bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Marker-Assisted Prediction of Genetic Value: Beyond the Ridge
Authors: Gianola Daniel , Perez-Enciso Miguel , Toro Miguel A 
Published: April 2021

Abstract
Marked-assisted genetic improvement of agricultural species exploits statistical dependencies in the joint distribution of marker genotypes and quantitative traits. An issue is how molecular (e.g., dense marker maps) and phenotypic information (e.g., some measure of yield in plants) is to be used for predicting the genetic value of candidates for selection. Multiple regression, selection index techniques, best linear unbiased prediction, and ridge regression of phenotypes on marker genotypes have been suggested, as well as more elaborate methods. Here, phenotype-marker associations are modeled hierarchically via multilevel models including chromosomal effects, a spatial covariance of marked effects within chromosomes, background genetic variability, and family heterogeneity. Lorenz curves and Gini coefficients are suggested for assessing the inequality of the contribution of different marked effects to genetic variability. Classical and Bayesian methods are presented. The Bayesian approach includes a Markov chain Monte Carlo implementation. The generality and flexibility of the Bayesian method is illustrated when a Lorenz curve is to be inferred.
A Diffusion Approximation for Selection and Drift in a Subdivided Population
Authors: Cherry Joshua L , Wakeley John 
Published: April 2021

Abstract
The population-genetic consequences of population structure are of great interest and have been studied extensively. An area of particular interest is the interaction among population structure, natural selection, and genetic drift. At first glance, different results in this area give very different impressions of the effect of population subdivision on effective population size (Ne), suggesting that no single value of Ne can completely characterize a structured population. Results presented here show that a population conforming to Wright’s island model of subdivision with genic selection can be related to an idealized panmictic population (a Wright-Fisher population). This equivalent panmictic population has a larger size than the actual population; i.e., Ne is larger than the actual population size, as expected from many results for this type of population structure. The selection coefficient in the equivalent panmictic population, referred to here as the effective selection coefficient (se), is smaller than the actual selection coefficient (s). This explains how the fixation probability of a selected allele can be unaffected by population subdivision despite the fact that subdivision increases Ne, for the product Nese is not altered by subdivision.
Genetic Diversity in Yeast Assessed With Whole-Genome Oligonucleotide Arrays
Authors: Winzeler Elizabeth A , Castillo-Davis Cristian I , Oshiro Guy , Liang David , Richards Daniel R , Zhou Yingyao , Hartl Daniel L 
Published: April 2021

Abstract
The availability of a complete genome sequence allows the detailed study of intraspecies variability. Here we use high-density oligonucleotide arrays to discover 11,115 single-feature polymorphisms (SFPs) existing in one or more of 14 different yeast strains. We use these SFPs to define regions of genetic identity between common laboratory strains of yeast. We assess the genome-wide distribution of genetic variation on the basis of this yeast population. We find that genome variability is biased toward the ends of chromosomes and is more likely to be found in genes with roles in fermentation or in transport. This subtelomeric bias may arise through recombination between nonhomologous sequences because full-gene deletions are more common in these regions than in more central regions of the chromosome.
An Analysis of Why Highly Similar Enzymes Evolve Differently
Authors: Majiduddin Fahd K , Palzkill Timothy 
Published: April 2021

Abstract
The TEM-1 and SHV-1 β-lactamases are important contributors to resistance to β-lactam antibiotics in gram-negative bacteria. These enzymes share 68% amino acid sequence identity and their atomic structures are nearly superimposable. Extended-spectrum cephalosporins were introduced to avoid the action of these β-lactamases. The widespread use of antibiotics has led to the evolution of variant TEM and SHV enzymes that can hydrolyze extended-spectrum antibiotics. Despite being highly similar in structure, the TEM and SHV enzymes have evolved differently in response to the selective pressure of antibiotic therapy. Examples of this are at residues Arg164 and Asp179. Among TEM variants, substitutions are found only at position 164, while among SHV variants, substitutions are found only at position 179. To explain this observation, the effects of substitutions at position 164 in both TEM-1 and SHV-1 on antibiotic resistance and on enzyme catalytic efficiency were examined. Competition experiments were performed between mutants to understand why certain substitutions preferentially evolve in response to the selective pressure of antibiotic therapy. The data presented here indicate that substitutions at position Asp179 in SHV-1 and Arg164 in TEM-1 are more beneficial to bacteria because they provide increased fitness relative to either wild type or other mutants.
Short-Chain Fatty Acid Activation by Acyl-Coenzyme A Synthetases Requires SIR2 Protein Function in Salmonella enterica and Saccharomyces cerevisiae
Authors: Starai Vincent J , Takahashi Hidekazu , Boeke Jef D , Escalante-Semerena Jorge C 
Published: April 2021

Abstract
SIR2 proteins have NAD+-dependent histone deacetylase activity, but no metabolic role has been assigned to any of these proteins. In Salmonella enterica, SIR2 function was required for activity of the acetyl-CoA synthetase (Acs) enzyme. A greater than two orders of magnitude increase in the specific activity of Acs enzyme synthesized by a sirtuin-deficient strain was measured after treatment with homogeneous S. enterica SIR2 protein. Human SIR2A and yeast SIR2 proteins restored growth of SIR2-deficient S. enterica on acetate and propionate, suggesting that eukaryotic cells may also use SIR2 proteins to control the synthesis of acetyl-CoA by the level of acetylation of acetyl-CoA synthetases. Consistent with this idea, growth of a quintuple sir2 hst1 hst2 hst3 hst4 mutant strain of the yeast Saccharomyces cerevisiae on acetate or propionate was severely impaired. The data suggest that the Hst3 and Hst4 proteins are the most important for allowing growth on these short-chain fatty acids.
Deficiencies in C20 Polyunsaturated Fatty Acids Cause Behavioral and Developmental Defects inCaenorhabditis elegans fat-3Mutants
Authors: Watts Jennifer L , Phillips Eric , Griffing Katharine R , Browse John 
Published: April 2021

AbstractArachidonic acid and other long-chain polyunsaturated fatty acids (PUFAs) are important structural components of membranes and are implicated in diverse signaling pathways. The Δ6 desaturation of linoleic and linolenic acids is the rate-limiting step in the synthesis of these molecules. C. elegans fat-3 mutants lack Δ6 desaturase activity and fail to produce C20 PUFAs. We examined these mutants and found that development and behavior were affected as a consequence of C20 PUFA deficiency. While fat-3 mutants are viable, they grow slowly, display considerably less spontaneous movement, have an altered body shape, and produce fewer progeny than do wild type. In addition, the timing of an ultradian rhythm, the defecation cycle, is lengthened compared to wild type. Since all these defects can be ameliorated by supplementing the nematode diet with gamma-linolenic acid or C20 PUFAs of either the n6 or the n3 series, we can establish a causal link between fatty acid deficiency and phenotype. Similar epidermal tissue defects and slow growth are hallmarks of human fatty acid deficiency.
Evidence of a High Rate of Selective Sweeps in African Drosophila melanogaster
Authors: Mousset Sylvain , Brazier Lionel , Cariou Marie-Louise , Chartois Frédérique , Depaulis Frantz , Veuille Michel 
Published: April 2021

Abstract
Assessing the rate of evolution depends on our ability to detect selection at several genes simultaneously. We summarize DNA sequence variation data in three new and six previously published data sets from the left arm of the second chromosome of Drosophila melanogaster in a population from West Africa, the presumed area of origin of this species. Four loci [Acp26Aa, Fbp2, Vha68-1, and Su(H)] were previously found to deviate from a neutral mutation-drift equilibrium as a consequence of one or several selective sweeps. Polymorphism data from five loci from intervening regions (dpp, Acp26Ab, Acp29AB, GH10711, and Sos) did not show the characteristic deviation from neutrality caused by local selective sweeps. This genomic region is polymorphic for the In(2L)t inversion. Four loci located near inversion breakpoints [dpp, sos, GH10711, and Su(H)] showed significant structuring between the two arrangements or significant deviation from neutrality in the inverted class, probably as a result of a recent shift in inversion frequency. Overall, these patterns of variation suggest that the four selective events were independent. Six loci were observed with no a priori knowledge of selection, and independent selective sweeps were detected in three of them. This suggests that a large part of the D. melanogaster genome has experienced the effect of positive selection in its ancestral African range.
piggyBac-Based Insertional Mutagenesis and Enhancer Detection as a Tool for Functional Insect Genomics
Authors: Horn Carsten , Offen Nils , Nystedt Sverker , Häcker Udo , Wimmer Ernst A 
Published: April 2021

AbstractTransposon mutagenesis provides a fundamental tool for functional genomics. Here we present a non-species-specific, combined enhancer detection and binary expression system based on the transposable element piggyBac: For the different components of this insertional mutagenesis system, we used widely applicable transposons and distinguishable broad-range transformation markers, which should enable this system to be operational in nonmodel arthropods. In a pilot screen in Drosophila melanogaster, piggyBac mutator elements on the X chromosome were mobilized in males by a Hermes-based jumpstarter element providing piggyBac transposase activity under control of the α1-tubulin promoter. As primary reporters in the piggyBac mutator elements, we employed the heterologous transactivators GAL4Δ or tTA. To identify larval and adult enhancer detectors, strains carrying UASp-EYFP or TRE-EYFP as secondary reporter elements were used. Tissue-specific enhancer activities were readily observed in the GAL4Δ/UASp-based systems, but only rarely in the tTA/TRE system. Novel autosomal insertions were recovered with an average jumping rate of 80%. Of these novel insertions, 3.8% showed homozygous lethality, which was reversible by piggyBac excision. Insertions were found in both coding and noncoding regions of characterized genes and also in noncharacterized and non-P-targeted CG-number genes. This indicates that piggyBac will greatly facilitate the intended saturation mutagenesis in Drosophila.
Gene Duplication and Spectral Diversification of Cone Visual Pigments of Zebrafish
Authors: Chinen Akito , Hamaoka Takanori , Yamada Yukihiro , Kawamura Shoji 
Published: April 2021

AbstractZebrafish is becoming a powerful animal model for the study of vision but the genomic organization and variation of its visual opsins have not been fully characterized. We show here that zebrafish has two red (LWS-1 and LWS-2), four green (RH2-1, RH2-2, RH2-3, and RH2-4), and single blue (SWS2) and ultraviolet (SWS1) opsin genes in the genome, among which LWS-2, RH2-2, and RH2-3 are novel. SWS2, LWS-1, and LWS-2 are located in tandem and RH2-1, RH2-2, RH2-3, and RH2-4 form another tandem gene cluster. The peak absorption spectra (λmax) of the reconstituted photopigments from the opsin cDNAs differed markedly among them: 558 nm (LWS-1), 548 nm (LWS-2), 467 nm (RH2-1), 476 nm (RH2-2), 488 nm (RH2-3), 505 nm (RH2-4), 355 nm (SWS1), 416 nm (SWS2), and 501 nm (RH1, rod opsin). The quantitative RT-PCR revealed a considerable difference among the opsin genes in the expression level in the retina. The expression of the two red opsin genes and of three green opsin genes, RH2-1, RH2-3, and RH2-4, is significantly lower than that of RH2-2, SWS1, and SWS2. These findings must contribute to our comprehensive understanding of visual capabilities of zebrafish and the evolution of the fish visual system and should become a basis of further studies on expression and developmental regulation of the opsin genes.
Alternative Transcription Initiation Sites and Polyadenylation Sites Are Recruited During Mu Suppression at the rf2a Locus of Maize
Authors: Cui Xiangqin , Hsia An-Ping , Liu Feng , Ashlock Daniel A , Wise Roger P , Schnable Patrick S 
Published: April 2021

Abstract
Even in the absence of excisional loss of the associated Mu transposons, some Mu-induced mutant alleles of maize can lose their capacity to condition a mutant phenotype. Three of five Mu-derived rf2a alleles are susceptible to such Mu suppression. The suppressible rf2a-m9437 allele has a novel Mu transposon insertion (Mu10) in its 5′ untranslated region (UTR). The suppressible rf2a-m9390 allele has a Mu1 insertion in its 5′ UTR. During suppression, alternative transcription initiation sites flanking the Mu1 transposon yield functional transcripts. The suppressible rf2a-m8110 allele has an rcy/Mu7 insertion in its 3′ UTR. Suppression of this allele occurs via a previously unreported mechanism; sequences in the terminal inverted repeats of rcy/Mu7 function as alternative polyadenylation sites such that the suppressed rf2a-m8110 allele yields functional rf2a transcripts. No significant differences were observed in the nucleotide compositions of these alternative polyadenylation sites as compared with 94 other polyadenylation sites from maize genes.
Selection on Rapidly Evolving Proteins in the Arabidopsis Genome
Authors: Barrier Marianne , Bustamante Carlos D , Yu Jiaye , Purugganan Michael D 
Published: April 2021

Abstract
Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (ω = Ka/Ks). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of ω among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (∼5%) have an estimated ω &gt; 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci.
Genome-Wide Analysis of mariner-Like Transposable Elements in Rice Reveals Complex Relationships With Stowaway Miniature Inverted Repeat Transposable Elements (MITEs)
Authors: Feschotte Cédric , Swamy Lakshmi , Wessler Susan R 
Published: April 2021

Abstract
Stowaway is a superfamily of miniature inverted repeat transposable elements (MITEs) that is widespread and abundant in plant genomes. Like other MITEs, however, its origin and mode of amplification are poorly understood. Several lines of evidence point to plant mariner-like elements (MLEs) as the autonomous partners of the nonautonomous Stowaway MITEs. To better understand this relationship, we have taken advantage of the nearly complete genome sequences of two rice subspecies to generate the first inventory of virtually all MLEs and Stowaway families coexisting in a single plant species. Thirty-four different MLEs were found to group into three major clades and 25 families. More than 22,000 Stowaway MITEs were identified and classified into 36 families. On the basis of detailed sequence comparisons, MLEs were confirmed to be the best candidate autonomous elements for Stowaway MITEs. Surprisingly, however, sequence similarity between MLE and Stowaway families was restricted to the terminal inverted repeats (TIRs) and, in a few cases, to adjacent subterminal sequences. These data suggest a model whereby most of the Stowaway MITEs in rice were cross-mobilized by MLE transposases encoded by distantly related elements.
The Coalescent and Infinite-Site Model of a Small Multigene Family
Authors: Innan Hideki 
Published: April 2021

Abstract
The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage disequilibrium are obtained, and a coalescent-based method for simulating patterns of polymorphism in a small multigene family is developed. The pattern of DNA variation is much more complicated than that in a single-copy gene, which can be simulated by the standard coalescent. Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered.
Delineation by Fluorescence in Situ Hybridization of a Single Hemizygous Chromosomal Region Associated With Aposporous Embryo Sac Formation in Pennisetum squamulatum and Cenchrus ciliaris
Authors: Goel Shailendra , Chen Zhenbang , Conner Joann A , Akiyama Yukio , Hanna Wayne W , Ozias-Akins Peggy 
Published: April 2021

Abstract
Apomixis is a means of asexual reproduction by which plants produce embryos without meiosis and fertilization; thus the embryo is of clonal, maternal origin. We previously reported molecular markers showing no recombination with the trait for aposporous embryo sac development in Pennisetum squamulatum and Cenchrus ciliaris, and the collective single-dose alleles defined an apospory-specific genomic region (ASGR). Fluorescence in situ hybridization (FISH) was used to confirm that the ASGR is a hemizygous genomic region and to determine its chromosomal position with respect to rDNA loci and centromere repeats. We also documented chromosome transmission from P. squamulatum in several backcrosses (BCs) with P. glaucum using genomic in situ hybridization (GISH). One to three complete P. squamulatum chromosomes were detected in BC6, but only one of the three hybridized with the ASGR-linked markers. In P. squamulatum and in all BCs examined, the apospory-linked markers were located in the distal region of the short arm of a single chromosome. All alien chromosomes behaved as univalents during meiosis and segregated randomly in BC3 and later BC generations, but presence of the ASGR-carrier chromosome alone was sufficient to confer apospory. FISH results support our hypotheses that hemizygosity, proximity to centromeric sequences, and chromosome structure may all play a role in low recombination in the ASGR.
The Maize Unstable factor for orange1 Is a Dominant Epigenetic Modifier of a Tissue Specifically Silent Allele of pericarp color1
Authors: Chopra Surinder , Cocciolone Suzy M , Bushman Shaun , Sangar Vineet , McMullen Michael D , Peterson Thomas 
Published: April 2021

Abstract
We have characterized Unstable factor for orange1 (Ufo1), a dominant, allele-specific modifier of expression of the maize pericarp color1 (p1) gene. The p1 gene encodes an Myb-homologous transcriptional activator of genes required for biosynthesis of red phlobaphene pigments. The P1-wr allele specifies colorless kernel pericarp and red cobs, whereas Ufo1 modifies P1-wr expression to confer pigmentation in kernel pericarp, as well as vegetative tissues, which normally do not accumulate significant amounts of phlobaphene pigments. In the presence of Ufo1, P1-wr transcript levels and transcription rate are increased in kernel pericarp. The P1-wr allele contains approximately six p1 gene copies present in a hypermethylated and multicopy tandem array. In P1-wr Ufo1 plants, methylation of P1-wr DNA sequences is reduced, whereas the methylation state of other repetitive genomic sequences was not detectably affected. The phenotypes produced by the interaction of P1-wr and Ufo1 are unstable, exhibiting somatic mosaicism and variable penetrance. Moreover, the changes in P1-wr expression and methylation are not heritable: meiotic segregants that lack Ufo1 revert to the normal P1-wr expression and methylation patterns. These results demonstrate the existence of a class of modifiers of gene expression whose effects are associated with transient changes in DNA methylation of specific loci.
The Genealogy of Sequences Containing Multiple Sites Subject to Strong Selection in a Subdivided Population
Authors: Nordborg Magnus , Innan Hideki 
Published: April 2021

AbstractA stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.
Nonrandom Homolog Segregation at Meiosis I in Schizosaccharomyces pombe Mutants Lacking Recombination
Authors: Davis Luther , Smith Gerald R 
Published: April 2021

Abstract
Physical connection between homologous chromosomes is normally required for their proper segregation to opposite poles at the first meiotic division (MI). This connection is generally provided by the combination of reciprocal recombination and sister-chromatid cohesion. In the absence of meiotic recombination, homologs are predicted to segregate randomly at MI. Here we demonstrate that in rec12 mutants of the fission yeast Schizosaccharomyces pombe, which are devoid of meiosis-induced recombination, homologs segregate to opposite poles at MI 63% of the time. Residual, Rec12-independent recombination appears insufficient to account for the observed nonrandom homolog segregation. Dyad asci are frequently produced by rec12 mutants. More than half of these dyad asci contain two viable homozygous-diploid spores, the products of a single reductional division. This set of phenotypes is shared by other S. pombe mutants that lack meiotic recombination, suggesting that nonrandom MI segregation and dyad formation are a general feature of meiosis in the absence of recombination and are not peculiar to rec12 mutants. Rec8, a meiosis-specific sister-chromatid cohesin, is required for the segregation phenotypes displayed by rec12 mutants. We propose that S. pombe possesses a system independent of recombination that promotes homolog segregation and discuss possible mechanisms.