bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multipartite Mitochondrial Genome in the Potato Cyst Nematode Globodera pallida
Authors: Armstrong Miles R , Blok Vivian C , Phillips Mark S 
Published: April 2021

AbstractThe mitochondrial genome (mtDNA) of the plant parasitic nematode Globodera pallida exists as a population of small, circular DNAs that, taken individually, are of insufficient length to encode the typical metazoan mitochondrial gene complement. As far as we are aware, this unusual structural organization is unique among higher metazoans, although interesting comparisons can be made with the multipartite mitochondrial genome organizations of plants and fungi. The variation in frequency between populations displayed by some components of the mtDNA is likely to have major implications for the way in which mtDNA can be used in population and evolutionary genetic studies of G. pallida.
A Reexamination of Spreading of Position-Effect Variegation in the white-roughest Region of Drosophila melanogaster
Authors: Talbert Paul B , Henikoff Steven 
Published: April 2021

Abstract
In Drosophila, heterochromatin causes mosaic silencing of euchromatic genes brought next to it by chromosomal rearrangements. Silencing has been observed to “spread”: genes closer to the heterochromatic rearrangement breakpoint are silenced more frequently than genes farther away. We have examined silencing of the white and roughest genes in the variegating rearrangements In(1)wm4, In(1)wmMc, and In(1)wm51b. Eleven stocks bearing these chromosomes differ widely in the strength of silencing of white and roughest. Stock-specific differences in the relative frequencies of inactivation of white and roughest were found that map to the white-roughest region or the adjacent heterochromatin. Most stock-specific differences did not correlate with gross differences in the heterochromatic content of the rearranged chromosomes; however, two stocks, In(1)wm51b and In(1)wmMc, were found to have anomalous additional heterochromatin that may act in trans to suppress variegating alleles. In comparing different stocks, the frequency of silencing of the roughest gene, which is more distant from heterochromatin, does not correlate with the frequency of silencing of the more proximal white gene on the same chromosome, in contradiction to the expectation of models of continuous linear propagation of silencing. We frequently observed rough eye tissue that is pigmented, as though an active white gene is skipped.
Some Features of the Mutability of Bacteria During Nonlethal Selection
Authors: Godoy V G , Gizatullin F S , Fox Maurice S 
Published: April 2021

Abstract
We describe the mutability of the Trp− chromosomal +1 frameshift mutation trpE7999 during nonlethal selection, finding that the appearance of Trp+ revertants behaves similarly to that of episomal Lac+ revertants. In addition, we show that a feature of the Lac+ and Trp+ mutability is the accumulation of Trp+ and Lac+ revertants with additional unselected mutations, most of which are not due to heritable mutators. The cells undergoing nonlethal selection apparently experience an epigenetic change resulting in a subset of bacteria with elevated mutability that often remain hypermutable for the duration of selection. The epigenetic change provoked by nonlethal selection appears to be mediated by a unique function provided by the F'128 episome.
Mechanisms of Dinucleotide Repeat Instability in Escherichia coli
Authors: Bichara Marc , Pinet Isabelle , Schumacher Sylvie , Fuchs Robert P P 
Published: April 2021

Abstract
The high level of polymorphism of microsatellites has been used for a variety of purposes such as positional cloning of genes associated with diseases, forensic medicine, and phylogenetic studies. The discovery that microsatellites are associated with human diseases, not only as markers of risk but also directly in disease pathogenesis, has triggered a renewed interest in understanding the mechanism of their instability. In this work we have investigated the role of DNA replication, long patch mismatch repair, and transcription on the genetic instability of all possible combinations of dinucleotide repeats in Escherichia coli. We show that the (GpC) and (ApT) self-complementary sequence repeats are the most unstable and that the mode of replication plays an important role in their instability. We also found that long patch mismatch repair is involved in avoiding both short deletion and expansion events and also in instabilities resulting from the processing of bulges of 6 to 8 bp for the (GpT/ApC)- and (ApG/CpT)-containing repeats. For each dinucleotide sequence repeat, we propose models for instability that involve the possible participation of unusual secondary structures.
The G Protein-Coupled Receptor Gpr1 Is a Nutrient Sensor That Regulates Pseudohyphal Differentiation in Saccharomyces cerevisiae
Authors: Lorenz Michael C , Pan Xuewen , Harashima Toshiaki , Cardenas Maria E , Xue Yong , Hirsch Jeanne P , Heitman Joseph 
Published: April 2021

Abstract
Pseudohyphal differentiation in the budding yeast Saccharomyces cerevisiae is induced in diploid cells in response to nitrogen starvation and abundant fermentable carbon source. Filamentous growth requires at least two signaling pathways: the pheromone responsive MAP kinase cascade and the Gpa2p-cAMP-PKA signaling pathway. Recent studies have established a physical and functional link between the Gα protein Gpa2 and the G protein-coupled receptor homolog Gpr1. We report here that the Gpr1 receptor is required for filamentous and haploid invasive growth and regulates expression of the cell surface flocculin Flo11. Epistasis analysis supports a model in which the Gpr1 receptor regulates pseudohyphal growth via the Gpa2p-cAMP-PKA pathway and independently of both the MAP kinase cascade and the PKA related kinase Sch9. Genetic and physiological studies indicate that the Gpr1 receptor is activated by glucose and other structurally related sugars. Because expression of the GPR1 gene is known to be induced by nitrogen starvation, the Gpr1 receptor may serve as a dual sensor of abundant carbon source (sugar ligand) and nitrogen starvation. In summary, our studies reveal a novel G protein-coupled receptor senses nutrients and regulates the dimorphic transition to filamentous growth via a Gα protein-cAMP-PKA signal transduction cascade.
Nested Cladistic Analysis Indicates Population Fragmentation Shapes Genetic Diversity in a Freshwater Mussel
Authors: Turner Thomas F , Trexler Joel C , Harris John L , Haynes Jody L 
Published: April 2021

Abstract
Recently developed phylogeographic analyses that incorporate genealogical relationships of alleles offer the exciting prospect of disentangling historical from contemporary events. However, the relative advantages and shortfalls of this approach remain to be studied. We compared the nested cladistic method to the more traditional analysis of variance approach in a study of intraspecific genetic variation in the freshwater mussel, Lampsilis hydiana. We surveyed 257 specimens for nucleotide sequence level variation in a fragment of the mitochondrial 16S rRNA gene. When compared side by side, nested cladistic analysis and analysis of molecular variance (AMOVA) identified fragmentation of Arkansas river populations from remaining populations to the southwest. Nested cladistic analysis identified a second, more recent separation of Ouachita and Upper Saline river populations that was not detected by AMOVA. Differences among analytical methods probably arise from treatment of spatial hierarchical information: hierarchical groups emerge via a parsimony criterion in nested cladistic analysis but must be specified a priori in AMOVA. Both methods identified significant genetic structure among localities within hierarchical groups. Results from AMOVA suggested little gene flow among local populations with an island model. However, inferences about process that gave rise to patterns at this level were not possible in nested cladistic analysis, because an ancestral (interior) haplotype was not observed for a key one-step clade in the parsimony network. Our results suggest that, under some circumstances, nested cladistic analysis has lower power than more traditional analysis of variance to infer processes at the local population level.
Isolation and Characterization of par1+ and par2+: Two Schizosaccharomyces pombe Genes Encoding B′ Subunits of Protein Phosphatase 2A
Authors: Jiang Wei , Hallberg Richard L 
Published: April 2021

Abstract
Protein phosphatase 2A (PP2A) is one of the major serine/threonine phosphatases found in eukaryotic cells. We cloned two genes, par1+ and par2+, encoding distinct B′ subunits of PP2A in fission yeast. They share 52% identity at the amino acid sequence level. Neither gene is essential but together they are required for normal septum positioning and cytokinesis, for growth at both high and low temperature, and for growth under a number of stressful conditions. Immunofluorescence microscopy revealed that Par2p has a cell-cycle-related localization pattern, being localized at cell ends during interphase and forming a medial ring in cells that are undergoing septation and cytokinesis. Our analyses also indicate that Par1p is more abundant than Par2p in the cell. Cross-organism studies showed that both par1+ and par2+ could complement the rts1Δ allele in Saccharomyces cerevisiae, albeit to different extents, in spite of the fact that neither contains a serine/threonine-rich N-terminal domain like that found in the S. cerevisiae homolog Rts1p. Thus, while Schizosaccharomyces pombe is more similar to higher eukaryotes with respect to its complement of B′-encoding genes, the function of those proteins is conserved relative to that of Rts1p.
Effect of a Neuropeptide Gene on Behavioral States in Caenorhabditis elegans Egg-Laying
Authors: Waggoner Laura E , Hardaker Laura Anne , Golik Steven , Schafer William R 
Published: April 2021

Abstract
Egg-laying behavior in the nematode Caenorhabditis elegans involves fluctuation between alternative behavioral states: an inactive state, during which eggs are retained in the uterus, and an active state, during which eggs are laid in bursts. We have found that the flp-1 gene, which encodes a group of structurally related neuropeptides, functions specifically to promote the switch from the inactive to the active egg-laying state. Recessive mutations in flp-1 caused a significant increase in the duration of the inactive phase, yet egg-laying within the active phase was normal. This pattern resembled that previously observed in mutants defective in the biosynthesis of serotonin, a neuromodulator implicated in induction of the active phase. Although flp-1 mutants were sensitive to stimulation of egg-laying by serotonin, the magnitude of their serotonin response was abnormally low. Thus, the flp-1-encoded peptides and serotonin function most likely function in concert to facilitate the onset of the active egg-laying phase. Interestingly, we observed that flp-1 is necessary for animals to down-regulate their rate of egg-laying in the absence of food. Because flp-1 is known to be expressed in interneurons that are postsynaptic to a variety of chemosensory cells, the FLP-1 peptides may function to regulate the activity of the egg-laying circuitry in response to sensory cues.
A Recombination Repair Gene of Schizosaccharomyces pombe, rhp57, Is a Functional Homolog of the Saccharomyces cerevisiae RAD57 Gene and Is Phylogenetically Related to the Human XRCC3 Gene
Authors: Tsutsui Yasuhiro , Morishita Takashi , Iwasaki Hiroshi , Toh Hiroyuki , Shinagawa Hideo 
Published: April 2021

Abstract
To identify Schizosaccharomyces pombe genes involved in recombination repair, we identified seven mutants that were hypersensitive to both methyl methanesulfonate (MMS) and γ-rays and that contained mutations that caused synthetic lethality when combined with a rad2 mutation. One of the mutants was used to clone the corresponding gene from a genomic library by complementation of the MMS-sensitive phenotype. The gene obtained encodes a protein of 354 amino acids whose sequence is 32% identical to that of the Rad57 protein of Saccharomyces cerevisiae. An rhp57 (RAD57 homolog of S. pombe) deletion strain was more sensitive to MMS, UV, and γ-rays than the wild-type strain and showed a reduction in the frequency of mitotic homologous recombination. The MMS sensitivity was more severe at lower temperature and was suppressed by the presence of a multicopy plasmid bearing the rhp51 gene. An rhp51 rhp57 double mutant was as sensitive to UV and γ-rays as an rhp51 single mutant, indicating that rhp51 function is epistatic to that of rhp57. These characteristics of the rhp57 mutants are very similar to those of S. cerevisiae rad57 mutants. Phylogenetic analysis suggests that Rhp57 and Rad57 are evolutionarily closest to human Xrcc3 of the RecA/Rad51 family of proteins.
The Fission Yeast git5 Gene Encodes a Gβ Subunit Required for Glucose-Triggered Adenylate Cyclase Activation
Authors: Landry Sheila , Pettit Maria T , Apolinario Ethel , Hoffman Charles S 
Published: April 2021

Abstract
Fission yeast adenylate cyclase is activated by the gpa2 Gα subunit of a heterotrimeric guanine-nucleotide binding protein (G protein). We show that the git5 gene, also required for this activation, encodes a Gβ subunit. In contrast to another study, we show that git5 is not a negative regulator of the gpa1 Gα involved in the pheromone response pathway. While 43% identical to mammalian Gβ's, the git5 protein lacks the amino-terminal coiled-coil found in other Gβ subunits, yet the gene possesses some of the coding capacity for this structure 5′ to its ORF. Although both gpa2 (Gα) and git5 (Gβ) are required for adenylate cyclase activation, only gpa2 is needed to maintain basal cAMP levels. Strains bearing a git5 disruption are derepressed for fbp1 transcription and sexual development even while growing in a glucose-rich environment, although fbp1 derepression is half that observed in gpa2 deletion strains. Multicopy gpa2 partially suppresses the loss of git5, while the converse is not true. These data suggest that Gβ is required for activation of adenylate cyclase either by promoting the activation of Gα or by independently activating adenylate cyclase subsequent to Gα stimulation as seen in type II mammalian adenylate cyclase activation.
The End of the LINE?: Lack of Recent L1 Activity in a Group of South American Rodents
Authors: Casavant N Carol , Scott LuAnn , Cantrell Michael A , Wiggins Lara E , Baker Robert J , Wichman Holly A 
Published: April 2021

Abstract
L1s (LINE-1: Long Interspersed Nuclear Element 1) are present in all mammals examined to date. They occur in both placental mammals and marsupials and thus are thought to have been present in the genome prior to the mammalian radiation. This unusual conservation of a transposable element family for over 100 million years has led to speculation that these elements provide an advantage to the genomes they inhabit. We have recently identified a group of South American rodents, including rice rats (Oryzomys), in which L1s appear to be quiescent or extinct. Several observations support this conclusion. First, genomic Southern blot analysis fails to reveal genus-specific bands in Oryzomys. Second, we were unable to find recently inserted elements. Procedures to enrich for young elements did not yield any with an intact open reading frame for reverse transcriptase; all elements isolated had numerous insertions, deletions, and stop codons. Phylogenetic analysis failed to yield species-specific clusters among the L1 elements isolated, and all Oryzomys sequences had numerous private mutations. Finally, in situ hybridization of L1 to Oryzomys chromosomes failed to reveal the characteristic L1 distribution in Oryzomys with either a homologous or heterologous probe. Thus, Oryzomys is a viable candidate for L1 extinction from a mammalian host.
Regulatory Elements Required for Development of Caenorhabditis elegans Hermaphrodites Are Conserved in the tra-2 Homologue of C. remanei, a Male/Female Sister Species
Authors: Haag Eric S , Kimble Judith 
Published: April 2021

Abstract
The Caenorhabditis elegans hermaphrodite is essentially a female that produces sperm. In C. elegans, tra-2 promotes female fates and must be repressed to achieve hermaphrodite spermatogenesis. In an effort to learn how mating systems evolve, we have cloned tra-2 from C. remanei, the closest gonochoristic relative of C. elegans. We found its structure to be similar to that of Ce-tra-2 but its sequence to be divergent. RNA interference demonstrates that Cr-tra-2 promotes female fates. Two sites of tra-2 regulation are required for the onset of hermaphrodite spermatogenesis in C. elegans. One, the MX region of TRA-2, is as well conserved in C. remanei as it is in C. briggsae (another male/hermaphrodite species), suggesting that this control is not unique to hermaphrodites. Another, the DRE/TGE element of the tra-2 3′ UTR, was not detected by sequence analysis. However, gel-shift assays demonstrate that a factor in C. remanei can bind specifically to the Cr-tra-2 3′ UTR, suggesting that this translational control is also conserved. We propose that both controls are general and do not constitute a novel “switch” that enables sexual mosaicism in hermaphrodites. However, subtle quantitative or qualitative differences in their employment may underlie differences in mating system seen in Caenorhabditis.
The Drosophila fl(2)d Gene, Required for Female-Specific Splicing of Sxl and tra Pre-mRNAs, Encodes a Novel Nuclear Protein With a HQ-Rich Domain
Authors: Penalva Luiz O F , Ruiz M Fernanda , Ortega Angeles , Granadino Begoña , Vicente Luis , Segarra Carmen , Valcárcel Juán , Sánchez Lucas 
Published: April 2021

Abstract
The Drosophila gene female-lethal(2)d [fl(2)d] interacts genetically with the master regulatory gene for sex determination, Sex-lethal. Both genes are required for the activation of female-specific patterns of alternative splicing on transformer and Sex-lethal pre-mRNAs. We have used P-element-mediated mutagenesis to identify the fl(2)d gene. The fl(2)d transcription unit generates two alternatively spliced mRNAs that can encode two protein isoforms differing at their amino terminus. The larger isoform contains a domain rich in histidine and glutamine but has no significant homology to proteins in databases. Several lines of evidence indicate that this protein is responsible for fl(2)d function. First, the P-element insertion that inactivates fl(2)d interrupts this ORF. Second, amino acid changes within this ORF have been identified in fl(2)d mutants, and the nature of the changes correlates with the severity of the mutations. Third, all of the phenotypes associated with fl(2)d mutations can be rescued by expression of this cDNA in transgenic flies. Fl(2)d protein can be detected in extracts from Drosophila cell lines, embryos, larvae, and adult animals, without apparent differences between sexes, as well as in adult ovaries. Consistent with a possible function in posttranscriptional regulation, Fl(2)d protein has nuclear localization and is enriched in nuclear extracts.
Quantitative Trait Loci Mapping in F2 Crosses Between Outbred Lines
Authors: Pérez-Enciso Miguel , Varona Luis 
Published: April 2021

Abstract
We develop a mixed-model approach for QTL analysis in crosses between outbred lines that allows for QTL segregation within lines as well as for differences in mean QTL effects between lines. We also propose a method called “segment mapping” that is based in partitioning the genome in a series of segments. The expected change in mean according to percentage of breed origin, together with the genetic variance associated with each segment, is estimated using maximum likelihood. The method also allows the estimation of differences in additive variances between the parental lines. Completely fixed random and mixed models together with segment mapping are compared via simulation. The segment mapping and mixed-model behaviors are similar to those of classical methods, either the fixed or random models, under simple genetic models (a single QTL with alternative alleles fixed in each line), whereas they provide less biased estimates and have higher power than fixed or random models in more complex situations, i.e., when the QTL are segregating within the parental lines. The segment mapping approach is particularly useful to determining which chromosome regions are likely to contain QTL when these are linked.
Heterochromatin Protein 1 Is Required for the Normal Expression of Two Heterochromatin Genes in Drosophila
Authors: Lu Brett Y , Emtage Peter C R , Duyf Brenda J , Hilliker Arthur J , Eissenberg Joel C 
Published: April 2021

Abstract
The Su(var)2-5 locus, an essential gene in Drosophila, encodes the heterochromatin-associated protein HP1. Here, we show that the Su(var)2-5 lethal period is late third instar. Maternal HP1 is still detectable in first instar larvae, but disappears by third instar, suggesting that developmentally late lethality is probably the result of depletion of maternal protein. We demonstrate that heterochromatic silencing of a normally euchromatic reporter gene is completely lost by third instar in zygotically HP1 mutant larvae, implying a defect in heterochromatin-mediated transcriptional regulation in these larvae. However, expression of the essential heterochromatic genes rolled and light is reduced in Su(var)2-5 mutant larvae, suggesting that reduced expression of essential heterochromatic genes could underlie the recessive lethality of Su(var)2-5 mutations. These results also show that HP1, initially recognized as a transcriptional silencer, is required for the normal transcriptional activation of heterochromatic genes.
Selective Genotyping With Epistasis Can Be Utilized for a Major Quantitative Trait Locus Mapping in Hypertension in Rats
Authors: Ohno Yoichi , Tanase Hisao , Nabika Toru , Otsuka Keiichi , Sasaki Takayuki , Suzawa Taichi , Morii Toshiyuki , Yamori Yukio , Saruta Takao 
Published: April 2021

Abstract
Epistasis used to be considered an obstacle in mapping quantitative trait loci (QTL) despite its significance. Numerous epistases have proved to be involved in quantitative genetics. We established a backcross model that demonstrates a major QTL for hypertension (Ht). Seventy-eight backcrossed rats (BC), derived from spontaneously hypertensive rats (SHR) and normotensive Fischer 344 rats, showed bimodal distribution of systolic blood pressure (BP) values and a phenotypic segregation ratio consistent with 1:1. In this backcross analysis, sarco(endo)plasmic reticulum Ca2+-dependent ATPase (Serca) II heterozygotes showed widespread bimodality in frequency distribution of BP values and obviously demonstrated Ht. First, in genome-wide screening, Mapmaker/QTL analysis mapped Ht at a locus between D1Mgh8 and D1Mit4 near Sa in all 78 BC. The peak logarithm of the odds (LOD) score reached 5.3. Second, Serca II heterozygous and homozygous BC were analyzed separately using Mapmaker/QTL. In the 35 Serca II heterozygous BC, the peak LOD score was 3.8 at the same locus whereas it did not reach statistical significance in the 43 Serca II homozygotes. Third, to map Ht efficiently, we selected 18 Serca II heterozygous BC with 9 highest and 9 lowest BP values. In these 18 BC, the peak LOD score reached 8.1. In 17 of the 18, D1Mgh8 genotypes (homo or hetero) qualitatively cosegregated with BP phenotypes (high or low) (P &lt; 0.0001, by chi-square analysis). In conclusion, selective genotyping with epistasis can be utilized for a major QTL mapping near Sa on chromosome 1 in SHR.