bluuebunny/crossref_metadata_2025 huggingface dataset:
Caenorhabditis elegans lin-45 raf Is Essential for Larval Viability, Fertility and the Induction of Vulval Cell Fates
Authors: Hsu Virginia , Zobel Cheri L , Lambie Eric J , Schedl Tim , Kornfeld Kerry
Published: April 2021

The protein kinase Raf is an important signaling protein. Raf activation is initiated by an interaction with GTP-bound Ras, and Raf functions in signal transmission by phosphorylating and activating a mitogen-activated protein (MAP) kinase kinase named MEK. We identified 13 mutations in the Caenorhabditis elegans lin-45 raf gene by screening for hermaphrodites with abnormal vulval formation or germline function. Weak, intermediate, and strong loss-of-function or null mutations were isolated. The phenotype caused by the most severe mutations demonstrates that lin-45 is essential for larval viability, fertility, and the induction of vulval cell fates. The lin-45(null) phenotype is similar to the mek-2(null) and mpk-1(null) phenotypes, indicating that LIN-45, MEK-2, and MPK-1 ERK MAP kinase function in a predominantly linear signaling pathway. The lin-45 alleles include three missense mutations that affect the Ras-binding domain, three missense mutations that affect the protein kinase domain, two missense mutations that affect the C-terminal 14-3-3 binding domain, three nonsense mutations, and one small deletion. The analysis of the missense mutations indicates that Ras binding, 14-3-3-binding, and protein kinase activity are necessary for full Raf function and suggests that a 14-3-3 protein positively regulates Raf-mediated signaling during C. elegans development.
Recombinogenic Effects of Suppressors of Position-Effect Variegation in Drosophila
Authors: Westphal Thomas , Reuter Gunter
Published: April 2021

Compact chromatin structure, induction of gene silencing in position-effect variegation (PEV), and crossing-over suppression are typical features of heterochromatin. To identify genes affecting crossing-over suppression by heterochromatin we tested PEV suppressor mutations for their effects on crossing over in pericentromeric regions of Drosophila autosomes. From the 46 mutations (28 loci) studied, 16 Su(var) mutations of the nine genes Su(var)2-1, Su(var)2-2, Su(var)2-5, Su(var)2-10, Su(var)2-14, Su(var) 2-15, Su(var)3-3, Su(var)3-7, and Su(var)3-9 significantly increase in heterozygotes or by additive effects in double and triple heterozygotes crossing over in the ri-pp region of chromosome 3. Su(var)2-201 and Su(var) 2-1401 display the strongest recombinogenic effects and were also shown to enhance recombination within the light-rolled heterochromatic region of chromosome 2. The dominant recombinogenic effects of Su(var) mutations are most pronounced in proximal euchromatin and are accompanied with significant reduction of meiotic nondisjunction. Our data suggest that crossing-over suppression by heterochromatin is controlled at chromatin structure as well as illustrate the possible effects of heterochromatin on total crossing-over frequencies in the genome.
Precocious Expression of the Glide/Gcm Glial-Promoting Factor in Drosophila Induces Neurogenesis
Authors: Van De Bor Véronique , Heitzler Pascal , Leger Sophie , Plessy Charles , Giangrande Angela
Published: April 2021

Neurons and glial cells depend on similar developmental pathways and often originate from common precursors; however, the differentiation of one or the other cell type depends on the activation of cell-specific pathways. In Drosophila, the differentiation of glial cells depends on a transcription factor, Glide/Gcm. This glial-promoting factor is both necessary and sufficient to induce the central and peripheral glial fates at the expense of the neuronal fate. In a screen for mutations affecting the adult peripheral nervous system, we have found a dominant mutation inducing supernumerary sensory organs. Surprisingly, this mutation is allelic to glide/gcm and induces precocious glide/gcm expression, which, in turn, activates the proneural genes. As a consequence, sensory organs are induced. Thus, temporal misregulation of the Glide/Gcm glial-promoting factor reveals a novel potential for this cell fate determinant. At the molecular level, this implies unpredicted features of the glide/gcm pathway. These findings also emphasize the requirement for both spatial and temporal glide/gcm regulation to achieve proper cell specification within the nervous system.
Fission Yeast Mutants Affecting Telomere Clustering and Meiosis-Specific Spindle Pole Body Integrity
Authors: Jin Ye , Uzawa Satoru , Cande W Z
Published: April 2021

In meiotic prophase of many eukaryotic organisms, telomeres attach to the nuclear envelope and form a polarized configuration called the bouquet. Bouquet formation is hypothesized to facilitate homologous chromosome pairing. In fission yeast, bouquet formation and telomere clustering occurs in karyogamy and persists throughout the horsetail stage. Here we report the isolation and characterization of six mutants from our screen for meiotic mutants. These mutants show defective telomere clustering as demonstrated by mislocalization of Swi6::GFP, a heterochromatin-binding protein, and Taz1p::GFP, a telomere-specific protein. These mutants define four complementation groups and are named dot1 to dot4—defective organization of telomeres. dot3 and dot4 are allelic to mat1-Mm and mei4, respectively. Immunolocalization of Sad1, a protein associated with the spindle pole body (SPB), in dot mutants showed an elevated frequency of multiple Sad1-nuclei signals relative to wild type. Many of these Sad1 foci were colocalized with Taz1::GFP. Impaired SPB structure and function were further demonstrated by failure of spore wall formation in dot1, by multiple Pcp1::GFP signals (an SPB component) in dot2, and by abnormal microtubule organizations during meiosis in dot mutants. The coincidence of impaired SPB functions with defective telomere clustering suggests a link between the SPB and the telomere cluster.
Genetic and Physical Interactions Between DPB11 and DDC1 in the Yeast DNA Damage Response Pathway
Authors: Wang Hong , Elledge Stephen J
Published: April 2021

DPB11 is essential for DNA replication and S/M checkpoint control in Saccharomyces cerevisiae. The Dpb11 protein contains four BRCT domains, which have been proposed to be involved in protein-protein interactions. To further investigate the regulation and function of Dpb11, a yeast two-hybrid screen was carried out to identify proteins that physically interact with Dpb11. One positive clone isolated from the screen encoded a carboxyl-terminal fragment of Ddc1 (339–612 aa). Ddc1 is a DNA damage checkpoint protein, which, together with Mec3 and Rad17, has been proposed to form a PCNA-like complex and acts upstream in the DNA damage checkpoint pathways. We further determined that the carboxyl region of Dpb11 is required for its interaction with Ddc1. DDC1 and DPB11 also interact genetically. The Δddc1 dpb11-1 double mutant is more UV and MMS sensitive than the Δddc1 or the dpb11-1 single mutants. Furthermore, the double mutant is more hydroxyurea sensitive and displayed a lower restrictive temperature than dpb11-1. These results suggest that DPB11 and DDC1 may function in the same or parallel pathways after DNA damage and that DDC1 may play a role in responding to replication defects.
The Function of the frizzled Pathway in the Drosophila Wing Is Dependent on inturned and fuzzy
Authors: Lee Haeryun , Adler Paul N
Published: April 2021

The Drosophila epidermis is characterized by a dramatic planar or tissue polarity. The frizzled pathway has been shown to be a key regulator of planar polarity for hairs on the wing, ommatidia in the eye, and sensory bristles on the notum. We have investigated the genetic relationships between putative frizzled pathway downstream genes inturned, fuzzy, and multiple wing hairs (inturned-like genes) and upstream genes such as frizzled, prickle, and starry night (frizzled-like genes). Previous data showed that the inturned-like genes were epistatic to the frizzled-like genes when the entire wing was mutant. We extended those experiments and examined the behavior of frizzled clones in mutant wings. We found the domineering nonautonomy of frizzled clones was not altered when the clone cells were simultaneously mutant for inturned, multiple wing hairs, or dishevelled but it was blocked when the entire wing was mutant for inturned, fuzzy, multiple wing hairs, or dishevelled. Thus, for the domineering nonautonomy phenotype of frizzled, inturned and multiple wing hairs are needed in the responding cells but not in the clone itself. Expressing a number of frizzled pathway genes in a gradient across part of the wing repolarizes wing cells in that region. We found inturned, fuzzy, and multiple wing hairs were required for a gradient of frizzled, starry night, prickle, or spiny-legs expression to repolarize wing cells. These data argue that inturned, fuzzy, and multiple wing hairs are downstream components of the frizzled pathway. To further probe the relationship between the frizzled-like and inturned-like genes we determined the consequences of altering the activity of frizzled-like genes in wings that carried weak alleles of inturned or fuzzy. Interestingly, both increasing and decreasing the activity of frizzled and other upstream genes enhanced the phenotypes of hypomorphic inturned and fuzzy mutants. We also examined the relationship between the frizzled-like and inturned-like genes in other regions of the fly. For some body regions and cell types (e.g., abdomen) the inturned-like genes were epistatic to the frizzled-like genes, but in other body regions (e.g., eye) that was not the case. Thus, the genetic control of tissue polarity is body region specific.
Multilocus Self-Recognition Systems in Fungi as a Cause of Trans-Species Polymorphism
Authors: Muirhead Christina A , Glass N Louise , Slatkin Montgomery
Published: April 2021

Trans-species polymorphism, meaning the presence of alleles in different species that are more similar to each other than they are to alleles in the same species, has been found at loci associated with vegetative incompatibility in filamentous fungi. If individuals differ at one or more of these loci (termed het for heterokaryon), they cannot form stable heterokaryons after vegetative fusion. At the het-c locus in Neurospora crassa and related species there is clear evidence of trans-species polymorphism: three alleles have persisted for ∼30 million years. We analyze a population genetic model of multilocus vegetative incompatibility and find the conditions under which trans-species polymorphism will occur. In the model, several unlinked loci determine the vegetative compatibility group (VCG) of an individual. Individuals of different VCGs fail to form productive heterokaryons, while those of the same VCG form viable heterokaryons. However, viable heterokaryon formation between individuals of the same VCG results in a loss in fitness, presumably via transfer of infectious agents by hyphal fusion or exploitation by aggressive genotypes. The result is a form of balancing selection on all loci affecting an individual's VCG. We analyze this model by making use of a Markov chain/strong selection, weak mutation (SSWM) approximation. We find that trans-species polymorphism of the type that has been found at the het-c locus is expected to occur only when the appearance of new incompatibility alleles is strongly constrained, because the rate of mutation to such alleles is very low, because the number of possible incompatibility alleles at each locus is restricted, or because the number of incompatibility loci is limited.
A Defect of Kap104 Alleviates the Requirement of Mitotic Exit Network Gene Functions in Saccharomyces cerevisiae
Authors: Asakawa Kazuhide , Toh-e Akio
Published: April 2021

A subgroup of the karyopherin β (also called importin β) protein that includes budding yeast Kap104 and human transportin/karyopherin β2 is reported to function as a receptor for the transport of mRNA-binding proteins into the nucleus. We identified KAP104 as a responsible gene for a suppressor mutation of cdc15-2. We found that the kap104-E604K mutation suppressed the temperature-sensitive growth of cdc15-2 cells by promoting the exit from mitosis and suppressed the temperature sensitivity of various mitoticexit mutations. The cytokinesis defect of these mitotic-exit mutants was not suppressed by kap104-E604K. Furthermore, the kap104-E604K mutation delays entry into DNA synthesis even at a permissive temperature. In cdc15-2 kap104-E604K cells, SWI5 and SIC1, but not CDH1, became essential at a high temperature, suggesting that the kap104-E604K mutation promotes mitotic exit via the Swi5-Sic1 pathway. Interestingly, SPO12, which is involved in the release of Cdc14 from the nucleolus during early anaphase, also became essential in cdc15-2 kap104-E604K cells at a high temperature. The kap104-E604K mutation caused a partial delocalization of Cdc14 from the nucleolus during interphase. This delocalization of Cdc14 was suppressed by the deletion of SPO12. These results suggest that a mutation in Kap104 stimulates exit from mitosis through the activation of Cdc14 and implies a novel role for Kap104 in cell-cycle progression in budding yeast.
SPN1, a Conserved Gene Identified by Suppression of a Postrecruitment-Defective Yeast TATA-Binding Protein Mutant
Authors: Fischbeck Julie A , Kraemer Susan M , Stargell Laurie A
Published: April 2021

Little is known about TATA-binding protein (TBP) functions after recruitment to the TATA element, although several TBP mutants display postrecruitment defects. Here we describe a genetic screen for suppressors of a postrecruitment-defective TBP allele. Suppression was achieved by a single point mutation in a previously uncharacterized Saccharomyces cerevisiae gene, SPN1 (suppresses postrecruitment functions gene number 1). SPN1 is an essential yeast gene that is highly conserved throughout evolution. The suppressing mutation in SPN1 substitutes an asparagine for an invariant lysine at position 192 (spn1K192N). The spn1K192N strain is able to suppress additional alleles of TBP that possess postrecruitment defects, but not a TBP allele that is postrecruitment competent. In addition, Spn1p does not stably associate with TFIID in vivo. Cells containing the spn1K192N allele exhibit a temperature-sensitive phenotype and some defects in activated transcription, whereas constitutive transcription appears relatively robust in the mutant background. Consistent with an important role in postrecruitment functions, transcription from the CYC1 promoter, which has been shown to be regulated by postrecruitment mechanisms, is enhanced in spn1K192N cells. Moreover, we find that SPN1 is a member of the SPT gene family, further supporting a functional requirement for the SPN1 gene product in transcriptional processes.
Telomeric P elements Associated With Cytotype Regulation of the P Transposon Family in Drosophila melanogaster
Authors: Stuart Jeremy R , Haley Kevin J , Swedzinski Douglas , Lockner Samuel , Kocian Paul E , Merriman Peter J , Simmons Michael J
Published: April 2021

P elements inserted at the left end of the Drosophila X chromosome were isolated genetically from wild-type P strains. Stocks carrying these elements were tested for repression of P-strain-induced gonadal dysgenesis in females and for repression of transposase-catalyzed P-element excision in males and females. Both traits were repressed by stocks carrying either complete or incomplete P elements inserted near the telomere of the X chromosome in cytological region 1A, but not by stocks carrying only nontelomeric X-linked P elements. All three of the telomeric P elements that were analyzed at the molecular level were inserted in one of the 1.8-kb telomere-associated sequence (TAS) repeats near the end of the X chromosome. Stocks with these telomeric P elements strongly repressed P-element excision induced in the male germline by a P strain or by the transposase-producing transgenes H(hsp/CP)2, H(hsp/CP)3, a combination of these two transgenes, and P(ry+, Δ2-3)99B. For H(hsp/CP)2 and P(ry+, Δ2-3)99B, the repression was also effective when the flies were subjected to heat-shock treatments. However, these stocks did not repress the somatic transposase activity of P(ry+, Δ2-3)99B. Repression of transposase activity in the germline required maternal transmission of the telomeric P elements themselves. Paternal transmission of these elements, or maternal transmission of the cytoplasm from carriers, both were insufficient to repress transposase activity. Collectively, these findings indicate that the regulatory abilities of telomeric P elements are similar to those of the P cytotype.
A Drosophila Homolog of the Polyglutamine Disease Gene SCA2 Is a Dosage-Sensitive Regulator of Actin Filament Formation
Authors: Satterfield Terrence F , Jackson Stephen M , Pallanck Leo J
Published: April 2021

Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disorder caused by the expansion of a CAG repeat encoding a polyglutamine tract in ataxin-2, the SCA2 gene product. The normal cellular function of ataxin-2 and the mechanism by which polyglutamine expansion of ataxin-2 causes neurodegeneration remain unknown. In this study we have used genetic and molecular approaches to investigate the function of a Drosophila homolog of the SCA2 gene (Datx2). Like human ataxin-2, Datx2 is found throughout development in a variety of tissue types and localizes to the cytoplasm. Mutations that reduce Datx2 activity or transgenic overexpression of Datx2 result in female sterility, aberrant sensory bristle morphology, loss or degeneration of tissues, and lethality. These phenotypes appear to result from actin filament formation defects occurring downstream of actin synthesis. Further studies demonstrate that Datx2 does not assemble with actin filaments, suggesting that the role of Datx2 in actin filament formation is indirect. These results indicate that Datx2 is a dosage-sensitive regulator of actin filament formation. Given that loss of cytoskeleton-dependent dendritic structure defines an early event in SCA2 pathogenesis, our findings suggest the possibility that dysregulation of actin cytoskeletal structure resulting from altered ataxin-2 activity is responsible for neurodegeneration in SCA2.
A Cluster of Four Receptor-Like Genes Resides in the Vf Locus That Confers Resistance to Apple Scab Disease
Authors: Xu Mingliang , Korban Schuyler S
Published: April 2021

The Vf locus, derived from the crabapple species Malus floribunda 821, confers resistance to five races of the fungal pathogen Venturia inaequalis, the causal agent of apple scab disease. In our previous research, the Vf locus was restricted to a BAC contig of ∼290 kb covered by five overlapping BAC clones. Here, we report on cloning of the resistance gene(s) present in the Vf BAC contig using a highly reliable and straightforward approach. This approach relies on hybridization of labeled cDNAs to amplified inserts of subclones derived from BAC inserts, followed by recovery of full-size transcripts by rapid amplification of cDNA ends (RACE). A cluster of four resistance paralogs (Vfa1, Vfa2, Vfa3, and Vfa4) was identified in the Vf locus. Vfa1, Vfa2 and Vfa4 had no introns and are predicted to encode proteins characterized with extracellular leucine-rich repeats (LRRs) and transmembrane (TM) domains. However, Vfa3 contains an insertion of 780 bp at the end of the LRR motif, resulting in multiple truncated transcripts. Comparison of Vfa1, Vfa2, and Vfa4 paralogs revealed a high degree of overall homology in their deduced amino acid sequences, while divergences were mainly restricted within LRR domains, including variable LRR units, numerous amino acid substitutions, and several residue deletions/duplications. Differential expression profiles among the four paralogs were observed during leaf development. Vfa1, Vfa2, and Vfa3 were active in immature leaves, but slightly expressed in mature leaves, while Vfa4 was active in immature leaves and was highly expressed in mature leaves.
Changing Effective Population Size and the McDonald-Kreitman Test
Authors: Eyre-Walker Adam
Published: April 2021

Artifactual evidence of adaptive amino acid substitution can be generated within a McDonald-Kreitman test if some amino acid mutations are slightly deleterious and there has been an increase in effective population size. Here I investigate the conditions under which this occurs. I show that fairly small increases in effective population size can generate artifactual evidence of positive selection if there is no selection upon synonymous codon use. This problem is exacerbated by the removal of low-frequency polymorphisms. However, selection on synonymous codon use restricts the conditions under which artifactual evidence of adaptive evolution is produced.
The Global Transcriptional Activator of Saccharomyces cerevisiae, Gcr1p, Mediates the Response to Glucose by Stimulating Protein Synthesis and CLN-Dependent Cell Cycle Progression
Authors: Willis Kristine A , Barbara Kellie E , Menon Balaraj B , Moffat Jason , Andrews Brenda , Santangelo George M
Published: April 2021

Growth of Saccharomyces cerevisiae requires coordination of cell cycle events (e.g., new cell wall deposition) with constitutive functions like energy generation and duplication of protein mass. The latter processes are stimulated by the phosphoprotein Gcr1p, a transcriptional activator that operates through two different Rap1p-mediated mechanisms to boost expression of glycolytic and ribosomal protein genes, respectively. Simultaneous disruption of both mechanisms results in a loss of glucose responsiveness and a dramatic drop in translation rate. Since a critical rate of protein synthesis (CRPS) is known to mediate passage through Start and determine cell size by modulating levels of Cln3p, we hypothesized that GCR1 regulates cell cycle progression by coordinating it with growth. We therefore constructed and analyzed gcr1Δ cln3Δ and gcr1Δ cln1Δ cln2Δ strains. Both strains are temperature and cold sensitive; interestingly, they exhibit different arrest phenotypes. The gcr1Δ cln3Δ strain becomes predominantly unbudded with 1N DNA content (G1 arrest), whereas gcr1Δ cln1Δ cln2Δ cells exhibit severe elongation and apparent M phase arrest. Further analysis demonstrated that the Rap1p/Gcr1p complex mediates rapid growth in glucose by stimulating both cellular metabolism and CLN transcription.
Suppressor Mutations Bypass the Requirement of fluG for Asexual Sporulation and Sterigmatocystin Production in Aspergillus nidulans
Authors: Seo Jeong-Ah , Guan Yajun , Yu Jae-Hyuk
Published: April 2021

Asexual sporulation (conidiation) in the filamentous fungus Aspergillus nidulans requires the early developmental activator fluG. Loss of fluG results in the blockage of both conidiation and production of the mycotoxin sterigmatocystin (ST). To investigate molecular mechanisms of fluG-dependent developmental activation, 40 suppressors of fluG (SFGs) that conidiate without fluG have been isolated and characterized. Genetic analyses showed that an individual suppression is caused by a single second-site mutation, and that all sfg mutations but one are recessive. Pairwise meiotic crosses grouped mutations to four loci, 31 of them to sfgA, 6 of them to sfgB, and 1 each to sfgC and sfgD, respectively. The only dominant mutation, sfgA38, also mapped to the sfgA locus, suggesting a dominant negative mutation. Thirteen sfgA and 1 sfgC mutants elaborated conidiophores in liquid submerged culture, indicating that loss of either of these gene functions not only bypasses fluG function but also results in hyperactive conidiation. While sfg mutants show varying levels of restored conidiation, all recovered the ability to produce ST at near wild-type levels. The fact that at least four loci are defined by recessive sfg mutations indicates that multiple genes negatively regulate conidiation downstream of fluG and that the activity of fluG is required to remove such repressive effects.
Quantitative Classification and Natural Clustering of Caenorhabditis elegans Behavioral Phenotypes
Authors: Geng Wei , Cosman Pamela , Baek Joong-Hwan , Berry Charles C , Schafer William R
Published: April 2021

Genetic analysis of nervous system function relies on the rigorous description of behavioral phenotypes. However, standard methods for classifying the behavioral patterns of mutant Caenorhabditis elegans rely on human observation and are therefore subjective and imprecise. Here we describe the application of machine learning to quantitatively define and classify the behavioral patterns of C. elegans nervous system mutants. We have used an automated tracking and image processing system to obtain measurements of a wide range of morphological and behavioral features from recordings of representative mutant types. Using principal component analysis, we represented the behavioral patterns of eight mutant types as data clouds distributed in multidimensional feature space. Cluster analysis using the k-means algorithm made it possible to quantitatively assess the relative similarities between different behavioral phenotypes and to identify natural phenotypic clusters among the data. Since the patterns of phenotypic similarity identified in this study closely paralleled the functional similarities of the mutant gene products, the complex phenotypic signatures obtained from these image data appeared to represent an effective diagnostic of the mutants' underlying molecular defects.
Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes
Authors: Sheldahl Lea A , Weinreich Daniel M , Rand David M
Published: April 2021

Surveys of nucleotide polymorphism and divergence indicate that the average selection coefficient on Drosophila proteins is weakly positive. Similar surveys in mitochondrial genomes and in the selfing plant Arabidopsis show that weak negative selection has operated. These differences have been attributed to the low recombination environment of mtDNA and Arabidopsis that has hindered adaptive evolution through the interference effects of linkage. We test this hypothesis with new sequence surveys of proteins lying in low recombination regions of the Drosophila genome. We surveyed >3800 bp across four proteins at the tip of the X chromosome and >3600 bp across four proteins on the fourth chromosome in 24 strains of D. melanogaster and 5 strains of D. simulans. This design seeks to study the interaction of selection and linkage by comparing silent and replacement variation in semihaploid (X chromosome) and diploid (fourth chromosome) environments lying in regions of low recombination. While the data do indicate very low rates of exchange, all four gametic phases were observed both at the tip of the X and across the fourth chromosome. Silent variation is very low at the tip of the X (θS = 0.0015) and on the fourth chromosome (θS = 0.0002), but the tip of the X shows a greater proportional loss of variation than the fourth shows relative to normal-recombination regions. In contrast, replacement polymorphism at the tip of the X is not reduced (θR = 0.00065, very close to the X chromosome average). MK and HKA tests both indicate a significant excess of amino acid polymorphism at the tip of the X relative to the fourth. Selection is significantly negative at the tip of the X (Nes =-1.53) and nonsignificantly positive on the fourth (Nes ∼ 2.9), analogous to the difference between mtDNA (or Arabidopsis) and the Drosophila genome average. Our distal X data are distinct from regions of normal recombination where the X shows a deficiency of amino acid polymorphism relative to the autosomes, suggesting more efficient selection against recessive deleterious replacement mutations. We suggest that the excess amino acid polymorphism on the distal X relative to the fourth chromosome is due to (1) differences in the mutation rate for selected mutations on the distal X or (2) a greater relaxation of selection from stronger linkage-related interference effects on the distal X. This relaxation of selection is presumed to be greater in magnitude than the difference in efficiency of selection between X-linked vs. autosomal selection.
Mapping of Quantitative Trait Loci Controlling Adaptive Traits in Coastal Douglas Fir. III. Quantitative Trait Loci-by-Environment Interactions
Authors: Jermstad Kathleen D , Bassoni Daniel L , Jech Keith S , Ritchie Gary A , Wheeler Nicholas C , Neale David B
Published: April 2021

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring temperatures. A three-generation mapping population of 460 cloned progeny was used for genetic mapping and phenotypic evaluations. An all-marker interval mapping method was used for scanning the genome for the presence of QTL and single-factor ANOVA was used for estimating QTL-by-environment interactions. A modest number of QTL were detected per trait, with individual QTL explaining up to 9.5% of the phenotypic variation. Two QTL-by-treatment interactions were found for growth initiation, whereas several QTL-by-treatment interactions were detected among growth cessation traits. This is the first report of QTL interactions with specific environmental signals in forest trees and will assist in the identification of candidate genes controlling these important adaptive traits in perennial plants.
A Consensus Linkage Map for Sugi (Cryptomeria japonica) From Two Pedigrees, Based on Microsatellites and Expressed Sequence Tags
Authors: Tani Naoki , Takahashi Tomokazu , Iwata Hiroyoshi , Mukai Yuzuru , Ujino-Ihara Tokuko , Matsumoto Asako , Yoshimura Kensuke , Yoshimaru Hiroshi , Murai Masafumi , Nagasaka Kazutoshi , Tsumura Yoshihiko
Published: April 2021

A consensus map for sugi (Cryptomeria japonica) was constructed by integrating linkage data from two unrelated third-generation pedigrees, one derived from a full-sib cross and the other by self-pollination of F1 individuals. The progeny segregation data of the first pedigree were derived from cleaved amplified polymorphic sequences, microsatellites, restriction fragment length polymorphisms, and single nucleotide polymorphisms. The data of the second pedigree were derived from cleaved amplified polymorphic sequences, isozyme markers, morphological traits, random amplified polymorphic DNA markers, and restriction fragment length polymorphisms. Linkage analyses were done for the first pedigree with JoinMap 3.0, using its parameter set for progeny derived by cross-pollination, and for the second pedigree with the parameter set for progeny derived from selfing of F1 individuals. The 11 chromosomes of C. japonica are represented in the consensus map. A total of 438 markers were assigned to 11 large linkage groups, 1 small linkage group, and 1 nonintegrated linkage group from the second pedigree; their total length was 1372.2 cM. On average, the consensus map showed 1 marker every 3.0 cM. PCR-based codominant DNA markers such as cleaved amplified polymorphic sequences and microsatellite markers were distributed in all linkage groups and occupied about half of mapped loci. These markers are very useful for integration of different linkage maps, QTL mapping, and comparative mapping for evolutional study, especially for species with a large genome size such as conifers.
Effect of Misoriented Sites on Neutrality Tests With Outgroup
Authors: Baudry Emmanuelle , Depaulis Frantz
Published: April 2021

Several neutrality tests use outgroups to infer the ancestral and derived states for polymorphism data. However, homoplasy can result in the incorrect inference of the derived variant. We show that empirically derived rates of misorientation strongly influence Fay and Wu's H-test, especially when the sample size is large.
Activity of Mitochondrially Synthesized Reporter Proteins Is Lower Than That of Imported Proteins and Is Increased by Lowering cAMP in Glucose-Grown Saccharomyces cerevisiae Cells
Authors: Demlow Christina M , Fox Thomas D
Published: April 2021

We selected for increased phenotypic expression of a synthetic cox2::arg8m-G66S reporter gene inserted into Saccharomyces cerevisiae mtDNA in place of COX2. Recessive mutations in ras2 and cyr1, as well as elevated dosage of PDE2, allowed cox2::arg8m-G66S to support Arg prototrophy. Each of these genetic alterations should decrease cellular cAMP levels. The resulting signal was transduced through redundant action of the three cAMP-dependent protein kinases, TPK1, TPK2, and TPK3. ras2 had little or no effect on the level of wild-type Arg8p encoded by cox2::ARG8m, but did increase Arg8p activity, as judged by growth phenotype. ras2 also caused increased fluorescence in cells carrying the synthetic cox3::GFPm reporter in mtDNA, but had little effect on the steady-state level of GFP polypeptide detected immunologically. Thus, decreased cAMP levels did not affect the synthesis of mitochondrially coded protein reporters in glucose-grown cells, but rather elevated activities in the matrix that promote efficient folding. Furthermore, we show that when Arg8p is synthesized in the cytoplasm and imported into mitochondria, it has greater activity than when it is synthesized in the matrix. Thus, mitochondrially synthesized proteins may not have the same access to matrix chaperones as cytoplasmically synthesized proteins emerging from the import apparatus.
Rights, proportionality, and process in EU counterterrorism lawmaking
Authors: de Londras Fiona , Tregidga Jasmin
Published: April 2021

Proportionality is a key principle of EU law. However, in spite of procedural requirements intended to ensure the full integration of proportionality as a design principle in EU law, the European Union continues to pass disproportionate counterterrorism laws. If proportionality is a fundamental constitutional principle of the European Union, and if lawmaking processes at EU level have been designed expressly with this in mind, then why do the EU’s counterterrorism laws consistently raise issues of disproportionate interference with rights? Taking as a case study the passage of the EU Directive on Combating Terrorism, this article argues that at least part of the answer lies in the curtailment and adjustment, in the counterterrorism field, of lawmaking processes that are designed to be participatory, evidence-based, and informed by proportionality.
Clinical Management of Gastrointestinal Disease in the Common Marmoset (Callithrix jacchus)
Authors: Fitz Casey , Goodroe Anna , Wierenga Lauren , Mejia Andres , Simmons Heather
Published: April 2021

Gastrointestinal disease is a frequently encountered problem among captive common marmoset (Callithrix jacchus) colonies. Management can be challenging due to the number of etiologies responsible for gastrointestinal disease in this species, limitations on diagnostic capabilities, and lack of effective treatments. Understanding commonly described GI diseases in the captive marmoset can provide insight on the impact these diseases have on research studies and aid in the development of appropriate management strategies. A review of commonly encountered GI disease processes as well as routinely implicated causes of GI disease in the common marmoset are provided. Current strategies in clinical management of GI disease in the common marmoset, including approaches to colony health, diagnostic testing, and commonly employed treatments are discussed.
Molecular and Binding Characteristics of OBP5 ofBradysia odoriphaga(Diptera: Sciaridae)
Authors: Yuting Yang , Dengke Hua , Caihua Shi , Wen Xie , Youjun Zhang
Published: April 2021

Odorant-binding proteins (OBPs) capture and transport semiochemicals to olfactory receptors (OR) and function in the ﬁrst step in insect olfaction. In the present study, we cloned a full-length cDNA sequence of BodoOBP5 from the insect pest Bradysia odoriphaga (Diptera: Sciaridae). Real-time PCR (qRT-PCR) analysis revealed that BodoOBP5 was expressed at higher levels in female adults than in other developmental stages. In the different tissues, BodoOBP5 was highly expressed in the female antennae, whereas low levels were expressed in the head and the male antennae, expression was negligible in other tissues. The recombinant protein of BodoOBP5 was successfully expressed with a bacterial system. Competitive binding assays with nine host plant volatiles and a putative sex pheromone revealed that purified BodoOBP5 strongly bound to two sulfur compounds (methyl allyl disulfide and diallyl disulfide); the corresponding dissolution constants (Ki) were 10.38 and 9.23 μM, respectively. Molecular docking indicated that Leu99, Leu103, Ala143, Tyr107, Phe142, and Trp144 in the hydrophobic cavity of BodoOBP5 are the key residues mediating the interaction of BodoOBP5 with methyl allyl disulfide and diallyl disulfide. RNAi-based Y-tube olfactometer assay indicated that there is no significant difference in methyl allyl disulfide and diallyl disulfide. The results of this study increase our understanding of the binding of BodoOBP5 with plant volatiles, facilitating the development of novel ways to control B. odoriphaga.
Rubinstein as Composer for the Pianoforte
Authors: Maclean Charles
Published: April 2021

The aim of this lecture-recital is to throw a stone, however small, on the cairn of a great, though for the moment much obliterated, memory. As a matter of interest, I propose to play pieces the great majority of which are likely to be unfamiliar. The interspersed remarks will be biographical and illustrative. As a preliminary I would establish three theses:—(a) Rubinstein is at the present date unduly neglected; (b) the meaning of original creative power in music is not sufficiently understood and recognised; (c) the influence of race as affecting musical composition, especially on the point of originality, is ignored.
Latin Church Music by Early English Composers
Authors: Collins H. B.
Published: April 2021

When I had the honour of an invitation to read a paper here this evening, the subject suggested to me was “Early English Church Music.” The idea conveyed to my mind by this title was that of a survey of English Church music of the polyphonic period, with an attempt perhaps to compare it with the contemporary Continental schools. It is hardly necessary for me to say that the data at my command are quite insufficient for carrying out any such ambitious scheme, even if it could be brought within the limits of a short paper. It occurred to me, however, that I might make some small contribution to the subject, which might be of assistance to its more adequate treatment in the future. With this view, I propose to confine myself this evening principally to Latin Church music—that is, to music written for the Catholic Liturgy during the 16th and 17th centuries; and to a few of the more representative composers.
Evaluation of the Preanalytical Interference of Hemoglobin, Bilirubin, or Lipids in Therapeutic Drug Monitoring Assays on Beckman Coulter AU Analyzers
Authors: Li Jieli , Rietschlin Jacqua , Miller Irene , Weber Charlene , Scheidegger Matt , Barringer Stephanie , Kerlin Rae , Williams JoAnna
Published: April 2021

Objective

The aim of this study was to evaluate the influence of hemolysis, icterus, and lipemia (HIL) interferences on 8 therapeutic drug monitoring (TDM) assays.

Methods

Amikacin, carbamazepine, digoxin, lidocaine, lithium, methotrexate, phenobarbital, and theophylline were spiked in specimen pools at the clinical decision cutoff values. The interferents were spiked in vitro in specimen pools. All analytes were tested on Beckman Coulter AU analyzers.

Results

Hemolysis interference was detected in quantitative microsphere system (QMS) amikacin at 55.59 μg/mL at a concentration of 500 mg/dL hemoglobin. Icterus interference was detected in enzyme multiplied immunoassay technique amikacin at 43.62 μg/mL and in QMS amikacin at 55.59 μg/mL, at a concentration of 20 mg/dL bilirubin.

Conclusion

Although the reference range value is recommended for clinical significance bias assessment for HIL interferences on most chemistry assays, an important investigation of the HIL interferences on TDM assays is to establish interferent thresholds at the clinical critical cutoff values.
COVID-19 and the Mental Health of Canadian Armed Forces Veterans: A Cross-Sectional Survey
Authors: Mahar Alyson L , Rindlisbacher Christina R , Edgelow Megan , Siddhpuria Shailee , Hallet Julie , Rochon Paula A , Cramm Heidi
Published: April 2021

Background

There are no data on the impact of COVID-19 and associated public health measures, including sheltering at home, travel restrictions, and changes in health care provision, on the mental health of older veterans. This information is necessary for government and philanthropic agencies to tailor mental health supports, services, and resources for veterans in the peri- and post-pandemic periods. The objective of this study was to compare mental health symptoms between Canadian Armed Forces (CAFs) veterans and the general Canadian older adult population in the early months of the COVID-19 pandemic.

Materials and Methods

This was a secondary analysis of a cross-sectional study of older adults in the national Canadian COVID-19 Coping Study. Individuals aged 55 years and older were eligible. A convenience sample of older adults was recruited through a web-based survey administered between May 01, 2020 and June 30, 2020. Canadian Armed Force military service history status (yes/no) was ascertained. The eight-item Center for Epidemiological Studies Depression Scale, the five-item Beck Anxiety Inventory, and the three-item Loneliness Scale were used to measure mental health symptoms. Multivariable logistic regression compared the odds of screening positive for depression, anxiety, and loneliness between veterans and non-veterans.

Results

Of 1,541 respondents who answered the final question (87% survey completeness rate), 210 were veterans. Forty percent of veterans met criteria for at least one of the mental health diagnoses compared to 46% of non-veterans (P = .12). The odds of reporting elevated symptoms of depression, anxiety, and loneliness were similar for veteran and non-veteran respondents after adjusting for confounders.

Conclusion

Veterans’ report of mental health symptoms was similar to the general population Spring 2020 of the COVID-19 pandemic. Although veterans’ military training may better prepare them to adapt in the face of a pandemic, additional research is needed to understand the longitudinal impacts on physical and mental health.
Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton
Authors: Wang Maojun , Li Jianying , Wang Pengcheng , Liu Fang , Liu Zhenping , Zhao Guannan , Xu Zhongping , Pei Liuling , Grover Corrinne E , Wendel Jonathan F , Wang Kunbo , Zhang Xianlong
Published: April 2021

Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the consequences for shaping 3D genomic architecture remains largely unknown in plants. Here, we report reference-grade genome assemblies for three species of cotton ranging 3-fold in genome size, namely Gossypium rotundifolium (K2), G. arboreum (A2), and G. raimondii (D5), using Oxford Nanopore Technologies. Comparative genome analyses document the details of lineage-specific TE amplification contributing to the large genome size differences (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb) and indicate relatively conserved gene content and synteny relationships among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status change between active (“A”) and inactive (“B”) compartments, and TE amplification was associated with the increase of the proportion of A compartment in gene regions (∼7,000 genes) in K2 and A2 relative to D5. Only 42% of topologically associating domain (TAD) boundaries were conserved among the three genomes. Our data implicate recent amplification of TEs following the formation of lineage-specific TAD boundaries. This study sheds light on the role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.
SARS-CoV-2 IgG response in symptomatic and asymptomatic COVID-19-infected healthcare workers
Authors: Cordova E , Bacelar B , Nieto F , Garibaldi F , Aguirre V , Machuca M , Badia M , Rodriguez C
Published: April 2021

Background

Healthcare workers (HCWs) accounted for a significant proportion of COVID-19 infections worldwide. Retrospective seroprevalence surveys are often used to screen for unidentified previous infection with SARS-CoV-2. However, the rate of humoral response in HCWs affected by COVID-19 is not well-defined.

Aims

To assess the specific IgG humoral response in symptomatic and asymptomatic SARS-CoV-2-infected HCWs and identify potential factors associated with humoral response.

Methods

We prospectively recruited 204 HCWs with RT-PCR-confirmed COVID-19 infection to evaluate SARS-CoV-2 humoral response. Serum-IgG antibodies against SARS-CoV-2 were analysed using two commercially available serological assays. A logistic regression was performed to identify independent factors associated with positive IgG serology test.

Results

Overall, the SARS-CoV-2 IgG seropositivity rate was 77%. This seropositivity rate was higher in symptomatic than in asymptomatic COVID-19 infection (83% versus 57%; P < 0.001) and in older HCWs.. The seropositivity rate did not diminish with time. In logistic regression, only a history of COVID-19 symptoms and age were identified as independent factors associated with the detection of anti-SARS-CoV-2 IgG antibodies.

Conclusions

SARS-CoV-2 IgG antibodies are found significantly more frequently in symptomatic and in older HCWs. The fact that not all COVID-19 HCWs develop detectable IgG is vital for the interpretation of COVID-19 seroprevalence surveys.
Community characteristics of forest understory birds along an elevational gradient in the Horn of Africa: A multi-year baseline
Authors: Kittelberger Kyle D , Neate-Clegg Montague H C , Buechley Evan R , Hakkı Şekercioğlu Çağan
Published: April 2021

Tropical mountains are global hotspots for birdlife. However, there is a dearth of baseline avifaunal data along elevational gradients, particularly in Africa, limiting our ability to observe and assess changes over time in tropical montane avian communities. In this study, we undertook a multi-year assessment of understory birds along a 1,750 m elevational gradient (1,430–3,186 m) in an Afrotropical moist evergreen montane forest within Ethiopia’s Bale Mountains. Analyzing 6 years of systematic bird-banding data from 5 sites, we describe the patterns of species richness, abundance, community composition, and demographic rates over space and time. We found bimodal patterns in observed and estimated species richness across the elevational gradient (peaking at 1,430 and 2,388 m), although no sites reached asymptotic species richness throughout the study. Species turnover was high across the gradient, though forested sites at mid-elevations resembled each other in species composition. We found significant variation across sites in bird abundance in some of the dietary and habitat guilds. However, we did not find any significant trends in species richness or guild abundances over time. For the majority of analyzed species, capture rates did not change over time and there were no changes in species’ mean elevations. Population growth rates, recruitment rates, and apparent survival rates averaged 1.02, 0.52, and 0.51 respectively, and there were no elevational patterns in demographic rates. This study establishes a multi-year baseline for Afrotropical birds along an elevational gradient in an under-studied international biodiversity hotspot. These data will be critical in assessing the long-term responses of tropical montane birdlife to climate change and habitat degradation.