bluuebunny/crossref_metadata_2025_split huggingface dataset:
The specificity of topoisomerase-mediated DNA cleavage defines acridine-induced frameshift specificity within a hotspot in bacteriophage T4.
Authors: Masurekar M , Kreuzer K N , Ripley L S 
Published: January 2021

Abstract
Acridine-induced frameshift mutations in bacteriophage T4 occur at the precise location in the DNA at which acridines stimulate DNA cleavage by the T4-encoded type II topoisomerase in vitro. The mutations are duplications or deletions that begin precisely at the broken phosphodiester bond. In vivo, acridine-induced frameshift mutagenesis is reduced nearly to background levels when the topoisomerase is genetically inactivated. These observations are consistent with a model in which cleaved DNA, induced by the topoisomerase and acridine, serves as the substrate for the production of frameshift mutations at the same site. Our model predicts that the specificity and frequency of cleavage direct the specificity and frequency of mutagenesis. This prediction was tested by examining the influence of DNA sequence changes on topoisomerase-mediated cleavage and on mutagenesis in the T4 rIIB gene. The model successfully predicted the results. When DNA sequence changes altered the position of acridine-induced, topoisomerase-mediated DNA cleavage in vitro, frameshift mutations were found at the new positions. DNA sequence changes that strongly decreased in vitro cleavage also reduced mutagenesis at that site. These results demonstrate that acridine-induced frameshift mutation specificity is directed by the characteristics of the acridine-topoisomerase reaction and do not suggest that slipped pairing in repeated sequences plays a major role in acridine-induced frameshifts in bacteriophage T4.
Functional analysis of mutations of murine chromosome 17 with the use of tertiary trisomy.
Authors: Ruvinsky A , Agulnik A , Agulnik S , Rogachova M 
Published: January 2021

Abstract
Analysis of the functional nature of mutations can be based on comparisons of their manifestation in organisms with a deletion or duplication of a particular chromosome segment. With the use of reciprocal translocation T(16;17)43H, it is feasible to produce mice with tertiary trisomy of the proximal region of chromosome 17. The mutations on chromosome 17 we tested included brachyury (T), hairpin tail (Thp), kinky (Fuki), quaking (qk), tufted (tf), as well as tct (t complex tail interaction), and tcl (t complex lethal) that are specific to t haplotypes. The set of dominant and recessive mutations was assigned to two groups: one obligatory, manifesting itself in the phenotype independently of the number of normal alleles in di- and trisomics, and the other facultative, phenotypically manifesting itself depending upon the dosage of mutant alleles. A model was derived from analysis of the interaction of the T and Thp mutations with t haplotypes. It seeks to explain the morphogenetic effects of the mutations observed in mice of different genotypes. The tir gene is postulated to reside on chromosome 17 within its framework. It is suggested that the gene dosage ratio at the tir and tct loci determines tail length.
Isolation of mutants defective in early steps of meiotic recombination in the yeast Saccharomyces cerevisiae.
Authors: Malone R E , Bullard S , Hermiston M , Rieger R , Cool M , Galbraith A 
Published: January 2021

Abstract
Using a selection based upon the ability of early Rec- mutations (e.g., rad50) to rescue the meiotic lethality of a rad52 spo13 strain, we have isolated 177 mutants. Analysis of 56 of these has generated alleles of the known Rec genes SPO11, ME14 and MER1, as well as defining five new genes: REC102, REC104, REC107, REC113 and REC114. Mutations in all of the new genes appear to specifically affect meiosis; they do not have any detectable mitotic phenotype. Mutations in REC102, REC104 and REC107 reduce meiotic recombination several hundred fold. No alleles of RED1 or HOP1 were isolated, consistent with the proposal that these genes may be primarily involved with chromosome pairing and not exchange.
Dominant and recessive suppressors that restore glucose transport in a yeast snf3 mutant.
Authors: Marshall-Carlson L , Neigeborn L , Coons D , Bisson L , Carlson M 
Published: January 2021

Abstract
The SNF3 gene of Saccharomyces cerevisiae encodes a high-affinity glucose transporter that is homologous to mammalian glucose transporters. To identify genes that are functionally related to SNF3, we selected for suppressors that remedy the growth defect of snf3 mutants on low concentrations of glucose or fructose. We recovered 38 recessive mutations that fall into a single complementation group, designated rgt1 (restores glucose transport). The rgt1 mutations suppress a snf3 null mutation and are not linked to snf3. A naturally occurring rgt1 allele was identified in a laboratory strain. We also selected five dominant suppressors. At least two are tightly linked to one another and are designated RGT2. The RGT2 locus was mapped 38 cM from SNF3 on chromosome IV. Kinetic analysis of glucose uptake showed that the rgt1 and RGT2 suppressors restore glucose-repressible high-affinity glucose transport in a snf3 mutant. These mutations identify genes that may regulate or encode additional glucose transport proteins.
Genetic interactions at the FLA10 locus: suppressors and synthetic phenotypes that affect the cell cycle and flagellar function in Chlamydomonas reinhardtii.
Authors: Lux F G , Dutcher S K 
Published: January 2021

Abstract
Through the isolation of suppressors of temperature-sensitive flagellar assembly mutations at the FLA10 locus of Chlamydomonas reinhardtii, we have identified six other genes involved in flagellar assembly. Mutations at these suppressor loci, termed SUF1-SUF6, display allele specificity with respect to which fla10- mutant alleles they suppress. An additional mutation, apm1-122, which confers resistance to the plant herbicides amiprophos-methyl and oryzalin, was also found to interact with mutations at the FLA10 locus. The apm1-122 mutation in combination with three fla10- mutant alleles results in synthetic cold-sensitive cell division defects, and in combination with an additional pseudo-wild-type fla10- allele yields a synthetic temperature-sensitive flagellar motility phenotype. Based upon the genetic interactions of these loci, we propose that the FLA10 gene product interacts with multiple components of the flagellar apparatus and plays a role both in flagellar assembly and in the cell cycle.
Length and sequence variation in evening bat D-loop mtDNA.
Authors: Wilkinson G S , Chapman A M 
Published: January 2021

Abstract
Length variation in D-loop mitochondrial DNA was observed after amplification with the polymerase chain reaction (PCR) in 28% of 195 evening bats, Nycticeius humeralis, from seven colonies. Nucleotide sequences of PCR products show that this heteroplasmy is characterized by an 81-bp region which is tandemly repeated five to eight times. Southern blots using PCR products as probes on HaeIII genomic digests confirm the presence of heteroplasmy. Furthermore, densitometry of electrophoresed PCR products from 109 mother-offspring pairs indicate that heteroplasmy is stably transmitted from mother to offspring with one exception: a heteroplasmic offspring had a homoplastic mother and sib. Nucleotide sequences from this family reveal that a repeat duplication and deletion occurred. The observed mutation rate per generation, mu, for length polymorphism is comparable to an independent estimate, mu = 10(-2), based on hierarchical diversity statistics. With the exception of the repeat nearest the proline tRNA gene, sequence similarities between repeats within bats are consistent with a model of concerted evolution due to unidirectional replication slippage. Selection is inferred to act on the first repeat because in comparison to other repeats it has the least sequence divergence among bats, the fewest transversions, and the lowest minimum free energy associated with folding.
Specific DNA alterations associated with the environmental induction of heritable changes in flax.
Authors: Schneeberger R G , Cullis C A 
Published: January 2021

Abstract
Several flax varieties have been shown to undergo environmentally induced heritable changes resulting in stable lines termed genotrophs. The most notable of these is the variety Stormont Cirrus, also termed "plastic" or Pl. A number of morphological, biochemical and genetic differences are associated with environmental induction of heritable changes in flax. We have studied 5S rDNA alterations as a model system for understanding environmental induction of heritable changes in flax. This paper reports the isolation of a flax 5S rRNA gene variant which identifies genotroph specific restriction fragment length polymorphisms (RFLPs) in flax. Restriction fragment patterns for several enzymes were observed in both large and small genotrophs which consistently differed from the progenitor, Stormont Cirrus. Identical RFLP profiles for all restriction endonucleases tested were observed in four small genotrophs produced from separate environmental induction experiments. Comparison between Stormont Cirrus and these small genotrophs showed at least six differing bands in addition to several high molecular weight polymorphisms. Genetic data indicate that the polymorphisms were all produced from a repetitive 5S rRNA gene cluster at a single chromosomal locus. Similar, but not identical, polymorphisms are also detected in other flax varieties and Linum species suggesting that the induced variation is related to that which occurs naturally. The results are evidence that a specific set of DNA alterations occur in association with the induction of heritable changes in flax. This is the first genetic marker which is altered to an identical state in one type of genotroph. The results are discussed with respect to mechanisms for environmentally induced heritable change in plants.
On the components of segregation distortion in Drosophila melanogaster. V. Molecular analysis of the Sd locus.
Authors: Powers P A , Ganetzky B 
Published: January 2021

Abstract
Segregation Distorter (SD) is a naturally occurring meiotic drive system comprising at least three distinct loci: Sd, Rsp and E(SD). Heterozygous SD/SD+ males transmit the SD chromosome in vast excess over the normal homolog. The distorted transmission involves the induced dysfunction of the spermatids that receive the SD+ chromosome. In the 220-kb region of DNA that contains the Sd gene, we identified a 5-kb tandem duplication that is uniquely associated with all SD chromosomes, absent in SD+ chromosomes, and detectably altered in Sd revertants. On northern blots, genomic probes from the tandem duplication detect an SD-specific 4-kb transcript in addition to several smaller transcripts present in both SD and SD+. Seven classes of cDNAs derived from these transcripts have been isolated. All of these cDNAs share extensive sequence identity at their 3' ends but differ at their 5' ends. Sequence analysis indicates that these cDNAs potentially encode four distinct, but related, polypeptides. Introduction of the tandem duplication into SD+ flies by germline transformation did not confer the dominant gain-of-function Sd phenotype. This result, taken together with our analysis of the Sd cDNAs, suggests that the duplication is part of a much larger gene that encodes several different polypeptides.
Expression of meiotic drive elements Spore killer-2 and Spore killer-3 in asci of Neurospora tetrasperma.
Authors: Raju N B , Perkins D D 
Published: January 2021

Abstract
It was shown previously that when a chromosomal Spore killer factor is heterozygous in Neurospora species with eight-spored asci, the four sensitive ascospores in each ascus die and the four survivors are all killers. Sk-2K and Sk-3K are nonrecombining haplotypes that segregate with the centromere of linkage group III. No killing occurs when either one of these killers is homozygous, but each is sensitive to killing by the other in crosses of Sk-2K x Sk-3K. In the present study, Sk-2K and Sk-3K were transferred by recurrent backcrosses from the eight-spored species Neurospora crassa into Neurospora tetrasperma, a pseudohomothallic species which normally makes asci with four large spores, each heterokaryotic for mating type and for any other centromere-linked genes that are heterozygous in the cross. The action of Sk-2K and Sk-3K in N. tetrasperma is that predicted from their behavior in eight-spored species. A sensitive nucleus is protected from killing if it is enclosed in the same ascospore with a killer nucleus. Crosses of Sk-2K x Sk-2S, Sk-3K x Sk-3S, and Sk-sK x Sk-3K all produce four-spored asci that are wild type in appearance, with the ascospores heterokaryotic and viable. The Eight-spore gene E, which shows variable penetrance, was used to obtain N. tetrasperma asci in which two to eight spores are small and homokaryotic. When killer and sensitive alleles are segregating in the presence of E, only those ascospores that contain a killer allele survive. Half of the small ascospores are killed. In crosses of Sk-2K x Sk-3K (with E heterozygous), effectively all small ascospores are killed. The ability of N. tetrasperma to carry killer elements in cryptic condition suggests a possible role for Spore killers in the origin of pseudohomothallism, with adoption of the four-spored mode restoring ascospore viability of crosses in which killing would otherwise occur.
Tel-1 transposon-like elements of Tetrahymena thermophila are associated with micronuclear genome rearrangements.
Authors: Wyman C , Blackburn E H 
Published: January 2021

Abstract
The micronuclear genome of Tetrahymena thermophila contains Tel-1 elements that structurally resemble transposons. Here we present molecular evidence that Tel-1 transposon-like elements are mobile. The arrangements of Tel-1 elements in the micronuclear genomes of several T. thermophila strains and cell lines were assayed by Southern blotting. The molecular evidence for Tel-1 transposition is most striking in strains that have undergone unusual laboratory-induced meioses. The genetic history of the strains exhibiting evidence of Tel-1 transposition is consistent with periods of genome restructuring in response to genomic "shock" that B. McClintock has suggested could result in transposon activation.
Genetic analysis of a temporally transcribed chemotaxis gene cluster in Caulobacter crescentus.
Authors: Alley M R , Gomes S L , Alexander W , Shapiro L 
Published: January 2021

Abstract
Caulobacter crescentus performs chemotaxis by short intermittent reversals of rotation of its single polar flagellum. Tn5 insertions causing a general chemotaxis phenotype, an inability to reverse swimming direction and to form large swarm colonies, have been mapped to an 8-kb region of the C. crescentus genome. These Tn5 mutations had different effects on the methyl-accepting chemotaxis proteins (MCP), and the activities of methyltransferase and methylesterase. The Tn5 insertion mutant SC1130 had no cross-reacting MCP and had reduced levels of activity of the methyltransferase and methylesterase. Other mutants bearing Tn5 insertions retained cross-reacting MCP activity and were altered only in their methyltransferase and methylesterase activities. Using a cosmid library we isolated a clone that complemented SC1130. Complementation studies of the Tn5 mutants using derivatives of the cosmid clone showed that all the Tn5 insertions lie within a single operon that appears to encode many chemotaxis genes. The first gene in this operon was shown to encode an MCP by immuno-blot analysis of strains carrying beta-galactosidase protein fusions to portions of the operon. The promoter of this operon was located by chromosomal integration of subclones of this region and by identifying DNA fragments that were capable of expressing lacZ transcriptional fusions. The transcription of the che operon occurred at a defined time in the cell cycle, prior to cell division.
Variance of neutral genetic variances within and between populations for a quantitative character.
Authors: Zeng Z B , Cockerham C C 
Published: January 2021

Abstract
The variances of genetic variances within and between finite populations were systematically studied using a general multiple allele model with mutation in terms of identity by descent measures. We partitioned the genetic variances into components corresponding to genetic variances and covariances within and between loci. We also analyzed the sampling variance. Both transient and equilibrium results were derived exactly and the results can be used in diverse applications. For the genetic variance within populations, sigma 2 omega, the coefficient of variation can be very well approximated as [formula: see text] for a normal distribution of allelic effects, ignoring recurrent mutation in the absence of linkage, where m is the number of loci, N is the effective population size, theta 1(0) is the initial identity by descent measure of two genes within populations and t is the generation number. The first term is due to genic variance, the second due to linkage disequilibrium, and third due to sampling. In the short term, the variation is predominantly due to linkage disequilibrium and sampling; but in the long term it can be largely due to genic variance. At equilibrium with mutation [formula: see text] where u is the mutation rate. The genetic variance between populations is a parameter. Variance arises only among sample estimates due to finite sampling of populations and individuals. The coefficient of variation for sample gentic variance between populations, sigma 2b, can be generally approximated as [formula: see text] when the number of loci is large where S is the number of sampling populations.
A mathematical model of interference for use in constructing linkage maps from tetrad data.
Authors: King J S , Mortimer R K 
Published: January 2021

Abstract
In determining genetic map distances it is necessary to infer crossover frequencies from the ratios of recombinant and parental progeny. To do this accurately, in intervals where multiple crossovers may occur, a mathematical model of chiasma interference must be assumed when mapping in organisms displaying such interference. In Saccharomyces cerevisiae the model most frequently used is that of R.W. Barratt. An alternative to this model is presented. This new model is implemented using a microcomputer and standard numerical methods. It is demonstrated to fit ranked tetrad data from Saccharomyces more closely than the Barratt model and thus generates more accurate estimates of map distances when used with two-point data. A computer program implementing the model has been developed for use in calculating map distances from tetrad data in Saccharomyces.
Mapping by transposons of the inversion termini in Escherichia coli K-12 strain 1485IN.
Authors: Enomoto M , Komoda Y , Tominaga A 
Published: January 2021

Abstract
Strain 1485IN carries a chromosomal inversion which corresponds to 35% of the chromosome and includes proC, trp and his genes. The termini of the inversion lie between the lac and proC loci and between his and cdd of the normal strain. Using Tn10 and Tn5 in transduction crosses between the normal and inversion strains, the termini were mapped to sites located approximately 0.25 min and 1.6 min away from proC and his, respectively within a region of roughly 4 kb long. The crosses where the normal strains carrying Tn10 near the terminus are donors and the inversion strain is a recipient, yielded unusual Tetr His- recombinants, which arose from illegitimate recombination leading to the replacement of a chromosomal his+ region with a transducing fragment carrying proC. Another rearrangement was detected between the normal and inversion strains in a region outside the inverted segment near the cdd locus.
Mutant bias in nonlethal selections results from selective recovery of mutants.
Authors: Benson S A , DeCloux A M , Munro J 
Published: January 2021

Abstract
We have characterized a nonlethal selection for mutations that allow Escherichia coli to grow on large maltodextrins (Dex+) in the absence of the lamB encoded maltoporin LamB. These Dex+ mutations occur before and after imposition of the selection and the selection does not result in a general increase in mutagenesis. The recovered Dex+ mutations are almost exclusively mutations that alter the ompF gene that encodes a major E. coli porin, OmpF even though analogous mutations in the homologous ompC gene, which encodes the OmpC porin, can confer a Dex+ phenotype. We show that the bias for ompF mutations results from a biased recovery and that the genetic background of the starting strain and the selection itself influences the type of mutants that are recovered. When we use a strain carrying an amber mutation in the lamB gene we observe the same preference for ompF mutations as when we start with a lamB deletion strain. In addition, we show that there is no preferential mutagenesis of the lamB gene during the selection which induces transcription of the lamB gene. We present evidence that the biased recovery of mutants observed in this selection does not result from adaptive or directed mutagenesis and that the phenotypic fitness which allows recovery of Dex+ mutants involves more than the increased ability to take up maltodextrins.
Molecular analysis of the hot spot region related to length mutations in wheat chloroplast DNAs. I. Nucleotide divergence of genes and intergenic spacer regions located in the hot spot region.
Authors: Ogihara Y , Terachi T , Sasakuma T 
Published: January 2021

Abstract
The nucleotide divergence of chloroplast DNAs around the hot spot region related to length mutation in Triticum (wheat) and Aegilops was analyzed. DNA sequences (ca. 4.5 kbp) of three chloroplast genome types of wheat complex were compared with one another and with the corresponding region of other grasses. The sequences region contained rbcL and psaI, two open reading frames, and a pseudogene, rpl23' (pseudogene for ribosomal protein L23) disrupted by AT-rich intergic spacer regions. The evolution of these genes in the closely related wheat complex is characterized by nonbiased nucleotide substitutions in terms of being synonymous/nonsynonymous, having A-T pressure transitions over transversions, and frequent changes at the third codon position, in contrast with the gene evolution among more distant plant groups where biased nucleotide substitutions have frequently occurred. The sequences of these genes had diverged almost in proportion to taxonomic distance. The sequence of the pseudogene rpl23' changed approximately two times faster than that of the coding region. Sequence comparison between the pseudogene and its protein-coding counterpart revealed different degrees of nucleotide homology in wheat, rice and maize, suggesting that the transposition timing of the pseudogene differed and/or that different rates of gene conversion operated on the pseudogene in the cpDNA of the three plant groups in Gramineae. The intergenic spacer regions diverged approximately ten times faster than the genes. The divergence of wheat from barley, and that from rice are estimated based on the nucleotide similarity to be 1.5, 10 and 40 million years, respectively.