bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific Genetic Interference With Behavioral Rhythms in Drosophila by Expression of Inverted Repeats
Authors: Martinek Sebastian , Young Michael W 
Published: April 2021

Abstract
We describe a new experimental technique that allows for a tissue-specific reduction of gene activity in the Drosophila nervous system. On the basis of the observation that certain gene functions can be ubiquitously blocked by injecting double-stranded RNA into Drosophila embryos, we employed a method to interfere with an individual gene function permanently in a predetermined cell type. This was achieved by the formation of an inverted-repeat RNA sequence in the tissue of interest under control of the GAL4/UAS binary expression system. As an example, we show that inverted-repeat-mediated interference with the period gene produces a hypomorphic period phenotype. A selective decrease of period RNA appears to be a component of the cellular response.
Extragenic Bypass Suppressors of Mutations in the Essential Gene BLD2 Promote Assembly of Basal Bodies With Abnormal Microtubules in Chlamydomonas reinhardtii
Authors: Preble Andrea M , Giddings Thomas H , Dutcher Susan K 
Published: April 2021

Abstract
bld2-1 mutant Chlamydomonas reinhardtii strains assemble basal bodies with singlet microtubules; bld2-1 cells display flagellar assembly defects as well as positioning defects of the mitotic spindle and cleavage furrow. To further understand the role of the BLD2 gene, we have isolated three new bld2 alleles and three partially dominant extragenic suppressors, rgn1-1, rgn1-2, and rgn1-3. bld2 rgn1-1 strains have phenotypes intermediate between those of bld2 and wild-type strains with respect to flagellar number, microtubule rootlet organization, cleavage furrow positioning, and basal body structural phenotypes. Instead of the triplet microtubules of wild-type cells, bld2 rgn1-1 basal bodies have mixtures of no, singlet, doublet, and triplet microtubules. The bld2-4 allele was made by insertional mutagenesis and identified in a noncomplementation screen in a diploid strain. The bld2-4 allele has a lethal phenotype based on mitotic segregation in diploid strains and in haploid strains generated by meiotic recombination. The lethal phenotype in haploid strains is suppressed by rgn1-1; these suppressed strains have similar phenotypes to other bld2 rgn1-1 double mutants. It is likely that BLD2 is an essential gene that is needed for basal body assembly and function.
An STE12 Homolog From the Asexual, Dimorphic Fungus Penicillium marneffei Complements the Defect in Sexual Development of an Aspergillus nidulans steA Mutant
Authors: Borneman Anthony R , Hynes Michael J , Andrianopoulos Alex 
Published: April 2021

Abstract
Penicillium marneffei is an opportunistic fungal pathogen of humans and the only dimorphic species identified in its genus. At 25° P. marneffei exhibits true filamentous growth, while at 37° P. marneffei undergoes a dimorphic transition to produce uninucleate yeast cells that divide by fission. Members of the STE12 family of regulators are involved in controlling mating and yeast-hyphal transitions in a number of fungi. We have cloned a homolog of the S. cerevisiae STE12 gene from P. marneffei, stlA, which is highly conserved. The stlA gene, along with the A. nidulans steA and Cryptococcus neoformans STE12α genes, form a distinct subclass of STE12 homologs that have a C2H2 zinc-finger motif in addition to the homeobox domain that defines STE12 genes. To examine the function of stlA in P. marneffei, we isolated a number of mutants in the P. marneffei-type strain and, in combination with selectable markers, developed a highly efficient DNA-mediated transformation procedure and gene deletion strategy. Deletion of the stlA gene had no detectable effect on vegetative growth, asexual development, or dimorphic switching in P. marneffei. Despite the lack of a detectable function, the P. marneffei stlA gene complemented the sexual defect of an A. nidulans steA mutant. In addition, substitution rate estimates indicate that there is a significant bias against nonsynonymous substitutions. These data suggest that P. marneffei may have a previously unidentified cryptic sexual cycle.
Integration of the Aedes aegypti Mosquito Genetic Linkage and Physical Maps
Authors: Brown S E , Severson D W , Smith L A , Knudson D L 
Published: April 2021

Abstract
Two approaches were used to correlate the Aedes aegypti genetic linkage map to the physical map. STS markers were developed for previously mapped RFLP-based genetic markers so that large genomic clones from cosmid libraries could be found and placed to the metaphase chromosome physical maps using standard FISH methods. Eight cosmids were identified that contained eight RFLP marker sequences, and these cosmids were located on the metaphase chromosomes. Twenty-one cDNAs were mapped directly to metaphase chromosomes using a FISH amplification procedure. The chromosome numbering schemes of the genetic linkage and physical maps corresponded directly and the orientations of the genetic linkage maps for chromosomes 2 and 3 were inverted relative to the physical maps. While the chromosome 2 linkage map represented essentially 100% of chromosome 2, ∼65% of the chromosome 1 linkage map mapped to only 36% of the short p-arm and 83% of the chromosome 3 physical map contained the complete genetic linkage map. Since the genetic linkage map is a RFLP cDNA-based map, these data also provide a minimal estimate for the size of the euchromatic regions. The implications of these findings on positional cloning in A. aegypti are discussed.
Overexpression of Translation Elongation Factor 1A Affects the Organization and Function of the Actin Cytoskeleton in Yeast
Authors: Munshi Raj , Kandl Kimberly A , Carr-Schmid Anne , Whitacre Johanna L , Adams Alison E M , Kinzy Terri Goss 
Published: April 2021

Abstract
The translation elongation factor 1 complex (eEF1) plays a central role in protein synthesis, delivering aminoacyl-tRNAs to the elongating ribosome. The eEF1A subunit, a classic G-protein, also performs roles aside from protein synthesis. The overexpression of either eEF1A or eEF1Bα, the catalytic subunit of the guanine nucleotide exchange factor, in Saccharomyces cerevisiae results in effects on cell growth. Here we demonstrate that overexpression of either factor does not affect the levels of the other subunit or the rate or accuracy of protein synthesis. Instead, the major effects in vivo appear to be at the level of cell morphology and budding. eEF1A overexpression results in dosage-dependent reduced budding and altered actin distribution and cellular morphology. In addition, the effects of excess eEF1A in actin mutant strains show synthetic growth defects, establishing a genetic connection between the two proteins. As the ability of eEF1A to bind and bundle actin is conserved in yeast, these results link the established ability of eEF1A to bind and bundle actin in vitro with nontranslational roles for the protein in vivo.
Functional Contacts With a Range of Splicing Proteins Suggest a Central Role for Brr2p in the Dynamic Control of the Order of Events in Spliceosomes of Saccharomyces cerevisiae
Authors: van Nues Rob W , Beggs Jean D 
Published: April 2021

Abstract
Mapping of functional protein interactions will help in understanding conformational rearrangements that occur within large complexes like spliceosomes. Because the U5 snRNP plays a central role in pre-mRNA splicing, we undertook exhaustive two-hybrid screening with Brr2p, Prp8p, and other U5 snRNP-associated proteins. DExH-box protein Brr2p interacted specifically with five splicing factors: Prp8p, DEAH-box protein Prp16p, U1 snRNP protein Snp1p, second-step factor Slu7p, and U4/U6.U5 tri-snRNP protein Snu66p, which is required for splicing at low temperatures. Co-immunoprecipitation experiments confirmed direct or indirect interactions of Prp16p, Prp8p, Snu66p, and Snp1p with Brr2p and led us to propose that Brr2p mediates the recruitment of Prp16p to the spliceosome. We provide evidence that the prp8-1 allele disrupts an interaction with Brr2p, and we propose that Prp8p modulates U4/U6 snRNA duplex unwinding through another interaction with Brr2p. The interactions of Brr2p with a wide range of proteins suggest a particular function for the C-terminal half, bringing forward the hypothesis that, apart from U4/U6 duplex unwinding, Brr2p promotes other RNA rearrangements, acting synergistically with other spliceosomal proteins, including the structurally related Prp2p and Prp16p. Overall, these protein interaction studies shed light on how splicing factors regulate the order of events in the large spliceosome complex.
Statistical Approaches to Paternity Analysis in Natural Populations and Applications to the North Atlantic Humpback Whale
Authors: Nielsen Rasmus , Mattila David K , Clapham Philip J , Palsbøll Per J 
Published: April 2021

Abstract
We present a new method for paternity analysis in natural populations that is based on genotypic data that can take the sampling fraction of putative parents into account. The method allows paternity assignment to be performed in a decision theoretic framework. Simulations are performed to evaluate the utility and robustness of the method and to assess how many loci are necessary for reliable paternity inference. In addition we present a method for testing hypotheses regarding relative reproductive success of different ecologically or behaviorally defined groups as well as a new method for estimating the current population size of males from genotypic data. This method is an extension of the fractional paternity method to the case where only a proportion of all putative fathers have been sampled. It can also be applied to provide abundance estimates of the number of breeding males from genetic data. Throughout, the methods were applied to genotypic data collected from North Atlantic humpback whales (Megaptera novaeangliae) to test if the males that appear dominant during the mating season have a higher reproductive success than the subdominant males.
Fidelity of Mitotic Double-Strand-Break Repair in Saccharomyces cerevisiae: A Role for SAE2/COM1
Authors: Rattray Alison J , McGill Carolyn B , Shafer Brenda K , Strathern Jeffrey N 
Published: April 2021

Abstract
Errors associated with the repair of DNA double-strand breaks (DSBs) include point mutations caused by misincorporation during repair DNA synthesis or novel junctions made by nonhomologous end joining (NHEJ). We previously demonstrated that DNA synthesis is ∼100-fold more error prone when associated with DSB repair. Here we describe a genetic screen for mutants that affect the fidelity of DSB repair. The substrate consists of inverted repeats of the trp1 and CAN1 genes. Recombinational repair of a site-specific DSB within the repeat yields TRP1 recombinants. Errors in the repair process can be detected by the production of canavanine-resistant (can1) mutants among the TRP1 recombinants. In wild-type cells the recombinational repair process is efficient and fairly accurate. Errors resulting in can1 mutations occur in &lt;1% of the TRP1 recombinants and most appear to be point mutations. We isolated several mutant strains with altered fidelity of recombination. Here we characterize one of these mutants that revealed an ∼10-fold elevation in the frequency of can1 mutants among TRP1 recombinants. The gene was cloned by complementation of a coincident sporulation defect and proved to be an allele of SAE2/COM1. Physical analysis of the can1 mutants from sae2/com1 strains revealed that many were a novel class of chromosome rearrangement that could reflect break-induced replication (BIR) and NHEJ. Strains with either the mre11s-H125N or rad50s-K81I alleles had phenotypes in this assay that are similar to that of the sae2/com1Δ strain. Our data suggest that Sae2p/Com1p plays a role in ensuring that both ends of a DSB participate in a recombination event, thus avoiding BIR, possibly by regulating the nuclease activity of the Mre11p/Rad50p/Xrs2p complex.
Partitioning of N-Ethylmaleimide-Sensitive Fusion (NSF) Protein Function in Drosophila melanogaster: dNSF1 Is Required in the Nervous System, and dNSF2 Is Required in Mesoderm
Authors: Golby Jessica A , Tolar Leigh Anna , Pallanck Leo 
Published: April 2021

Abstract
The N-ethylmaleimide-sensitive fusion protein (NSF) promotes the fusion of secretory vesicles with target membranes in both regulated and constitutive secretion. While it is thought that a single NSF may perform this function in many eukaryotes, previous work has shown that the Drosophila genome contains two distinct NSF genes, dNSF1 and dNSF2, raising the possibility that each plays a specific secretory role. To explore this possibility, we generated mutations in the dNSF2 gene and used these and novel dNSF1 loss-of-function mutations to analyze the temporal and spatial requirements and the degree of functional redundancy between dNSF1 and dNSF2. Results of this analysis indicate that dNSF1 function is required in the nervous system beginning at the adult stage of development and that dNSF2 function is required in mesoderm beginning at the first instar larval stage of development. Additional evidence suggests that dNSF1 and dNSF2 may play redundant roles during embryonic development and in the larval nervous system. Ectopic expression studies demonstrate that the dNSF1 and dNSF2 gene products can functionally substitute for one another. These results indicate that the Drosophila NSF proteins exhibit similar functional properties, but have evolved distinct tissue-specific roles.
Characterization of the S-Locus Region of Almond (Prunus dulcis): Analysis of a Somaclonal Mutant and a Cosmid Contig for an S Haplotype
Authors: Ushijima Koichiro , Sassa Hidenori , Tamura Mihoko , Kusaba Makoto , Tao Ryutaro , Gradziel Thomas M , Dandekar Abhaya M , Hirano Hisashi 
Published: April 2021

Abstract
Almond has a self-incompatibility system that is controlled by an S locus consisting of the S-RNase gene and an unidentified “pollen S gene.” An almond cultivar “Jeffries,” a somaclonal mutant of “Nonpareil” (ScSd), has a dysfunctional Sc haplotype both in pistil and pollen. Immunoblot and genomic Southern blot analyses detected no Sc haplotype-specific signal in Jeffries. Southern blot showed that Jeffries has an extra copy of the Sd haplotype. These results indicate that at least two mutations had occurred to generate Jeffries: (1) deletion of the Sc haplotype and (2) duplication of the Sd haplotype. To analyze the extent of the deletion in Jeffries and gain insight into the physical limit of the S locus region, ∼200 kbp of a cosmid contig for the Sc haplotype was constructed. Genomic Southern blot analyses showed that the deletion in Jeffries extends beyond the region covered by the contig. Most cosmid end probes, except those near the Sc-RNase gene, cross-hybridized with DNA fragments from different S haplotypes. This suggests that regions away from the Sc-RNase gene can recombine between different S haplotypes, implying that the cosmid contig extends to the borders of the S locus.
Comparative Gene Expression Profiles Following UV Exposure in Wild-Type and SOS-Deficient Escherichia coli
Authors: Courcelle Justin , Khodursky Arkady , Peter Brian , Brown Patrick O , Hanawalt Philip C 
Published: April 2021

Abstract
The SOS response in UV-irradiated Escherichia coli includes the upregulation of several dozen genes that are negatively regulated by the LexA repressor. Using DNA microarrays containing amplified DNA fragments from 95.5% of all open reading frames identified on the E. coli chromosome, we have examined the changes in gene expression following UV exposure in both wild-type cells and lexA1 mutants, which are unable to induce genes under LexA control. We report here the time courses of expression of the genes surrounding the 26 documented lexA-regulated regions on the E. coli chromosome. We observed 17 additional sites that responded in a lexA-dependent manner and a large number of genes that were upregulated in a lexA-independent manner although upregulation in this manner was generally not more than twofold. In addition, several transcripts were either downregulated or degraded following UV irradiation. These newly identified UV-responsive genes are discussed with respect to their possible roles in cellular recovery following exposure to UV irradiation.
Dissecting the Genetic Pathway to Extreme Fruit Size in Tomato Using a Cross Between the Small-Fruited Wild SpeciesLycopersicon pimpinellifoliumandL. esculentumvar. Giant Heirloom
Authors: Lippman Zachary , Tanksley Steven D 
Published: April 2021

AbstractIn an effort to determine the genetic basis of exceptionally large tomato fruits, QTL analysis was performed on a population derived from a cross between the wild species Lycopersicon pimpinellifolium (average fruit weight, 1 g) and the L. esculentum cultivar var. Giant Heirloom, which bears fruit in excess of 1000 g. QTL analysis revealed that the majority (67%) of phenotypic variation in fruit size could be attributed to six major loci localized on chromosomes 1-3 and 11. None of the QTL map to novel regions of the genome—all have been reported in previous studies involving moderately sized tomatoes. This result suggests that no major QTL beyond those already reported were involved in the evolution of extremely large fruit. However, this is the first time that all six QTL have emerged in a single population, suggesting that exceptionally large-fruited varieties, such as Giant Heirloom, are the result of a novel combination of preexisting QTL alleles. One of the detected QTL, fw2.2, has been cloned and exerts its effect on fruit size through global control of cell division early in carpel/fruit development. However, the most significant QTL detected in this study (fw11.3, lcn11.1) maps to the bottom of chromosome 11 and seems to exert its effect on fruit size through control of carpel/locule number. A second major locus, also affecting carpel number (and hence fruit size), was mapped to chromosome 2 (fw2.1, lcn2.1). We propose that these two carpel number QTL correspond to the loci described by early classical geneticists as fasciated (f) and locule number (lc), respectively.
Detection of Closely Linked Multiple Quantitative Trait Loci Using a Genetic Algorithm
Authors: Nakamichi Reiichiro , Ukai Yasuo , Kishino Hirohisa 
Published: April 2021

Abstract
The existence of a quantitative trait locus (QTL) is usually tested using the likelihood of the quantitative trait on the basis of phenotypic character data plus the recombination fraction between QTL and flanking markers. When doing this, the likelihood is calculated for all possible locations on the linkage map. When multiple QTL are suspected close by, it is impractical to calculate the likelihood for all possible combinations of numbers and locations of QTL. Here, we propose a genetic algorithm (GA) for the heuristic solution of this problem. GA can globally search the optimum by improving the “genotype” with alterations called “recombination” and “mutation.” The “genotype” of our GA is the number and location of QTL. The “fitness” is a function based on the likelihood plus Akaike’s information criterion (AIC), which helps avoid false-positive QTL. A simulation study comparing the new method with existing QTL mapping packages shows the advantage of the new GA. The GA reliably distinguishes multiple QTL located in a single marker interval.
A Frameshift Mutation in MC1R and a High Frequency of Somatic Reversions Cause Black Spotting in Pigs
Authors: Kijas J M H , Moller M , Plastow G , Andersson L 
Published: April 2021

Abstract
Black spotting on a red or white background in pigs is determined by the EP allele at the MC1R/Extension locus. A previous comparison of partial MC1R sequences revealed that EP shares a missense mutation (D121N) with the ED2 allele for dominant black color. Sequence analysis of the entire coding region now reveals a second mutation in the form of a 2-bp insertion at codon 23 (nt67insCC). This mutation expands a tract of six C nucleotides to eight and introduces a premature stop codon at position 56. This frameshift mutation is expected to cause a recessive red color, which was in fact observed in some breeds with the EP allele present (Tamworth and Hereford). RT-PCR analyses were conducted using skin samples taken from both spotted and background areas of spotted pigs. The background red area had transcript only from the mutant nt67insCC MC1R allele, whereas the black spot also contained a transcript without the 2-bp insertion. This indicates that black spots are due to somatic reversion events that restore the frame and MC1R function. The phenotypic expression of the EP allele is highly variable and the associated coat color ranges from red, red with black spots, white with black spots, to almost completely solid black. In several breeds of pigs the phenotypic manifestation of this allele has been modified by selection for or against black spots.
Estimating the Time to the Most Recent Common Ancestor for the Y chromosome or Mitochondrial DNA for a Pair of Individuals
Authors: Walsh Bruce 
Published: April 2021

Abstract
Bayesian posterior distributions are obtained for the time to the most recent common ancestor (MRCA) for a nonrecombining segment of DNA (such as the nonpseudoautosomal arm of the Y chromosome or the mitochondrial genome) for two individuals given that they match at k out of n scored markers. We argue that the distribution of the time t to the MRCA is the most natural measure of relatedness for such nonrecombining regions. Both an infinite-alleles (no recurring mutants) and stepwise mutation model are examined, and these agree well when n is moderate to large and k/n is close to one. As expected, the infinite alleles model underestimates t relative to the stepwise model. Using a modest number (20) of microsatellite markers is sufficient to obtain reasonably precise estimates of t for individuals separated by 200 or less generations. Hence, the multilocus haplotypes of two individuals can be used not only to date very deep ancestry but also rather recent ancestry as well. Finally, our results have forensic implications in that a complete match at all markers between a suspect and a sample excludes only a modest subset of the population unless a very large number of markers (&gt;500 microsatellites) are used.
Multiple Signaling Mechanisms of the UNC-6/netrin Receptors UNC-5 and UNC-40/DCC in Vivo
Authors: Merz David C , Zheng Hong , Killeen Marie T , Krizus Aldis , Culotti Joseph G 
Published: April 2021

Abstract
Cell and growth cone migrations along the dorsoventral axis of Caenorhabditis elegans are mediated by the UNC-5 and UNC-40 receptor subtypes for the secreted UNC-6 guidance cue. To characterize UNC-6 receptor function in vivo, we have examined genetic interactions between unc-5 and unc-40 in the migrations of the hermaphrodite distal tip cells. We report that cell migration defects as severe as those associated with a null mutation in unc-6 are produced only by null mutations in both unc-5 and unc-40, indicating that either receptor retains some partial function in the absence of the other. We show that hypomorphic unc-5 alleles exhibit two distinct types of interallelic genetic interactions. In an unc-40 wild-type genetic background, some pairs of hypomorphic unc-5 alleles exhibit a partial allelic complementation. In an unc-40 null background, however, we observed that unc-5 hypomorphs exhibit dominant negative effects. We propose that the UNC-5 and UNC-40 netrin receptors can function to mediate chemorepulsion in DTC migrations either independently or together, and the observed genetic interactions suggest that this flexibility in modes of signaling results from the formation of a variety of oligomeric receptor complexes.