A mechanism for gene conversion in fungi

A mechanism for gene conversion is proposed which overcomes many of the difficulties that any copy choice model encounters. It is suggested that along with general genetic pairing of homologous genomes at meiosis, effective pairing over short regions of the genetic material occurs at the molecular level by the separation of the strands of the DNA double helices, followed by the annealing of strands from two homologous chromatids. If the annealed region happens to span a heterozygous site, mispairing of bases will occur. Such a situation may be analogous to that in DNA which is damaged by mutagens; the same or similar repair mechanisms may operate, and these, by adjusting the base sequences in order to restore normal base pairing, would bring about gene conversion in the absence of any genetic replication. The model indicates how precise breakage and rejoining of chromatids could occur in the vicinity of the conversion, so that conversion would frequently be accompanied by the recombination of outside markers. The model also proposes that the distance between two mutant sites on a fine structure map depends not so much on the frequency of a recombinational event occurring between them, but rather on the degree of inhibition of the processes of genetic pairing by the mutants themselves.The model will explain almost all the data in a formal way, and it has the advantage over copy choice mechanisms for gene conversion in (1) being compatible with semi-conservative replication of DNA, (2) not invoking DNA synthesis during or after genetic pairing, (3) providing a molecular mechanism for close specific pairing, (4) making it unnecessary to postulate sister strand exchange or a process akin to this, (5) suggesting why rates of gene conversion in opposite directions are sometimes unequal and (6) providing an explanation of the clustering of mutant sites, a basis for map expansion and for the apparently capricious departure of fine structure maps from additivity. Although the model proposed is a general rather than a specific one, it suggests that the process of conversion and intragenic recombination is more complex than is usually believed, since it depends on several interacting factors. Nevertheless, it is hoped that the introduction of a model with this complexity will help to stimulate specific experiments, and that these will provide definitive information which would never be obtained if simpler models of conversion and intragenic recombination were believed to explain the genetic data sufficiently well.

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GENETIC ORGANIZATION IN CAENORHABDITIS ELEGANS: FINE-STRUCTURE ANALYSIS OF THE unc-22 GENE

Genetics ◽

10.1093/genetics/91.1.95 ◽

1979 ◽

Vol 91 (1) ◽

pp. 95-103 ◽

Cited By ~ 4

Author(s):

D G Moerman ◽

D L Baillie

Keyword(s):

Drosophila Melanogaster ◽

Fine Structure ◽

Caenorhabditis Elegans ◽

Gene Conversion ◽

Structure Analysis ◽

Intragenic Recombination ◽

Preliminary Estimate ◽

Recessive Mutations ◽

Fine Structure Analysis ◽

New Alleles

ABSTRACT Fine-structure analysis of the unc-22 gene of Caenorhabditis elegarns has revealed a number of sites that are separable by recombination. Eight new ethyl methanesulfonate-induced recessive mutations of the unc-22 gene have been isolated. Using these new alleles, as well as e66, a number of separable sites have been identified and positioned relative to one another. The map distances obtained are found to be comparable to those associated with intragenic recombination in Drosophila melanogaster, indicating that genetic finestructure analysis is feasible in Caenorhabditis elegans. Evidence of possible gene conversion is presented. A preliminary estimate of the unc-22 gene size is 2.4 × 10-2 map units.

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Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽

10.1093/genetics/129.4.1021 ◽

1991 ◽

Vol 129 (4) ◽

pp. 1021-1032 ◽

Cited By ~ 4

Author(s):

M J Mahan ◽

J R Roth

Keyword(s):

Homologous Recombination ◽

Parent Strain ◽

Genetic Material ◽

Chromosomal Inversion ◽

Chromosome Segment ◽

Bacterial Chromosome ◽

Flanking Sequence ◽

Flanking Sequences ◽

Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

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Why Do People Stay Poor?

The Quarterly Journal of Economics ◽

10.1093/qje/qjab045 ◽

2021 ◽

Cited By ~ 1

Author(s):

Clare Balboni ◽

Oriana Bandiera ◽

Robin Burgess ◽

Maitreesh Ghatak ◽

Anton Heil

Keyword(s):

Occupational Choice ◽

Large Scale ◽

Choice Model ◽

Effective Means ◽

Threshold Level ◽

Poverty Traps ◽

Asset Transfer ◽

Small Livestock ◽

Program Costs ◽

Almost All

Abstract There are two broad views as to why people stay poor. One emphasizes differences in fundamentals, such as ability, talent, or motivation. The other, the poverty traps view, emphasizes differences in opportunities which stem from access to wealth. To test between these two views, we exploit a large-scale, randomized asset transfer and an 11-year panel of 6,000 households who begin in extreme poverty. The setting is rural Bangladesh and the assets are cows. The data supports the poverty traps view—we identify a threshold level of initial assets above which households accumulate assets, take on better occupations (from casual labor in agriculture or domestic services to running small livestock businesses), and grow out of poverty. The reverse happens for those below the threshold. Structural estimation of an occupational choice model reveals that almost all beneficiaries are misallocated in the work they do at baseline and that the gains arising from eliminating misallocation would far exceed the program costs. Our findings imply that large transfers which create better jobs for the poor are an effective means of getting people out of poverty traps and reducing global poverty.

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Fine-structure genetics of ama-1, an essential gene encoding the amanitin-binding subunit of RNA polymerase II in Caenorhabditis elegans.

Genetics ◽

10.1093/genetics/120.2.423 ◽

1988 ◽

Vol 120 (2) ◽

pp. 423-434

Author(s):

A M Bullerjahn ◽

D L Riddle

Keyword(s):

Fine Structure ◽

Caenorhabditis Elegans ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Essential Gene ◽

Resistance Mutation ◽

Lethal Mutation ◽

Intragenic Recombination ◽

Lethal Mutations ◽

Binding Subunit

Abstract A fine-structure genetic map has been constructed for ama-1 IV, an essential gene in Caenorhabditis elegans encoding the amanitin-binding subunit of RNA polymerase II. Sixteen EMS-induced recessive-lethal mutations have been positioned in the gene by determining their intragenic recombination frequencies with m118, a mutation that confers dominant resistance to alpha-amanitin. The 16 mutants, all isolated in the ama-1(m118) background, include 13 that are early larval lethals, and three that are mid-larval lethals, at 25 degrees. Six of the mutants exhibit temperature-dependence in the severity of their phenotype. Intragenic recombination between the lethal site and the parental resistance mutation was detected by means of resistance to amanitin. Recombinants were detected at frequencies as low as 2 X 10(-6). The segregation of the closely linked flanking markers, unc-17 and unc-5, revealed whether the lethal mutation was to the left or the right of m118. By adding the distances between the extreme left and right mutations, the ama-1 gene is estimated to be 0.011 map unit long, with m118 positioned 0.004 map unit from the left-most lethal mutation. To order the lethal mutations with respect to each other, viable heteroallelic strains were constructed using the free duplication, mDp1[unc-17(e113) dpy-13(+) ama-1(+)]. The heteroallelic strains were sensitive to amanitin, and recombination events between the lethal mutations were specifically selected by means of the dominant amanitin resistance encoded on the recombinant chromosome. The segregation of outside markers revealed the left-right order of the lethal mutations. The position of mutations within the gene is nonrandom. Functional domains of the ama-1 gene indicated by the various lethal phenotypes are discussed.

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The Spermatozoon of Actinia Equina L. Var. Mesembryanthemum

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315400024255 ◽

1980 ◽

Vol 60 (1) ◽

pp. 193-204 ◽

Cited By ~ 18

Author(s):

A. U. Larkman ◽

M. A. Carter

Keyword(s):

Fine Structure ◽

Sexual Reproduction ◽

Recent Work ◽

Developmental Stages ◽

Early Stage ◽

Genetic Material ◽

Sea Anemones ◽

Free Living ◽

Pass Through ◽

Parent Female

Actinia equina var. mesembryanthemum, the beadlet anemone (Stephenson, 1935), is a very common and widely distributed littoral anthozoan, whose sexual reproduction shows several interesting characteristics. Adult sea anemones of both sexes brood planulae and more advanced developmental stages within the gastrovascular cavity, although earlier embryonic stages are rarely found brooded in this way. Chia & Rostron (1970) suggest that embryos are expelled from the parent female anemone at an early stage and pass through a free-living phase before re-entering anemones of either sex for brooding. However, recent work (Cain, 1974) suggests that juvenile anemones are genetically related to the adult anemones in which they are brooded, and also the distribution of genetic material during sexual reproduction appears to be abnormal (Carter & Thorp, 1979). In an attempt to achieve a better understanding of the unusual sexual reproduction of this species, an ultrastructural investigation of gametogenesis was undertaken. This paper describes the fine structure of the spermatozoon within the testis.

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An apparent case of nonsymmetrical and sustained strand-specific hemimethylation in the Dc8 gene of carrot

Genome ◽

10.1139/g97-100 ◽

1998 ◽

Vol 41 (1) ◽

pp. 23-33 ◽

Cited By ~ 6

Author(s):

Yuanxiang Zhou ◽

Clint W Magill ◽

Jane M Magill ◽

Ronald J Newton

Keyword(s):

Pcr Amplification ◽

Daucus Carota L ◽

Template Strand ◽

Bisulfite Treatment ◽

Base Sequences ◽

Pcr Products ◽

Specific Amplification ◽

The Difference ◽

Almost All ◽

Methylation Patterns

The Dc8 gene of carrot (Daucus carota L.) shows differential expression during embryo development. Changes in methylation patterns of a segment of about 500 bp (from base + 120 to base -446) of Dc8 allele 6 were investigated by treating genomic DNA, extracted from embryogenic callus at different stages of development, with sodium bisulfite to modify nonmethylated cytosines. Following asymmetric (strand-specific) amplification, base sequences for samples from each developmental stage were determined for each strand directly from the PCR products or from cloned PCR products. Different methylation patterns were detected in the two strands. The 5' to 3' sense (coding) strand was almost completely nonmethylated, whereas almost all the cytosines in the 3' to 5' (template) strand were methylated. By 71 days after transfer to embryo-inducing medium, few methylcytosines remained; those that were present were generally near the TATA box or in a region beyond -300. The cytosines that were methylated were not limited to CG or CNG sequences. The difference in the extent of methylation between the two complementary strands implies either that there is a mechanism for strand-specific methylation, or that complementary sequences can differ greatly in sensitivity to bisulfite treatment or PCR amplification.

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Further observations on intragenic recombination in Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300020619 ◽

1981 ◽

Vol 38 (3) ◽

pp. 281-296 ◽

Cited By ~ 27

Author(s):

Arthur J. Hilliker ◽

Arthur Chovnick

Keyword(s):

Drosophila Melanogaster ◽

Fine Structure ◽

Meiotic Recombination ◽

Intragenic Recombination ◽

Crossing Over ◽

Marker Exchange ◽

Conversion Frequency ◽

Co Conversion ◽

Higher Eukaryotes ◽

Postmeiotic Segregation

SUMMARYThis report examines several issues bearing upon intragenic recombination in higher eukaryotes. The fine structure data accumulated in our analysis of the genetic organization of the rosy locus in Drosophila melanogaster. Firstly, we confirm that a conversion event has a markedly less than 50% probability of resulting in flanking marker exchange, a finding consistent with more recent analyses of the available Saccharomyces data (e.g. Fogel et al. 1978). As reported earlier, co-conversion of recombinationally separable sites within the rosy locus occurs (McCarron, Gelbart & Chovnick, 1974). In this report, we demonstrate that the frequency of co-conversion is inversely proportional to the distance between co-converting sites. As in fungi, real conversion frequency differences are observed among rosy mutant alleles, and the data suggest that there may be a relationship between allele conversion frequency and map position. Unlike Neurospora and Saccharomyces, only one flanking marker exchange class is recovered from any given mutant heteroallele recombination experiment. In this respect, the Drosophila system resembles Aspergillus. As in Neurospora and Saccharomyces, rosy locus intragenic recombinants associated with flanking marker exchange exhibit interference with crossing over in adjacent regions, while no interference is seen among recombinants exhibiting parental flanking markers. Finally, experimental results are discussed which demonstrate the occurrence of postmeiotic segregation in Drosophila. These analogies between Drosophila and fungi provide further evidence in support of the notion that eukaryotes share common molecular mechanism(s) of meiotic recombination.

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CHANGES IN CELL FINE STRUCTURE OF LIMA BEAN AXES DURING EARLY GERMINATION

Canadian Journal of Botany ◽

10.1139/b66-039 ◽

1966 ◽

Vol 44 (3) ◽

pp. 331-340 ◽

Cited By ~ 21

Author(s):

Shimon Klein ◽

Yehuda Ben-Shaul

Keyword(s):

Endoplasmic Reticulum ◽

Fine Structure ◽

Cell Walls ◽

Lipid Droplets ◽

Lima Bean ◽

Amorphous Substance ◽

Golgi Bodies ◽

Early Germination ◽

Almost All ◽

Vacuolar Content

Changes in cell fine structure were studied in axes of green lima bean seeds soaked in water for 1–48 hours. At the beginning of the imbibition period the cortical and pith cells and to a smaller degree the cells of the future conductive tissues contain several vacuoles filled with an amorphous substance. Almost all of the cells contain lipid droplets arranged exclusively along cell walls. The endoplasmic reticulum appears in the form of long tubules, predominantly occupying the peripheral parts of the cell, surrounding the nucleus. A large concentration of ribosomes, mostly unattached, can be found in the cytoplasm. Similar particles make up the bulk of the nucleolus, but could not be found in plastids, which frequently contained starch, but were devoid of internal membranes. Only very few Golgi bodies occur. No changes in fine structure seem to occur during the first 4 hours of imbibition, but after 24 hours the lipid droplets and the vacuolar content have disappeared, the endoplasmic reticulum is more evenly distributed throughout the cells, and a large number of Golgi bodies can be seen.

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Detection of Coxiella burnetii in ticks collected from cattle in several provinces of the Republic of Guinea

Epidemiology and Infectious Diseases (Russian Journal) ◽

10.17816/eid34806 ◽

2019 ◽

Vol 24 (5-6) ◽

pp. 234-239

Author(s):

Yulia A. Panferova ◽

Olga A. Freylikhman ◽

Nikolay K. Tokarevich ◽

Ekaterina V. Naydenova ◽

Kirill S. Zakharov ◽

...

Keyword(s):

Coxiella Burnetii ◽

Geographical Origin ◽

Q Fever ◽

Local Population ◽

Genetic Material ◽

Clinical Signs ◽

Republic Of Guinea ◽

Plasmid Analysis ◽

The Republic ◽

Almost All

Background. Q fever, or coxiellosis, is a natural focal disease characterized by polymorphism of clinical signs and can affect not only humans but also many species of animals. This infection is spread almost all over the world. On the African continent, the foci of coxiellosis infection endanger the local population and people arriving for temporary stay. Given that sick agricultural animals and their ectoparasites are markers of the presence of infection in the region, a study of the latter may be relevant to identify the potential foci of Q fever. This work aimed to identify Coxiella burnetii DNA from ixodic ticks collected from cattle in several provinces of Republic of Guinea and to type isolates using genetic markers (plasmid type) to enable their comparison with strains of different geographical origin. Methods. Using amplification technologies, we investigated the ticks obtained from cattle in the provinces of Boke and Kindia to detect Coxiella DNA. Results. The genetic material of the Q fever causative agent was detected in no more than 5% of the total number of samples studied. For positive samples, typing was performed using plasmid analysis. The isolates with the plasmid type QpH1 circulate in the Republic of Guinea. Conclusion. The findings were analyzed along with data from other researchers on the spread of Q fever in subequatorial Africa. The differences in the levels of prevalence of Coxiella in ticks in the territories of not only different countries but also within the same state can be determined by the prevalence among the hosts within herds. The risk of contamination with Q fever in endemic regions should be considered.

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Cosi2 : An efficient simulator of exact and approximate coalescent with selection

10.1101/005090 ◽

2014 ◽

Author(s):

Ilya Shlyakhter ◽

Pardis C. Sabeti ◽

Stephen F. Schaffner

Keyword(s):

Gene Conversion ◽

Genetic Material ◽

Small Subset ◽

Demographic Model ◽

Coalescent Simulation ◽

Recombination Rates ◽

Wide Range ◽

Selection Gene ◽

And Migration ◽

Recombination Hot Spots

Motivation: Efficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection. Gene conversion is not supported by any published coalescent simulators that support selection. Results: We describe cosi2 , an efficient simulator that supports both exact and approximate coalescent simulation with positive selection. cosi2 improves on the speed of existing exact simulators, and permits further speedup in approximate mode while retaining support for selection. cosi2 supports a wide range of demographic scenarios including recombination hot spots, gene conversion, population size changes, population structure and migration. cosi2 implements coalescent machinery efficiently by tracking only a small subset of the Ancestral Recombination Graph, sampling only relevant recombination events, and using augmented skip lists to represent tracked genetic segments. To preserve support for selection in approximate mode, the Markov approximation is implemented not by moving along the chromosome but by performing a standard backwards-in-time coalescent simulation while restricting coalescence to node pairs with overlapping or near-overlapping genetic material. We describe the algorithms used by cosi2 and present comparisons with existing selection simulators.

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