bluuebunny/crossref_metadata_2025 huggingface dataset:
High-Resolution Mapping of Quantitative Trait Loci by Selective Recombinant Genotyping
Authors: Ronin Y , Korol A , Shtemberg M , Nevo E , Soller M
Published: April 2021

Selective recombinant genotyping (SRG) is a three-stage procedure for high-resolution mapping of a QTL that has previously been mapped to a known confidence interval (target C.I.). In stage 1, a large mapping population is accessed and phenotyped, and a proportion, P, of the high and low tails is selected. In stage 2, the selected individuals are genotyped for a pair of markers flanking the target C.I., and a group of R individuals carrying recombinant chromosomes in the target interval are identified. In stage 3, the recombinant individuals are genotyped for a set of M markers spanning the target C.I. Extensive simulations showed that: (1) Standard error of QTL location (SEQTL) decreased when QTL effect (d) or population size (N) increased, but was constant for given “power factor” (PF = d2N); (2) increasing the proportion selected in the tails beyond 0.25 had only a negligible effect on SEQTL; and (3) marker spacing in the target interval had a remarkably powerful effect on SEQTL, yielding a reduction of up to 10-fold in going from highest (24 cM) to lowest (0.29 cM) spacing at given population size and QTL effect. At the densest marker spacing, SEQTL of 1.0-0.06 cM were obtained at PF = 500-16,000. Two new genotyping procedures, the half-section algorithm and the golden section/half-section algorithm, allow the equivalent of complete haplotyping of the target C.I. in the recombinant individuals to be achieved with many fewer data points than would be required by complete individual genotyping.
Estimating the Time Since the Fixation of a Beneficial Allele
Authors: Przeworski Molly
Published: April 2021

The fixation of a beneficial allele in a population leaves a well-characterized signature in patterns of nucleotide variation at linked sites. This signature can be used to estimate the time since fixation from patterns of polymorphism in extant individuals. I introduce a method to assess the support in polymorphism data for a recent episode of directional positive selection and to estimate the time since fixation. I summarize the polymorphism data by three statistics that carry information about levels of diversity, the allele frequency spectrum, and the extent of allelic associations. Simulations are then used to obtain a sample from the posterior distribution of the time since fixation, conditional on the observed summaries. I test the performance of the approach on simulated data and apply it to the gene tb1 in maize. The data support the recent fixation of a favored allele, consistent with what is known about the importance of tb1 in the domestication process of maize.
The AF-6 Homolog Canoe Acts as a Rap1 Effector During Dorsal Closure of the Drosophila Embryo
Authors: Boettner Benjamin , Harjes Phoebe , Ishimaru Satoshi , Heke Michael , Fan Hong Qing , Qin Yi , Van Aelst Linda , Gaul Ulrike
Published: April 2021

Rap1 belongs to the highly conserved Ras subfamily of small GTPases. In Drosophila, Rap1 plays a critical role in many different morphogenetic processes, but the molecular mechanisms executing its function are unknown. Here, we demonstrate that Canoe (Cno), the Drosophila homolog of mammalian junctional protein AF-6, acts as an effector of Rap1 in vivo. Cno binds to the activated form of Rap1 in a yeast two-hybrid assay, the two molecules colocalize to the adherens junction, and they display very similar phenotypes in embryonic dorsal closure (DC), a process that relies on the elongation and migration of epithelial cell sheets. Genetic interaction experiments show that Rap1 and Cno act in the same molecular pathway during DC and that the function of both molecules in DC depends on their ability to interact. We further show that Rap1 acts upstream of Cno, but that Rap1, unlike Cno, is not involved in the stimulation of JNK pathway activity, indicating that Cno has both a Rap1-dependent and a Rap1-independent function in the DC process.
DNA Methylation in Placentas of Interspecies Mouse Hybrids
Authors: Schütt Sabine , Florl Andrea R , Shi Wei , Hemberger Myriam , Orth Annie , Otto Sabine , Schulz Wolfgang A , Fundele Reinald H
Published: April 2021

Interspecific hybridization in the genus Mus results in several hybrid dysgenesis effects, such as male sterility and X-linked placental dysplasia (IHPD). The genetic or molecular basis for the placental phenotypes is at present not clear. However, an extremely complex genetic system that has been hypothesized to be caused by major epigenetic changes on the X chromosome has been shown to be active. We have investigated DNA methylation of several single genes, Atrx, Esx1, Mecp2, Pem, Psx1, Vbp1, Pou3f4, and Cdx2, and, in addition, of LINE-1 and IAP repeat sequences, in placentas and tissues of fetal day 18 mouse interspecific hybrids. Our results show some tendency toward hypomethylation in the late gestation mouse placenta. However, no differential methylation was observed in hyper- and hypoplastic hybrid placentas when compared with normal-sized littermate placentas or intraspecific Mus musculus placentas of the same developmental stage. Thus, our results strongly suggest that generalized changes in methylation patterns do not occur in trophoblast cells of such hybrids.
Identification of Cis-regulatory Elements in the Mouse Pax9/Nkx2-9 Genomic Region: Implication for Evolutionary Conserved Synteny
Authors: Santagati Fabio , Abe Kuniya , Schmidt Volker , Schmitt-John Thomas , Suzuki Misao , Yamamura Ken-ichi , Imai Kenji
Published: April 2021

We previously reported close physical linkage between Pax9 and Nkx2-9 in the human, mouse, and pufferfish (Fugu rubripes) genomes. In this study, we analyzed cis-regulatory elements of the two genes by comparative sequencing in the three species and by transgenesis in the mouse. We identified two regions including conserved noncoding sequences that possessed specific enhancer activities for expression of Pax9 in the medial nasal process and of Nkx2-9 in the ventral neural tube. Remarkably, the latter contained the consensus Gli-binding motif. Interestingly, the identified Pax9 cis-regulatory sequences were located in an intron of the neighboring gene Slc25a21. Close examination of an extended genomic interval around Pax9 revealed the presence of strong synteny conservation in the human, mouse, and Fugu genomes. We propose such an intersecting organization of cis-regulatory sequences in multigenic regions as a possible mechanism that maintains evolutionary conserved synteny.
Heterogeneous Selection at Specific Loci in Natural Environments in Arabidopsis thaliana
Authors: Weinig Cynthia , Dorn Lisa A , Kane Nolan C , German Zachary M , Halldorsdottir Solveig S , Ungerer Mark C , Toyonaga Yuko , Mackay Trudy F C , Purugganan Michael D , Schmitt Johanna
Published: April 2021

Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.
Post-transcriptional Cosuppression of Ty1 Retrotransposition
Authors: Garfinkel David J , Nyswaner Katherine , Wang Jun , Cho Jae-Yong
Published: April 2021

To determine whether homology-dependent gene silencing or cosuppression mechanisms underlie copy number control (CNC) of Ty1 retrotransposition, we introduced an active Ty1 element into a naïve strain. Single Ty1 element retrotransposition was elevated in a Ty1-less background, but decreased dramatically when additional elements were present. Transcription from the suppressing Ty1 elements enhanced CNC but translation or reverse transcription was not required. Ty1 CNC occurred with a transcriptionally active Ty2 element, but not with Ty3 or Ty5 elements. CNC also occurred when the suppressing Ty1 elements were transcriptionally silenced, fused to the constitutive PGK1 promoter, or contained a minimal segment of mostly TYA1-gag sequence. Ty1 transcription of a multicopy element expressed from the GAL1 promoter abolished CNC, even when the suppressing element was defective for transposition. Although Ty1 RNA and TyA1-gag protein levels increased with the copy number of expressible elements, a given element's transcript level varied less than twofold regardless of whether the suppressing elements were transcriptionally active or repressed. Furthermore, a decrease in the synthesis of Ty1 cDNA is strongly associated with Ty1 CNC. Together our results suggest that Ty1 cosuppression can occur post-transcriptionally, either prior to or during reverse transcription.
The Role of Cdh1p in Maintaining Genomic Stability in Budding Yeast
Authors: Ross Karen E , Cohen-Fix Orna
Published: April 2021

Cdh1p, a substrate specificity factor for the cell cycle-regulated ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C), promotes exit from mitosis by directing the degradation of a number of proteins, including the mitotic cyclins. Here we present evidence that Cdh1p activity at the M/G1 transition is important not only for mitotic exit but also for high-fidelity chromosome segregation in the subsequent cell cycle. CDH1 showed genetic interactions with MAD2 and PDS1, genes encoding components of the mitotic spindle assembly checkpoint that acts at metaphase to prevent premature chromosome segregation. Unlike cdh1Δ and mad2Δ single mutants, the mad2Δ cdh1Δ double mutant grew slowly and exhibited high rates of chromosome and plasmid loss. Simultaneous deletion of PDS1 and CDH1 caused extensive chromosome missegregation and cell death. Our data suggest that at least part of the chromosome loss can be attributed to kinetochore/spindle problems. Our data further suggest that Cdh1p and Sic1p, a Cdc28p/Clb inhibitor, have overlapping as well as nonoverlapping roles in ensuring proper chromosome segregation. The severe growth defects of both mad2Δ cdh1Δ and pds1Δ cdh1Δ strains were rescued by overexpressing Swe1p, a G2/M inhibitor of the cyclin-dependent kinase, Cdc28p/Clb. We propose that the failure to degrade cyclins at the end of mitosis leaves cdh1Δ mutant strains with abnormal Cdc28p/Clb activity that interferes with proper chromosome segregation.
The Promotion of Gonadal Cell Divisions by the Caenorhabditis elegans TRPM Cation Channel GON-2 Is Antagonized by GEM-4 Copine
Authors: Church Diane L , Lambie Eric J
Published: April 2021

The initiation of postembryonic cell divisions by the gonadal precursors of C. elegans requires the activity of gon-2. gon-2 encodes a predicted cation channel (GON-2) of the TRPM subfamily of TRP proteins and is likely to mediate the influx of Ca2+ and/or Mg2+. We report here that mutations in gem-4 (gon-2 extragenic modifier) are capable of suppressing loss-of-function alleles of gon-2. gem-4 encodes a member of the copine family of Ca2+-dependent phosphatidylserine binding proteins. Overall, our data indicate that GEM-4 antagonizes GON-2. This antagonism could be mediated by a direct inhibition of GON-2 by GEM-4, since both proteins are predicted to be localized to the plasma membrane. Alternatively, GEM-4 could affect GON-2 activity levels by either promoting endocytosis or inhibiting exocytosis of vesicles that carry GON-2. It is also possible that GEM-4 and GON-2 act in parallel to each other. Mutation of gem-4 does not suppress the gonadal defects produced by inactivation of gon-4, suggesting that gon-4 either acts downstream of gem-4 and gon-2 or acts in a parallel regulatory pathway.
A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae
Authors: Dorer Douglas R , Rudnick Jamie A , Moriyama Etsuko N , Christensen Alan C
Published: April 2021

Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.
A Function for Subtelomeric DNA in Saccharomyces cerevisiae
Authors: Barton Arnold B , Su Yuping , Lamb Jacque , Barber Dianna , Kaback David B
Published: April 2021

The subtelomeric DNA sequences from chromosome I of Saccharomyces cerevisiae are shown to be inherently poor substrates for meiotic recombination. On the basis of these results and prior observations that crossovers near telomeres do not promote efficient meiosis I segregation, we suggest that subtelomeric sequences evolved to prevent recombination from occurring where it cannot promote efficient segregation.
Teaching Advanced Genetics Without Lectures
Authors: Cameron Vicki L
Published: April 2021

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

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

The 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

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

Intron 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 (<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

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

In 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

The 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

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

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

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

Restorer-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

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

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

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 < 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.
Ketamine for Bipolar Depression: A Systematic Review
Authors: Bahji Anees , Zarate Carlos A , Vazquez Gustavo H
Published: April 2021

Background

Ketamine appears to have a therapeutic role in certain mental disorders, most notably unipolar major depressive disorder. However, its efficacy in bipolar depression is less clear. This study aimed to assess the efficacy and tolerability of ketamine for bipolar depression.

Methods

We conducted a systematic review of experimental studies using ketamine for the treatment of bipolar depression. We searched PubMed, MEDLINE, Embase, PsycINFO, and the Cochrane Central Register for relevant studies published since each database’s inception. We synthesized evidence regarding efficacy (improvement in depression rating scores) and tolerability (adverse events, dissociation, dropouts) across studies.

Results

We identified 6 studies, with 135 participants (53% female; 44.7 years; standard deviation, 11.7 years). All studies used 0.5 mg/kg of add-on intravenous racemic ketamine, with the number of doses ranging from 1 to 6; all participants continued a mood-stabilizing agent. The overall proportion achieving a response (defined as those having a reduction in their baseline depression severity of at least 50%) was 61% for those receiving ketamine and 5% for those receiving a placebo. The overall response rates varied from 52% to 80% across studies. Ketamine was reasonably well tolerated; however, 2 participants (1 receiving ketamine and 1 receiving placebo) developed manic symptoms. Some participants developed significant dissociative symptoms at the 40-minute mark following ketamine infusion in 2 trials.

Conclusions

There is some preliminary evidence supporting use of intravenous racemic ketamine to treat adults with bipolar depression. There is a need for additional studies exploring longer-term outcomes and alterative formulations of ketamine.
Antibacterial use in the age of SARS-CoV-2
Authors: Angell Kathleen E , Lawler James V , Hewlett Angela L , Rupp Mark E , Bergman Scott J , Van Schooneveld Trevor C , Broadhurst M Jana , Brett-Major David M
Published: April 2021

Background

Balancing the use of antibacterial therapy against selection for resistance in this pandemic era has introduced both questions and guidelines. In this project, we explored how prescription of empirical antibacterial therapy differs between those with and without SARS-CoV-2 infection.

Methods

Multivariable logistic regression was used to determine whether COVID-19 status and other factors play a role in the prescription of antibacterial therapy in an inpatient setting at a large referral academic medical centre. Further analysis was conducted to determine whether these factors differ between those testing positive and negative for SARS-CoV-2.

Results

Of 405 patients in the cohort, 175 received antibacterial therapy and 296 tested positive for SARS-CoV-2. A positive SARS-CoV-2 test carried an OR of 0.3 (95% CI: 0.19, 0.49) for receiving antibacterial treatment in the first 48 h after admission (P < 0.0001) adjusting for age and procalcitonin results. Patients were 1% and 3% less likely to receive antibacterials for every year increase in age in the overall group and among those testing negative for SARS-CoV-2, respectively. Younger age was found to impact use of antibacterial therapy in both the overall analysis as well as the SARS-CoV-2 negative subgroup (P = 0.03 and P = 0.01). High procalcitonin values were found to be associated with increased antibacterial therapy use in both the overall and stratified analyses.

Conclusions

Antibacterial therapy prescription differs by COVID-19 disease status, and procalcitonin results are most highly associated with antibacterial use across strata.
A Fatal Case of Toxic Epidermal Necrolysis Combined With Vanishing Bile Duct Syndrome and Hemophagocytic Lymphohistiocytosis
Authors: Wier Julian , Lacey Alexandra , Yenikomshian Haig , Gillenwater Justin
Published: April 2021

This case report describes a case of fatal toxic epidermal necrolysis complicated by both vanishing bile duct syndrome and hemophagocytic lymphohistiocytosis due to Influenza B infection. Here we highlight the potential for complex morbidity secondary to underlying autoimmune hypersensitivity. Furthermore, the stepwise progression of these pathologies is noted, with the initial epidermal lesions first progressing to cholestatic injury and then subsequently to the hematologic manifestations.
Optimization of a Larval Sampling Method for Monitoring Drosophila suzukii (Diptera: Drosophilidae) in Blueberries
Authors: Van Timmeren Steven , Davis Amelia R , Isaacs Rufus
Published: April 2021

Managing spotted-wing drosophila, Drosophila suzukii (Matsumura), in fruit crops is complicated by the unreliability of currently available traps for monitoring adult flies, combined with the difficulty of detecting larval infestation before fruit damage is apparent. A simple method to extract larvae from fruit in liquid, strain the solution, then count them in a coffee filter was developed recently for use in integrated pest management programs. Here, we present a series of experiments conducted to improve fruit sampling by making it faster, less expensive, and more accurate. The volume of blueberries sampled (59–473 ml) did not significantly affect the detection of second and third instars, but we found that 118-ml samples were best for detecting the smallest larvae. These small instars were more detectable when berries were lightly squeezed before immersion, whereas larger instars were similarly detectable without using this step. We also found that immersing fruit for 30 min was sufficient before counting larvae, and similar numbers of larvae were found in the filter using room temperature water rather than a salt solution. The process of filtering, detection, and counting larvae took only 2–4 min per sample to process, depending on larval density. Using a microscope to count the larvae was consistently the best approach for detecting D. suzukii larvae. Based on these results, we discuss how fruit sampling can be streamlined within IPM programs, so growers and their advisors can improve control and reduce the cost of monitoring this invasive pest.
MHC Reflects Fine-Scale Habitat Structure in White-Tailed Eagles,Haliaeetus albicilla
Authors: Minias Piotr , Janiszewska Aleksandra , Pikus Ewa , Zadworny Tomasz , Anderwald Dariusz
Published: April 2021

The major histocompatibility complex (MHC) genes code for key immune receptors responsible for recognition of intra- and extracellular pathogens (MHC class I and class II, respectively). It was hypothesized that MHC polymorphism can be maintained via fluctuating selection resulting from between-habitat variation in pathogen regimes. We examined associations between MHC class I and class II genes and habitat structure in an apex avian predator, the white-tailed eagle, Haliaeetus albicilla. We genotyped MHC class I and class II genes in ca. 150 white-tailed eagle chicks from nearly 100 nesting territories distributed across 3 distinct populations in Poland. Habitat structure was quantified at the level of foraging territories and directly at the nest sites. We found strong support for associations of habitat traits with diversity and allelic composition at the MHC class II. Forest area within territory and forest productivity were identified as the major habitat predictors of MHC class II polymorphism, whereas other habitat traits (distance to nearest open water, grassland, and water area within territory or understory presence) showed fewer associations with class II alleles. In contrast, there was little support for associations between MHC class I genes and habitat structure. All significant associations were apparent at the within-population level rather than between populations. Our results suggest that extracellular (rather than intracellular) pathogens may exert much stronger selective pressure on the white-tailed eagle. Associations of habitat structure with MHC class II may reflect fluctuating (balancing) selection, which maintains MHC diversity within populations.
The Family Borreliaceae (Spirochaetales), a Diverse Group in Two Genera of Tick-Borne Spirochetes of Mammals, Birds, and Reptiles
Authors: Barbour Alan G , Gupta Radhey S
Published: April 2021

Spirochetes of the family Borreliaceae are, with one exception, tick-borne pathogens of a variety of vertebrates. The family at present comprises two genera: Borrelia (Swellengrebel), which includes the agents of relapsing fever, avian spirochetosis, and bovine borreliosis, and Borreliella (Gupta et al.), which includes the agents of Lyme disease and was formerly known as ‘Borrelia burgdorferi sensulato complex’. The two genera are distinguished not only by their disease associations but also biological features in the tick vector, including tissue location in unfed ticks and transovarial transmission. Borrelia species transmitted by argasid (soft) ticks tend to have more exclusive relationships with their tick vectors than do other Borrelia species and all Borreliella species that have ixodid (hard) ticks as vectors. The division of genera is supported by phylogenomic evidence from whole genomes and by several specific molecular markers. These distinguishing phylogenetic criteria also applied to three new species or isolates of Borrelia that were discovered in ixodid ticks of reptiles, a monotreme, and birds. Although the deep branching of the family from other spirochetes has been a challenge for inferences about evolution of the family, the discovery of related microorganisms in the gut microbiota of other arachnids suggests an ancestral origin for the family as symbionts of ticks and other arachnids.