bluuebunny/crossref_metadata_2025 huggingface dataset:
Melatonin alleviates deoxynivalenol-induced apoptosis of human granulosa cells by reducing mutually accentuated FOXO1 and ER stress
Authors: Xue Rufeng , Li Shuhang , Zou Huijuan , Ji Dongmei , Lv Mingrong , Zhou Ping , Wei Zhaolian , Zhang Zhiguo , Cao Yunxia
Published: April 2021

Deoxynivalenol (DON) is one of the most prevalent Fusarium mycotoxins, which cause detrimental effects on human and animal reproductive systems by inducing oxidative stress. Increasing evidence has suggested the potential roles of melatonin in protecting granulosa cells from oxidative injury, but the underlying mechanisms remain largely elusive. Here, we demonstrated that suppression of FOXO1 and endoplasmic reticulum (ER) stress was engaged in melatonin-mediated protection against oxidative damage in human granulosa cells upon DON exposure in vitro. DON induced excess reactive oxygen species accumulation, cells viability loss, reduced estradiol-17β, and progesterone production in human granulosa cells, whereas melatonin ameliorated these phenotypes. Next, we found that the protective effect of melatonin against apoptosis was via reducing ER stress because the inhibition of ER stress displayed similar protective effects during DON treatment. Moreover, melatonin provided no additional protection when ER stress was inhibited. We further found that FOXO1 is a pivotal downstream effector of melatonin and ER stress in regulating DON-induced apoptosis in human granulosa cells. Blocking of FOXO1 reduced DON-induced cells death and FOXO1 activation could be suppressed by melatonin or ER stress inhibitor. However, melatonin failed to further restore cells viability in the presence of FOXO1 inhibitor. Collectively, our results reveal a new mechanism of melatonin in protecting against DON-induced apoptosis and dysfunction by suppressing ER stress and FOXO1 in human granulosa cells.
O15: DISRUPTION OF THE BLOOD-SPINAL CORD BARRIER PREDICTS PERMANENT PARAPLEGIA AFTER THORACOABDOMINAL AORTIC ANEURYSM REPAIR
Authors: Kelly J , Patel A , Onadim I , Abisi S , Bell R , Tyrrell M , Sallam M , Salih M , Mayr M , Bradbury E , Cho J , Gworzdz A , Booth T , Smith A , Modarai B
Published: April 2021

Introduction

Paraplegia post-thoracoabdominal aortic aneurysm (TAAA) repair remains both a devastating and poorly understood complication. We related temporal changes in cellular and protein composition of cerebrospinal fluid (CSF) to neurological outcomes after TAAA repair to gain mechanistic insights driving paraplegia.

Method

Patients undergoing TAAA repair (open or endovascular) with a CSF drain were prospectively recruited between 2016-2018. CSF was collected pre-operatively and 24-hourly until removal. Daily neurological examinations were performed by blinded neurologists to the study. CSF cell content was characterised by flow cytometry and proteome analysed by tandem-mass-tag proteomics. An in-vivo rat model was modified using 15 minutes of aortic occlusion to produce consistent paraplegia. Rats were analysed neuro-behaviourally and histologically.

Result

CSF was analysed from 52 patients (age: 70.27+/-11.4; 66% male; open (n=9), endovascular (n=43)). 12 developed paraplegia of whom 5 remained permanently-paraplegic. Demographics were comparable between paraplegics, those who recovered and without post-op neurology. Permanent paraplegia was associated with a significant infiltration of CSF CD45+ leucocytes (P<0.0001). Levels of ADVS-1 was >3-fold higher in permanent-paraplegics CSF versus those who recovered (P=0.0008). ADVS-1 >15ng/ml predicted permanent paraplegia with 100% specificity. Pre-treatment with ADVS-1 inhibition significantly improved walking (<0.001) and increased astrocytic staining in the lateral corticospinal, reticulospinal and rubrospinal tracts versus controls (P=0.03, 0.04, 0.04 respectively).

Conclusion

Permanent paraplegia is associated with shedding of ADVS-1 from parenchymal cord into CSF and blood/spinal-cord barrier disruption leading to cord oedema/leucocyte infiltration. Pre-treatment with ADVS-1 inhibition led to neurobehavioural and histological improvements offering translational hope for this devastating complication.

Take-home message

ADVS-1 is a novel biomarker of paraplegia where accurate biomarkers have proven challenging but more importantly it has proven a therapeutic target with genuine translational potential.
Robust and Dynamic Graph Convolutional Network For Multi-view Data Classification
Authors: Peng Liang , Kong Fei , Liu Chongzhi , Kuang Ping
Published: April 2021

Since graph learning could preserve the structure information of the samples to improve the learning ability, it has been widely applied in both shallow learning and deep learning. However, the current graph learning methods still suffer from the issues such as outlier influence and model robustness. In this paper, we propose a new dynamic graph neural network (DGCN) method to conduct semi-supervised classification on multi-view data by jointly conducting the graph learning and the classification task in a unified framework. Specifically, our method investigates three strategies to improve the quality of the graph before feeding it into the GCN model: (i) employing robust statistics to consider the sample importance for reducing the outlier influence, i.e. assigning every sample with soft weights so that the important samples are with large weights and outliers are with small or even zero weights; (ii) learning the common representation across all views to improve the quality of the graph for every view; and (iii) learning the complementary information from all initial graphs on multi-view data to further improve the learning of the graph for every view. As a result, each of the strategies could improve the robustness of the DGCN model. Moreover, they are complementary for reducing outlier influence from different aspects, i.e. the sample importance reduces the weights of the outliers, both the common representation and the complementary information improve the quality of the graph for every view. Experimental result on real data sets demonstrates the effectiveness of our method, compared to the comparison methods, in terms of multi-class classification performance.
A Survey of Privacy Solutions using Blockchain for Recommender Systems: Current Status, Classification and Open Issues
Authors: Abduljabbar Tamara Abdulmunim , Tao Xiaohui , Zhang Ji , Zhou Xujuan , Li Lin , Cai Yi
Published: April 2021

Due to the rapid growth of Internet, E-commerce and Internet of Things, people use Web based services for most of their needs including buying items, reading books, watching online shows etc. Several companies are using recommender systems to influence people’s choices based on their likings, behaviours etc. Hence, people fear that their privacy is violated. Also, some of the online applications are not safe and secure. One way to overcome the privacy related issues is using secured solutions such as incorporating blockchain technologies for privacy-based applications. The decentralized nature of blockchain technologies have resolved several security, and authentication problems of Internet of Things systems. In this paper, we conduct a comprehensive survey on the privacy solutions for recommender systems emphasising current status, classification and open issues. We also discuss blockchain technology, including its structure as well as applications of blockchain technology for privacy solutions of recommender systems. Furthermore, we discuss the limitations and delve into future trends that blockchain technology can be adapted for privacy-base applications in the years to come.
Characterization of robustness and resilience in graphs: a mini-review
Authors: Schaeffer S E , Valdés V , Figols J , Bachmann I , Morales F , Bustos-Jiménez J
Published: April 2021

We briefly survey recent proposals that seek to capture in numerical terms the resilience and the robustness of a graph. After a brief introduction and the establishment of notation and terminology, we catalogue characterizations proposed in journal articles published within the last two decades. We then describe some of the numerous application areas for such characterizations. We experiment with implementations of numerous characteristics on several graph-generation models, after which we conclude with a discussion of open problems and future directions.
Thymomectomy plus total thymectomy versus simple thymomectomy for early-stage thymoma without myasthenia gravis: a European Society of Thoracic Surgeons Thymic Working Group Study
Authors: Guerrera Francesco , Falcoz Pierre Emmanuel , Moser Bernhard , van Raemdonck Dirk , Bille’ Andrea , Toker Alper , Spaggiari Lorenzo , Ampollini Luca , Filippini Claudia , Thomas Pascal Alexandre , Verdonck Bram , Mendogni Paolo , Aigner Clemens , Voltolini Luca , Novoa Nuria , Patella Miriam , Mantovani Sara , Bravio Ivan Gomes , Zisis Charalambos , Guirao Angela , Londero Francesco , Congregado Miguel , Rocco Gaetano , Du Pont Bert , Martucci Nicola , Esch Matthias , Brunelli Alessandro , Detterbeck Frank C , Venuta Federico , Weder Walter , Ruffini Enrico ,   the European Society of Thoracic Surgeons (ESTS) Thymic Working Group Participating Centers, Klepetko Walter , Olland Anne , Du Pont Bert , Nonaka Daisuke , Ozkan Berker , Lo Iacono Giorgio , Braggio Cesare , Filosso Pier Luigi , Brioude Geoffrey , van Schil Paul , Nosotti Mario , Valdivia Daniel , Bongiolatti Stefano , Inci Ilhan , Dimitra Rontogianni , Sànchez David , Grossi William , Moreno-Merino Sergio , Teschner Martin
Published: April 2021

OBJECTIVES

Resection of thymic tumours including the removal of both the tumour and the thymus gland (thymothymectomy; TT) is the procedure of choice and is recommended in most relevant articles in the literature. Nevertheless, in recent years, some authors have suggested that resection of the tumour (simple thymomectomy; ST) may suffice from an oncological standpoint in patients with early-stage thymoma who do not have myasthenia gravis (MG) (non-MG). The goal of our study was to compare the short- and long-term outcomes of ST versus TT in non-MG early-stage thymomas using the European Society of Thoracic Surgeons thymic database.

METHODS

A total of 498 non-MG patients with pathological stage I thymoma were included in the study. TT was performed in 466 (93.6%) of 498 patients who had surgery with curative intent; ST was done in 32 (6.4%). The completeness of resection, the rate of complications, the 30-day mortality, the overall recurrence and the freedom from recurrence were compared. We performed crude and propensity score-adjusted comparisons by surgical approach (ST vs TT).

RESULTS

TT showed the same rate of postoperative complications, 30-day mortality and postoperative length of stay as ST. The 5-year overall survival rate was 89% in the TT group and 55% in the ST group. The 5-year freedom from recurrence was 96% in the TT group and 79% in the ST group.

CONCLUSION

Patients with early-stage thymoma without MG who have a TT show significantly better freedom from recurrence than those who have an ST, without an increase in postoperative morbidity rate.
The influence of maize genotype on the rhizosphere eukaryotic community
Authors: Matus-Acuña Violeta , Caballero-Flores Gustavo , Martínez-Romero Esperanza
Published: April 2021

The microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.
Isolation of the Gene Encoding the Drosophila melanogaster Homolog of the Saccharomyces cerevisiae GCN2 eIF-2α Kinase
Authors: Olsen DeAnne S , Jordan Barbara , Chen Dreeny , Wek Ronald C , Cavener Douglas R
Published: April 2021

Genomic and cDNA clones homologous to the yeast GCN2 eIF-2α kinase (yGCN2) were isolated from Drosophila melanogaster. The identity of the Drosophila GCN2 (dGCN2) gene is supported by the unique combination of sequence encoding a protein kinase catalytic domain and a domain homologous to histidyl-tRNA synthetase and by the ability of dGCN2 to complement a deletion mutant of the yeast GCN2 gene. Complementation of Δgcn2 in yeast by dGCN2 depends on the presence of the critical regulatory phosphorylation site (serine 51) of eIF-2α. dGCN2 is composed of 10 exons encoding a protein of 1589 amino acids. dGCN2 mRNA is expressed throughout Drosophila development and is particularly abundant at the earliest stages of embryogenesis. The dGCN2 gene was cytogenetically and physically mapped to the right arm of the third chromosome at 100C3 in STS Dm2514. The discovery of GCN2 in higher eukaryotes is somewhat unexpected given the marked differences between the amino acid biosynthetic pathways of yeast vs. Drosophila and other higher eukaryotes. Despite these differences, the presence of GCN2 in Drosophila suggests at least partial conservation from yeast to multicellular organisms of the mechanisms responding to amino acid deprivation.
Nonneutral Evolution and Differential Mutation Rate of Gender-Associated Mitochondrial DNA Lineages in the Marine Mussel Mytilus
Authors: Quesada Humberto , Warren Mary , Skibinski David O F
Published: April 2021

Mussels have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally, and the F type is transmitted maternally. To test hypotheses of the molecular evolution of both mtDNA genomes, 50 nucleotide sequences were obtained for 396 bp of the COIII gene of European populations of Mytilus edulis and the Atlantic and Mediterranean forms of M. galloprovincialis. Analysis based on the proportion of synonymous and nonsynonymous substitutions indicate that mtDNA is evolving in a non-neutral and complex fashion. Previous studies on American mussels demonstrated that the F genome experiences a higher purifying selection and that the M genome evolves faster. Here we show that these patterns also hold in European populations. However, in contrast to American populations, where an excess of replacement substitution between F and M lineages has been reported, a significant excess of replacement polymorphism within mtDNA lineages is observed in European populations of M. galloprovincialis.European populations also show an excess of replacement polymorphism within the F but not within the M genome with respect to American M. trossulus, as well as a consistent pattern of excess of rare variants in both F and M genomes. These results are consistent with a nearly neutral model of molecular evolution and a recent relaxation of selective constraints on European mtDNA. Levels of diversity are significantly higher for the M than F genome, and the M genome also accumulates synonymous and nonsynonymous substitutions at a higher rate, in contrast with earlier reports where no difference for the synonymous rate was observed. It is suggested that a subtle balance between relaxed selection and a higher mutation rate explains the faster evolutionary rate of the M lineage.
The Expected Number of Heterozygous Sites in a Subdivided Population
Authors: Nagylaki Thomas
Published: April 2021

A simple, exact formula is derived for the expected number of heterozygous sites per individual at equilibrium in a subdivided population. The model of infinitely many neutral sites is posited; the linkage map is arbitrary. The monoecious, diploid population is subdivided into a finite number of panmictic colonies that exchange gametes. The backward migration matrix is arbitrary, but time independent and ergodic (i.e., irreducible and aperiodic). With suitable weighting, the expected number of heterozygous sites is 4Neu, where Ne denotes the migration effective population number and u designates the total mutation rate per gene (or DNA sequence). For diploid migration, this formula is a good approximation if Ne ⪢ 1.
The Schizosaccharomyces pombe S-Phase Checkpoint Differentiates Between Different Types of DNA Damage
Authors: Rhind Nicholas , Russell Paul
Published: April 2021

We have identified an S-phase DNA damage checkpoint in Schizosaccharomyces pombe. This checkpoint is dependent on Rad3, the S. pombe homolog of the mammalian ATM/ATR checkpoint proteins, and Cds1. Cds1 had previously been believed to be involved only in the replication checkpoint. The requirement of Cds1 in the DNA damage checkpoint suggests that Cds1 may be a general target of S-phase checkpoints. Unlike other checkpoints, the S. pombe S-phase DNA damage checkpoint discriminates between different types of damage. UV-irradiation, which causes base modification that can be repaired during G1 and S-phase, invokes the checkpoint, while γ-irradiation, which causes double-stranded breaks that cannot be repaired by a haploid cell if induced before replication, does not invoke the checkpoint. Because the same genes are required to respond to UV- and γ-irradiation during G2, this discrimination may represent an active suppression of the γ response during S-phase.
Genetic Mechanisms Underlying Apimaysin and Maysin Synthesis and Corn Earworm Antibiosis in Maize (Zea mays L.)
Authors: Lee E A , Byrne P F , McMullen M D , Snook M E , Wiseman B R , Widstrom N W , Coe E H
Published: April 2021

C-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14.1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.
A Bayesian Characterization of Hardy-Weinberg Disequilibrium
Authors: Shoemaker Jennifer , Painter Ian , Weir B S
Published: April 2021

A Bayesian method for determining if there are large departures from independence between pairs of alleles at a locus, Hardy-Weinberg equilibrium (HWE), is presented. We endorse the view that a population will never be exactly in HWE and that there will be occasions when there is a need for an alternative to the usual hypothesis-testing setting. Bayesian methods provide such an alternative, and our approach differs from previous Bayesian treatments in using the disequilibrium and inbreeding coefficient parameterizations. These are easily interpretable but may be less mathematically tractable than other parameterizations. We examined the posterior distributions of our parameters for evidence that departures from HWE were large. For either parameterization, when a conjugate prior was used, the prior probability for small departures was itself small, i.e., the prior was weighted against small departures from independence. We could avoid this uneven weighting by using a step prior which gave equal weighting to both small and large departures from HWE. In most cases, the Bayesian methodology makes it clear that there are not enough data to draw a conclusion.
Selfish Genes, Pleiotropy and the Origin of Recombination
Authors: Hey Jody
Published: April 2021

If multiple linked polymorphisms are under natural selection, then conflicts arise and the efficiency of natural selection is hindered relative to the case of no linkage. This simple interaction between linkage and natural selection creates an opportunity for mutations that raise the level of recombination to increase in frequency and have an enhanced chance of fixation. This important finding by S. Otto and N. Barton means that mutations that raise the recombination rate, but are otherwise neutral, will be selectively favored under fairly general circumstances of multilocus selection and linkage. The effect described by Otto and Barton, which was limited to neutral modifiers, can also be extended to include all modifiers of recombination, both beneficial and deleterious. Computer simulations show that beneficial mutations that also increase recombination have an increased chance of fixation. Similarly, deleterious mutations that also decrease recombination have an increased chance of fixation. The results suggest that a simple model of recombination modifiers, including both neutral and pleiotropic modifiers, is a necessary explanation for the evolutionary origin of recombination.
Van Gogh: A New Drosophila Tissue Polarity Gene
Authors: Taylor Job , Abramova Natasha , Charlton Jeannette , Adler Paul N
Published: April 2021

Mutations in the Van Gogh gene result in the altered polarity of adult Drosophila cuticular structures. On the wing, Van Gogh mutations cause an altered polarity pattern that is typical of mutations that inactivate the frizzled signaling/signal transduction pathway. The phenotype however, differs from those seen previously, as the number of wing cells forming more than one hair is intermediate between that seen previously for typical frizzled-like or inturned-like mutations. Consistent with Van Gogh being involved in the function of the frizzled signaling/signal transduction pathway, Van Gogh mutations show strong interactions with mutations in frizzled and prickle. Mitotic clones of Van Gogh display domineering cell nonautonomy. In contrast to frizzled clones, Van Gogh clones alter the polarity of cells proximal (and in part anterior and posterior) but not distal to the clone. In further contrast to frizzled clones, Van Gogh clones cause neighboring wild-type hairs to point away from rather than toward the clone. This anti-frizzled type of domineering nonautonomy and the strong genetic interactions seen between frizzled and Van Gogh suggested the possibility that Van Gogh was required for the noncell autonomous function of frizzled. As a test of this possibility we induced frizzled clones in a Van Gogh mutant background and Van Gogh clones in a frizzled mutant background. In both cases the domineering nonautonomy was suppressed consistent with Van Gogh being essential for frizzled signaling.
A Genetic Screen for Novel Components of the Notch Signaling Pathway During Drosophila Bristle Development
Authors: Go Masahiro J , Artavanis-Tsakonas Spyros
Published: April 2021

The Notch receptor is the central element in a cell signaling mechanism controlling a broad spectrum of cell fate choices. Genetic modifier screens in Drosophila and subsequent molecular studies have identified several Notch pathway components, but the biochemical nature of signaling is still elusive. Here, we report the results of a genetic modifier screen of the bristle phenotype of a gain-of-function Notch allele, Abruptex16. Abruptex mutations interfere with lateral inhibition/specification events that control the segregation of epidermal and sensory organ precursor lineages, thus inhibiting bristle formation. Mutations that reduce Notch signaling suppress this phenotype. This screen of approximately 50,000 flies led to the identification of a small number of dominant suppressors in seven complementation groups. These include known components in the pathway, Notch, mastermind, Delta, and Hairless, as well as two novel mutations. The first, A122, appears to interact with Notch only during bristle development. The other, M285, displays extensive genetic interactions with the Notch pathway elements and appears, in general, capable of suppressing Notch gain-of-function phenotypes while enhancing Notch loss-of-function phenotypes, suggesting that it plays an important role in Notch signaling.
Deleterious Mutations at the Mitochondrial ND3 Gene in South American Marsh Rats (Holochilus)
Authors: Kennedy Patricia , Nachman Michael W
Published: April 2021

Statistical analyses of DNA sequences have revealed patterns of nonneutral evolution in mitochondrial DNA of mice, humans, and Drosophila. Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus Holochilus). We sequenced the complete mitochondrial ND3 gene in 82 Holochilus brasiliensis and 21 H. vulpinus to test the neutral prediction that the ratio of nonsynonymous to synonymous nucleotide changes is the same within and between species. Within H. brasiliensis we observed a greater number of amino acid polymorphisms than expected based on interspecific comparisons. This contingency table analysis suggests that many amino acid polymorphisms are mildly deleterious. Several tests of the frequency distribution also revealed departures from a neutral, equilibrium model, and these departures were observed for both nonsynonymous and synonymous sites. In general, an excess of rare sites was observed, consistent with either a recent selective sweep or with populations not at mutation-drift equilibrium.
Mechanism and Control of Interspecies Recombination in Escherichia coli. I. Mismatch Repair, Methylation, Recombination and Replication Functions
Authors: Štambuk Snježana , Radman Miroslav
Published: April 2021

A genetic analysis of interspecies recombination in Escherichia coli between the linear Hfr DNA from Salmonella typhimurium and the circular recipient chromosome reveals some fundamental aspects of recombination between related DNA sequences. The MutS and MutL mismatch binding proteins edit (prevent) homeologous recombination between these 16% diverged genomes by at least two distinct mechanisms. One is MutH independent and presumably acts by aborting the initiated recombination through the UvrD helicase activity. The RecBCD nuclease might contribute to this editing step, presumably by preventing reiterated initiations of recombination at a given locus. The other editing mechanism is MutH dependent, requires unmethylated GATC sequences, and probably corresponds to an incomplete long-patch mismatch repair process that does not depend on UvrD helicase activity. Insignificant effects of the Dam methylation of parental DNAs suggest that unmethylated GATC sequences involved in the MutH-dependent editing are newly synthesized in the course of recombination. This hypothetical, recombination-associated DNA synthesis involves PriA and RecF functions, which, therefore, determine the extent of MutH effect on interspecies recombination. Sequence divergence of recombining DNAs appears to limit the frequency, length, and stability of early heteroduplex intermediates, which can be stabilized, and the recombinants mature via the initiation of DNA replication.
Alteration of N-Terminal Phosphoesterase Signature Motifs Inactivates Saccharomyces cerevisiae Mre11
Authors: Bressan Debra A , Olivares Heidi A , Nelms Benjamin E , Petrini John H J
Published: April 2021

Saccharomyces cerevisiae Mre11, Rad50, and Xrs2 function in a protein complex that is important for nonhomologous recombination. Null mutants of MRE11, RAD50, and XRS2 are characterized by ionizing radiation sensitivity and mitotic interhomologue hyperrecombination. We mutagenized the four highly conserved phosphoesterase signature motifs of Mre11 to create mre11-11, mre11-2, mre11-3, and mre11-4 and assessed the functional consequences of these mutant alleles with respect to mitotic interhomologue recombination, chromosome loss, ionizing radiation sensitivity, double-strand break repair, and protein interaction. We found that mre11 mutants that behaved as the null were sensitive to ionizing radiation and deficient in double-strand break repair. We also observed that these null mutants exhibited a hyperrecombination phenotype in mitotic cells, consistent with previous reports, but did not exhibit an increased frequency of chromosome loss. Differential ionizing radiation sensitivities among the hypomorphic mre11 alleles correlated with the trends observed in the other phenotypes examined. Two-hybrid interaction testing showed that all but one of the mre11 mutations disrupted the Mre11-Rad50 interaction. Mutagenesis of the phosphoesterase signatures in Mre11 thus demonstrated the importance of these conserved motifs for recombinational DNA repair.
Identification of High-Copy Disruptors of Telomeric Silencing in Saccharomyces cerevisiae
Authors: Singer Miriam S , Kahana Alon , Wolf Alexander J , Meisinger Lia L , Peterson Suzanne E , Goggin Colin , Mahowald Maureen , Gottschling Daniel E
Published: April 2021

The ends of chromosomes in Saccharomyces cerevisiae initiate a repressive chromatin structure that spreads internally and inhibits the transcription of nearby genes, a phenomenon termed telomeric silencing. To investigate the molecular basis of this process, we carried out a genetic screen to identify genes whose overexpression disrupts telomeric silencing. We thus isolated 10 DOT genes (disruptor of telomeric silencing). Among these were genes encoding chromatin component Sir4p, DNA helicase Dna2p, ribosomal protein L32, and two proteins of unknown function, Asf1p and Ifh1p. The collection also included genes that had not previously been identified: DOT1, DOT4, DOT5, DOT6, and TLC1, which encodes the RNA template component of telomerase. With the exception of TLC1, all these genes, particularly DOT1 and DOT4, also reduced silencing at other repressed loci (HM loci and rDNA) when overexpressed. Moreover, deletion of the latter two genes weakened silencing as well, suggesting that DOT1 and DOT4 normally play important roles in gene repression. DOT1 deletion also affected telomere tract length. The function of Dot1p is not known. The sequence of Dot4p suggests that it is a ubiquitin-processing protease. Taken together, the DOT genes include both components and regulators of silent chromatin.
Epigenetic Allelic States of a Maize Transcriptional Regulatory Locus Exhibit Overdominant Gene Action
Authors: Hollick Jay B , Chandler Vicki L
Published: April 2021

Using alleles of the maize purple plant locus (pl), which encodes a transcriptional regulator of anthocyanin pigment synthesis, we describe a case of single-locus heterosis, or overdominance, where the heterozygote displays a phenotype that is greater than either homozygote. The Pl-Rhoades (Pl-Rh) allele is subject to epigenetic changes in gene expression, resulting in quantitatively distinct expression states. Allelic states with low-expression levels, designated Pl′-mahogany (Pl′-mah), are dominant to the high-expression state of Pl-Rh. Pl′-mah states retain low-expression levels in subsequent generations when homozygous or heterozygous with Pl-Rh. However, Pl′-mah alleles frequently exhibit higher expression levels when heterozygous with other pl alleles; illustrating an overdominant allelic relationship. Higher expression levels are also observed when Pl′-mah is hemizygous. These results suggest that persistent allelic interactions between Pl′-mah and Pl-Rh are required to maintain the low-expression state and that other pl alleles are missing sequences required for this interaction. The Pl-Rh state can be sexually transmitted from Pl′-mah/pl heterozygotes, but not from Pl′-mah hemizygotes, suggesting that fixation of the high-expression state may involve synapsis. The existence of such allele-dependent regulatory mechanisms implicates a novel importance of allele polymorphisms in the genesis and maintenance of genetic variation.
Analysis of Population Structure in Autotetraploid Species
Authors: Ronfort Joëlle , Jenczewski Eric , Bataillon Thomas , Rousset François
Published: April 2021

Population structure parameters commonly used for diploid species are reexamined for the particular case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution of identity probabilities for neutral genes in an “island model” of population structure are derived assuming tetrasomic inheritance. The expected equilibrium value of FST is computed. In contrast to diploids, the correlation of genes between individuals within populations with respect to genes between populations (FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance and is consequently inappropriate for estimating demographic parameters in such populations. We thus define a new parameter (ρ) and derive its relationship withNm. This relationship is shown to be independent from both the selfing rate and the proportion of double reduction. Finally, the statistical procedure required to evaluate these parameters using data on gene frequencies distribution among autotetraploid populations is developed.
Characterization of Functional Regions in the Schizosaccharomyces pombe mei3 Developmental Activator
Authors: Wang Wei , Li Peng , Schettino Annette , Peng Zhe , McLeod Maureen
Published: April 2021

The Schizosaccharomyces pombe mei3+ gene is expressed only in diploid cells undergoing meiosis. Ectopic expression of mei3+ in haploid cells causes meiotic catastrophe. Mei3 is an inhibitor of Ran1/Pat1 kinase and contains a nine-amino-acid motif, Mei3-RKDIII, that resembles two regions in the Ste11 substrate for Ran1/Pat1. Substitution of serine for Arg-81 within Mei3-RKDIII transforms the inhibitor into a substrate for Ran1/Pat1. Thus, it is likely that Mei3-RKDIII defines a pseudosubstrate sequence. In this study, we constructed a series of mei3 deletion mutations and assayed each for activity. This analysis indicates that the carboxy-terminal domain of Mei3 is sufficient for function in vivo. Alanine-scanning mutagenesis identifies critical residues within the inhibitory domain. Two mutations, SM1 and SM8, fail to cause meiotic catastrophe. The SM1 mutation contains alterations of amino acid residues in Mei3-RKDIII. Recombinant SM1 protein exhibits reduced ability to inhibit Ran1/Pat1 kinase in vitro and interacts inefficiently with the kinase in a two-hybrid assay. The SM8 protein binds to Ran1/Pat1 in a two-hybrid assay but fails to inhibit Ran1/Pat1 substrate phosphorylation in vitro. These findings provide evidence that Mei3-RKDIII defines a Ran1/Pat1-binding site that is necessary but not sufficient for inhibition of the kinase. Using fusions to green fluorescent protein, the cellular localization of Ran1 and Mei3 was examined in living cells. Ran1 is concentrated in the nucleus. Mei3 is also enriched in the nucleus and, consistent with the genetic and biochemical results, the inhibitory domain of Mei3 is sufficient for nuclear localization.
Chromosomal Heterozygosity and Fertility in House Mice (Mus musculus domesticus) From Northern Italy
Authors: Hauffe Heidi C , Searle Jeremy B
Published: April 2021

Following the discovery of over 40 Robertsonian (Rb) races of Mus musculus domesticus in Europe and North Africa, the house mouse has been studied extensively as an ideal model to determine the chromosomal changes that may cause or accompany speciation. Current models of chromosomal speciation are based on the assumption that heterozygous individuals have a particularly low fertility, although recent studies indicate otherwise. Despite their importance, fertility estimates for the house mouse are incomplete because traditional measurements, such as anaphase I nondisjunction and germ cell death, are rarely estimated in conjunction with litter size. In an attempt to bridge this gap, we have taken advantage of the house mouse hybrid zone in Upper Valtellina (Lombardy, Italy) in which five Rb races interbreed. We present data on the fertility of naturally occurring (“wild-caught”) hybrids and of offspring from laboratory crosses of wild-caught mice (“laboratory-reared”), using various measurements. Wild-caught mice heterozygous for one fusion were more infertile than predicted from past studies, possibly due to genic hybridity; laboratory-reared heterozygotes carrying seven or eight trivalents at meiosis I and heterozygotes carrying one pentavalent also had low fertilities. These low fertilities are especially significant given the probable occurrence of a reinforcement event in Upper Valtellina.
Effect of the Pairing Gene Ph1 and Premeiotic Colchicine Treatment on Intra- and Interchromosome Pairing of Isochromosomes in Common Wheat
Authors: Vega Juan M , Feldman Moshe
Published: April 2021

The analysis of the pattern of isochromosome pairing allows one to distinguish factors affecting presynaptic alignment of homologous chromosomes from those affecting synapsis and crossing-over. Because the two homologous arms in an isochromosome are invariably associated by a common centromere, the suppression of pairing between these arms (intrachromosome pairing) would indicate that synaptic or postsynaptic events were impaired. In contrast, the suppression of pairing between an isochromosome and its homologous chromosome (interchromosome pairing), without affecting intrachromosome pairing, would suggest that homologous presynaptic alignment was impaired. We used such an isochromosome system to determine which of the processes associated with chromosome pairing was affected by the Ph1 gene of common wheat—the main gene that restricts pairing to homologues. Ph1 reduced the frequency of interchromosome pairing without affecting intrachromosome pairing. In contrast, intrachromosome pairing was strongly reduced in the absence of the synaptic gene Syn-B1. Premeiotic colchicine treatment, which drastically decreased pairing of conventional chromosomes, reduced interchromosome but not intrachromosome pairing. The results support the hypothesis that premeiotic alignment is a necessary stage for the regularity of meiotic pairing and that Ph1 relaxes this alignment. We suggest that Ph1 acts on premeiotic alignment of homologues and homeologues as a means of ensuring diploid-like meiotic behavior in polyploid wheat.
Comparative Mapping Between Arabidopsis thaliana and Brassica nigra Indicates That Brassica Genomes Have Evolved Through Extensive Genome Replication Accompanied by Chromosome Fusions and Frequent Rearrangements
Authors: Lagercrantz Ulf
Published: April 2021

Chromosome organization and evolution in the Brassicaceae family was studied using comparative linkage mapping. A total of 160 mapped Arabidopsis thaliana DNA fragments identified 284 homologous loci covering 751 cM in Brassica nigra. The data support that modern diploid Brassica species are descended from a hexaploid ancestor, and that the A. thaliana genome is similar in structure and complexity to those of each of the hypothetical diploid progenitors of the proposed hexaploid. Thus, the Brassica lineage probably went through a triplication after the divergence of the lineages leading to A. thaliana and B. nigra. These duplications were also accompanied by an exceptionally high rate of chromosomal rearrangements. The average length of conserved segments between A. thaliana and B. nigra was estimated at 8 cM. This estimate corresponds to ∼90 rearrangements since the divergence of the two species. The estimated rate of chromosomal rearrangements is higher than any previously reported data based on comparative mapping. Despite the large number of rearrangements, fine-scale comparative mapping between model plant A. thaliana and Brassica crops is likely to result in the identification of a large number of genes that affect important traits in Brassica crops.
Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice
Authors: Wu Jianzhong , Kurata Nori , Tanoue Hiroshi , Shimokawa Takanori , Umehara Yosuke , Yano Masahiro , Sasaki Takuji
Published: April 2021

Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.
Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines
Authors: Wu Junyuan , Krutovskii Konstantin V , Strauss Steven H
Published: April 2021

We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that >90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.
Extraordinary Ribosomal Spacer Length Heterogeneity in a Neotyphodium Endophyte Hybrid: Implications for Concerted Evolution
Authors: Ganley Austen R D , Scott Barry
Published: April 2021

An extraordinary level of length heterogeneity was found in the ribosomal DNA (rDNA) of an asexual hybrid Neotyphodium grass endophyte, isolate Lp1. This hybrid Neotyphodium endophyte is an interspecific hybrid between two grass endophytes, Neotyphodium lolii, and a sexual form, Epichlöe typhina, and the length heterogeneity was not found in either of these progenitor species. The length heterogeneity in the hybrid is localized to the intergenic spacer (IGS) and is the result of copy-number variation of a tandemly repeated subrepeat class within the IGS, the 111-/119-bp subrepeats. Copy number variation of this subrepeat class appears to be a consequence of mitotic unequal crossing over that occurs between these subrepeats. This implies that unequal crossing over plays a role in the concerted evolution of the whole rDNA. Changes in the pattern of IGS length variants occurred in just two rounds of single-spore purification. Analysis of the IGS length heterogeneity revealed features that are unexpected in a simple model of unequal crossing over. Potential refinements of the molecular details of unequal crossing over are presented, and we also discuss evidence for a combination of homogenization mechanisms that drive the concerted evolution of the Lp1 rDNA.
Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice
Authors: Wu Wei-Ren , Li Wei-Ming , Tang Ding-Zhong , Lu Hao-Ran , Worland A J
Published: April 2021

Using time-related phenotypic data, methods of composite interval mapping and multiple-trait composite interval mapping based on least squares were applied to map quantitative trait loci (QTL) underlying the development of tiller number in rice. A recombinant inbred population and a corresponding saturated molecular marker linkage map were constructed for the study. Tiller number was recorded every 4 or 5 days for a total of seven times starting at 20 days after sowing. Five QTL were detected on chromosomes 1, 3, and 5. These QTL explained more than half of the genetic variance at the final observation. All the QTL displayed an S-shaped expression curve. Three QTL reached their highest expression rates during active tillering stage, while the other two QTL achieved this either before or after the active tillering stage.
The Effect of Mating System Differences on Nucleotide Diversity at the Phosphoglucose Isomerase Locus in the Plant Genus Leavenworthia
Authors: Liu F , Charlesworth D , Kreitman M
Published: April 2021

To test the theoretical prediction that highly inbreeding populations should have low neutral genetic diversity relative to closely related outcrossing populations, we sequenced portions of the cytosolic phosphoglucose isomerase (PgiC) gene in the plant genus Leavenworthia, which includes both self-incompatible and inbreeding taxa. On the basis of sequences of intron 12 of this gene, the expected low diversity was seen in both populations of the selfers Leavenworthia uniflora and L. torulosa and in three highly inbreeding populations of L. crassa, while high diversity was found in self-incompatible L. stylosa, and moderate diversity in L. crassa populations with partial or complete self-incompatibility. In L. stylosa, the nucleotide diversity was strongly structured into three haplotypic classes, differing by several insertion/deletion sequences, with linkage disequilibrium between sequences of the three types in intron 12, but not in the adjacent regions. Differences between the three kinds of haplotypes are larger than between sequences of this gene region from different species. The haplotype divergence suggests the presence of a balanced polymorphism at this locus, possibly predating the split between L. stylosa and its two inbreeding sister taxa, L. uniflora and L. torulosa. It is therefore difficult to distinguish between different potential causes of the much lower sequence diversity at this locus in inbreeding than outcrossing populations. Selective sweeps during the evolution of these populations are possible, or background selection, or merely loss of a balanced polymorphism maintained by overdominance in the populations that evolved high selfing rates.