bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Conditionally Dispensable Chromosome Controls Host-Specific Pathogenicity in the Fungal Plant Pathogen Alternaria alternata
Authors: Hatta Rieko , Ito Kaoru , Hosaki Yoshitsugu , Tanaka Takayoshi , Tanaka Aiko , Yamamoto Mikihiro , Akimitsu Kazuya , Tsuge Takashi 
Published: April 2021

Abstract
The filamentous fungus Alternaria alternata contains seven pathogenic variants (pathotypes), which produce host-specific toxins and cause diseases on different plants. Previously, the gene cluster involved in host-specific AK-toxin biosynthesis of the Japanese pear pathotype was isolated, and four genes, named AKT genes, were identified. The AKT homologs were also found in the strawberry and tangerine pathotypes, which produce AF-toxin and ACT-toxin, respectively. This result is consistent with the fact that the toxins of these pathotypes share a common 9,10-epoxy-8-hydroxy-9-methyl-decatrienoic acid structural moiety. In this study, three of the AKT homologs (AFT1-1, AFTR-1, and AFT3-1) were isolated on a single cosmid clone from strain NAF8 of the strawberry pathotype. In NAF8, all of the AKT homologs were present in multiple copies on a 1.05-Mb chromosome. Transformation-mediated targeting of AFT1-1 and AFT3-1 in NAF8 produced AF-toxin-minus, nonpathogenic mutants. All of the mutants lacked the 1.05-Mb chromosome encoding the AFT genes. This chromosome was not essential for saprophytic growth of this pathogen. Thus, we propose that a conditionally dispensable chromosome controls host-specific pathogenicity of this pathogen.
Inferences About Human Demography Based on Multilocus Analyses of Noncoding Sequences
Authors: Pluzhnikov Anna , Di Rienzo Anna , Hudson Richard R 
Published: April 2021

Abstract
Data from 10 unlinked autosomal noncoding regions, resequenced in 15 individuals from each of three populations, were used in a multilocus analysis to test models of human demography. Each of the 10 regions consisted of ~2500 bp. The multilocus analysis, based on summary statistics (average and variance of Tajima's D and Fu and Li's D*), was used to test a family of models with recent population expansion. The African sample (Hausa of Cameroon) is compatible with a constant population size model and a range of models with recent expansion. For this population sample, we estimated confidence sets that showed the limited range of parameter values compatible with growth. For an exponential growth rate as low as 1 × 10−3/generation, population growth is unlikely to have started prior to 50,000 years ago. For higher growth rates, the onset of growth must be more recent. On the basis of the average value of Tajima's D, our sample from an Italian population was found to be incompatible with a constant population size model or any simple expansion model. In the Chinese sample, the variance of Tajima's D was too large to be compatible with the constant population size model or any simple expansion model.
Genetic Architecture of Plastic Methyl Jasmonate Responses in Arabidopsis thaliana
Authors: Kliebenstein Daniel J , Figuth Antje , Mitchell-Olds Thomas 
Published: April 2021

Abstract
The ability of a single genotype to generate different phenotypes in disparate environments is termed phenotypic plasticity, which reflects the interaction of genotype and environment on developmental processes. However, there is controversy over the definition of plasticity genes. The gene regulation model states that plasticity loci influence trait changes between environments without altering the means within a given environment. Alternatively, the allelic sensitivity model argues that plasticity evolves due to selection of phenotypic values expressed within particular environments; hence plasticity must be controlled by loci expressed within these environments. To identify genetic loci controlling phenotypic plasticity and address this controversy, we analyzed the plasticity of glucosinolate accumulation under methyl jasmonate (MeJa) treatment in Arabidopsis thaliana. We found genetic variation influencing multiple MeJa signal transduction pathways. Analysis of MeJa responses in the Landsberg erecta × Columbia recombinant inbred lines identified a number of quantitative trait loci (QTL) that regulate plastic MeJa responses. All significant plasticity QTL also impacted the mean trait value in at least one of the two “control” or “MeJa” environments, supporting the allelic sensitivity model. Additionally, we present an analysis of MeJa and salicylic acid cross-talk in glucosinolate regulation and describe the implications for glucosinolate physiology and functional understanding of Arabidopsis MeJa signal transduction.
A Bacterial Artificial Chromosome-Based Genetic Linkage Map of the Nematode Pristionchus pacificus
Authors: Srinivasan Jagan , Sinz Waltraud , Lanz Christa , Brand Alexandra , Nandakumar Ramkumar , Raddatz Günter , Witte Hanh , Keller Heike , Kipping Isabel , Pires-daSilva André , Jesse Taco , Millare Jun , de Both Michiel , Schuster Stephan C , Sommer Ralf J 
Published: April 2021

Abstract
To understand the evolution of developmental processes, nonmodel organisms in the nematodes, insects, and vertebrates are compared with established model systems. Often, these comparisons suffer from the inability to apply sophisticated technologies to these nonmodel species. In the nematode Pristionchus pacificus, cellular and genetic analyses are used to compare vulva development to that of Caenorhabditis elegans. However, substantial changes in gene function between P. pacificus and C. elegans limit the use of candidate gene approaches in studying P. pacificus mutations. To facilitate map-based cloning of mutations in P. pacificus, we constructed a BAC-based genetic linkage map. A BAC library of 13,440 clones was generated and completely end sequenced. By comparing BAC end and EST sequences between the “wild-type” strain P. pacificus var. California and the polymorphic strain P. pacificus var. Washington, 133 single-stranded conformational polymorphisms were identified. These markers were tested on a meiotic mapping panel of 46 randomly picked F2 animals after a cross of the two strains, providing the first genetic linkage map of P. pacificus. A mapping strategy using two selected markers per chromosome was devised and the efficiency of this approach was illustrated by the mapping of the Ppa-unc-1/Twitchin gene.
Effective Population Size and Population Subdivision in Demographically Structured Populations
Authors: Laporte Valérie , Charlesworth Brian 
Published: April 2021

Abstract
A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.
Coexistence of Bos taurus and B. indicus Mitochondrial DNAs in Nuclear Transfer-Derived Somatic Cattle Clones
Authors: Steinborn Ralf , Schinogl Pamela , Wells David N , Bergthaler Andreas , Müller Mathias , Brem Gottfried 
Published: April 2021

Abstract
We investigated the mitochondrial DNA (mtDNA) composition in one of the largest adult somatic mammalian clones (n = 20) reported so far. The healthy cloned cattle were derived from nuclear transfer of an identical nuclear genetic background (mural granulosa donor cells including surrounding cytoplasm) into enucleated oocytes with either Bos indicus or B. taurus mtDNA. Here we report the first cases of coexisting mtDNAs of two closely related subspecies following nuclear transfer. Heteroplasmy (0.6-2.8%) was found in 4 out of 11 cross-subspecies cloned cattle. Quantitation was performed using “amplification refractory mutation system (ARMS) allele-specific real-time PCR.” We determined that the ratio of donor cell to recipient cytoplast mtDNA copy number was 0.9% before nuclear transfer. Therefore, we concluded that the percentage of donor cell mtDNA in the heteroplasmic intersubspecific cloned animals is in accordance with neutral transmission of donor mtDNA. We determined an amino acid sequence divergence of up to 1.3% for the two subspecies-specific mtDNA haplotypes. In addition, intrasubspecific B. indicus heteroplasmy of ∼1% (but up to 7.3 and 12.7% in muscle and follicular cells of one animal) was detected in 7 out of the 9 B. indicus intrasubspecific cloned cattle.
A Novel Class of secA Alleles That Exert a Signal-Sequence-Dependent Effect on Protein Export in Escherichia coli
Authors: Khatib Karim , Belin Dominique 
Published: April 2021

Abstract
The murine plasminogen activator inhibitor 2 (PAI2) signal sequence inefficiently promotes the export of E. coli alkaline phosphatase (AP). High-level expression of PAI2::AP chimeric proteins from the arabinose PBAD promoter is toxic and confers an AraS phenotype. Most AraR suppressors map to secA, as determined by sequencing 21 independent alleles. Mutations occur throughout the gene, including both nucleotide binding domains (NBDI and NBDII) and the putative signal sequence binding domain (SSBD). Using malE and phoA signal sequence mutants, we showed that the vast majority of these secA suppressors exhibit weak Sec phenotypes. Eight of these secA mutations were further characterized in detail. Phenotypically, these eight suppressors can be divided into three groups, each localized to one domain of SecA. Most mutations allow near-normal levels of wild-type preprotein export, but they enhance the secretion defect conferred by signal sequence mutations. Interestingly, one group exerts a selective effect on the export of PAI2::AP when compared to that of AP. In conclusion, this novel class of secA mutations, selected as suppressors of a toxic signal sequence, differs from the classical secA (prlD) mutations, selected as suppressors of defective signal sequences, although both types of mutations affect signal sequence recognition.
A Novel System of Fertility Rescue in Drosophila Hybrids Reveals a Link Between Hybrid Lethality and Female Sterility
Authors: Barbash Daniel A , Ashburner Michael 
Published: April 2021

Abstract
Hybrid daughters of crosses between Drosophila melanogaster females and males from the D. simulans species clade are fully viable at low temperature but have agametic ovaries and are thus sterile. We report here that mutations in the D. melanogaster gene Hybrid male rescue (Hmr), along with unidentified polymorphic factors, rescue this agametic phenotype in both D. melanogaster/D. simulans and D. melanogaster/D. mauritiana F1 female hybrids. These hybrids produced small numbers of progeny in backcrosses, their low fecundity being caused by incomplete rescue of oogenesis as well as by zygotic lethality. F1 hybrid males from these crosses remained fully sterile. Hmr+ is the first Drosophila gene shown to cause hybrid female sterility. These results also suggest that, while there is some common genetic basis to hybrid lethality and female sterility in D. melanogaster, hybrid females are more sensitive to fertility defects than to lethality.
Molecular and Cytological Analyses of Large Tracks of Centromeric DNA Reveal the Structure and Evolutionary Dynamics of Maize Centromeres
Authors: Nagaki Kiyotaka , Song Junqi , Stupar Robert M , Parokonny Alexander S , Yuan Qiaoping , Ouyang Shu , Liu Jia , Hsiao Joseph , Jones Kristine M , Dawe R Kelly , Buell C Robin , Jiang Jiming 
Published: April 2021

Abstract
We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of ∼200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed ∼3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.
A GENETIC AND BIOCHEMICAL ANALYSIS OF THE TEMPERATURE SENSITIVE, NORMAL-WINGED ALLELES OF THE RUDIMENTARY LOCUS OF DROSOPHILA MELANOGASTER
Authors: Falk Darrel R , McCaughin Gary , Cogley Thomas 
Published: April 2021

ABSTRACT
The genetic and biochemical characteristics of a particular class of mutants at the rudimentary locus are described. The mutants are pyrimidine auxotrophs, like classical rudimentary alleles, but they are unique in that they do not alter the size or shape of the wing (Falk and Nash 1974b). Aspartate transcarbamylase and dihydroorotase activities have been measured in seven different normal-winged mutants, and the results indicate that these strains are enzymologically "leaky" mutants.
Previous studies have shown that three genetic functions (corresponding to the first three enzymes of pyrimidine synthesis) are associated with the rudimentary locus. Four of the seven mutants appear to affect all three of these functions. Each of the four is temperature sensitive, and a biochemical analysis of the temperature sensitivity of one of these mutants, (r)pyr1-3, suggests that a process affecting the synthesis or assembly of these enzymes is altered at high temperatures.
ON THE INTERPRETATION OF MUTAGENICALLY INDUCED MOSAICISM IN DROSOPHILA
Authors: Nissani M 
Published: April 2021

ABSTRACT
This paper draws attention to the formal parallelism that exists between chromosomal-loss mosaicism and mutagenically induced mosaicism in Drosophila and suggests that, although the underlying processes by which these two types of genetic mosaics are generated are very different, the more refined methodology employed in developmental analyses of genetically induced chromosomal-loss mosaics may be profitably extrapolated to mutagenesis studies. Results obtained from various studies of genetically induced mosaics and from a previous EMS mutation induction experiment at the yellow locus are utilized to illustrate this methodology and to estimate the total mutagenicity rates of EMS.—The following are some of the tentative conclusions that have been drawn in this report regarding an EMS concentration that produced 31% F2 lethals in the standard X-linked recessive lethal test: (1) The frequency of cuticular mosaics is at least 5 times that of F3 lethals. (2) At least 60% of all cuticular mosaics go undetected in the standard X-linked recessive lethal test since their mutant tissue does not extend into the germ line. (3) The frequency of EMS-induced cryptic mosaics is probably less than 10% the frequency of cuticular mosaics. (4) Some EMS-induced mutations are probably bona fide completes; if confirmed, this inference must be taken into consideration in estimating the total mutagenicity rates of this agent and in molecular interpretations of its mechanism of action. (5) The fact that the proportion of mutant tissue in EMS-induced mosaics is greater than 25% is consistent with the suggestion that the action of EMS is occasionally delayed until after the first cleavage division of the embryo. (6) Such an EMS concentration causes on the average more than 5 independent genetic alterations in the entire haploid genome of an X-bearing sperm.—This report clarifies the experimental evidence that must be generated, and the methodology that can be used to analyze this evidence, if it is of interest to render these and related conclusions regarding the effect of EMS on D. melanogaster more accurate, or if it is of interest to conduct a similar analysis for other mutagens that cause a significant degree of mosaicism.
GENETIC MODULATION OF RNA METABOLISM IN DROSOPHILA. II. COORDINATE RATE CHANGE IN 4S, 5S, AND POLY-A ASSOCIATED RNA SYNTHESIS
Authors: Clark Stephen H , Kiefer Barry I 
Published: April 2021

ABSTRACT
It has been demonstrated that a particular rDNA-deficient Y chromosome (YbbSuVar-5) increases the rate of ribosomal RNA synthesis in adult testes (Shermoen and Kiefer 1975) and in whole flies (Clark, Strausbaugh and Kiefer 1977). As an initial attempt to explore the molecular basis of this phenomenon, experiments were designed to determine if the rate increase was specific for rRNA as opposed to the other species of RNA. The genotypes used in these studies were car bb/Ybb-, car bb/YbbSuVar-5, and Sam+ iso. car bb/YbbSuVar-5 and car bb/Ybb- are deficient to the same extent in rDNA and Sam+ iso is a wild-type stock. Following isotope incorporation, total RNA was extracted by a phenol:chloroform method and separated by polyacrylamide gel electrophoresis. The various RNA species were quantified by UV absorption and their radioactivity determined by gel fractionation and liquid scintillation counting. The resulting data permitted the calculation of a specific activity (i.e., dpm/µg RNA) which was defined as synthetic rate. Polyadenylated RNA was isolated using a poly-U sepharose column and similar rate calculations were made. The data from these studies indicate that the rate of synthesis of all species of RNA examined (28S + 18S, 5S, 4S transfer RNA and polyadenylated RNA) is increased by the presence of the YbbSuVar-5 chromosome. Genetic and molecular mechanisms are discussed.
BEHAVIORAL MUTANTS OF DROSOPHILA MELANOGASTER. II. BEHAVIORAL ANALYSIS AND FOCUS MAPPING
Authors: Homyk Theodore 
Published: April 2021

ABSTRACT
Several simple tests have been applied to study the behavior and performance of mutants of Drosophila melanogaster isolated in the preceding study (Homyk and Sheppard 1977). The tests showed that many mutants have specific behavioral abnormalities and that most mutants can easily be distinguished from an Oregon-R control on the basis of their behavioral phenotypes. Mutants representing six genes hop poorly and are unable to initiate wing oscillation when tethered. Mutations in four genes reduce the level of spontaneous motor activity of flies and increase the excitability threshold necessary to induce high activity motor functions such as running and flying. The latter mutants are referred to as hypoactive. Another class, stress-sensitive, including mutations in three genes, are reversibly paralyzed by mechanical shock. Mosaic analyses suggest that six mutations affect muscular tissue and two others affect neural tissue. It is also shown that tan mutants fail to retract their forelegs during flight and that the focus responsible for this behavioral phenotype is the compound eye. Specific behavioral abnormalities of several mutants are discussed in conjunction with previous studies from many laboratories concerning the participation of neural, sensory and muscular elements producing behavior in normal (nonmutant) insects. Such considerations are an essential prelude to anatomical and physiological studies of the mutants in Drosophila.
GENETIC EVIDENCE OF UNUSUAL MEIOSIS IN THE DINOFLAGELLATE CRYPTHECODINIUM COHNII
Authors: Beam C A , Himes M , Himelfarb J , Link C , Shaw K 
Published: April 2021

ABSTRACT
Genetic analysis of the homothallic dinoflagellate, Crypthecodinium cohnii, using 16 nonallelic motility mutants, revealed (1) virtual absence of second division segregation and (2) independent assortment of all genes except for: (a) three cases of cross specific, "false" linkage and (b) one possible case of linkage with a high percentage of crossing over. The probability that at least two of the 16 genes studied are on one of the approximately 50 (minimal) chromosomes is extremely high and, since recombination is observed between all pairs of markers, it is highly probable that some results from crossing over. This likelihood plus the observed absence of second division segregation and the significant number of two-celled zygotic cysts support the view that the "meiosis" of C. cohnii is a one-division process.
THE RELATIONSHIPS AMONG TRANSMISSION FREQUENCY, MALE RECOMBINATION AND PROGENY PRODUCTION IN DROSOPHILA MELANOGASTER
Authors: Hiraizumi Yuichiro 
Published: April 2021

ABSTRACT
The T-007 second chromosome line, which was originally isolated in 1970 from a natural population of Drosophila melanogasterat Harlingen, south Texas, has previously been shown to be associated with several unusual genetic phenomena. In the present study, two characteristics, distorted transmission frequency and male recombination, were analyzed in relation to the progeny production of T-007 heterozygous individuals. The following points were established: (1) Distorted transmission frequency in the T-007 heterozygous male was mainly due to "elimination" of T-007 chromosomes among the progeny, while no such elimination occurred for the normal partner chromosome. (2) Transmission frequency and progeny production of the T-007 heterozygous females were normal, or at least almost normal. (3) The frequency of male recombination increased with an increasing degree of distortion. This was due to an increased number of recombinants produced per male and to a decreased number of progeny receiving the T-007 chromosome.
SEGREGATION OF CYTOPLASMIC INCOMPATIBILITY PROPERTIES IN CULEX PIPIENS FATIGANS
Authors: Subbarao Sarala K , Krishnamurthy B S , Curtis C F , Adak T , Chandrahas R K 
Published: April 2021

ABSTRACT
Maternally inherited variants, which arose within a laboratory colony of Culex pipiens fatigans, have been studied by rearing cultures from single egg rafts. Segregation, i.e., variation of cytoplasmic incompatibility properties between the male progeny of individual females, was demonstrated. Also, from the daughters of individual females, sub-lines were derived within which all the males showed the same incompatibility or compatibility properties. Among the descendants of tetracycline-treated individuals were lines which superficially simulated these phenomena, but these lines ultimately reverted to the cytoplasmic compatibility type of the strain which was submitted to the treatment. The types of variations in cytoplasmic incompatibility properties that have been studied are discussed.