bluuebunny/crossref_metadata_2025 huggingface dataset:
The Estimation of the Number and the Length Distribution of Gene Conversion Tracts From Population DNA Sequence Data
Authors: Betrán Esther , Rozas Julio , Navarro Arcadio , Barbadilla Antonio
Published: January 2021

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: ψ, which measures the probability of detecting a converted site, and φ the parameter of the geometric distribution, from which the average true tract length, 1 / (1 – φ), can be estimated. Expressions are provided for estimating φ by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of φ for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.
A Putative Rhamnogalacturonase Required for Sexual Development of Neurospora crassa
Authors: Nelson Mary Anne , Merino Sandra T , Metzenberg Robert L
Published: January 2021

In previous work, the asd-1 (ascus development) gene of the filamentous fungus Neurospora crassa was identified as a gene expressed preferentially during the sexual cycle and shown to be essential for normal sexual development. The asd-1 gene has been sequenced and further characterized. It contains two introns, the first of which is in-frame and inefficiently or differentially spliced. The predicted ASD-1 protein has extensive homology with rhamnogalacturonase B of Aspergillus aculeatus, which cleaves the backbone within the ramified hairy regions of pectin. In homozygous asd-1 crosses, sexual development is initiated and large numbers of normal-sized asci are formed. Ascospore delineation does not occur, however, and no sexual progeny are produced. As most asd-1 asci contain eight nuclei, the two meiotic divisions and subsequent mitotic division typical of normal crosses seem to occur, but the haploid nuclei are not partitioned into ascospores. In wild-type crosses, the ASD-1 protein is present in large amounts in croziers and young asci, but it is only faintly detectable in more mature asci containing developing ascospores. Models to explain the possible role of a rhamnogalacturonase in sexual development are presented.
Ras1-Mediated Modulation of Drosophila Homeotic Function in Cell and Segment Identity
Authors: Boube Muriel , Benassayag Corinne , Seroude Laurent , Cribbs David L
Published: January 2021

Mutations of the Drosophila homeotic proboscipedia gene (pb; the Hox-A2/B2 homologue) provoke dose-sensitive defects. These were used to search for dose-sensitive dominant modifiers of pb function. Two identified interacting genes were the proto-oncogene Ras1 and its functional antagonist Gap1, prominent intermediaries in known signal transduction pathways. Ras1+ is a positive modifier of pb activity both in normal and ectopic cell contexts, while the Ras1-antagonist Gap1 has an opposite effect. A general role for Ras1 in homeotic function is likely, since Ras1+ activity also modulates functions of the homeotic loci Sex combs reduced and Ultrabithorax. Our data suggest that the modulation occurs by a mechanism independent of transcriptional control of the homeotic loci themselves, or of the Ras1/Gap1 genes. Taken together our data support a role for Ras1-mediated cell signaling in the homeotic control of segmental differentiation.
Recombination Creates Novel L1 (LINE-1) Elements in Rattus norvegicus
Authors: Hayward Bruce E , Zavanelli Mary , Furano Anthony V
Published: January 2021

Mammalian L1 (long interspersed repeated DNA, LINE-1) retrotransposons consist of a 5′ untranslated region (UTR) with regulatory properties, two protein encoding regions (ORF I, ORF II, which encodes a reverse transcriptase) and a 3′ UTR. L1 elements have been evolving in mammals for >100 million years and this process continues to generate novel L1 subfamilies in modern species. Here we characterized the youngest known subfamily in Rattus norvegicus, L1mlvi2, and unexpectedly found that this element has a dual ancestry. While its 3′ UTR shares the same lineage as its nearest chronologically antecedent subfamilies, L13 and L14, its ORF I sequence does not. The L1mlvi2 ORF I was derived from an ancestral ORF I sequence that was the evolutionary precursor of the L13 and L14 ORF I. We suggest that an ancestral ORF I sequence was recruited into the modern L1mlvi2 subfamily by recombination that possibly could have resulted from template strand switching by the reverse transcriptase during L1 replication. This mechanism could also account for some of the structural features of rodent L1 5′ UTR and ORF I sequences including one of the more dramatic features of L1 evolution in mammals, namely the repeated acquisition of novel 5′ UTRs.
A Likelihood Approach to Populations Samples of Microsatellite Alleles
Authors: Nielsen Rasmus
Published: January 2021

This paper presents a likelihood approach to population samples of microsatellite alleles. A Markov chain recursion method previously published by Griffiths and Tavaré applied to estimate the likelihood function under different models of microsatellite evolution. The method presented can be applied to estimate a fundamental population genetics parameter θ as well as parameters of the mutational model. The new likelihood estimator provides a better estimator of θ in terms of the mean square error than previous approaches. Furthermore, it is demonstrated how the method may easily be applied to test models of microsatellite evolution. In particular it is shown how to compare a one-step model of microsatellite evolution to a multi-step model by a likelihood ratio test.
Cloning of the Arabidopsis and Rice Formaldehyde Dehydrogenase Genes: Implications for the Origin of Plant ADH Enzymes
Authors: Dolferus R , Osterman J C , Peacock W J , Dennis E S
Published: January 2021

This article reports the cloning of the genes encoding the Arabidopsis and rice class III ADH enzymes, members of the alcohol dehydrogenase or medium chain reductase/dehydrogenase superfamily of proteins with glutathione-dependent formaldehyde dehydrogenase activity (GSH-FDH). Both genes contain eight introns in exactly the same positions, and these positions are conserved in plant ethanolactive Adh genes (class P). These data provide further evidence that plant class P genes have evolved from class III genes by gene duplication and acquisition of new substrate specificities. The position of introns and similarities in the nucleic acid and amino acid sequences of the different classes of ADH enzymes in plants and humans suggest that plant and animal class I11 enzymes diverged before they duplicated to give rise to plant and animal ethanol-active ADH enzymes. Plant class P ADH enzymes have gained substrate specificities and evolved promoters with different expression properties, in keeping with their metabolic function as part of the alcohol fermentation pathway.
A Population Genetics Model of Marker-Assisted Selection
Authors: Luo Z W , Thompson R , Woolliams J A
Published: January 2021

A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.
A Sex-Influenced Modifier in Drosophila That Affects a Broad Spectrum of Target Loci Including the Histone Repeats
Authors: Bhadra Utpal , Pal-Bhadra Manika , Birchler James A
Published: January 2021

A second chromosomal trans-acting modifier, Lightener of white (Low), modulates the phenotypic expression of various alleles of the white eye color gene. This modifier has an unusually broad spectrum of affected genes including white, brown, scarlet and the eye developmental genes, Bar and Lobe. In addition, Low weakly suppresses position effect variegation. Northern blot hybridization with different X and autosomal probes reveals that Low modulates genes of independent expression patterns. Interestingly, many of the modulations of gene expression are developmentally restricted and differ in intensity between the sexes. Low also elevates the expression of the histone tandem repeats in three distinct developmental stages. A deficiency encompassing the histone cluster reduces their transcript levels and significantly alters the expression of some of the tested genes. Thus, Low is a modifier that plays a role in modulating the expression of genes governing various processes including pigment deposition, eye development, chromosomal proteins and position effect variegation.
Molecular and Genetic Analysis of REC103, an Early Meiotic Recombination Gene in Yeast
Authors: Gardiner Jack M , Bullard Steven A , Chrome Chris , Malone Robert E
Published: January 2021

In the yeast Saccharomyces cerevisiae at least 10 genes are required to begin meiotic recombination. A new early recombination gene REC103 is described in this paper. It was initially defined by the rec103-1 mutation found in a selection for mutations overcoming the spore inviability of a rad52 spo13 haploid strain. Mutations in REC103 also rescue rad52 in spo13 diploids. rec103 spo13 strains produce viable spores; these spores show no evidence of meiotic recombination. rec103 SPO13 diploids produce no viable spores, consistent with the loss of recombination. Mutations in REC103 do not affect mitotic recombination, growth, or repair. These phenotypes are identical to those conferred by mutations in several other early meiotic recombination genes (e.g., REC102, REC104, REC114, MEI4, MER-2, and SPO11). REC103 maps to chromosome VII between ADE5 and RAD54. Cloning and sequencing of REC103 reveals that REC103 is identical to SK18, a gene that depresses the expression of yeast double-stranded (“killer”) (ds)RNA viruses. REC103/SK18 is transcribed in mitotic cells and is induced ∼15-fold in meiosis. REC103 has 26% amino acid identity to the Schizosaccharomyces pombe rec14  + gene; mutations in both genes confer similar meiotic phenotypes, suggesting that they may play similar roles in meiotic recombination.
The vrille Gene of Drosophila Is a Maternal Enhancer of decapentaplegic and Encodes a New Member of the bZIP Family of Transcription Factors
Authors: George Hélène , Terracol Régine
Published: January 2021

We report here the genetical and molecular characterization of a new Drosophila zygotic lethal locus, vrille (vri). vri alleles act not only as dominant maternal enhancers of embryonic dorsoventral patterning defects caused by easter and decapentaplegic (dpp) mutations, but also as dominant zygotic enhancers of dpp alleles for phenotypes in wing. The vri gene encodes a new member of the bZIP family of transcription factors closely related to gene 9 of Xenopus laevis, induced by thyroid hormone during the tadpole tail resorption program, and NF-IL3A, a human T cell transcription factor that transactivates the interleukin-3 promoter. NF-IL3A shares 93% similarity and 60% identity with Vri for a stretch of 68 amino acids that includes the bZIP domain. Although all the alleles tested behave like antimorphs, the dominant enhancement is also seen with a nonsense mutation allele that prevents translation of the bZIP domain. Because of the strong dominant enhancement of dpp phenotypes by vri alleles in both embryo and wing, and also the similarity between the wing vein phenotypes caused by the vri and shortvein dpp alleles, we postulate that vri interacts either directly or indirectly with certain components of the dpp (a TGFβ homologue) signal transduction pathway.
Occurrence of Repeat Induced Point Mutation in Long Segmental Duplications of Neurospora
Authors: Perkins David D , Margolin Brian S , Selker Eric U , Haedo S D
Published: January 2021

Previous studies of repeat induced point mutation (RIP) have typically involved gene-size duplications resulting from insertion of transforming DNA at ectopic chromosomal positions. To ascertain whether genes in larger duplications are subject to RIP, progeny were examined from crosses heterozygous for long segmental duplications obtained using insertional or quasiterminal translocations. Of 17 distinct mutations from crossing 11 different duplications, 13 mapped within the segment that was duplicated in the parent, one was closely linked, and three were unlinked. Half of the mutations in duplicated segments were at previously unknown loci. The mutations were recessive and were expressed both in haploid and in duplication progeny from Duplication × Normal, suggesting that both copies of the wild-type gene had undergone RIP. Seven transition mutations characteristic of RIP were found in 395 base pairs (bp) examined in one ro-11 allele from these crosses and three were found in ~750 bp of another. A single chain-terminating C to T mutation was found in 800 bp of arg-6. RIP is thus responsible. These results are consistent with the idea that the impaired fertility that is characteristic of segmental duplications is due to inactivation by RIP of genes needed for progression through the sexual cycle.
Identification of Genes Controlling Growth Polarity in the Budding Yeast Saccharomyces cerevisiae: A Possible Role of N-Glycosylation and Involvement of the Exocyst Complex
Authors: Mondésert G , Clarke D J , Reed S I
Published: January 2021

The regulation of secretion polarity and cell surface growth during the cell cycle is critical for proper morphogenesis and viability of Saccharomyces cerevisiae. A shift from isotropic cell surface growth to polarized growth is necessary for bud emergence and a repolarization of secretion to the bud neck is necessary for cell separation. Although alterations in the actin cytoskeleton have been implicated in these changes in secretion polarity, clearly other cellular systems involved in secretion are likely to be targets of cell cycle regulation. To investigate mechanisms coupling cell cycle progression to changes in secretion polarity in parallel with and downstream of regulation of actin polarization, we implemented a screen for mutants defective specifically in polarized growth but with normal actin cytoskeleton structure. These mutants fell into three classes: those partially defective in N-glycosylation, those linked to specific defects in the exocyst, and a third class neither defective in glycosylation nor linked to the exocyst. These results raise the possibility that changes in N-linked glycosylation may be involved in a signal linking cell cycle progression and secretion polarity and that the exocyst may have regulatory functions in coupling the secretory machinery to the polarized actin cytoskeleton.
Genetic Interactions Between a pep7 Mutation and the PEP12 and VPS45 Genes: Evidence for a Novel SNARE Component in Transport Between the Saccharomyces cerevisiae Golgi Complex and Endosome
Authors: Webb Gene C , Hoedt Marloes , Poole Lynn J , Jones Elizabeth W
Published: January 2021

The PEP7 gene from Saccharomyces cerevisiae encodes a 59-kD hydrophilic polypeptide that is required for transport of soluble vacuolar hydrolase precursors from the TGN to the endosome. This study presents the results of a high-copy suppression analysis of pep7-20 mutant phenotypes. This analysis demonstrated that both VPS45 and PEP12 are allele-specific high-copy suppressors of pep7-20 mutant phenotypes. Overexpression of VPS45 was able to completely suppress the Zn2+ sensitivity and partially suppress the carboxypeptidase Y deficiency. Overexpression of PEP12 was able to do the same, but to a lesser extent. Vps45p and Pep12p are Sec1p and syntaxin (t-SNARE) homologues, respectively, and are also thought to function in transport between the TGN and endosome. Two additional vacuole pathway SNARE complex homologues, Vps33p (Sec1p) and Pth1p (syntaxin), when overexpressed, were unable to suppress pep7-20 or any other pep7 allele, further supporting the specificity of the interactions of pep7-20 with PEP12 and VPS45. Because several other vesicle docking/fusion reactions take place in the cell without discernible participation of Pep7p homologues, we suggest that Pep7p is a step-specific regulator of docking and/or fusion of TGN-derived transport vesicles onto the endosome.
Mating-Type Genes From the Homothallic Fungus Sordaria macrospora Are Functionally Expressed in a Heterothallic Ascomycete
Authors: Pöggeler Stefanie , Risch Siegfried , Kück Ulrich , Osiewacz Heinz D
Published: January 2021

Homokaryons from the homothallic ascomycte Sordaria macrospora are able to enter the sexual pathway and to form fertile fruiting bodies. To analyze the molecular basis of homothallism and to elucidate the role of mating-products during fruiting body development, we cloned and sequenced the entire S. macrospora mating-type locus. Comparison of the Sordaria mating-type locus with mating-type idiomorphs from the heterothallic ascomycetes Neurospora crassa and Podospora anserina revealed that sequences from both idiomorphs (A/a and mat–/mat+, respectively) are contiguous in S. macrospora. DNA sequencing of the S. macrospora mating-type region allowed the identification of four open reading frames (ORFs), which were termed Smt-a1, SmtA-1, SmtA-2 and SmtA-3. While Smt-a1, SmtA-1, and SmtA-2 show strong sequence similarities with the corresponding N. crassa mating-type ORFs, SmtA-3 has a chimeric character. It comprises sequences that are similar to the A and a mating-type idiomorph from N. crassa. To determine functionality of the S. macrospora mating-type genes, we show that all ORFs are transcriptionally expressed. Furthermore, we transformed the S. macrospora mating-type genes into mat– and mat+ strains of the closely related heterothallic fungus P. anserina. The transformation experiments show that mating-type genes from S. macrospora induce fruiting body formation in P. anserina.
A Mutation in an HSP90 Gene Affects the Sexual Cycle and Suppresses Vegetative Incompatibility in the Fungus Podospora anserina
Authors: Loubradou Gabriel , Bégueret Joel , Turcq Béatrice
Published: January 2021

Vegetative incompatibility is widespread in fungi but its molecular mechanism and biological function are still poorly understood. A way to study vegetative incompatibility is to investigate the function of genes whose mutations suppress this phenomenon. In Podospora anserina, these genes are known as mod genes. In addition to suppressing vegetative incompatibility, mod mutations cause some developmental defects. This suggests that the molecular mechanisms of vegetative incompatibility and development pathways are interconnected. The mod-E1 mutation was isolated as a suppressor of the developmental defects of the mod-D2 strain. We show here that mod-E1 also partially suppresses vegetative incompatibility, strengthening the link between development and vegetative incompatibility. mod-E1 is the first suppressor of vegetative incompatibility characterized at the molecular level. It encodes a member of the Hsp90 family, suggesting that development and vegetative incompatibility use common steps of a signal transduction pathway. The involvement of mod-E in the sexual cycle has also been further investigated.
The Ac-st2 Element of Maize Exhibits a Positive Dosage Effect and Epigenetic Regulation
Authors: Brutnell Thomas P , May Bruce P , Dellaporta Stephen L
Published: January 2021

A novel derivative of the maize transposable element Ac, termed Ac-st2, that displays a positive dosage effect in maize has been identified. Although identical in sequence to other Ac elements, increasing the copy number of the element in the endosperm results in earlier and more frequent Ds excisions. Ac-st2 autonomously transposes and catalyzes somatic excisions of Ds elements. Germinal transpositions of either Ac-st2 or Ds, however, were not observed. The Ac-st2 phenotype includes a reduction in Ac transcript accumulation that is associated with increased methylation at specific sites in the promoter region of the major transcriptional start site within Ac (ORFa). This element differs from metastable (cycling) Ac derivatives in that Ac-st2 conditions a uniform transposition pattern throughout endosperm and plant development. Ac-st2 undergoes frequent increases in activity after its association with an active Ac element. This change in activity correlates with reduced levels of methylation in the ORFa promoter region. Using a competitive PCR assay, Ac transcript accumulation was followed through endosperm development. From these data, a model is proposed to explain the patterns of variegation associated with both “wild type” active Ac and Ac-st2 elements.
Mutational Analysis of Cdc19p, a Schizosaccharomyces pombe MCM Protein
Authors: Forsburg Susan L , Sherman Daniel A , Ottilie Sabine , Yasuda J Randy , Hodson Jeffrey A
Published: January 2021

The cdc19  + gene encodes an essential member of the MCM family of replication proteins in Schizosaccharomyces pombe. We have examined the structure and function of the Cdc19p protein using molecular and genetic approaches. We find that overproduction of wild-type Cdc19p in wild-type cells has no effect, but cdc19-P1 mutant cells do not tolerate elevated levels of other MCM proteins or overexpression of mutant forms of Cdc19p. We have found genetic interactions between cdc19  + and genes encoding subunits of DNA polymerase δ and the replication initiator cdc18  +. We have constructed a series of point mutations and sequence deletions throughout Cdc19p, which allow us to distinguish essential from nonessential regions of the protein. Not surprisingly, conserved residues in the MCM homology domain are required for protein function, but some residues outside the core homology domain are dispensable.
Extended Reproductive Roles of the fruitless Gene in Drosophila melanogaster Revealed by Behavioral Analysis of New fru Mutants
Authors: Villella Adriana , Gailey Donald A , Berwald Barbra , Ohshima Saiyou , Barnes Phillip T , Hall Jeffrey C
Published: January 2021

The fruitless mutants fru3 and fru4 were assessed for sex-specific reproductive-behavioral phenotypes and compared to the previously reported fru mutants. Among the several behavioral anomalies exhibited by males expressing these relatively new mutations, some are unique. fru3 and fru4 males are less stimulated to court females than and fru1 and fru2. No courtship pulse song is generated by either fru3 or fru4 males, even though they perform brief wing extensions. fru3 and fru4 males display significantly less chaining behavior than do fru1 males. The hierarchy of courtship responses by fru males directed toward females vs. males, when presented with both sexes simultaneously, is that fru1 males perform vigorous and indiscriminant courtship directed at either sex; fru4 males are similarly indiscriminant, but courtship levels were lower than fru1; fru2 males prefer females; fru3 males show a courtship bias toward males. fru3 and fru4 males essentially lack the Muscle of Lawrence (MOL). On several reproductive criteria, there was no difference between fru-variant females and fru  +. The increases in phenotypic severity measured for the new mutants are discussed in the context of the emerging molecular genetics of fru and with regard to the gene's position within the sex-determination pathway.
Variation of Dominance of Newly Arisen Adaptive Genes
Authors: Bourguet Denis , Lenormand Thomas , Guillemaud Thomas , Marcel Véronique , Fournier Didier , Raymond Michel
Published: January 2021

Newly arisen adaptive alleles such as insecticide resistance genes represent a good opportunity to investigate the theories put forth to explain the molecular basis of dominance and its possible evolution. Dominance levels of insecticide resistance conferred by insensitive alleles of the acetylcholinesterase gene were analyzed in five resistant strains of the mosquito Culex pipiens. Dominance levels were found to differ between strains, varying from partial recessivity to complete dominance. This variation was not explained by differences in catalytic properties of the enzyme, since four of the five resistant strains had identical inhibition properties for the insensitive acetylcholinesterase. Among these four laboratory strains and in individuals collected from natural populations, we found a correlation between increased acetylcholinesterase activities and higher dominance levels. We propose a molecular explanation for how variation in acetylcholinesterase activity may result in variation of dominance level. We also conjecture that the four resistant strains did not differ in their amino acid sequence in the catalytically active regions of acetylcholinesterase, but that the expression of the gene was regulated by either neighboring or distant sites, thereby modifying the dominance level. Under this interpretation, dominance levels may evolve in this system, since heritable variation in acetylcholinesterase activity was found.
Historical Analysis of Genetic Variation Reveals Low Effective Population Size in a Northern Pike (Esox lucius) Population
Authors: Miller Loren M , Kapuscinski Anne R
Published: January 2021

Effective population size (Ne) of a natural fish population was estimated from temporal changes in allele frequencies at seven microsatellite loci. Use of a historical collection of fish scales made it possible to increase the precision of estimates by increasing the time interval between samples and to use an equation developed for discrete generations without correcting for demographic parameters. Estimates of Ne for the time intervals 1961–1977 and 1977–1993 were 35 and 72, respectively. For the entire interval, 1961–1993, the estimate of Ne was 48 when based on a weighted mean derived from the above two estimates or 125 when calculated from 1961 and 1993 samples only. Corresponding ratios of effective size to adult census size ranged from 0.03 to 0.14. An Ne of 48 over a 32-year period would imply that this population lost as much as 8% of its heterozygosity in that time. Results suggest the potential for using genetic methods based on microsatellite loci data to compare historical trends in Ne with population dynamic parameters. Such comparisons will help to evaluate the relationship between genetic diversity and long-term persistence of natural populations.
Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution
Authors: Nadeau Joseph H , Sankoff David
Published: January 2021

Duplicated genes are an important source of new protein functions and novel developmental and physiological pathways. Whereas most models for fate of duplicated genes show that they tend to be rapidly lost, models for pathway evolution suggest that many duplicated genes rapidly acquire novel functions. Little empirical evidence is available, however, for the relative rates of gene loss vs. divergence to help resolve these contradictory expectations. Gene families resulting from genome duplications provide an opportunity to address this apparent contradiction. With genome duplication, the number of duplicated genes in a gene family is at most 2n, where n is the number of duplications. The size of each gene family, e.g., 1, 2, 3,..., 2n, reflects the patterns of gene loss vs. functional divergence after duplication. We focused on gene families in humans and mice that arose from genome duplications in early vertebrate evolution and we analyzed the frequency distribution of gene family size, i.e., the number of families with two, three or four members. All the models that we evaluated showed that duplicated genes are almost as likely to acquire a new and essential function as to be lost through acquisition of mutations that compromise protein function. An explanation for the unexpectedly high rate of functional divergence is that duplication allows genes to accumulate more neutral than disadvantageous mutations, thereby providing more opportunities to acquire diversified functions and pathways.
DNA Sequence Analysis of Sry Alleles (Subgenus Mus) Implicates Misregulation as the Cause of C57BL/6J-YPOS Sex Reversal and Defines the SRY Functional Unit
Authors: Albrecht Kenneth H , Eicher Eva M
Published: January 2021

The Sry (sex determining region, Y chromosome) open reading frame from mice representing four species of the genus Mus was sequenced in an effort to understand the conditional dysfunction of some M. domesticus Sry alleles when present on the C57BL/6J inbred strain genetic background and to delimit the functionally important protein regions. Twenty-two Sry alleles were sequenced, most from wild-derived Y chromosomes, including 11 M. domesticus alleles, seven M. musculus alleles and two alleles each from the related species M. spicilegus and M. spretus. We found that the HMG domain (high mobility group DNA binding domain) and the unique regions are well conserved, while the glutamine repeat cluster (GRC) region is quite variable. No correlation was found between the predicted protein isoforms and the ability of a Sry allele to allow differentiation of ovarian tissue when on the C57BL/6J genetic background, strongly suggesting that the cause of this sex reversal is not the Sry protein itself, but rather the regulation of SRY expression. Furthermore, our interspecies sequence analysis provides compelling evidence that the M. musculus and M. domesticus SRY functional domain is contained in the first 143 amino acids, which includes the HMG domain and adjacent unique region (UR-2).
The Amounts of Nucleotide Variation Within and Between Allelic Classes and the Reconstruction of the Common Ancestral Sequence in a Population
Authors: Innan Hideki , Tajima Fumio
Published: January 2021

The amounts of nucleotide variation within and between allelic classes were studied. The expectation and variance of the number of segregating sites and the expectation of the average number of pairwise differences among a sample of DNA sequences were obtained by using the theory of gene genealogy with no recombination. When the ancestral allelic class is unknown, it was found that the amount of variation within an allelic class increases with its frequency in the sample, while the amount of variation between two allelic classes is the largest when the two allelic classes exist equally. On the other hand, if we know the ancestral allelic class, as the frequency of the mutant allelic class increases, the amounts of variation within the mutant allelic class and between two allelic classes increase and the amount of variation within the ancestral allelic class decreases. As an example, we analyzed the polymorphism in the ND5 gene of Drosophila melanogaster and constructed the common ancestral sequence with high confidence, suggesting that the pattern of polymorphism within species gives useful information to know the ancestral sequence of the species.
Size and Sequence Polymorphism in the Isocitrate Dehydrogenase Kinase/Phosphatase Gene (aceK) and Flanking Regions in Salmonella enterica and Escherichia coli
Authors: Nelson Kimberlyn , Wang Fu-Sheng , Boyd E Fidelma , Selander Robert K
Published: January 2021

The sequence of aceK, which codes for the regulatory catalytic enzyme isocitrate dehydrogenase kinase/phosphatase (IDH K/P), and sequences of the 5′ flanking region and part or all of the 3′ flanking region were determined for 32 strains of Salmonella enterica and Escherichia coli. In E. coli, the aceK gene was 1734 bp long in 13 strains, but in three strains it was 12 bp shorter and the stop codon was TAA rather than TGA. Strains with the shorter aceK lacked an open reading frame (f728) downstream between aceK and iclR that was present, in variable length, in the other strains. Among the 72 ECOR strains, the truncated aceK gene was present in all isolates of the B2 group and half of those of the D group. Other variant conditions included the presence of IS1 elements in two strains and large deletions in two strains. The aceK-aceA intergenic region varied in length from 48 to 280 bp in E. coli, depending largely on the number of repetitive extragenic palindromic (REP) sequences present. Among the ECOR strains, the number of REP elements showed a high degree of phylogenetic association, and sequencing of the region in the ECOR strains permitted partial reconstruction of its evolutionary history. In S. enterica, the normal length of aceK was 1752 bp, but three other length variants, ranging from 1746 to 1785 bp, were represented in five of the 16 strains examined. The flanking intergenic regions showed relatively minor variation in length and sequence. The occurrence of several nonrandom patterns of distribution of polymorphic synonymous nucleotide sites indicated that intragenic recombination of horizontally exchanged DNA has contributed to the generation of allelic diversity at the aceK locus in both species.
Identification and Characterization of Genes That Interact With lin-12 in Caenorhabditis elegans
Authors: Tax Frans E , Thomas James H , Ferguson Edwin L , Horvitzt H Robert
Published: January 2021

We identified and characterized 14 extragenic mutations that suppressed the dominant egg-laying defect of certain lin-12 gain-of-function mutations. These suppressors defined seven genes: sup-l7, lag-2, sel-4, sel-5, sel-6, sel-7 and sel-8. Mutations in six of the genes are recessive suppressors, whereas the two mutations that define the seventh gene, lag-2, are semi-dominant suppressors. These suppressor mutations were able to suppress other lin-12 gain-of-function mutations. The suppressor mutations arose at a very low frequency per gene, 10-50 times below the typical loss-of-function mutation frequency. The suppressor mutations in sup1 7 and lag-2 were shown to be rare non-null alleles, and we present evidence that null mutations in these two genes cause lethality. Temperature-shift studies for two suppressor genes, sup1 7and lag-2, suggest that both genes act at approximately the same time as lin-12in specifying a cell fate. Suppressor alleles of six of these genes enhanced a temperature-sensitive loss-of-function allele of glp-1, a gene related to lin-12 in structure and function. Our analysis of these suppressors suggests that the majority of these genes are part of a shared lin-12/glp-1 signal transduction pathway, or act to regulate the expression or stability of lin-12 and glp-1.
P-Element Insertion Alleles of Essential Genes on the Third Chromosome of Drosophila melanogaster: Mutations Affecting Embryonic PNS Development
Authors: Salzberg Adi , Prokopenko Sergei N , He Yuchun , Tsai Peter , Pál Margit , Maróy Péter , Glover David M , Deák Péter , Bellen Hugo J
Published: January 2021

To identify novel genes and to isolate tagged mutations in known genes that are required for the development of the peripheral nervous system (PNS), we have screened a novel collection of 2460 strains carrying lethal or semilethal P-element insertions on the third chromosome. Monoclonal antibody 22C10 was used as a marker to visualize the embryonic PNS. We identified 109 mutant strains that exhibited reproducible phenotypes in the PNS. Cytological and genetic analyses of these strains indicated that 87 mutations affect previously identified genes: tramtrack (n = 18 alleles), string (n = 15), cyclin A (n = 13), single-minded (n = 13), Delta (n = 9), neuralized (n = 4), pointed (n = 4), extra macrochaetae (n = 4), pospero (n = 3), tartan (n = 2), and pebble (n = 2). In addition, 13 mutations affect genes that we identified recently in a chemical mutagenesis screen designed to isolate similar mutants: hearty (n = 3), dursotonals (n = 2), pauarotti (n = 2), sanpodo (n = 2), dalmatian (n = 1), missensed (n = 1), senseless (n = 1), and sticky chl (n = 1). The remaining nine mutations define seven novel complementation groups. The data presented here demonstrate that this collection of Pelements will be useful for the identification and cloning of novel genes on the third chromosome, since >70% of mutations identified in the screen are caused by the insertion of a Pelement. A comparison between this screen and a chemical mutagenesis screen undertaken earlier highlights the complementarity of the two types of genetic screens.
Bayesian Procedures for Discriminating Among Hypotheses With Discrete Distributions: Inheritance in the Tetraploid Astilbe biternata
Authors: Olson Matthew S
Published: January 2021

Discrimination between disomic and tetrasomic inheritance aids in determining whether tetraploids originated by allotetraploidy or autotetraploidy, respectively. Past assessments of inheritance in tetraploids have used analyses whereby each inheritance hypothesis is tested independently. I present a Bayesian analysis that is appropriate for discriminating among several inheritance hypotheses and can be used in any case where hypotheses are defined by discrete distributions. The Bayesian approach incorporates prior knowledge of the probability of occurrence of disomic and tetrasomic hypotheses so that the results of the analysis are not biased by the fact that there is a single tetrasomic hypothesis and multiple disomic hypotheses. This analysis is used to interpret data from crosses in the tetraploid Astilbe biternata, a herbaceous plant native to the southern Appalachians. The progeny ratios from all crosses favored the hypothesis of disomic inheritance at both the PGM and slow-PGI loci. These results support earlier cytogenetic evidence for the allotetraploid origin of Astilbe biternata.
1. Family Law Practice and the First Interview
Authors: Hodgson Roiya
Published: January 2021

This chapter begins by identifying the various skills that family lawyers must possess. These include technical skills such as advocacy, interviewing, negotiation, and writing; and ‘soft skills’. The discussion then turns to the professional conduct issues that are crucial to seeing a client for the first time, including confidentiality and money laundering. It includes the General Data Protection Regulation (GDPR) The Divorce, Dissolution and Separation Act 2020 is mentioned as well as the new Solicitors Regulatory Authority’s (SRA) Standards and Regulationswhich came into force in November 2019. Litigants in person are also explained and discussed.
5. Separation and Nullity
Authors: Hodgson Roiya
Published: January 2021

This chapter considers some parts of the law and procedure following the breakdown of a relationship. It discusses the remedy of separation as an alternative to divorce proceedings. It explains the term ‘separation’ and the two main statutes relating to these areas. The chapter also discusses the bars to petition and also examines nullity as a remedy, including void and voidable marriages and the different grounds for finding a marriage void or voidable. It looks at nullity and civil partnerships, as well as a remedy for escaping forced marriages and some statistics on forced marriages. The Civil Partnership (Opposite-sex Couples) Regulations 2019 (SI 2019/1458) are mentioned. Case law is also used.
6. Divorce
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the grounds for divorce under the Matrimonial Causes Act 1973. These include adultery, unreasonable behaviour, desertion, two years’ separation plus consent, and five years’ separation. It also outlines the first year bar on divorce and the ground for divorce being that the marriage has broken down irretrievably. The chapter explores each of the five possible facts that prove the ground for divorce and explains the relevance of continued cohabitation between the parties in relation to unreasonable behaviour and adultery. It also discusses continuous separation. Some discussion of the proposals for no-fault divorce is also included in this chapter.
8. Jurisdiction
Authors: Hodgson Roiya
Published: January 2021

This chapter deals with the European law governing jurisdiction in divorce and the international law concepts that are a feature of this area of law. It discusses the increasingly important question of jurisdiction in divorce proceedings, and explains the concepts of ‘domicile’which includes domicile of origin, domicile of dependence, and domicile of choice. It also explains the concept of ‘habitual residence’ as how both domicile and habitual residence apply to divorce proceedings. There is finally an outline of jurisdiction in practice and the rule that if the domicile of a client is uncertain then habitual residence is usually easier to establish. There is some mention of Brexit.
9. Procedure for a Matrimonial Order
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the procedure for obtaining a divorce or dissolving a civil partnership, which is governed by the Family Procedure Rules 2010. It outlines the main steps a solicitor should take before issuing divorce proceedings and explores the complete procedure for obtaining an undefended divorce. It explains that the procedure for divorce is governed by the Family Procedure Rules (FPR) 2010, which came into force in 2011. The FPR refers to ‘matrimonial orders’ which includes a decree of divorce, a decree of nullity, and a decree of judicial separation. Service of the petition is also discussed, as well as the various forms used.
10. Civil Partnership Act 2004
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the scope of the Civil Partnership Act 2004 (CPA 2004) which came into force on 5 December 2005 and the formation of civil partnerships. It outlines civil partnership and same-sex marriage under The Marriage (Same-Sex Couples) Act 2013. It also explains the differences between civil partnership and marriage. Once a partnership has been formed, civil partners assume many legal rights and responsibilities for each other, third parties, and the State. It does explain that adultery, however, is not a fact to establish the ground for dissolution of a civil partnership as it is in marriage. The Civil Partnership (Opposite-sex Couples) Regulations 2019 are also outlined.
11. Financial Orders Following Divorce or Dissolution
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the factors that a court will take into account when deciding on the division of money and property following a divorce or dissolution of a civil partnership. It introduces the main concepts in proceedings for financial orders under the Matrimonial Causes Act 1973, which includes all of the circumstances of the case, children, and the factors for orders involving children. It examines the factors considered by the court when deciding on financial orders and these are explained in detail. It looks at the clean break principle, pensions, and the principal case-law arising from proceedings for financial orders.
21. Welfare Benefits
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the main types of welfare benefits that are available to family law clients. It explains the importance of welfare benefits in relation to areas of family law, and that a family lawyer must have a working knowledge of these areas in particular with regards to financial remedy. The eligibility of benefits and what the client will receive is discussed. The chapter explains that the main benefit which is now in place is universal credit, but also mentions the ‘legacy benefits’, including income support, jobseeker’s allowance, tax credits, employment and support allowance, housing benefit, council tax reduction, and child benefit.
23. Cohabitation and Finance
Authors: Hodgson Roiya
Published: January 2021

Cohabiting couples do not have any intrinsic legal rights by simply cohabiting. The ‘common law wife/husband’ does not exist in law, despite many believing that it does. This chapter discusses the legal position of cohabitants and financial remedies. This includes the Law Commission Proposals in order to try and allow cohabitants to gain some financial relief in certain circumstances. The legal remedies available to separating cohabitants including establishing legal title and a beneficial interest, is outlined. This also includes resulting and constructive trusts. Finally, the position of cohabitants in relation to the family home and Trusts of Land and Appointment of Trustees Act is discussed.
36. Protection under the Family Law Act 1996: Procedure
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the procedure for obtaining orders under the Family Law Act 1996 without notice, on notice, and when enforcing orders. Proceedings are commenced using a Form FL401 and a statement in support. Proceedings are commenced in the family court. Funding is available for those eligible for CLS funding. The respondent should be personally served with the FL401 and the statement in support unless the application is to be made without notice. Police should be contacted if a non-molestation order is breached and if an occupation order has a power of arrest attached to it. Warrant of arrest and committal proceedings are also discussed.
Assisted Reproductive Techniques and Genetic Manipulation in the Common Marmoset
Authors: Park Jung Eun , Sasaki Erika
Published: January 2021

Genetic modification of nonhuman primate (NHP) zygotes is a useful method for the development of NHP models of human diseases. This review summarizes the recent advances in the development of assisted reproductive and genetic manipulation techniques in NHP, providing the basis for the generation of genetically modified NHP disease models. In this study, we review assisted reproductive techniques, including ovarian stimulation, in vitro maturation of oocytes, in vitro fertilization, embryo culture, embryo transfer, and intracytoplasmic sperm injection protocols in marmosets. Furthermore, we review genetic manipulation techniques, including transgenic strategies, target gene knock-out and knock-in using gene editing protocols, and newly developed gene-editing approaches that may potentially impact the production of genetically manipulated NHP models. We further discuss the progress of assisted reproductive and genetic manipulation techniques in NHP; future prospects on genetically modified NHP models for biomedical research are also highlighted.