bluuebunny/crossref_metadata_2025 huggingface dataset:
The results of aortic arch replacement using antegrade cerebral perfusion in haemodialysis patients: analysis of the Japan cardiovascular surgery database
Authors: Saito Yoshiaki , Yamamoto Hiroyuki , Fukuda Ikuo , Miyata Hiroaki , Minakawa Masahito , Motomura Noboru
Published: April 2021

OBJECTIVES

There have been limited data available regarding aortic arch replacement in dialysis patients. The purpose of this study was to examine real-world data and to determine the impact of preoperative dialysis status and other risks on surgical aortic arch replacement using the Japan Cardiovascular Surgery Database.

METHODS

A total of 5044 patients who underwent elective, isolated aortic arch replacement using antegrade cerebral perfusion during 2014–2017 were eligible for the study. Of these, 89 patients received haemodialysis preoperatively. The patients were divided into 6 groups according to their preoperative estimated glomerular filtration rate and dialysis status for comparison. Preoperative and postoperative data were examined using a multivariable regression model.

RESULTS

The overall surgical mortality rates of non-Chronic Kidney Disease (CKD) (estimated glomerular filtration rate >60 ml/min/1.73 m2), stage 3A, stage 3B, stage 4, stage 5 CKD and dialysis patients were 2.6%, 3.1%, 6.8%, 11.6%, 16.7% and 13.5%, respectively. After risk adjustment, dialysis was shown to be strongly associated with surgical mortality (odds ratio 4.39 and 95% confidence interval 2.22–8.72) and have a trend to be associated with postoperative stroke (odds ratio 2.02, 95% confidence interval 1.00–4.10, P = 0.051) when compared to the non-CKD group. As predictors of mortality, male sex, peripheral arterial disease, preoperative liver dysfunction and impaired left ventricular function were identified.

CONCLUSIONS

The Japanese nationwide database revealed the outcomes of aortic arch replacement in dialysis patients. Appropriate counselling and an alternative strategy should be considered for such patients with multiple risks for mortality.
When Ethnicity and Gender Align: Classroom Composition, Friendship Segregation, and Collective Identities in European Schools
Authors: Kroneberg Clemens , Kruse Hanno , Wimmer Andreas
Published: April 2021

Using survey data on school classes in four European countries, we study how the social relations and identities of adolescents develop depending on the degree to which ethnic and gender boundaries align with each other. Minority students will have mostly same-ethnic friends, we find, when classmates of different ethnic origins tend to be of the opposite sex as well. Within such local topographies of boundaries, minority students will also end up identifying less as members of the nation. In contrast, majority students are not affected by the alignment of ethnic and gender boundaries, and gender identities of both minorities and majorities are less malleable as well: Neither friendship segregation along gender divides nor the development of gender role attitudes depend on the degree to which gender and ethnic origin align. We argue that gender boundaries and feelings of national belonging among majority students are widely taken for granted and thus less sensitive to attribute alignment at the local level. The article builds a bridge between the literatures on ethnic segregation of friendship networks, adolescent ethnic identities, and gender role attitudes by integrating them into a structuralist framework that identifies the conditions under which the local configuration of boundaries affects social life.
MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions
Authors: Milkevych Viktor , Karaman Emre , Sahana Goutam , Janss Luc , Cai Zexi , Lund Mogens Sandø
Published: April 2021

This work represents a novel mechanistic approach to simulate and study genomic networks with accompanying regulatory interactions and complex mechanisms of quantitative trait formation. The approach implemented in MeSCoT software is conceptually based on the omnigenic genetic model of quantitative (complex) trait, and closely imitates the basic in vivo mechanisms of quantitative trait realization. The software provides a framework to study molecular mechanisms of gene-by-gene and gene-by-environment interactions underlying quantitative trait’s realization and allows detailed mechanistic studies of impact of genetic and phenotypic variance on gene regulation. MeSCoT performs a detailed simulation of genes’ regulatory interactions for variable genomic architectures and generates complete set of transcriptional and translational data together with simulated quantitative trait values. Such data provide opportunities to study, for example, verification of novel statistical methods aiming to integrate intermediate phenotypes together with final phenotype in quantitative genetic analyses or to investigate novel approaches for exploiting gene-by-gene and gene-by-environment interactions.
Simultaneous Estimation of All the Parameters of a Stepwise Mutation Model
Authors: Fu Yun-Xin , Chakraborty Ranajit
Published: April 2021

Minisatellite and microsatellite are short tandemly repetitive sequences dispersed in eukaryotic genomes, many of which are highly polymorphic due to copy number variation of the repeats. Because mutation changes copy numbers of the repeat sequences in a generalized stepwise fashion, stepwise mutation models are widely used for studying the dynamics of these loci. We propose a minimum chi-square (MCS) method for simultaneous estimation of all the parameters in a stepwise mutation model and the ancestral allelic type of a sample. The MCS estimator requires knowing the mean number of alleles of a certain size in a sample, which can be estimated using Monte Carlo samples generated by a coalescent algorithm. The method is applied to samples of seven (CA)n repeat loci from eight human populations and one chimpanzee population. The estimated values of parameters suggest that there is a general tendency for microsatellite alleles to expand in size, because (1) each mutation has a slight tendency to cause size increase and (2) the mean size increase is larger than the mean size decrease for a mutation. Our estimates also suggest that most of these CA-repeat loci evolve according to multistep mutation models rather than single-step mutation models. We also introduced several quantities for measuring the quality of the estimation of ancestral allelic type, and it appears that the majority of the estimated ancestral allelic types are reasonably accurate. Implications of our analysis and potential extensions of the method are discussed.
Locating Regions of Differential Variability in DNA and Protein Sequences
Authors: Tang Hua , Lewontin R C
Published: April 2021

In the comparison of DNA and protein sequences between species or between paralogues or among individuals within a species or population, there is often some indication that different regions of the sequence are divergent or polymorphic to different degrees, indicating differential constraint or diversifying selection operating in different regions of the sequence. The problem is to test statistically whether the observed regional differences in the density of variant sites represent real differences and then to estimate as accurately as possible the location of the differential regions. A method is given for testing and locating regions of differential variation. The method consists of calculating G(xk) = k/n – xk/N, where xk is the position of the kth variant site along the sequence, n is the total number of variant sites, and N is the total sequence length. The estimated region is the longest stretch of adjacent sequence for which G(xk) is monotonically increasing (a hot spot) or decreasing (a cold spot). Critical values of this length for tests of significance are given, a sequential method is developed for locating multiple differential regions, and the power of the method against various alternatives is explored. The method locates the endpoints of hot spots and cold spots of variation with high accuracy.
Role of Exonucleolytic Degradation in Group I Intron Homing in Phage T4
Authors: Huang Yi-Jiun , Parker Monica M , Belfort Marlene
Published: April 2021

Homing of the phage T4 td intron is initiated by the intron-encoded endonuclease I-TevI, which cleaves the intronless allele 23 and 25 nucleotides upstream of the intron insertion site (IS). The distance between the I-TevI cleavage site (CS) and IS implicates endo- and/or exonuclease activities to resect the DNA segment between the IS and CS. Furthermore, 3′ tails must presumably be generated for strand invasion by 5′-3′ exonuclease activity. Three experimental approaches were used to probe for phage nucleases involved in homing: a comparative analysis of in vivo homing levels of nuclease-deficient phage, an in vitro assay of nuclease activity and specificity, and a coconversion analysis of flanking exon markers. It was thereby demonstrated that T4 RNase H, a 5′-3′ exonuclease, T4 DNA exonuclease A (DexA) and the exonuclease activity of T4 DNA polymerase (43Exo), 3′-5′ exonucleases, play a role in intron homing. The absence of these functions impacts not only homing efficiency but also the extent of degradation and flanking marker coconversion. These results underscore the critical importance of the 3′ tail in intron homing, and they provide the first direct evidence of a role for 3′ single-stranded DNA ends as intermediates in T4 recombination. Also, the involvement of RNase H, DexA, and 43Exo in homing provides a clear example of the harnessing of functions variously involved in phage nucleic acid metabolism for intron propagation.
Identification of Ascorbic Acid-Deficient Arabidopsis thaliana Mutants
Authors: Conklin Patricia L , Saracco Scott A , Norris Susan R , Last Robert L
Published: April 2021

Vitamin C (l-ascorbic acid) is a potent antioxidant and cellular reductant present at millimolar concentrations in plants. This small molecule has roles in the reduction of prosthetic metal ions, cell wall expansion, cell division, and in the detoxification of reactive oxygen generated by photosynthesis and adverse environmental conditions. However, unlike in animals, the biosynthesis of ascorbic acid (AsA) in plants is only beginning to be unraveled. The previously described AsA-deficient Arabidopsis mutant vtc1 (vitamin c-1) was recently shown to have a defect in GDP-mannose pyrophosphorylase, providing strong evidence for the recently proposed role of GDP-mannose in AsA biosynthesis. To genetically define other AsA biosynthetic loci, we have used a novel AsA assay to isolate four vtc mutants that define three additional VTC loci. We have also isolated a second mutant allele of VTC1. The four loci represented by the vtc mutant collection have been genetically characterized and mapped onto the Arabidopsis genome. The vtc mutants have differing ozone sensitivities. In addition, two of the mutants, vtc2-1 and vtc2-2, have unusually low levels of AsA in the leaf tissue of mature plants.
Biased Estimation of the Recombination Fraction Using Half-Sib Families and Informative Offspring
Authors: Gomez-Raya L
Published: April 2021

A maximum-likelihood method to estimate the recombination fraction and its sampling variance using informative and noninformative half-sib offspring is derived. Estimates of the recombination fraction are biased up to 20 cM when noninformative offspring are discarded. In certain scenarios, the sampling variance can be increased or reduced up to fivefold due to the bias in estimating the recombination fraction and the LOD score can be reduced up to 5 units when discarding noninformative offspring. Comparison of the estimates of recombination fraction, map distance, and LOD score when constructing a genetic map with 251 two-point linkage analyses and six families of Norwegian cattle was carried out to evaluate the implications of discarding noninformative offspring in practical situations. The average discrepancies in absolute value (average difference when using and neglecting noninformative offspring) were 0.0146, 1.64 cM, and 2.61 for the recombination fraction, map distance, and the LOD score, respectively. A method for simultaneous estimation of allele frequencies in the dam population and a transmission disequilibrium parameter is proposed. This method might account for the bias in estimating allele frequencies in the dam population when the half-sib offspring is selected for production traits.
Theory of Time-Resolved Somatic Complementation and Its Use to Explore the Sporulation Control Network in Physarum polycephalum
Authors: Marwan Wolfgang
Published: April 2021

Mutants of Physarum polycephalum can be complemented by fusion of plasmodial cells followed by cytoplasmic mixing. Complementation between strains carrying different mutational defects in the sporulation control network may depend on the signaling state of the network components. We have previously suggested that time-resolved somatic complementation (TRSC) analysis with such mutants may be used to probe network architecture and dynamics. By computer simulation it is now shown how and under which conditions the regulatory hierarchy of genes can be determined experimentally. A kinetic model of the sporulation control network is developed, which is then used to demonstrate how the mechanisms of TRSC can be understood and simulated at the kinetic level. On the basis of theoretical considerations, experimental parameters that determine whether functional complementation of two mutations will occur are identified. It is also shown how gene dosage-effect relationships can be employed for network analysis. The theoretical framework provided may be used to systematically analyze network structure and dynamics through time-resolved somatic complementation studies. The conclusions drawn are of general relevance in that they do not depend on the validity of the model from which they were derived.
Single-Nucleotide Polymorphisms of the Trypanosoma cruzi MSH2 Gene Support the Existence of Three Phylogenetic Lineages Presenting Differences in Mismatch-Repair Efficiency
Authors: Augusto-Pinto Luiz , Teixeira Santuza M R , Pena Sérgio D J , Machado Carlos Renato
Published: April 2021

We have identified single-nucleotide polymorphisms (SNPs) in the mismatch-repair gene TcMSH2 from Trypanosoma cruzi. Phylogenetic inferences based on the SNPs, confirmed by RFLP analysis of 32 strains, showed three distinct haplogroups, denominated A, B, and C. Haplogroups A and C presented strong identity with the previously described T. cruzi lineages I and II, respectively. A third haplogroup (B) was composed of strains presenting hybrid characteristics. All strains from a haplogroup encoded the same specific protein isoform, called, respectively, TcMHS2a, TcMHS2b, and TcMHS2c. The classification into haplogroups A, B, and C correlated with variation in the efficiency of mismatch repair in these cells. When microsatellite loci of strains representative of each haplogroup were analyzed after being cultured in the presence of hydrogen peroxide, new microsatellite alleles were definitely seen in haplogroups B and C, while no evidence of microsatellite instability was found in haplogroup A. Also, cells from haplogroups B and C were considerably more resistant to cisplatin treatment, a characteristic known to be conferred by deficiency of mismatch repair in eukaryotic cells. Altogether, our data suggest that strains belonging to haplogroups B and C may have decreased mismatch-repair ability when compared with strains assigned to the haplogroup A lineage.
New Genes That Interact With lin-35 Rb to Negatively Regulate the let-60 ras Pathway in Caenorhabditis elegans
Authors: Thomas Jeffrey H , Ceol Craig J , Schwartz Hillel T , Horvitz H Robert
Published: April 2021

Previous studies have shown that a synthetic multivulva phenotype results from mutations in genes that antagonize the ras-mediated intercellular signaling system responsible for vulval induction in Caenorhabditis elegans. Synthetic multivulva mutations define two classes of genes, A and B, and a mutation in a gene of each class is required to produce the multivulva phenotype. The ectopic vulval tissue in multivulva animals is generated by vulval precursor cells that in the wild type do not generate vulval tissue. One of the class B synthetic multivulva genes, lin-35, encodes a protein similar to the retinoblastoma (Rb) protein. In this article, we describe the isolation and characterization of 50 synthetic multivulva mutations, the identification of new components of both the class A and class B lin-35 Rb pathways, and the cloning of lin-52, a class B gene that may have a conserved role in Rb-mediated signaling.
Mechanosensory Inputs Influence Caenorhabditis elegans Pharyngeal Activity via Ivermectin Sensitivity Genes
Authors: Keane John , Avery Leon
Published: April 2021

Mechanical stimulation induces opposite behavioral responses in the adult and dauer pharynx. Tail tap of adults inhibits pharyngeal pumping via a pathway involving the innexin gene unc-7 and components of the glutamatergic pathway encoded by the genes avr-14 and avr-15. Tail tap of dauers stimulates pumping through a mechanism involving Gαo and Gαq. The nematocidal drug ivermectin is believed to kill worms by opening a glutamate-gated chloride channel (AVR-15) on pharyngeal muscle, causing complete pumping inhibition. However, ivermectin can also inhibit pumping in the absence of this channel. We propose that one of the ways ivermectin could prevent pumping, in the absence of the AVR-15 ivermectin-binding channel on pharynx muscle, is to target AVR-14 and AVR-15, which are expressed in the inhibitory pathway linking mechanosensation and pumping activity.
Telomeric Associated Sequences of Drosophila Recruit Polycomb-Group Proteins in Vivo and Can Induce Pairing-Sensitive Repression
Authors: Boivin Antoine , Gally Christelle , Netter Sophie , Anxolabéhère Dominique , Ronsseray Stéphane
Published: April 2021

In Drosophila, relocation of a euchromatic gene near centromeric or telomeric heterochromatin often leads to its mosaic silencing. Nevertheless, modifiers of centromeric silencing do not affect telomeric silencing, suggesting that each location requires specific factors. Previous studies suggest that a subset of Polycomb-group (PcG) proteins could be responsible for telomeric silencing. Here, we present the effect on telomeric silencing of 50 mutant alleles of the PcG genes and of their counteracting trithorax-group genes. Several combinations of two mutated PcG genes impair telomeric silencing synergistically, revealing that some of these genes are required for telomeric silencing. In situ hybridization and immunostaining experiments on polytene chromosomes revealed a strict correlation between the presence of PcG proteins and that of heterochromatic telomeric associated sequences (TASs), suggesting that TASs and PcG complexes could be associated at telomeres. Furthermore, lines harboring a transgene containing an X-linked TAS subunit and the mini-white reporter gene can exhibit pairing-sensitive repression of the white gene in an orientation-dependent manner. Finally, an additional binding site for PcG proteins was detected at the insertion site of this type of transgene. Taken together, these results demonstrate that PcG proteins bind TASs in vivo and may be major players in Drosophila telomeric position effect (TPE).
The SHOOTLESS2 and SHOOTLESS1 Genes Are Involved in Both Initiation and Maintenance of the Shoot Apical Meristem Through Regulating the Number of Indeterminate Cells
Authors: Satoh Namiko , Itoh Jun-Ichi , Nagato Yasuo
Published: April 2021

To characterize the SHL2 and SHL1 genes in detail, we analyzed three strains carrying weak alleles of SHL2, shl2-6, shl2-7, and shl2-8, and one weak allele of SHL1, shl1-3. In contrast to strong alleles, which result in lack of shoot meristem, strains bearing these weak alleles formed shoot meristem frequently during embryogenesis. In shl2-6 and shl2-7 mutants, the meristem was lost during seed development. Only the shl2-8 mutant could survive after germination, but it showed abnormal initiation pattern and morphology of leaves. In strains bearing the weak alleles, the shoot meristem was composed of a small number of indeterminate cells and ultimately converted into leaf primordium. The shl1-3 mutant showed phenotypes similar to those of shl2-8. Thus SHL2 and SHL1 are required for both initiation and maintenance of shoot meristem. In shl2 mutants, there was a positive correlation between the size of the expression domain of OSH1 representing the number of indeterminate cells, the frequency of shoot meristem initiation, and the duration of meristem survival. Thus the shoot meristem will not initiate in an “all-or-nothing” fashion, but is formed in various degrees depending on the strength of the alleles. Double-mutant analyses indicate that SHL2 functions upstream of SHO to establish proper organization of the shoot meristem.
The Mus81/Mms4 Endonuclease Acts Independently of Double-Holliday Junction Resolution to Promote a Distinct Subset of Crossovers During Meiosis in Budding Yeast
Authors: Santos Teresa de los , Hunter Neil , Lee Cindy , Larkin Brittany , Loidl Josef , Hollingsworth Nancy M
Published: April 2021

Current models for meiotic recombination require that crossovers derive from the resolution of a double-Holliday junction (dHJ) intermediate. In prokaryotes, enzymes responsible for HJ resolution are well characterized but the identification of a eukaryotic nuclear HJ resolvase has been elusive. Indirect evidence suggests that MUS81 from humans and fission yeast encodes a HJ resolvase. We provide three lines of evidence that Mus81/Mms4 is not the major meiotic HJ resolvase in S. cerevisiae: (1) MUS81/MMS4 is required to form only a distinct subset of crossovers; (2) rather than accumulating, dHJ intermediates are reduced in an mms4 mutant; and (3) expression of a bacterial HJ resolvase has no suppressive effect on mus81 meiotic phenotypes. Our analysis also reveals the existence of two distinct classes of crossovers in budding yeast. Class I is dependent upon MSH4/MSH5 and exhibits crossover interference, while class II is dependent upon MUS81/MMS4 and exhibits no interference. mms4 specifically reduces crossing over on small chromosomes, which are known to undergo less interference. The correlation between recombination rate and degree of interference to chromosome size may therefore be achieved by modulating the balance between class I/class II crossovers.
COM, a Heterochromatic Locus Governing the Control of Independent Endogenous Retroviruses From Drosophila melanogaster
Authors: Desset Sophie , Meignin Carine , Dastugue Bernard , Vaury Chantal
Published: April 2021

ZAM and Idefix are two endogenous retroviruses whose expression is tightly controlled in Drosophila melanogaster. However, a line exists in which this control has been perturbed, resulting in a high mobilization rate for both retroviruses. This line is called the U (unstable) line as opposed to the other S (stable) lines. In the process of analyzing this control and tracing the genetic determinant involved, we found that ZAM and Idefix expression responded to two types of controls: one restricting their expression to specific somatic cells in the ovaries and the other silencing their expression in S lines but permitting it in U lines. While studying this second control in the U or S backgrounds, we found that the heterochromatic locus 20A2-3 on the X chromosome, previously implicated in the regulation of a third retroelement, gypsy, also controlled both ZAM and Idefix. We report here that genetic determinants necessary for endogenous retrovirus silencing occur at the 20A2-3 locus, which we call COM, for centre organisateur de mobilisation. We propose that if this point of control becomes mutated during the life of the fly, it may trigger processes reactivating dormant endogenous retroviruses and thus bring about sudden bursts of mobilization.
Map-Based Cloning of Leaf Rust Resistance Gene Lr21 From the Large and Polyploid Genome of Bread Wheat
Authors: Huang Li , Brooks Steven A , Li Wanlong , Fellers John P , Trick Harold N , Gill Bikram S
Published: April 2021

We report the map-based cloning of the leaf rust resistance gene Lr21, previously mapped to a generich region at the distal end of chromosome arm 1DS of bread wheat (Triticum aestivum L.). Molecular cloning of Lr21 was facilitated by diploid/polyploid shuttle mapping strategy. Cloning of Lr21 was confirmed by genetic transformation and by a stably inherited resistance phenotype in transgenic plants. Lr21 spans 4318 bp and encodes a 1080-amino-acid protein containing a conserved nucleotide-binding site (NBS) domain, 13 imperfect leucine-rich repeats (LRRs), and a unique 151-amino-acid sequence missing from known NBS-LRR proteins at the N terminus. Fine-structure genetic analysis at the Lr21 locus detected a noncrossover (recombination without exchange of flanking markers) within a 1415-bp region resulting from either a gene conversion tract of at least 191 bp or a double crossover. The successful map-based cloning approach as demonstrated here now opens the door for cloning of many crop-specific agronomic traits located in the gene-rich regions of bread wheat.
Four Loci on Abnormal Chromosome 10 Contribute to Meiotic Drive in Maize
Authors: Hiatt Evelyn N , Dawe R Kelly
Published: April 2021

We provide a genetic analysis of the meiotic drive system on maize abnormal chromosome 10 (Ab10) that causes preferential segregation of specific chromosomal regions to the reproductive megaspore. The data indicate that at least four chromosomal regions contribute to meiotic drive, each providing distinct functions that can be differentiated from each other genetically and/or phenotypically. Previous reports established that meiotic drive requires neocentromere activity at specific tandem repeat arrays (knobs) and that two regions on Ab10 are involved in trans-activating neocentromeres. Here we confirm and extend data suggesting that only one of the neocentromere-activating regions is sufficient to move many knobs. We also confirm the localization of a locus/loci on Ab10, thought to be a prerequisite for meiotic drive, which promotes recombination in structural heterozygotes. In addition, we identified two new and independent functions required for meiotic drive. One was identified through the characterization of a deletion derivative of Ab10 [Df(L)] and another as a newly identified meiotic drive mutation (suppressor of meiotic drive 3). In the absence of either function, meiotic drive is abolished but neocentromere activity and the recombination effect typical of Ab10 are unaffected. These results demonstrate that neocentromere activity and increased recombination are not the only events required for meiotic drive.
Functional Redundancy Within roX1, a Noncoding RNA Involved in Dosage Compensation in Drosophila melanogaster
Authors: Stuckenholz Carsten , Meller Victoria H , Kuroda Mitzi I
Published: April 2021

Drosophila melanogaster males dosage compensate by twofold upregulation of the expression of genes on their single X chromosome. This process requires at least five proteins and two noncoding RNAs, roX1 and roX2, which paint the male X chromosome. We used a deletion analysis to search for functional RNA domains within roX1, assaying RNA stability, targeting of the MSL proteins to the X, and rescue of male viability in a roX1-  roX2- mutant background. We found that deletion of 10% segments of the RNA did not dramatically reduce function in most cases, suggesting extensive internal redundancy. The 3′ 600 nt of roX1 were most sensitive to mutations, affecting proper localization and 3′ processing of the RNA. Disruption of an inverted repeat predicted to form a stem-loop structure was found partially responsible for the defects observed.
Stochastic Search Variable Selection for Identifying Multiple Quantitative Trait Loci
Authors: Yi Nengjun , George Varghese , Allison David B
Published: April 2021

In this article, we utilize stochastic search variable selection methodology to develop a Bayesian method for identifying multiple quantitative trait loci (QTL) for complex traits in experimental designs. The proposed procedure entails embedding multiple regression in a hierarchical normal mixture model, where latent indicators for all markers are used to identify the multiple markers. The markers with significant effects can be identified as those with higher posterior probability included in the model. A simple and easy-to-use Gibbs sampler is employed to generate samples from the joint posterior distribution of all unknowns including the latent indicators, genetic effects for all markers, and other model parameters. The proposed method was evaluated using simulated data and illustrated using a real data set. The results demonstrate that the proposed method works well under typical situations of most QTL studies in terms of number of markers and marker density.
The Evolution of Mutator Genes in Bacterial Populations: The Roles of Environmental Change and Timing
Authors: Tanaka Mark M , Bergstrom Carl T , Levin Bruce R
Published: April 2021

Recent studies have found high frequencies of bacteria with increased genomic rates of mutation in both clinical and laboratory populations. These observations may seem surprising in light of earlier experimental and theoretical studies. Mutator genes (genes that elevate the genomic mutation rate) are likely to induce deleterious mutations and thus suffer an indirect selective disadvantage; at the same time, bacteria carrying them can increase in frequency only by generating beneficial mutations at other loci. When clones carrying mutator genes are rare, however, these beneficial mutations are far more likely to arise in members of the much larger nonmutator population. How then can mutators become prevalent? To address this question, we develop a model of the population dynamics of bacteria confronted with ever-changing environments. Using analytical and simulation procedures, we explore the process by which initially rare mutator alleles can rise in frequency. We demonstrate that subsequent to a shift in environmental conditions, there will be relatively long periods of time during which the mutator subpopulation can produce a beneficial mutation before the ancestral subpopulations are eliminated. If the beneficial mutation arises early enough, the overall frequency of mutators will climb to a point higher than when the process began. The probability of producing a subsequent beneficial mutation will then also increase. In this manner, mutators can increase in frequency over successive selective sweeps. We discuss the implications and predictions of these theoretical results in relation to antibiotic resistance and the evolution of mutation rates.
The Mitotic DNA Damage Checkpoint Proteins Rad17 and Rad24 Are Required for Repair of Double-Strand Breaks During Meiosis in Yeast
Authors: Shinohara Miki , Sakai Kazuko , Ogawa Tomoko , Shinohara Akira
Published: April 2021

We show here that deletion of the DNA damage checkpoint genes RAD17 and RAD24 in Saccharomyces cerevisiae delays repair of meiotic double-strand breaks (DSBs) and results in an altered ratio of crossover-to-noncrossover products. These mutations also decrease the colocalization of immunostaining foci of the RecA homologs Rad51 and Dmc1 and cause a delay in the disappearance of Rad51 foci, but not of Dmc1. These observations imply that RAD17 and RAD24 promote efficient repair of meiotic DSBs by facilitating proper assembly of the meiotic recombination complex containing Rad51. Consistent with this proposal, extra copies of RAD51 and RAD54 substantially suppress not only the spore inviability of the rad24 mutant, but also the γ-ray sensitivity of the mutant. Unexpectedly, the entry into meiosis I (metaphase I) is delayed in the checkpoint single mutants compared to wild type. The control of the cell cycle in response to meiotic DSBs is also discussed.
Telomerase-Independent Proliferation Is Influenced by Cell Type in Saccharomyces cerevisiae
Authors: Lowell Joanna E , Roughton Alexander I , Lundblad Victoria , Pillus Lorraine
Published: April 2021

Yeast strains harboring mutations in genes required for telomerase function (TLC1 and the EST genes) exhibit progressive shortening of telomeric DNA and replicative senescence. A minority of cells withstands loss of telomerase through RAD52-dependent amplification of telomeric and subtelomeric sequences; such survivors are now capable of long-term propagation with telomeres maintained by recombination rather than by telomerase. Here we report that simultaneous expression in haploid cells of both MATa and MATα information suppresses the senescence of telomerase-deficient mutants, with suppression occurring via the RAD52-dependent survivor pathway(s). Such suppression can be mimicked by deletion of SIR1-SIR4, genes that function in transcriptional silencing of several loci including the silent mating-type loci. Furthermore, telomerase-defective diploid strains that express only MATa or MATα information senesce at a faster rate than telomerase-defective diploids that are heterozygous at the MAT locus. This suggests that the RAD52-dependent pathway(s) for telomere maintenance respond to changes in the levels of recombination, a process regulated in part by the hierarchy of gene control that includes MAT regulation. We propose that cell-type-specific regulation of recombination at human telomeres may similarly contribute to the tissue-specific patterns of disease found in telomerase-deficient tumors.
An N-Ethyl-N-Nitrosourea Mutagenesis Screen for Epigenetic Mutations in the Mouse
Authors: Percec Ivona , Thorvaldsen Joanne L , Plenge Robert M , Krapp Christopher J , Nadeau Joseph H , Willard Huntington F , Bartolomei Marisa S
Published: April 2021

The mammalian epigenetic phenomena of X inactivation and genomic imprinting are incompletely understood. X inactivation equalizes X-linked expression between males and females by silencing genes on one X chromosome during female embryogenesis. Genomic imprinting functionally distinguishes the parental genomes, resulting in parent-specific monoallelic expression of particular genes. N-ethyl-N-nitrosourea (ENU) mutagenesis was used in the mouse to screen for mutations in novel factors involved in X inactivation. Previously, we reported mutant pedigrees identified through this screen that segregate aberrant X-inactivation phenotypes and we mapped the mutation in one pedigree to chromosome 15. We now have mapped two additional mutations to the distal chromosome 5 and the proximal chromosome 10 in a second pedigree and show that each of the mutations is sufficient to induce the mutant phenotype. We further show that the roles of these factors are specific to embryonic X inactivation as neither genomic imprinting of multiple genes nor imprinted X inactivation is perturbed. Finally, we used mice bearing selected X-linked alleles that regulate X chromosome choice to demonstrate that the phenotypes of all three mutations are consistent with models in which the mutations have affected molecules involved specifically in the choice or the initiation of X inactivation.
Low Nucleotide Diversity in Chimpanzees and Bonobos
Authors: Yu Ning , Jensen-Seaman Michael I , Chemnick Leona , Kidd Judith R , Deinard Amos S , Ryder Oliver , Kidd Kenneth K , Li Wen-Hsiung
Published: April 2021

Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.
Isolation and Characterization of High-Temperature-Induced Dauer Formation Mutants in Caenorhabditis elegans
Authors: Ailion Michael , Thomas James H
Published: April 2021

Dauer formation in Caenorhabditis elegans is regulated by at least three signaling pathways, including an insulin receptor-signaling pathway. These pathways were defined by mutants that form dauers constitutively (Daf-c) at 25°. Screens for Daf-c mutants at 25° have probably been saturated, but failed to identify all the components involved in regulating dauer formation. Here we screen for Daf-c mutants at 27°, a more strongly dauer-inducing condition. Mutations identified include novel classes of alleles for three known genes and alleles defining at least seven new genes, hid-1–hid-7. Many of the genes appear to act in the insulin branch of the dauer pathway, including pdk-1, akt-1, aex-6, and hid-1. We also molecularly identify hid-1 and show that it encodes a novel highly conserved putative transmembrane protein expressed in neurons.
The Drosophila spn-D Gene Encodes a RAD51C-Like Protein That Is Required Exclusively During Meiosis
Authors: Abdu Uri , González-Reyes Acaimo , Ghabrial Amin , Schüpbach Trudi
Published: April 2021

In Drosophila, mutations in double-strand DNA break (DSB) repair enzymes, such as spn-B, activate a meiotic checkpoint leading to dorsal-ventral patterning defects in the egg and an abnormal appearance of the oocyte nucleus. Mutations in spn-D cause an array of ovarian phenotypes similar to spn-B. We have cloned the spn-D locus and found that it encodes a protein of 271 amino acids that shows significant homology to the human RAD51C protein. In mammals the spn-B and spn-D homologs, XRCC3 and RAD51C, play a role in genomic stability in somatic cells. To test for a similar role for spn-B and spn-D in double-strand DNA repair in mitotic cells, we analyzed the sensitivity of single and double mutants to DSBs induced by exposure to X rays and MMS. We found that neither singly mutant nor doubly mutant animals were significantly sensitized to MMS or X rays. These results suggest that spn-B and spn-D act in meiotic recombination but not in repair of DSBs in somatic cells. As there is no apparent ortholog of the meiosis-specific DMC1 gene in the Drosophila genome, and given their meiosis-specific requirement, we suggest that spn-B and spn-D may have a function comparable to DMC1.
Analysis of the Generation and Segregation of Propagons: Entities That Propagate the [PSI+] Prion in Yeast
Authors: Cox Brian , Ness Frederique , Tuite Mick
Published: April 2021

The propagation of the prion form of the yeast Sup35p protein, the so-called [PSI+] determinant, involves the generation and partition of a small number of particulate determinants that we propose calling “propagons.” The numbers of propagons in [PSI+] cells can be inferred from the kinetics of elimination of [PSI+] during growth in the presence of a low concentration of guanidine hydrochloride (GdnHCl). Using this and an alternative method of counting the numbers of propagons, we demonstrate considerable clonal variation in the apparent numbers of propagons between different [PSI+] yeast strains, between different cultures of the same [PSI+] yeast strain, and between different cells of the same [PSI+] culture. We provide further evidence that propagon generation is blocked by growth in GdnHCl and that it is largely confined to the S phase of the cell cycle. In addition, we show that at low propagon number there is a bias toward retention of propagons in mother cells and that production of new propagons is very rapid when cells with depleted numbers of propagons are rescued into normal growth medium. The implications of our findings with respect to yeast prion propagation mechanisms are discussed.
Transposon Mutagenesis of the Mouse Germline
Authors: Carlson Corey M , Dupuy Adam J , Fritz Sabine , Roberg-Perez Kevin J , Fletcher Colin F , Largaespada David A
Published: April 2021

Sleeping Beauty is a synthetic “cut-and-paste” transposon of the Tc1/mariner class. The Sleeping Beauty transposase (SB) was constructed on the basis of a consensus sequence obtained from an alignment of 12 remnant elements cloned from the genomes of eight different fish species. Transposition of Sleeping Beauty elements has been observed in cultured cells, hepatocytes of adult mice, one-cell mouse embryos, and the germline of mice. SB has potential as a random germline insertional mutagen useful for in vivo gene trapping in mice. Previous work in our lab has demonstrated transposition in the male germline of mice and transmission of novel inserted transposons in offspring. To determine sequence preferences and mutagenicity of SB-mediated transposition, we cloned and analyzed 44 gene-trap transposon insertion sites from a panel of 30 mice. The distribution and sequence content flanking these cloned insertion sites was compared to 44 mock insertion sites randomly selected from the genome. We find that germline SB transposon insertion sites are AT-rich and the sequence ANNTANNT is favored compared to other TA dinucleotides. Local transposition occurs with insertions closely linked to the donor site roughly one-third of the time. We find that ∼27% of the transposon insertions are in transcription units. Finally, we characterize an embryonic lethal mutation caused by endogenous splicing disruption in mice carrying a particular intron-inserted gene-trap transposon.
The Extent of Linkage Disequilibrium and Haplotype Sharing Around a Polymorphic Site
Authors: Innan Hideki , Nordborg Magnus
Published: April 2021

Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has occurred in a sample or subsample. We obtain an approximation for the probability that no recombination that could give rise to a detectable recombination event (through the four-gamete test) has occurred. The probabilities can be used to obtain approximate distributions for the length of variously defined haplotypes around a polymorphic site. The implications of our results for data analysis, and in particular for detecting selection, are discussed.
Limitations of Allotopic Expression of Mitochondrial Genes in Mammalian Cells
Authors: Oca-Cossio Jose , Kenyon Lesley , Hao Huiling , Moraes Carlos T
Published: April 2021

The possibility of expressing mitochondrial DNA-coded genes in the nuclear-cytoplasmic compartment provides an attractive system for genetic treatment of mitochondrial disorders associated with mitochondrial DNA mutations. In theory, by recoding mitochondrial genes to adapt them to the universal genetic code and by adding a DNA sequence coding for a mitochondrial-targeting sequence, one could achieve correct localization of the gene product. Such transfer has occurred in nature, and certain species of algae and plants express a number of polypeptides that are commonly coded by mtDNA in the nuclear-cytoplasmic compartment. In the present study, allotopic expression of three different mtDNA-coded polypeptides (ATPase8, apocytochrome b, and ND4) into COS-7 and HeLa cells was analyzed. Among these, only ATPase8 was correctly expressed and localized to mitochondria. The full-length, as well as truncated forms, of apocytochrome b and ND4 decorated the periphery of mitochondria, but also aggregated in fiber-like structures containing tubulin and in some cases also vimentin. The addition of a hydrophilic tail (EGFP) to the C terminus of these polypeptides did not change their localization. Overexpression of molecular chaperones also did not have a significant effect in preventing aggregations. Allotopic expression of apocytochrome b and ND4 induced a loss of mitochondrial membrane potential in transfected cells, which can lead to cell death. Our observations suggest that only a subset of mitochondrial genes can be replaced allotopically. Analyses of the hydrophobic patterns of different polypeptides suggest that hydrophobicity of the N-terminal segment is the main determinant for the importability of peptides into mammalian mitochondria.
A General Statistical Framework for Mapping Quantitative Trait Loci in Nonmodel Systems: Issue for Characterizing Linkage Phases
Authors: Lin Min , Lou Xiang-Yang , Chang Myron , Wu Rongling
Published: April 2021

Because of uncertainty about linkage phases of founders, linkage mapping in nonmodel, outcrossing systems using molecular markers presents one of the major statistical challenges in genetic research. In this article, we devise a statistical method for mapping QTL affecting a complex trait by incorporating all possible QTL-marker linkage phases within a mapping framework. The advantage of this model is the simultaneous estimation of linkage phases and QTL location and effect parameters. These estimates are obtained through maximum-likelihood methods implemented with the EM algorithm. Extensive simulation studies are performed to investigate the statistical properties of our model. In a case study from a forest tree, this model has successfully identified a significant QTL affecting wood density. Also, the probability of the linkage phase between this QTL and its flanking markers is estimated. The implications of our model and its extension to more general circumstances are discussed.
The Divergent Orphan Nuclear Receptor ODR-7 Regulates Olfactory Neuron Gene Expression via Multiple Mechanisms in Caenorhabditis elegans
Authors: Colosimo Marc E , Tran Susan , Sengupta Piali
Published: April 2021

Nuclear receptors regulate numerous critical biological processes. The C. elegans genome is predicted to encode ∼270 nuclear receptors of which >250 are unique to nematodes. ODR-7 is the only member of this large divergent family whose functions have been defined genetically. ODR-7 is expressed in the AWA olfactory neurons and specifies AWA sensory identity by promoting the expression of AWA-specific signaling genes and repressing the expression of an AWC-specific olfactory receptor gene. To elucidate the molecular mechanisms of action of a divergent nuclear receptor, we have identified residues and domains required for different aspects of ODR-7 function in vivo. ODR-7 utilizes an unexpected diversity of mechanisms to regulate the expression of different sets of target genes. Moreover, these mechanisms are distinct in normal and heterologous cellular contexts. The odr-7 ortholog in the closely related nematode C. briggsae can fully substitute for all ODR-7-mediated functions, indicating conservation of function across 25–120 million years of divergence.