bluuebunny/crossref_metadata_2025 huggingface dataset:
Isolation and Characterization of a Temperature-Sensitive Circadian Clock Mutant of Neurospora crassa
Authors: Morgan Louis W , Feldman Jerry F
Published: January 2021

A new circadian clock mutant has been isolated in Neurospora crassa. This new mutation, called period-6 (pd-6), has two features novel to known clock mutations. First, the mutation is temperature sensitive. At restrictive temperatures (above 21°) the mutation shortens circadian period length from a wild-type value of 21.5 hr to 18 hr. At permissive temperatures (below 21°) the mutant has a 20.5-hr period length close to that of the wild-type strain. Second, the prd-6 mutation is epistatic to the previously isolated clock mutation period-2 (prd-2). This epistasis is unusual in that the prd-2 prd-6 double mutant strain has an 18-hr period length at both the restrictive and permissive temperatures. That is, the temperature-sensitive aspect of the phenotype of the prd-6 strain is lost in the prd-2 prd-6 double mutant strain. This suggests that the gene products of the prd-2 and prd-6 loci may interact physically and that the presence of a normal prd-2+ protein is required for low temperature to “rescue” the prd-6 mutant phenotype. These results, combined with our recent finding that prd-2 and some alleles of the frq gene show genetic synergy, suggest that it may be possible to establish a more comprehensive model of the Neurospora circadian clock.
Multiple Genes Encoding Pheromones and a Pheromone Receptor Define the Bβ1 Mating-Type Specificity in Schizophyllum commune
Authors: Vaillancourt Lisa J , Raudaskoski Marjatta , Specht Charles A , Raper Carlene A
Published: January 2021

The genes defining multiple B mating types in the wood-rotting mushroom Schizophyllum commune are predicted to encode multiple pheromones and pheromone receptors. These genes are clustered in each of two recombinable and independently functioning loci, Bα and Bβ. A difference in specificity at either locus between a mated pair of individuals initiates an identical series of events in sexual morphogenesis. The Bα1 locus was recently found to contain genes predicted to encode three lipopeptide pheromones and a pheromone receptor with a seven-transmembrane domain. These gene products interact in heterospecific pairs, the pheromone of one Bα specificity with the receptor of any one of the other eight Bα specificities, and are likely to activate a signaling cascade similar to that known for mating in Saccharomyces cerevisiae. We report here that the Bβ1 locus also contains at least three pheromone genes and one pheromone receptor gene, which function similarly to the genes in the Bα1 locus, but only within the series of Bβ specificities. A comparison of the DNA sequences of the Bα1 and Bβ1 loci suggests that each arose from a common ancestral sequence, allowing us to speculate about the evolution of this unique series of regulatory genes.
Genetic and Molecular Analysis of smooth, a Quantitative Trait Locus Affecting Bristle Number in Drosophila melanogaster
Authors: Lage Petra zur , Shrimpton Antony D , Flavell Andrew J , Mackay Trudy F C , Brown Andrew J Leigh
Published: January 2021

A semi-lethal, sterile allele of the smooth locus (2-91.5), sm3, was discovered in an artificial selection line for low abdominal bristle number that had been started from a P-M dysgenic cross. The fitness effects and extremely low bristle number phenotype of the allele could not be separated by recombination from a P-element insertion at cytological location 56E, and precise excision of the P element at this site was associated with reversion to wild type. The smooth gene was cloned using the P-element insertion as a tag. The gene encodes a 2.6-kb transcript derived from 10 exons and covers a genomic region of at least 80 kb. The Drosophila smooth gene shares substantial sequence identity with a group of RNA binding proteins, with the closest relationship being to the human heterogeneous nuclear ribonucleoprotein L gene. The smooth gene is by definition an abdominal bristle number quantitative trait locus, but further work is required to discern whether naturally occurring allelic variation at this locus is a source of genetic variation for abdominal bristle number in natural populations.
Morph-Specific Proteins in Pollen and Styles of Distylous Turnera (Turneraceae)
Authors: Athanasiou Andreas , Shore Joel S
Published: January 2021

We used nondenaturing isoelectric focusing (IEF) in a survey of plants from 11 populations to identify style and pollen proteins unique to the short-styled morph of Turnera scabra, T. subulata and T. krapovickasii. Three protein bands [approximately isoelectric points (pIs) 6.1, 6.3 and 6.5] were found only in styles and stigmas of short-styled plants while two bands (approximately pIs 6.7 and 6.8, M  r 56 and 59 kD) occur only in pollen of short-styled plants. Some of these bands appear very late in development, within 24 hr before flowering. Two isozyme loci were mapped to an 8.7 cM region spanning the distyly locus. Using these isozyme markers we identified progeny exhibiting recombination adjacent to the distyly locus. No recombinants between the distyly locus and the locus or loci controlling the presence of the short-styled morph-specific proteins were obtained. This suggests that the loci encoding these proteins are either extremely tightly linked to the distyly locus and in complete disequilibrium with the S allele or exhibit morph-limited expression. Crosses to a plant showing an unusual style protein phenotype demonstrated that an additional unlinked locus is required for full expression of the style proteins. The function of the morph-specific proteins is unknown
A New Enhancer of Position-Effect Variegation in Drosophila melanogaster Encodes a Putative RNA Helicase That Binds Chromosomes and Is Regulated by the Cell Cycle
Authors: Eberl Daniel F , Lorenz Lori J , Melnick Michael B , Sood Vanita , Lasko Paul , Perrimon Norbert
Published: January 2021

In Drosophila melanogaster, position-effect variegation of the white gene has been a useful phenomenon by which to study chromosome structure and the genes that modify it. We have identified a new enhancer of variegation locus, Dmrnahel (hel). Deletion or mutation of hel enhances white variegation, and this can be reversed by a transformed copy of her  +. In the presence of two endogenous copies, the transformed her  + behaves as a suppressor of variegation. hel is an essential gene and functions both maternally and zygotically. The HEL protein is similar to known RNA helicases, but contains an unusual variant (DECD) of the DEAD motif common to these proteins. Potential HEL homologues have been found in mammals, yeast and worms. HEL protein associates with salivary gland chromosomes and locates to nuclei of embryos and ovaries, but disappears in mitotic domains of embryos as chromosomes condense. We propose that the HEL protein promotes an open chromatin structure that favors transcription during development by regulating the spread of heterochromatin, and that HEL is regulated by, and may have a role in, the mitotic cell cycle during embryogenesis.
Mutational Analysis of the Drosophila Sister-Chromatid Cohesion Protein ORD and Its Role in the Maintenance of Centromeric Cohesion
Authors: Bickel Sharon E , Wyman Dudley W , Orr-Weaver Terry L
Published: January 2021

The ord gene is required for proper segregation of all chromosomes in both male and female Drosophila meiosis. Here we describe the isolation of a null ord allele and examine the consequences of ablating ord function. Cytologically, meiotic sister-chromatid cohesion is severely disrupted in flies lacking ORD protein. Moreover, the frequency of missegregation in genetic tests is consistent with random segregation of chromosomes through both meiotic divisions, suggesting that sister cohesion may be completely abolished. However, only a slight decrease in viability is observed for ord null flies, indicating that ORD function is not essential for cohesion during somatic mitosis. In addition, we do not observe perturbation of germ-line mitotic divisions in flies lacking ORD activity. Our analysis of weaker ord alleles suggests that ORD is required for proper centromeric cohesion after arm cohesion is released at the metaphase I/anaphase I transition. Finally, although meiotic cohesion is abolished in the ord null fly, chromosome loss is not appreciable. Therefore, ORD activity appears to promote centromeric cohesion during meiosis II but is not essential for kinetochore function during anaphase.
Mating in Saccharomyces cerevisiae: The Role of the Pheromone Signal Transduction Pathway in the Chemotropic Response to Pheromone
Authors: Schrick Kathrin , Garvik Barbara , Hartwell Leland H
Published: January 2021

The mating process in yeast has two distinct aspects. One is the induction and activation of proteins required for cell fusion in response to a pheromone signal; the other is chemotropism, i.e., detection of a pheromone gradient and construction of a fusion site available to the signaling cell. To determine whether components of the signal transduction pathway necessary for transcriptional activation also play a role in chemotropism, we examined strains with null mutations in components of the signal transduction pathway for diploid formation, prezygote formation and the chemotropic process of mating partner discrimination when transcription was induced downstream of the mutation. Cells mutant for components of the mitogen-activated protein (MAP) kinase cascade (ste5, ste20, ste11, ste7 or fus3 kss1) formed diploids at a frequency 1% that of the wild-type control, but formed prezygotes as efficiently as the wild-type control and showed good mating partner discrimination, suggesting that the MAP kinase cascade is not essential for chemotropism. In contrast, cells mutant for the receptor (ste2) or the β or γ subunit (ste4 and stel8) of the G protein were extremely defective in both diploid and prezygote formation and discriminated poorly between signaling and nonsignaling mating partners, implying that these components are important for chemotropism.
Rules of Donor Preference in Saccharomyces Mating-Type Gene Switching Revealed by a Competition Assay Involving Two Types of Recombination
Authors: Wu Xiaohua , Wu Cherry , Haber James E
Published: January 2021

Mating type (MAT) switching in Saccharomyces cerevisiae is initiated by a double-strand break (DSB) created at MAT by HO endonuclease. MAT  a cells activate the entire left arm of chromosome III; thus MAT  a preferentially recombines with the silent donor HML. In contrast, MATα cells inactivate the left arm, including HML, and thus preferentially recombine with HMR, 100 kb to the right of MAT. We present a novel competition assay, in which the DSB at MAT can be repaired either by MAT switching or by single-strand annealing (SSA) between two URA3 genes flanking MAT. With preferred donors, MAT  a or MATα switching occurs 65–70% of the time in competition with SSA. When HML is deleted, 40% of MAT  a cells recombine with the “wrong” donor HMR; however, when HMR is deleted, only 18% of MATα cells recombine with HML. In interchromosomal switching, with donors on chromosome III and MAT on chromosome V, MAT  a retains its strong preference for HML and switching is efficient, when the chromosome III recombination enhancer is present. However, MATα donor preference is lost and interchromosomal switching is very inefficient. These experiments demonstrate the utility of using competition between two outcomes to measure the relative efficiency of recombination.
Large Scale Identification of Genes Involved in Cell Surface Biosynthesis and Architecture in Saccharomyces cerevisiae
Authors: Lussier Marc , White Ann-Marie , Sheraton Jane , di Paolo Tiziano , Treadwell Julie , Southard Susan B , Horenstein Craig I , Chen-Weiner Joan , Ram Arthur F J , Kapteyn Johan C , Roemer Terry W , Vo Dahn H , Bondoc Dana C , Hall John , Zhong Wu Wei , Sdicu Anne-Marie , Davies Julian , Klis Frans M , Robbins Phillips W , Bussey Howard
Published: January 2021

The sequenced yeast genome offers a unique resource for the analysis of eukaryotic cell function and enables genome-wide screens for genes involved in cellular processes. We have identified genes involved in cell surface assembly by screening transposon-mutagenized cells for altered sensitivity to calcofluor white, followed by supplementary screens to further characterize mutant phenotypes. The mutated genes were directly retrieved from genomic DNA and then matched uniquely to a gene in the yeast genome database. Eighty-two genes with apparent perturbation of the cell surface were identified, with mutations in 65 of them displaying at least one further cell surface phenotype in addition to their modified sensitivity to calcofluor. Fifty of these genes were previously known, 17 encoded proteins whose function could be anticipated through sequence homology or previously recognized phenotypes and 15 genes had no previously known phenotype.
Genetic and Environmental Factors Affecting the de novo Appearance of the [PSI
+
] Prion in Saccharomyces cerevisiae
Authors: Derkatch Irina L , Bradley Michael E , Zhou Ping , Chernoff Yury O , Liebman Susan W
Published: January 2021

It has previously been shown that yeast prion [PSI  +  ] is cured by GuHCl, although reports on reversibility of curing were contradictory. Here we show that GuHCl treatment of both [PSI  +  ] and [psi  –  ] yeast strains results in two classes of [psi  –  ] derivatives: Pin+, in which [PSI  +  ] can be reinduced by Sup35p overproduction, and Pin–, in which overexpression of the complete SUP35 gene does not lead to the [PSI  +  ] appearance. However, in both Pin+ and Pin– derivatives [PSI  +  ] is reinduced by overproduction of a short Sup35p N-terminal fragment, thus, in principle, [PSI  +  ] curing remains reversible in both cases. Neither suppression nor growth inhibition caused by SUP35 overexpression in Pin+  [psi  –  ] derivatives are observed in Pin–  [psi  –  ] derivatives. Genetic analyses show that the Pin+ phenotype is determined by a non-Mendelian factor, which, unlike the [PSI  +  ] prion, is independent of the Sup35p N-terminal domain. A Pin–  [psi  –  ] derivative was also generated by transient inactivation of the heat shock protein, Hsp104, while [PSI  +  ] curing by Hsp104 overproduction resulted exclusively in Pin+  [psi  –  ] derivatives. We hypothesize that in addition to the [PSI  +  ] prion-determining domain in the Sup35p N-terminus, there is another self-propagating conformational determinant in the C-proximal part of Sup35p and that this second prion is responsible for the Pin+ phenotype.
High Frequency cDNA Recombination of the Saccharomyces Retrotransposon Ty5: The LTR Mediates Formation of Tandem Elements
Authors: Ke Ning , Voytas Daniel F
Published: January 2021

Retroelement cDNA can integrate into the genome using the element-encoded integrase, or it can recombine with preexisting elements using the recombination system of the host. Recombination is a particularly important pathway for the yeast retrotransposon Ty5 and accounts for ∼30% of the putative transposition events when a homologous substrate is carried on a plasmid and ∼7% when the substrate is located at the chromosomal URA3 locus. Characterization of recombinants revealed that they are either simple replacements of the marker gene or tandem elements. Using an assay system in which the donor element and recombination substrates are separated, we found that the long terminal repeats (LTRs) are critical for tandem element formation. LTR-containing substrates generate tandem elements at frequencies more than 10-fold higher than similarly sized internal Ty5 sequences. Internal sequences, however, facilitate tandem element formation when associated with an LTR, and there is a linear relationship between frequencies of tandem element formation and the length of LTR-containing substrates. We propose that recombination is initiated between the LTRs of the cDNA and substrate and that internal sequences promote tandem element formation by facilitating sequence alignment. Because of its location in subtelomeric regions, recombinational amplification of Ty5 may contribute to the organization of chromosome ends.
Enhancement of Overgrowth by Gene Interactions in lethal(2)giant discs Imaginal Discs From Drosophila melanogaster
Authors: Buratovich Michael A , Bryant Peter J
Published: January 2021

Recessive lethal mutations of the lethal(2)giant discs (l(2)gd) and lethal(2)fat (l(2)ft) loci of Drosophila melanogaster cause imaginal disc hyperplasia during a prolonged larval stage. Imaginal discs from l(2)ft l(2)gd or G l(2)gd double homozygotes show more extensive overgrowth than in either single homozygote, and double homozygous l(2)ft l(2)gd mitotic clones in adult flies show much more overgrowth than is seen in clones homozygous for either l(2)gd or l(2)ft alone. dachsous (ds) also acts as an enhancer of l(2)gd, producing dramatically overgrown discs and causing failure to pupariate in double homozygotes. The comb gap (cg) mutation, which also interacts with ds, greatly enhances the tendency of imaginal discs from l(2)gd larvae to duplicate as they overgrow. If l(2)gd homozygotes are made heterozygous for l(2)ft, then several discs duplicate, indicating that l(2)ft acts as a dominant enhancer of l(2)gd. l(2)ft also acts as a dominant enhancer of l(2)gd, and conversely l(2)gd acts as a dominant modifier of l(2)ft. The enhancement of overgrowth caused by various mutant combinations is accompanied by changes in expression of Decapentaplegic and Wingless. These results show that tumor suppressor genes act in combination to control cell proliferation, and that tissue hyperplasia can be associated with ectopic expression of genes involved in pattern formation.
An Interspecific Backcross of Lycopersicon esculentum × L. hirsutum: Linkage Analysis and a QTL Study of Sexual Compatibility Factors and Floral Traits
Authors: Bernacchi Dario , Tanksley Steven D
Published: January 2021

A BC1, population of the self-compatible tomato Lycopersicon esculentum and its wild self-incompatible relative L. hirsutum f. typicum was used for restriction fragment length polymorphism linkage analysis and quantitative trait loci (QTL) mapping of reproductive behavior and floral traits. The self-incompatibility locus, S, on chromosome 1 harbored the only QTL for self-incompatibility indicating that the transition to self-compatibility in the lineage leading to the cultivated tomato was primarily the result of mutations at the S locus. Moreover, the major QTL controlling unilateral incongruity also mapped to the S locus, supporting the hypothesis that self-incompatibility and unilateral incongruity are not independent mechanisms. The mating behavior of near-isogenic lines carrying the L. hirsutum allele for the S locus on chromosome 1 in an otherwise L. esculentum background support these conclusions. The S locus region of chromosome 1 also harbors most major QTL for several floral traits important to pollination biology (e.g., number and size of flowers), suggesting a gene complex controlling both genetic and morphological mechanisms of reproduction control. Similar associations in other flowering plants suggest that such complex may have been conserved since early periods of plant evolution or else reflect a convergent evolutionary process.
Dominant Enhancers of Egfr in Drosophila melanogaster: Genetic Links Between the Notch and Egfr Signaling Pathways
Authors: Price James V , Savenye Edward D , Lum David , Breitkreutz Ashton
Published: January 2021

The Drosophila epidermal growth factor receptor (EGFR) is a key component of a complex signaling pathway that participates in multiple developmental processes. We have performed and F1 screen for mutations that cause dominant enhancement of wing vein phenotypes associated with mutations in Egfr. With this screen, we have recovered mutations in Hairless (H), vein, groucho (gro), and three apparently novel loci. All of the E(Egfr)s we have identified show dominant interactions in transheterozygous combinations with each other and with alleles of N or Su(H), suggesting that they are involved in cross-talk between the N and EGFR signaling pathways. Further examination of the phenotypic interactions between Egfr, H, and gro revealed that reductions in Egfr activity enhanced both the bristle loss associated with H mutations, and the bristle hyperplasia and ocellar hypertrophy associated with gro mutations. Double mutant combinations of Egfr and gro hypomorphic alleles led to the formation of ectopic compound eyes in a dosage sensitive manner. Our findings suggest that these E(Egfr)s represent links between the Egfr and Notch signaling pathways, and that Egfr activity can either promote or suppress Notch signaling, depending on its developmental context.
Sex Chromosome Meiotic Drive in Stalk-Eyed Flies
Authors: Presgraves Daven C , Severance Emily , Willrinson Gerald S
Published: January 2021

Meiotically driven sex chromosomes can quickly spread to fixation and cause population extinction unless balanced by selection or suppressed by genetic modifiers. We report results of genetic analyses that demonstrate that extreme female-biased sex ratios in two sister species of stalk-eyed flies, Cyrtodiopsis dalmanni and C. whitei, are due to a meiotic drive element on the X chromosome (Xd). Relatively high frequencies of Xd in C. dalmanni and C. whitei (13–17% and 29%, respectively) cause female-biased sex ratios in natural populations of both species. Sex ratio distortion is associated with spermatid degeneration in male carriers of Xd. Variation in sex ratios is caused by Y-linked and autosomal factors that decrease the intensity of meiotic drive. Y-linked polymorphism for resistance to drive exists in C. dalmanni in which a resistant Y chromosome reduces the intensity and reverses the direction of meiotic drive. When paired with Xd, modifying Y chromosomes (Ym) cause the transmission of predominantly Y-bearing sperm, and on average, production of 63% male progeny. The absence of sex ratio distortion in closely related monomorphic outgroup species suggests that this meiotic drive system may predate the origin of C. whitei and C. dalmanni. We discuss factors likely to be involved in the persistence of these sex-linked polymorphisms and consider the impact of Xd on the operational sex ratio and the intensity of sexual selection in these extremely sexually dimorphic flies.
Role of knot (kn) in Wing Patterning in Drosophila
Authors: Nestoras Katerina , Lee Helena , Mohler Jym
Published: January 2021

We have undertaken a genetic analysis of new strong alleles of knot (kn). The original kn1 mutation causes an alteration of wing patterning similar to that associated with mutations of fused (fu), an apparent fusion of veins 3 and 4 in the wing. However, unlike fu, strong kn mutations do not affect embryonic segmentation and indicate that kn is not a component of a general Hh (Hedgehog)-signaling pathway. Instead we find that kn has a specific role in those cells of the wing imaginal disc that are subject to ptc-mediated Hh-signaling. Our results suggest a model for patterning the medial portion of the Drosophila wing, whereby the separation of veins 3 and 4 is maintained by kn activation in the intervening region in response to Hh-signaling across the adjacent anterior-posterior compartment boundary.
Genetic Variation Segregating in Natural Populations of Tribolium castaneum Affecting Traits Observed in Hybrids With T. freemani
Authors: Wade Michael J , Johnson Norman A , Jones Rachel , Siguel Vera , McNaughton Michael
Published: January 2021

We investigated patterns of within-species genetic variation for traits observed in hybrids (hybrid numbers, hybrid sex ratios, and hybrid male deformities) between two species of flour beetles, Tribolium castaneum and T. freemani. We found genetic variation segregating among four natural populations of T. castaneum as well as within these populations. For some hybrid traits, we observed as much variation among populations 750 km apart as between populations on different continents, suggesting genetic differentiation at a local scale. Within natural populations, the variation segregating among sires is greater than that found in an earlier study for an outbred laboratory population and comparable to that observed between inbred lines derived from the outbred stock by eight generations of brother-sister mating. When sires from T. castaneum are mated to conspecific and heterospecific females, we do not observe a significant correlation at the level of the family mean between the intraspecific and interspecific phenotypes, suggesting the independence of the hybrid traits from comparable traits within species. We discuss our findings in relation to the evolutionary genetics of speciation and the expression of epistatic genetic variance in interspecific crosses.
Chromosomal Transmission Bias in Laboratory Hybrids Between Wild Strains of the Two European Subspecies of House Mice
Authors: Lenormand Thomas , Fel-Clair Fabienne , Manolakou Katerina , Alibert Paul , Britton-Davidian Janice
Published: January 2021

Laboratory crosses between wild strains of the two European house mouse subspecies Mus musculus domesticus (2n = 34) and M. m. musculus (2n = 40) were performed to analyze the selective processes involved in the non-introgression of centromeric regions of Robertsonian (Rb) fusions in the Danish hybrid zone. The chromosomal analysis of 226 backcross progeny from 22 reciprocal crosses showed that the segregation of the three Rb fusions present did not significantly differ from Mendelian expectations. However, a significant negative correlation was found between Rb transmission rates and the average litter sizes of the F1 pairs. Among the different models of selection discussed, the most likely one supported the existence of two opposing selective factors resulting in an overall compensation of chromosomal types in the backcross progeny. A two-phase selective process involving embryo competition was postulated with non-Rb carriers being favored during pre-implantation but disadvantaged after implantation. Such balanced selective pressures acting on musculus non-Rb centromeres are compatible with the steep slope and off-centered position of the chromosomal cline observed in the Danish hybrid zone. These results suggested that these selective factors may be more related to centromere origin (musculus or domesticus) than to centromere structure (Rb or non-Rb).
Patterns of DNA Variability at X-Linked Loci in Mus domesticus
Authors: Nachman Michael W
Published: January 2021

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.
Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes
Authors: Feldman Moshe , Liu Bao , Segal Gregorio , Abbo Shahal , Levy Avraham A , Vega Juan M
Published: January 2021

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, lowcopy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.
UV- and Gamma-Radiation Sensitive Mutants of Arabidopsis thaliana
Authors: Jiang C-Z , Yen C-N , Cronin K , Mitchell D , Britt A B
Published: January 2021

Arabidopsis seedlings repair UV-induced DNA damage via light-dependent and -independent pathways. The mechanism of the “dark repair” pathway is still unknown. To determine the number of genes required for dark repair and to investigate the substrate-specificity of this process we isolated mutants with enhanced sensitivity to UV radiation in the absence of photoreactivating light. Seven independently derived UV sensitive mutants were isolated from EMS-mutagenized population. These fell into six complementation groups, two of which (UVR1 and UVH1) have previously been defined. Four of these mutants are defective in the dark repair of UV-induced pyrimidine [6-4]pyrimidinone dimers. These four mutant lines are sensitive to the growth-inhibitory effects of gamma radiation, suggesting that this repair pathway is also involved in the repair of some type of gamma-induced DNA damage product. The requirement for the coordinate action of several different gene products for effective repair of pyrimidine dimers, as well as the nonspecific nature of the repair activity, is consistent with nucleotide excision repair mechanisms previously described in Saccharomyces cerevisiae and nonplant higher eukaryotes and inconsistent with substrate-specific base excision repair mechanisms found in some bacteria, bacteriophage, and fungi.
A Limited Number of Caenorhabditis elegans Genes Are Readily Mutable to Dominant, Temperature-Sensitive Maternal-Effect Embryonic Lethality
Authors: Mitenko Nancy L , Eisner James R , Swiston John R , Mains Paul E
Published: January 2021

Dominant gain-of-function mutations can give unique insights into the study of gene function. In addition, gain-of-function mutations, unlike loss-of-function alleles, are not biased against the identification of genetically redundant loci. To identify novel genetic functions active during Caenorhabditis elegans embryogenesis, we have collected a set of dominant temperature-sensitive maternal-effect embryonic lethal mutations. In a previous screen, we isolated eight such mutations, distributed among six genes. In the present study, we describe eight new dominant mutations that identify only three additional genes, yielding a total of 16 dominant mutations found in nine genes. Therefore, it appears that a limited number of C. elegans genes mutate to this phenotype at appreciable frequencies. Five of the genes that we identified by dominant mutations have loss-of-function alleles. Two of these genes may lack loss-of-function phenotypes, indicating that they are nonessential and so may represent redundant loci. Loss-of-function mutations of three other genes are associated with recessive lethality, indicating nonredundancy.
Drosophila Male-Specific Lethal-4 Protein: Structure/Function Analysis and Dependence on MSL-1 for Chromosome Association
Authors: Lyman Laura M , Copps Kyle , Rastelli Luca , Kelly Richard L , Kuroda Mitzi I
Published: January 2021

MSL-2 is required for the male-specific assembly of a dosage compensation regulatory complex on the X chromosome of Drosophila melanogaster. We found that MSL-2 binds in a reproducible, partial pattern to the male Xchromosome in the absence of MLE or MSL-3, or when ectopically expressed at a low level in females. Moreover, the pattern of MSL-2 binding corresponds precisely in each case to that of MSL-1, suggesting that the two proteins function together to associate with the X. Consistent with this hypothesis, we isolated EMSinduced loss of function msl-1 and msl-2 alleles in a screen for suppressors of the toxic effects of MSL-2 expression in females. We also used sitedirected mutagenesis to determine the importance of the MSL-2 RING finger domain and second cysteine-rich motif. The mutations, including those in conserved zinc coordinating cysteines, confirm that the RING finger is essential for MSL-2 function, while suggesting a less stringent requirement for an intact second motif.
Patterns of Mitochondrial Variation Within and Between African Malaria Vectors, Anopheles gambiae and An. arabiensis, Suggest Extensive Gene Flow
Authors: Besansky Nora J , Lehmann Tovi , Fahey G Thomas , Fontenille Didier , Braack Lawrence E O , Hawley William A , Collins Frank H
Published: January 2021

Anopheles gambiae and An. arabiensis are mosquito species responsible for most malaria transmission in sub-Saharan Africa. They are also closely related sibling species that share chromosomal and molecular polymorphisms as a consequence of incomplete lineage sorting or introgressive hybridization. To help resolve these processes, this study examined the partitioning of mtDNA sequence variation within and between species across Africa, from both population genetic and phylogeographic perspectives. Based on partial gene sequences from the cytochrome b, ND1 and ND5 genes, haplotype diversity was high but sequences were very closely related. Within species, little or no population subdivision was detected, and there was no evidence for isolation by distance. Between species, there were no fixed nucleotide differences, a high proportion of shared polymorphisms, and eight haplotypes in common over distances as great as 6000 km. Only one of 16 shared polymorphisms led to an amino acid difference, and there was no compelling evidence for nonneutral variation. Parsimony networks constructed of haplotypes from both species revealed no correspondence of haplotype with either geography or taxonomy. This trend of low intraspecific genetic divergence is consistent with evidence from allozyme and microsatellite data and is interpreted in terms of both extensive gene flow and recent range expansion from relatively large, stable populations. We argue that retention of ancestral polymorphisms is a plausible but insufficient explanation for low interspecific genetic divergence, and that extensive hybridization is a contributing factor.
DNA Polymorphism at the Pgi Locus of a Wild Yam, Dioscorea tokoro
Authors: Terauchi Ryohei , Terachi Tom , Miyashita Naohiko T
Published: January 2021

To study the origin and maintenance mechanisms of the PGI allozyme polymorphism of a wild plant, Dioscorea tokoro, DNA sequences of the entire coding region (1701 bp) and two intronic regions (total 2049 bp) of the Pgi gene as well as a part of the Adh gene (590 bp) were analyzed. Two replacement substitutions were revealed to be responsible for the differentiation of three allozymes alleles (Pgi-a, Pgi-b and Pgi-c) that occur in natural population in intermediate frequencies. Interspecific comparison of DNA sequences identified Pgi-6 as the oldest allele, from which two other alleles were derived probably within the last 150,000 years. The level of DNA polymorphism at D. tokoro Pgi locus was low. No elevated level of DNA polymorphism was detected in the close vicinity of the two replacement sites differentiating the three allozymes. Departures from the neutral mutation hypothesis were detected by Fu and Li's and MK tests. The observed patterns of DNA polymorphism are explainable by both (1) the neutral mutation hypothesis with an assumption of small effective size of D. tokoro population, and (2) the positive selection hypothesis that the allele frequencies of Pgi-a and Pgi-c have increased in a short time by their selective advantages.
Cognitive Stimulation Therapy for Older Adults With Mild-to-Moderate Dementia in Italy: Effects on Cognitive Functioning, and on Emotional and Neuropsychiatric Symptoms
Authors: Carbone Elena , Gardini Simona , Pastore Massimiliano , Piras Federica , Vincenzi Margherita , Borella Erika
Published: January 2021

Objectives

Cognitive Stimulation Therapy (CST) is one of the most popular evidence-based interventions for people with dementia. The aim of the present study was to assess the effectiveness in the short- and long-term (on completing the treatment and 3 months later) of an Italian adaptation of the CST protocol (CST-IT).

Method

Older adults with mild-to-moderate dementia at 16 residential care homes were randomly assigned to a CST-IT group (N = 123) or an active control group (N = 102). The following domains were examined for potential benefits: general cognitive functioning (Mini-Mental State Examination [MMSE] and the Alzheimer’s Disease Assessment Scale—Cognitive subscale [ADAS-Cog]), language (Narrative Language Test), mood and behavior (Cornell scale and Neuropsychiatric Inventory), everyday life functioning (Disability Assessment for Dementia), and quality of life (Quality of Life—Alzheimer’s Disease scale).

Results

At both the short- and long-term assessments, the CST-IT group’s MMSE scores remained stable, while the control group’s scores decreased slightly from pretest to posttest and at follow-up. The CST-IT group also had short-term benefits in other cognitive measures (ADAS-Cog and Narrative Language Test) and mood and behavior measures, which were generally maintained at follow-up. No other differences were observed.

Discussion

The effectiveness of CST in sustaining cognitive and emotional functioning, and counteracting the progression of behavioral/neuropsychiatric symptoms in people with dementia was confirmed, and a long-term benefit was demonstrated. CST is a promising option for the treatment of people with dementia in clinical practice.
The Effect of Lifestyle Interventions on the International Classification of Functioning, Disability and Health Participation Domain in Older Adults: A Systematic Review and Meta-Analysis
Authors: O’Hoski Sachi , Chauvin Stephanie , Vrkljan Brenda , Beauchamp Marla K
Published: January 2021

Background and Objectives

The World Health Organization’s International Classification of Functioning, Disability and Health (ICF) recognizes participation in life situations as a major component of health. Identifying interventions that target this component is critical, particularly in older adulthood, where declines in physical functioning can impact participation. The purpose of this study was to evaluate the effectiveness of lifestyle or behavior change interventions on the ICF participation domain in older adults.

Research Design and Methods

MEDLINE (Ovid), Embase (Ovid), CINAHL (EBSCO), AgeLine (EBSCO), PsycINFO (Ovid), and AMED (Ovid) were searched from inception to April 2020 for randomized controlled trials comparing the effects of any behavior change or lifestyle intervention to usual care among community-dwelling adults ≥60 years with respect to participation-related domains of the ICF. The protocol was registered with Prospero (CRD42019125334).

Results

Eight studies with a total of 1,548 participants were included. No significant effect on participation outcomes was found (standardized mean difference 0.04; 95% CI −0.19 to 0.26; p = .76) and the quality of evidence was judged to be very low.

Discussion and Implications

Lifestyle or behavior change interventions showed limited effect on participation in later life. However, there remains much uncertainty in the estimate of this effect due, in part, to the low quality of the included studies. Measurement tools that are responsive to changes in participation in older adulthood should be used to determine the effect of such interventions. Improving study design will lead to more efficacious interventions that promote participation for our aging population.
PM4NGS, a project management framework for next-generation sequencing data analysis
Authors: Vera Alvarez Roberto , Pongor Lorinc , Mariño-Ramírez Leonardo , Landsman David
Published: January 2021

Background

FAIR (Findability, Accessibility, Interoperability, and Reusability) next-generation sequencing (NGS) data analysis relies on complex computational biology workflows and pipelines to guarantee reproducibility, portability, and scalability. Moreover, workflow languages, managers, and container technologies have helped address the problem of data analysis pipeline execution across multiple platforms in scalable ways.

Findings

Here, we present a project management framework for NGS data analysis called PM4NGS. This framework is composed of an automatic creation of a standard organizational structure of directories and files, bioinformatics tool management using Docker or Bioconda, and data analysis pipelines in CWL format. Pre-configured Jupyter notebooks with minimum Python code are included in PM4NGS to produce a project report and publication-ready figures. We present 3 pipelines for demonstration purposes including the analysis of RNA-Seq, ChIP-Seq, and ChIP-exo datasets.

Conclusions

PM4NGS is an open source framework that creates a standard organizational structure for NGS data analysis projects. PM4NGS is easy to install, configure, and use by non-bioinformaticians on personal computers and laptops. It permits execution of the NGS data analysis on Windows 10 with the Windows Subsystem for Linux feature activated. The framework aims to reduce the gap between researcher in experimental laboratories producing NGS data and workflows for data analysis. PM4NGS documentation can be accessed at https://pm4ngs.readthedocs.io/.
Broad Specifications and Intent to Use: Is the EU Trade Mark System Credible?
Authors: Arnold Richard
Published: January 2021

An assessment of the credibility of the EU trade mark system in the light of the ruling of the Court of Justice of the European Union in Case C-371/18 Sky v SkyKick leads to the following conclusions: the decisions that lack of clarity and precision of specifications of goods and services is not a ground of invalidity and that partial bad faith when applying to register a trade mark leads to partial invalidity are unsurprising; the decision that applying to register a trade mark without intending to use it can amount to bad faith, at least in some circumstances, is an important step forward that gives national courts a tool with which to combat unjustifiably broad specifications of goods and services; but the jury is still out with regard to the EU trade mark system’s acceptance of broad terms such as ‘computer software’ in specifications.
19. Pensions in Financial Proceedings
Authors: Hodgson Roiya
Published: January 2021

This chapter covers pensions and pension orders available to the court. It discusses what a pension is, the pension as a financial instrument, and how a pension is valued. The cash equivalent transfer value (CETV) is explained. The chapter explains how pensions are dealt with following divorce or dissolution and the various options for pensions in financial proceedings. One of the options includes pension offsetting, which is the least complex option. The other two options that are discussed are pension attachment and pension sharing. It is explained that pension sharing was the solution to the problems and unpopularity of the pension attachment order.
28. Child Abduction
Authors: Hodgson Roiya
Published: January 2021

This chapter focuses on the issue of parental child abduction, i.e. the removal of children by a parent to another country without the permission of the other parent or the permission of the court. It looks at jurisdiction, in which circumstances removal may be lawful, passports, and port alerts. It examines the phenomenon of parental child abduction; the national and international law assisting parents seeking the return of a child; and the law and procedure relevant to preventing child abduction. Hague and non-Hague convention countries are also discussed, as well as what can be done if a child is abducted to a non-Hague convention country.
29. Children in Local Authority Care
Authors: Hodgson Roiya
Published: January 2021

This chapter examines the role of local authorities in protecting the child from harm and the orders available under the Children Act 1989, which are used in cases of alleged harm to children. It explains the nature of public child law proceedings and goes into detail to discuss the definition of the ‘threshold criteria’—the standard that the court uses to decide whether an order should be made. It also discusses the investigations which can be carried out by the local authority in relation to a child and parental contact with children in care, and compares a care order and a supervision order.
30. Emergency Protection of Children
Authors: Hodgson Roiya
Published: January 2021

When a child is in imminent need of protection, the order used to protect the child is an emergency protection order (EPO) under s44 of the Children Act 1989. This chapter discusses the use of emergency protection orders in public law for children and examines the factors a court will consider when asked to make an emergency order. It looks at contact when an EPO is in place, duration and discharge of an application, and procedure. Case-law is used to provide guidance. It also looks at the powers available to the police when faced with a child in need of protection.
32. Child Protection Conferences
Authors: Hodgson Roiya
Published: January 2021

A local authority’s investigation into a child’s health and development includes a case conference so that information about the child can be shared by those involved with the child and family. This chapter discusses the function of a child protection conference in public children law and the role of a solicitor in the conference. Family group conferences are also discussed, as well as who attends the child protection conference, their contributions to it, and when a child protection conference will be held. Confidentiality in the child protection and parents being excludes from all or parts of the conference is explained.
34. Protection under the Family Law Act 1996: Occupation Orders
Authors: Hodgson Roiya
Published: January 2021

The Family Law Act 1996 allows a court to make occupation orders to regulate the occupation of the family home. This chapter discusses the effect of occupation orders in that the general aim is to regulate the occupation of the family home. The tests for each order, duration, and which order to choose for the client are outlined under each section. What the court can order is also explained as well as ancillary orders and transfer of tenancies. A flowchart is provided in order to help work out which order to apply for, depending on the circumstances of the case.