bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporation of Large Heterologies Into Heteroduplex DNA During Double-Strand-Break Repair in Mouse Cells
Authors: Raynard Steven J , Baker Mark D 
Published: April 2021

AbstractIn this study, the formation and repair of large (&gt;1 kb) insertion/deletion (I/D) heterologies during double-strand-break repair (DSBR) was investigated using a gene-targeting assay that permits efficient recovery of sequence insertion events at the haploid chromosomal immunoglobulin (Ig) μ-locus in mouse hybridoma cells. The results revealed that (i) large I/D heterologies were generated on one or both sides of the DSB and, in some cases, formed symmetrically in both homology regions; (ii) large I/D heterologies did not negatively affect the gene targeting frequency; and (iii) prior to DNA replication, the large I/D heterologies were rectified.
Maintenance of Mitochondrial Morphology Is Linked to Maintenance of the Mitochondrial Genome in Saccharomyces cerevisiae
Authors: Hanekamp Theodor , Thorsness Mary K , Rebbapragada Indrani , Fisher Elizabeth M , Seebart Corrine , Darland Monica R , Coxbill Jennifer A , Updike Dustin L , Thorsness Peter E 
Published: April 2021

Abstract
In the yeast Saccharomyces cerevisiae, certain mutant alleles of YME4, YME6, and MDM10 cause an increased rate of mitochondrial DNA migration to the nucleus, carbon-source-dependent alterations in mitochondrial morphology, and increased rates of mitochondrial DNA loss. While single mutants grow on media requiring mitochondrial respiration, any pairwise combination of these mutations causes a respiratory-deficient phenotype. This double-mutant phenotype allowed cloning of YME6, which is identical to MMM1 and encodes an outer mitochondrial membrane protein essential for maintaining normal mitochondrial morphology. Yeast strains bearing null mutations of MMM1 have altered mitochondrial morphology and a slow growth rate on all carbon sources and quantitatively lack mitochondrial DNA. Extragenic suppressors of MMM1 deletion mutants partially restore mitochondrial morphology to the wild-type state and have a corresponding increase in growth rate and mitochondrial DNA stability. A dominant suppressor also suppresses the phenotypes caused by a point mutation in MMM1, as well as by specific mutations in YME4 and MDM10.
Sex-RatioDrive inDrosophila simulans: Variation in Segregation Ratio ofXChromosomes From a Natural Population
Authors: Montchamp-Moreau Catherine , Cazemajor Michel 
Published: April 2021

AbstractThe sex-ratio trait that exists in a dozen Drosophila species is a case of naturally occurring X chromosome drive that causes males to produce female-biased progeny. Autosomal and Y polymorphism for suppressors are known to cause variation in drive expression, but the X chromosome polymorphism has never been thoroughly investigated. We characterized 41 X chromosomes from a natural population of Drosophila simulans that had been transferred to a suppressor-free genetic background. We found two clear-cut groups of chromosomes, sex-ratio and standard. The sex-ratio X chromosomes differed in their segregation ratio (81-96% females in the progeny), the less powerful drivers being less stable in their expression. A sib analysis, using a moderate driver, indicated that within-X variation in drive expression depended on genetic (autosomal) or epigenetic factors and that the age of the males also affected the trait. The other X chromosomes produced equal or roughly equal sex ratios, but again with significant variation. The continuous pattern of variation observed within both groups suggested that, in addition to a major sex-ratio gene, many X-linked loci of small effect modify the segregation ratio of this chromosome and are maintained in a polymorphic state. This was also supported by the frequency distribution of sex ratios produced by recombinant X chromosomes.
Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species
Authors: Sivasundar Arjun , Hey Jody 
Published: April 2021

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.
The Rad27 (Fen-1) Nuclease Inhibits Ty1 Mobility in Saccharomyces cerevisiae
Authors: Sundararajan Anuradha , Lee Bum-Soo , Garfinkel David J 
Published: April 2021

Abstract
Although most Ty1 elements in Saccharomyces cerevisiae are competent for retrotransposition, host defense genes can inhibit different steps of the Ty1 life cycle. Here, we demonstrate that Rad27, a structure-specific nuclease that plays an important role in DNA replication and genome stability, inhibits Ty1 at a posttranslational level. We have examined the effects of various rad27 mutations on Ty1 element retrotransposition and cDNA recombination, termed Ty1 mobility. The point mutations rad27-G67S, rad27-G240D, and rad27-E158D that cause defects in certain enzymatic activities in vitro result in variable increases in Ty1 mobility, ranging from 4- to 22-fold. The C-terminal frameshift mutation rad27-324 confers the maximum increase in Ty1 mobility (198-fold), unincorporated cDNA, and insertion at preferred target sites. The null mutation differs from the other rad27 alleles by increasing the frequency of multimeric Ty1 insertions and cDNA recombination with a genomic element. The rad27 mutants do not markedly alter the levels of Ty1 RNA or the TyA1-gag protein. However, there is an increase in the stability of unincorporated Ty1 cDNA in rad27-324 and the null mutant. Our results suggest that Rad27 inhibits Ty1 mobility by destabilizing unincorporated Ty1 cDNA and preventing the formation of Ty1 multimers.
Lateral Elements Inside Synaptonemal Complex-Like Polycomplexes in ndt80 Mutants of Yeast Bind DNA
Authors: Bhuiyan Hasanuzzaman , Dahlfors Gunilla , Schmekel Karin 
Published: April 2021

Abstract
The synaptonemal complex (SC) keeps the synapsed homologous chromosomes together during pachytene in meiotic prophase I. Structures that resemble stacks of SCs, polycomplexes, are sometimes found before or after pachytene. We have investigated ndt80 mutants of yeast, which arrest in pachytene. SCs appear normal in spread chromosome preparations, but are only occasionally found in intact nuclei examined in the electron microscope. Instead, large polycomplexes occur in almost every ndt80 mutant nucleus. Immunoelectron microscopy using DNA antibodies show strong preferential labeling to the lateral element parts of the polycomplexes. In situ hybridization using chromosome-specific probes confirms that the chromosomes in ndt80 mutants are paired and attached to the SCs. Our results suggest that polycomplexes can be involved in binding of chromosomes and possibly also in synapsis.
Female Site-Specific Transposase-Induced Recombination: A High-Efficiency Method for Fine Mapping Mutations on the X Chromosome in Drosophila
Authors: Marcus Jeffrey M 
Published: April 2021

Abstract
P-element transposons in the Drosophila germline mobilize only in the presence of the appropriate transposase enzyme. Sometimes, instead of mobilizing completely, P elements will undergo site-specific recombination with the homologous chromosome. Site-specific recombination is the basis for male recombination mapping, since the male germline does not normally undergo recombination. Site-specific recombination also takes place in females, but this has been difficult to study because of the obscuring effects of meiotic recombination. Using map functions, I demonstrate that it is possible to employ female site-specific transposase-induced recombination (FaSSTIR) to map loci on the X chromosome and predict that FaSSTIR mapping should be more efficient than meiotic mapping over short genetic intervals. Both FaSSTIR mapping and meiotic mapping were used to fine map the crossveinless locus on the X chromosome. Both techniques identified the same 10-kb interval as the probable location of the crossveinless mutation. Over short intervals (&lt; ∼7.6 cM), FaSSTIR produces more informative recombination events than does meiotic recombination. Over longer intervals, FaSSTIR is not always more efficient than meiotic mapping, but it produces the correct gene order. FaSSTIR matches the expectations suggested by the map functions and promises to be a useful technique, particularly for mapping X-linked loci.
Knockout Targeting of the Drosophila Nap1 Gene and Examination of DNA Repair Tracts in the Recombination Products
Authors: Lankenau Susanne , Barnickel Thorsten , Marhold Joachim , Lyko Frank , Mechler Bernard M , Lankenau Dirk-Henner 
Published: April 2021

Abstract
We used ends-in gene targeting to generate knockout mutations of the nucleosome assembly protein 1 (Nap1) gene in Drosophila melanogaster. Three independent targeted null-knockout mutations were produced. No wild-type NAP1 protein could be detected in protein extracts. Homozygous Nap1KO knockout flies were either embryonic lethal or poorly viable adult escapers. Three additional targeted recombination products were viable. To gain insight into the underlying molecular processes we examined conversion tracts in the recombination products. In nearly all cases the I-SceI endonuclease site of the donor vector was replaced by the wild-type Nap1 sequence. This indicated exonuclease processing at the site of the double-strand break (DSB), followed by replicative repair at donor-target junctions. The targeting products are best interpreted either by the classical DSB repair model or by the break-induced recombination (BIR) model. Synthesis-dependent strand annealing (SDSA), which is another important recombinational repair pathway in the germline, does not explain ends-in targeting products. We conclude that this example of gene targeting at the Nap1 locus provides added support for the efficiency of this method and its usefulness in targeting any arbitrary locus in the Drosophila genome.
The Promoter of the Heterochromatic Drosophila Telomeric Retrotransposon, HeT-A, Is Active When Moved Into Euchromatic Locations
Authors: George Janet A , Pardue Mary-Lou 
Published: April 2021

Abstract
The Drosophila telomeric retrotransposon, HeT-A, is found only in heterochromatin; therefore, its promoter must function in this chromatin environment. Studies of position effect variegation suggest that promoters of heterochromatic genes are very different from euchromatic promoters, but this idea has not been tested with isolated promoter sequences. The HeT-A promoter is the first heterochromatin promoter to be isolated and it is of interest to investigate its activity when removed from telomeric heterochromatin. This promoter was initially characterized by testing reporter constructs in transient transfection of cultured cells, an environment that may approximate its endogenous heterochromatin. We now report P-element-mediated transpositions of these constructs, testing the function of different parts of the putative promoter in euchromatin. Expression of endogenous HeT-A RNA shows marked developmental regulation and accumulates preferentially in replicating diploid tissues. HeT-A promoter constructs are active in all euchromatic locations tested and some display aspects of endogenous HeT-A stage- and cell-type expression programs. The activity of each promoter construct in euchromatic locations is also generally consistent with its activity in the transient transfection tests; a possibly significant exception is one sequence segment that appreciably enhanced activity in transient transfection but repressed promoter activity in euchromatin.
Chromatin Immunoprecipitation Reveals That the 180-bp Satellite Repeat Is the Key Functional DNA Element of Arabidopsis thaliana Centromeres
Authors: Nagaki Kiyotaka , Talbert Paul B , Zhong Cathy Xiaoyan , Dawe R Kelly , Henikoff Steven , Jiang Jiming 
Published: April 2021

Abstract
The centromeres of Arabidopsis thaliana chromosomes contain megabases of complex DNA consisting of numerous types of repetitive DNA elements. We developed a chromatin immunoprecipitation (ChIP) technique using an antibody against the centromeric H3 histone, HTR12, in Arabidopsis. ChIP assays showed that the 180-bp centromeric satellite repeat was precipitated with the antibody, suggesting that this repeat is the key component of the centromere/kinetochore complex in Arabidopsis.
The Rise and Fall of Isolation by Distance in the Anadromous Brook Charr (Salvelinus fontinalisMitchill)
Authors: Castric Vincent , Bernatchez Louis 
Published: April 2021

AbstractGeographic patterns of genetic diversity depend on a species’ demographic properties in a given habitat, which may change over time. The rates at which patterns of diversity respond to changes in demographic properties and approach equilibrium are therefore pivotal in our understanding of spatial patterns of diversity. The brook charr Salvelinus fontinalis is a coastal fish exhibiting limited marine movements, such that a stable one-dimensional isolation-by-distance (IBD) pattern should be observed over the whole range. Its range, however, recently shifted northward such that northern populations may still be in the process of reaching equilibrium. We investigated variation in IBD patterns, genetic divergence, and allelic richness at six microsatellite markers in 2087 anadromous brook charr from 59 rivers along the most likely postglacial colonization route. We observed a decrease in allelic richness, together with an increase in differentiation and a decrease in IBD in the most recently colonized northern populations, as expected following recent colonization. Contrary to expectation, however, similar patterns were also observed at the southernmost part of the range, despite the fact that these populations are not considered to be newly colonized. We propose that the loss of dispersal capabilities associated with anadromy may have caused the southernmost populations to evolve relatively independently of one another. This study thus demonstrated that changes in a species’ geographic range and dispersal capabilities may contribute to shaping geographic patterns of genetic diversity.
Transvection at the End of the Truncated Chromosome in Drosophila melanogaster
Authors: Savitsky Mikhail , Kahn Tatyana , Pomerantseva Ekaterina , Georgiev Pavel 
Published: April 2021

Abstract
The phenomenon of transvection is well known for the Drosophila yellow locus. Thus enhancers of a promoterless yellow locus in one homologous chromosome can activate the yellow promoter in the other chromosome where the enhancers are inactive or deleted. In this report, we examined the requirements for trans-activation of the yellow promoter at the end of the deficient chromosome. A number of truncated chromosomes ending in different areas of the yellow regulatory region were examined in combination with the promoterless y alleles. We found that trans-activation of the yellow promoter at the end of a deficient chromosome required ∼6 kb of an additional upstream sequence. The nature of upstream sequences affected the strength of transvection: addition of gypsy sequences induced stronger trans-activation than addition of HeT-A or yellow sequences. Only the promoter proximal region (within -158 bp of the yellow transcription start) was essential for trans-activation; i.e., transvection did not require extensive homology in the yellow upstream region. Finally, the yellow enhancers located on the two pairing chromosomes could cooperatively activate one yellow promoter.
Microsatellite Allele Sizes: A Simple Test to Assess Their Significance on Genetic Differentiation
Authors: Hardy Olivier J , Charbonnel Nathalie , Fréville Hélène , Heuertz Myriam 
Published: April 2021

AbstractThe mutation process at microsatellite loci typically occurs at high rates and with stepwise changes in allele sizes, features that may introduce bias when using classical measures of population differentiation based on allele identity (e.g., FST, Nei’s Ds genetic distance). Allele size-based measures of differentiation, assuming a stepwise mutation process [e.g., Slatkin’s RST, Goldstein et al.’s (δμ)2], may better reflect differentiation at microsatellite loci, but they suffer high sampling variance. The relative efficiency of allele size- vs. allele identity-based statistics depends on the relative contributions of mutations vs. drift to population differentiation. We present a simple test based on a randomization procedure of allele sizes to determine whether stepwise-like mutations contributed to genetic differentiation. This test can be applied to any microsatellite data set designed to assess population differentiation and can be interpreted as testing whether FST = RST. Computer simulations show that the test efficiently identifies which of FST or RST estimates has the lowest mean square error. A significant test, implying that RST performs better than FST, is obtained when the mutation rate, μ, for a stepwise mutation process is (a) ≥ m in an island model (m being the migration rate among populations) or (b) ≥ 1/t in the case of isolated populations (t being the number of generations since population divergence). The test also informs on the efficiency of other statistics used in phylogenetical reconstruction [e.g., Ds and (δμ)2], a nonsignificant test meaning that allele identity-based statistics perform better than allele size-based ones. This test can also provide insights into the evolutionary history of populations, revealing, for example, phylogeographic patterns, as illustrated by applying it on three published data sets.
Local Superimpositions Facilitate Morphometric Analysis of Complex Articulating Structures
Authors: Rhoda Daniel , Segall Marion , Larouche Olivier , Evans Kory , Angielczyk Kenneth D 
Published: April 2021

Synopsis
Articulating structures, such as the vertebrate skeleton or the segmented arthropod exoskeleton, comprise a majority of the morphological diversity across the eukaryotic tree of life. Quantifying the form of articulating structures is therefore imperative for a fuller understanding of the factors influencing biological form. A wealth of freely available 3D data capturing this morphological diversity is stored in online repositories such as Morphosource, but the geometric morphometric analysis of an articulating structure is impeded by arbitrary differences in the resting positions of its individual articulating elements. In complex articulating structures, where the angles between articulating elements cannot be standardized, landmarks on articulating elements must be Procrustes superimposed independently (locally) and then recombined to quantify variation in the entire articulating structure simultaneously. Here, we discuss recent advances in local superimposition techniques, namely the “matched local superimpositions” approach, which incorporates anatomically accurate relative sizes, positions, and orientations of locally-superimposed landmarks, enabling clearer biological interpretation. We also use simulations to evaluate the consequences of choice of superimposition approach. Our results show that local superimpositions will isolate shape variation within locally-superimposed landmark subsets by sacrificing size and positional variation. They may also create morphometric “modules” when there are none by increasing integration within the locally-superimposed subsets; however, this effect is no greater than the spurious between-module integration created when superimposing landmark subsets (i.e., articulating elements) together. Taken together, our results show that local superimposition techniques differ from conventional Procrustes superimpositions in predictable ways. Finally, we use empirical datasets of the skulls of wrasses and colubriform snakes to highlight the promise of local superimpositions and their utility. Complex articulating structures must be studied, and the only current solution to do so is local superimpositions.
Identifying Hospitals in Nepal for Acute Burn Care and Stabilization Capacity Development: Location-Allocation Modeling for Strategic Service Delivery
Authors: Li Kevin , Mehta Kajal , Wright Ada , Lee Joohee , Yadav Manish , Pham Tam N , Rai Shankar M , Nakarmi Kiran , Stewart Barclay 
Published: April 2021

AbstractIn Nepal, preventable death and disability from burn injuries are common due to poor population-level spatial access to organized burn care. Most severe burns are referred to a single facility nationwide, often after suboptimal burn stabilization and/or significant care delay. Therefore, we aimed to identify existing first-level hospitals within Nepal that would optimize population-level access as “burn stabilization points” if their acute burn care capabilities are strengthened. A location-allocation model was created using designated first-level candidate hospitals, a population density grid for Nepal, and road network/travel speed data. Six models (A–F) were developed using cost-distance and network analyses in ArcGIS to identify the three vs five candidate hospitals at ≤2, 6, and 12 travel-hour thresholds that would optimize population-level spatial access. The baseline model demonstrated that currently 20.3% of the national population has access to organized burn care within 2 hours of travel, 37.2% within 6 travel-hours, and 72.6% within 12 travel-hours. If acute burn stabilization capabilities were strengthened, models A to C of three chosen hospitals would increase population-level burn care access to 45.2, 89.4, and 99.8% of the national population at ≤2, 6, and 12 travel-hours, respectively. In models D to F, five chosen hospitals would bring access to 53.4, 95.0, and 99.9% of the national population at ≤2, 6, and 12 travel-hours, respectively. These models demonstrate developing capabilities in three to five hospitals can provide population-level spatial access to acute burn care for most of Nepal’s population. Organized efforts to increase burn stabilization points are feasible and imperative to reduce the rates of preventable burn-related death and disability country-wide.
The Geography of Knowledge and R&D-led Growth
Authors: Aloi Marta , Poyago-Theotoky Joanna , Tournemaine Frédéric 
Published: April 2021

Abstract
We analyse how spatial disparities in innovation activities, coupled with migration costs, affect economic geography, market structure, growth and regional inequality. We provide conditions for existence and uniqueness of a spatial equilibrium, and for the endogenous emergence of industry clusters. Spatial variations in knowledge spillovers lead to spatial concentration of more innovative firms. Migration costs, however, limit the concentration of economic activities in the most productive region. Narrowing the gap in knowledge spillovers across regions raises growth, and reduces regional inequality by making firms more sensitive to wage differentials. The associated change in the industry concentration has positive welfare effects.