bluuebunny/crossref_metadata_2025 huggingface dataset:
Rap1p Requires Gcr1p and Gcr2p Homodimers to Activate Ribosomal Protein and Glycolytic Genes, Respectively
Authors: Deminoff Stephen J , Santangelo George M
Published: April 2021

Efficient transcription of ribosomal protein (RP) and glycolytic genes requires the Rap1p/Gcr1p regulatory complex. A third factor, Gcr2p, is required for only the glycolytic (specialized) mode of transcriptional activation. It is recruited to the complex by Gcr1p and likely mediates a change in the phosphorylation state and/or conformation of the latter. We show here that leucine zipper motifs in Gcr1p and Gcr2p (1LZ and 2LZ) are each specific to one of the two activation mechanisms—mutations in 1LZ and 2LZ impair transcription of RP and glycolytic genes, respectively. Although neither class of mutations causes more than a mild growth defect, simultaneous impairment of 1LZ and 2LZ results in a severe synthetic defect and a reduction in the expression of both sets of genes. Intracistronic complementation by point mutations in the charged e and g positions confirmed that Gcr1p/Gcr1p and Gcr2p/Gcr2p homodimers are the forms required for the different roles of the activator complex. Direct heterodimerization between 1LZ and 2LZ apparently does not occur. Dichotomous Rap1p activation and its striking requirement for distinct homodimeric subunits give cells the capacity to switch between coordinated and uncoupled RP and glycolytic gene regulation.
Identification of a Mutant DNA Polymerase δ in Saccharomyces cerevisiae With an Antimutator Phenotype for Frameshift Mutations
Authors: Hadjimarcou Michalis I , Kokoska Robert J , Petes Thomas D , Reha-Krantz Linda J
Published: April 2021

We propose that a β-turn-β structure, which plays a critical role in exonucleolytic proofreading in the bacteriophage T4 DNA polymerase, is also present in the Saccharomyces cerevisiae DNA pol δ. Site-directed mutagenesis was used to test this proposal by introducing a mutation into the yeast POL3 gene in the region that encodes the putative β-turn-β structure. The mutant DNA pol δ has a serine substitution in place of glycine at position 447. DNA replication fidelity of the G447S-DNA pol δ was determined in vivo by using reversion and forward assays. An antimutator phenotype for frameshift mutations in short homopolymeric tracts was observed for the G447S-DNA pol δ in the absence of postreplication mismatch repair, which was produced by inactivation of the MSH2 gene. Because the G447S substitution reduced frameshift but not base substitution mutagenesis, some aspect of DNA polymerase proofreading appears to contribute to production of frameshifts. Possible roles of DNA polymerase proofreading in frameshift mutagenesis are discussed.
Many Genomic Regions Are Required for Normal Embryonic Programmed Cell Death in Caenorhabditis elegans
Authors: Sugimoto Asako , Kusano Ayumi , Hozak Rebecca R , Derry W Brent , Zhu Jiangwen , Rothman Joel H
Published: April 2021

To identify genes involved in programmed cell death (PCD) in Caenorhabditis elegans, we screened a comprehensive set of chromosomal deficiencies for alterations in the pattern of PCD throughout embryonic development. From a set of 58 deficiencies, which collectively remove ∼74% of the genome, four distinct classes were identified. In class I (20 deficiencies), no significant deviation from wild type in the temporal pattern of cell corpses was observed, indicating that much of the genome does not contain zygotic genes that perform conspicuous roles in embryonic PCD. The class II deficiencies (16 deficiencies defining at least 11 distinct genomic regions) led to no or fewer-than-normal cell corpses. Some of these cause premature cell division arrest, probably explaining the diminution in cell corpse number; however, others have little effect on cell proliferation, indicating that the reduced cell corpse number is not a direct result of premature embryonic arrest. In class III (18 deficiencies defining at least 16 unique regions), an excess of cell corpses was observed. The developmental stage at which the extra corpses were observed varied among the class III deficiencies, suggesting the existence of genes that perform temporal-specific functions in PCD. The four deficiencies in class IV (defining at least three unique regions), showed unusually large corpses that were, in some cases, attributable to extremely premature arrest in cell division without a concomitant block in PCD. Deficiencies in this last class suggest that the cell death program does not require normal embryonic cell proliferation to be activated and suggest that while some genes required for cell division might also be required for cell death, others are not. Most of the regions identified by these deficiencies do not contain previously identified zygotic cell death genes. There are, therefore, a substantial number of as yet unidentified genes required for normal PCD in C. elegans.
Rpm2, the Protein Subunit of Mitochondrial RNase P in Saccharomyces cerevisiae, Also Has a Role in the Translation of Mitochondrially Encoded Subunits of Cytochrome c Oxidase
Authors: Stribinskis Vilius , Gao Guo-Jian , Ellis Steven R , Martin Nancy C
Published: April 2021

RPM2 is a Saccharomyces cerevisiae nuclear gene that encodes the protein subunit of mitochondrial RNase P and has an unknown function essential for fermentative growth. Cells lacking mitochondrial RNase P cannot respire and accumulate lesions in their mitochondrial DNA. The effects of a new RPM2 allele, rpm2-100, reveal a novel function of RPM2 in mitochondrial biogenesis. Cells with rpm2-100 as their only source of Rpm2p have correctly processed mitochondrial tRNAs but are still respiratory deficient. Mitochondrial mRNA and rRNA levels are reduced in rpm2-100 cells compared to wild type. The general reduction in mRNA is not reflected in a similar reduction in mitochondrial protein synthesis. Incorporation of labeled precursors into mitochondrially encoded Atp6, Atp8, Atp9, and Cytb protein was enhanced in the mutant relative to wild type, while incorporation into Cox1p, Cox2p, Cox3p, and Var1p was reduced. Pulse-chase analysis of mitochondrial translation revealed decreased rates of translation of COX1, COX2, and COX3 mRNAs. This decrease leads to low steady-state levels of Cox1p, Cox2p, and Cox3p, loss of visible spectra of aa3 cytochromes, and low cytochrome c oxidase activity in mutant mitochondria. Thus, RPM2 has a previously unrecognized role in mitochondrial biogenesis, in addition to its role as a subunit of mitochondrial RNase P. Moreover, there is a synthetic lethal interaction between the disruption of this novel respiratory function and the loss of wild-type mtDNA. This synthetic interaction explains why a complete deletion of RPM2 is lethal.
Conserved Vertebrate Chromosome Segments in the Large Salamander Genome
Authors: Voss S Randal , Smith Jeramiah J , Gardiner David M , Parichy David M
Published: April 2021

Urodele amphibians (salamanders) are important models for embryological, physiological, and natural history research and are also a biomedically important group because they are the only vertebrates capable of regenerating entire organ systems. To enhance the utility of salamanders for biomedical research and for understanding genome evolution, genetic linkage analysis was used to identify chromosome segments that are homologous between ambystomatid salamanders and distantly related vertebrate model organisms. A total of 347 loci (AFLPs, RAPDs, and protein-coding loci) were mapped using an interspecific meiotic mapping panel (Ambystoma mexicanum and A. tigrinum tigrinum; family Ambystomatidae). Genome size in Ambystoma was estimated to be 7291 cM, the largest linkage map estimate reported for any organism. However, the relatively large size of the salamander genome did not hinder efforts to map and identify conserved syntenies from a small sample of 24 protein-coding loci. Chromosomal segments that are conserved between fishes and mammals are also conserved in these salamanders. Thus, comparative gene mapping appears to be an efficient strategy for identifying orthologous loci between ambystomatid salamanders and genomically well-characterized vertebrate model organisms.
Tc8, a Tourist-like Transposon in Caenorhabditis elegans
Authors: Le Quang Hien , Turcotte Kime , Bureau Thomas
Published: April 2021

Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.
Genetic Analysis of Endocytosis in Caenorhabditis elegans: Coelomocyte Uptake Defective Mutants
Authors: Fares Hanna , Greenwald Iva
Published: April 2021

The coelomocytes of Caenorhabditis elegans are scavenger cells that continuously and nonspecifically endocytose fluid from the pseudocoelom (body cavity). Green fluorescent protein (GFP) secreted into the pseudocoelom from body wall muscle cells is endocytosed and degraded by coelomocytes. We show that toxin-mediated ablation of coelomocytes results in viable animals that fail to endocytose pseudocoelomic GFP, indicating that endocytosis by coelomocytes is not essential for growth or survival of C. elegans under normal laboratory conditions. We examined known viable endocytosis mutants, and performed RNAi for other known endocytosis genes, for coelomocyte uptake defective (Cup) phenotypes. We also screened for new genes involved in endocytosis by isolating viable mutants with Cup defects; this screen identified 14 different genes, many with multiple alleles. A variety of Cup terminal phenotypes were observed, consistent with defects at various steps in the endocytic pathway. Available molecular information indicates that the Cup mutant screen has identified novel components of the endocytosis machinery that are conserved in mammals but not in Saccharomyces cerevisiae, the only other organism for which large-scale genetic screens for endocytosis mutants have been performed.
Drosophila Immunity: Genes on the Third Chromosome Required for the Response to Bacterial Infection
Authors: Wu Louisa P , Choe Kwang-Min , Lu Yiran , Anderson Kathryn V
Published: April 2021

We have screened the third chromosome of Drosophila melanogaster for mutations that prevent the normal immune response. We identified mutant lines on the basis of their failure to induce transcription of an antibacterial peptide gene in response to infection or their failure to form melanized clots at the site of wounding. These mutations define 14 genes [immune response deficient (ird) genes] that have distinct roles in the immune response. We have identified the molecular basis of several ird phenotypes. Two genes, scribble and kurtz/modulo, affect the cellular organization of the fat body, the tissue responsible for antimicrobial peptide production. Two ird genes encode components of the signaling pathways that mediate responses to bacterial infection, a Drosophila gene encoding a homolog of IκB kinase (DmIkkβ) and Relish, a Rel-family transcription factor. These genetic studies should provide a basis for a comprehensive understanding of the genetic control of immune responses in Drosophila.
Quantitative Trait Locus Analysis in Crosses Between Outbred Lines With Dominance and Inbreeding
Authors: Pérez-Enciso Miguel , Fernando Rohan L , Bidanel Jean-Pierre , Le Roy Pascale
Published: April 2021

We provide a theoretical framework for quantitative trait locus (QTL) analysis of a crossed population where parental lines may be outbred and dominance as well as inbreeding are allowed for. It can be applied to any pedigree. A biallelic QTL is assumed, and the QTL allele frequencies can be different in each breed. The genetic covariance between any two individuals is expressed as a nonlinear function of the probability of up to 15 possible identity modes and of the additive and dominance effects, together with the allelic frequencies in each of the two parental breeds. The probabilities of each identity mode are obtained at the desired genome positions using a Monte Carlo Markov chain method. Unbiased estimates of the actual genetic parameters are recovered in a simulated F2 cross and in a six-generation complex pedigree under a variety of genetic models (allele fixed or segregating in the parental populations and additive or dominance action). Results from analyzing an F2 cross between Meishan and Large White pigs are also presented.
Are the Dominant and Recessive Plant Disease Resistance Genes Similar?: A Case Study of Rice R Genes and Xanthomonas oryzae pv. oryzae Races
Authors: Li Zhi-Kang , Sanchez Alma , Angeles E , Singh Sukhwider , Domingo Jessica , Huang Ning , Khush Gurdev S
Published: April 2021

The resistance of rice to its bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) has both qualitative and quantitative components that were investigated using three near-isogenic line sets for four resistance (R) genes (Xa4, xa5, xa13, and Xa21) and 12 Xoo races. Our results indicate that these two resistance components of rice plants were associated with the properties of the R genes. The qualitative component of the R genes was reflected by their large effects against corresponding avirulent Xoo races. The quantitative component of the R genes was their residual effects against corresponding virulent races and their epistatic effects, which together could lead to high-level resistance in a race-specific manner. Our results revealed important differences between the different types of R genes. Two R genes, Xa4 and Xa21, showed complete dominance against the avirulent Xoo races and had large residual effects against virulent ones. They acted independently and cumulatively, suggesting they are involved in different pathways of the rice defensive system. The third R gene, xa5, showed partial dominance or additivity to the avirulent Xoo races and had relatively small but significant residual effects against the virulent races. In contrast, xa13 was completely recessive, had no residual effects against the virulent races, and showed more pronounced race specificity. There was a strong interaction leading to increased resistance between xa13 and xa5 and between either of them and Xa4 or Xa21, suggesting their regulatory roles in the rice defensive pathway(s). Our results indicated that high-level and durable resistance to Xoo should be more efficiently achieved by pyramiding different types of R genes.
Overactivation of the Protein Kinase C-Signaling Pathway Suppresses the Defects of Cells Lacking the Rho3/Rho4-GAP Rgd1p in Saccharomyces cerevisiae
Authors: de Bettignies Geoffroy , Thoraval Didier , Morel Carine , Peypouquet Marie France , Crouzet Marc
Published: April 2021

The nonessential RGD1 gene encodes a Rho-GTPase activating protein for the Rho3 and Rho4 proteins in Saccharomyces cerevisiae. Previous studies have revealed genetic interactions between RGD1 and the SLG1 and MID2 genes, encoding two putative sensors for cell integrity signaling, and VRP1 encoding an actin and myosin interacting protein involved in polarized growth. To better understand the role of Rgd1p, we isolated multicopy suppressor genes of the cell lethality of the double mutant rgd1Δ mid2Δ. RHO1 and RHO2 encoding two small GTPases, MKK1 encoding one of the MAP-kinase kinases in the protein kinase C (PKC) pathway, and MTL1, a MID2-homolog, were shown to suppress the rgd1Δ defects strengthening the functional links between RGD1 and the cell integrity pathway. Study of the transcriptional activity of Rlm1p, which is under the control of Mpk1p, the last kinase of the PKC pathway, and follow-up of the PST1 transcription, which is positively regulated by Rlm1p, indicate that the lack of RGD1 function diminishes the PKC pathway activity. We hypothesize that the rgd1Δ inactivation, at least through the hyperactivation of the small GTPases Rho3p and Rho4p, alters the secretory pathway and/or the actin cytoskeleton and decreases activity of the PKC pathway.
Sit4p Protein Phosphatase Is Required for Sensitivity of Saccharomyces cerevisiae to Kluyveromyces lactis Zymocin
Authors: Jablonowski Daniel , Butler Andrew R , Fichtner Lars , Gardiner Donald , Schaffrath Raffael , Stark Michael J R
Published: April 2021

We have identified two Saccharomyces cerevisiae genes that, in high copy, confer resistance to Kluyveromyces lactis zymocin, an inhibitor that blocks cells in the G1 phase of the cell cycle prior to budding and DNA replication. One gene (GRX3) encodes a glutaredoxin and is likely to act at the level of zymocin entry into sensitive cells, while the other encodes Sap155p, one of a family of four related proteins that function positively and interdependently with the Sit4p protein phosphatase. Increased SAP155 dosage protects cells by influencing the sensitivity of the intracellular target and is unique among the four SAP genes in conferring zymocin resistance in high copy, but is antagonized by high-copy SAP185 or SAP190. Since cells lacking SIT4 or deleted for both SAP185 and SAP190 are also zymocin resistant, our data support a model whereby high-copy SAP155 promotes resistance by competition with the endogenous levels of SAP185 and SAP190 expression. Zymocin sensitivity therefore requires a Sap185p/Sap190p-dependent function of Sit4p protein phosphatase. Mutations affecting the RNA polymerase II Elongator complex also confer K. lactis zymocin resistance. Since sit4Δ and SAP-deficient strains share in common several other phenotypes associated with Elongator mutants, Elongator function may be a Sit4p-dependent process.
The N Terminus of Saccharomyces cerevisiae Sst2p Plays an RGS-Domain-Independent, Mpt5p-Dependent Role in Recovery From Pheromone Arrest
Authors: Xu Bing-E , Skowronek Karlheinz R , Kurjan Janet
Published: April 2021

The Saccharomyces cerevisiae RGS protein Sst2p is involved in desensitization to pheromone and acts as a GTPase-activating protein for the Gα subunit Gpa1p. Other results indicate that Sst2p acts through Mpt5p and that this action occurs downstream of Fus3p and through Cln3p/Cdc28p. Our results indicate that the interaction of Sst2p with Mpt5p requires the N-terminal MPI (Mpt5p-interacting) domain of Sst2p and is independent of the C-terminal RGS domain. Overexpression of the MPI domain results in an Mpt5p-dependent increase in recovery from pheromone arrest. Overexpression of either intact Sst2p or the MPI domain leads to partial suppression of a gpa1 growth defect, and this suppression is dependent on Mpt5p, indicating that MPI function occurs downstream of Gpa1p and through Mpt5p. Combination of an mpt5 mutation with the GPA1G302S mutation, which uncouples Gpa1p from Sst2p, results in pheromone supersensitivity similar to the sst2 mutant, and promotion of recovery by overexpression of Sst2p is dependent on both Mpt5p and the Gpa1p interaction. These results indicate that Sst2p is a bifunctional protein and that the MPI domain acts through Mpt5p independently of the RGS domain. RGS family members from other fungi contain N-terminal domains with sequence similarity to the Sst2p MPI domain, suggesting that MPI function may be conserved.
Multiple Mechanisms for Degradation of Bacteriophage T4 soc mRNA
Authors: Kai Toshie , Yonesaki Tetsuro
Published: April 2021

The dmd gene of bacteriophage T4 is required for regulation of mRNA stability in a stage-dependent manner during infection. When this gene is mutated, late genes are globally silenced because of rapid degradation of mRNAs. To investigate the mechanism of such mRNA degradation, we analyzed the late gene soc transcripts. The degradation of soc mRNA was remarkably stabilized when its ability to be translated was impaired; either disruption of translation initiation signals or elimination of termination codons was effective in stabilization of soc mRNA and removal of elongation modestly stabilized it. Even in the absence of translation, however, the residual activity was still significant. These results suggested that the degradation of soc transcripts was promoted by two different mechanisms; one is dependent on translation and the other independent of translation. We found several cleavages introduced into soc RNA specifically when the dmd gene was mutated; some of them could be linked to polypeptide chain elongation and termination, suggesting the correlation with ribosomal action, and the others were independent of translation.
A Haplolethal Locus Uncovered by Deletions in the Mouse t Complex
Authors: Browning Victoria L , Bergstrom Rebecca A , Daigle Sandra , Schimenti John C
Published: April 2021

Proper levels of gene expression are important for normal mammalian development. Typically, altered gene dosage caused by karyotypic abnormalities results in embryonic lethality or birth defects. Segmental aneuploidy can be compatible with life but often results in contiguous gene syndromes. The ability to manipulate the mouse genome allows the systematic exploration of regions that are affected by alterations in gene dosage. To explore the effects of segmental haploidy in the mouse t complex on chromosome 17, radiation-induced deletion complexes centered at the Sod2 and D17Leh94 loci were generated in embryonic stem (ES) cells. A small interval was identified that, when hemizygous, caused specific embryonic lethal phenotypes (exencephaly and edema) in most fetuses. The penetrance of these phenotypes was background dependent. Additionally, evidence for parent-of-origin effects was observed. This genetic approach should be useful for identifying genes that are imprinted or whose dosage is critical for normal embryonic development.
A Misexpression Study Examining Dorsal Thorax Formation in Drosophila melanogaster
Authors: Peña-Rangel María Teresa , Rodriguez Isabel , Riesgo-Escovar Juan Rafael
Published: April 2021

We studied thorax formation in Drosophila melanogaster using a misexpression screen with EP lines and thoracic Gal4 drivers that provide a genetically sensitized background. We identified 191 interacting lines showing alterations of thoracic bristles (number and/or location), thorax and scutellum malformations, lethality, or suppression of the thoracic phenotype used in the screen. We analyzed these lines and showed that known genes with different functional roles (selector, prepattern, proneural, cell cycle regulation, lineage restriction, signaling pathways, transcriptional control, and chromatin organization) are among the modifier lines. A few lines have previously been identified in thorax formation, but others, such as chromatin-remodeling complex genes, are novel. However, most of the interacting loci are uncharacterized, providing a wealth of new genetic data. We also describe one such novel line, poco pelo (ppo), where both misexpression and loss-of-function phenotypes are similar: loss of bristles and scutellum malformation.
A Novel Selection System for Chromosome Translocations in Saccharomyces cerevisiae
Authors: Tennyson Rachel B , Ebran Nathalie , Herrera Anissa E , Lindsley Janet E
Published: April 2021

Chromosomal translocations are common genetic abnormalities found in both leukemias and solid tumors. While much has been learned about the effects of specific translocations on cell proliferation, much less is known about what causes these chromosome rearrangements. This article describes the development and use of a system that genetically selects for rare translocation events using the yeast Saccharomyces cerevisiae. A translocation YAC was created that contains the breakpoint cluster region from the human MLL gene, a gene frequently involved in translocations in leukemia patients, flanked by positive and negative selection markers. A translocation between the YAC and a yeast chromosome, whose breakpoint falls within the MLL DNA, physically separates the markers and forms the basis for the selection. When RAD52 is deleted, essentially all of the selected and screened cells contain simple translocations. The detectable translocation rates are the same in haploids and diploids, although the mechanisms involved and true translocation rates may be distinct. A unique double-strand break induced within the MLL sequences increases the number of detectable translocation events 100- to 1000-fold. This novel system provides a tractable assay for answering basic mechanistic questions about the development of chromosomal translocations.
Genetic Analysis of Drosophila melanogaster Polytene Chromosome Region 44D–45F: Loci Required for Viability and Fertility
Authors: Mohr Stephanie E , Boswell Robert E
Published: April 2021

A genetic screen to identify mutations in genes in the 45A region on the right arm of chromosome 2 that are involved in oogenesis in Drosophila was undertaken. Several lethal but no female sterile mutations in the region had previously been identified in screens for P-element insertion or utilizing X rays or EMS as a mutagen. Here we report the identification of EMS-induced mutations in 21 essential loci in the 45D–45F region, including 13 previously unidentified loci. In addition, we isolated three mutant alleles of a newly identified locus required for fertility, sine prole. Mutations in sine prole disrupt spermatogenesis at or before individualization of spermatozoa and cause multiple defects in oogenesis, including inappropriate division of the germline cyst and arrest of oogenesis at stage 4.
The Genetic Architecture of Drosophila Sensory Bristle Number
Authors: Dilda Christy L , Mackay Trudy F C
Published: April 2021

We have mapped quantitative trait loci (QTL) for Drosophila mechanosensory bristle number in six recombinant isogenic line (RIL) mapping populations, each of which was derived from an isogenic chromosome extracted from a line selected for high or low, sternopleural or abdominal bristle number and an isogenic wild-type chromosome. All RILs were evaluated as male and female F1 progeny of crosses to both the selected and the wild-type parental chromosomes at three developmental temperatures (18°, 25°, and 28°). QTL for bristle number were mapped separately for each chromosome, trait, and environment by linkage to roo transposable element marker loci, using composite interval mapping. A total of 53 QTL were detected, of which 33 affected sternopleural bristle number, 31 affected abdominal bristle number, and 11 affected both traits. The effects of most QTL were conditional on sex (27%), temperature (14%), or both sex and temperature (30%). Epistatic interactions between QTL were also common. While many QTL mapped to the same location as candidate bristle development loci, several QTL regions did not encompass obvious candidate genes. These features are germane to evolutionary models for the maintenance of genetic variation for quantitative traits, but complicate efforts to understand the molecular genetic basis of variation for complex traits.
lingerer, a Drosophila Gene Involved in Initiation and Termination of Copulation, Encodes a Set of Novel Cytoplasmic Proteins
Authors: Kuniyoshi Hisato , Baba Kotaro , Ueda Ryu , Kondo Shunzo , Awano Wakae , Juni Naoto , Yamamoto Daisuke
Published: April 2021

In an effort to uncover genetic components underlying the courtship behavior of Drosophila melanogaster, we have characterized a novel gene, lingerer (lig), mutations of which result in abnormal copulation. Males carrying a hypomorphic mutation in lig fail to withdraw their genitalia upon termination of copulation, but display no overt abnormalities in their genitalia. A severe reduction in the dosage of the lig gene causes repeated attempted copulations but no successful copulations. Complete loss of lig function results in lethality during early pupal stages. lig is localized to polytene segment 44A on the second chromosome and encodes three alternatively spliced transcripts that generate two types of 150-kD proteins, Lig-A and Lig-B, differing only at the C terminus. Lig proteins show no similarity to known proteins. However, a set of homologous proteins in mammals suggest that Drosophila Lig belongs to a family of proteins that share five highly conserved domains. Lig is a cytoplasmic protein expressed in the central nervous system (CNS), imaginal discs, and gonads. Lig-A expression is selectively reduced in lig mutants and the ubiquitous supply of this protein at the beginning of metamorphosis restores the copulatory defects of the lig mutant. We propose that lig may act in the nervous system to mediate the control of copulatory organs during courtship.
Cellular Differentiation in Response to Nutrient Availability: The Repressor of Meiosis, Rme1p, Positively Regulates Invasive Growth in Saccharomyces cerevisiae
Authors: van Dyk Dewald , Hansson Guy , Pretorius Isak S , Bauer Florian F
Published: April 2021

In the yeast Saccharomyces cerevisiae, the transition from a nutrient-rich to a nutrient-limited growth medium typically leads to the implementation of a cellular adaptation program that results in invasive growth and/or the formation of pseudohyphae. Complete depletion of essential nutrients, on the other hand, leads either to entry into a nonbudding, metabolically quiescent state referred to as G0 in haploid strains or to meiosis and sporulation in diploids. Entry into meiosis is repressed by the transcriptional regulator Rme1p, a zinc-finger-containing DNA-binding protein. In this article, we show that Rme1p positively regulates invasive growth and starch metabolism in both haploid and diploid strains by directly modifying the transcription of the FLO11 (also known as MUC1) and STA2 genes, which encode a cell wall-associated protein essential for invasive growth and a starch-degrading glucoamylase, respectively. Genetic evidence suggests that Rme1p functions independently of identified signaling modules that regulate invasive growth and of other transcription factors that regulate FLO11 and that the activation of FLO11 is dependent on the presence of a promoter sequence that shows significant homology to identified Rme1p response elements (RREs). The data suggest that Rme1p functions as a central switch between different cellular differentiation pathways.
Patterns of Selection Against Transposons Inferred From the Distribution of Tc1, Tc3 and Tc5 Insertions in the mut-7 Line of the Nematode Caenorhabditis elegans
Authors: Rizzon Carène , Martin Edwige , Marais Gabriel , Duret Laurent , Ségalat Laurent , Biémont Christian
Published: April 2021

To identify the factors (selective or mutational) that affect the distribution of transposable elements (TEs) within a genome, it is necessary to compare the pattern of newly arising element insertions to the pattern of element insertions that have been fixed in a population. To do this, we analyzed the distribution of recent mutant insertions of the Tc1, Tc3, and Tc5 elements in a mut-7 background of the nematode Caenorhabditis elegans and compared it to the distribution of element insertions (presumably fixed) within the sequenced genome. Tc1 elements preferentially insert in regions with high recombination rates, whereas Tc3 and Tc5 do not. Although Tc1 and Tc3 both insert in TA dinucleotides, there is no clear relationship between the frequency of insertions and the TA dinucleotide density. There is a strong selection against TE insertions within coding regions: the probability that a TE will be fixed is at least 31 times lower in coding regions than in noncoding regions. Contrary to the prediction of theoretical models, we found that the selective pressure against TE insertions does not increase with the recombination rate. These findings indicate that the distribution of these three transposon families in the genome of C. elegans is determined essentially by just two factors: the pattern of insertions, which is a characteristic of each family, and the selection against insertions within coding regions.
Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda
Authors: Bachtrog Doris
Published: April 2021

The neo-sex chromosomes of Drosophila miranda constitute an ideal system to study the effects of recombination on patterns of genome evolution. Due to a fusion of an autosome with the Y chromosome, one homolog is transmitted clonally. Here, I compare patterns of molecular evolution of 18 protein-coding genes located on the recombining neo-X and their homologs on the nonrecombining neo-Y chromosome. The rate of protein evolution has significantly increased on the neo-Y lineage since its formation. Amino acid substitutions are accumulating uniformly among neo-Y-linked genes, as expected if all loci on the neo-Y chromosome suffer from a reduced effectiveness of natural selection. In contrast, there is significant heterogeneity in the rate of protein evolution among neo-X-linked genes, with most loci being under strong purifying selection and two genes showing evidence for adaptive evolution. This observation agrees with theory predicting that linkage limits adaptive protein evolution. Both the neo-X and the neo-Y chromosome show an excess of unpreferred codon substitutions over preferred ones and no difference in this pattern was observed between the chromosomes. This suggests that there has been little or no selection maintaining codon bias in the D. miranda lineage. A change in mutational bias toward AT substitutions also contributes to the decline in codon bias. The contrast in patterns of molecular evolution between amino acid mutations and synonymous mutations on the neo-sex-linked genes can be understood in terms of chromosome-specific differences in effective population size and the distribution of selective effects of mutations.
Genetic Modifiers of Tauopathy in Drosophila
Authors: Shulman Joshua M , Feany Mel B
Published: April 2021

In Alzheimer's disease and related disorders, the microtubule-associated protein Tau is abnormally hyperphosphorylated and aggregated into neurofibrillary tangles. Mutations in the tau gene cause familial frontotemporal dementia. To investigate the molecular mechanisms responsible for Tau-induced neurodegeneration, we conducted a genetic modifier screen in a Drosophila model of tauopathy. Kinases and phosphatases comprised the major class of modifiers recovered, and several candidate Tau kinases were similarly shown to enhance Tau toxicity in vivo. Despite some clinical and pathological similarities among neurodegenerative disorders, a direct comparison of modifiers between different Drosophila disease models revealed that the genetic pathways controlling Tau and polyglutamine toxicity are largely distinct. Our results demonstrate that kinases and phosphatases control Tau-induced neurodegeneration and have important implications for the development of therapies in Alzheimer's disease and related disorders.
Partial Diploidization of Meiosis in Autotetraploid Arabidopsis thaliana
Authors: Santos J L , Alfaro D , Sanchez-Moran E , Armstrong S J , Franklin F C H , Jones G H
Published: April 2021

Meiosis was analyzed cytogenetically in autotetraploids of Arabidopsis, including both established lines and newly generated autotetraploid plants. Fluorescent in situ hybridization with 5S and 45S rDNA probes was used to identify the different chromosomes at metaphase I of meiosis. Multivalents were observed frequently in all the lines analyzed, but there were significant differences in multivalent frequency not only between the newly generated tetraploids and the established lines but also among the different established lines. The new tetraploids showed high multivalent frequencies, exceeding the theoretical 66.66% predicted by the simple random-end pairing model, in some cases significantly, thus indicating that Arabidopsis autotetraploids have more than two autonomous pairing sites per chromosome, despite their small sizes. The established lines showed fewer multivalents than the new autotetraploids did, but the extent of this reduction was strongly line and chromosome dependent. One line in particular showed a large reduction in multivalents and a concomitant increase in bivalents, while the other lines showed lesser reductions in multivalents. The reduction in multivalents was not uniformly distributed across chromosomes. The smaller chromosomes, especially chromosomes 2 and 4, showed the most marked reductions while the largest chromosome (1) showed virtually no reduction compared to the new tetraploids. It is concluded that the established autotetraploid lines have undergone a partial diploidization of meiosis, but not necessarily genetical diploidization, since their creation. Possible mechanisms for the resulting change in meiotic chromosome behavior are discussed.
Preclinical Testing of Vaccines and Therapeutics for Gonorrhea in Female Mouse Models of Lower and Upper Reproductive Tract Infection
Authors: Connolly Kristie L , Pilligua-Lucas Michelle , Gomez Carolina , Costenoble-Caherty Allison C , Soc Anthony , Underwood Knashka , Macintyre Andrew N , Sempowski Gregory D , Jerse Ann E
Published: April 2021

Murine models of Neisseria gonorrhoeae lower reproductive tract infection are valuable systems for studying N. gonorrhoeae adaptation to the female host and immune responses to infection. These models have also accelerated preclinical testing of candidate therapeutic and prophylactic products against gonorrhea. However, because N. gonorrhoeae infection is restricted to the murine cervicovaginal region, there is a need for an in vivo system for translational work on N. gonorrhoeae pelvic inflammatory disease (PID). Here we discuss the need for well-characterized preclinical upper reproductive tract infection models for developing candidate products against N. gonorrhoeae PID, and report a refinement of the gonorrhea mouse model that supports sustained upper reproductive tract infection. To establish this new model for vaccine testing, we also tested the licensed meningococcal 4CMenB vaccine, which cross-protects against murine N. gonorrhoeae lower reproductive tract infection, for efficacy against N. gonorrhoeae in the endometrium and oviducts following transcervical or vaginal challenge.
Evaluating resampling methods and structured features to improve fall incident report identification by the severity level
Authors: Liu Jiaxing , Wong Zoie S Y , So H Y , Tsui Kwok Leung
Published: April 2021

Objective

This study aims to improve the classification of the fall incident severity level by considering data imbalance issues and structured features through machine learning.

Materials and Methods

We present an incident report classification (IRC) framework to classify the in-hospital fall incident severity level by addressing the imbalanced class problem and incorporating structured attributes. After text preprocessing, bag-of-words features, structured text features, and structured clinical features were extracted from the reports. Next, resampling techniques were incorporated into the training process. Machine learning algorithms were used to build classification models. IRC systems were trained, validated, and tested using a repeated and randomly stratified shuffle-split cross-validation method. Finally, we evaluated the system performance using the F1-measure, precision, and recall over 15 stratified test sets.

Results

The experimental results demonstrated that the classification system setting considering both data imbalance issues and structured features outperformed the other system settings (with a mean macro-averaged F1-measure of 0.733). Considering the structured features and resampling techniques, this classification system setting significantly improved the mean F1-measure for the rare class by 30.88% (P value < .001) and the mean macro-averaged F1-measure by 8.26% from the baseline system setting (P value < .001). In general, the classification system employing the random forest algorithm and random oversampling method outperformed the others.

Conclusions

Structured features provide essential information for categorizing the fall incident severity level. Resampling methods help rebalance the class distribution of the original incident report data, which improves the performance of machine learning models. The IRC framework presented in this study effectively automates the identification of fall incident reports by the severity level.
Neuroblastoma Screening at 1 Year of Age: The Final Results of a Controlled Trial
Authors: Berthold Frank , Spix Claudia , Erttmann Rudolf , Hero Barbara , Michaelis Joerg , Treuner Joern , Ernst Angela , Schilling Freimut H
Published: April 2021

Background

Neuroblastoma screening aims to reduce neuroblastoma-related mortality. A controlled trial showed no reduction in stage 4 disease incidence and preliminary mortality data. This article presents epidemiologic and clinical data 20 years after cessation of the screening program.

Methods

The patients with detected disease in the screening area were compared with the clinically diagnosed patients in the control area and in the prestudy and poststudy cohorts. All statistical tests were 2-sided.

Results

The cumulative incidence for children aged 1 to 6 years in the birth study cohorts (1994-1999) in the screening arm was 13.4 cases per 100 000 births (95% confidence interval [CI] = 12.2 to 14.6) based on 61.2% of screening participants and 38.8% of nonparticipants. Screening participants had a cumulative incidence of 15.7 (95% CI = 14.0 to 17.4) per 100 000 births. The cumulative incidence in the contemporary control cohort was 9.3 (95% CI = 8.2 to 10.3) per 100 000 births, 7.6 (95% CI = 6.8 to 8.4) in the prestudy cohort, and 8.1 (95% CI = 7.4 to 8.9) in the poststudy cohort from 2000 to 2004 (P < .001 each). The increased incidence in the screening cohort was restricted to stages 1 through 3, while stage 4 incidence was not reduced. The cumulative mortality for deaths within 10 years from diagnosis and per 100 000 births remained unchanged. Patients with stage 4 disease detected by screening had better biological characteristics and an improved outcome compared with those stage 4 cases not detected by screening.

Conclusions

Neuroblastoma screening at 1 year of age reduced neither stage 4 incidence nor neuroblastoma mortality and was affected by overdiagnosis, leading to unnecessary treatment. A few screening-detected stage 4 cases represent a biologically interesting subgroup but do not change the recommendation to close the “catecholamine-based neuroblastoma screening book.”
Education of Musical Sensitiveness
Authors: Westharp Alfred
Published: April 2021

“Education of Musical Sensitiveness—is there not enough to be learned in actual music !” exclaims the musical amateur in reading this title. “Music, is it not learned enough ? Is it not already difficult enough to understand something of it ?”
Can improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation inSorghum bicolor
Authors: Jaikumar Nikhil S , Stutz Samantha S , Fernandes Samuel B , Leakey Andrew D B , Bernacchi Carl J , Brown Patrick J , Long Stephen P
Published: April 2021

Previous studies have found that maximum quantum yield of CO2 assimilation (Φ CO2,max,app) declines in lower canopies of maize and miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear whether the maladaptive shade response is a general property of this C4 grass tribe, the Andropogoneae. We explored the generality of this maladaptation by testing the hypothesis that erect leaf forms (erectophiles), which allow more light into the lower canopy, suffer less of a decline in photosynthetic efficiency than drooping leaf (planophile) forms. On average, Φ CO2,max,app declined 27% in lower canopy leaves across 35 accessions, but the decline was over twice as great in planophiles than in erectophiles. The loss of photosynthetic efficiency involved a decoupling between electron transport and assimilation. This was not associated with increased bundle sheath leakage, based on 13C measurements. In both planophiles and erectophiles, shaded leaves had greater leaf absorptivity and lower activities of key C4 enzymes than sun leaves. The erectophile form is considered more productive because it allows a more effective distribution of light through the canopy to support photosynthesis. We show that in sorghum, it provides a second benefit, maintenance of higher Φ CO2,max,app to support efficient use of that light resource.
Melatonin promotes Arabidopsis primary root growth in an IAA-dependent manner
Authors: Yang Li , You Jun , Li Jinzhu , Wang Yanping , Chan Zhulong
Published: April 2021

Melatonin has been characterized as a growth regulator in plants. Melatonin shares tryptophan as the precursor with the auxin indole-3-acetic acid (IAA), but the interplay between melatonin and IAA remains controversial. In this study, we aimed to dissect the relationship between melatonin and IAA in regulating Arabidopsis primary root growth. We observed that melatonin concentrations ranging from 10–9 to 10–6 M functioned as IAA mimics to promote primary root growth in Arabidopsis wild type, as well as in pin-formed (pin) single and double mutants. Transcriptome analysis showed that changes in gene expression after melatonin and IAA treatment were moderately correlated. Most of the IAA-regulated genes were co-regulated by melatonin, indicating that melatonin and IAA regulated a similar subset of genes. Melatonin partially rescued primary root growth defects in pin single and double mutant plants. However, melatonin treatment had little effect on primary root growth in the presence of high concentrations of auxin biosynthesis inhibitors, or polar transport inhibitor, and could not rescue the root length defect of the IAA biosynthesis quintuple mutant yucQ. Therefore, we propose that melatonin promotes primary root growth in an IAA-dependent manner.
A PPMAP analysis of the filamentary structures in Ophiuchus L1688 and L1689
Authors: Howard A D P , Whitworth A P , Griffin M J , Marsh K A , Smith M W L
Published: April 2021

We use the Point Process MAPping (PPMAP) algorithm to reanalyse the Herschel and SCUBA-2 observations of the L1688 and L1689 subregions of the Ophiuchus molecular cloud. PPMAP delivers maps with high resolution (here 14 arcsec, corresponding to ${\sim}0.01\, {\rm pc}$ at ${\sim}140\, {\rm pc}$), by using the observations at their native resolutions. PPMAP also delivers more accurate dust optical depths, by distinguishing dust of different types and at different temperatures. The filaments and pre-stellar cores almost all lie in regions with $N_{\rm H_2}\gtrsim 7\times 10^{21}\, {\rm cm}^{-2}$ (corresponding to AV ≳ 7). The dust temperature, T, tends to be correlated with the dust opacity index, β, with low T and low β concentrated in the interiors of filaments. The one exception to this tendency is a section of filament in L1688 that falls – in projection – between the two B stars: S1 and HD147889; here T and β are relatively high, and there is compelling evidence that feedback from these two stars has heated and compressed the filament. Filament fwhms are typically in the range $0.10$ to $0.15\, {\rm pc}$. Most filaments have line-densities in the range $25$ to $65\, {\rm M_{\odot }\, pc^{-1}}$. If their only support is thermal gas pressure, and the gas is at the canonical temperature of $10\, {\rm K}$, the filaments are highly supercritical. However, there is some evidence from ammonia observations that the gas is significantly warmer than this, and we cannot rule out the possibility of additional support from turbulence and/or magnetic fields. On the basis of their spatial distribution, we argue that most of the starless cores are likely to disperse (rather than evolving to become pre-stellar).