bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci.
Authors: Hughes A L , Hughes M K , Watkins D I 
Published: January 2021

Abstract
A statistical study of DNA sequences of alleles at the highly polymorphic class I MHC loci of humans, HLA-A and HLA-B, showed evidence of both large-scale recombination events (involving recombination of exons 1-2 of one allele with exons 3-8 of another) and small-scale recombination events (involving apparent exchange of short DNA segments). The latter events occurred disproportionately in the region of the gene encoding the antigen recognition site (ARS) of the class I molecule. Furthermore, they involved the ARS codons which are under the strongest selection favoring allelic diversity at the amino acid level. Thus, the frequency of recombinant alleles appears to have been increased by some form of balancing selection (such as overdominant selection) favoring heterozygosity in the ARS. These analyses also revealed a striking difference between the A and B loci. Recombination events appear to have occurred about twice as frequently at the B locus, and recombinants at the B locus were significantly more likely to affect polymorphic sites in the ARS. At the A locus, there are well-defined allelic lineages that have persisted since prior to the human-chimpanzee divergence; but at the B locus, there is no evidence for such long-lasting allelic lineages. Thus, relatively frequent interallelic recombination has apparently been a feature of the long-term evolution of the B locus but not of the A locus.
Mutation models and quantitative genetic variation.
Authors: Zeng Z B , Cockerham C C 
Published: January 2021

Abstract
Analyses of evolution and maintenance of quantitative genetic variation depend on the mutation models assumed. Currently two polygenic mutation models have been used in theoretical analyses. One is the random walk mutation model and the other is the house-of-cards mutation model. Although in the short term the two models give similar results for the evolution of neutral genetic variation within and between populations, the predictions of the changes of the variation are qualitatively different in the long term. In this paper a more general mutation model, called the regression mutation model, is proposed to bridge the gap of the two models. The model regards the regression coefficient, gamma, of the effect of an allele after mutation on the effect of the allele before mutation as a parameter. When gamma = 1 or 0, the model becomes the random walk model or the house-of-cards model, respectively. The additive genetic variances within and between populations are formulated for this mutation model, and some insights are gained by looking at the changes of the genetic variances as gamma changes. The effects of gamma on the statistical test of selection for quantitative characters during macroevolution are also discussed. The results suggest that the random walk mutation model should not be interpreted as a null hypothesis of neutrality for testing against alternative hypotheses of selection during macroevolution because it can potentially allocate too much variation for the change of population means under neutrality.
A conditional allele of the Saccharomyces cerevisiae HOP1 gene is suppressed by overexpression of two other meiosis-specific genes: RED1 and REC104.
Authors: Hollingsworth N M , Johnson A D 
Published: January 2021

Abstract
The HOP1 gene of Saccharomyces cerevisiae is believed to encode a protein component of the synaptonemal complex, the structure formed when homologous chromosomes synapse during meiotic prophase. Five new mutant alleles (three conditional, two nonconditional) of HOP1 were identified by screening EMS-mutagenized cells for a failure to complement the spore viability defect of a hop1 null allele. Two high copy plasmids were found that partially suppress the temperature-sensitive spore inviability phenotype of one of these alleles, hop1-628. The suppression is allele-specific; no effect of the plasmids is observed in hop1 null diploids. Mutation of either of the two suppressor genes results in recessive spore lethality, indicating that these genes play important roles during meiosis. The DNA sequence of one high copy suppressor gene matched that of RED1, a previously identified meiosis-specific gene. Our data strongly support the idea that RED1 protein is also a component of the synaptonemal complex and further suggest that the RED1 and HOP1 gene products may interact. The second suppressor maps to the right arm of chromosome VIII distal to CDC12 and is REC104, a meiosis-specific gene believed to act early in meiosis.
The mog-1 gene is required for the switch from spermatogenesis to oogenesis in Caenorhabditis elegans.
Authors: Graham P L , Kimble J 
Published: January 2021

Abstract
Caenorhabditis elegans hermaphrodites make first sperm, then oocytes. By contrast, animals homozygous for any of six loss-of-function mutations in the gene mog-1 (for masculinization of the germ line) make sperm continuously and do not switch into oogenesis. Therefore, in mog-1 mutants, germ cells that normally would become oocytes are transformed into sperm. By contrast, somatic sexual fates are normal, suggesting that mog-1 plays a germ line-specific role in sex determination. Analyses of double mutants suggest that mog-1 negatively regulates the fem genes and/or fog-1: mog-1; fem and mog-1; fog-1 double mutants all make oocytes rather than sperm. Therefore, we propose that wild-type mog-1 is required in the hermaphrodite germ line for regulation of the switch from spermatogenesis to oogenesis rather than for specification of oogenesis per se. In addition to its role in germline sex determination, maternal mog-1 is required for embryogenesis: most progeny of a mog-1; fem or mog-1; fog-1 mother die as embryos. How might the roles of mog-1 in the sperm/oocyte switch and embryogenesis be linked? Previous work showed that fem-3 is regulated post-transcriptionally to achieve the sperm/oocyte switch. We speculate that mog-1 may function in the post-transcriptional regulation of numerous germ-line RNAs, including fem-3. A loss of mog-1 might inappropriately activate fem-3 and thereby abolish the sperm/oocyte switch; its loss might also lead to misregulation of maternal RNAs and thus embryonic death.
Unusual variability of the Drosophila melanogaster ref(2)P protein which controls the multiplication of sigma rhabdovirus.
Authors: Dru P , Bras F , Dezélée S , Gay P , Petitjean A M , Pierre-Deneubourg A , Teninges D , Contamine D 
Published: January 2021

Abstract
The ref(2)P gene of Drosophila melanogaster was identified by the discovery of two alleles, Po and Pp, respectively, permissive and restrictive for sigma rhabdovirus multiplication. A surprising variability of this gene was first noticed by the observation of size differences between the transcripts of permissive and restrictive alleles. In this paper, another restrictive allele, Pn, clearly distinct from Pp, is described: it exhibits a weaker antiviral effect than Pp and differs from Pp by its molecular structure. Five types of alleles were distinguished on the basis of their molecular structure, as revealed by S1 nuclease analysis of 17 D. melanogaster strains; three alleles were permissive and two restrictive. Comparison of the sequences of four haplotypes revealed numerous point mutations, two deletions (21 and 24 bp) and a complex event involving a 3-bp deletion, all affected the coding region. The unusual variability of the ref(2)P locus was confirmed by the high ratio of amino acid replacements to synonymous mutations (7:1), as compared to that of other genes, such as the Adh (2:42). Nevertheless, nucleotide sequence comparison with the Drosophila erecta ref(2)P gene shows that selective pressures are exerted to maintain the existence of a functional protein. The effects of this high variability on the ref(2)P protein are discussed in relation to its specific antiviral properties and to its function in D. melanogaster, where it is required for male fertility.
A genetic analysis of the stoned locus and its interaction with dunce, shibire and Suppressor of stoned variants of Drosophila melanogaster.
Authors: Petrovich T Z , Merakovsky J , Kelly L E 
Published: January 2021

Abstract
The genetic complementation patterns of both behavioral and lethal alleles at the stoned locus have been characterized. Mosaic analysis of a stoned lethal allele suggests that stoned functions either in the nervous system or in both the nervous system and musculature, but is not required for gross neural development. The behavioral alleles stnts and stnC, appear to be defective in a diametrically opposite sense, show interallelic complementation, and indicate distinct roles for the stoned gene product in the visual system and in motor coordination. A number of other neurological mutations have been investigated for their possible interaction with the viable stoned alleles. Mutations at two loci, dunce and shibire, act synergistically with the stnts mutations to cause lethality, but fail to interact with stnC. A third variant (Suppressor of stoned) has been identified which can suppress the debilitation associated with the stnts mutations. These data, together with a previously identified interaction between the stnts and tan mutants, indicate a central role for the stoned gene product in neuronal function, and suggests that the stoned gene product interacts, either directly or indirectly, with the neural cAMP second messenger system, with the synaptic membrane recycling pathway via dynamin, and with biogenic amine metabolism.
Observations on the induction of position effect variegation of euchromatic genes in Drosophila melanogaster.
Authors: Pokholkova G V , Makunin I V , Belyaeva E S , Zhimulev I F 
Published: January 2021

Abstract
In the T(1;2)dorvar7 translocation, the 1A-2B7-8 segment of the X chromosome is brought to the vicinity of 2R-chromosome heterochromatin resulting in position effect variegation of dor, BR-C and more distal genes, as well as compaction of chromatin in this segment. By irradiation of T(1;2)dorvar7, nine reversions (rev) to a normal phenotype were recovered. In two cases (rev27, rev226), the 1A-2B7-8 section is relocated to the 19A region of the X chromosome, forming free duplications (1A-2B7-8/19A-20F-X-het). Modifiers of position effect do not change the normal expression of the BR-C and dor genes in these duplications. In five reversions (rev3, rev40, rev60, rev167, rev175), free duplications have formed from the 1A-2B7-8 fragment and X chromosome heterochromatin. In these rearrangements, modifiers of position effect (low temperature, removal of Y and 2R-chromosome heterochromatin and a genetic enhancer (E-var(3)201) induce position-effect again. Two reversions (rev45 and rev110) are associated with additional inversions in the original dorvar7 chromosomes. The inversions relocate part of the heterochromatin adjacent to the 1A-2B7-8 section into new positions. In T(1;2)dorrev45, position-effect is seen in the 2B7-8-7A element as compaction spreading from 2B7-8 proximally in some cases as far as the 5D region. Thus, in rev45 the pattern of euchromatin compaction is reciprocal to that of the initial dorvar7 strain. Apparently, it is due to the same variegation-evoking center near the 2R centromere in both cases. In all nine revertants, weakening or complete disappearance of the position-effect is observed despite retention of the 20-kb heterochromatic segment adjacent to the 1A-2B7-8 region. Thus, a 20-kb heterochromatic sequence does not inactivate euchromatin joined to it.
Suppression of a lethal trisomic phenotype in Drosophila melanogaster by increased dosage of an unlinked locus.
Authors: Dorer D R , Cadden M A , Gordesky-Gold B , Harries G , Christensen A C 
Published: January 2021

Abstract
One of the most extreme examples of gene dosage sensitivity is the Triplo-lethal locus (Tpl) on the third chromosome of Drosophila melanogaster, which is lethal when present in either one or three copies. Increased dosage of an unlinked locus, Isis, suppresses the triplo-lethal phenotype of Tpl, but not the haplo-lethal phenotype. We have mapped Isis to the X chromosome region 7E3-8A5, and shown that the suppression is a gene dosage effect. Altered dosage of Isis in the presence of two copies of Tpl has no obvious effects. By examining the interactions between Isis dosage and Tpl we suggest that Isis does not directly repress Tpl expression, but acts downstream on the triplo-lethal phenotype of Tpl.
The genetic basis of Haldane's rule and the nature of asymmetric hybrid male sterility among Drosophila simulans, Drosophila mauritiana and Drosophila sechellia.
Authors: Zeng L W , Singh R S 
Published: January 2021

Abstract
Haldane's rule (i.e., the preferential hybrid sterility and inviability of heterogametic sex) has been known for 70 years, but its genetic basis, which is crucial to the understanding of the process of species formation, remains unclear. In the present study, we have investigated the genetic basis of hybrid male sterility using Drosophila simulans, Drosophila mauritiana and Drosophila sechellia. An introgression of D. sechellia Y chromosome into a fairly homogenous background of D. simulans did not show any effect of the introgressed Y on male sterility. The substitution of D. simulans Y chromosome into D. sechellia, and both reciprocal Y chromosome substitutions between D. simulans and D. mauritiana were unsuccessful. Introgressions of cytoplasm between D. simulans and D. mauritiana (or D. sechellia) also did not have any effect on hybrid male sterility. These results rule out the X-Y interaction hypothesis as a general explanation of Haldane's rule in this species group and indicate an involvement of an X-autosome interaction. Models of symmetrical and asymmetrical X-autosome interaction have been developed which explain the Y chromosome substitution results and suggest that evolution of interactions between different genetic elements in the early stages of speciation is more likely to be of an asymmetrical nature. The model of asymmetrical X-autosome interaction also predicts that different sets of interacting genes may be involved in different pairs of related species and can account for the observation that hybrid male sterility in many partially isolated species is often nonreciprocal or unidirectional.
Stage-specific effects of X-irradiation on yeast meiosis.
Authors: Thorne L W , Byers B 
Published: January 2021

Abstract
Previous work has shown that cdc13 causes meiotic arrest of Saccharomyces cerevisiae following DNA replication by a RAD9-dependent mechanism. In the present work, we have further investigated the implicit effects of chromosomal lesions on progression through meiosis by exposing yeast cells to X-irradiation at various times during sporulation. We find that exposure of RAD9 cells to X-irradiation early in meiosis prevents sporulation, arresting the cells at a stage prior to premeiotic DNA replication. rad9 meiotic cells are much less responsive to X-irradiation damage, completing sporulation after treatment with doses sufficient to cause arrest of RAD9 strains. These findings thereby reveal a RAD9-dependent checkpoint function in meiosis that is distinct from the G2 arrest previously shown to result from cdc13 dysfunction. Analysis of the spores that continued to be produced by either RAD9 or rad9 cultures that were X-irradiated in later stages of sporulation revealed most spores to be viable, even after exposure to radiation doses sufficient to kill most vegetative cells. This finding demonstrates that the lesions induced by X-irradiation at later times fail to trigger the checkpoint function revealed by cdc13 arrest and suggests that the lesions may be subject to repair by serving as intermediates in the recombination process. Strains mutant for chromosomal synapsis and recombination, and therefore defective in meiotic disjunction, were tested for evidence that X-ray-induced lesions might alleviate inviability by promoting recombination. Enhancement of spore viability when spo11 (but not hop 1) diploids were X-irradiated during meiosis indicates that induced lesions may partially substitute for SPO11-dependent functions that are required for the initiation of recombination.
Using yeast genetics to generate a research environment.
Authors: Manney T R , Manney M L 
Published: January 2021

Abstract
Many of the same features of the yeast Saccharomyces cerevisiae that have made it so useful as a genetics and molecular biology research organism make it equally useful as a teaching organism. Furthermore, the fact that it is a modern research organism makes it all the more exciting to students and teachers. The unique characteristic of yeast as a unicellular, eukaryotic organism with a complete sexual life cycle is ideal for teaching. A simple monohybrid cross to explore dominance and recessiveness, a dihybrid cross to demonstrate independent assortment, pigmented adenine auxotrophs for investigating the fundamentals of gene action, and easily measured responses to ultraviolet radiation provide an array of appropriate laboratory tools that put real science in the hands of students and teachers. Direct collaborations between scientists and science teachers bring together complementing knowledge and experience, providing an effective and efficient way to adapt and simplify techniques and procedures to accommodate time and money constraints. Collaborations quickly identify technical and theoretical problems that must be solved for implementation in classrooms. They also provide a continuing stimulus to teachers and students to participate in the research process.
Instability of a plasmid-borne inverted repeat in Saccharomyces cerevisiae.
Authors: Henderson S T , Petes T D 
Published: January 2021

Abstract
Inverted repeated DNA sequences are common in both prokaryotes and eukaryotes. We found that a plasmid-borne 94 base-pair inverted repeat (a perfect palindrome of 47 bp) containing a poly GT sequence is unstable in S. cerevisiae, with a minimal deletion frequency of about 10(-4)/mitotic division. Ten independent deletions had identical end points. Sequence analysis indicated that all deletions were the result of a DNA polymerase slippage event (or a recombination event) involving a 5-bp repeat (5' CGACG 3') that flanked the inverted repeat. The deletion rate and the types of deletions were unaffected by the rad52 mutation. Strains with the pms1 mutation had a 10-fold elevated frequency of instability of the inverted repeat. The types of sequence alterations observed in the pms1 background, however, were different than those seen in either the wild-type or rad52 genetic backgrounds.
SID1-1: a mutation affecting meiotic sister-chromatid association in yeast.
Authors: Flatters M , Dawson D 
Published: January 2021

Abstract
Meiotic chromosome segregation must occur with high fidelity in order to prevent the generation of deleterious aneuploidies. In meiosis I, homologous chromosomes pair, then migrate to opposite poles of the spindle. This process uses a collection of unique structures and mechanisms that have yet to be thoroughly characterized. To acquire a collection of informative meiotic mutants, we carried out a novel genetic screen in Saccharomyces cerevisiae. This screen was designed to identify dominant mutants in which meiosis I chromosome segregation occurs with decreased fidelity. One mutant recovered using this screen, SID1-1 (sister disjunction), showed an incidence of spores disomic for a marked chromosome III that was 25-fold greater than the wild-type level. Crossing-over is slightly, but not dramatically, reduced in SID1-1. Both recombinant and nonrecombinant chromosomes segregate with reduced fidelity in the presence of SID1-1. We present evidence that the mutant is defective in sister-chromatid association.
A duplication including the Y allele of Lcp2 and the TRIM retrotransposon at the Lcp locus on the degenerating neo-Y chromosome of Drosophila miranda: molecular structure and mechanisms by which it may have arisen.
Authors: Steinemann M , Steinemann S 
Published: January 2021

Abstract
Evolutionary changes during the process of sex chromosome differentiation in Drosophila miranda are associated with massive DNA rearrangements. Comparing the DNA structure of the larval cuticle protein (Lcp) region from the X2 and neo-Y chromosome pair, we observed insertions, deletions and a large duplication at the neo-Y chromosomal locus. The duplication encompasses a complete copy of the neo-Y allele of Lcp2, and the ISY3 and the ISY4 insertion sequences. The latter was identified as a retrotransposon, termed TRIM. ISY3 shows DNA sequence similarity to P element homologs identified in the Drosophila obscura species group. We were interested in mechanistic aspects generating the duplication. We cannot exclude unequivocally that unequal sister-chromatid exchange could give rise to the observed duplication; however, recombination is a rare event in Drosophila males. Location and sequence of the retrotransposon TRIM served as molecular markers allowing us to reconstruct two intrachromosomal transposition events that could lead to the observed duplication.
QTL analysis of transgressive segregation in an interspecific tomato cross.
Authors: deVicente M C , Tanksley S D 
Published: January 2021

Abstract
Two accessions, representing the species Lycopersicon esculentum (cultivated tomato) and Lycopersicon pennellii (a wild relative), were evaluated for 11 quantitative traits and found to be significantly different for 10 of the traits. Transgressive segregation was observed for eight of the traits in a large interspecific F2 population. When restriction fragment length polymorphism markers were used as probes for the quantitative trait loci (QTL) underlying the traits, 74 significant QTL (LOD &gt; 2) were detected. Thirty-six percent of those QTL had alleles with effects opposite to those predicted by the parental phenotypes. These QTL were directly related to the appearance of transgressive individuals in the F2 for those traits which showed transgressive segregation. However, the same types of QTL (with allelic effects opposite to those predicted by the parents) were also observed for traits that did not display transgressive segregation in the F2. One such trait was dry weight accumulation. When two overdominant QTL (detected in the F2) for this trait were backcrossed into the L. esculentum genetic background, transgressive individuals were recovered and their occurrence was associated with the two QTL demonstrating the potential for transgressive segregation for all characters and implicating overdominance as a second cause of transgressive segregation. Epistasis was not implicated in transgressive segregation in either the F2 or backcross generations. Results from this research not only reveal the basis of wide-cross transgressive segregation, but demonstrate that molecular markers can be used to identify QTL (from wild species) responsible for transgressive phenotypes and to selectively transfer them into crop species. This strategy might be used to improve many traits of economic importance including those for which wild species appear phenotypically inferior to their cultivated counterparts.
Genetic variation and random drift in autotetraploid populations.
Authors: Moody M E , Mueller L D , Soltis D E 
Published: January 2021

Abstract
The rate of decay of genetic variation is determined for randomly mating autotetraploid populations of finite size, and the equilibrium homozygosity under mutation and random drift is calculated. It is shown that heterozygosity is lost at a slower rate than in diploid populations, and that the equilibrium heterozygosity with mutation and random drift is higher than for diploids. Outcrossing populations as well as populations that randomly self are analyzed. A method of comparing genetic variation between autotetraploid and diploid populations is proposed. Our treatment suggests that the "gametic homozygosity" provides a unified approach for comparing genotypes within a population as well as comparing genetic variation between populations with different levels of ploidy.