bluuebunny/crossref_metadata_2025 huggingface dataset:
Reinforcement methods designed to increase the residual life expectation of rigid pavements
Authors: Zghibarcea S , Taranu N , Ungureanu D , Boboc A , Boboc V
Published: April 2021

The lifespan of a road structure can be evaluated only based on a traffic forecast. After a road is open to traffic, degradations are starting to developed, even at light and moderate traffic levels. Thus, at a specific time moment during the structure’s lifespan, the residual life expectation of a road can be determined as a function of the degradation state and the forecasted traffic. The degradation state can be evaluated either by using the approximated characteristics of the road construction materials or, based on the real material properties that are experimentally determined on core samples. If the residual life is estimated based on up-to-date traffic forecasts and real road materials properties, the common reinforcement methods used to prologue the lifespan of the structure can be optimized and adapted to the specific conditions of each type of pavement.
Activated carbon and halloysite nanotubes membrane for CO2 and CH4 separation
Authors: Gunasakaran A , Jafa J , Saalah S , Sipaut C S , Yusof N , Aziz F , Ismail A F , Bilad M R , Yahya N Y , Ismail N M
Published: April 2021

In this study, mixed matrix membranes (MMMs) were prepared where activated carbon and halloysite nanotubes with a loading of 1 wt% is incorporated into the polysulfone membrane, and the performance of each membrane was investigated. The morphological properties, mechanical strength and their correlations with the gas separation performance for CO2 and CH4 for halloysite-mixed matrix membrane (MMMs-HNT) and activated carbon-mixed matrix membrane (MMMs-AC) was studied by using Scanning Electron Microscopy (SEM-EDX), tensile test and gas permeation test. From the characterization of MMMs, SEM shows an increase of 30.77% on the thickness of the dense layer of MMMs-HNTs compared to neat membrane and MMMs-AC. The EDX results also showed that HNTs evenly distributed in the polymeric matrix without any sign of agglomeration. Elongation at the break for MMMs-HNTs also decreases to 11.38%. The gas separation performance for MMMs-HNTs increased by about 55.43% compared to MMMs-AC at 2 bar. Furthermore, MMMs-HNTs also showed in increase in the selectivity of membrane towards CO2 and CH4 from 0.82 to 15.83 at 2 bar. In conclusion, the addition of 1 wt% of HNTs into PSF polymeric matrix showed a better permeance of CO2 and a greater selectivity compared to the neat membrane and the MMMs-AC and thus is the optimum inorganic filler for the mixed matrix membrane.
Retraction: LCA-SEM Energy Petrochemical Product Structure: A Research on Optimization Model of Low Carbon Economy Urban Agglomeration Supply Chain (IOP Conf. Ser.: Mater. Sci. Eng.
439 052041)
Authors: Yucong You , Luxia Yi
Published: April 2021

IOP Publishing Limited ("IOPP") is retracting this paper following an investigation which revealed that sections of the manuscript are computer generated. IOP Publishing is investigating why this was not identified during the submission and peer review process by the conference. As a member of the Committee for Publication Ethics (COPE) this has been investigated in accordance with COPE guidelines and it was agreed the article should be retracted.

IOPP expresses its thanks to the independent advisors who have shared their thoughts regarding this paper during the course of the investigation.

Retraction published: 28 April 2021
Beam collapse and refractive index changes inside fused silica induced by loosely focused femtosecond laser
Authors: Zhang Lin , Liu Jiamin , Zhong Zhicheng , Jiang Hao , Gu Honggang , Chen Xiuguo , Liu Shiyuan
Published: April 2021

Femtosecond laser-induced optical and structural changes inside transparent materials are crucial to ultrafast laser micromachining. In this work, on-axis beam collapse has been predicted by theoretical simulations and further demonstrated by the experimental results where a femtosecond pulse was loosely focused into a fused silica with the energy far above the self-focusing threshold. A detailed discussion of the energy thresholds and the starting locations on the optical axis of beam collapse for different beam waist radiuses is given. In addition, the spatial distribution of the refractive index has been determined using a spectroscopic ellipsometer and a roughly uniform decrease of 0.1 has been observed in the laser-modified region. Further, the relationship between the spatial distribution of the refractive index and the pulse energy density has been discussed quantitatively. The observed modulation of the beam collapse and the refractive index distribution can be expected to be a useful tool for femtosecond laser micromachining.
Influence of heat treatment on creep behavior of IN625 coating on a Ni3Al-base superalloy
Authors: Taheri Morteza , Rasoulpouraghdam Arash , Lohrasbi-Nejad Azadeh , Kashani-Bozorg Seyed Farshid , Panahi Liavoli Rohallah
Published: April 2021

IN625 coatings applied by selective laser melting show high resistance at high temperatures but the creep behavior of such coatings is not well understood. In this paper, the microstructure and creep behavior of this coating applied to Rene80 alloy under different heat treatment conditions, were investigated by a small punch creep test. The results show that coating application in the form of solution heat treatment + coating + aging heat treatment leads the maximum creep life of about 135 h. In cast-coated specimens, liquation cracks due to incomplete solution of γ-γ′ eutectic, γ′ phase, Cr-Mo boride, and MC carbide in heat affected zone reduced the creep life by about 63 h. In these samples, unlike the heat treatment sample, which experienced inter-granular creep failure, the failure occurred exactly from the coating-substrate interface.
Anti-condensation behavior of bamboo leaf surface (backside) and its bionic preparation
Authors: Wan Yanling , Zhang Caiyun , Zhang Meng , Xu Jinkai
Published: April 2021

Condensation often leads to a decrease in the efficiency of engineering equipment and an increase in energy consumption. Therefore, preventing or delaying condensation on the metal surface is of great significance for practical applications. Here, we report that the main microstructures on the bamboo leaves(backside) are microgrooves, pores and nano needle-like waxy layers, which have good hydrophobicity and anti-condensation performance. Combined experiments and theoretical analyses reveal that, the hydrophobic surface increases the thermodynamic barrier during the condensation process, which makes the liquid droplets appear in a dropwise condensation mode on the surface, thereby increasing the heat transfer coefficient. In addition, when the condensed droplets merge, their low surface energy and nano-needle structure drive their spontaneous bounce. Here, imitated the backside surface of bamboo leaf, an anti-condensation on the aluminum alloy surface is achieved by laser processing and sol-gel method-hydrothermal method.
Recent progress of triboelectrification-induced electroluminescence: from fundaments to applications
Authors: Su Li , Wang Haojie , Zi Yunlong
Published: April 2021

Luminescence is the premise for humans and even all creatures in the world to survive, as well as a crucial means for humans to interact with the environment. Recently, triboelectrification-induced electroluminescence (TIEL) has been applied in anti-counterfeiting, real-time vision sensor, human/machine interactive system, as well as self-powered illumination and display, thus attracting significant attention. It can convert kinetic energy into light through the coupling effects of triboelectrification and electroluminescence. In this review, we focus on the latest advancements of TIEL, including its fundaments, novel applications, and outlook. It is predicted that TIEL will be widely applied in daily activities and industrial productions, so as to achieve self-powered smart systems.
Advances on gradient scaffolds for osteochondral tissue engineering
Authors: Oliveira Joaquim M , Ribeiro Viviana P , Reis Rui L
Published: April 2021

The osteochondral (OC) tissue is one of the most hierarchical and complex structures known and it is composed by two main compartments of hyaline articular cartilage and subchondral bone. It exhibits unique cellular and molecular transitions from the cartilage to the bone layers. OC diseases such as osteoarthritis and traumatic lesions may affect the articular cartilage, calcified cartilage (interface region) and subchondral bone, thus posing great regenerative challenges. Tissue engineering (TE) principles can offer novel technologies and combinatorial approaches that can better recapitulate the biological OC challenges and complexity in terms of biochemical, mechanical, structural and metabolic gradients, and ultimately can provide biofunctional 3D scaffolds with high reproducibility, versatility and adaptability to each patient’s needs, as it occurs in OC tissue defects. The recent reports and future directions dealing with gradient scaffolds for OCTE strategies are overviewed herein. A special focus on clinical translation/regulatory approval is given.
Novel simple topology coreless TMR array current sensor
Authors: Xu X P , Liu T Z , Zhu M , Wangs J G
Published: April 2021

Traditional coreless current sensors have multiple magnetic sensors, the same number of operational amplifier and analog-to-digital converter (ADC). This requires more components and basically cannot meet the practical use because of area-effective and cost-effective requirements. In this paper a novel coreless tunnel magnetoresistance (TMR) array current sensor has the characteristics of simple N-1-1 topology, light weight, and low power consumption. Three TMRs are directly connected in parallel and unified only by one programmable amplifier to directly output to meet the current measurement. A relatively simple circuit structure is adopted and a good result is obtained. Finally, the applicability of the scheme is verified by theoretical analysis and actual measurement.
Characterization and comparison of gene-centered human interactomes
Authors: Mosca Ettore , Bersanelli Matteo , Matteuzzi Tommaso , Di Nanni Noemi , Castellani Gastone , Milanesi Luciano , Remondini Daniel
Published: April 2021

The complex web of macromolecular interactions occurring within cells—the interactome—is the backbone of an increasing number of studies, but a clear consensus on the exact structure of this network is still lacking. Different genome-scale maps of human interactome have been obtained through several experimental techniques and functional analyses. Moreover, these maps can be enriched through literature-mining approaches, and different combinations of various ‘source’ databases have been used in the literature. It is therefore unclear to which extent the various interactomes yield similar results when used in the context of interactome-based approaches in network biology. We compared a comprehensive list of human interactomes on the basis of topology, protein complexes, molecular pathways, pathway cross-talk and disease gene prediction. In a general context of relevant heterogeneity, our study provides a series of qualitative and quantitative parameters that describe the state of the art of human interactomes and guidelines for selecting interactomes in future applications.
Attentional Modulation of Hierarchical Speech Representations in a Multitalker Environment
Authors: Kiremitçi Ibrahim , Yilmaz Özgür , Çelik Emin , Shahdloo Mo , Huth Alexander G , Çukur Tolga
Published: April 2021

Humans are remarkably adept in listening to a desired speaker in a crowded environment, while filtering out nontarget speakers in the background. Attention is key to solving this difficult cocktail-party task, yet a detailed characterization of attentional effects on speech representations is lacking. It remains unclear across what levels of speech features and how much attentional modulation occurs in each brain area during the cocktail-party task. To address these questions, we recorded whole-brain blood-oxygen-level-dependent (BOLD) responses while subjects either passively listened to single-speaker stories, or selectively attended to a male or a female speaker in temporally overlaid stories in separate experiments. Spectral, articulatory, and semantic models of the natural stories were constructed. Intrinsic selectivity profiles were identified via voxelwise models fit to passive listening responses. Attentional modulations were then quantified based on model predictions for attended and unattended stories in the cocktail-party task. We find that attention causes broad modulations at multiple levels of speech representations while growing stronger toward later stages of processing, and that unattended speech is represented up to the semantic level in parabelt auditory cortex. These results provide insights on attentional mechanisms that underlie the ability to selectively listen to a desired speaker in noisy multispeaker environments.
Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology
Authors: Karaba Andrew H , Zhou Weiqiang , Hsieh Leon L , Figueroa Alexis , Massaccesi Guido , Rothman Richard E , Fenstermacher Katherine Z J , Sauer Lauren , Shaw-Saliba Kathryn , Blair Paul W , Robinson Matthew L , Leung Sherry , Wesson Russell , Alachkar Nada , El-Diwany Ramy , Ji Hongkai , Cox Andrea L
Published: April 2021

Background

Several inflammatory cytokines are upregulated in severe coronavirus disease 2019 (COVID-19). We compared cytokines in COVID-19 versus influenza to define differentiating features of the inflammatory response to these pathogens and their association with severe disease. Because elevated body mass index (BMI) is a known risk factor for severe COVID-19, we examined the relationship of BMI to cytokines associated with severe disease.

Methods

Thirty-seven cytokines and chemokines were measured in plasma from 135 patients with COVID-19, 57 patients with influenza, and 30 healthy controls. Controlling for BMI, age, and sex, differences in cytokines between groups were determined by linear regression and random forest prediction was used to determine the cytokines most important in distinguishing severe COVID-19 and influenza. Mediation analysis was used to identify cytokines that mediate the effect of BMI and age on disease severity.

Results

Interleukin-18 (IL-18), IL-1β, IL-6, and tumor necrosis factor-α (TNF-α) were significantly increased in COVID-19 versus influenza patients, whereas granulocyte macrophage colony-stimulating factor, interferon-γ (IFN-γ), IFN-λ1, IL-10, IL-15, and monocyte chemoattractant protein 2 were significantly elevated in the influenza group. In subgroup analysis based on disease severity, IL-18, IL-6, and TNF-α were elevated in severe COVID-19, but not in severe influenza. Random forest analysis identified high IL-6 and low IFN-λ1 levels as the most distinct between severe COVID-19 and severe influenza. Finally, IL-1RA was identified as a potential mediator of the effects of BMI on COVID-19 severity.

Conclusions

These findings point to activation of fundamentally different innate immune pathways in severe acute respiratory syndrome coronavirus 2 and influenza infection, and emphasize drivers of severe COVID-19 to focus both mechanistic and therapeutic investigations.
Improving the Outcomes of Immunocompromised Patients With Coronavirus Disease 2019
Authors: Haidar Ghady , Mellors John W
Published: April 2021

Recent case studies have highlighted the fact that certain immunocompromised individuals are at risk for prolonged SARS-CoV-2 replication, intrahost viral evolution of multiply-mutated variants, and poor clinical outcomes. The immunologic determinants of this risk, the duration of infectiousness, and optimal treatment and prevention strategies in immunocompromised hosts are ill defined. Of additional concern is the widespread use of immunosuppressive medications to treat COVID-19, which may enhance and prolong viral replication in the context of immunodeficiency. We outline the rationale for 4 interrelated approaches to usher in an era of evidence-based medicine for optimal management of immunocompromised patients with COVID-19: multicenter pathogenesis and outcomes studies to relate the risk of severe disease to the type and degree of immunodeficiency, studies to evaluate immunologic responses to SARS-CoV-2 vaccines, studies to evaluate the efficacy of monoclonal antibodies for primary prophylaxis, and clinical trials of novel antiviral agents for the treatment of COVID-19.
On the Quantity and Quality of Girls: Fertility, Parental Investments and Mortality
Authors: Anukriti S , Bhalotra Sonia , Tam Eddy H F
Published: April 2021

Access to prenatal sex-detection technology in India has led to a phenomenal increase in abortion of girls. We find that it has also narrowed the gender gap in under-five mortality, consistent with surviving girls being more wanted than aborted girls. For every three aborted girls, one additional girl survived to age five. Mechanisms include moderation of son-biased fertility stopping and narrowing of gender gaps in parental investments. However, surviving girls are more likely to be born in lower-status families. Our findings have implications not only for counts of missing girls but also for the later life outcomes of girls.
Gender differences in the association between physical activity and obesity in adults with vision and hearing losses
Authors: Pardhan Shahina , Smith Lee , Davis Adrian , Bourne Rupert , Barnett Yvonne , Jacob Louis , Koyanagi Ai , Radzimiński Łukasz , Skalska Maria , Jastrzębska Joanna , Jastrzębski Zbigniew , López-Sánchez Guillermo F
Published: April 2021

Background

Physical inactivity is strongly associated with obesity, which in turn is a major risk factor for many non-communicable diseases. We examined associations between physical inactivity and obesity in Spanish adults with vision and hearing difficulties and explored differences between men and women.

Methods

Data from the Spanish National Health Survey 2017 were analyzed [n = 23 089 adults (15–103 years, mean age 53.4 ± 18.9 years, 45.9% men)]. Participants self-reported difficulties in seeing and hearing. Physical inactivity (exposure) was evaluated with the International Physical Activity Questionnaire Short Form. Obesity (outcome) was defined as body mass index ≥30 kg m−2 based on self-reported weight and height. The association between physical inactivity and obesity was assessed with multivariable logistic regression in people with difficulties seeing and hearing, adjusting for significant covariates.

Results

Multivariable logistic regression analyses showed that the association between physical inactivity and obesity was stronger in those with difficulty hearing (OR 1.778, 95% CI 1.215–2.602) compared with difficulty seeing (OR 1.375, 95% CI 1.076–1.756). Gender-stratified analyses showed significant association between physical inactivity and obesity in men who reported difficulty hearing (OR 2.319, 95% CI 1.441–3.735) and difficulty seeing (OR 1.556, 95% CI 1.079–2.244), but not in women.

Conclusions

A significant association between physical inactivity and obesity was observed in Spanish men with vision and hearing difficulties. Physical activity has an important role in the prevention of obesity in men with seeing and hearing difficulties. Active steps should be taken to encourage physical activity to reduce the risk of obesity in people with sensory impairments.
Survival of young, dense Betula ermanii stands after wildfire at top soil removal sites
Authors: Hayamizu Masato , Nakata Yasutaka , Torita Hiroyuki
Published: April 2021

A forest fire in a cool-temperate broadleaved forest in northern Japan, from 26 May to 19 June 2019, provided an opportunity to examine the post-fire dynamics of young, dense birch (Betula ermanii Cham.) stands that had previously undergone top soil removal through soil scarification. To characterize the post-fire responses (survival and resprouting) of birch trees, we set up two plots, 6 months after the fire. We investigated the trunk diameter at breast height and burn marks on the trunks (scorch height and bole charring percentage) of all B. ermanii trees in both plots. Survival and resprouting of each tree were monitored over a 10-month period (6 and 16 months after the fire). To quantify post-fire vegetation recovery of the forest floor, we manually mapped the dominant understory plant, dwarf bamboo (i.e. Sasa kurilensis (Rupr.) Makino et Shibata), from orthomosaic images obtained using an unmanned aircraft vehicle, and estimated the recovery rate in the second year after the fire. Additionally, the seedlings of woody species were counted in both plots. A logistic generalized linear model revealed that the size-dependent survival rates of the plants in each plots were similar in the first year after fire. All B. ermanii trees died without resprouting in the second year after the fire, indicating the lethal effects of fire on young birch trees in top soil removal sites. Moreover, a high recovery rate of dwarf bamboo over 2 years in both plots and limited woody seedling establishment of woody plants suggest that the fire resulted in the regeneration failure of young stands in the top soil removal sites. Based on these findings, we suggest that the vulnerability of young trees can lead to the rapid change in vegetation from young forest to dense dwarf bamboo cover after a fire.
Transvection in the Drosophila Abd-B Domain: Extensive Upstream Sequences Are Involved in Anchoring Distant cis-Regulatory Regions to the Promoter
Authors: Sipos László , Mihály József , Karch François , Schedl Paul , Gausz János , Gyurkovics Henrik
Published: April 2021

The Abd-B gene, one of the three homeotic genes in the Drosophila bithorax complex (BX-C), is required for the proper identity of the fifth through the eighth abdominal segments (corresponding to parasegments 10–14) of the fruitfly. The morphological difference between these four segments is due to the differential expression of Abd-B, which is achieved by the action of the parasegment-specific cisregulatory regions infra-abdominal-5 (iab-5), -6, -7 and -8. The dominant gain-of-function mutation Frontabdominal-7 (Fab-7) removes a boundary separating two of these cis-regulatory regions, iab-6 and iab-7. As a consequence of the Fab-7 deletion, the parasegment 12- (PS12-) specific iab-7 is ectopically activated in PS11. This results in the transformation of the sixth abdominal segment (A6) into the seventh (A7) in Fab-7 flies. Here we report that point mutations of the Abd-B gene in trans suppress the Fab-7 phenotype in a pairing-dependent manner and thus represent a type of transvection. We show that the observed suppression is the result of trans-regulation of the defective Abd-B gene by the ectopically activated iab-7. Unlike previously demonstrated cases of trans-regulation in the Abd-B locus, trans-suppression of Fab-7 is sensitive to heterozygosity for chromosomal rearrangements that disturb homologous pairing at the nearby Ubx locus. However, in contrast to Ubx, the transvection we observed in the Abd-B locus is insensitive to the allelic status of zeste. Analysis of different deletion alleles of Abd-B that enhance trans-regulation suggests that an extensive upstream region, different from the sequences required for transcription initiation, mediates interactions between the iab cis-regulatory regions and the proximal Abd-B promoter. Moreover, we find that the amount of DNA deleted in the upstream region is roughly proportional to the strength of trans-interaction, suggesting that this region consists of numerous discrete elements that cooperate in tethering the iab regulatory domains to Abd-B. Possible implications of the tethering complex for the regulation of Abd-B are discussed. In addition, we present evidence that the tenacity of trans-interactions in the Abd-B gene may vary, depending upon the tissue and stage of development.
Mutational Analysis of the Yeast DEAH-Box Splicing Factor Prp16
Authors: Hotz Hans-Rudolf , Schwer Beate
Published: April 2021

Prp16 is an essential yeast splicing factor that catalyzes RNA-dependent hydrolysis of nucleoside triphosphates. Prp16 is a member of the DEAH-box protein family, which is defined by six collinear sequence motifs. The importance of residues within four of the conserved motifs was assessed by alanine-scanning mutagenesis. Mutant alleles of PRP16 were tested for in vivo function by complementation of a Δprp16 null strain. In motif I (GETGSGKT), alanine substitutions at Gly-378, Lys-379, and Thr-380 were lethal, whereas replacement of the amino acids in positions 373–377 were viable. In the signature DEAH-box (motif II), Asp-473 and Glu-474 were essential, whereas the H476A mutant was viable. The S505A and T507A mutants in motif III (SAT) were viable. In motif VI (QRSGRAGRTAPG), mutants Q685A, R686A, G688A, R689A, and R692A were lethal, whereas G691A, P695A, and G696A supported growth. Instructive structure-function relationships were established by conservative substitutions at essential residues identified by alanine scan. Overexpression of nonviable alleles impaired the growth of wild-type PRP16 cells. Deletion analysis of the 1071-amino-acid Prp16 protein revealed that the N-terminal 204 amino acids and the C-terminal 100 residues were dispensable for PRP16 function in vivo. These studies provide an instructive framework for functional analysis of other DEAH-box splicing factors.
Meiotic Chromosome Morphology and Behavior in zip1 Mutants of Saccharomyces cerevisiae
Authors: Tung Kuei-Shu , Roeder G Shirleen
Published: April 2021

The yeast Zip1 protein (Zip1p) is a component of the central region of the synaptonemal complex (SC). Zip1p is predicted to form a dimer consisting of a coiled-coil domain flanked by globular domains. To analyze the organization of Zip1p within the SC, in-frame deletions of ZIP1 were constructed and analyzed. The results demonstrate that the C terminus but not the N terminus of Zip1p is required for its localization to chromosomes. Deletions in the carboxy half of the predicted coiled-coil region cause decreases in the width of the SC. Based on these results, a model for the organization of Zip1p within the SC is proposed. zip1 deletion mutations were also examined for their effects on sporulation, spore viability, crossing over, and crossover interference. The results demonstrate that the extent of synapsis is positively correlated with the levels of spore viability, crossing over, and crossover interference. In contrast, the role of Zip1p in synapsis is separable from its role in meiotic cell cycle progression. zip1 mutants display interval-specific effects on crossing over.
Sir- and Silencer-Independent Disruption of Silencing in Saccharomyces by Sas10p
Authors: Kamakaka Rohinton T , Rine Jasper
Published: April 2021

A promoter fusion library of Saccharomyces cerevisiae genes was used to exploit phenotypes associated with altered protein dosage. We identified a novel gene, SAS10, by the ability of Sas10p, when overproduced, to disrupt silencing. The predicted Sas10p was 70,200 kD and strikingly rich in charged amino acids. Sas10p was exclusively nuclear in all stages of the cell cycle. Overproduction of Sas10p caused derepression of mating type genes at both HML and HMR, as well as of URA3, TRP1, and ADE2 when inserted near a telomere or at HMR or the rDNA locus. Repressed genes not associated with silenced chromatin were unaffected. Sas10p was essential for viability, and the termination point following Sas10p depletion was as large budded cells. Remarkably, Sas10p overproduction disrupted silencing even under conditions that bypassed the requirement for Sir proteins, ORC, and Rap1p in silencing. These data implied that Sas10p function was intimately connected with the structure of silenced chromatin.
Rate Variation of DNA Sequence Evolution in the Drosophila Lineages
Authors: Takano Toshiyuki S
Published: April 2021

Rate constancy of DNA sequence evolution was examined for three species of Drosophila, using two samples: the published sequences of eight genes from regions of the normal recombination rates and new data of the four AS-C (ac, sc, l'sc and ase) and ci genes. The AS-C and ci genes were chosen because these genes are located in the regions of very reduced recombination in Drosophila melanogaster and their locations remain unchanged throughout the entire lineages involved, yielding less effect of ancestral polymorphism in the study of rate constancy. The synonymous substitution pattern of the three lineages was found to be erratic in both samples. The dispersion index for replacement substitution was relatively high for the per, G6pd and ac genes. A significant heterogeneity was found in the number of synonymous substitutions in the three lineages between the two samples of genes with different recombination rates. This is partly due to a lack of the lineage effect in the D. melanogaster and Drosophila simulans lineages in the AS-C and ci genes in contrast to Akashi's observation of genes in regions of normal recombination. The higher codon bias in Drosophila yakuba as compared with D. melanogaster and D. simulans was observed in the four AS-C genes, which suggests change(s) in action of natural selection involved in codon usage on these genes. Fluctuating selection intensity may also be responsible for the observed locus-lineage interaction effects in synonymous substitution.
A Methylated Neurospora 5S rRNA Pseudogene Contains a Transposable Element Inactivated by Repeat-Induced Point Mutation
Authors: Margolin Brian S , Garrett-Engele Phillip W , Stevens Judith N , Fritz Deborah Y , Garrett-Engele Carrie , Metzenberg Robert L , Selker Eric U
Published: April 2021

In an analysis of 22 of the roughly 100 dispersed 5S rRNA genes in Neurospora crassa, a methylated 5S rRNA pseudogene, Ψ63, was identified. We characterized the Ψ63 region to better understand the control and function of DNA methylation. The 120-bp 5S rRNA-like region of Ψ63 is interrupted by a 1.9-kb insertion that has characteristics of sequences that have been modified by repeat-induced point mutation (RIP). We found sequences related to this insertion in wild-type strains of N. crassa and other Neurospora species. Most showed evidence of RIP; but one, isolated from the N. crassa host of Ψ63, showed no evidence of RIP. A deletion from near the center of this sequence apparently rendered it incapable of participating in RIP with the related full-length copies. The Ψ63 insertion and the related sequences have features of transposons and are related to the Fot1 class of fungal transposable elements. Apparently Ψ63 was generated by insertion of a previously unrecognized Neurospora transposable element into a 5S rRNA gene, followed by RIP. We name the resulting inactivated Neurospora transposon PuntRIP1 and the related sequence showing no evidence of RIP, but harboring a deletion that presumably rendered it defective for transposition, dPunt.
Repression of Hybrid Dysgenesis in Drosophila melanogaster by Combinations of Telomeric P-Element Reporters and Naturally Occurring P Elements
Authors: Ronsseray Stéphane , Marin Laurent , Lehmann Monique , Anxolabéhère Dominique
Published: April 2021

In Drosophila melanogaster, hybrid dysgenesis occurs in the germline of flies produced by crosses between females lacking P elements and males carrying 25–55 P elements. We have previously shown that a complete maternally inherited repression of P transposition in the germline (P cytotype) can be elicited by only two autonomous P elements located at the X chromosome telomere (cytological site 1A). We have tested whether P transgenes at 1A, unable to code for a P-repressor, may contribute to the repression of P elements. Females carrying a P-lacZ transgene at 1A [“P-lacZ(1A)”], crossed with P males, do not repress dysgenic sterility in their progeny. However, these P-lacZ(1A) insertions, maternally or paternally inherited, contribute to P-element repression when they are combined with other regulatory P elements. This combination effect is not seen when the P-lacZ transgene is located in pericentromeric heterochromatin or in euchromatin; however a P-w,ry transgene located at the 3R chromosome telomere exhibits the combination effect. The combination effect with the P-lacZ(1A) transgene is impaired by a mutant Su(var)205 allele known to impair the repression ability of the autonomous P elements at 1A. We hypothesized that the combination effect is due to modification of the chromatin structure or nuclear location of genomic P elements.
Genotype-Environment Interaction at Quantitative Trait Loci Affecting Sensory Bristle Number in Drosophila melanogaster
Authors: Gurganus Marjorie C , Fry James D , Nuzhdin Sergey V , Pasyukova Elena G , Lyman Richard F , Mackay Trudy F C
Published: April 2021

The magnitude of segregating variation for bristle number in Drosophila melanogaster exceeds that predicted from models of mutation-selection balance. To evaluate the hypothesis that genotype-environment interaction (GEI) maintains variation for bristle number in nature, we quantified the extent of GEI for abdominal and sternopleural bristles among 98 recombinant inbred lines, derived from two homozygous laboratory strains, in three temperature environments. There was considerable GEI for both bristle traits, which was mainly attributable to changes in rank order of line means. We conducted a genome-wide screen for quantitative trait loci (QTLs) affecting bristle number in each sex and temperature environment, using a dense (3.2-cM) marker map of polymorphic insertion sites of roo transposable elements. Nine sternopleural and 11 abdominal bristle number QTLs were detected. Significant GEI was exhibited by 14 QTLs, but there was heterogeneity among QTLs in their sensitivity to thermal and sexual environments. To further evaluate the hypothesis that GEI maintains variation for bristle number, we require estimates of allelic effects across environments at genetic loci affecting the traits. This level of resolution may be achievable for Drosophila bristle number because candidate loci affecting bristle development often map to the same location as bristle number QTLs.
The Genetic Basis of Drosophila sechellia's Resistance to a Host Plant Toxin
Authors: Jones Corbin D
Published: April 2021

Unlike its close relatives, Drosophila sechellia is resistant to the toxic effects of the fruit of its host plant, Morinda citrifolia. Using 15 genetic markers, I analyze the genetic basis of D. sechellia's resistance to this fruit's primary toxin, octanoic acid. D. sechellia's resistance is dominant in F1 hybrids between it and its sister species D. simulans. All chromosomes, except the Y and the dot fourth, carry genes affecting resistance. The third chromosome has the greatest effect and carries at least two factors. The X chromosome has an intermediate effect and harbors at least two genes, whereas the second chromosome carries at least one gene of weak effect. Thus, at least five loci are involved in this adaptation. However, I also identified large chromosome regions having no effect on resistance, suggesting that D. sechellia's resistance is neither very simple nor highly polygenic. Instead, resistance appears to have an oligogenic basis. D. sechellia's resistance to its host may contribute to ecological isolation between it and D. simulans.
Evolution of Multigene Families by Gene Duplication: A Haploid Model
Authors: Tachida Hidenori , Kuboyama Tohru
Published: April 2021

Evolution of multigene families by gene duplication and subsequent diversification is analyzed assuming a haploid model without interchromosomal crossing over. Chromosomes with more different genes are assumed to have higher fitness. Advantageous and deleterious mutations and duplication/deletion also affect the evolution, as in previous studies. In addition, negative selection on the total number of genes (copy number selection) is incorporated in the model. First, a Markov chain approximation is used to obtain formulas for the average numbers of different alleles, genes without pseudogene mutations, and pseudogenes assuming that mutation rates and duplication/deletion rates are all very small. Computer simulation shows that the approximation works well if the products of population size with mutation and duplication/deletion rates are all small compared to 1. However, as they become large, the approximation underestimates gene numbers, especially the number of pseudogenes. Based on the approximation, the following was found: (1) Gene redundancy measured by the average number of redundant genes decreases as advantageous selection becomes stronger. (2) The number of different genes can be approximately described by a linear pure-birth process and thus has a coefficient of variation around 1. (3) The birth rate is an increasing function of population size without copy number selection, but not necessarily so otherwise. (4) Copy number selection drastically decreases the number of pseudogenes. Available data of mutation rates and duplication/deletion rates suggest much faster increases of gene numbers than those observed in the evolution of currently existing multigene families. Various explanations for this discrepancy are discussed based on our approximate analysis.
Bottleneck Effect on Genetic Variance: A Theoretical Investigation of the Role of Dominance
Authors: Wang Jinliang , Caballero Armando , Keightley Peter D , Hill William G
Published: April 2021

The phenomenon that the genetic variance of fitness components increase following a bottleneck or inbreeding is supported by a growing number of experiments and is explained theoretically by either dominance or epistasis. In this article, diffusion approximations under the infinite sites model are used to quantify the effect of dominance, using data on viability in Drosophila melanogaster. The model is based on mutation parameters from mutation accumulation experiments involving balancer chromosomes (set I) or inbred lines (set II). In essence, set I assumes many mutations of small effect, whereas set II assumes fewer mutations of large effect. Compared to empirical estimates from large outbred populations, set I predicts reasonable genetic variances but too low mean viability. In contrast, set II predicts a reasonable mean viability but a low genetic variance. Both sets of parameters predict the changes in mean viability (depression), additive variance, between-line variance and heritability following bottlenecks generally compatible with empirical results, and these changes are mainly caused by lethals and deleterious mutants of large effect. This article suggests that dominance is the main cause for increased genetic variances for fitness components and fitness-related traits after bottlenecks observed in various experiments.
SPE3, Which Encodes Spermidine Synthase, Is Required for Full Repression Through NREDIT in Saccharomyces cerevisiae
Authors: Friesen Helena , Tanny Jason C , Segall Jacqueline
Published: April 2021

We previously identified a transcriptional regulatory element, which we call NREDIT, that is required for repression of the sporulation-specific genes, DIT1 and DIT2, during vegetative growth of Saccharomyces cerevisiae. Repression through this element is dependent on the Ssn6-Tup1 corepressor. In this study, we show that SIN4 contributes to NREDIT-mediated repression, suggesting that changes in chromatin structure are, at least in part, responsible for regulation of DIT gene expression. In a screen for additional genes that function in repression of DIT (FRD genes), we recovered alleles of TUP1, SSN6, SIN4, and ROX3 and identified mutations comprising eight complementation groups of FRD genes. Four of these FRD genes appeared to act specifically in NREDIT-mediated repression, and four appeared to be general regulators of gene expression. We cloned the gene complementing the frd3-1 phenotype and found that it was identical to SPE3, which encodes spermidine synthase. Mutant spe3 cells not only failed to support complete repression through NREDIT but also had modest defects in repression of some other genes. Addition of spermidine to the medium partially restored repression to spe3 cells, indicating that spermidine may play a role in vivo as a modulator of gene expression. We suggest various mechanisms by which spermidine could act to repress gene expression.
Functional Analysis of the Fibrinogen-Related scabrous Gene From Drosophila melanogaster Identifies Potential Effector and Stimulatory Protein Domains
Authors: Lee E-Chiang , Yu Sung-Yun , Hu Xiaoxi , Mlodzik Marek , Baker Nicholas E
Published: April 2021

The scabrous (sca) gene encodes a secreted dimeric glycoprotein with putative coiled-coil domains N-terminally and a C-terminal region related to the blood clot protein fibrinogen. Homozygous sca mutants have extra bristle organs and rough eyes. We describe a GAL4-based expression system for testing rescue of the sca mutant phenotype by altered SCA proteins and for misexpression. We find that deletion of the fibrinogen-related domain (FReD) greatly decreases SCA function, confirming the importance of this conserved region. SCA function could not be restored by FReDs from human fibrinogen chain genes. However, proteins lacking any FReD still showed some function in both rescue and misexpression experiments, suggesting that putative effector-binding regions lie outside this domain. Consistent with this, proteins expressing only the FReD had no rescuing activity but were recessive negative; i.e., they enhanced the phenotype of sca mutations but had no phenotype in the presence of a wild-type sca allele. This suggests that the FReD contributes to SCA function by binding to other components of the bristle determination pathway, increasing the activity of the linked N-terminal region.
Speciation and Domestication in Maize and Its Wild Relatives: Evidence From the Globulin-1 Gene
Authors: Hilton Holly , Gaut Brandon S
Published: April 2021

The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa—maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged ∼700,000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.
Chromosome Walking to the AVR1-CO39 Avirulence Gene of Magnaporthe grisea: Discrepancy Between the Physical and Genetic Maps
Authors: Farman Mark L , Leong Sally A
Published: April 2021

The avrCO39 gene conferring avirulence toward rice cultivar CO39 was previously mapped to chromosome 1 of Magnaporthe grisea between cosegregating markers CH5-120H and 1.2H and marker 5-10-F. In the present study, this region of the chromosome was physically mapped using RecA-mediated Achilles’ cleavage. Cleavage of genomic DNA sequences within CH5-120H and 5-10-F liberated a 610-kb restriction fragment, representing the physical distance between these markers. Chromosome walking was initiated from both markers but was curtailed due to the presence of repetitive DNA sequences and the absence of overlapping clones in cosmid libraries representing several genome equivalents. These obstacles were overcome by directly subcloning the target region after release by Achilles’ cleavage and a contig spanning avrCO39 was thus assembled. Transformation of two cosmids into a virulent recipient strain conferred a cultivar-specific avirulence phenotype thus confirming the cloning of avrCO39. Meiotic crossover points were unevenly distributed across this chromosomal region and were clustered around the avrCO39 locus. A 14-fold variation in the relationship between genetic and physical distance was measured over the avrCO39 chromosomal region. Thus the poor correlation of physical to genetic distance previously observed in M. grisea appears to be manifested over relatively short distances.
Transposable Element Insertions Respecify Alternative Exon Splicing in Three Drosophila Myosin Heavy Chain Mutants
Authors: Davis Mary Beth , Dietz Jon , Standiford David M , Emerson Charles P
Published: April 2021

Insertions of transposable elements into the myosin heavy chain (Mhc) locus disrupt the regulation of alternative pre-mRNA splicing for multi-alternative exons in the Mhc2, Mhc3, and Mhc4 mutants in Drosophila. Sequence and expression analyses show that each inserted element introduces a strong polyadenylation signal that defines novel terminal exons, which are then differentially recognized by the alternative splicing apparatus. Mhc2 and Mhc4 have insertion elements located within intron 7c and exon 9a, respectively, and each expresses a single truncated transcript that contains an aberrant terminal exon defined by the poly(A) signal of the inserted element and the 3′ acceptor of the upstream common exon. In Mhc3, a poly(A) signal inserted into Mhc intron 7d defines terminal exons using either the upstream 3′ acceptor of common exon 6 or the 7d acceptor, leading to the expression of 4.1- and 1.7-kb transcripts, respectively. Acceptor selection is regulated in Mhc3 transcripts, where the 3′ acceptor of common Mhc exon 6 is preferentially selected in larvae, whereas the alternative exon 7d acceptor is favored in adults. These results reflect the adult-specific use of exon 7d and suggest that the normal exon 7 alternative splicing mechanism continues to influence the selection of exon 7d in Mhc3 transcripts. Overall, transposable element-induced disruptions in alternative processing demonstrate a role for the nonconsensus 3′ acceptors in Mhc exons 7 and 9 alternative splicing regulation.
A Dense Genetic Map of the Silkworm, Bombyx mori, Covering All Chromosomes Based on 1018 Molecular Markers
Authors: Yasukochi Yuji
Published: April 2021

A dense linkage map was constructed for the silkworm, Bombyx mori, containing 1018 genetic markers on all 27 autosomes and the Z chromosome. Most of the markers, covering ∼2000 cM, were randomly amplified polymorphic DNAs amplified with primer-pairs in combinations of 140 commercially available decanucleotides. In addition, eight known genes and five visible mutations were mapped. Bombyx homologues of engrailed and invected genes were found to be closely linked, as in Drosophila melanogaster. The average interval between markers was ∼2 cM, equal to ∼500 kb. The correspondence of seven linkage groups to counterparts of the conventional linkage map was determined. This map is the first linkage map in insects having a large number of chromosomes (n = 28) that covers all chromosomes without any gaps.