bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms.
Authors: Helentjaris T , Weber D , Wright S 
Published: January 2021

Abstract
While preparing a linkage map for maize based upon loci detected through the use of restriction fragment length polymorphisms (RFLPs), it was found that 62 of the 217 cloned maize sequences tested (29%) detected more than one fragment on genomic Southern blots. Thus, more than one nucleotide sequence is present within the maize genome which is in part homologous to each of these cloned sequences. The genomic locations of these ;;duplicate'' sequences were determined and it was found that they usually originated from different chromosomes. The process which produced them did not operate randomly as some pairs of chromosomes share many duplicate sequences while many other pairs share none. Furthermore, these shared duplicate sequences are generally arrayed in an ordered arrangement along these chromosomes. It is believed that chromosomal segments which contain several duplicate loci in a generally ordered arrangement must have had a common origin. The presence of these duplicated segments supports the idea that allopolyploidy may have been involved in the evolution of maize. Nevertheless, the duplicate loci do not primarily involve five pairs of chromosomes and thus, five pairs of homeologous chromosomes are not currently present within the maize genome. The data clearly indicate that maize is not a recent allotetraploid produced by hybridization between two individuals with similar genomic structures; however, the data are also consistent with the possibility of these shared duplicate chromosomal segments having been generated through internal duplication.
A selective screen to recover chromosomal deletions and duplications in Drosophila melanogaster.
Authors: Gubb D , McGill S , Ashburner M 
Published: January 2021

Abstract
A screen is described that will select for breakpoints within a restricted chromosomal region in Drosophila. The aberrations recovered can be used to construct chromosomes carrying synthetic duplications and deletions. Such chromosomes have applications in the mapping of complementation groups at both the genetic and molecular level. In particular, breakpoints recovered after P element hybrid dysgenesis tend to be associated with P element insertion sites. Such aberration breakpoints can be genetically mapped, as synthetic deletions, and then used as transposon-tagged sites for the recovery of genomic clones.
The discoidin I gene family of Dictyostelium discoideum is linked to genes regulating its expression.
Authors: Welker D L 
Published: January 2021

Abstract
The discoidin I protein has been studied extensively as a marker of early development in the cellular slime mold Dictyostelium discoideum. However, like most other developmentally regulated proteins in this system, no reliable information was available on the linkage of the discoidin genes to other known genes. Analysis of the linkage of the discoidin I genes by use of restriction fragment length polymorphisms revealed that all three discoidin I genes as well as a pseudogene are located on linkage group II. This evidence is consistent with the discoidin I genes forming a gene cluster that may be under the control of a single regulatory element. The discoidin I genes are linked to three genetic loci (disA, motA, daxA) that affect the expression of the discoidin I protein. Linkage of the gene family members to regulatory loci may be important in the coordinate maintenance of the gene family and regulatory loci. A duplication affecting the entire discoidin gene family is also linked to group II; this appears to be a small tandem duplication. This duplication was mapped using a DNA polymorphism generated by insertion of the Tdd-3 mobile genetic element into a Tdd-2 element flanking the gamma gene. A probe for Tdd-2 identified a restriction fragment length polymorphism in strain AX3K that was consistent with generation by a previously proposed Tdd-3 insertion event. A putative duplication or rearrangement of a second Tdd-2 element on linkage group IV of strain AX3K was also identified. This is the first linkage information available for mobile genetic elements in D. discoideum.
Variation among extracted lines of Drosophila melanogaster in triacylglycerol and carbohydrate storage.
Authors: Clark A G , Keith L E 
Published: January 2021

Abstract
Whole larvae and whole adult extracts from 26 second chromosome replacement lines of Drosophila melanogaster were analyzed to determine the amounts of stored triacylglycerols and carbohydrates as well as the activities of 13 enzymes in relevant biochemical pathways. Analysis of covariance revealed significant differences among lines in stored lipids and carbohydrates, as well as in activities of most of the enzymes. Significant broad-sense genetic correlations (among adjusted line means) were detected for a number of enzyme pairs. Multiple regression techniques were applied to assess the extent to which the amounts of stored triacylglycerols and carbohydrates could be predicted from the enzyme activities. Significant regressions were found in both adults and larvae, suggesting that modulation of enzyme activities is reflected in different sizes of storage pools. The population genetic consequences of natural selection acting on a phenotype such as energy storage is considered in light of models of metabolic flux in biochemical pathways.
A sex chromosomal restriction-fragment-length marker linked to melanoma-determining Tu loci in Xiphophorus.
Authors: Schartl M 
Published: January 2021

Abstract
In Xiphophorus, the causative genetic information for melanoma formation has been assigned by classical genetics to chromosomal loci, which are located on the sex chromosomes. In our attempts to molecularly clone these melanoma-determining loci, named Tu, we have looked for restriction-fragment-length markers (RFLMs) linked to the Tu loci. These RFLMs should be useful in obtaining a physical map of a Tu locus, which will aid in the cloning of the corresponding sequences. DNA samples from various Xiphophorus strains and hybrids including those bearing different Tu wild-type, deletion and translocation chromosomes, were screened for the presence of random RFLMs using homologous or heterologous sequences as hybridization probes. We find an EcoRI restriction fragment which shows limited crosshybridization to the v-erb B gene--but not representing the authentic c-erb B gene of Xiphophorus--to be polymorphic with respect to different sex chromosomes. Linkage analysis revealed that a 5-kb fragment is linked to the Tu-Sd locus on the X chromosome, a 7-kb fragment is linked to the Tu-Sr locus on the Y chromosome, both of Xiphophorus maculatus, and that a 12-kb fragment is linked to the Tu-Li locus on the X chromosome of Xiphophorus variatus. Using different chromosomal mutants this RFLM has been mapped to a frequent deletion/translocation breakpoint of the X chromosome, less than 0.3 cM apart from the Tu locus.
The evolution of the Y chromosome with X-Y recombination.
Authors: Clark A G 
Published: January 2021

Abstract
A theoretical population genetic model is developed to explore the consequences of X-Y recombination in the evolution of sex chromosome polymorphism. The model incorporates one sex-determining locus and one locus subject to natural selection. Both loci have two alleles, and the rate of classical meiotic recombination between the loci is r. The alleles at the sex-determining locus specify whether the chromosome is X or Y, and the alleles at the selected locus are arbitrarily labeled A and a. Natural selection is modeled as a process of differential viabilities. The system can be expressed in terms of three recurrence equations, one for the frequency of A on the X-bearing gametes produced by females, one for each of the frequency of A on the X- and Y-bearing gametes produced by males. Several special cases are examined, including X chromosome dominance and symmetric selection. Unusual equilibria are found with the two sexes having very different allele frequencies at the selected locus. A significant finding is that the allowance of recombination results in a much greater opportunity for polymorphism of the Y chromosome. Tighter linkage results in a greater likelihood for equilibria with a large difference between the sex chromosomes in allele frequency.
Cytoplasmic leucyl-tRNA synthetase of Neurospora crassa is not specified by the leu-5 locus.
Authors: Benarous R , Chow C M , RajBhandary U L 
Published: January 2021

Abstract
We generated a lambda gt11 Neurospora crassa cDNA library and screened the library for the cytoplasmic leucyl-tRNA synthetase (cyto LeuRS) clones using cyto LeuRS specific antibody. Two clones, lambda NCLRSC1 and lambda NCLRSC2, were obtained which have inserts of approximately 2 kbp and approximately 1.3 kbp, and which overlap by about 0.6 kbp. The following lines of evidence indicate that lambda NCLRSC1 and lambda NCLRSC2 encode parts of cyto LeuRS. (1) Antibodies affinity purified using either of the fusion proteins encoded by lambda NCLRSC1 or lambda NCLRSC2 inhibit cyto LeuRS activity. Thus, the fusion protein and cyto LeuRS share immunological determinants. (2) The same antibodies also react with an approximately 115-kDa protein, which comigrates with purified cyto LeuRS, in immunoblots of total N. crassa proteins. We used the cDNA clones to probe a N. crassa genomic DNA library and isolated two genomic DNA clones. Partial sequence analysis of cDNA and genomic DNA clones shows a methionine initiated open reading frame, which includes a stretch of amino acid residues that are highly conserved and that are at the ATP binding site in aminoacyl-tRNA synthetases. Using the cloned DNA as probe, we show that the cyto LeuRS mRNA is approximately 3900 nucleotides long. Finally, we have used restriction fragment length polymorphism mapping to show that the cyto LeuRS gene resides on the far right of linkage group II and not on linkage group V where the leu-5 mutation, which was previously reported to specify cyto LeuRS, is located.
Reciprocality of recombination events that rearrange the chromosome.
Authors: Mahan M J , Roth J R 
Published: January 2021

Abstract
We describe a genetic system for studying the reciprocality of chromosomal recombination; all substrates and recombination functions involved are provided exclusively by the bacterial chromosome. The genetic system allows the recovery of both recombinant products from a single recombination event. The system was used to demonstrate the full reciprocality of three different types of recombination events: (1) intrachromosomal recombination between direct repeats, causing deletions; (2) intrachromosomal recombination between inverse homologies, causing inversion of a segment of the bacterial chromosome; and (3) circle to circle recombination (in the absence of any plasmid or phage functions). Results suggest that intrachromosomal recombination in bacteria is frequently fully reciprocal.
Many protein products from a few loci: assignment of human salivary proline-rich proteins to specific loci.
Authors: Lyons K M , Azen E A , Goodman P A , Smithies O 
Published: January 2021

Abstract
Earlier studies of protein polymorphisms led to the description of 13 linked loci thought to encode the human salivary proline-rich proteins (PRPs). However, more recent studies at the DNA level have shown that there are only six genes which encode PRPs. The present study was undertaken in order to reconcile these observations. Nucleotide and decoded amino acid sequences from each of the six genes were compared with the available protein sequence data for PRPs. This analysis allowed assignment of the PmF, PmS and Pe proteins to the PRB1 locus, the G1 protein to the PRB3 locus, the Po protein to the PRB4 locus, the Ps protein to the PRB2 locus, and the CON1 and CON2 proteins to the PRB4 locus. Correlations between insertion/deletion RFLPs and PRP protein phenotypes were observed for the PmF, PmS, Gl and CON2 proteins. Our overall analysis indicates that in many instances several proteins previously considered to be the products of separate loci are actually proteolytic cleavage products of a large precursor specified by one or other of the six genes identified at the DNA level. Our analysis also demonstrates that some of the "null" alleles proposed to occur at 11 of the 13 loci in the earlier genetic studies, are actually productive alleles having alterations at proteolytic cleavage sites within the relevant precursor protein. The absence of cleavage leads to the persistence of longer precursor peptides not resolved electrophoretically, concurrently with an absence of the smaller PRPs seen when cleavage occurs.
Gene conversion, linkage, and the evolution of multigene families.
Authors: Nagylaki T 
Published: January 2021

Abstract
The evolution of the probabilities of genetic identity within and between the loci of a multigene family is investigated. Unbiased gene conversion, equal crossing over, random genetic drift, and mutation to new alleles are incorporated. Generations are discrete and nonoverlapping; the diploid, monoecious population mates at random. The linkage map is arbitrary, and the location dependence of the probabilities of identity is formulated exactly. The greatest of the rates of gene conversion, random drift, and mutation is epsilon much less than 1. For interchromosomal conversion, the equilibrium probabilities of identity are within order epsilon [i.e., O(epsilon)] of those in a simple model that has no location dependence and, at equilibrium, no linkage disequilibrium. At equilibrium, the linkage disequilibria are of O(epsilon); they are evaluated explicitly with an error of O(epsilon 2); they may be negative if symmetric heteroduplexes occur. The ultimate rate and pattern of convergence to equilibrium are within O(epsilon 2) and O(epsilon), respectively, of that of the same simple model. If linkage is loose (i.e., all the crossover rates greatly exceed epsilon, though they may still be much less than 1/2), the linkage disequilibria are reduced to O(epsilon) in a time of O(-ln epsilon). If intrachromosomal conversion is incorporated, the same results hold for loose linkage, except that, if the crossover rates are much less than 1/2, then the linkage disequilibria generally exceed those for pure interchromosomal conversion.
Studies of the genetic organization of the vestigial microregion of Drosophila melanogaster.
Authors: Lasko P F , Pardue M L 
Published: January 2021

Abstract
The region of the second chromosome of Drosophila melanogaster defined by Df(2R)vgB was screened for recessive lethal and visible mutations. Fifty-eight new recessive alleles fall into 17 complementation groups. Many new vg alleles were also isolated in a screen for new vg deficiencies. The breakpoints of the new vg deficiencies were nonrandomly distributed. The distal breakpoints of twelve of 20 deficiencies overlapping Df(2R)vgB are genetically identical to that of Df(2R)vgD, coinciding with the position of a complex, pleiotropic locus, l(2)49Ea-Psc-Su(z)2.
The Ultrastructure of the Nictitating Membrane of the Little Penguin (Eudyptula minor, Aves)
Authors: Collin S P , Collin H B 
Published: January 2021

Synopsis
The ultrastructure of the nictitating membrane in the little penguin Eudyptula minor was studied using both scanning and transmission electron microscopy to improve our understanding of the function of ocular adnexa in diving birds. Following euthanasia, eyes were enucleated and immersion fixed in Karnovsky’s fixative. The nictitating membrane and conjunctiva were embedded in araldite and semi- or ultra-thin sections were stained and photographed using compound and transmission electron microscopes, respectively. Ultrastructural dimensions were measured directly from digital photographs. Surface ultrastructure was examined using scanning electron microscopy. The transparent nictitating membrane consists of a dense stroma surrounded by epithelia on both the external (conjunctival) and internal (bulbar) surfaces. The conjunctival surface of the membrane near the leading edge is covered by microvilli, which transition to microplicae and finally to microridges in the periphery. Beneath the epithelial cells, there is a well-developed basement membrane. Scattered throughout this epithelium are a few goblet cells. The surface of the bulbar epithelium is covered by microvilli near the leading edge, which become denser peripherally. The stroma consists of densely-packed collagen fibrils, which are randomly oriented in bundles near the leading edge but are aligned in the same direction parallel with the epithelial and corneal surfaces and with the leading edge, when the membrane is extended. The ultrastructure of the nictitating membrane in the little penguin differs from other birds and its function is predominantly protective, while preserving clear vision in both water and air.
Predicting the observability of population III stars with ELT-HARMONI via the helium 1640 Å emission line
Authors: Grisdale Kearn , Thatte Niranjan , Devriendt Julien , Pereira-Santaella Miguel , Slyz Adrianne , Kimm Taysun , Dubois Yohan , Yi Sukyoung K 
Published: January 2021

ABSTRACT
Population III (Pop. III) stars, as of yet, have not been detected, however as we move into the era of extremely large telescopes this is likely to change. One likely tracer for Pop. III stars is the He iiλ1640 emission line, which will be detectable by the HARMONI spectrograph on the European Extremely Large Telescope (ELT) over a broad range of redshifts (2 ≤ z ≤ 14). By post-processing galaxies from the cosmological, AMR-hydrodynamical simulation newhorizon with theoretical spectral energy distributions (SED) for Pop. III stars and radiative transfer (i.e. the Yggdrasil Models and cloudy look-up tables, respectively) we are able to compute the flux of He iiλ1640 for individual galaxies. From mock 10 h observations of these galaxies we show that HARMONI will be able to detect Pop. III stars in galaxies up to z ∼ 10 provided Pop. III stars have a top heavy initial mass function (IMF). Furthermore, we find that should Pop. III stars instead have an IMF similar to those of the Pop. I stars, the He iiλ1640 line would only be observable for galaxies with Pop. III stellar masses in excess of $10^{7}\, {\rm M}_\odot$, average stellar age $\lt 1\, {\rm Myr}$ at z = 4. Finally, we are able to determine the minimal intrinsic flux required for HARMONI to detect Pop. III stars in a galaxy up to z = 10.
Dynamical modelling of CXOGBS J175553.2−281633: a 10 h long orbital period cataclysmic variable
Authors: Gomez Sebastian , Torres Manuel A P , Jonker Peter G , Kostrzewa-Rutkowska Zuzanna , van Grunsven Theo F J , Udalski Andrzej , Hynes Robert I , Heinke Craig O , Maccarone Thomas J , Salinas Ricardo , Strader Jay 
Published: January 2021

ABSTRACT
We present modelling of the long-term optical light and radial velocity curves of the binary stellar system CXOGBS J175553.2−281633, first detected in X-rays in the Chandra Galactic Bulge Survey. We analysed 7 yr of optical I-band photometry from Optical Gravitational Lensing Experiment and found long-term variations from year to year. These long-term variations can most likely be explained with by either variations in the luminosity of the accretion disc or a spotted secondary star. The phased light curve has a sinusoidal shape, which we interpret as being due to ellipsoidal modulations. We improve the orbital period to be P = 10.34488 ± 0.00006 h with a time of inferior conjunction of the secondary star T0 = HJD 2455260.8204 ± 0.0008. Moreover, we collected 37 spectra over 6 non-consecutive nights. The spectra show evidence for an evolved K7 secondary donor star, from which we obtain a semi-amplitude for the radial velocity curve of K2 = 161 ± 6 km s−1. Using the light-curve synthesis code xrbinary, we derive the most likely orbital inclination for the binary of i = 63.0 ± 0.7 deg, a primary mass of M1 = 0.83 ± 0.06 M⊙, consistent with a white dwarf accretor, and a secondary donor mass of M2 = 0.65 ± 0.07 M⊙, consistent with the spectral classification. Therefore, we identify the source as a long orbital period cataclysmic variable star.
Constraining stellar population parameters from narrow band photometric surveys using convolutional neural networks
Authors: Liew-Cain Choong Ling , Kawata Daisuke , Sánchez-Blázquez Patricia , Ferreras Ignacio , Symeonidis Myrto 
Published: January 2021

ABSTRACT
Upcoming large-area narrow band photometric surveys, such as Javalambre Physics of the Accelerating Universe Astrophysical Survey (J-PAS), will enable us to observe a large number of galaxies simultaneously and efficiently. However, it will be challenging to analyse the spatially resolved stellar populations of galaxies from such big data to investigate galaxy formation and evolutionary history. We have applied a convolutional neural network (CNN) technique, which is known to be computationally inexpensive once it is trained, to retrieve the metallicity and age from J-PAS-like narrow-band images. The CNN was trained using synthetic photometry from the integral field unit spectra of the Calar Alto Legacy Integral Field Area survey and the age and metallicity obtained in a full spectral fitting on the same spectra. We demonstrate that our CNN model can consistently recover age and metallicity from each J-PAS-like spectral energy distribution. The radial gradients of the age and metallicity for galaxies are also recovered accurately, irrespective of their morphology. However, it is demonstrated that the diversity of the data set used to train the neural networks has a dramatic effect on the recovery of galactic stellar population parameters. Hence, future applications of CNNs to constrain stellar populations will rely on the availability of quality spectroscopic data from samples covering a wide range of population parameters.
Solar dynamo cycle variations with a rotational period
Authors: Pipin V V 
Published: January 2021

ABSTRACTUsing non-linear mean-field dynamo models, we calculate magnetic cycle parameters, such as the dynamo cycle period, the amplitude of the total magnetic energy and the Poynting flux luminosity from the surface, for solar analogues with rotation periods in the range of 1–30 d. We perform simulations for both kinematic and non-kinematic dynamo models. The kinematic dynamo models, which take into account the non-linear α-effect and the loss of the magnetic flux due to magnetic buoyancy, show a decrease of the magnetic cycle with the decrease of the stellar rotation period. Stars with a rotational period of fewer than 10 d show non-stationary long-term variations of magnetic activity. The non-kinematic dynamo models take into account the magnetic field feedback on the large-scale flow and heat transport inside the convection zone. They show the non-monotonic variation of the dynamo period with the rotation rate. The models for rotational periods fewer than 10 d show non-stationary evolution with a slight increase in the primary dynamo period with the increase of the rotation rate. The non-kinematic models show the growth of the dynamo-generated magnetic flux with the increase of the rotation rate. There is a dynamo saturation for a star rotating with a period of 2 d or less. The saturation of the magnetic activity parameters is accompanied by a depression of the differential rotation.