bluuebunny/crossref_metadata_2025 huggingface dataset:
Interspecific Transfer of Wolbachia Between Two Lepidopteran Insects Expressing Cytoplasmic Incompatibility: A Wolbachia Variant Naturally InfectingCadra cautellaCauses Male Killing inEphestia kuehniella
Authors: Sasaki Tetsuhiko , Kubo Takeo , Ishikawa Hajime
Published: April 2021

Wolbachia is known as the causative agent of various reproductive alterations in arthropods. The almond moth Cadra cautella is doubly infected with A- and B-group Wolbachia and expresses complete cytoplasmic incompatibility (CI). The Mediterranean flour moth Ephestia kuehniella carries A-group Wolbachia and expresses partial CI. In the present study, the Wolbachia in C. cautella was transferred to E. kuehniella from which the original Wolbachia had been removed. We obtained transfected lines of three different infection states: single infection with A, single infection with B, and double infection with A and B. The doubly transfected lines and those transfected with only A produced exclusively female progeny. Two lines of evidence suggested that the sex ratio distortion was due to male killing. First, reduced egg hatch rate was observed. Second, removal of the Wolbachia from the transfected lines resulted in the recovery of a normal sex ratio of ∼1:1. The occurrence of male killing following transfection showed that host factors influence the determination of the reproductive phenotype caused by Wolbachia. The transfected E. kuehniella males carrying exclusively B-group Wolbachia expressed partial incompatibility when crossed with the uninfected females. In addition, the transfected lines were bidirectionally incompatible with the naturally infected strain, which was the first demonstration of bidirectional CI in a lepidopteran.
Chromosomal Rearrangements and Evolution of Recombination: Comparison of Chiasma Distribution Patterns in Standard and Robertsonian Populations of the House Mouse
Authors: Dumas David , Britton-Davidian Janice
Published: April 2021

The effects of chromosomal rearrangements on recombination rates were tested by the analysis of chiasma distribution patterns in wild house mice. Males and females of two chromosomal races from Tunisia differing by nine pairs of Robertsonian (Rb) fusions (standard all-acrocentric, 2N = 40 and 2N = 22) were studied. A significant decrease in chiasma number (CN) was observed in Rb mice compared to standard ones for both sexes. The difference in CN was due to a reduction in the number of proximal chiasmata and was associated with an overall more distal redistribution. These features were related to distance of chiasmata to the centromere, suggesting that the centromere effect was more pronounced in Rb fusions than in acrocentric chromosomes. These modifications were interpreted in terms of structural meiotic constraints, although genic factors were likely involved in patterning the observed differences between sexes within races. Thus, the change in chromosomal structure in Rb mice was associated with a generalized decrease in recombination due to a reduction in diploid number, a lower CN, and a decrease in the efficiency of recombination. The effects of such modifications on patterns of genic diversity are discussed in the light of models of evolution of recombination.
The Use of Genetic Markers to Measure Genomic Response to Selection in Livestock
Authors: Gomez-Raya Luis , Olsen Hanne Gro , Lingaas Frode , Klungland Helge , Våge Dag Inge , Olsaker Ingrid , Talle Seblewengel Bekele , Aasland Monica , Lien Sigbjørn
Published: April 2021

A method to measure genomic response to natural and artificial selection by means of genetic markers in livestock is proposed. Genomic response through several levels of selection was measured using sequential testing for distorted segregation of alleles among selected and nonselected sons, single-sperm typing, and a test with records for growth performance. Statistical power at a significance level of 0.05 was >0.5 for a marker linked to a QTL with recombination fractions 0, 0.10, and 0.20 for detecting genomic responses for gene effects of 0.6, 0.7, and 1.0 phenotypic standard deviations, respectively. Genomic response to artificial selection in six commercial bull sire families comprising 285 half-sib sons selected for growth performance was measured using 282 genetic markers evenly distributed over the cattle genome. A genome-wide test using selected sons was significant (P < 0.001), indicating that selection induces changes in the genetic makeup of commercial cattle populations. Markers located in chromosomes 6, 10, and 16 identified regions in those chromosomes that are changing due to artificial selection as revealed by the association of records of performance with alleles at specific markers. Either natural selection or genetic drift may cause the observed genomic response for markers in chromosomes 1, 7, and 17.
Different Types and Rates of Genome Evolution Detected by Comparative Sequence Analysis of Orthologous Segments From Four Cereal Genomes
Authors: Ramakrishna Wusirika , Dubcovsky Jorge , Park Yong-Jin , Busso Carlos , Emberton John , SanMiguel Phillip , Bennetzen Jeffrey L
Published: April 2021

Orthologous regions in barley, rice, sorghum, and wheat were studied by bacterial artificial chromosome sequence analysis. General microcolinearity was observed for the four shared genes in this region. However, three genic rearrangements were observed. First, the rice region contains a cluster of 48 predicted small nucleolar RNA genes, but the comparable region from sorghum contains no homologous loci. Second, gene 2 was inverted in the barley lineage by an apparent unequal recombination after the ancestors of barley and wheat diverged, 11-15 million years ago (mya). Third, gene 4 underwent direct tandem duplication in a common ancestor of barley and wheat 29-41 mya. All four of the shared genes show the same synonymous substitution rate, but nonsynonymous substitution rates show significant variations between genes 4a and 4b, suggesting that gene 4b was largely released from the strong purifying selection that acts on gene 4a in both barley and wheat. Intergenic retrotransposon blocks, many of them organized as nested insertions, mostly account for the lower gene density of the barley and wheat regions. All but two of the retrotransposons were found in the regions between genes, while all but 2 of the 51 inverted repeat transposable elements were found as insertions in genic regions and outside the retrotransposon blocks.
Patterns of Diversity and Recombination Along Chromosome 1 of Maize (Zea mays ssp. mays L.)
Authors: Tenaillon Maud I , Sawkins Mark C , Anderson Lorinda K , Stack Stephen M , Doebley John , Gaut Brandon S
Published: April 2021

We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. mays). Genetic diversity was measured in three types of markers: single-nucleotide polymorphisms, indels, and microsatellites. All three were examined in a sample of previously published DNA sequences from 21 loci on maize chromosome 1. Small indels (1-5 bp) were numerous and far more common than large indels. Furthermore, large indels (>100 bp) were infrequent in the population sample, suggesting they are slightly deleterious. The 21 loci also contained 47 microsatellites, of which 33 were polymorphic. Diversity in SNPs, indels, and microsatellites was compared to two measures of recombination: C (=4Nc) estimated from DNA sequence data and R based on a quantitative recombination nodule map of maize synaptonemal complex 1. SNP diversity was correlated with C (r = 0.65; P = 0.007) but not with R (r =-0.10; P = 0.69). Given the lack of correlation between R and SNP diversity, the correlation between SNP diversity and C may be driven by demography. In contrast to SNP diversity, microsatellite diversity was correlated with R (r = 0.45; P = 0.004) but not C (r =-0.025; P = 0.55). The correlation could arise if recombination is mutagenic for microsatellites, or it may be consistent with background selection that is apparent only in this class of rapidly evolving markers.
Roles for WHITE COLLAR-1 in Circadian and General Photoperception in Neurospora crassa
Authors: Lee Kwangwon , Dunlap Jay C , Loros Jennifer J
Published: April 2021

The transcription factors WHITE COLLAR-1 (WC-1) and WHITE COLLAR-2 (WC-2) interact to form a heterodimeric complex (WCC) that is essential for most of the light-mediated processes in Neurospora crassa. WCC also plays a distinct non-light-related role as the transcriptional activator in the FREQUENCY (FRQ)/WCC feedback loop that is central to the N. crassa circadian system. Although an activator role was expected for WC-1, unanticipated phenotypes resulting from some wc-1 alleles prompted a closer examination of an allelic series for WC-1 that has uncovered roles for this central regulator in constant darkness and in response to light. We analyzed the phenotypes of five different wc-1 mutants for expression of FRQ and WC-1 in constant darkness and following light induction. While confirming the absolute requirement of WC-1 for light responses, the data suggest multiple levels of control for light-regulated genes.
Genetic Analysis of Caenorhabditis elegans glp-1 Mutants Suggests Receptor Interaction or Competition
Authors: Pepper Anita S-R , Killian Darrell J , Hubbard E Jane Albert
Published: April 2021

glp-1 encodes a member of the highly conserved LIN-12/Notch family of receptors that mediates the mitosis/meiosis decision in the C. elegans germline. We have characterized three mutations that represent a new genetic and phenotypic class of glp-1 mutants, glp-1(Pro). The glp-1(Pro) mutants display gain-of-function germline pattern defects, most notably a proximal proliferation (Pro) phenotype. Each of three glp-1(Pro) alleles encodes a single amino acid change in the extracellular part of the receptor: two in the LIN-12/Notch repeats (LNRs) and one between the LNRs and the transmembrane domain. Unlike other previously described gain-of-function mutations that affect this region of LIN-12/Notch family receptors, the genetic behavior of glp-1(Pro) alleles is not consistent with simple hypermorphic activity. Instead, the mutant phenotype is suppressed by wild-type doses of glp-1. Moreover, a trans-heterozygous combination of two highly penetrant glp-1(Pro) mutations is mutually suppressing. These results lend support to a model for a higher-order receptor complex and/or competition among receptor proteins for limiting factors that are required for proper regulation of receptor activity. Double-mutant analysis with suppressors and enhancers of lin-12 and glp-1 further suggests that the functional defect in glp-1(Pro) mutants occurs prior to or at the level of ligand interaction.
Sequence Variation of Alcohol Dehydrogenase (Adh) Paralogs in Cactophilic Drosophila
Authors: Matzkin Luciano M , Eanes Walter F
Published: April 2021

This study focuses on the population genetics of alcohol dehydrogenase (Adh) in cactophilic Drosophila. Drosophila mojavensis and D. arizonae utilize cactus hosts, and each host contains a characteristic mixture of alcohol compounds. In these Drosophila species there are two functional Adh loci, an adult form (Adh-2) and a larval and ovarian form (Adh-1). Overall, the greater level of variation segregating in D. arizonae than in D. mojavensis suggests a larger population size for D. arizonae. There are markedly different patterns of variation between the paralogs across both species. A 16-bp intron haplotype segregates in both species at Adh-2, apparently the product of an ancient gene conversion event between the paralogs, which suggests that there is selection for the maintenance of the intron structure possibly for the maintenance of pre-mRNA structure. We observe a pattern of variation consistent with adaptive protein evolution in the D. mojavensis lineage at Adh-1, suggesting that the cactus host shift that occurred in the divergence of D. mojavensis from D. arizonae had an effect on the evolution of the larval expressed paralog. Contrary to previous work we estimate a recent time for both the divergence of D. mojavensis and D. arizonae (2.4 ± 0.7 MY) and the age of the gene duplication (3.95 ± 0.45 MY).
Interallelic Complementation at the Mouse Mitf Locus
Authors: Steingrímsson Eiríkur , Arnheiter Heinz , Hallsson Jón Hallsteinn , Lamoreux M Lynn , Copeland Neal G , Jenkins Nancy A
Published: April 2021

Mutations at the mouse microphthalmia locus (Mitf) affect the development of different cell types, including melanocytes, retinal pigment epithelial cells of the eye, and osteoclasts. The MITF protein is a member of the MYC supergene family of basic-helix-loop-helix-leucine-zipper (bHLHZip) transcription factors and is known to regulate the expression of cell-specific target genes by binding DNA as homodimer or as heterodimer with related proteins. The many mutations isolated at the locus have different effects on the phenotype and can be arranged in an allelic series in which the phenotypes range from near normal to white microphthalmic animals with osteopetrosis. Previous investigations have shown that certain combinations of Mitf alleles complement each other, resulting in a phenotype more normal than that of each homozygote alone. Here we analyze this interallelic complementation in detail and show that it is limited to one particular allele, MitfMi-white (MitfMi-wh), a mutation affecting the DNA-binding domain. Both loss- and gain-of-function mutations are complemented, as are other Mitf mutations affecting the DNA-binding domain. Furthermore, this behavior is not restricted to particular cell types: Both eye development and coat color phenotypes are complemented. Our analysis suggests that MitfMi-wh-associated interallelic complementation is due to the unique biochemical nature of this mutation.
Effects of Genetic Background on Response to Selection in Experimental Populations of Arabidopsis thaliana
Authors: Ungerer Mark C , Linder C Randal , Rieseberg Loren H
Published: April 2021

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.
The Inheritance of Chemical Phenotype in Cannabis sativa L.
Authors: de Meijer Etienne P M , Bagatta Manuela , Carboni Andrea , Crucitti Paola , Moliterni V M Cristiana , Ranalli Paolo , Mandolino Giuseppe
Published: April 2021

Four crosses were made between inbred Cannabis sativa plants with pure cannabidiol (CBD) and pure Δ-9-tetrahydrocannabinol (THC) chemotypes. All the plants belonging to the F1’s were analyzed by gas chromatography for cannabinoid composition and constantly found to have a mixed CBD-THC chemotype. Ten individual F1 plants were self-fertilized, and 10 inbred F2 offspring were collected and analyzed. In all cases, a segregation of the three chemotypes (pure CBD, mixed CBD-THC, and pure THC) fitting a 1:2:1 proportion was observed. The CBD/THC ratio was found to be significantly progeny specific and transmitted from each F1 to the F2’s derived from it. A model involving one locus, B, with two alleles, BD and BT, is proposed, with the two alleles being codominant. The mixed chemotypes are interpreted as due to the genotype BD/BT at the B locus, while the pure-chemotype plants are due to homozygosity at the B locus (either BD/BD or BT/BT). It is suggested that such codominance is due to the codification by the two alleles for different isoforms of the same synthase, having different specificity for the conversion of the common precursor cannabigerol into CBD or THC, respectively. The F2 segregating groups were used in a bulk segregant analysis of the pooled DNAs for screening RAPD primers; three chemotype-associated markers are described, one of which has been transformed in a sequence-characterized amplified region (SCAR) marker and shows tight linkage to the chemotype and codominance.
SOD2 Functions Downstream of Sch9 to Extend Longevity in Yeast
Authors: Fabrizio Paola , Liou Lee-Loung , Moy Vanessa N , Diaspro Alberto , Valentine Joan Selverstone , Gralla Edith Butler , Longo Valter D
Published: April 2021

Signal transduction pathways inactivated during periods of starvation are implicated in the regulation of longevity in organisms ranging from yeast to mammals, but the mechanisms responsible for life-span extension are poorly understood. Chronological life-span extension in S. cerevisiae cyr1 and sch9 mutants is mediated by the stress-resistance proteins Msn2/Msn4 and Rim15. Here we show that mitochondrial superoxide dismutase (Sod2) is required for survival extension in yeast. Deletion of SOD2 abolishes life-span extension in sch9Δ mutants and decreases survival in cyr1:mTn mutants. The overexpression of Sods—mitochondrial Sod2 and cytosolic CuZnSod (Sod1)—delays the age-dependent reversible inactivation of mitochondrial aconitase, a superoxide-sensitive enzyme, and extends survival by 30%. Deletion of the RAS2 gene, which functions upstream of CYR1, also doubles the mean life span by a mechanism that requires Msn2/4 and Sod2. These findings link mutations that extend chronological life span in S. cerevisiae to superoxide dismutases and suggest that the induction of other stress-resistance genes regulated by Msn2/4 and Rim15 is required for maximum longevity extension.
Bayesian Analysis of Genetic Differentiation Between Populations
Authors: Corander Jukka , Waldmann Patrik , Sillanpää Mikko J
Published: April 2021

We introduce a Bayesian method for estimating hidden population substructure using multilocus molecular markers and geographical information provided by the sampling design. The joint posterior distribution of the substructure and allele frequencies of the respective populations is available in an analytical form when the number of populations is small, whereas an approximation based on a Markov chain Monte Carlo simulation approach can be obtained for a moderate or large number of populations. Using the joint posterior distribution, posteriors can also be derived for any evolutionary population parameters, such as the traditional fixation indices. A major advantage compared to most earlier methods is that the number of populations is treated here as an unknown parameter. What is traditionally considered as two genetically distinct populations, either recently founded or connected by considerable gene flow, is here considered as one panmictic population with a certain probability based on marker data and prior information. Analyses of previously published data on the Moroccan argan tree (Argania spinosa) and of simulated data sets suggest that our method is capable of estimating a population substructure, while not artificially enforcing a substructure when it does not exist. The software (BAPS) used for the computations is freely available from http://www.rni.helsinki.fi/~mjs.
Estimating Ancestral Population Sizes and Divergence Times
Authors: Wall Jeffrey D
Published: April 2021

This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly >10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.
Specialization of Function Among Aldehyde Dehydrogenases: The ALD2 and ALD3 Genes Are Required for β-Alanine Biosynthesis in Saccharomyces cerevisiae
Authors: White W Hunter , Skatrud Paul L , Xue Zhixiong , Toyn Jeremy H
Published: April 2021

The amino acid β-alanine is an intermediate in pantothenic acid (vitamin B5) and coenzyme A (CoA) biosynthesis. In contrast to bacteria, yeast derive the β-alanine required for pantothenic acid production via polyamine metabolism, mediated by the four SPE genes and by the FAD-dependent amine oxidase encoded by FMS1. Because amine oxidases generally produce aldehyde derivatives of amine compounds, we propose that an additional aldehyde-dehydrogenase-mediated step is required to make β-alanine from the precursor aldehyde, 3-aminopropanal. This study presents evidence that the closely related aldehyde dehydrogenase genes ALD2 and ALD3 are required for pantothenic acid biosynthesis via conversion of 3-aminopropanal to β-alanine in vivo. While deletion of the nuclear gene encoding the unrelated mitochondrial Ald5p resulted in an enhanced requirement for pantothenic acid pathway metabolites, we found no evidence to indicate that the Ald5p functions directly in the conversion of 3-aminopropanal to β-alanine. Thus, in Saccharomyces cerevisiae, ALD2 and ALD3 are specialized for β-alanine biosynthesis and are consequently involved in the cellular biosynthesis of coenzyme A.
RecFOR Function Is Required for DNA Repair and Recombination in a RecA Loading-Deficient recB Mutant of Escherichia coli
Authors: Ivančić-Baće Ivana , Peharec Petra , Moslavac Sunčana , Škrobot Nikolina , Salaj-Šmic† Erika , Brčić-Kostić Krunoslav
Published: April 2021

The RecA loading activity of the RecBCD enzyme, together with its helicase and 5′ → 3′ exonuclease activities, is essential for recombination in Escherichia coli. One particular mutant in the nuclease catalytic center of RecB, i.e., recB1080, produces an enzyme that does not have nuclease activity and is unable to load RecA protein onto single-stranded DNA. There are, however, previously published contradictory data on the recombination proficiency of this mutant. In a recF– background the recB1080 mutant is recombination deficient, whereas in a recF+ genetic background it is recombination proficient. A possible explanation for these contrasting phenotypes may be that the RecFOR system promotes RecA-single-strand DNA filament formation and replaces the RecA loading defect of the RecB1080CD enzyme. We tested this hypothesis by using three in vivo assays. We compared the recombination proficiencies of recB1080, recO, recR, and recF single mutants and recB1080 recO, recB1080 recR, and recB1080 recF double mutants. We show that RecFOR functions rescue the repair and recombination deficiency of the recB1080 mutant and that RecA loading is independent of RecFOR in the recB1080 recD double mutant where this activity is provided by the RecB1080C(D–) enzyme. According to our results as well as previous data, three essential activities for the initiation of recombination in the recB1080 mutant are provided by different proteins, i.e., helicase activity by RecB1080CD, 5′ → 3′ exonuclease by RecJ- and RecA-single-stranded DNA filament formation by RecFOR.
MLH1 Mutations Differentially Affect Meiotic Functions in Saccharomyces cerevisiae
Authors: Hoffmann Eva R , Shcherbakova Polina V , Kunkel Thomas A , Borts Rhona H
Published: April 2021

To test whether missense mutations in the cancer susceptibility gene MLH1 adversely affect meiosis, we examined 14 yeast MLH1 mutations for effects on meiotic DNA transactions and gamete viability in the yeast Saccharomyces cerevisiae. Mutations analogous to those associated with hereditary nonpolyposis colorectal cancer (HNPCC) or those that reduce Mlh1p interactions with ATP or DNA all impair replicative mismatch repair as measured by increased mutation rates. However, their effects on meiotic heteroduplex repair, crossing over, chromosome segregation, and gametogenesis vary from complete loss of meiotic functions to no meiotic defect, and mutants defective in one meiotic process are not necessarily defective in others. DNA binding and ATP binding but not ATP hydrolysis are required for meiotic crossing over. The results reveal clear separation of different Mlh1p functions in mitosis and meiosis, and they suggest that some, but not all, MLH1 mutations may be a source of human infertility.
Characterization of Caenorhabditis elegans Homologs of the Down Syndrome Candidate Gene DYRK1A
Authors: Raich William B , Moorman Celine , Lacefield Clay O , Lehrer Jonah , Bartsch Dusan , Plasterk Ronald H A , Kandel Eric R , Hobert Oliver
Published: April 2021

The pathology of trisomy 21/Down syndrome includes cognitive and memory deficits. Increased expression of the dual-specificity protein kinase DYRK1A kinase (DYRK1A) appears to play a significant role in the neuropathology of Down syndrome. To shed light on the cellular role of DYRK1A and related genes we identified three DYRK/minibrain-like genes in the genome sequence of Caenorhabditis elegans, termed mbk-1, mbk-2, and hpk-1. We found these genes to be widely expressed and to localize to distinct subcellular compartments. We isolated deletion alleles in all three genes and show that loss of mbk-1, the gene most closely related to DYRK1A, causes no obvious defects, while another gene, mbk-2, is essential for viability. The overexpression of DYRK1A in Down syndrome led us to examine the effects of overexpression of its C. elegans ortholog mbk-1. We found that animals containing additional copies of the mbk-1 gene display behavioral defects in chemotaxis toward volatile chemoattractants and that the extent of these defects correlates with mbk-1 gene dosage. Using tissue-specific and inducible promoters, we show that additional copies of mbk-1 can impair olfaction cell-autonomously in mature, fully differentiated neurons and that this impairment is reversible. Our results suggest that increased gene dosage of human DYRK1A in trisomy 21 may disrupt the function of fully differentiated neurons and that this disruption is reversible.
Trichothecene Nonproducer Gibberella Species Have Both Functional and Nonfunctional 3-O-Acetyltransferase Genes
Authors: Kimura Makoto , Tokai Takeshi , Matsumoto Gentaro , Fujimura Makoto , Hamamoto Hiroshi , Yoneyama Katsuyoshi , Shibata Takehiko , Yamaguchi Isamu
Published: April 2021

The trichothecene 3-O-acetyltransferase gene (FgTri101) required for trichothecene production by Fusarium graminearum is located between the phosphate permease gene (pho5) and the UTP-ammonia ligase gene (ura7). We have cloned and sequenced the pho5-to-ura7 regions from three trichothecene nonproducing Fusarium (i.e., F. oxysporum, F. moniliforme, and Fusarium species IFO 7772) that belong to the teleomorph genus Gibberella. BLASTX analysis of these sequences revealed portions of predicted polypeptides with high similarities to the TRI101 polypeptide. While FspTri101 (Fusarium species Tri101) coded for a functional 3-O-acetyltransferase, FoTri101 (F. oxysporum Tri101) and FmTri101 (F. moniliforme Tri101) were pseudogenes. Nevertheless, F. oxysporum and F. moniliforme were able to acetylate C-3 of trichothecenes, indicating that these nonproducers possess another as yet unidentified 3-O-acetyltransferase gene. By means of cDNA expression cloning using fission yeast, we isolated the responsible FoTri201 gene from F. oxysporum; on the basis of this sequence, FmTri201 has been cloned from F. moniliforme by PCR techniques. Both Tri201 showed only a limited level of nucleotide sequence similarity to FgTri101 and FspTri101. The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species.
Natural Selection for Polymorphism in the Disease Resistance Gene Rps2 of Arabidopsis thaliana
Authors: Mauricio Rodney , Stahl Eli A , Korves Tonia , Tian Dacheng , Kreitman Martin , Bergelson Joy
Published: April 2021

Pathogen resistance is an ecologically important phenotype increasingly well understood at the molecular genetic level. In this article, we examine levels of avrRpt2-dependent resistance and Rps2 locus DNA sequence variability in a worldwide sample of 27 accessions of Arabidopsis thaliana. The rooted parsimony tree of Rps2 sequences drawn from a diverse set of ecotypes includes a deep bifurcation separating major resistance and susceptibility clades of alleles. We find evidence for selection maintaining these alleles and identify the N-terminal part of the leucine-rich repeat region as a probable target of selection. Additional protein variants are found within the two major clades and correlate well with measurable differences among ecotypes in resistance to the avirulence gene avrRpt2 of the pathogen Pseudomonas syringae. Long-lived polymorphisms have been observed for other resistance genes of A. thaliana; the Rps2 data suggest that the long-term maintenance of phenotypic variation in resistance genes may be a general phenomenon and are consistent with diversifying selection acting in concert with selection to maintain variation.
The Evolution of Sex Dimorphism in Recombination
Authors: Lenormand Thomas
Published: April 2021

Sex dimorphism in recombination is widespread on both sex chromosomes and autosomes. Various hypotheses have been proposed to explain these dimorphisms. Yet no theoretical model has been explored to determine how heterochiasmy—the autosomal dimorphism—could evolve. The model presented here shows three circumstances in which heterochiasmy is likely to evolve: (i) a male-female difference in haploid epistasis, (ii) a male-female difference in cis-epistasis minus trans-epistasis in diploids, or (iii) a difference in epistasis between combinations of genes inherited maternally or paternally. These results hold even if sources of linkage disequilibria besides epistasis, such as migration or Hill-Robertson interference, are considered and shed light on previous verbal models of sex dimorphism in recombination rates. Intriguingly, these results may also explain why imprinted regions on the autosomes of humans or sheep are particularly heterochiasmate.
Molecular Population Genetics of the Arabidopsis CLAVATA2 Region: The Genomic Scale of Variation and Selection in a Selfing Species
Authors: Shepard Kristen A , Purugganan Michael D
Published: April 2021

The Arabidopsis thaliana CLAVATA2 (CLV2) gene encodes a leucine-rich repeat protein that regulates the development of the shoot meristem. The levels and patterns of nucleotide variation were assessed for CLV2 and 10 flanking genes that together span a 40-kb region of chromosome I. A total of 296 out of 7959 sequenced nucleotide sites were polymorphic. The mean levels of sequence diversity of the contiguous genes in this region are approximately twofold higher than those of other typical Arabidopsis nuclear loci. There is, however, wide variation in the levels and patterns of sequence variation among the 11 linked genes in this region, and adjacent genes appear to be subject to contrasting evolutionary forces. CLV2 has the highest levels of nucleotide variation in this region, a significant excess of intermediate frequency polymorphisms, and significant levels of intragenic linkage disequilibrium. Most alleles at CLV2 are found in one of three haplotype groups of moderate (>15%) frequency. These features suggest that CLV2 may harbor a balanced polymorphism.
A High-Copy-Number CACTA Family Transposon in Temperate Grasses and Cereals
Authors: Langdon Tim , Jenkins Glyn , Hasterok Robert , Jones R Neil , King Ian P
Published: April 2021

A lineage of CACTA family transposons has been identified in temperate grasses and cereals, and a full-length representative of the subfamily from Lolium perenne has been sequenced. Both the size and internal organization of the L. perenne element are typical of other CACTA family elements but its high copy number and strong conservation are unexpected. Comparison with homologs in other species suggests that this lineage has adopted a distinct and novel evolutionary strategy, which has allowed it to maintain its presence in genomes over long periods of time.
Regulating General Mutation Rates: Examination of the Hypermutable State Model for Cairnsian Adaptive Mutation
Authors: Roth John R , Kofoid Eric , Roth Frederick P , Berg Otto G , Seger Jon , Andersson Dan I
Published: April 2021

In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis suffered by the selected mutants has been interpreted as support for the idea that E. coli possesses an evolved (and therefore beneficial) mechanism that increases the mutation rate in response to stress (the hypermutable state model, HSM). This mechanism is proposed to allow faster genetic adaptation to stressful conditions and to explain why mutations appear directed to useful sites. Analysis of the HSM reveals that it requires implausibly intense mutagenesis (105 times the unselected rate) and even then cannot account for the behavior of the Cairns system. The assumptions of the HSM predict that selected revertants will carry an average of eight deleterious null mutations and thus seem unlikely to be successful in long-term evolution. The experimentally observed 35-fold increase in the level of general mutagenesis cannot account for even one Lac+ revertant from a mutagenized subpopulation of 105 cells (the number proposed to enter the hypermutable state). We conclude that temporary general mutagenesis during stress is unlikely to provide a long-term selective advantage in this or any similar genetic system.
Evolutionary, Structural and Biochemical Evidence for a New Interaction Site of the Leptin Obesity Protein
Authors: Gaucher Eric A , Miyamoto Michael M , Benner Steven A
Published: April 2021

The Leptin protein is central to the regulation of energy metabolism in mammals. By integrating evolutionary, structural, and biochemical information, a surface segment, outside of its known receptor contacts, is predicted as a second interaction site that may help to further define its roles in energy balance and its functional differences between humans and other mammals.
Prodigal Children: Why Older Mothers Favor Their Once-Deviant Adult Children
Authors: Kincaid Reilly , Rurka Marissa , Suitor J Jill , Gilligan Megan , Pillemer Karl , Mohebbi Liam , Mundell Nicholas
Published: April 2021

Objectives

Past research suggests that adult children who reform their deviant behaviors (i.e., problems with drugs/alcohol or the law) are more likely to become favored by their mothers, yet the reasons underlying this phenomenon are unclear. This study employs a longitudinal, qualitative approach to explore why adult children’s behavioral reforms shape changes in maternal favoritism.

Method

Analyses are based on qualitative interview data collected at 2 points 7 years apart from older mothers regarding their adult children in 20 families. Each of these families had a “prodigal child”—a child for whom desistance from deviant behaviors between the 2 waves was accompanied by newfound maternal favoritism.

Results

Findings revealed 2 conditions under which mothers came to favor reformed deviants over their siblings. First, this occurred when adult children’s behavioral reformations were accompanied by mothers’ perceptions of these children as having grown more family-oriented. Second, this occurred when mothers came to see reformed deviants as exhibiting a stronger need and appreciation for maternal support, relative to their siblings.

Discussion

Mothers’ perceptions of children’s behavioral reformations as being accompanied by greater dedication to family or reflecting a need for their mothers’ support offer 2 explanations for why previously deviant adult children may become mothers’ favored offspring. These findings contribute to a growing body of scholarship on the complexity of intergenerational relations by shedding new light on changing patterns of favoritism in families with a history of parental disappointment, conflict, and strain.
Noncovalent microarrays from synthetic amino-terminating glycans: Implications in expanding glycan microarray diversity and platform comparison
Authors: Li Chunxia , Palma Angelina S , Zhang Pengtao , Zhang Yibing , Gao Chao , Silva Lisete M , Li Zhen , Trovão Filipa , Weishaupt Markus , Seeberger Peter H , Likhosherstov Leonid M , Piskarev Vladimir , Yu Jin , Westerlind Ulrika , Chai Wengang
Published: April 2021

Glycan microarrays have played important roles in detection and specificity assignment of glycan recognition by proteins. However, the size and diversity of glycan libraries in current microarray systems are small compared to estimated glycomes, and these may lead to missed detection or incomplete assignment. For microarray construction, covalent and noncovalent immobilization are the two types of methods used, but a direct comparison of results from the two platforms is required. Here we develop a chemical strategy to prepare lipid-linked probes from both naturally derived aldehyde-terminating and synthetic amino-terminating glycans that addresses the two aspects: expansion of sequence-defined glycan libraries and comparison of the two platforms. We demonstrate the specific recognition by plant and mammalian lectins, carbohydrate-binding modules and antibodies and the overall similarities from the two platforms. Our results provide new knowledge on unique glycan-binding specificities for the immune receptor Dectin-1 toward β-glucans and the interaction of rotavirus P[19] adhesive protein with mucin O-glycan cores.
Cis-acting modifiers in the ABCA4 locus contribute to the penetrance of the major disease-causing variant in Stargardt disease
Authors: Lee Winston , Zernant Jana , Nagasaki Takayuki , Molday Laurie L , Su Pei-Yin , Fishman Gerald A , Tsang Stephen H , Molday Robert S , Allikmets Rando
Published: April 2021

Over 1200 variants in the ABCA4 gene cause a wide variety of retinal disease phenotypes, the best known of which is autosomal recessive Stargardt disease (STGD1). Disease-causing variation encompasses all mutation categories, from large copy number variants to very mild, hypomorphic missense variants. The most prevalent disease-causing ABCA4 variant, present in ~ 20% of cases of European descent, c.5882G > A p.(Gly1961Glu), has been a subject of controversy since its minor allele frequency (MAF) is as high as ~ 0.1 in certain populations, questioning its pathogenicity, especially in homozygous individuals. We sequenced the entire ~140Kb ABCA4 genomic locus in an extensive cohort of 644 bi-allelic, i.e. genetically confirmed, patients with ABCA4 disease and analyzed all variants in 140 compound heterozygous and 10 homozygous cases for the p.(Gly1961Glu) variant. A total of 23 patients in this cohort additionally harbored the deep intronic c.769-784C > T variant on the p.(Gly1961Glu) allele, which appears on a specific haplotype in ~ 15% of p.(Gly1961Glu) alleles. This haplotype was present in 5/7 of homozygous cases, where the p.(Gly1961Glu) was the only known pathogenic variant. Three cases had an exonic variant on the same allele with the p.(Gly1961Glu). Patients with the c.[769-784C > T;5882G > A] complex allele exhibit a more severe clinical phenotype, as seen in compound heterozygotes with some more frequent ABCA4 mutations, e.g. p.(Pro1380Leu). Our findings indicate that the c.769-784C > T variant is major cis-acting modifier of the p.(Gly1961Glu) allele. The absence of such additional allelic variation on most p.(Gly1961Glu) alleles largely explains the observed paucity of affected homozygotes in the population.
Protein instability associated with AARS1 and MARS1 mutations causes trichothiodystrophy
Authors: Botta Elena , Theil Arjan F , Raams Anja , Caligiuri Giuseppina , Giachetti Sarah , Bione Silvia , Accadia Maria , Lombardi Anita , Smith Desiree E C , Mendes Marisa I , Swagemakers Sigrid M A , van der Spek Peter J , Salomons Gajja S , Hoeijmakers Jan H J , Yesodharan Dhanya , Nampoothiri Sheela , Ogi Tomoo , Lehmann Alan R , Orioli Donata , Vermeulen Wim
Published: April 2021

Trichothiodystrophy (TTD) is a rare hereditary neurodevelopmental disorder defined by sulfur-deficient brittle hair and nails and scaly skin, but with otherwise remarkably variable clinical features. The photosensitive TTD (PS-TTD) forms exhibits in addition to progressive neuropathy and other features of segmental accelerated aging and is associated with impaired genome maintenance and transcription. New factors involved in various steps of gene expression have been identified for the different non-photosensitive forms of TTD (NPS-TTD), which do not appear to show features of premature aging. Here, we identify alanyl-tRNA synthetase 1 and methionyl-tRNA synthetase 1 variants as new gene defects that cause NPS-TTD. These variants result in the instability of the respective gene products alanyl- and methionyl-tRNA synthetase. These findings extend our previous observations that TTD mutations affect the stability of the corresponding proteins and emphasize this phenomenon as a common feature of TTD. Functional studies in skin fibroblasts from affected individuals demonstrate that these new variants also impact on the rate of tRNA charging, which is the first step in protein translation. The extension of reduced abundance of TTD factors to translation as well as transcription redefines TTD as a syndrome in which proteins involved in gene expression are unstable.
Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)
Authors: Shaheen John , Mudd Austin B , Diekwisch Thomas G H , Abramyan John
Published: April 2021

Synopsis

Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary time line of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In this study, we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison with functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46–60 million years ago in the lineage leading to modern true toads, a time line that coincides with the rise of the family Bufonidae.
Biometric encryption of smartphones: a charted ship in the ocean of adversarial system?
Authors: Bhalotia Kartikey Sanjeev , Pareek Divyansh
Published: April 2021

India has recently been flooded with smartphones having features of biometric encryption that allows users to encrypt the data on their devices using their biometric features, such as finger impressions or iris patterns. This technology assures users of precluding impermissible intrusions into their private data. However, this idea behind biometric encryption has witnessed critical considerations in the recent past, when Courts of various jurisdictions in the USA were faced with the issue of whether an investigating agency has the power to unlock such smartphones by compelling an accused to depress his fingerprints on the touch ID of the same. The courts have tried to strike a balance between the competing interests of the State and of the accused. While on the one side is the consideration that such power to the investigating agencies are essential for combating crime, on the other, there are the individualistic fundamental rights of the accused. The courts have weighed the prospective impact of giving the investigating agency the said power against an accused’s fundamental rights against self-incrimination, and privacy. This article, after analysing these judgments, endeavours to provide answers to the questions that Indian Courts might face in future concerning search and seizure of smartphones and its implications on the fundamental rights of an accused. This discussion becomes important especially due to the absence of any judicial pronouncements on the issue in India and more so, because even existing pronouncements by the courts in the USA have been quite contradictory.
A discrete dynamics approach to interbank financial contagion
Authors: Leventides John , Poulios Costas , Camouzis Elias
Published: April 2021

The purpose of this paper is to describe in terms of mathematical models and systems theory the dynamics of interbank financial contagion. Such a description gives rise to a model that can be studied with mathematical tools and will provide a new framework for the study of contagion dynamics complementary to research by simulation studied so far. It provides a better understanding of such financial networks and a unifying network for the research of financial contagion. The mathematical description we present is in terms of Boolean dynamical systems and a linear operator. We relate the properties of the dynamical systems to the properties of the operator.