bluuebunny/crossref_metadata_2025 huggingface dataset:
Six Decades of Human Adenovirus Type 4 Infections Reviewed: Increasing Infections Among Civilians Are a Matter of Concern
Authors: Coleman Kristen K , Robie Emily R , Abdelgadir Anfal , Kozhumam Arthi S , Binder Raquel A , Gray Gregory C
Published: February 2021

Human adenovirus type 4 (HAdV-E4) frequently causes epidemics among military and civilian populations. We conducted a systematic review of 144 peer-reviewed articles reporting HAdV-E4 infections, published during the years 1960–2020. More than 24 500 HAdV-E4 infections, including 27 associated deaths, were documented. HAdV-E4 infections were reported from all geographic regions of the world except Central America and the Caribbean. The number of publications reporting civilian infections tripled in the last decade, with a steady increase in reported civilian infections over time. Infections commonly caused respiratory and ocular disease. North America reported the most infections, followed by Asia and Europe. The majority of deaths were reported in the United States, followed by China and Singapore. Civilians seem to increasingly suffer HAdV-E4 disease, with recent epidemics among US college students. Public health officials should consider seeking emergency use authorization for the adenovirus vaccine such that it might be available to mitigate civilian epidemics.
Effect of Body Weight and Age on the Pharmacokinetics of Dihydroartemisinin: Food and Drug Administration Basis for Dose Determination of Artesunate for Injection in Pediatric Patients With Severe Malaria
Authors: Kitabi Eliford , Bensman Timothy J , Earp Justin C , Chilukuri Dakshina M , Smith Heidi , Ball Leslie , O’Shaughnessy Elizabeth , Yasinskaya Yuliya , Colangelo Philip M , Reynolds Kellie S
Published: February 2021

For treatment of severe malaria, the World Health Organization recommends 3 mg/kg intravenous artesunate in pediatric patients weighing less than 20 kg. Here we describe the Food and Drug Administration’s rationale for selecting 2.4 mg/kg in pediatric patients weighing less than 20 kg based on literature review and independent analyses.
Regenerative potential of epicardium-derived extracellular vesicles mediated by conserved miRNA transfer
Authors: del Campo Cristina Villa , Liaw Norman Y , Gunadasa-Rohling Mala , Matthaei Moritz , Braga Luca , Kennedy Tahnee , Salinas Gabriela , Voigt Niels , Giacca Mauro , Zimmermann Wolfram-Hubertus , Riley Paul Richard
Published: February 2021

Aims

After a myocardial infarction, the adult human heart lacks sufficient regenerative capacity to restore lost tissue, leading to heart failure progression. Finding novel ways to reprogram adult cardiomyocytes into a regenerative state is a major therapeutic goal. The epicardium, the outermost layer of the heart, contributes cardiovascular cell types to the forming heart and is a source of trophic signals to promote heart muscle growth during embryonic development. The epicardium is also essential for heart regeneration in zebrafish and neonatal mice and can be reactivated after injury in adult hearts to improve outcome. A recently identified mechanism of cell–cell communication and signalling is that mediated by extracellular vesicles (EVs). Here, we aimed to investigate epicardial signalling via EV release in response to cardiac injury and as a means to optimize cardiac repair and regeneration.

Methods and results

We isolated epicardial EVs from mouse and human sources and targeted the cardiomyocyte population. Epicardial EVs enhanced proliferation in H9C2 cells and in primary neonatal murine cardiomyocytes in vitro and promoted cell cycle re-entry when injected into the injured area of infarcted neonatal hearts. These EVs also enhanced regeneration in cryoinjured engineered human myocardium (EHM) as a novel model of human myocardial injury. Deep RNA-sequencing of epicardial EV cargo revealed conserved microRNAs (miRs) between human and mouse epicardial-derived exosomes, and the effects on cell cycle re-entry were recapitulated by administration of cargo miR-30a, miR-100, miR-27a, and miR-30e to human stem cell-derived cardiomyocytes and cryoinjured EHM constructs.

Conclusion

Here, we describe the first characterization of epicardial EV secretion, which can signal to promote proliferation of cardiomyocytes in infarcted mouse hearts and in a human model of myocardial injury, resulting in enhanced contractile function. Analysis of exosome cargo in mouse and human identified conserved pro-regenerative miRs, which in combination recapitulated the therapeutic effects of promoting cardiomyocyte proliferation.
Severity of GERD and disease progression
Authors: Fuchs K H , DeMeester T R , Otte F , Broderick R C , Breithaupt W , Varga G , Musial F
Published: February 2021

Background

Many factors may play a role in the severity and progression of gastroesophageal reflux disease (GERD) since pathophysiology is multifactorial. Data regarding the progression of GERD are controversial: some reports of increased esophageal acid exposure (EAE) and mucosal damage were considered as evidence for a stable disease course, while others interprete these findings as disease progression. The aim of this study is to analyze a large patient-population with persisting symptoms indicative of GERD under protonpumpinhibitor-therapy and identify components characterizing disease severity and progression.

Methods

Patients with symptoms indicative of GERD were included in the study in a tertiary referral center (Frankfurt, Germany). All selected patients were under long-term protonpumpinhibitor-therapy with persistant symptoms. All patients underwent investigations to collect data on their physical status, EAE, severity of esophagitis, anatomical changes, and esophageal functional defects as well as their relation to the duration of the disease. Incidence over time was plotted as survival curves and tested with Log-rank tests for the four main disease markers. Multivariate modeling with COX-regression model was used to estimate the general impact of the four main disease markers on the time course of the disease. In order to elucidate possible causal relationships over time, a path analysis (structural equation model) was calculated.

Results

From the database with 1480 data sets, 972 patients were evaluated (542 males, 430 females). The mean age was 50.5 years (range18–89). The mean body mass index was 27.2(19–48). The mean time between the onset of symptoms and the diagnostic investigations was 8.2 years (1–50). A longer disease history for GERD was significantly associated with a higher risk for LES-incompetence. The mean duration from symptom onset to the time of clinical investigation was 9 years for patients with LES-incompetence (n = 563), compared to a mean of 6 years for those with mechanically intact LES (n = 95). A longer period from symptom onset to diagnostics was significantly associated with higher acid exposure. The pathway analysis was significant for the following model: ‘history’ (P < 0.001➔LES-incompetence & Hiatal Hernia➔(p < 0,001)➔pH-score (P < 0.001).

Conclusion: LES-incompetence, the functional deterioration of the LES, and the anatomical alteration at the esophagogastric junction (Hiatal Hernia) as well as an increased EAE were associated with a long history of suffering from GERD. Path modeling suggests a causal sequence overtime of the main disease-parameters, tentatively allowing for a prediction of the course of the disease.
Prediction for future occurrence of type A aortic dissection using computational fluid dynamics
Authors: Hohri Yu , Numata Satoshi , Itatani Keiichi , Kanda Keiichi , Yamazaki Sachiko , Inoue Tomoya , Yaku Hitoshi
Published: February 2021

OBJECTIVES

The actual underlying mechanisms of acute type A aortic dissection (AAAD) are not well understood. The present study aimed to elucidate the mechanism of AAAD using computational fluid dynamics (CFD) analysis.

METHODS

We performed CFD analysis using patient-specific computed tomography imaging in 3 healthy control cases and 3 patients with AAAD. From computed tomography images, we made a healthy control model or pre-dissection model for CFD analysis. Pulsatile cardiac flow during one cardiac cycle was simulated, and a three-dimensional flow streamline was visualized to evaluate flow velocity, wall shear stress and oscillatory shear index (OSI).

RESULTS

In healthy controls, the transvalvular aortic flow was parallel to the ascending aorta. There was no spotty high OSI area at the ascending aorta. In pre-dissection patients, accelerated transvalvular aortic flow was towards the posterolateral ascending aorta. The vortex flow was observed on the side of the lesser curvature in mid-systole and expanded throughout the entire ascending aorta during diastole. Systolic wall shear stress was high due to the accelerated aortic blood flow on the side of the greater curvature of the ascending aorta. On the side of the lesser curvature, high OSI areas were observed around the vortex flow. In all pre-dissection cases, a spotty high OSI area was in close proximity to the actual primary entry site of the future AAAD.

CONCLUSIONS

The pre-onset high OSI area with vortex flow is closely associated with the future primary entry site. Therefore, we can elucidate the mechanism of AAAD with CFD analysis.
The efficacy of sinus plication in aortic valvuloplasty for bicuspid aortic valve: experiments in a pulsatile flow simulation model
Authors: Arimura Satoshi , Takada Jumpei , Nishimura Gohki , Nakama Natsuki , Kawasaki Eita , Matsuhama Minoru , Iwasaki Kiyotaka , Kasegawa Hitoshi , Kunihara Takashi
Published: February 2021

OBJECTIVES

Sinus plication has emerged as a promising tool that can lead to better stability in bicuspid aortic valve (BAV) repair. However, the mechanisms underlying the efficacy of this technique are unclear. We evaluated the hydrodynamic effect of sinus plication using the experimental pulsatile flow simulator and our original BAV model in vitro.

METHODS

Based on the computed tomography data of a BAV patient who had undergone aortic valvuloplasty, a BAV model (group C, n = 6) was developed with bovine pericardium and vascular prosthesis (J-graft Shield Neo Valsalva 24 mm). We performed sinus plication (group SP, n = 6) in the BAV model and compared hydrodynamic data with the control model in the pulsatile flow simulator. Non-fused cusp angle, annulus diameter and effective height were measured by ultrasonography.

RESULTS

The average flow was significantly increased in group SP compared to group C (4.24 ± 0.14 l/min vs 4.14 ± 0.15 l/min, respectively, P = 0.034). The mean transvalvular pressure gradient and regurgitant fraction were significantly decreased in group SP compared to group C (11.6 ± 4.3 mmHg vs 16.6 ± 5.0 mmHg, respectively, P = 0.009 and 14.1 ± 2.0% vs 17.4 ± 2.1%, respectively, P = 0.001). Ultrasound measurement indicated that non-fused cusp angle was significantly increased in group SP compared to group C (163.8° ± 9.2° vs 153.0° ± 4.6°, respectively, P = 0.012).

CONCLUSIONS

Sinus plication in the BAV model significantly increased the commissural angle. It was effective in not only controlling regurgitation but also improving valve opening. These finding should be confirmed by evaluating cusp stress and/or long-term durability in the future studies.
The relationship between self-care, long-term mortality, and heart failure hospitalization: insights from a real-world cohort study
Authors: Calero-Molina Esther , Hidalgo Encarna , Rosenfeld Laia , Verdú-Rotellar Jose Maria , Verdú-Soriano Jose , Garay Alberto , Alcoberro Lidia , Jimenez-Marrero Santiago , Garcimartin Paloma , Yun Sergi , Guerrero Carmen , Moliner Pedro , Delso Cristina , Alcober Laia , Enjuanes Cristina , Comin-Colet Josep
Published: February 2021

Aims

The assumption that improved self-care in the setting of heart failure (HF) care necessarily translates into improvements in long-term mortality and/or hospitalization is not well established. We aimed to study the association between self-care and long-term mortality and other major adverse HF events (MAHFE).

Methods and results

We conducted an observational, prospective, cohort study of 1123 consecutive patients with chronic HF. The primary endpoint was all-cause mortality. We used the European Heart Failure Self-care Behaviour Scale 9-item version (EHFSCBS-9) to measure global self-care (overall score) and three specific dimensions of self-care including autonomy-based adherence, consulting behaviour and provider-based adherence. After a mean follow-up of 3.3 years, all-cause death occurred in 487 patients (43%). In adjusted analysis, higher EHFScBS-9 scores (better self-care) at baseline were associated with lower risk of all-cause death [hazard ratio (HR) 0.993, 95% confidence interval (CI) (0.988–0.997), P-value = 0.002], cardiovascular (CV) death [HR 0.989, 95% CI (0.981–0.996), P-value = 0.003], HF hospitalization [HR 0.993, 95% CI (0.988–0.998), P-value = 0.005], and the combination of MAHFE [HR 0.995, 95% CI (0.991–0.999), P-value = 0.018]. Similarly, impaired global self-care [HR 1.589, 95% CI (1.201–2.127), P-value = 0.001], impaired autonomy-based adherence [HR 1.464, 95% CI (1.114–1.923), P-value = 0.006], and impaired consulting behaviour dimensions [HR 1.510, 95% CI (1.140–1.923), P-value = 0.006] were all associated with higher risk of all-cause mortality.

Conclusion

In this study, we have shown that worse self-care is an independent predictor of long-term mortality (both, all-cause and CV), HF hospitalization, and the combinations of these endpoints in patients with chronic HF. Important dimensions of self-care such as autonomy-based adherence and consulting behaviour also determine the risk of all these outcomes in the long term.
In vitro antimicrobial activity and comparison of the herbal extracts and sodium hypochlorite against primary plaque colonizers
Authors: Rafi Shaik Mohammed , Sharaf Mohammed A F , Li Xianping , Yousuf Syed , Pan Su-Shuang
Published: February 2021

NaClO is not suitable as a root canal irrigant because of its cytotoxicity. Good biocompatibility irrigants are required to have antibacterial activity. Many herbal products like Bee glue, Noni juice and Azadirachta indica have such properties. This study aims to investigate the possible effects of propolis, MCJ and Neem on bacterial infections and cytotoxicity in primary plaque colonizers. Direct contact and agar diffusion tests evaluated the antibacterial activity of herbal products against Fusobacterium, Candida albicans and Prevotella. The CCK 8 test determined the influence of these herbal products on the proliferation of human apical papilla stem cells (hSCAPs) and human periodontal fibroblasts (hPDLFs). A migration assay test was performed in addition to quantitative real-time PCR which measured osteogenic differentiation in hSCAPs. All herbal extracts tested in this study exhibited antibacterial activity comparable to NaClO against bacterial infections, while the strongest bacteriostatic effect was shown in the herbal treated group. These extracts had much weaker effects on the proliferation and migration of hSCAPs and hPDLFs as calculated by the CCK-8 assay against NaClO. Bee glue treatment had the most potent effect on osteogenic differentiation, followed by treatment with Noni juice and Azadirachta indica (Neem), while NaClO showed the lowest effect. For primary plaque colonizers of immature or advanced permanent teeth, Bee glue, Noni juice, and Azadirachta indica can be promising irrigants with good biocompatibility. Direct contact process and agar diffusion studies have tested the antibacterial activity against Fusobacterium, Candida albicans and Prevotella. The CCK 8 test determined the influence of these three plants on the proliferation of human apical papilla stem cells (hSCAPs) and human periodontal fibroblasts (hPDLFs). In order to examine migration ability, migration assay test was performed. Alizarin red staining, alkaline phosphatase (ALP) staining and quantitative real-time PCR measured osteo-/odontogenic differentiation in hSCAPs. All herbal extracts tested in this study exhibited antibacterial activity comparable to NaClO against bacterial infections, while the strongest bacteriostatic effect was shown in the treated group. These extracts had much weaker effects on the proliferation and migration of hSCAPs and hPDLFs as calculated by the CCK-8 assay against NaClO. Bee glue treatment had the most potent effect on osteo-odontogenic differentiation, followed by treatment with Noni juice and Azadirachta indica (Neem), while NaClO showed the lowest effect. For primary plaque colonizers of immature or advanced permanent teeth, Bee glue, Noni juice and Azadirachta indica (Neem) can be promising irrigants.
The ‘sustainable’ video-narratives of Greenpeace – an ecolinguistic investigation
Authors: Abbamonte Lucia
Published: February 2021

The ‘sustainable’ narratives of Greenpeace, as they unfold in thousands of short videos retrievable from both YouTube and Greenpeace’s official websites, are ultimately meant to engage more volunteers and donors. Accordingly, their affinities with some advertising languages are easily discernible, such as the use of topics that appeal to the public, for example idyllic natural settings. The multimodal composition of these videos deploys appealing film sequences of landscapes, alternately marked and unmarked by human interventions, whose meanings are reinforced through the lexico-grammar of the verbal level, which is notionally salient and rich in intertextual allusions. The purposes of the present study are to analyse their discursive and multimedia features through the lens of ecolinguistics, a relatively recent approach that is positioned within the wide domain of discourse analysis, and to investigate the cultural-linguistic implications of Greenpeace’s proactive communication. A major focus of attention is on the advertised visions of better worlds and the new stories we should live by, where nature is not to be used for profit but treated as the ecosystem that our lives depend on.
Analysis of osm-6, a Gene That Affects Sensory Cilium Structure and Sensory Neuron Function in Caenorhabditis elegans
Authors: Collet Joan , Spike Caroline A , Lundquist Erik A , Shaw Jocelyn E , Herman Robert K
Published: February 2021

Mutation in the Caenorhabditis elegans gene osm-6 was previously shown to result in defects in the ultrastructure of sensory cilia and defects in chemosensory and mechanosensory behaviors. We have cloned osm-6 by transposon tagging and transformation rescue and have identified molecular lesions associated with five osm-6 mutations. The osm-6 gene encodes a protein that is 40% identical in amino acid sequence to a predicted mammalian protein of unknown function. We fused osm-6 with the gene for green fluorescent protein (GFP); the fusion gene rescued the osm-6 mutant phenotype and showed accumulation of GFP in ciliated sensory neurons exclusively. The OSM-6::GFP protein was localized to cytoplasm, including processes and dendritic endings where sensory cilia are situated. Mutations in other genes known to cause ciliary defects led to changes in the appearance of OSM-6::GFP in dendritic endings or, in the case of daf-19, reduced OSM-6::GFP accumulation. We conclude from an analysis of genetic mosaics that osm-6 acts cell autonomously in affecting cilium structure.
Quantitative Genetics of Ovariole Number in Drosophila melanogaster. II. Mutational Variation and Genotype-Environment Interaction
Authors: Wayne Marta L , Mackay Trudy F C
Published: February 2021

The rare alleles model of mutation-selection balance (MSB) hypothesis for the maintenance of genetic variation was evaluated for two quantitative traits, ovariole number and body size. Mutational variances (VM) for these traits, estimated from mutation accumulation lines, were 4.75 and 1.97 × 10−4 times the environmental variance (VE), respectively. The mutation accumulation lines were studied in three environments to test for genotype × environment interaction (GEI) of new mutations; significant mutational GEI was found for both traits. Mutations for ovariole number have a quadratic relationship with competitive fitness, suggesting stabilizing selection for the trait; there is no significant correlation between mutations for body size and competitive fitness. Under MSB, the ratio of segregating genetic variance, VG, to mutational variance, VM, estimates the inverse of the selection coefficient against a heterozygote for a new mutation. Estimates of VG/VM for ovariole number and body size were both approximately 1.1 × 104. Thus, MSB can explain the level of variation, if mutations affecting these traits are under very weak selection, which is inconsistent with the empirical observation of stabilizing selection, or if the estimate of VM is biased downward by two orders of magnitude. GEI is a possible alternative explanation.
Polycomb Group Repression Is Blocked by the Drosophila suppressor of Hairy-wing [su(Hw)] Insulator
Authors: Mallin Daniel R , Myung Jane S , Patton J Scott , Geyer Pamela K
Published: February 2021

The suppressor of Hairy-wing [SU(HW)] binding region disrupts communication between a large number of enhancers and promoters and protects transgenes from chromosomal position effects. These properties classify the SU(HW) binding region as an insulator. While enhancers are blocked in a general manner, protection from repressors appears to be more variable. In these studies, we address whether repression resulting from the Polycomb group genes can be blocked by the SU(HW) binding region. The effects of this binding region on repression established by an Ultrabithorax Polycomb group Response Element were examined. A transposon carrying two reporter genes, the yellow and white genes, was used so that repression and insulation could be assayed simultaneously. We demonstrate that the SU(HW) binding region is effective at preventing Polycomb group repression. These studies suggest that one role of the su(Hw) protein may be to restrict the range of action of repressors, such as the Polycomb group proteins, throughout the euchromatic regions of the genome.
Departure from Neutrality at the Mitochondrial NADH Dehydrogenase Subunit 2 Gene in Humans, but Not in Chimpanzees
Authors: Wise Cheryl A , Sraml Michaela , Easteal Simon
Published: February 2021

To test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution, nucleotide sequences were determined for the 1041 bp of the NADH dehydrogenase subunit 2 (ND2) gene in 20 geographically diverse humans and 20 common chimpanzees. Contingency tests of neutrality were performed using four mutational categories for the ND2 molecule: synonymous and nonsynonymous mutations in the transmembrane regions, and synonymous and nonsynonymous mutations in the surface regions. The following three topological mutational categories were also used: intraspecific tips, intraspecific interiors, and interspecific fixed differences. The analyses reveal a significantly greater number of nonsynonymous polymorphisms within human transmembrane regions than expected based on interspecific comparisons, and they are inconsistent with a neutral equilibrium model. This pattern of excess nonsynonymous polymorphism is not seen within chimpanzees. Statistical tests of neutrality, such as Tajima's D test, and the D and F tests proposed by Fu and Li, indicate an excess of low frequency polymorphisms in the human data, but not in the chimpanzee data. This is consistent with recent directional selection, a population bottleneck or background selection of slightly deleterious mutations in human mtDNA samples. The analyses further support the idea that mitochondrial genome evolution is governed by selective forces that have the potential to affect its use as a “neutral” marker in evolutionary and population genetic studies.
Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice
Authors: Chen Mingsheng , SanMiguel Phillip , Bennetzen Jeffrey L
Published: February 2021

Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leviathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.
Epigenetic Instability and Trans-Silencing Interactions Associated With an SPT::Ac T-DNA Locus in Tobacco
Authors: English James J , Jones Jonathan D G
Published: February 2021

Progeny of tobacco line 2853.6, which carries a streptomycin phosphotransferase (SPT) gene interrupted by the maize element Activator (Ac), were selected for streptomycin resistance (Spr) because of germinal Ac excision. Some events gave rise to Spr alleles that were unstable and exhibited a mottled phenotype on streptomycin-containing medium due to somatic loss of SPT function. This instability was most pronounced in one particular line, Spr12F. Other Spr alleles rarely exhibited silencing of SPT. Streptomycin-sensitive, homozygous Spr12F plants were recovered, and crosses were performed with other, more stable Spr lines. A high proportion of the resulting heterozygous progeny were silenced for SPT expression. The silenced state was heritable even after the Spr12F allele segregated away. No correlation could be made between silencing and methylation of the SPT gene. Structural analysis of allele Spr12F showed that the SPT gene from which Ac had excised was flanked by direct repeats of Ac. A search was carried out among 110 additional Spr alleles for new independent unstable alleles, and four were identified. All of these alleles also carried an SPT gene flanked by direct repeats of Ac. Thus, there is a strong correlation between this structure and instability of SPT expression.
Empirical Nonparametric Bootstrap Strategies in Quantitative Trait Loci Mapping: Conditioning on the Genetic Model
Authors: Lebreton Claude M , Visscher Peter M
Published: February 2021

Several nonparametric bootstrap methods are tested to obtain better confidence intervals for the quantitative trait loci (QTL) positions, i.e., with minimal width and unbiased coverage probability. Two selective resampling schemes are proposed as a means of conditioning the bootstrap on the number of genetic factors in our model inferred from the original data. The selection is based on criteria related to the estimated number of genetic factors, and only the retained bootstrapped samples will contribute a value to the empirically estimated distribution of the QTL position estimate. These schemes are compared with a nonselective scheme across a range of simple configurations of one QTL on a one-chromosome genome. In particular, the effect of the chromosome length and the relative position of the QTL are examined for a given experimental power, which determines the confidence interval size. With the test protocol used, it appears that the selective resampling schemes are either unbiased or least biased when the QTL is situated near the middle of the chromosome. When the QTL is closer to one end, the likelihood curve of its position along the chromosome becomes truncated, and the nonselective scheme then performs better inasmuch as the percentage of estimated confidence intervals that actually contain the real QTL's position is closer to expectation. The nonselective method, however, produces larger confidence intervals. Hence, we advocate use of the selective methods, regardless of the QTL position along the chromosome (to reduce confidence interval sizes), but we leave the problem open as to how the method should be altered to take into account the bias of the original estimate of the QTL's position.
Identification of GCD14 and GCD15, Novel Genes Required for Translational Repression of GCN4 mRNA in Saccharomyces cerevisiae
Authors: Cuesta Rafael , Hinnebusch Alan G , Tamame Mercedes
Published: February 2021

In Saccharomyces cerevisiae, expression of the transcriptional activator GCN4 increases at the translational level in response to starvation for an amino acid. The products of multiple GCD genes are required for efficient repression of GCN4 mRNA translation under nonstarvation conditions. The majority of the known GCD genes encode subunits of the general translation initiation factor eIF-2 or eIF-2B. To identify additional initiation factors in yeast, we characterized 65 spontaneously arising Gcd− mutants. In addition to the mutations that were complemented by known GCD genes or by GCN3, we isolated mutant alleles of two new genes named GCD14 and GCD15. Recessive mutations in these two genes led to highly unregulated GCN4 expression and to derepressed transcription of genes in the histidine biosynthetic pathway under GCN4 control. The derepression of GCN4 expression in gcd14 and gcd15 mutants occurred with little or no increase in GCN4 mRNA levels, and it was dependent on upstream open reading frames (uORFs) in GCN4 mRNA that regulate its translation. We conclude that GCD14 and GCD15 are required for repression of GCN4 mRNA translation by the uORFs under conditions of amino acid sufficiency. The gcd14 and gcd15 mutations confer a slow-growth phenotype on nutrient-rich medium, and gcd15 mutations are lethal when combined with a mutation in gcd13. Like other known GCD genes, GCD14 and GCD15 are therefore probably required for general translation initiation in addition to their roles in GCN4-specific translational control.
High Frequency Intragenic Recombination During Macronuclear Development in Tetrahymena thermophila Restores the Wild-type SerH1 Gene
Authors: Deak J C , Doerder F P
Published: February 2021

Macronuclear development in ciliates is characterized by extensive rearrangement of genetic material, including sequence elimination, chromosome fragmentation and telomere addition. Intragenic recombination is a relatively rare, but evolutionarily important phenomenon occurring in mitosis and meiosis in a wide variety of organisms. Here, we show that high frequency intragenic recombination, on the order of 30%, occurs in the developing amitotic macronucleus of the ciliate Tetrahymena thermophila. Such recombination, occurring between two nonsense transition mutations separated by 726 nucleotides, reproducibly restores wild-type expression of the SerH1 surface protein gene, thus mimicking complementation in trans heterozygotes. Recombination must be considered a potentially important aspect of macronuclear development, producing gene combinations not present in the germinal micronucleus.
Heterosis for Viability, Fecundity, and Male Fertility in Drosophila melanogaster: Comparison of Mutational and Standing Variation
Authors: Fry James D , Heinsohn Stefanie L , Mackay Trudy F C
Published: February 2021

If genetic variation for fitness traits in natural populations (“standing” variation) is maintained by recurrent mutation, then quantitative-genetic properties of standing variation should resemble those of newly arisen mutations. One well-known property of standing variation for fitness traits is inbreeding depression, with its converse of heterosis or hybrid vigor. We measured heterosis for three fitness traits, pre-adult viability, female fecundity, and male fertility, among a set of inbred Drosophilia melanogaster lines recently derived from the wild, and also among a set of lines that had been allowed to accumulate spontaneous mutations for over 200 generations. The inbred lines but not the mutation-accumulation (MA) lines showed heterosis for pre-adult viability. Both sets of lines showed heterosis for female fecundity, but heterosis for male fertility was weak or absent. Crosses among a subset of the MA lines showed that they were strongly differentiated for male fertility, with the differences inherited in autosomal fashion; the absence of heterosis for male fertility among the MA lines was therefore not caused by an absence of mutations affecting this trait. Crosses among the inbred lines also gave some, albeit equivocal, evidence for male fertility variation. The contrast between the results for female fecundity and those for male fertility suggests that mutations affecting different fitness traits may differ in their average dominance properties, and that such differences may be reflected in properties of standing variation. The strong differentiation among the MA lines in male fertility further suggests that mutations affecting this trait occur at a high rate.
Ribosomal Protein Insufficiency and the Minute Syndrome in Drosophila: A Dose-Response Relationship
Authors: Sæbøe-Larssen Stein , Lyamouri May , Merriam John , Oksvold Morten P , Lambertsson Andrew
Published: February 2021

Minutes comprise >50 phenotypically similar mutations scattered throughout the genome of Drosophila, many of which are identified as mutations in ribosomal protein (rp) genes. Common traits of the Minute phenotype are short and thin bristles, slow development, and recessive lethality. By mobilizing a P element inserted in the 5′ UTR of M(3)95A, the gene encoding ribosomal protein S3 (RPS3), we have generated two homozygous viable heteroalleles that are partial revertants with respect to the Minute phenotype. Molecular characterization revealed both alleles to be imprecise excisions, leaving 40 and 110 bp, respectively, at the P-element insertion site. The weaker allele (40 bp insert) is associated with a ~15% decrease in RPS3 mRNA abundance and displays a moderate Minute phenotype. In the stronger allele (110 bp insert) RPS3 mRNA levels are reduced by ~60%, resulting in an extreme Minute phenotype that includes many morphological abnormalities as well as sterility in both males and females due to disruption of early gametogenesis. The results show that there is a correlation between reduced RPS3 mRNA levels and the severity of the Minute phenotype, in which faulty differentiation of somatic tissues and arrest of gametogenesis represent the extreme case. That heteroalleles in M(3)95A can mimic the phenotypic variations that exist between different Minute/rp-gene mutations strongly suggests that all phenotypes primarily are caused by reductions in maximum protein synthesis rates, but that the sensitivity for reduced levels of the individual rp-gene products is different.
Radiation-Induced Chromosome Aberrations in Saccharomyces cerevisiae: Influence of DNA Repair Pathways
Authors: Friedl Anna A , Kiechle Markus , Fellerhoff Barbara , Eckardt-Schupp Friederike
Published: February 2021

Radiation-induced chromosome aberrations, particularly exchange-type aberrations, are thought to result from misrepair of DNA double-strand breaks. The relationship between individual pathways of break repair and aberration formation is not clear. By electrophoretic karyotyping of single-cell clones derived from irradiated cells, we have analyzed the induction of stable aberrations in haploid yeast cells mutated for the RAD52 gene, the RAD54 gene, the HDF1(=YKU70) gene, or combinations thereof. We found low and comparable frequencies of aberrational events in wildtype and hdf1 mutants, and assume that in these strains most of the survivors descended from cells that were in G2 phase during irradiation and therefore able to repair breaks by homologous recombination between sister chromatids. In the rad52 and the rad54 strains, enhanced formation of aberrations, mostly exchange-type aberrations, was detected, demonstrating the misrepair activity of a rejoining mechanism other than homologous recombination. No aberration was found in the rad52 hdf1 double mutant, and the frequency in the rad54 hdf1 mutant was very low. Hence, misrepair resulting in exchange-type aberrations depends largely on the presence of Hdf1, a component of the nonhomologous end-joining pathway in yeast.
DNA Sequence Analysis of Spontaneous Mutagenesis in Saccharomyces cerevisiae
Authors: Kunz Bernard A , Ramachandran Karthikeyan , Vonarx Edward J
Published: February 2021

To help elucidate the mechanisms involved in spontaneous mutagenesis, DNA sequencing has been applied to characterize the types of mutation whose rates are increased or decreased in mutator or antimutator strains, respectively. Increased spontaneous mutation rates point to malfunctions in genes that normally act to reduce spontaneous mutation, whereas decreased rates are associated with defects in genes whose products are necessary for spontaneous mutagenesis. In this article, we survey and discuss the mutational specificities conferred by mutator and antimutator genes in the budding yeast Saccharomyces cerevisiae. The implications of selected aspects of the data are considered with respect to the mechanisms of spontaneous mutagenesis.
Topical Reversion at the HIS1 Locus of Saccharomyces cerevisiae • A Tale of Three Mutants
Authors: von Borstel R C , Savage Elizabeth A , Wang Qi , Hennig Ursula G G , Ritzel R Gary , Lee Grace S-F , Hamilton Michael D , Chrenek Micah A , Tomaszewski Robert W , Higgins John A , Tenove Christopher J , Liviero Lucia , Hastings Philip J , Korch Christopher T , Steinberg C M
Published: February 2021

Mutants of the HIS1 locus of the yeast Saccharomyces cerevisiae are suitable reporters for spontaneous reversion events because most reversions are topical, that is, within the locus itself. Thirteen mutations of his1-1 now have been identified with respect to base sequence. Revertants of three mutants and their spontaneous reversion rates are presented: (1) a chain termination mutation (his1-208, née his1-1) that does not revert by mutations of tRNA loci and reverts only by intracodonic suppression; (2) a missense mutation (his1-798, née his1-7) that can revert by intragenic suppression by base substitutions of any sort, including a back mutation as well as one three-base deletion; and (3) a −1 frameshift mutation (his1-434, née his1-19) that only reverts topically by +1 back mutation, +1 intragenic suppression, or a −2 deletion. Often the +1 insertion is accompanied by base substitution events at one or both ends of a run of A's. Missense suppressors of his1-798 are either feeders or nonfeeders, and at four different locations within the locus, a single base substitution encoding an amino acid alteration will suffice to turn the nonfeeder phenotype into a feeder phenotype. Late-appearing revertants of his1-798 were found to be slowly growing leaky mutants rather than a manifestation of adaptive mutagenesis. Spontaneous revertants of his1-208 and his1-434 produced no late-arising colonies.
Isolation and Characterization of Fission Yeast sns Mutants Defective at the Mitosis-to-Interphase Transition
Authors: Matynia Anna , Mueller Ulrich , Ong Ngoctuyen , Demeter Janos , Granger Aaron L , Hinata Kaede , Sazer Shelley
Published: February 2021

pim1-d1ts was previously identified in a visual screen for fission yeast mutants unable to complete the mitosis-to-interphase transition. pim1+ encodes the guanine nucleotide exchange factor (GEF) for the spi1 GTPase. Perturbations of this GTPase system by either mutation or overproduction of its regulatory proteins cause cells to arrest with postmitotic condensed chromosomes, an unreplicated genome, and a wide medial septum. The septation phenotype of pim1-d1ts was used as the basis for a more extensive screen for this novel class of sns (septated, not in S-phase) mutants. Seventeen mutants representing 14 complementation groups were isolated. Three strains, sns-A3, sns-A5, and sns-A6, representing two different alleles, are mutated in the pim1+ gene. Of the 13 non-pim1ts sns complementation groups, 11 showed genetic interactions with the spi1 GTPase system. The genes mutated in 10 sns strains were synthetically lethal with pim1-d1, and six sns strains were hypersensitive to overexpression of one or more of the known components of the spi1 GTPase system. Epistasis analysis places the action of the genes mutated in nine of these strains downstream of pim1+ and the action of one gene upstream of pim1+. Three strains, sns-A2, sns-B1, and sns-B9, showed genetic interaction with the spi1 GTPase system in every test performed. sns-B1 and sns-B9 are likely to identify downstream targets, whereas sns-A2 is likely to identify upstream regulators of the spi1 GTPase system that are required for the mitosis-to-interphase transition.
Physical Mapping of the liguleless Linkage Group in Sorghum bicolor Using Rice RFLP-Selected Sorghum BACs
Authors: Zwick Michael S , Islam-Faridi M Nurul , Czeschin Don G , Wing Rod A , Hart Gary E , Stelly David M , Price H James
Published: February 2021

Physical mapping of BACs by fluorescent in situ hybridization (FISH) was used to analyze the liguleless (lg-1) linkage group in sorghum and compare it to the conserved region in rice and maize. Six liguleless-associated rice restriction fragment length polymorphism (RFLP) markers were used to select 16 homeologous sorghum BACs, which were in turn used to physically map the liguleless linkage group in sorghum. Results show a basic conservation of the liguleless region in sorghum relative to the linkage map of rice. One marker which is distal in rice is more medial in sorghum, and another marker which is found within the linkage group in rice is on a different chromosome in sorghum. BACs associated with linkage group I hybridize to chromosome It, which was identified by using FISH in a sorghum cytogenetic stock trisomic for chromosome I (denoted It), and a BAC associated with linkage group E hybridized to an unidentified chromosome. Selected BACs, representing RFLP loci, were end-cloned for RFLP mapping, and the relative linkage order of these clones was in full agreement with the physical data. Similarities in locus order and the association of RFLP-selected BAC markers with two different chromosomes were found to exist between the linkage map of the liguleless region in maize and the physical map of the liguleless region in sorghum.
Identification of Chromosomal Regions Involved in decapentaplegic Function in Drosophila
Authors: Nicholls Russell E , Gelbart William M
Published: February 2021

Signaling molecules of the transforming growth factor β (TGF-β) family contribute to numerous developmental processes in a variety of organisms. However, our understanding of the mechanisms which regulate the activity of and mediate the response to TGF-β family members remains incomplete. The product of the Drosophila decapentaplegic (dpp) locus is a well-characterized member of this family. We have taken a genetic approach to identify factors required for TGF-β function in Drosophila by testing for genetic interactions between mutant alleles of dpp and a collection of chromosomal deficiencies. Our survey identified two deficiencies that act as maternal enhancers of recessive embryonic lethal alleles of dpp. The enhanced individuals die with weakly ventralized phenotypes. These phenotypes are consistent with a mechanism whereby the deficiencies deplete two maternally provided factors required for dpp's role in embryonic dorsal-ventral pattern formation. One of these deficiencies also appears to delete a factor required for dpp function in wing vein formation. These deficiencies remove material from the 54F-55A and 66B-66C polytene chromosomal regions, respectively. As neither of these regions has been previously implicated in dpp function, we propose that each of the deficiencies removes a novel factor or factors required for dpp function.
Bayesian Inference of Genetic Parameters and Selection Response for Litter Size Components in Pigs
Authors: Blasco A , Sorensen D , Bidanel J P
Published: February 2021

Three contemporary lines were formed from the progeny of 50 French Large White sows. In the first line, gilts were selected for ovulation rate at puberty. In the second line, they were selected for prenatal survival of the first two parities, corrected for ovulation rate. The control constituted the third line. Ovulation rate at puberty was analyzed using an animal model with a batch effect. Prenatal survival was analyzed with a repeatability animal model that included batch and parity effects. Flat priors were used to represent vague previous knowledge about parity and batch effects. Additive and residual effects were represented assuming that they were a priori normally distributed. Variance components were assumed to follow either uniform or inverted chi-square distributions, a priori. The use of different priors did not affect the results substantially. Heritabilities for ovulation rate ranged from 0.32 to 0.39, and from 0.11 to 0.16 for prenatal survival, depending on the prior used. The mean of the marginal posterior distribution of response to four generations of selection ranged from 0.38 to 0.40 ova per generation, and from 1.1 to 1.3% of the mean survival rate for average survival per generation.
Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)
Authors: Bradshaw H D , Otto Kevin G , Frewen Barbara E , McKay John K , Schemske Douglas W
Published: February 2021

Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining ≥25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.
Yeast dom34 Mutants Are Defective in Multiple Developmental Pathways and Exhibit Decreased Levels of Polyribosomes
Authors: Davis Luther , Engebrecht JoAnne
Published: February 2021

The DOM34 gene of Saccharomyces cerevisiae is similar togenes found in diverse eukaryotes and archaebacteria. Analysis of dom34 strains shows that progression through the G1 phase of the cell cycle is delayed, mutant cells enter meiosis aberrantly, and their ability to form pseudohyphae is significantly diminished. RPS30A, which encodes ribosomal protein S30, was identified in a screen for high-copy suppressors of the dom34Δ growth defect. dom34Δ mutants display an altered polyribosome profile that is rescued by expression of RPS30A. Taken together, these data indicate that Dom34p functions in protein translation to promote G1 progression and differentiation. A Drosophila homolog of Dom34p, pelota, is required for the proper coordination of meiosis and spermatogenesis. Heterologous expression of pelota in dom34Δ mutants restores wild-type growth and differentiation, suggesting conservation of function between the eukaryotic members of the gene family.