bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonrandom Segregation of the Mouse Univalent X Chromosome: Evidence of Spindle-Mediated Meiotic Drive
Authors: LeMaire-Adkins Renée , Hunt Patricia A 
Published: April 2021

Abstract
A fundamental principle of Mendelian inheritance is random segregation of alleles to progeny; however, examples of distorted transmission either of specific alleles or of whole chromosomes have been described in a variety of species. In humans and mice, a distortion in chromosome transmission is often associated with a chromosome abnormality. One such example is the fertile XO female mouse. A transmission distortion effect that results in an excess of XX over XO daughters among the progeny of XO females has been recognized for nearly four decades. Utilizing contemporary methodology that combines immunofluorescence, FISH, and three-dimensional confocal microscopy, we have readdressed the meiotic segregation behavior of the single X chromosome in oocytes from XO females produced on two different inbred backgrounds. Our studies demonstrate that segregation of the univalent X chromosome at the first meiotic division is nonrandom, with preferential retention of the X chromosome in the oocyte in ∼60% of cells. We propose that this deviation from Mendelian expectations is facilitated by a spindle-mediated mechanism. This mechanism, which appears to be a general feature of the female meiotic process, has implications for the frequency of nondisjunction in our species.
Hierarchical Patterns of Transgene Expression Indicate Involvement of Developmental Mechanisms in the Regulation of the Maize P1-rr Promoter
Authors: Cocciolone Suzy M , Sidorenko Lyudmila V , Chopra Surinder , Dixon Philip M , Peterson Thomas 
Published: April 2021

Abstract
The maize P1-rr gene encodes a Myb-homologous transcription factor that regulates the synthesis of red flavonoid pigments. Maize plants transformed with segments of the P1-rr promoter driving a GUS reporter gene exhibit significant variation in transgene expression, both between independent transformation events and among sibling plants derived from a single event. Interestingly, variability in spatial expression is not random; rather, transgene activity occurs predominantly in five patterns that fit a hierarchy: expression is most common in kernel pericarp, with sequential addition of expression in cob glumes, husk, silk, and tassel. The hierarchical expression pattern of P-rr::GUS transgenes suggests a possible model for developmental regulation of the P1-rr gene. Our results demonstrate that variability in transgene expression, a common occurrence in transgenic plant studies, can be informative if adequately analyzed to uncover underlying patterns of gene expression.
New Insights on Homology-Dependent Silencing of I Factor Activity by Transgenes Containing ORF1 in Drosophila melanogaster
Authors: Malinsky Sophie , Bucheton Alain , Busseau Isabelle 
Published: April 2021

Abstract
I factors in Drosophila melanogaster are non-LTR retrotransposons that transpose at very high frequencies in the germ line of females resulting from crosses between reactive females (devoid of active I factors) and inducer males (containing active I factors). Constructs containing I factor ORF1 under the control of the hsp70 promoter repress I factor activity. This repressor effect is maternally transmitted and increases with the transgene copy number. It is irrespective of either frame integrity or transcriptional orientation of ORF1, suggesting the involvement of a homology-dependent trans-silencing mechanism. A promoterless transgene displays no repression. The effect of constructs in which ORF1 is controlled by the hsp70 promoter does not depend upon heat-shock treatments. No effect of ORF1 is detected when it is controlled by the I factor promoter. We discuss the relevance of the described regulation to the repression of I factors in I strains.
A Genetic Screen for Modifiers of a Kinase Suppressor of Ras-Dependent Rough Eye Phenotype in Drosophila
Authors: Therrien Marc , Morrison Deborah K , Wong Allan M , Rubin Gerald M 
Published: April 2021

Abstract
kinase suppressor of Ras (ksr) encodes a putative protein kinase that by genetic criteria appears to function downstream of RAS in multiple receptor tyrosine kinase (RTK) pathways. While biochemical evidence suggests that the role of KSR is closely linked to the signal transduction mechanism of the MAPK cascade, the precise molecular function of KSR remains unresolved. To further elucidate the role of KSR and to identify proteins that may be required for KSR function, we conducted a dominant modifier screen in Drosophila based on a KSR-dependent phenotype. Overexpression of the KSR kinase domain in a subset of cells during Drosophila eye development blocks photoreceptor cell differentiation and results in the external roughening of the adult eye. Therefore, mutations in genes functioning with KSR might modify the KSR-dependent phenotype. We screened ∼185,000 mutagenized progeny for dominant modifiers of the KSR-dependent rough eye phenotype. A total of 15 complementation groups of Enhancers and four complementation groups of Suppressors were derived. Ten of these complementation groups correspond to mutations in known components of the Ras1 pathway, demonstrating the ability of the screen to specifically identify loci critical for Ras1 signaling and further confirming a role for KSR in Ras1 signaling. In addition, we have identified 4 additional complementation groups. One of them corresponds to the kismet locus, which encodes a putative chromatin remodeling factor. The relevance of these loci with respect to the function of KSR and the Ras1 pathway in general is discussed.
DNA Polymorphism at the Cytosolic Phosphoglucose Isomerase (PgiC) Locus of the Wild Plant Arabidopsis thaliana
Authors: Kawabe Akira , Yamane Kyoko , Miyashita Naohiko T 
Published: April 2021

Abstract
DNA variation in a 4.7-kb region of the cytosolic phosphoglucose isomerase (PgiC) locus was investigated for 21 ecotypes of Arabidopsis thaliana. The estimated nucleotide diversity was 0.0038, which was one-third of those in previously investigated loci. Since most of the nucleotide variations (93%) were singleton and doubleton, Tajima's test statistic was significantly negative. About 50% of nucleotide polymorphisms in exons were replacement, which caused significance in McDonald and Kreitman's test when compared with Arabis gemmifera and Cardaminopsis petraea. These results indicated that DNA polymorphism at the PgiC locus was not under neutrality. There were two divergent sequence types in the PgiC region, which were associated with allozyme variation. The Fast allozyme was shown to have originated from the Slow allozyme, since two outgroup species had the Slow form. A phylogenetic tree of ecotypes with the Fast allozyme had the shape of a star phylogeny. Mismatch distribution of the Fast allozyme ecotypes resembled that expected under an expanding population model. These results suggest positive selection for the Fast allozyme of the PGIC in A. thaliana.
Null Mutations in the lin-31 Gene Indicate Two Functions During Caenorhabditis elegans Vulval Development
Authors: Miller Leilani M , Hess Heather A , Doroquez David B , Andrews Noelle M 
Published: April 2021

Abstract
The lin-31 gene is required for the proper specification of vulval cell fates in the nematode Caenorhabditis elegans and encodes a member of the winged-helix family of transcription factors. Members of this important family have been identified in many organisms and are known to bind specific DNA targets involved in a variety of developmental processes. DNA sequencing of 13 lin-31 alleles revealed six nonsense mutations and two missense mutations within the DNA-binding domain, plus three deletions, one transposon insertion, and one frameshift mutation that all cause large-scale disruptions in the gene. The missense mutations are amino acid substitutions in the DNA-binding domain and probably disrupt interactions of the LIN-31 transcription factor with its DNA target. In addition, detailed phenotypic analysis of all 19 alleles showed similar penetrances for several characteristics examined. From our analysis we conclude: (1) the null phenotype of lin-31 is the phenotype displayed by almost all of the existing alleles, (2) the DNA-binding domain plays a critical role in LIN-31 function, and (3) direct screens for multivulva and vulvaless mutants will probably yield only null (or strong) alleles of lin-31.
Toward a Physical Map ofDrosophila buzzatii: Use of Randomly Amplified Polymorphic DNA Polymorphisms and Sequence-Tagged Site Landmarks
Authors: Laayouni Hafid , Santos Mauro , Fontdevila Antonio 
Published: April 2021

AbstractWe present a physical map based on RAPD polymorphic fragments and sequence-tagged sites (STSs) for the repleta group species Drosophila buzzatii. One hundred forty-four RAPD markers have been used as probes for in situ hybridization to the polytene chromosomes, and positive results allowing the precise localization of 108 RAPDs were obtained. Of these, 73 behave as effectively unique markers for physical map construction, and in 9 additional cases the probes gave two hybridization signals, each on a different chromosome. Most markers (68%) are located on chromosomes 2 and 4, which partially agree with previous estimates on the distribution of genetic variation over chromosomes. One RAPD maps close to the proximal breakpoint of inversion 2z3 but is not included within the inverted fragment. However, it was possible to conclude from this RAPD that the distal breakpoint of 2z3 had previously been wrongly assigned. A total of 39 cytologically mapped RAPDs were converted to STSs and yielded an aggregate sequence of 28,431 bp. Thirty-six RAPDs (25%) did not produce any detectable hybridization signal, and we obtained the DNA sequence from three of them. Further prospects toward obtaining a more developed genetic map than the one currently available for D. buzzatii are discussed.
Evolution of Dosage Compensation in Diptera: The Gene maleless Implements Dosage Compensation in Drosophila (Brachycera Suborder) but Its Homolog in Sciara (Nematocera Suborder) Appears to Play No Role in Dosage Compensation
Authors: Ruiz M Fernanda , Esteban M Rosario , Doñoro Carmen , Goday Clara , Sánchez Lucas 
Published: April 2021

Abstract
In Drosophila melanogaster and in Sciara ocellaris dosage compensation occurs by hypertranscription of the single male X chromosome. This article reports the cloning and characterization in S. ocellaris of the gene homologous to maleless (mle) of D. melanogaster, which implements dosage compensation. The Sciara mle gene produces a single transcript, encoding a helicase, which is present in both male and female larvae and adults and in testes and ovaries. Both Sciara and Drosophila MLE proteins are highly conserved. The affinity-purified antibody to D. melanogaster MLE recognizes the S. ocellaris MLE protein. In contrast to Drosophila polytene chromosomes, where MLE is preferentially associated with the male X chromosome, in Sciara MLE is found associated with all chromosomes. Anti-MLE staining of Drosophila postblastoderm male embryos revealed a single nuclear dot, whereas Sciara male and female embryos present multiple intranuclear staining spots. This expression pattern in Sciara is also observed before blastoderm stage, when dosage compensation is not yet set up. The affinity-purified antibodies against D. melanogaster MSL1, MSL3, and MOF proteins involved in dosage compensation also revealed no differences in the staining pattern between the X chromosome and the autosomes in both Sciara males and females. These results lead us to propose that different proteins in Drosophila and Sciara would implement dosage compensation.
Inferring Recent Outcrossing Rates Using Multilocus Individual Heterozygosity: Application to Evolving Wheat Populations
Authors: Enjalbert Jérôme , David Jacques L 
Published: April 2021

Abstract
Using multilocus individual heterozygosity, a method is developed to estimate the outcrossing rates of a population over a few previous generations. Considering that individuals originate either from outcrossing or from n successive selfing generations from an outbred ancestor, a maximum-likelihood (ML) estimator is described that gives estimates of past outcrossing rates in terms of proportions of individuals with different n values. Heterozygosities at several unlinked codominant loci are used to assign n values to each individual. This method also allows a test of whether populations are in inbreeding equilibrium. The estimator’s reliability was checked using simulations for different mating histories. We show that this ML estimator can provide estimates of outcrossing rates for the final generation outcrossing rate (t0) and a mean of the preceding rates (tp) and can detect major temporal variation in the mating system. The method is most efficient for low to intermediate outcrossing levels. Applied to nine populations of wheat, this method gave estimates of t0 and tp. These estimates confirmed the absence of outcrossing (t0 = 0) in the two populations subjected to manual selfing. For free-mating wheat populations, it detected lower final generation outcrossing rates (t0 = 0-0.06) than those expected from global heterozygosity (t = 0.02-0.09). This estimator appears to be a new and efficient way to describe the multilocus heterozygosity of a population, complementary to Fis and progeny analysis approaches.
The teflon Gene Is Required for Maintenance of Autosomal Homolog Pairing at Meiosis I in Male Drosophila melanogaster
Authors: Tomkiel John E , Wakimoto Barbara T , Briscoe Albert 
Published: April 2021

Abstract
In recombination-proficient organisms, chiasmata appear to mediate associations between homologs at metaphase of meiosis I. It is less clear how homolog associations are maintained in organisms that lack recombination, such as male Drosophila. In lieu of chiasmata and synaptonemal complexes, there must be molecules that balance poleward forces exerted across homologous centromeres. Here we describe the genetic and cytological characterization of four EMS-induced mutations in teflon (tef), a gene involved in this process in Drosophila melanogaster. All four alleles are male specific and cause meiosis I-specific nondisjunction of the autosomes. They do not measurably perturb sex chromosome segregation, suggesting that there are differences in the genetic control of autosome and sex chromosome segregation in males. Meiotic transmission of univalent chromosomes is unaffected in tef mutants, implicating the tef product in a pairing-dependent process. The segregation of translocations between sex chromosomes and autosomes is altered in tef mutants in a manner that supports this hypothesis. Consistent with these genetic observations, cytological examination of meiotic chromosomes suggests a role of tef in regulating or mediating pairing of autosomal bivalents at meiosis I. We discuss implications of this finding in regard to the evolution of heteromorphic sex chromosomes and the mechanisms that ensure chromosome disjunction in the absence of recombination.
Diverging Trends Between Heterozygosity and Allelic Richness During Postglacial Colonization in the European Beech
Authors: Comps B , Gömöry D , Letouzey J , Thiébaut B , Petit R J 
Published: April 2021

Abstract
Variation at 12 polymorphic isozyme loci was studied in the European beech on the basis of an extensive sample of 389 populations distributed throughout the species range. Special emphasis was given to the analysis of the pattern of geographic variation on the basis of two contrasting measures of genetic diversity, gene diversity (H) and allelic richness, and to their relationship. Measures of allelic richness were corrected for variation in sample size by using the rarefaction method. As expected, maximum allelic richness was found in the southeastern part of the range (southern Italy and the Balkans), where beech was confined during the last ice age. Surprisingly, H was lower in refugia than in recently colonized regions, resulting in a negative correlation between the two diversity measures. The decrease of allelic richness and the simultaneous increase of H during postglacial recolonization was attributed to several processes that differentially affect the two diversity parameters, such as bottlenecks due to long-distance founding events, selection during population establishment, and increased gene flow at low population densities.
Estimates of the Rate and Distribution of Fitness Effects of Spontaneous Mutation in Saccharomyces cerevisiae
Authors: Zeyl Clifford , DeVisser J Arjan G M 
Published: April 2021

Abstract
The per-genome, per-generation rate of spontaneous mutation affecting fitness (U) and the mean fitness cost per mutation (s) are important parameters in evolutionary genetics, but have been estimated for few species. We estimated U and sh (the heterozygous effect of mutations) for two diploid yeast strains differing only in the DNA mismatch-repair deficiency used to elevate the mutation rate in one (mutator) strain. Mutations were allowed to accumulate in 50 replicate lines of each strain, during 36 transfers of randomly chosen single colonies (∼600 generations). Among wild-type lines, fitnesses were bimodal, with one mode showing no change in mean fitness. The other mode showed a mean 29.6% fitness decline and the petite phenotype, usually caused by partial deletion of the mitochondrial genome. Excluding petites, maximum-likelihood estimates adjusted for the effect of selection were U = 9.5 × 10-5 and sh = 0.217 for the wild type. Among the mutator lines, the best fit was obtained with 0.005 ≤ U ≤ 0.94 and 0.049 ≥ sh ≥ 0.0003. Like other recently tested model organisms, wild-type yeast have low mutation rates, with high mean fitness costs per mutation. Inactivation of mismatch repair increases the frequency of slightly deleterious mutations by approximately two orders of magnitude.
Analysis of the pdx-1 (snz-1/sno-1) Region of the Neurospora crassa Genome: Correlation of Pyridoxine-Requiring Phenotypes With Mutations in Two Structural Genes
Authors: Bean Laura E , Dvorachek William H , Braun Edward L , Errett Allison , Saenz Gregory S , Giles Mara D , Werner-Washburne Margaret , Nelson Mary Anne , Natvig Donald O 
Published: April 2021

Abstract
We report the analysis of a 36-kbp region of the Neurospora crassa genome, which contains homologs of two closely linked stationary phase genes, SNZ1 and SNO1, from Saccharomyces cerevisiae. Homologs of SNZ1 encode extremely highly conserved proteins that have been implicated in pyridoxine (vitamin B6) metabolism in the filamentous fungi Cercospora nicotianae and in Aspergillus nidulans. In N. crassa, SNZ and SNO homologs map to the region occupied by pdx-1 (pyridoxine requiring), a gene that has been known for several decades, but which was not sequenced previously. In this study, pyridoxine-requiring mutants of N. crassa were found to possess mutations that disrupt conserved regions in either the SNZ or SNO homolog. Previously, nearly all of these mutants were classified as pdx-1. However, one mutant with a disrupted SNO homolog was at one time designated pdx-2. It now appears appropriate to reserve the pdx-1 designation for the N. crassa SNZ homolog and pdx-2 for the SNO homolog. We further report annotation of the entire 36,030-bp region, which contains at least 12 protein coding genes, supporting a previous conclusion of high gene densities (12,000-13,000 total genes) for N. crassa. Among genes in this region other than SNZ and SNO homologs, there was no evidence of shared function. Four of the genes in this region appear to have been lost from the S. cerevisiae lineage.
Regulatory Mechanisms Controlling Expression of the DAN/TIR Mannoprotein Genes During Anaerobic Remodeling of the Cell Wall in Saccharomyces cerevisiae
Authors: Abramova Natalia E , Cohen Brian D , Sertil Odeniel , Kapoor Rachna , Davies Kelvin J A , Lowry Charles V 
Published: April 2021

Abstract
The DAN/TIR genes of Saccharomyces cerevisiae encode homologous mannoproteins, some of which are essential for anaerobic growth. Expression of these genes is induced during anaerobiosis and in some cases during cold shock. We show that several heme-responsive mechanisms combine to regulate DAN/TIR gene expression. The first mechanism employs two repression factors, Mox1 and Mox2, and an activation factor, Mox4 (for mannoprotein regulation by oxygen). The genes encoding these proteins were identified by selecting for recessive mutants with altered regulation of a dan1::ura3 fusion. MOX4 is identical to UPC2, encoding a binucleate zinc cluster protein controlling expression of an anaerobic sterol transport system. Mox4/Upc2 is required for expression of all the DAN/TIR genes. It appears to act through a consensus sequence termed the AR1 site, as does Mox2. The noninducible mox4Δ allele was epistatic to the constitutive mox1 and mox2 mutations, suggesting that Mox1 and Mox2 modulate activation by Mox4 in a heme-dependent fashion. Mutations in a putative repression domain in Mox4 caused constitutive expression of the DAN/TIR genes, indicating a role for this domain in heme repression. MOX4 expression is induced both in anaerobic and cold-shocked cells, so heme may also regulate DAN/TIR expression through inhibition of expression of MOX4. Indeed, ectopic expression of MOX4 in aerobic cells resulted in partially constitutive expression of DAN1. Heme also regulates expression of some of the DAN/TIR genes through the Rox7 repressor, which also controls expression of the hypoxic gene ANB1. In addition Rox1, another heme-responsive repressor, and the global repressors Tup1 and Ssn6 are also required for full aerobic repression of these genes.
The ste3 Pheromone Receptor Gene of Pneumocystis carinii Is Surrounded by a Cluster of Signal Transduction Genes
Authors: Smulian A George , Sesterhenn Thomas , Tanaka Reiko , Cushion Melanie T 
Published: April 2021

Abstract
Although the clinical aspects of Pneumocystis carinii pneumonia are well characterized, the basic biology of the causative organism is poorly understood. Most proposed life cycles of P. carinii include both asexual and sexual replicative cycles. The two most prominent morphological forms are a trophic form, thought to undergo asexual replication by binary fission, and a cystic form or ascus containing intracystic bodies or ascospores, the products of sexual replication. To facilitate the Pneumocystis genome project, a P. carinii f. sp. carinii genomic cosmid library and an additional λ cDNA library were generated. A partial expressed sequence tag database, created as part of the genome project, revealed the transcription of meiosis-specific genes and other genes related to sexual reproduction. The ortholog of Ste3, an a-factor pheromone receptor, was cloned and genes surrounding the ste3 locus were examined. Clustered around the ste3 gene are genes encoding elements functional in the pheromone response signal transduction cascade of model fungal organisms. These include the Ste20 protein kinase, the Ste12 homoeodomain transcriptional regulator, a potential pheromone mating factor, and other DNA-binding proteins. The genomic organization of the ste3 locus bears significant similarity to that of the mating locus recently described in Cryptococcus neoformans. The P. carinii genome contains much of the genetic machinery necessary for pheromone responsiveness, and these data support the existence of a sexual replication cycle.