutations (BRIMs) are point mutations and have a higher proportion of frameshifts than do spontaneous mutations of the same substrate. Although the REV3 translesion DNA polymerase is not required for recombination, it introduces ∼75% of the BRIMs and ∼90% of the base substitution mutations. Recombinational repair of the DSB is strongly dependent upon genes of the RAD52 epistasis group; however, the residual recombinants present in rad57 mutants are associated with a 5- to 20-fold increase in BRIMs. The spectrum of mutations in rad57 mutants is similar to that seen in the wild-type strain and is similarly affected by REV3. We also find that REV3 is required for the repair of MMS-induced lesions when recombinational repair is compromised. Our data suggest that Rad55p/Rad57p help limit the generation of substrates that require pol ζ during recombination.
The Y Chromosome of Drosophila melanogaster Exhibits Chromosome-Wide Imprinting
Authors: Maggert Keith A , Golic Kent G
Published: April 2021

Genomic imprinting is well known as a regulatory property of a few specific chromosomal regions and leads to differential behavior of maternally and paternally inherited alleles. We surveyed the activity of two reporter genes in 23 independent P-element insertions on the heterochromatic Y chromosome of Drosophila melanogaster and found that all but one location showed differential expression of one or both genes according to the parental source of the chromosome. In contrast, genes inserted in autosomal heterochromatin generally did not show imprint-regulated expression. The imprints were established on Y-linked transgenes inserted into many different sequences and locations. We conclude that genomic imprinting affecting gene expression is a general property of the Drosophila Y chromosome and distinguishes the Y from the autosomal complement.
Quantitative Trait Loci for Maternal Performance for Offspring Survival in Mice
Authors: Peripato Andréa C , de Brito Reinaldo A , Vaughn Ty T , Pletscher L Susan , Matioli Sergio R , Cheverud James M
Published: April 2021

Maternal performance refers to the effect that the environment provided by mothers has on their offspring’s phenotypes, such as offspring survival and growth. Variations in maternal behavior and physiology are responsible for variations in maternal performance, which in turn affects offspring survival. In our study we found females that failed to nurture their offspring and showed abnormal maternal behaviors. The genetic architecture of maternal performance for offspring survival was investigated in 241 females of an F2 intercross of the SM/J and LG/J inbred mouse strains. Using interval-mapping methods we found two quantitative trait loci (QTL) affecting maternal performance at D2Mit17 + 6 cM and D7Mit21 + 2 cM on chromosomes 2 and 7, respectively. In a two-way genome-wide epistasis scan we found 15 epistatic interactions involving 23 QTL distributed across all chromosomes except 12, 16, and 17. These loci form several small sets of interacting QTL, suggesting a complex set of mechanisms operating to determine maternal performance for offspring survival. Taken all together and correcting for the large number of significant factors, QTL and their interactions explain almost 35% of the phenotypic variation for maternal performance for offspring survival in this cross. This study allowed the identification of many possible candidate genes, as well as the relative size of gene effects and patterns of gene action affecting maternal performance in mice. Detailed behavior observation of mothers from later generations suggests that offspring survival in the first week is related to maternal success in building nests, grooming their pups, providing milk, and/or manifesting aggressive behavior against intruders.
Sex-Specific Differences in Meiotic Chromosome Segregation Revealed by Dicentric Bridge Resolution in Mice
Authors: Koehler Kara E , Millie Elise A , Cherry Jonathan P , Burgoyne Paul S , Evans Edward P , Hunt Patricia A , Hassold Terry J
Published: April 2021

The meiotic properties of paracentric inversion heterozygotes have been well studied in insects and plants, but not in mammalian species. In essence, a single meiotic recombination event within the inverted region results in the formation of a dicentric chromatid, which usually breaks or is stretched between the two daughter nuclei during the first meiotic anaphase. Here, we provide evidence that this is not the predominant mode of exchange resolution in female mice. In sharp contrast to previous observations in other organisms, we find that attempts to segregate the dicentric chromatid frequently result not in breakage, stretching, or loss, but instead in precocious separation of the sister centromeres of at least one homolog. This often further results in intact segregation of the dicentric into one of the meiotic products, where it can persist into the first few embryonic divisions. These novel observations point to an unusual mechanism for the processing of dicentric chromosomes in mammalian oogenesis. Furthermore, this mechanism is rare or nonexistent in mammalian spermatogenesis. Thus, our results provide additional evidence of sexual dimorphism in mammalian meiotic chromosome behavior; in “stressful” situations, meiotic sister chromatid cohesion is apparently handled differently in males than in females.
Characterization and Effects of the Replicated Flowering Time Gene FLC in Brassica rapa
Authors: Schranz M Eric , Quijada Pablo , Sung Si-Bum , Lukens Lewis , Amasino Richard , Osborn Thomas C
Published: April 2021

Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time.
Control of Vulval Competence and Centering in the Nematode Oscheius sp. 1 CEW1
Authors: Louvet-Vallée Sophie , Kolotuev Irina , Podbilewicz Benjamin , Félix Marie-Anne
Published: April 2021

To compare vulva development mechanisms in the nematode Oscheius sp. 1 to those known in Caenorhabditis elegans, we performed a genetic screen for vulva mutants in Oscheius sp. 1 CEW1. Here we present one large category of mutations that we call cov, which affect the specification of the Pn.p ventral epidermal cells along the antero-posterior axis. The Pn.p cells are numbered from 1 to 12 from anterior to posterior. In wild-type Oscheius sp. 1 CEW1, the P(4-8).p cells are competent to form the vulva and the progeny of P(5-7).p actually form the vulva, with the descendants of P6.p adopting a central vulval fate. Among the 17 mutations (defining 13 genes) that we characterize here, group 1 mutations completely or partially abolish P(4-8).p competence, and this correlates with early fusion of the Pn.p cells to the epidermal syncytium. In this group, we found a putative null mutation in the lin-39 HOM-C homolog, the associated phenotype of which could be weakly mimicked by injection of a morpholino against Osp1-lin-39 in the mother’s germ line. Using cell ablation in a partially penetrant competence mutant, we show that vulval competence is partially controlled by a gonadal signal. Most other mutants found in the screen display phenotypes unknown in C. elegans. Group 2 mutants show a partial penetrance of Pn.p competence loss and an abnormal centering of the vulva on P5.p, suggesting that these two processes are coregulated by the same pathway in Oscheius sp. 1. Group 3 mutants display an enlarged competence group that includes P3.p, thus demonstrating the existence of a specific mechanism inhibiting P3.p competence. Group 4 mutants display an abnormal centering of the vulval pattern on P7.p and suggest that a specific mechanism centers the vulval pattern on a single Pn.p cell.
A P-Element Insertion Screen Identified Mutations in 455 Novel Essential Genes in Drosophila
Authors: Oh Su-Wan , Kingsley Tracy , Shin Hyun-hee , Zheng Zhiyu , Chen Hua-Wei , Chen Xiu , Wang Hong , Ruan Peizheng , Moody Michelle , Hou Steven X
Published: April 2021

With the completion of the nucleotide sequences of several complex eukaryotic genomes, tens of thousands of genes have been predicted. However, this information has to be correlated with the functions of those genes to enhance our understanding of biology and to improve human health care. The Drosophila transposon P-element-induced mutations are very useful for directly connecting gene products to their biological function. We designed an efficient transposon P-element-mediated gene disruption procedure and performed genetic screening for single P-element insertion mutations, enabling us to recover 2500 lethal mutations. Among these, 2355 are second chromosome mutations. Sequences flanking >2300 insertions that identify 850 different genes or ESTs (783 genes on the second chromosome and 67 genes on the third chromosome) have been determined. Among these, 455 correspond to genes for which no lethal mutation has yet been reported. The Drosophila genome is thought to contain ∼3600 vital genes; 1400 are localized on the second chromosome. Our mutation collection represents ∼56% of the second chromosome vital genes and ∼24% of the total vital Drosophila genes.
Loss of CDC5 Function in Saccharomyces cerevisiae Leads to Defects in Swe1p Regulation and Bfa1p/Bub2p-Independent Cytokinesis
Authors: Park Chong Jin , Song Sukgil , Lee Philip R , Shou Wenying , Deshaies Raymond J , Lee Kyung S
Published: April 2021

In many organisms, polo kinases appear to play multiple roles during M-phase progression. To provide new insights into the function of budding yeast polo kinase Cdc5p, we generated novel temperature-sensitive cdc5 mutants by mutagenizing the C-terminal domain. Here we show that, at a semipermissive temperature, the cdc5-3 mutant exhibited a synergistic bud elongation and growth defect with loss of HSL1, a component important for normal G2/M transition. Loss of SWE1, which phosphorylates and inactivates the budding yeast Cdk1 homolog Cdc28p, suppressed the cdc5-3 hsl1Δ defect, suggesting that Cdc5p functions at a point upstream of Swe1p. In addition, the cdc5-4 and cdc5-7 mutants exhibited chained cell morphologies with shared cytoplasms between the connected cell bodies, indicating a cytokinetic defect. Close examination of these mutants revealed delayed septin assembly at the incipient bud site and loosely organized septin rings at the mother-bud neck. Components in the mitotic exit network (MEN) play important roles in normal cytokinesis. However, loss of BFA1 or BUB2, negative regulators of the MEN, failed to remedy the cytokinetic defect of these mutants, indicating that Cdc5p promotes cytokinesis independently of Bfa1p and Bub2p. Thus, Cdc5p contributes to the activation of the Swe1p-dependent Cdc28p/Clb pathway, normal septin function, and cytokinesis.
In VivoIntroduction of Unpreferred Synonymous Codons Into the DrosophilaAdhGene Results in Reduced Levels of ADH Protein
Authors: Carlini David B , Stephan Wolfgang
Published: April 2021

The evolution of codon bias, the unequal usage of synonymous codons, is thought to be due to natural selection for the use of preferred codons that match the most abundant species of isoaccepting tRNA, resulting in increased translational efficiency and accuracy. We examined this hypothesis by introducing 1, 6, and 10 unpreferred codons into the Drosophila alcohol dehydrogenase gene (Adh). We observed a significant decrease in ADH protein production with number of unpreferred codons, confirming the importance of natural selection as a mechanism leading to codon bias. We then used this empirical relationship to estimate the selection coefficient (s) against unpreferred synonymous mutations and found the value (s ≥ 10-5) to be approximately one order of magnitude greater than previous estimates from population genetics theory. The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster.
Unexpected Complexity of Poly(A)-Binding Protein Gene Families in Flowering Plants: Three Conserved Lineages That Are at Least 200 Million Years Old and Possible Auto- and Cross-Regulation
Authors: Belostotsky Dmitry A
Published: April 2021

Eukaryotic poly(A)-binding protein (PABP) is a ubiquitous, essential factor involved in mRNA biogenesis, translation, and turnover. Most eukaryotes examined have only one or a few PABPs. In contrast, eight expressed PABP genes are present in Arabidopsis thaliana. These genes fall into three distinct classes, based on highly concordant results of (i) phylogenetic analysis of the amino acid sequences of the encoded proteins, (ii) analysis of the intron number and placement, and (iii) surveys of gene expression patterns. Representatives of each of the three classes also exist in the rice genome, suggesting that the diversification of the plant PABP genes has occurred prior to the split of monocots and dicots ≥200 MYA. Experiments with the recombinant PAB3 protein suggest the possibility of a negative feedback regulation, as well as of cross-regulation between the Arabidopsis PABPs that belong to different classes but are simultaneously expressed in the same cell type. Such a high complexity of the plant PABPs might enable a very fine regulation of organismal growth and development at the post-transcriptional level, compared with PABPs of other eukaryotes.
Bounds on the Minimum Number of Recombination Events in a Sample History
Authors: Myers Simon R , Griffiths Robert C
Published: April 2021

Recombination is an important evolutionary factor in many organisms, including humans, and understanding its effects is an important task facing geneticists. Detecting past recombination events is thus important; this article introduces statistics that give a lower bound on the number of recombination events in the history of a sample, on the basis of the patterns of variation in the sample DNA. Such lower bounds are appropriate, since many recombination events in the history are typically undetectable, so the true number of historical recombinations is unobtainable. The statistics can be calculated quickly by computer and improve upon the earlier bound of Hudson and Kaplan (1985). A method is developed to combine bounds on local regions in the data to produce more powerful improved bounds. The method is flexible to different models of recombination occurrence. The approach gives recombination event bounds between all pairs of sites, to help identify regions with more detectable recombinations, and these bounds can be viewed graphically. Under coalescent simulations, there is a substantial improvement over the earlier method (of up to a factor of 2) in the expected number of recombination events detected by one of the new minima, across a wide range of parameter values. The method is applied to data from a region within the lipoprotein lipase gene and the amount of detected recombination is substantially increased. Further, there is strong clustering of detected recombination events in an area near the center of the region. A program implementing these statistics, which was used for this article, is available from http://www.stats.ox.ac.uk/mathgen/programs.html.
Polymorphism and Divergence for Island-Model Species
Authors: Wakeley John
Published: April 2021

Estimates of the scaled selection coefficient, γ of Sawyer and Hartl, are shown to be remarkably robust to population subdivision. Estimates of mutation parameters and divergence times, in contrast, are very sensitive to subdivision. These results follow from an analysis of natural selection and genetic drift in the island model of subdivision in the limit of a very large number of subpopulations, or demes. In particular, a diffusion process is shown to hold for the average allele frequency among demes in which the level of subdivision sets the timescale of drift and selection and determines the dynamic equilibrium of allele frequencies among demes. This provides a framework for inference about mutation, selection, divergence, and migration when data are available from a number of unlinked nucleotide sites. The effects of subdivision on parameter estimates depend on the distribution of samples among demes. If samples are taken singly from different demes, the only effect of subdivision is in the rescaling of mutation and divergence-time parameters. If multiple samples are taken from one or more demes, high levels of within-deme relatedness lead to low levels of intraspecies polymorphism and increase the number of fixed differences between samples from two species. If subdivision is ignored, mutation parameters are underestimated and the species divergence time is overestimated, sometimes quite drastically. Estimates of the strength of selection are much less strongly affected and always in a conservative direction.
Identification of a Functional Domain Within the Essential Core of Histone H3 That Is Required for Telomeric and HM Silencing in Saccharomyces cerevisiae
Authors: Thompson Jeffrey S , Snow Marilyn L , Giles Summer , McPherson Leslie E , Grunstein Michael
Published: April 2021

Fourteen novel single-amino-acid substitution mutations in histone H3 that disrupt telomeric silencing in Saccharomyces cerevisiae were identified, 10 of which are clustered within the α1 helix and L1 loop of the essential histone fold. Several of these mutations cause derepression of silent mating locus HML, and an additional subset cause partial loss of basal repression at the GAL1 promoter. Our results identify a new domain within the essential core of histone H3 that is required for heterochromatin-mediated silencing.
Large-Scale Functional Genomic Analysis of Sporulation and Meiosis in Saccharomyces cerevisiae
Authors: Enyenihi Akon H , Saunders William S
Published: April 2021

We have used a single-gene deletion mutant bank to identify the genes required for meiosis and sporulation among 4323 nonessential Saccharomyces cerevisiae annotated open reading frames (ORFs). Three hundred thirty-four sporulation-essential genes were identified, including 78 novel ORFs and 115 known genes without previously described sporulation defects in the comprehensive Saccharomyces Genome (SGD) or Yeast Proteome (YPD) phenotype databases. We have further divided the uncharacterized sporulation-essential genes into early, middle, and late stages of meiosis according to their requirement for IME1 induction and nuclear division. We believe this represents a nearly complete identification of the genes uniquely required for this complex cellular pathway. The set of genes identified in this phenotypic screen shows only limited overlap with those identified by expression-based studies.
Molecular Evolution of the Escherichia coli Chromosome. VI. Two Regions of High Effective Recombination
Authors: Milkman Roger , Jaeger Erich , McBride Ryan D
Published: April 2021

Two 6- to 8-min regions, centered respectively near 45 min (O-antigen region) and 99 min (restriction-modification region) on the Escherichia coli chromosome, display unusually high variability among 11 otherwise very similar strains. This variation, revealed by restriction fragment length polymorphism (RFLP) and nucleotide sequence comparisons, appears to be due to a great local increase in the retention frequency of recombinant replacements. We infer a two-step mechanism. The first step is the acquisition of a small stretch of DNA from a phylogenetically distant source. The second is the successful retransmission of the imported DNA, together with flanking native DNA, to other strains of E. coli. Each cell containing the newly transferred DNA has a very high selective advantage until it reaches a high frequency and (in the O-antigen case) is recognized by the new host's immune system. A high selective advantage increases the probability of retention greatly; the effective recombination rate is the product of the basic recombination rate and the probability of retention. Nearby nucleotide sequences clockwise from the O-antigen (rfb) region are correlated with specific O antigens, confirming local hitchhiking. Comparable selection involving imported restriction endonuclease genes is proposed for the region near 99 min.
Inbreeding and the Genetic Complexity of Human Hypertension
Authors: Rudan Igor , Smolej-Narancic Nina , Campbell Harry , Carothers Andrew , Wright Alan , Janicijevic Branka , Rudan Pavao
Published: April 2021

Considerable uncertainty exists regarding the genetic architecture underlying common late-onset human diseases. In particular, the contribution of deleterious recessive alleles has been predicted to be greater for late-onset than for early-onset traits. We have investigated the contribution of recessive alleles to human hypertension by examining the effects of inbreeding on blood pressure (BP) as a quantitative trait in 2760 adult individuals from 25 villages within Croatian island isolates. We found a strong linear relationship between the inbreeding coefficient (F) and both systolic and diastolic BP, indicating that recessive or partially recessive quantitative trait locus (QTL) alleles account for 10-15% of the total variation in BP in this population. An increase in F of 0.01 corresponded to an increase of ∼3 mm Hg in systolic and 2 mm Hg in diastolic BP. Regression of F on BP indicated that at least several hundred (300-600) recessive QTL contribute to BP variability. A model of the distribution of locus effects suggests that the 8-16 QTL of largest effect together account for a maximum of 25% of the dominance variation, while the remaining 75% of the variation is mediated by QTL of very small effect, unlikely to be detectable using current technologies and sample sizes. We infer that recent inbreeding accounts for 36% of all hypertension in this population. The global impact of inbreeding on hypertension may be substantial since, although inbreeding is declining in Western societies, an estimated 1 billion people globally show rates of consanguineous marriages >20%.
Analyses for the Presence of a Major Gene Affecting Uterine Capacity in Unilaterally Ovariectomized Rabbits
Authors: Argente M J , Blasco A , Ortega J A , Haley C S , Visscher P M
Published: April 2021

The presence of a major gene for uterine capacity (UC), ovulation rate (OR), number of implanted embryos (IE), embryo survival (ES), fetal survival (FS), and prenatal survival (PS) was investigated in a population of rabbits divergently selected for UC for 10 generations. Selection was performed on estimated breeding values for UC up to four parities. UC was estimated as litter size in the remaining overcrowded horn of unilaterally ovariectomized does. OR and IE were counted by means of laparoscopy. Bartlett’s test, Fain’s test, and a complex segregation analysis using Bayesian methods were used to test for the presence of a major gene. All three tests showed that the data appeared consistent with the presence of a major gene affecting UC and IE. The results of the complex segregation analysis suggested the presence of a major gene with large effect on IE and ES (a > 1σp), at high frequency (p = 0.70 and 0.68, respectively), and with a large contribution to the total variance (Rg = 0.39 and 0.47, respectively); and the presence of a major gene with moderate effect on each of OR, FS, PS, and UC. The results suggest that the studied reproductive traits are determined genetically by at least one gene of large effect.
Single-Nucleotide Polymorphisms in Soybean
Authors: Zhu Y L , Song Q J , Hyten D L , Van Tassell C P , Matukumalli L K , Grimm D R , Hyatt S M , Fickus E W , Young N D , Cregan P B
Published: April 2021

Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson’s θ was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r2) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.
Neutrality Tests Using DNA Polymorphism From Multiple Samples
Authors: Li Haipeng , Zhang Yunwu , Zhang Ya-Ping , Fu Yun-Xin
Published: April 2021

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data. This article provides a procedure to conduct a neutrality test and details are given for two commonly used tests. Applying the two new tests to the chemokine-receptor gene (CCR5) in humans, we found that the hypothesis that all mutations are selectively neutral cannot explain the observed pattern of DNA polymorphism.
Mapping Quantitative Trait Loci in the Case of a Spike in the Phenotype Distribution
Authors: Broman Karl W
Published: April 2021

A common departure from the usual normality assumption in QTL mapping concerns a spike in the phenotype distribution. For example, in measurements of tumor mass, some individuals may exhibit no tumors; in measurements of time to death after a bacterial infection, some individuals may recover from the infection and fail to die. If an appreciable portion of individuals share a common phenotype value (generally either the minimum or the maximum observed phenotype), the standard approach to QTL mapping can behave poorly. We describe several alternative approaches for QTL mapping in the case of such a spike in the phenotype distribution, including the use of a two-part parametric model and a nonparametric approach based on the Kruskal-Wallis test. The performance of the proposed procedures is assessed via computer simulation. The procedures are further illustrated with data from an intercross experiment to identify QTL contributing to variation in survival of mice following infection with Listeria monocytogenes.
Bayesian Sperm Competition Estimates
Authors: Jones Beatrix , Clark Andrew G
Published: April 2021

We introduce a Bayesian method for estimating parameters for a model of multiple mating and sperm displacement from genotype counts of brood-structured data. The model is initially targeted for Drosophila melanogaster, but is easily adapted to other organisms. The method is appropriate for use with field studies where the number of mates and the genotypes of the mates cannot be controlled, but where unlinked markers have been collected for a set of females and a sample of their offspring. Advantages over previous approaches include full use of multilocus information and the ability to cope appropriately with missing data and ambiguities about which alleles are maternally vs. paternally inherited. The advantages of including X-linked markers are also demonstrated.
Ku-Dependent and Ku-Independent End-Joining Pathways Lead to Chromosomal Rearrangements During Double-Strand Break Repair in Saccharomyces cerevisiae
Authors: Yu Xin , Gabriel Abram
Published: April 2021

Chromosomal double-strand breaks (DSBs) can be repaired by either homology-dependent or homology-independent pathways. Nonhomologous repair mechanisms have been relatively less well studied, despite their potential importance in generating chromosomal rearrangements. We have developed a Saccharomyces cerevisiae-based assay to identify and characterize homology-independent chromosomal rearrangements associated with repair of a unique DSB generated within an engineered URA3 gene. Approximately 1% of successfully repaired cells have accompanying chromosomal rearrangements consisting of large insertions, deletions, aberrant gene conversions, or other more complex changes. We have analyzed rearrangements in isogenic wild-type, rad52, yku80, and rad52 yku80 strains, to determine the types of events that occur in the presence or absence of these key repair proteins. Deletions were found in all strain backgrounds, but insertions were dependent upon the presence of Yku80p. A rare RAD52- and YKU80-independent form of deletion was present in all strains. These events were characterized by long one-sided deletions (up to 13 kb) and extensive imperfect overlapping sequences (7-22 bp) at the junctions. Our results demonstrate that the frequency and types of repair events depend on the specific genetic context. This approach can be applied to a number of problems associated with chromosome stability.
DIM-1, a Novel Immunoglobulin Superfamily Protein in Caenorhabditis elegans, Is Necessary for Maintaining Bodywall Muscle Integrity
Authors: Rogalski Teresa M , Gilbert Mary M , Devenport Danelle , Norman Kenneth R , Moerman Donald G
Published: April 2021

The UNC-112 protein is required during initial muscle assembly in C. elegans to form dense bodies and M-lines. Loss of this protein results in arrest at the twofold stage of embryogenesis. In contrast, a missense mutation in unc-112 results in viable animals that have disorganized bodywall muscle and are paralyzed as adults. Loss or reduction of dim-1 gene function can suppress the severe muscle disruption and paralysis exhibited by these mutant hermaphrodites. The overall muscle structure in hermaphrodites lacking a functional dim-1 gene is slightly disorganized, and the myofilament lattice is not as strongly anchored to the muscle cell membrane as it is in wild-type muscle. The dim-1 gene encodes two polypeptides that contain three Ig-like repeats. The short DIM-1 protein isoform consists entirely of three Ig repeats and is sufficient for wild-type bodywall muscle structure and stability. DIM-1(S) localizes to the region of the muscle cell membrane around and between the dense bodies, which are the structures that anchor the actin filaments and may play a role in stabilizing the thin rather than the thick filament components of the sarcomere.
Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool
Authors: Xu Zheng , Lance Britton , Vargas Claudia , Arpinar Budak , Bhandarkar Suchendra , Kraemer Eileen , Kochut Krys J , Miller John A , Wagner Jeff R , Weise Michael J , Wunderlich John K , Stringer James , Smulian George , Cushion Melanie T , Arnold Jonathan
Published: April 2021

A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock Ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.
Drosophila Tufted Is a Gain-of-Function Allele of the Proneural Gene amos
Authors: Lai Eric C
Published: April 2021

Tufted is a classical Drosophila mutant characterized by a large number of ectopic mechanosensory bristles on the dorsal mesothorax. Unlike other ectopic bristle mutants, Tufted is epistatic to achaete and scute, the proneural genes that normally control the development of these sensory organs. In this report, I present genetic and molecular evidence that Tufted is a gain-of-function allele of the proneural gene amos that ectopically activates mechanosensory neurogenesis. I also systematically examine the ability of the various proneural bHLH proteins to cross-activate each other and find that their ability to do so is in general relatively limited, despite their common ability to induce the formation of mechanosensory bristles. This phenomenon seems instead to be related to their shared ability to activate Asense and Senseless.
A Genetic Screen for Hedgehog Targets Involved in the Maintenance of the Drosophila Anteroposterior Compartment Boundary
Authors: Végh Mátyás , Basler Konrad
Published: April 2021

The development of multicellular organisms requires the establishment of cell populations with different adhesion properties. In Drosophila, a cell-segregation mechanism underlies the maintenance of the anterior (A) and posterior (P) compartments of the wing imaginal disc. Although engrailed (en) activity contributes to the specification of the differential cell affinity between A and P cells, recent evidence suggests that cell sorting depends largely on the transduction of the Hh signal in A cells. The activator form of Cubitus interruptus (Ci), a transcription factor mediating Hh signaling, defines anterior specificity, indicating that Hh-dependent cell sorting requires Hh target gene expression. However, the identity of the gene(s) contributing to distinct A and P cell affinities is unknown. Here, we report a genetic screen based on the FRT/FLP system to search for genes involved in the correct establishment of the anteroposterior compartment boundary. By using double FRT chromosomes in combination with a wing-specific FLP source we screened 250,000 mutagenized chromosomes. Several complementation groups affecting wing patterning have been isolated, including new alleles of most known Hh-signaling components. Among these, we identified a class of patched (ptc) alleles exhibiting a novel phenotype. These results demonstrate the value of our setup in the identification of genes involved in distinct wing-patterning processes.
Mutation Rate and Novel tt Mutants of Arabidopsis thaliana Induced by Carbon Ions
Authors: Shikazono Naoya , Yokota Yukihiko , Kitamura Satoshi , Suzuki Chihiro , Watanabe Hiroshi , Tano Shigemitsu , Tanaka Atsushi
Published: April 2021

Irradiation of Arabidopsis thaliana by carbon ions was carried out to investigate the mutational effect of ion particles in higher plants. Frequencies of embryonic lethals and chlorophyll-deficient mutants were found to be significantly higher after carbon-ion irradiation than after electron irradiation (11-fold and 7.8-fold per unit dose, respectively). To estimate the mutation rate of carbon ions, mutants with no pigments on leaves and stems (tt) and no trichomes on leaves (gl) were isolated at the M2 generation and subjected to analysis. Averaged segregation rate of the backcrossed mutants was 0.25, which suggested that large deletions reducing the viability of the gametophytes were not transmitted, if generated, in most cases. During the isolation of mutants, two new classes of flavonoid mutants (tt18, tt19) were isolated from carbon-ion-mutagenized M2 plants. From PCR and sequence analysis, two of the three tt18 mutant alleles were found to have a small deletion within the LDOX gene and the other was revealed to contain a rearrangement. Using the segregation rates, the mutation rate of carbon ions was estimated to be 17-fold higher than that of electrons. The isolation of novel mutants and the high mutation rate suggest that ion particles can be used as a valuable mutagen for plant genetics.
The Quality Measures Domain in Nursing Home Compare: Is High Performance Meaningful or Misleading?
Authors: Konetzka R Tamara , Davila Heather , Brauner Daniel J , Cursio John F , Sharma Hari , Werner Rachel M , Park Young Shin , Shippee Tetyana P
Published: April 2021

Background and Objectives

The reported percent of nursing home residents suffering adverse outcomes decreased dramatically since Nursing Home Compare began reporting them, but the validity of scores is questionable for nursing homes that score well on measures using facility-reported data but poorly on inspections. Our objective was to assess whether nursing homes with these “discordant” scores are meaningfully better than nursing homes that score poorly across domains.

Research Design and Methods

We used a convergent mixed-methods design, starting with quantitative analyses of 2012–2016 national data. We conducted in-depth interviews and observations in 12 nursing homes in 2017–2018, focusing on how facilities achieved their Nursing Home Compare ratings. Additional quantitative analyses were conducted in parallel to study performance trajectories over time. Quantitative and qualitative results were interpreted together.

Results

Discordant facilities engage in more quality improvement strategies than poor performers, but do not seem to invest in quality improvement in resource-intensive, broad-based ways that would spill over into other domains of quality and change their trajectory of improvement. Instead, they focus on lower-resource improvements related to data quality, staff training, leadership, and communication. In contrast, poor-performing facilities seemed to lack the leadership and continuity of staff required for even these low-resource interventions.

Discussion and Implications

High performance on the quality measures using facility-reported data is mostly meaningful rather than misleading to consumers who care about those outcomes, although discordant facilities still have quality deficits. The quality measures domain should continue to have a role in Nursing Home Compare.
A cross-tissue transcriptome-wide association study identifies novel susceptibility genes for lung cancer in Chinese populations
Authors: Zhu Meng , Fan Jingyi , Zhang Chang , Xu Jing , Yin Rong , Zhang Erbao , Wang Yuzhuo , Ji Mengmeng , Sun Qi , Dai Juncheng , Jin Guangfu , Chen Liang , Xu Lin , Hu Zhibin , Ma Hongxia , Shen Hongbing
Published: April 2021

Although dozens of susceptibility loci have been identified for lung cancer in genome-wide association studies (GWASs), the susceptibility genes and underlying mechanisms remain unclear. In this study, we conducted a cross-tissue transcriptome-wide association study (TWAS) with UTMOST based on summary statistics from 13 327 lung cancer cases and 13 328 controls and the genetic-expression matrix over 44 human tissues in the Genotype-Tissue Expression (GTEx) project. After further evaluating the associations in each tissue, we revealed 6 susceptibility genes in known loci and identified 12 novel ones. Among those, five novel genes, including DCAF16 (Pcross-tissue = 2.57 × 10−5, PLung = 2.89 × 10−5), CBL (Pcross-tissue = 5.08 × 10−7, PLung = 1.82 × 10−4), ATR (Pcross-tissue = 1.45 × 10−5, PLung = 9.68 × 10−5), GYPE (Pcross-tissue = 1.45 × 10−5, PLung = 2.17 × 10−3) and PARD3 (Pcross-tissue = 5.79 × 10−6, PLung = 4.05 × 10−3), were significantly associated with the risk of lung cancer in both cross-tissue and lung tissue models. Further colocalization analysis indicated that rs7667864 (C > A) and rs2298650 (G > T) drove the GWAS association signals at 4p15.31–32 (OR = 1.09, 95%CI: 1.04–1.12, PGWAS = 5.54 × 10−5) and 11q23.3 (OR = 1.08, 95%CI: 1.04–1.13, PGWAS = 5.55 × 10−5), as well as the expression of DCAF16 (βGTEx = 0.24, PGTEx = 9.81 × 10−15; βNJLCC = 0.29, PNJLCC = 3.84 × 10−8) and CBL (βGTEx = −0.17, PGTEx = 2.82 × 10−8; βNJLCC = −0.32, PNJLCC = 2.61 × 10−7) in lung tissue. Functional annotations and phenotype assays supported the carcinogenic effect of these novel susceptibility genes in lung carcinogenesis.
Fertility treatment with clomiphene citrate and childhood epilepsy: a nationwide cohort study
Authors: Kettner L O , Matthiesen N B , Ramlau-Hansen C H , Kesmodel U S , Henriksen T B
Published: April 2021

STUDY QUESTION

Is fertility treatment with clomiphene citrate associated with an increased risk of childhood epilepsy, including specific subtypes of epilepsy?

SUMMARY ANSWER

Fertility treatment with clomiphene citrate may be associated with a small increased risk of idiopathic generalized epilepsy and focal epilepsy in childhood.

WHAT IS KNOWN ALREADY

Clomiphene citrate is among the most commonly prescribed drugs for fertility treatment. However, concerns have been raised as to whether the treatment may harm the developing fetus.

STUDY DESIGN, SIZE, DURATION

This nationwide cohort study included all pregnancies in Denmark from 1 July 1995 resulting in a live-born singleton child before 31 December 2013. The children were followed until 31 December 2016.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Children conceived after fertility treatment with clomiphene citrate were identified from the Danish National Prescription Registry. The primary outcomes were childhood epilepsy, idiopathic generalized epilepsy, and focal epilepsy identified from the Danish National Patient Register and from antiepileptic drug prescriptions in the Danish National Prescription Registry. All analyses were conducted using Cox proportional hazards regression.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 1 081 291 pregnancies were included; 12 644 children (1.2%) developed epilepsy. Fertility treatment with clomiphene citrate was associated with a small increased risk of childhood epilepsy (hazard ratio [HR]: 1.10; 95% CI: 1.00–1.22), idiopathic generalized epilepsy (HR: 1.41; 95% CI: 1.16–1.72), and focal epilepsy (HR: 1.26; 95% CI: 1.04–1.53).

LIMITATIONS, REASONS FOR CAUTION

The increased risk of idiopathic generalized epilepsy may be due to confounding from time stable parental characteristics related to treatment with clomiphene citrate, since the association was strongest with the lowest administered dosage of clomiphene citrate prior to conception, and the association disappeared in a sibling analysis.

WIDER IMPLICATIONS OF THE FINDINGS

The increased risk of focal epilepsy may be related to the hormonal treatment, since the association tended to increase with increasing cumulative dosage of clomiphene citrate prior to conception, and the association persisted in a sibling analysis. This finding may be of clinical importance, since alternative hormones are available for fertility treatment.

STUDY FUNDING/COMPETING INTEREST(S)

Financial support from Aarhus University and the Aase and Ejnar Danielsen Foundation. U.S.K. received personal teaching fees from Merck, outside the submitted work.

TRIAL REGISTRATION NUMBER

N/A.
A Microscopic Derivation of Gibbs Measures for Nonlinear Schrödinger Equations with Unbounded Interaction Potentials
Authors: Sohinger Vedran
Published: April 2021

We study the derivation of the Gibbs measure for the nonlinear Schrödinger (NLS) equation from many-body quantum thermal states in the mean-field limit. In this paper, we consider the nonlocal NLS with defocusing and unbounded $L^p$ interaction potentials on $\mathbb{T}^d$ for $d=1,2,3$. This extends the author’s earlier joint work with Fröhlich et al. [ 45], where the regime of defocusing and bounded interaction potentials was considered. When $d=1$, we give an alternative proof of a result previously obtained by Lewin et al. [ 69]. Our proof is based on a perturbative expansion in the interaction. When $d=1$, the thermal state is the grand canonical ensemble. As in [ 45], when $d=2,3$, the thermal state is a modified grand canonical ensemble, which allows us to estimate the remainder term in the expansion. The terms in the expansion are analysed using a graphical representation and are resummed by using Borel summation. By this method, we are able to prove the result for the optimal range of $p$ and obtain the full range of defocusing interaction potentials, which were studied in the classical setting when $d=2,3$ in the work of Bourgain [ 15].
Gonococcal Pelvic Inflammatory Disease: Placing Mechanistic Insights Into the Context of Clinical and Epidemiological Observations
Authors: Xu Stacey X , Gray-Owen Scott D
Published: April 2021

While infection by Neisseria gonorrhoeae is often asymptomatic in women, undetected infections can ascend into the upper genital tract to elicit an inflammatory response that manifests as pelvic inflammatory disease, with the outcomes depending on the intensity and duration of inflammation and whether it is localized to the endometrial, fallopian tube, ovarian, and/or other tissues. This review examines the contribution of N. gonorrhoeae versus other potential causes of pelvic inflammatory disease by considering new insights gained through molecular, immunological, and microbiome-based analyses, and the current epidemiological burden of infection, with an aim to highlighting key areas for future study.