bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Trait Locus Mapping in Laboratory Mice Derived From a Replicated Selection Experiment for Open-Field Activity
Authors: Turri Maria Grazia , Henderson Norman D , DeFries John C , Flint Jonathan 
Published: April 2021

Abstract
Bidirectional selection in rodents has been used to derive animal models of human behavior. An important question is whether selection for behavior operates on a limited number of QTL or whether the number and individual contribution of QTL varies between selection experiments. To address this question, we mapped QTL in two large F2 intercrosses (N = 815 and 821) from the four lines derived from a replicated selection experiment for open-field activity, an animal model for susceptibility to anxiety. Our analyses indicate that selection operated on the same relatively small number of loci in both crosses. Haplotype information and the direction of effect of each QTL allele were used to confirm that the QTL mapped in the two crosses lie in the same chromosomal regions, although we were unable to determine whether QTL in the two crosses represent the same genes. We conclude that the genetic architecture of the selected strains is similar and relatively simple.
Localization of Male-Specifically Expressed MROS Genes of Silene latifolia by PCR on Flow-Sorted Sex Chromosomes and Autosomes
Authors: Kejnovský Eduard , Vrána Jan , Matsunaga Sachihiro , Souček Přemysl , Široký Jiří , Doležel Jaroslav , Vyskot Boris 
Published: April 2021

Abstract
The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that the MROS3 gene is located in at least two copies tandemly arranged on the X chromosome with additional copy(ies) on the autosome(s), while MROS1, MROS2, and MROS4 are exclusively autosomal. The specificity of PCR products was checked by digestion with a restriction enzyme or reamplification using nested primers. Homology search of databases has shown the presence of five MROS3 homologues in A. thaliana, four of them arranged in two tandems, each consisting of two copies. We conclude that MROS3 is a low-copy gene family, connected with the proper pollen development, which is present not only in dioecious but also in other dicot plant species.
Development of a Genetics Education Workshop Curriculum for Native American College and University Students
Authors: Burhansstipanov Linda , Bemis Lynne , Dignan Mark , Dukepoo Frank 
Published: April 2021

Abstract
The long-term goal of Genetic Education for Native Americans (GENA), a project funded by the National Human Genome Research Institute (NHGRI), is to provide a balance of scientific and cultural information about genetics and genetic research to Native Americans and thereby to improve informed decision making. The project provides culturally sensitive education about genetic research to Native American medical students and college and university students. Curriculum development included focus groups, extensive review of available curricula, and collection of information about career opportunities in genetics. Special attention was focused on genetic research to identify key concepts, instructional methods, and issues that are potentially troublesome or sensitive for Native Americans. Content on genetic research and careers in genetics was adapted from a wide variety of sources for use in the curriculum. The resulting GENA curriculum is based on 24 objectives arranged into modules customized for selected science-related conference participants. The curriculum was pretested with Native American students, medical and general university, health care professionals, and basic scientists. Implementation of the curriculum is ongoing. This article describes the development and pretesting of the genetics curriculum for the project with the expectation that the curriculum will be useful for genetics educators working in diverse settings.
Eukaryotic β-Alanine Synthases Are Functionally Related but Have a High Degree of Structural Diversity
Authors: Gojković Zoran , Sandrini Michael P B , Piškur Jure 
Published: April 2021

Abstract
β-Alanine synthase (EC 3.5.1.6), which catalyzes the final step of pyrimidine catabolism, has only been characterized in mammals. A Saccharomyces kluyveri pyd3 mutant that is unable to grow on N-carbamyl-β-alanine as the sole nitrogen source and exhibits diminished β-alanine synthase activity was used to clone analogous genes from different eukaryotes. Putative PYD3 sequences from the yeast S. kluyveri, the slime mold Dictyostelium discoideum, and the fruit fly Drosophila melanogaster complemented the pyd3 defect. When the S. kluyveri PYD3 gene was expressed in S. cerevisiae, which has no pyrimidine catabolic pathway, it enabled growth on N-carbamyl-β-alanine as the sole nitrogen source. The D. discoideum and D. melanogaster PYD3 gene products are similar to mammalian β-alanine synthases. In contrast, the S. kluyveri protein is quite different from these and more similar to bacterial N-carbamyl amidohydrolases. All three β-alanine synthases are to some degree related to various aspartate transcarbamylases, which catalyze the second step of the de novo pyrimidine biosynthetic pathway. PYD3 expression in yeast seems to be inducible by dihydrouracil and N-carbamyl-β-alanine, but not by uracil. This work establishes S. kluyveri as a model organism for studying pyrimidine degradation and β-alanine production in eukaryotes.
The nonA Gene in Drosophila Conveys Species-Specific Behavioral Characteristics
Authors: Campesan Susanna , Dubrova Yuri , Hall Jeffrey C , Kyriacou Charalambos P 
Published: April 2021

Abstract
The molecular basis of species-specific differences in courtship behavior, a critical factor in preserving species boundaries, is poorly understood. Genetic analysis of all but the most closely related species is usually impossible, given the inviability of hybrids. We have therefore applied interspecific transformation of a single candidate behavioral locus, no-on-transient A (nonA), between Drosophila virilis and D. melanogaster, to investigate whether nonA, like the period gene, might encode species-specific behavioral information. Mutations in nonA can disrupt both visual behavior and the courtship song in D. melanogaster. The lovesong of nonAdiss mutant males superficially resembles that of D. virilis, a species that diverged from D. melanogaster 40–60 mya. Transformation of the cloned D. virilis nonA gene into D. melanogaster hosts carrying a synthetic deletion of the nonA locus restored normal visual function (the phenotype most sensitive to nonA mutation). However, the courtship song of transformant males showed several features characteristic of the corresponding D. virilis signal, indicating that nonA can act as a reservoir for species-specific information. This candidate gene approach, together with interspecific transformation, can therefore provide a direct avenue to explore potential speciation genes in genetically and molecularly tractable organisms such as Drosophila.
The cyclope Gene of Drosophila Encodes a Cytochrome c Oxidase Subunit VIc Homolog
Authors: Szuplewski Sébastien , Terracol Régine 
Published: April 2021

Abstract
Cytochrome c oxidase is the terminal enzyme of the mitochondrial electron transfer chain. In eukaryotes, the enzyme is composed of 3 mitochondrial DNA-encoded subunits and 7–10 (in mammals) nuclear DNA-encoded subunits. This enzyme has been extensively studied in mammals and yeast but, in Drosophila, very little is known and no mutant has been described so far. Here we report the genetic and molecular characterization of mutations in cyclope (cype) and the cloning of the gene encoding a cytochrome c oxidase subunit VIc homolog. cype is an essential gene whose mutations are lethal and show pleiotropic phenotypes. The 77-amino acid peptide encoded by cype is 46% identical and 59% similar to the human subunit (75 amino acids). The transcripts are expressed maternally and throughout development in localized regions. They are found predominantly in the central nervous system of the embryo; in the central region of imaginal discs; in the germarium, follicular, and nurse cells of the ovary; and in testis. A search in the Genome Annotation Database of Drosophila revealed the absence of subunit VIIb and the presence of 9 putative nuclear cytochrome c oxidase subunits with high identity scores when compared to the 10 human subunits.
Overdominant Epistatic Loci Are the Primary Genetic Basis of Inbreeding Depression and Heterosis in Rice. II. Grain Yield Components
Authors: Luo L J , Li Z-K , Mei H W , Shu Q Y , Tabien R , Zhong D B , Ying C S , Stansel J W , Khush G S , Paterson A H 
Published: April 2021

AbstractThe genetic basis underlying inbreeding depression and heterosis for three grain yield components of rice was investigated in five interrelated mapping populations using a complete RFLP linkage map, replicated phenotyping, and the mixed model approach. The populations included 254 F10 recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica), two backcross (BC) and two testcross populations derived from crosses between the RILs and the parents plus two testers (Zhong413 and IR64). For the yield components, the RILs showed significant inbreeding depression and hybrid breakdown, and the BC and testcross populations showed high levels of heterosis. The average performance of the BC or testcross hybrids was largely determined by heterosis. The inbreeding depression values of individual RILs were negatively associated with the heterosis measurements of the BC or testcross hybrids. We identified many epistatic QTL pairs and a few main-effect QTL responsible for &gt;65% of the phenotypic variation of the yield components in each of the populations. Most epistasis occurred between complementary loci, suggesting that grain yield components were associated more with multilocus genotypes than with specific alleles at individual loci. Overdominance was also an important property of most loci associated with heterosis, particularly for panicles per plant and grains per panicle. Two independent groups of genes appeared to affect grain weight: one showing primarily nonadditive gene action explained 62.1% of the heterotic variation of the trait, and the other exhibiting only additive gene action accounted for 28.1% of the total trait variation of the F1 mean values. We found no evidence suggesting that pseudooverdominance from the repulsive linkage of completely or partially dominant QTL for yield components resulted in the overdominant QTL for grain yield. Pronounced overdominance resulting from epistasis expressed by multilocus genotypes appeared to explain the long-standing dilemma of how inbreeding depression could arise from overdominant genes.
Modeling Linkage Disequilibrium Between a Polymorphic Marker Locus and a Locus Affecting Complex Dichotomous Traits in Natural Populations
Authors: Luo Z W , Wu Chung-I 
Published: April 2021

AbstractLinkage disequilibrium is an important topic in evolutionary and population genetics. An issue yet to be settled is the theory required to extend the linkage disequilibrium analysis to complex traits. In this study, we present theoretical analysis and methods for detecting or estimating linkage disequilibrium (LD) between a polymorphic marker locus and any one of the loci affecting a complex dichotomous trait on the basis of samples randomly or selectively collected from natural populations. Statistical properties of these methods were investigated and their powers were compared analytically or by use of Monte Carlo simulations. The results show that the disequilibrium may be detected with a power of 80% by using phenotypic records and marker genotype when both the trait and marker variants are common (30%) and the LD is relatively high (40–100% of the theoretical maximum). The maximum-likelihood approach provides accurate estimates of the model parameters as well as detection of linkage disequilibrium. The likelihood method is preferred for its higher power and reliability in parameter estimation. The approaches developed in this article are also compared to those for analyzing a continuously distributed quantitative trait. It is shown that a larger sample size is required for the dichotomous trait model to obtain the same level of power in detecting linkage disequilibrium as the continuous trait analysis. Potential use of these estimates in mapping the trait locus is also discussed.
The Functional Impact of Pgm Amino Acid Polymorphism on Glycogen Content in Drosophila melanogaster
Authors: Verrelli Brian C , Eanes Walter F 
Published: April 2021

Abstract
Earlier studies of the common PGM allozymes in Drosophila melanogaster reported no in vitro activity differences. However, our study of nucleotide variation observed that PGM allozymes are a heterogeneous mixture of amino acid polymorphisms. In this study, we analyze 10 PGM protein haplotypes with respect to PGM activity, thermostability, and adult glycogen content. We find a twofold difference in activity among PGM protein haplotypes that is associated with a threefold difference in glycogen content. The latitudinal clines for several Pgm amino acid polymorphisms show that high PGM activity, and apparently higher flux to glycogen synthesis, parallel the low activity clines at G6PD for reduced pentose shunt flux in northern latitudes. This suggests that amino acid polymorphism is under selection at this branch point and may be favored for increased metabolic storage associated with stress resistance and adaptation to temperate regions.
Rejection of S-Heteroallelic Pollen by a Dual-Specific S-RNase in Solanum chacoense Predicts a Multimeric SI Pollen Component
Authors: Luu Doan-Trung , Qin Xike , Laublin Geneviève , Yang Qing , Morse David , Cappadocia Mario 
Published: April 2021

Abstract
S-heteroallelic pollen (HAP) grains are usually diploid and contain two different S-alleles. Curiously, HAP produced by tetraploids derived from self-incompatible diploids are typically self-compatible. The two different hypotheses previously advanced to explain the compatibility of HAP are the lack of pollen-S expression and the “competition effect” between two pollen-S gene products expressed in a single pollen grain. To distinguish between these two possibilities, we used a previously described dual-specific S11/13-RNase, termed HVapb-RNase, which can reject two phenotypically distinct pollen (P11 and P13). Since the HVapb-RNase does not distinguish between the two pollen types (it recognizes both), P11P13 HAP should be incompatible with the HVapb-RNase in spite of the competition effect. We show here that P11P13 HAP is accepted by S11S13 styles, but is rejected by the S11/13-RNase, which demonstrates that the pollen-S genes must be expressed in HAP. A model involving tetrameric pollen-S is proposed to explain both the compatibility of P11P13 HAP on S11S13-containing styles and the incompatibility of P11P13 HAP on styles containing the HVapb-RNase.
The Aspergillus nidulans snt Genes Are Required for the Regulation of Septum Formation and Cell Cycle Checkpoints
Authors: Kraus Peter R , Harris Steven D 
Published: April 2021

Abstract
In Aspergillus nidulans, germinating conidia undergo multiple rounds of nuclear division before forming a septum. Previous genetic results suggest that the ability to separate nuclear division and septum formation depends upon a threshold level of activity of the cyclin-dependent kinase NIMXcdk1. Mutations in nimX and nimT, the gene encoding the NIMXcdk1-activating phosphatase, have revealed that Tyr-15 phosphorylation is important for determining the timing of the formation of the first septum. Here, we describe a screen for suppressors of nimT23 (snt), designed to identify additional components of the pathway regulating septum formation. We show that a subset of the snt mutants are defective in the temporal regulation of septum formation and in cell cycle checkpoint responses. Molecular characterization of sntA shows that it is allelic to the previously described ankA gene, which encodes the NIMXcdk1 Tyr-15 kinase. Additional experiments described in this study show that nutritional conditions modulate the timing of septum formation and alter the phenotypes displayed by the snt mutants. A model that suggests that the timing of septum formation is influenced by DNA damage and glucose availability via the sntA and sntB gene products is proposed.
Reciprocal Mouse and Human Limb Phenotypes Caused by Gain- and Loss-of-Function Mutations Affecting Lmbr1
Authors: Clark Richard M , Marker Paul C , Roessler Erich , Dutra Amalia , Schimenti John C , Muenke Maximilian , Kingsley David M 
Published: April 2021

Abstract
The major locus for dominant preaxial polydactyly in humans has been mapped to 7q36. In mice the dominant Hemimelic extra toes (Hx) and Hammertoe (Hm) mutations map to a homologous chromosomal region and cause similar limb defects. The Lmbr1 gene is entirely within the small critical intervals recently defined for both the mouse and human mutations and is misexpressed at the exact time that the mouse Hx phenotype becomes apparent during limb development. This result suggests that Lmbr1 may underlie preaxial polydactyly in both mice and humans. We have used deletion chromosomes to demonstrate that the dominant mouse and human limb defects arise from gain-of-function mutations and not from haploinsufficiency. Furthermore, we created a loss-of-function mutation in the mouse Lmbr1 gene that causes digit number reduction (oligodactyly) on its own and in trans to a deletion chromosome. The loss of digits that we observed in mice with reduced Lmbr1 activity is in contrast to the gain of digits observed in Hx mice and human polydactyly patients. Our results suggest that the Lmbr1 gene is required for limb formation and that reciprocal changes in levels of Lmbr1 activity can lead to either increases or decreases in the number of digits in the vertebrate limb.
Transmission Genetics of Chromatin From a Synthetic Amphidiploid to Cultivated Peanut (Arachis hypogaeaL.): Broadening the Gene Pool of a Monophyletic Polyploid Species
Authors: Burow Mark D , Simpson Charles E , Starr James L , Paterson Andrew H 
Published: April 2021

AbstractPolyploidy creates severe genetic bottlenecks, contributing to the genetic vulnerability of leading crops. Cultivated peanut is thought to be of monophyletic origin, harboring relatively little genetic diversity. To introduce variability from diploid wild species into tetraploid cultivated Arachis hypogaea, a synthetic amphidiploid {[A. batizocoi K9484 × (A. cardenasii GKP10017 × A. diogoi GKP10602)]4×} was used as donor parent to generate a backcross population of 78 progeny. Three hundred seventy RFLP loci were mapped onto 23 linkage groups, spanning 2210 cM. Chromatin derived from the two A-genome diploid ancestors (A. cardenasii and A. diogoi) comprised mosaic chromosomes, reflecting crossing over in the diploid A-genome interspecific F1 hybrid. Recombination between chromosomes in the tetraploid progeny was similar to chromosome pairing reported for A. hypogaea, with recombination generally between chromosomes of the same subgenomic affinity. Segregation distortion was observed for 25% of the markers, distributed over 20 linkage groups. Unexpectedly, 68% of the markers deviating from expected segregation showed an excess of the synthetic parent allele. Genetic consequences, relationship to species origins, and significance for comparative genetics are discussed.
Depletion of a Novel SET-Domain Protein Enhances the Sterility of mes-3 and mes-4 Mutants of Caenorhabditis elegans
Authors: Xu Lei , Strome Susan 
Published: April 2021

Abstract
Four maternal-effect sterile genes, mes-2, mes-3, mes-4, and mes-6, are essential for germline development in Caenorhabditis elegans. Homozygous mes progeny from heterozygous mothers are themselves fertile but produce sterile progeny with underproliferated and degenerated germlines. All four mes genes encode chromatin-associated proteins, two of which resemble known regulators of gene expression. To identify additional components in the MES pathway, we used RNA-mediated interference (RNAi) to test candidate genes for enhancement of the Mes mutant phenotype. Enhancement in this assay was induction of sterility a generation earlier, in the otherwise fertile homozygous progeny of heterozygous mothers, which previous results had suggested represent a sensitized genetic background. We tested seven genes predicted to encode regulators of chromatin organization for RNAi-induced enhancement of mes-3 sterility and identified one enhancer, called set-2 after the SET domain encoded by the gene. Depletion of SET-2 also enhances the sterile phenotype of mes-4 but not of mes-2 or mes-6. set-2 encodes two alternatively spliced transcripts, set-2l and set-2s, both of which are enriched in the germline of adults. In the adult germline, SET-2L protein is localized in mitotic and mid-late-stage meiotic nuclei but is undetectable in early pachytene nuclei. SET-2L protein is localized in all nuclei of embryos. The localization of SET-2L does not depend on any of the four MES proteins, and none of the MES proteins depend on SET-2 for their normal localization. Our results suggest that SET-2 participates along with the MES proteins in promoting normal germline development.
Structural Features and Methylation Patterns Associated With Paramutation at the r1 Locus of Zea mays
Authors: Walker Elsbeth L , Panavas Tadas 
Published: April 2021

Abstract
In paramutation, two alleles of a gene interact and, during the interaction, one of them becomes epigenetically silenced. The various paramutation systems that have been studied to date exhibit intriguing differences in the physical complexity of the loci involved. B and Pl alleles that participate in paramutation are simple, single genes, while the R haplotypes that participate in paramutation contain multiple gene copies and often include rearrangements. The number and arrangement of the sequences in particular complex R haplotypes have been correlated with paramutation behavior. Here, the physical structures of 28 additional haplotypes of R were examined. A specific set of physical features is associated with paramutability (the ability to be silenced). However, no physical features were strongly correlated with paramutagenicity (the ability to cause silencing) or neutrality (the inability to participate in paramutation). Instead, paramutagenic haplotypes were distinguished by high levels of cytosine methylation over certain regions of the genes while neutral haplotypes were distinguished by lack of C-methylation over these regions. These findings suggest that paramutability of r1 is determined by the genetic structure of particular haplotypes, while paramutagenicity is determined by the epigenetic state.