bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conserved Regions of the timeless (tim) Clock Gene in Drosophila Analyzed Through Phylogenetic and Functional Studies
Authors: Ousley Andrea , Zafarullah Khaja , Chen Yifeng , Emerson Mark , Hickman Lesley , Sehgal Amita 
Published: April 2021

Abstract
Circadian (~24-hr) rhythms in Drosophila melanogaster depend upon cyclic expression of the period (per) and timeless (tim) genes, which encode interacting components of the endogenous clock. The per gene has been isolated from other insects and, more recently, a per ortholog was found in mammals where its expression oscillates in a circadian fashion. We report here the complete sequence of a tim gene from another species, Drosophila virilis. TIM is better conserved than the PER protein is between these two species (76 vs. 54% overall amino acid identity), and putative functional domains, such as the PER interaction domains and the nuclear localization signal, are highly conserved. The acidic domain and the cytoplasmic localization domain, however, are within the least conserved regions. In addition, the initiating methionine in the D. virilis gene lies downstream of the proposed translation start for the original D. melanogaster tim cDNA and corresponds to the one used by D. simulans and D. yakuba. Among the most conserved parts of TIM is a region of unknown function near the N terminus. We show here that deletion of a 32 amino acid segment within this region affects rescue of rhythms in arrhythmic tim01 flies. Flies carrying a full-length tim transgene displayed rhythms with ~24-hr periods, indicating that a fully functional clock can be restored in tim01 flies through expression of a tim transgene. Deletion of the segment mentioned above resulted in very long activity rhythms with periods ranging from 30.5 to 48 hr.
Intraspecific Variation in Symbiont Genomes: Bottlenecks and the Aphid-Buchnera Association
Authors: Funk Daniel J , Wernegreen Jennifer J , Moran Nancy A 
Published: April 2021

Abstract
Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced Ne as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced Ne at aphid and endosymbiont loci.
Fine Structure Analysis of the Yeast Centrin, Cdc31p, Identifies Residues Specific for Cell Morphology and Spindle Pole Body Duplication
Authors: Ivanovska Irena , Rose Mark D 
Published: April 2021

Abstract
Centrin/Cdc31p is a Ca2+-binding protein related to calmodulin found in the MTOC of diverse organisms. In yeast, Cdc31p localizes to the SPB where it interacts with Kar1p and is required for SPB duplication. Recent findings suggest that centrin also functions elsewhere in the cell. To dissect the functions of Cdc31p, we generated cdc31 mutations chosen only for temperature sensitivity, but otherwise unbiased as to phenotype. Three phenotypes of the cdc31 mutants, temperature sensitivity, G2/M arrest, and cell lysis, were not well correlated, indicating that the mutations may differentially affect Cdc31p's interactions with other proteins. Alleles near the C-terminal region exhibited high G2/M arrest and genetic interactions with kar1-Δ17, suggesting that this region modulates an SPB-related function. Alleles causing high lysis and reduced Kic1p kinase activity mapped to the middle of the gene, suggesting disruption of a KIC1-like function and defects in activating Kic1p. A third region conferred temperature sensitivity without affecting cell lysis or G2/M arrest, suggesting that it defines a third function. Mutations in the C-terminal region were also defective for interaction with Kic1p. Mapping the alleles onto a predicted structure of Cdc31p, we have identified surfaces likely to be important for interacting with both Kar1p and Kic1p.
Cell Polarity and Hyphal Morphogenesis Are Controlled by Multiple Rho-Protein Modules in the Filamentous Ascomycete Ashbya gossypii
Authors: Wendland J , Philippsen P 
Published: April 2021

Abstract
Polarized cell growth requires a polarized organization of the actin cytoskeleton. Small GTP-binding proteins of the Rho-family have been shown to be involved in the regulation of actin polarization as well as other processes. Hyphal growth in filamentous fungi represents an ideal model to investigate mechanisms involved in generating cell polarity and establishing polarized cell growth. Since a potential role of Rho-proteins has not been studied so far in filamentous fungi we isolated and characterized the Ashbya gossypii homologs of the Saccharomyces cerevisiae CDC42, CDC24, RHO1, and RHO3 genes. The AgCDC42 and AgCDC24 genes can both complement conditional mutations in the S. cerevisiae CDC42 and CDC24 genes and both proteins are required for the establishment of actin polarization in A. gossypii germ cells. Agrho1 mutants show a cell lysis phenotype. Null mutant strains of Agrho3 show periodic swelling of hyphal tips that is overcome by repolarization and polar hyphal growth in a manner resembling the germination pattern of spores. Thus different Rho-protein modules are required for distinct steps during polarized hyphal growth of A. gossypii.
ND9P, a Novel Protein With Armadillo-like Repeats Involved in Exocytosis: Physiological Studies Using Allelic Mutants in Paramecium
Authors: Froissard Marine , Keller Anne-Marie , Cohen Jean 
Published: April 2021

Abstract
In Paramecium, a number of mutants affected in the exocytotic membrane fusion step of the regulated secretory pathway have been obtained. Here, we report the isolation of one of the corresponding genes, ND9, previously suspected to encode a soluble protein interacting with both plasma and trichocyst membranes. Nd9p is a novel polypeptide that contains C-terminal Armadillo-like repeats. Point mutations were found in the first N-terminal quarter of the molecule and in the last putative Armadillo repeat, respectively, for the two thermosensitive mutants, nd9-1 and nd9-2. The different behaviors of these mutants in recovery experiments upon temperature shifts suggest that the N-terminal domain of the molecule may be involved in membrane binding activity, whereas the C-terminal domain is a candidate for protein-protein interactions. The nonsense nd9-3 mutation that produces a short N-terminal peptide has a dominant negative effect on the nd9-1 allele. We show here that, when overexpressed, the dominant negative effect can be produced even on the wild-type allele, suggesting competition for a common target. We suggest that Nd9p could act, like some SNARE proteins, at the membrane-cytosol interface to promote membrane fusion.
Molecular Evolution of Duplicated Amylase Gene Regions in Drosophila melanogaster: Evidence of Positive Selection in the Coding Regions and Selective Constraints in the cis-Regulatory Regions
Authors: Araki Hitoshi , Inomata Nobuyuki , Yamazaki Tsuneyuki 
Published: April 2021

Abstract
In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. Fst between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (Gst′=−0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5′ flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5′ flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster.
Molecular Identification of virilizer, a Gene Required for the Expression of the Sex-Determining Gene Sex-lethal in Drosophila melanogaster
Authors: Niessen Markus , Schneiter Roger , Nothiger Rolf 
Published: April 2021

Abstract
Sex-lethal (Sxl) is a central switch gene in somatic sexual development of Drosophila melanogaster. Female-specific expression of Sxl relies on autoregulatory splicing of Sxl pre-mRNA by SXL protein. This process requires the function of virilizer (vir). Besides its role in Sxl splicing, vir is essential for male and female viability and is also required for the production of eggs capable of embryonic development. We have identified vir molecularly and found that it produces a single transcript of 6 kb that is ubiquitously expressed in male and female embryos throughout development. This transcript encodes a nuclear protein of 210 kD that cannot be assigned to a known protein family. VIR contains a putative transmembrane domain, a coiled-coil region and PEST sequences. We have characterized five different alleles of vir. Those alleles that affect both sexes are associated with large truncations of the protein, while alleles that affect only the female-specific functions are missense mutations that lie relatively close to each other, possibly defining a region important for the regulation of Sxl.
Mutational Analysis of the Drosophila homothorax Gene
Authors: Kurant Estee , Eytan Dan , Salzberg Adi 
Published: April 2021

Abstract
The homothorax (hth) gene is involved in multiple aspects of embryonic and adult fly development. It encodes a homeodomain-containing protein of the MEIS family and was shown to regulate the subcellular localization of the homeotic protein cofactor Extradenticle (EXD). The HTH protein contains a TALE class homeodomain and a conserved MH domain, which is required for its interaction with EXD. In this work, we describe the structure of the hth locus, characterize at the molecular level a collection of mutant alleles of hth, and discuss the correlation between the identified structural defects and their consequent phenotypes. The hth locus spans more than 100 kb and contains 14 exons. Several of the exon-intron boundaries within the homeodomain and the MH domain-coding regions are conserved between Drosophila and Caenorhabditis elegans. The analysis of hth mutations demonstrates that the homeodomain of HTH is not required for nuclear localization of EXD and that the MH domain-containing first 240 residues are sufficient for nuclear localization of both EXD and HTH. Mutations that alter or delete the homeodomain cause only partial homeotic transformations in the PNS, whereas mutations affecting the MH domain cause distinct and more severe PNS phenotypes. These observations may suggest that driving nuclear localization of EXD is the main role of HTH in patterning the embryonic PNS. They may also suggest that homeodomain-defective HTH protein retains some of its transcription-regulating functions by binding DNA via its interaction with EXD.
Dual-Tagging Gene Trap of Novel Genes inDrosophila melanogaster
Authors: Lukacsovich Tamas , Asztalos Zoltan , Awano Wakae , Baba Kotaro , Kondo Shunzo , Niwa Suguri , Yamamoto Daisuke 
Published: April 2021

AbstractA gene-trap system is established for Drosophila. Unlike the conventional enhancer-trap system, the gene-trap system allows the recovery only of fly lines whose genes are inactivated by a P-element insertion, i.e., mutants. In the gene-trap system, the reporter gene expression reflects precisely the spatial and temporal expression pattern of the trapped gene. Flies in which gene trap occurred are identified by a two-step screening process using two independent markers, mini-w and Gal4, each indicating the integration of the vector downstream of the promoter of a gene (dual tagging). mini-w has its own promoter but lacks a polyadenylation signal. Therefore, mini-w mRNA is transcribed from its own promoter regardless of the vector integration site in the genome. However, the eyes of flies are not orange or red unless the vector is incorporated into a gene enabling mini-w to be spliced to a downstream exon of the host gene and polyadenylated at the 3′ end. The promoter-less Gal4 reporter is expressed as a fusion mRNA only when it is integrated downstream of the promoter of a host gene. The exons of trapped genes can be readily cloned by vectorette RT-PCR, followed by RACE and PCR using cDNA libraries. Thus, the dual-tagging gene-trap system provides a means for (i) efficient mutagenesis, (ii) unequivocal identification of genes responsible for mutant phenotypes, (iii) precise detection of expression patterns of trapped genes, and (iv) rapid cloning of trapped genes.
Comparative Analysis of the nonA Region in Drosophila Identifies a Highly Diverged 5′ Gene That May Constrain nonA Promoter Evolution
Authors: Campesan Susanna , Chalmers David , Sandrelli Federica , Megighian Aram , Peixoto Alexandre A , Costa Rodolfo , Kyriacou Charalambos P 
Published: April 2021

Abstract
A genomic fragment from Drosophila virilis that contained all the no-on-transientA (nonA) coding information, plus several kilobases of upstream material, was identified. Comparisons of nonA sequences and the gene nonA-like in D. melanogaster, a processed duplication of nonA, suggest that it arose before the split between D. melanogaster and D. virilis. In both species, another gene that lies &lt;350 bp upstream from the nonA transcription starts, and that probably corresponds to the lethal gene l(1)i19, was identified. This gene encodes a protein that shows similarities to GPI1, which is required for the biosynthesis of glycosylphosphatidylinositol (GPI), a component for anchoring eukaryotic proteins to membranes, and so we have named it dGpi1. The molecular evolution of nonA and dGpi1 sequences show remarkable differences, with the latter revealing a level of amino acid divergence that is as high as that of transformer and with extremely low levels of codon bias. Nevertheless, in D. melanogaster hosts, the D. virilis fragment rescues the lethality associated with a mutation of l(1)i19e, as well as the viability and visual defects produced by deletion of nonA–. The presence of dGpi1 sequences so close to nonA appears to have constrained the evolution of the nonA promoter.
Recombination and Spontaneous Mutation at the Major Cluster of Resistance Genes in Lettuce (Lactuca sativa)
Authors: Chin Doris B , Arroyo-Garcia Rosa , Ochoa Oswaldo E , Kesseli Rick V , Lavelle Dean O , Michelmore Richard W 
Published: April 2021

AbstractTwo sets of overlapping experiments were conducted to examine recombination and spontaneous mutation events within clusters of resistance genes in lettuce. Multiple generations were screened for recombinants using PCR-based markers flanking Dm3. The Dm3 region is not highly recombinagenic, exhibiting a recombination frequency 18-fold lower than the genome average. Recombinants were identified only rarely within the cluster of Dm3 homologs and no crossovers within genes were detected. Three populations were screened for spontaneous mutations in downy mildew resistance. Sixteen Dm mutants were identified corresponding to spontaneous mutation rates of 10–3 to 10–4 per generation for Dm1, Dm3, and Dm7. All mutants carried single locus, recessive mutations at the corresponding Dm locus. Eleven of the 12 Dm3 mutations were associated with large chromosome deletions. When recombination could be analyzed, deletion events were associated with exchange of flanking markers, consistent with unequal crossing over; however, although the number of Dm3 paralogs was changed, no novel chimeric genes were detected. One mutant was the result of a gene conversion event between Dm3 and a closely related homolog, generating a novel chimeric gene. In two families, spontaneous deletions were correlated with elevated levels of recombination. Therefore, the short-term evolution of the major cluster of resistance genes in lettuce involves several genetic mechanisms including unequal crossing over and gene conversion.
Population Admixture: Detection by Hardy-Weinberg Test and Its Quantitative Effects on Linkage-Disequilibrium Methods for Localizing Genes Underlying Complex Traits
Authors: Deng Hong-Wen , Chen Wei-Min , Recker Robert R 
Published: April 2021

Abstract
In association studies searching for genes underlying complex traits, the results are often inconsistent, and population admixture has been recognized qualitatively as one major potential cause. Hardy-Weinberg equilibrium (HWE) is often employed to test for population admixture; however, its power is generally unknown. Through analytical and simulation approaches, we quantify the power of the HWE test for population admixture and the effects of population admixture on increasing the type I error rate of association studies under various scenarios of population differentiation and admixture. We found that (1) the power of the HWE test for detecting population admixture is usually small; (2) population admixture seriously elevates type I error rate for detecting genes underlying complex traits, the extent of which depends on the degrees of population differentiation and admixture; (3) HWE testing for population admixture should be performed with random samples or only with controls at the candidate genes, or the test can be performed for combined samples of cases and controls at marker loci that are not linked to the disease; (4) testing HWE for population admixture generally reduces false positive association findings of genes underlying complex traits but the effect is small; and (5) with population admixture, a linkage disequilibrium method that employs cases only is more robust and yields many fewer false positive findings than conventional case-control analyses. Therefore, unless random samples are carefully selected from one homogeneous population, admixture is always a legitimate concern for positive findings in association studies except for the analyses that deliberately control population admixture.
Effects of pore water distributions on P-wave velocity–water saturation relations in partially saturated sandstones
Authors: Horikawa T , Katsura M , Yokota T , Nakashima S 
Published: April 2021

SUMMARY
We have developed a new method for introducing the effects of pore water distribution into the interpretation of P-wave velocity (VP) dispersion in a partially saturated rock. Pore water in an unsaturated rock is distributed as patches, and mesoscopic-scale wave-induced fluid flow (WIFF) from saturated patches to empty patches is known as a key mechanism for interpreting P-wave dispersion. Mesoscopic WIFF depends on permeability and the scale of the saturated patch, thus evaluating their influences is important for estimating the relationship between water saturation (${S_{\rm{w}}}$) and VP. The simplest and conventional law for simulating the ${S_{\rm{w}}} - {V_{{P}}}$ relation considering the mesoscopic WIFF is White's model, which describes the patch size changes proportional to the saturation. However, White's model assumes homogeneity in the size and distribution of pores, and does not consider the effects of pore water distribution in a partially saturated rock. In the rock, pore water is distributed heterogeneously according to the pore radius, causing non-linear changes in the permeability and size of the saturated patches against the water saturation. In this study, we modified White's model by introducing relative permeability and a new coefficient describing the nonlinear change of the patch size into the conventional version, and applied the modified model to better interpret our experimental ${S_{\rm{w}}} - {V_{{P}}}$ relations, which were measured by an ultrasonic technique at 200 and 500 kHz for two types of Berea sandstone samples with different permeabilities as their water saturation was decreased by evaporative drying. The relative permeabilities were determined by applying the Mualem–van Genuchten model into the capillary pressure curves from mercury intrusion porosimetry. Furthermore, we proposed a calculation method for the new coefficient using tortuosity, which corresponds to the pore water connection. The modified White's model could reproduce the experimental ${S_{\rm{w}}} - {V_{{P}}}$ relations better than other conventional models. Consequently, our modification, considering the effect of pore water distribution, would be useful for more quantitative interpretation of P-wave velocity and attenuation under coexisting multifluid conditions.
Two-dimensional meshless modelling and TE-mode inversion of magnetotelluric data
Authors: Wittke J , Tezkan B 
Published: April 2021

SUMMARY
We present a new 2-D forward modelling and inversion scheme to interpret magnetotelluric/radio-magnetotelluric data by utilizing a novel meshless forward operator. We use this discretization technique within an inverse scheme to recover conductivity structures from given magnetotelluric data. To approximate solutions of the partial differential equations that describe the magnetotelluric experiment, we discretize the subsurface only in terms of nodes. These node sets, which are simple to generate, are used to derive the differential operators’ approximations in a generalized meshless framework. First, we study and compare forward modelling calculations to an analytical and known solution from the literature. Several example calculations are given, which validate the proposed meshless forward operator. We then formulate our inverse scheme for TE-mode data, which uses only subsets of the nodal subsurface parametrization to generate conductivity structures from this given data. The inverse scheme consists of a Gauss–Newton algorithm combined with the generalized meshless framework. To validate the algorithm, we present inversion results from synthetic and field data. We compare our results to conductivity models calculated by established, well-known inversion schemes and literature results. We report that our algorithm can accurately model magnetotelluric responses and recover meaningful conductivity models, explaining given magnetotelluric data.