bluuebunny/crossref_metadata_2025_split huggingface dataset:
Teaching Advanced Genetics Without Lectures
Authors: Cameron Vicki L 
Published: April 2021

Abstract
In an effort to increase student engagement and therefore student learning, an advanced genetics course was developed in which traditional lectures were eliminated. Instead, students were required to complete reading assignments before each class meeting, and those readings were then the topic of group discussion. Assigned readings alternated between text assignments and articles from the primary literature. Students were made accountable for their own preparation by the administration of a quiz at the start of each class. Group discussion of the topics engaged students in the learning process and readministration of the quiz at the end of class allowed them to benefit from the group interaction and understanding. Interspersing text readings and primary literature led to student understanding of how genetic knowledge is acquired and interpreted and how experimental detail leads to the construction of general models.
Role of Mismatch Repair in the Fidelity of RAD51- and RAD59-Dependent Recombination in Saccharomyces cerevisiae
Authors: Spell Rachelle Miller , Jinks-Robertson Sue 
Published: April 2021

Abstract
To prevent genome instability, recombination between sequences that contain mismatches (homeologous recombination) is suppressed by the mismatch repair (MMR) pathway. To understand the interactions necessary for this regulation, the genetic requirements for the inhibition of homeologous recombination were examined using mutants in the RAD52 epistasis group of Saccharomyces cerevisiae. The use of a chromosomal inverted-repeat recombination assay to measure spontaneous recombination between 91 and 100% identical sequences demonstrated differences in the fidelity of recombination in pathways defined by their dependence on RAD51 and RAD59. In addition, the regulation of homeologous recombination in rad51 and rad59 mutants displayed distinct patterns of inhibition by different members of the MMR pathway. Whereas the requirements for the MutS homolog, MSH2, and the MutL homolog, MLH1, in the suppression of homeologous recombination were similar in rad51 strains, the loss of MSH2 caused a greater loss in homeologous recombination suppression than did the loss of MLH1 in a rad59 strain. The nonequivalence of the regulatory patterns in the wild-type and mutant strains suggests an overlap between the roles of the RAD51 and RAD59 gene products in potential cooperative recombination mechanisms used in wild-type cells.
Genome-Wide Amplifications Caused by Chromosomal Rearrangements Play a Major Role in the Adaptive Evolution of Natural Yeast
Authors: Infante Juan J , Dombek Kenneth M , Rebordinos Laureana , Cantoral Jesús M , Young Elton T 
Published: April 2021

AbstractThe relative importance of gross chromosomal rearrangements to adaptive evolution has not been precisely defined. The Saccharomyces cerevisiae flor yeast strains offer significant advantages for the study of molecular evolution since they have recently evolved to a high degree of specialization in a very restrictive environment. Using DNA microarray technology, we have compared the genomes of two prominent variants of S. cerevisiae flor yeast strains. The strains differ from one another in the DNA copy number of 116 genomic regions that comprise 38% of the genome. In most cases, these regions are amplicons flanked by repeated sequences or other recombination hotspots previously described as regions where double-strand breaks occur. The presence of genes that confer specific characteristics to the flor yeast within the amplicons supports the role of chromosomal rearrangements as a major mechanism of adaptive evolution in S. cerevisiae. We propose that nonallelic interactions are enhanced by ethanol- and acetaldehyde-induced double-strand breaks in the chromosomal DNA, which are repaired by pathways that yield gross chromosomal rearrangements. This mechanism of chromosomal evolution could also account for the sexual isolation shown among the flor yeast.
The Structure and Early Evolution of Recently Arisen Gene Duplicates in the Caenorhabditis elegans Genome
Authors: Katju Vaishali , Lynch Michael 
Published: April 2021

Abstract
The significance of gene duplication in provisioning raw materials for the evolution of genomic diversity is widely recognized, but the early evolutionary dynamics of duplicate genes remain obscure. To elucidate the structural characteristics of newly arisen gene duplicates at infancy and their subsequent evolutionary properties, we analyzed gene pairs with ≤10% divergence at synonymous sites within the genome of Caenorhabditis elegans. Structural heterogeneity between duplicate copies is present very early in their evolutionary history and is maintained over longer evolutionary timescales, suggesting that duplications across gene boundaries in conjunction with shuffling events have at least as much potential to contribute to long-term evolution as do fully redundant (complete) duplicates. The median duplication span of 1.4 kb falls short of the average gene length in C. elegans (2.5 kb), suggesting that partial gene duplications are frequent. Most gene duplicates reside close to the parent copy at inception, often as tandem inverted loci, and appear to disperse in the genome as they age, as a result of reduced survivorship of duplicates located in proximity to the ancestral copy. We propose that illegitimate recombination events leading to inverted duplications play a disproportionately large role in gene duplication within this genome in comparison with other mechanisms.
Selective Constraints on Intron Evolution in Drosophila
Authors: Parsch John 
Published: April 2021

AbstractIntron sizes show an asymmetrical distribution in a number of organisms, with a large number of “short” introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (&lt;10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.
l(3)malignant brain tumor and Three Novel Genes Are Required for Drosophila Germ-Cell Formation
Authors: Yohn Christopher B , Pusateri Leslie , Barbosa Vitor , Lehmann Ruth 
Published: April 2021

Abstract
To identify genes involved in the process of germ-cell formation in Drosophila, a maternal-effect screen using the FLP/FRT-ovoD method was performed on chromosome 3R. In addition to expected mutations in the germ-cell determinant oskar and in other genes known to be involved in the process, several novel mutations caused defects in germ-cell formation. Mutations in any of three genes [l(3)malignant brain tumor, shackleton, and out of sync] affect the synchronous mitotic divisions and nuclear migration of the early embryo. The defects in nuclear migration or mitotic synchrony result in a reduction in germ-cell formation. Mutations in another gene identified in this screen, bebra, do not cause mitotic defects, but appear to act upstream of the localization of oskar. Analysis of our mutants demonstrates that two unique and independent processes must occur to form germ cells—germ-plasm formation and nuclear division/migration.
Recruitment of the Proneural Genescuteto the Drosophila Sex-Determination Pathway
Authors: Wrischnik Lisa A , Timmer John R , Megna Lisa A , Cline Thomas W 
Published: April 2021

AbstractIn flies, scute (sc) works with its paralogs in the achaete-scute-complex (ASC) to direct neuronal development. However, in the family Drosophilidae, sc also acquired a role in the primary event of sex determination, X chromosome counting, by becoming an X chromosome signal element (XSE)—an evolutionary step shown here to have occurred after sc diverged from its closest paralog, achaete (ac). Two temperature-sensitive alleles, scsisB2 and scsisB3, which disrupt only sex determination, were recovered in a powerful F1 genetic selection and used to investigate how sc was recruited to the sex-determination pathway. scsisB2 revealed 3′ nontranscribed regulatory sequences likely to be involved. The scsisB2 lesion abolished XSE activity when combined with mutations engineered in a sequence upstream of all XSEs. In contrast, changes in Sc protein sequence seem not to have been important for recruitment. The observation that the other new allele, scsisB3, eliminates the C-terminal half of Sc without affecting neurogenesis and that scsisB1, the most XSE-specific allele previously available, is a nonsense mutant, would seem to suggest the opposite, but we show that housefly Sc can substitute for fruit fly Sc in sex determination, despite lacking Drosophilidae-specific conserved residues in its C-terminal half. Lack of synergistic lethality among mutations in sc, twist, and dorsal argue against a proposed role for sc in mesoderm formation that had seemed potentially relevant to sex-pathway recruitment. The screen that yielded new sc alleles also generated autosomal duplications that argue against the textbook view that fruit fly sex signal evolution recruited a set of autosomal signal elements comparable to the XSEs.
Expression of the Arabidopsis Transposable ElementTag1Is Targeted to Developing Gametophytes
Authors: Galli Mary , Theriault Angie , Liu Dong , Crawford Nigel M 
Published: April 2021

AbstractThe Arabidopsis transposon Tag1 undergoes late excision during vegetative and germinal development in plants containing 35S-Tag1-GUS constructs. To determine if transcriptional regulation can account for the developmental control of Tag1 excision, the transcriptional activity of Tag1 promoter-GUS fusion constructs of various lengths was examined in transgenic plants. All constructs showed expression in the reproductive organs of developing flowers but no expression in leaves. Expression was restricted to developing gametophytes in both male and female lineages. Quantitative RT-PCR analysis confirmed that Tag1 expression predominates in the reproductive organs of flower buds. These results are consistent with late germinal excision of Tag1, but they cannot explain the vegetative excision activity of Tag1 observed with 35S-Tag1-GUS constructs. To resolve this issue, Tag1 excision was reexamined using elements with no adjacent 35S promoter sequences. Tag1 excision in this context is restricted to germinal events with no detectable vegetative excision. If a 35S enhancer sequence is placed next to Tag1, vegetative excision is restored. These results indicate that the intrinsic activity of Tag1 is restricted to germinal excision due to targeted expression of the Tag1 transposase to developing gametophytes and that this activity is altered by the presence of adjacent enhancers or promoters.
Maize ROP2 GTPase Provides a Competitive Advantage to the Male Gametophyte
Authors: Arthur K M , Vejlupkova Z , Meeley R B , Fowler J E 
Published: April 2021

Abstract
Rop GTPases have been implicated in the regulation of plant signal transduction and cell morphogenesis. To explore ROP2 function in maize, we isolated five Mutator transposon insertions (rop2::Mu alleles). Transmission frequency through the male gametophyte, but not the female, was lower than expected in three of the rop2::Mu mutants. These three alleles formed an allelic series on the basis of the relative transmission rate of each when crossed as trans-heterozygotes. A dramatic reduction in the level of ROP2-mRNA in pollen was associated with the three alleles causing a transmission defect, whereas a rop2::Mu allele that did not result in a defect had wild-type transcript levels, thus confirming that mutation of rop2 causes the mutant phenotype. These data strongly support a role for rop2 in male gametophyte function, perhaps surprisingly, given the expression in pollen of the nearly identical duplicate gene rop9. However, the transmission defect was apparent only when a rop2::Mu heterozygote was used as the pollen donor or when a mixture of wild-type and homozygous mutant pollen was used. Thus, mutant pollen is at a competitive disadvantage compared to wild-type pollen, although mutant pollen grains lacked an obvious cellular defect. Our data demonstrate the importance in vivo of a specific Rop, rop2, in the male gametophyte.
The Genetics of Adaptation: The Roles of Pleiotropy, Stabilizing Selection and Drift in Shaping the Distribution of Bidirectional Fixed Mutational Effects
Authors: Griswold Cortland K , Whitlock Michael C 
Published: April 2021

Abstract
Pleiotropy allows for the deterministic fixation of bidirectional mutations: mutations with effects both in the direction of selection and opposite to selection for the same character. Mutations with deleterious effects on some characters can fix because of beneficial effects on other characters. This study analytically quantifies the expected frequency of mutations that fix with negative and positive effects on a character and the average size of a fixed effect on a character when a mutation pleiotropically affects from very few to many characters. The analysis allows for mutational distributions that vary in shape and provides a framework that would allow for varying the frequency at which mutations arise with deleterious and positive effects on characters. The results show that a large fraction of fixed mutations will have deleterious pleiotropic effects even when mutation affects as little as two characters and only directional selection is occurring, and, not surprisingly, as the degree of pleiotropy increases the frequency of fixed deleterious effects increases. As a point of comparison, we show how stabilizing selection and random genetic drift affect the bidirectional distribution of fixed mutational effects. The results are then applied to QTL studies that seek to find loci that contribute to phenotypic differences between populations or species. It is shown that QTL studies are biased against detecting chromosome regions that have deleterious pleiotropic effects on characters.
Rtg2 Protein Links Metabolism and Genome Stability in Yeast Longevity
Authors: Borghouts Corina , Benguria Alberto , Wawryn Jaroslaw , Jazwinski S Michal 
Published: April 2021

Abstract
Mitochondrial dysfunction induces a signaling pathway, which culminates in changes in the expression of many nuclear genes. This retrograde response, as it is called, extends yeast replicative life span. It also results in a marked increase in the cellular content of extrachromsomal ribosomal DNA circles (ERCs), which can cause the demise of the cell. We have resolved the conundrum of how these two molecular mechanisms of yeast longevity operate in tandem. About 50% of the life-span extension elicited by the retrograde response involves processes other than those that counteract the deleterious effects of ERCs. Deletion of RTG2, a gene that plays a central role in relaying the retrograde response signal to the nucleus, enhances the generation of ERCs in cells with (grande) or in cells without (petite) fully functional mitochondria, and it curtails the life span of each. In contrast, overexpression of RTG2 diminishes ERC formation in both grandes and petites. The excess Rtg2p did not augment the retrograde response, indicating that it was not engaged in retrograde signaling. FOB1, which is known to be required for ERC formation, and RTG2 were found to be in converging pathways for ERC production. RTG2 did not affect silencing of ribosomal DNA in either grandes or petites, which were similar to each other in the extent of silencing at this locus. Silencing of ribosomal DNA increased with replicative age in either the presence or the absence of Rtg2p, distinguishing silencing and ERC accumulation. Our results indicate that the suppression of ERC production by Rtg2p requires that it not be in the process of transducing the retrograde signal from the mitochondrion. Thus, RTG2 lies at the nexus of cellular metabolism and genome stability, coordinating two pathways that have opposite effects on yeast longevity.
Molecular-Genetic Characterization of CMS-SRestorer-of-FertilityAlleles Identified in Mexican Maize and Teosinte
Authors: Gabay-Laughnan Susan , Chase Christine D , Ortega Victor M , Zhao Liming 
Published: April 2021

AbstractRestorer-of-fertility (Rf) alleles for S-type cytoplasmic male sterility (CMS-S) are prevalent in Mexican races of maize and teosinte. Forty-five Rf alleles from 26 races of maize and 6 Rf alleles from different accessions of teosinte were found to be homozygous viable, consistent with the hypothesis that they are naturally occurring Rf alleles. Mapping and allelism studies were performed to assess the number of genes represented by these 51 alleles. Forty-two of the Rf alleles mapped to the long arm of chromosome 2 (2L), and 5 of these were further mapped to the whp1-rf3 region. The Rf3 restoring allele, found in some U.S. maize inbred lines, cosegregates with internal processing of CMS-S mitochondrial transcripts. Three of the 5 mapped Rf alleles were associated with a similar RNA processing event. Allelism or tight linkage was confirmed between Rf3 and 2 teosinte alleles (Rf K-69-6 and Rf 9477) and between Rf3 and the Cónico Norteño allele Rf C-N (GTO 22). The rf3 region of 2L potentially encodes a complex of linked rf genes. The prevalence of restoring alleles in this chromosomal region, among normal-cytoplasm accessions of Mexican maize and teosinte, supports the conclusion that these alleles have functions in normal mitochondrial gene expression that by chance allow them to restore male fertility in S cytoplasm.
Strategies for Avoiding Reinventing the Precollege Education and Outreach Wheel
Authors: Dolan Erin L , Soots Barbara E , Lemaux Peggy G , Rhee Seung Y , Reiser Leonore 
Published: April 2021

Abstract
The National Science Foundation’s recent mandate that all Principal Investigators address the broader impacts of their research has prompted an unprecedented number of scientists to seek opportunities to participate in precollege education and outreach. To help interested geneticists avoid duplicating efforts and make use of existing resources, we examined several precollege genetics, genomics, and biotechnology education efforts and noted the elements that contributed to their success, indicated by program expansion, participant satisfaction, or participant learning. Identifying a specific audience and their needs and resources, involving K–12 teachers in program development, and evaluating program efforts are integral to program success. We highlighted a few innovative programs to illustrate these findings. Challenges that may compromise further development and dissemination of these programs include absence of reward systems for participation in outreach as well as lack of training for scientists doing outreach. Several programs and institutions are tackling these issues in ways that will help sustain outreach efforts while allowing them to be modified to meet the changing needs of their participants, including scientists, teachers, and students. Most importantly, resources and personnel are available to facilitate greater and deeper involvement of scientists in precollege and public education.
Transposon-induced inversions activate gene expression in the maize pericarp
Authors: Sharma Sharu Paul , Zuo Tao , Peterson Thomas 
Published: April 2021

Abstract
Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression, and inhibited recombination. Here, we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p1 gene is null and the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. By screening for kernels with red pericarp, we identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp. To our knowledge, this is the first report of multiple recurrent inversions that change the position of a gene promoter relative to an enhancer to induce ectopic expression in a eukaryote.
Corroborating catch estimates to inform monitoring of a small-scale marine recreational fishery in a World Heritage property
Authors: Taylor S M , Smallwood C B , Desfosses C J , Ryan K L , Jackson G 
Published: April 2021

Abstract
Obtaining accurate estimates of catch can be challenging for small-scale recreational fisheries. Using inner Shark Bay as a case-study, we investigated whether a state-wide phone-diary (PD) survey could provide robust estimates of boat-based fishing effort and catch (kept and total) of pink snapper (Chrysophrys auratus) and grass emperor (Lethrinus laticaudis). Estimates were compared with those from concurrent surveys for two spatial scales corresponding to the fishery and the three pink snapper stocks within the fishery. A supplementary access point (SAP) survey incorporated remote camera data and interviews with fishers at boat ramps. An aerial survey was used to adjust the SAP estimates, accounting for catches from boat fishers launching from remote beaches (SAP_Aerial). The SAP survey provided the most precise estimates but underestimated catches for one of the stocks. Estimated fishing effort from the SAP_Aerial survey was comparable to the PD survey (3% lower) for inner Shark Bay, as was the estimated kept catch of pink snapper (7% lower) and these estimates were considered robust (Relative Standard Error &lt; 40% and sample size ≥ 30). In contrast, estimates of the total catch of pink snapper and the catch (kept and total) of grass emperor from the PD survey were consistently lower. While the on-site surveys generally provided robust estimates of catch for each stock, most PD estimates were not robust at this scale. The SAP_Aerial survey is considered to be the most appropriate for ongoing monitoring because it provides robust estimates for the spatial scales examined. However, estimates of catch from periodic PD surveys for the entire fishery could be adjusted using the on-site data to provide the stock-specific information required for ongoing assessments of sustainability. Our study demonstrates that corroborative studies assist in monitoring recreational fisheries.