bluuebunny/crossref_metadata_2025 huggingface dataset:
Speckle-tracking echocardiography in comparison with ejection fraction for prediction of cardiovascular mortality in patients with end-stage renal disease
Authors: Terhuerne Janna , van Diepen Merel , Kramann Rafael , Erpenbeck Johanna , Dekker Friedo , Marx Nikolaus , Floege Jürgen , Becker Michael , Schlieper Georg
Published: January 2021

Background

Cardiovascular disease is the major cause of death in end-stage renal disease (ESRD). To develop better means to assess cardiovascular risk in these patients, we compared conventional echocardiography-derived left ventricular ejection fraction (EF) with the novel method of 2D speckle-tracking echocardiography to determine cardiac strain.

Methods

Predictive performances of conventional EF and speckle-tracking echocardiography-derived global longitudinal strain (GLS) were compared using receiver-operator curve (ROC) analyses and calibration by calibration plots. We also took into account other known cardiovascular risk factors through multivariable logistic regression analysis.

Results

The study comprised 171 ESRD patients (mean age 64 years, 64% male) on maintenance dialysis therapy (93% haemodialysis, 7% peritoneal dialysis) for an average period of 39 months. During 2.1 years of follow-up, 42 patients (25%) died from cardiovascular disease. ROC analysis of GLS resulted in an area under the curve of 0.700 [95% confidence interval (CI) 0.603–0.797] compared with an area under the curve of EF of 0.615 (95% CI 0.514–0.716) (P = 0.059 for difference). The total absolute deviation between predicted and observed outcome frequencies obtained by calibration plots were 13.8% for EF compared with only 6.4% for GLS. Best results of ROC analysis (area under the curve = 0.759; P = 0.06), calibration and goodness-of-fit (χ2 = 28.34, P ≤ 0.0001, R2 = 0.25) were achieved for GLS added to a baseline model consisting of known cardiovascular risk factors in a multivariate regression analysis.

Conclusions

In summary, in chronic dialysis patients, GLS is a more precise predictor of cardiovascular mortality than conventional echocardiography-derived EF.
Roxadustat and thyroid-stimulating hormone suppression
Authors: Tokuyama Atsuyuki , Kadoya Hiroyuki , Obata Atsushi , Obata Takahiro , Sasaki Tamaki , Kashihara Naoki
Published: January 2021

Hypoxia-inducible factor prolyl-hydroxylase inhibitors belong to a new class of orally administered drugs for treating anemia in patients with chronic kidney disease (CKD). The prevalence of hypothyroidism is disproportionately high in patients with CKD on hemodialysis. We report a rapid suppression of thyroid-stimulating hormone (TSH) and decrease in free triiodothyronine (T3) and free tetraiodothyronine levels after switching from darbepoetin alfa to roxadustat in a hemodialysis patient with hypothyroidism on levothyroxine therapy. This was reversed after stopping roxadustat. Roxadustat has structural similarity with T3 and is a selective activating ligand for thyroid hormone receptor-β possibly suppressing TSH release.
Suboptimal personal protective equipment and SARS-CoV-2 infection in Nephrologists: a Spanish national survey
Authors: Quiroga Borja , Sánchez-Álvarez Emilio , Ortiz Alberto , de Sequera Patricia ,   the Spanish Society of Nephrology
Published: January 2021

Background

Healthcare workers have been overexposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the current pandemic, but there is little information on the impact of SARS-CoV-2 on nephrologists. The aim of this study was to assess SARS-CoV-2 infections in nephrologists in the first and second pandemic waves, describing risk factors and clinical features.

Methods

This national survey was sent to Spanish nephrologists. Epidemiological data, comorbidities and medications were collected and compared between infected and non-infected nephrologists. Symptoms, prescribed treatments and outcomes are described for infected nephrologists.

Results

Three hundred and twenty-seven nephrologists (66% female, age 46 ± 11 years) completed the survey. Of them, 62 (19%) were infected by SARS-CoV-2. Infection was detected by real-time reverse transcription-polymerase chain reaction in the 37 symptomatic patients (62%) and by serological tests in 25 (38%) asymptomatic individuals. Five (8%) of the infected nephrologists were hospitalized. Contrary to the general population, most infections occurred during the first pandemic wave and, specifically, during the first month, when personal protective equipment (PPE) shortages were more severe. Factors associated with infection in univariate analysis were younger age (P = 0.004), work in non-nephrology departments (P = 0.045), higher exposure to coronavirus disease 2019 patients (P < 0.001), lack of appropriate PPE (P < 0.001) and non-O ABO blood group. In an adjusted multivariate model, only lack of appropriate PPE remained predictive of infection [hazard ratio 3.5 (95% confidence interval 1.9–6.8), P < 0.0001].

Conclusions

SARS-CoV-2 infection was frequent among nephrologists, was frequently diagnosed late and was associated with working conditions.
Evaluation of Thyroid Function in Pregnant Women Using Automated Immunoassays
Authors: Geno K Aaron , Reed Matthew S , Cervinski Mark A , Nerenz Robert D
Published: January 2021

Introduction

Automated free thyroxine (FT4) immunoassays are widely available, but professional guidelines discourage their use in pregnant women due to theoretical under-recoveries attributed to increased thyroid hormone binding capacity and instead advocate the use of total T4 (TT4) or free thyroxine index (FTI). The impact of this recommendation on the classification of thyroid status in apparently euthyroid pregnant patients was evaluated.

Methods

After excluding specimens with thyroid autoantibody concentrations above reference limits, thyroid-stimulating hormone (TSH), FT4, TT4, and T-uptake were measured on the Roche Cobas® platform in remnant clinical specimens from at least 147 nonpregnant women of childbearing age and pregnant women at each trimester. Split-sample comparisons of FT4 as measured by the Cobas and equilibrium dialysis were performed.

Results

FT4 decreased with advancing gestational age by both immunoassay and equilibrium dialysis. TSH declined during the first trimester, remained constant in the second, and increased throughout the third, peaking just before delivery. Interpretation of TT4 concentrations using 1.5-times the nonpregnant reference interval classified 13.6% of first trimester specimens below the lower reference limit despite TSH concentrations within trimester-specific reference intervals. Five FTI results from 480 pregnant individuals (about 1.0%) fell outside the manufacturer’s reference interval.

Conclusions

Indirect FT4 immunoassay results interpreted in the context of trimester-specific reference intervals provide a practical and viable alternative to TT4 or FTI. Declining FT4 and increasing TSH concentrations near term suggest that declining FT4 is not an analytical artifact but represents a true physiological change in preparation for labor and delivery.
Predicting Damage to Hop Cones by Tetranychus urticae (Acari: Tetranychidae)
Authors: Woods Joanna L , Iskra Anne E , Gent David H
Published: January 2021

Twospotted spider mite (Tetranychus urticae Koch) is a cosmopolitan pest of numerous plants, including hop (Humulus lupulus L.). The most costly damage from the pest on hop results from infestation of cones, which are the harvested product, which can render crops unsalable if cones become discolored. We analyzed 14 yr of historical data from 312 individual experimental plots in western Oregon to identify risk factors associated with visual damage to hop cones from T. urticae. Logistic regression models were fit to estimate the probability of cone damage. The most predictive model was based on T. urticae-days during mid-July to harvest, which correctly predicted occurrence and nonoccurrence of cone damage in 91 and 93% of data sets, respectively, based on Youden’s index. A second model based on the ratio of T. urticae to predatory arthropods late in the season correctly predicted cone damage in 92% of data sets and nonoccurrence of damage in 77% of data sets. The model based on T. urticae abundance performed similarly when validated in 23 commercial hop yards, whereas the model based on the predator:prey ratio was relatively conservative and yielded false-positive predictions in 11 of the 23 yards. Antecedents of these risk factors were explored and quantified by structural equation modeling. A simple path diagram was constructed that conceptualizes T. urticae invasion of hop cones as dependent on prior density of the pest on leaves in early spring and summer, which in turn influences the development of predatory arthropods that mediate late-season density of the pest. In summary, the biological insights and models developed here provide guidance to pest managers on the likelihood of visual cone damage from T. urticae that can inform late-season management based on both abundance of the pest and its important predators. This is critically important because a formal economic threshold for T. urticae on hop does not exist and current management efforts may be mistimed to influence the pest when crop damage is most probable. More broadly, this research suggests that current management practices that target T. urticae early in the season may in fact predispose yards to later outbreaks of the pest.
Prevalence of diabetes and impact on cardiovascular events and mortality in patients with chronic coronary syndromes, across multiple geographical regions and ethnicities
Authors: Mak Koon-Hou , Vidal-Petiot Emmanuelle , Young Robin , Sorbets Emmanuel , Greenlaw Nicola , Ford Ian , Tendera Michal , Ferrari Roberto , Tardif Jean-Claude , Udell Jacob A , Escobedo Jorge , Fox Kim M , Steg Philippe Gabriel ,   the CLARIFY Investigators
Published: January 2021

Background

In contrast with the setting of acute myocardial infarction, there are limited data regarding the impact of diabetes mellitus on clinical outcomes in contemporary cohorts of patients with chronic coronary syndromes. We aimed to investigate the prevalence and prognostic impact of diabetes according to geographical regions and ethnicity.

Methods and results

CLARIFY is an observational registry of patients with chronic coronary syndromes, enrolled across 45 countries in Europe, Asia, America, Middle East, Australia, and Africa in 2009–2010, and followed up yearly for 5 years. Chronic coronary syndromes were defined by ≥1 of the following criteria: prior myocardial infarction, evidence of coronary stenosis >50%, proven symptomatic myocardial ischaemia, or prior revascularization procedure.

Among 32 694 patients, 9502 (29%) had diabetes, with a regional prevalence ranging from below 20% in Northern Europe to ∼60% in the Gulf countries. In a multivariable-adjusted Cox proportional hazards model, diabetes was associated with increased risks for the primary outcome (cardiovascular death, myocardial infarction, or stroke) with an adjusted hazard ratio of 1.28 (95% confidence interval 1.18, 1.39) and for all secondary outcomes (all-cause and cardiovascular mortality, myocardial infarction, stroke, heart failure, and coronary revascularization). Differences on outcomes according to geography and ethnicity were modest.

Conclusion

In patients with chronic coronary syndromes, diabetes is independently associated with mortality and cardiovascular events, including heart failure, which is not accounted by demographics, prior medical history, left ventricular ejection fraction, or use of secondary prevention medication. This is observed across multiple geographic regions and ethnicities, despite marked disparities in the prevalence of diabetes.

ClinicalTrials identifier

ISRCTN43070564
Female sterile mutations on the second chromosome of Drosophila melanogaster. I. Maternal effect mutations.
Authors: Schüpbach T , Wieschaus E
Published: January 2021

In mutagenesis screens for recessive female sterile mutations on the second chromosome of Drosophila melanogaster 529 chromosomes were isolated which allow the homozygous females to survive, but cause them to be sterile. In 136 of these lines, mutant females produce morphologically normal eggs which cannot support normal embryonic development. These "maternal-effect" mutations fall into 67 complementation groups which define 23 multiply hit and 44 singly hit loci. In eggs from 14 complementation groups development is blocked before the formation of a syncytial blastoderm. In eggs from 12 complementation groups development is abnormal before cellularization, 17 complementation groups cause abnormal cellularization, 12 complementation groups cause changes in cellular morphology in early gastrulation stages, and 12 complementation groups seem to affect later embryonic development.
Pattern of ac transposition in maize.
Authors: Schwartz D
Published: January 2021

Analysis of four nearby transpositions of Ac from the waxy locus indicate that the element can reinsert to either side. The cause of the asymmetry observed for P-VV transpositions is discussed and a model is presented to account for the high frequency of close reinsertions of Ac.
A cytogenetic analysis of the Punch-tudor region of chromosome 2R in Drosophila melanogaster.
Authors: O'Donnell J , Boswell R , Reynolds T , Mackay W
Published: January 2021

Eleven chromosomal deficiencies and several rearrangements in the Pu-tud region of chromosome 2R have been generated and examined cytologically. The Pu locus has been localized to chromosome bands 57C5-6 and tud to 57C7-8. Mutagenesis within the region defined by the deletion intervals has resulted in the isolation of 92 new lethal mutations. Seventy-six of these mutations have been separated into 16 complementation groups that have been ordered and placed cytologically by deletion mapping. All new alleles fully complement tud for both lethal and grandchildless phenotypes. The largest number of new mutations, a total of 25, are Pu alleles.
Spatial autocorrelation analysis of the distribution of genotypes within populations of lodgepole pine.
Authors: Epperson B K , Allard R W
Published: January 2021

Spatial autocorrelation analyses of point samples within two populations of lodgepole pine (Pinus contorta ssp. latifolia) indicate that single-locus mature tree and pollen genotypes are distributed in a nearly random fashion for most of the allozyme loci assayed. This lack of structure in the distributions of most genotypes is consistent with outcrossing rates that are very nearly 1.0 and with estimates indicating that both pollen and seed are dispersed over long distances in lodgepole pine. However, spatial autocorrelation of genotypes for a few loci suggests that genotypes at these loci may be under natural selection.
Ath-2, a second gene determining atherosclerosis susceptibility and high density lipoprotein levels in mice.
Authors: Paigen B , Nesbitt M N , Mitchell D , Albee D , LeBoeuf R C
Published: January 2021

Strain C57BL/6J and A/J differ at two genes determining atherosclerosis susceptibility. The first gene, Ath-1, was described earlier and this report characterizes Ath-2. The alleles at Ath-2 are r for resistance and s for susceptibility to atherosclerosis. The resistant phenotype in female mice is characterized by high plasma high density lipoprotein-cholesterol levels (74 mg/dl +/- SEM 2) and very few lesions/mouse after 14 weeks of consumption of an atherogenic diet (0.1 +/- SEM 0.1 in a predetermined region of the aorta). The susceptible phenotype in female mice is characterized by low levels of high density lipoprotein-cholesterol (35 mg/dl +/- SEM 1) and 1.2 lesions/mouse +/- SEM 0.2 in the same region of the aorta. In Ath-2 heterozygotes, resistance is dominant to susceptibility. Recombinant inbred strains derived from C57BL/6 and A were characterized for Apoa 1, Apoa 2 and susceptibility to atherosclerosis. Ath-1 and Ath-2 interact with each other so that resistant alleles at either locus confer a resistant phenotype to the animal. The map position of Ath-2 is not known, but Ath-2 does not map near genes determining the apolipoproteins for A-I, A-II, or E.
Amino acid sequence similarity between GCN3 and GCD2, positive and negative translational regulators of GCN4: evidence for antagonism by competition.
Authors: Paddon C J , Hannig E M , Hinnebusch A G
Published: January 2021

The GCD2 gene product is required in conditions of amino acid sufficiency to repress the synthesis of GCN4, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. GCD2 is also required unconditionally for cell viability. The constitutive derepression of GCN4 expression and temperature sensitivity for growth associated with GCD2 alleles, known as gcd12 mutations, are completely masked by wild-type GCN3, a positive regulator of GCN4 expression. This observation suggests that GCN3 can promote or at least partially substitute for GCD2 function in normal growth conditions, while acting as an antagonist of GCD2 in amino acid starvation conditions. We report here that the predicted amino acid sequence of GCN3 shows extensive similarity with the carboxyl-terminal portion of GCD2. Based on this finding, it seems likely that gcd12 mutations specifically affect the domain of GCD2 that is similar in sequence to GCN3. We propose that GCN3 can substitute for this domain in a gcd12 mutant grown in normal growth conditions, and that modification of GCN3 in starvation conditions causes it to interfere with, rather than substitute for GCD2 function. A gcd2 deletion and gcd2-1 are each expected to inactivate a second domain for which GCN3 cannot substitute, accounting for the inability of GCN3 to mask the phenotypes associated with these mutations.
The Caenorhabditis elegans gene sdc-2 controls sex determination and dosage compensation in XX animals.
Authors: Nusbaum C , Meyer B J
Published: January 2021

We have identified a new X-linked gene, sdc-2, that controls the hermaphrodite (XX) modes of both sex determination and X chromosome dosage compensation in Caenorhabditis elegans. Mutations in sdc-2 cause phenotypes that appear to result from a shift of both the sex determination and dosage compensation processes in XX animals to the XO modes of expression. Twenty-eight independent sdc-2 mutations have no apparent effect in XO animals, but cause two distinct phenotypes in XX animals: masculinization, reflecting a defect in sex determination, and lethality or dumpiness, reflecting a disruption in dosage compensation. The dosage compensation defect can be demonstrated directly by showing that sdc-2 mutations cause elevated levels of several X-linked transcripts in XX but not XO animals. While the masculinization is blocked by mutations in sex determining genes required for male development (her-1 and fem-3), the lethality, dumpiness and overexpression of X-linked genes are not, indicating that the effect of sdc-2 mutations on sex determination and dosage compensation are ultimately implemented by two independent pathways. We propose a model in which sdc-2 is involved in the coordinate control of both sex determination and dosage compensation in XX animals and acts in the regulatory hierarchy at a step prior to the divergence of the two pathways.
Ancient interlocus exon exchange in the history of the HLA-A locus.
Authors: Hughes A L , Nei M
Published: January 2021

The major histocompatibility complex (MHC) in humans and chimpanzees includes three classical class I loci, A, B and C, which encode glycoproteins expressed on the surface of all nucleated cells. There are also several nonclassical class I loci including E, which have more limited expression. By analyzing published sequences, we have shown that in exons 4 and 5, A locus alleles from both humans and chimpanzees are much more similar to E than to B or C alleles, whereas in exons 2 and 3 alleles from all three classical class I loci are much more similar to each other than any one is to E. We propose that some 20 million years ago, interlocus recombination led to the formation of a hybrid gene in which exons 2 and 3 were derived from the original A locus and exons 4 and 5 were derived from the E locus. The fact that such an ancient event can still be detected suggests that interlocus recombination is rare in the MHC and does not significantly contribute to MHC polymorphism, which is known to be extremely high. The present finding, however, supports Gilbert's idea that exons in a gene may occasionally be replaced by those from another gene in the evolutionary process.
Isolation and characterization of dominant female sterile mutations of Drosophila melanogaster. II. Mutations on the second chromosome.
Authors: Szabad J , Erdélyi M , Hoffmann G , Szidonya J , Wright T R
Published: January 2021

Twenty-four, second chromosome, dominant female sterile (Fs) mutations in Drosophila are described. Fs(2) were isolated at a frequency of approximately 1 per 1000 EMS-treated chromosomes screened. In comparison the isolation of frequency for second chromosome zygotic recessive lethal mutations was approximately 550 per 1000. Complementation analysis of the Fs(2) revertants showed that the 24 Fs(2) mutations identify 13-15 loci, calculated to be about 65-75% of the second chromosome genes EMS mutable to dominant female sterility. Two of the Fs(2) mutations are useful tools for the dominant female sterile technique: Fs(2)1 for induction and detection of germ-line clones and Fs(2)Ugra for follicle cell clones. Several of the Fs(2) mutations bring about novel mutant phenotypes. Seven of them alter egg shape, whereas the others arrest development primarily at two stages: around fertilization by five Fs(2) and during cleavage divisions [by Fs(2) in three loci]. The remaining that allow development to the larval stage of differentiation include four new dorsal alleles and one dominant torso allele. Analysis of germ-line chimeras revealed that with two exceptions all the Fs(2) mutations are germ-line dependent. The Fs(2) mutations were mapped mainly on the basis of mitotic recombination induced in the female germ-line cells of adult females. That most of the Fs(2) may be gain-of-function mutations is indicated by the unusual behavior of the Fs+ germ-line clones and also by the fact that 90% of the could be induced to revert.
The Drosophila zeste locus is nonessential.
Authors: Goldberg M L , Colvin R A , Mellin A F
Published: January 2021

Diepoxybutane-induced mutations of the Drosophila zeste locus were generated in an effort to obtain a null allele. Of 33 mutations of this X-linked gene isolated, 16 were associated with multilocus deletions of zeste and adjacent complementation groups, while the remainder were defects restricted to zeste undetectable by Southern blot analysis. Two of these multilocus deletions (Df(1)zdeb3 and Df(1)zdeb92) were employed in the synthesis of females completely deleted for zeste. Such "zesteless" flies were produced, though at frequencies lower than Mendelian expectations. zeste-deleted females are fertile, and can give rise to zeste-deleted female progeny. These results demonstrate that the product of the zeste gene is not essential to viability or to female fertility, even if absent both as a maternal contribution and as a product of the zygotic genome. However, the possibility that zeste may influence relative viability cannot be excluded. In spite of previous in vitro indications that the zeste protein may activate transcription of the Ultrabithorax (Ubx) gene, zeste -deleted flies are Ubx+ in phenotype. This suggests that the zeste protein normally is either a very weak transcription factor, or that its function can be substituted by that of other regulatory proteins.
The P-M and the 23.5 MRF (hobo) systems of hybrid dysgenesis in Drosophila melanogaster are independent of each other.
Authors: Stamatis N , Monastirioti M , Yannopoulos G , Louis C
Published: January 2021

Strains of Drosophila melanogaster bearing the male recombination factor 23.5 MRF induce hybrid dysgenesis in a way which is highly reminiscent of the P-M system, and, most probably, causally related to the activity of the transposable element hobo. We have investigated potential interactions between the two systems of hybrid dysgenesis by studying mixed lines derived from bidirectional crosses between 23.5 MRF and P strains, and analyzed their potentials to induce or suppress the occurrence of dysgenesis. All new lines possess the P induction abilities, as determined by two different procedures, and have also acquired a P cytotype. In contrast, some of them lost their ability to induce the non-P-M dysgenesis, as well as to suppress the action of 23.5 MRF. This loss of the 23.5 MRF induction abilities parallels the selective loss of full-length hobo elements from the genome of these lines, providing further substantiation to the notion that the 23.5 MRF activity is directly linked to this transposable element.
Genetic analysis of prototrophic natural variants of Candida albicans.
Authors: Goshorn A K , Scherer S
Published: January 2021

To facilitate genetic analysis of Candida albicans natural variants, we have isolated a dominant mycophenolic acid-resistant mutant. Mycophenolic acid-resistant auxotrophs were used to analyze prototrophic natural variants by spheroplast fusion. The fusion products were shown to be heterozygous for many of the parental chromosomes by molecular and genetic criteria. Using this approach, we have found that one type of morphologic variation is due to a recessive change and identified three dominant 5-fluorocytosine-resistant mutants. Rare fusion products express recessive parental markers. These exceptional progeny should be useful for linkage analysis and strain construction.
Characterization of triosephosphate isomerase mutants with reduced enzyme activity in Mus musculus.
Authors: Merkle S , Pretsch W
Published: January 2021

Four heterozygous triosephosphate isomerase (TPI) mutants with approximately 50% reduced activity in blood compared to wild type were detected in offspring of 1-ethyl-1-nitrosourea treated male mice. Breeding experiments displayed an autosomal, dominant mode of inheritance for the mutations. All mutations were found to be homozygous lethal at an early postimplantation stage of embryonic development, probably due to a total lack of TPI activity and consequently to the inability to utilize glucose as a source of metabolic energy. Although activity alteration was also found in liver, lung, kidney, spleen, heart, brain and muscle the TPI deficiency in heterozygotes has no influence on the following physiological traits: hematological parameters, plasma glucose, glucose consumption of blood cells, body weight and organo-somatic indices of liver, spleen, heart, kidney and lung. Biochemical investigations of TPI in the four mutant lines indicated no difference of physicochemical properties compared to the wild type. Results from immunoinactivation assays indicate that the decrease of enzyme activity corresponds to a decrease in the level of an immunologically active moiety. It is suggested that the mutations have affected the Tpi-1 structural locus and resulted in alleles which produce no detectable enzyme activity and no immunologically cross-reacting material. The study furthermore suggests one functional TPI gene per haploid genome in the erythrocyte and seven other tested organs of the mouse.
Quantitative genetics of doubled haploid populations and application to the theory of line development.
Authors: Gallais A
Published: January 2021

The line value of a genotype is defined as the expected value of all lines that can be derived from this genotype. Specific genetic effects are defined for this value: only additive and additive by additive epistatic effects are necessary. There is no dominance effect for such a value. A general expression for the covariances between related lines is given. From a design with several lines per haplodiploidized plant taken at random from a population it is possible to estimate the additive variance for line value and the variance of additive by additive epistasis for line value. Variances of higher order epistasis can be estimated with a two-factor mating design in which a cross is replaced by the population of lines that can be derived from it. With a diallel or a factorial design a direct test for the presence of homozygous by homozygous epistasis is possible. The application of the concept of line value to the theory of line development leads to simple expressions of genetic advance in one cycle of recurrent selection according to the testing system. A brief consideration of these expressions leads to the conclusion that single doubled haploid descent recurrent selection will be one of the most efficient methods for low heritabilities and with a rapid development of doubled haploid lines.
Consequences of growth media, gene copy number, and regulatory mutations on the expression of the PRB1 gene of Saccharomyces cerevisiae.
Authors: Moehle C M , Jones E W
Published: January 2021

Glucose represses PRB1 expression at the level of transcription. However, release from glucose repression initially does not result in accumulation of protease B (PrB) activity despite transcriptional derepression. PrB activity accumulates only upon a second transcriptional derepression as the cells approach stationary phase. Increasing the PRB1 gene dosage on 2 mu-based plasmids does not overcome glucose repression. Glucose-mediated repression of PRB1 is not subject to the same genetic controls as SUC2. Mutation of the HXK2 gene, which confers glucose-insensitive expression of secreted invertase, had no effect on PRB1 expression at the level of PrB activity. Strains bearing a mutation in any of the SNF1-SNF6 genes cannot derepress secreted invertase synthesis, but did derepress PrB synthesis when grown in the absence of glucose. Mutation of the SNF2 or SNF5 gene led to accumulation of PrB activity to levels ten times that of wild type. Polymorphism for a suppressor gene was observed: in snf5-bearing strains, one allele of this suppressor gene resulted in elevated levels of PrB and the other allele resulted in wild-type levels of PrB; neither allele suppressed the Suc- phenotype of the snf5 mutant. Re-examination of published data on SUC2 expression in snf2 and snf5 mutants and examination of PRB1 expression in these mutants paradoxically suggest that the SNF2 and SNF5 gene products might act as negative regulators of gene expression.
A linkage map of endogenous murine leukemia proviruses.
Authors: Frankel W N , Stoye J P , Taylor B A , Coffin J M
Published: January 2021

Thirty endogenous proviruses belonging to the modified polytropic (Mpmv) class of murine leukemia virus (MLV) were identified by proviral-cellular DNA junction fragment segregation in several sets of recombinant inbred mice. Twenty-six Mpmv loci were mapped to chromosomal regions by matching proviral strain distribution patterns to those of previously assigned genes. Like other endogenous nonecotropic MLVs, Mpmv loci were present on several chromosomes in all strains examined. We pooled recombinant inbred strain linkage data from 110 MLV loci and selected marker genes in order to construct a chromosomal linkage map. Every mouse chromosome was found to harbor at least one proviral insertion, and several regions contained multiple integrations. However, the overall distribution of the 110 mapped proviruses did not deviate significantly from a random distribution. Because of their polymorphism in inbred strains of mice, and the ability to score as many as 57 proviruses per strain using only three hybridization probes, the nonecotropic MLVs mapped in common strains of mice offer a significant advantage over older methods (e.g., biochemical or individual restriction fragment polymorphisms) as genetic markers. These endogenous insertion elements should also be useful for assessing strain purity, and for studying the relatedness of common and not-so-common inbred strains.
Mitotic chromosome transmission fidelity mutants in Saccharomyces cerevisiae.
Authors: Spencer F , Gerring S L , Connelly C , Hieter P
Published: January 2021

We have isolated 136 independent mutations in haploid yeast strains that exhibit decreased chromosome transmission fidelity in mitosis. Eighty-five percent of the mutations are recessive and 15% are partially dominant. Complementation analysis between MATa and MAT alpha isolates identifies 11 chromosome transmission fidelity (CTF) complementation groups, the largest of which is identical to CHL1. For 49 independent mutations, no corresponding allele has been recovered in the opposite mating type. The initial screen monitored the stability of a centromere-linked color marker on a nonessential yeast chromosome fragment; the mitotic inheritance of natural yeast chromosome III is also affected by the ctf mutations. Of the 136 isolates identified, seven were inviable at 37 degrees and five were inviable at 11 degrees. In all cases tested, these temperature conditional lethalities cosegregated with the chromosome instability phenotype. Five additional complementation groups (ctf12 through ctf16) have been defined by complementation analysis of the mutations causing inviability at 37 degrees. Twenty-three of the 136 isolates exhibited growth defects at concentrations of benomyl permissive for the parent strain, and nine appeared to be tolerant of inhibitory levels of benomyl. All of the mutant strains showed normal sensitivity to ultraviolet and gamma-irradiation. Further characterization of these mutant strains will describe the functions of gene products crucial to the successful execution of processes required for aspects of the chromosome cycle that are important for chromosome transmission fidelity in mitosis.
The relationship between P elements and male recombination in Drosophila melanogaster.
Authors: Duttaroy A , McCarron M , Sitaraman K , Doughty G , Chovnick A
Published: January 2021

P element dysgenesis associated male recombination in Drosophila was examined with a selective system focused upon 5% of the standard female genetic map divided into eight recombination segments. We found no correspondence between P element mobilization events and recombination in males in the intervals monitored. We defined two adjacent short genetic and molecular regions, one devoid of male recombination and the other acting as a "hot spot" for exchange in the absence of supporting P element insertion and excision activity. These data suggest that, even in the presence of mobilizing P elements, transposase may be active at non-P element sites, and that the genome may harbor sequences ranging from highly responsive to completely unresponsive to transposase action. A viewpoint is presented wherein P elements, with sequences that bind transposase, serve to focus the recombination action of transposase to encompass a region of DNA radiating outward from the initial binding site. We suggest that this region is measured in terms of chromosomal segments rather than limited to P element sequences.
DNA methylation in eukaryotes: kinetics of demethylation and de novo methylation during the life cycle.
Authors: Otto S P , Walbot V
Published: January 2021

We present a model for the kinetics of methylation and demethylation of eukaryotic DNA; the model incorporates values for de novo methylation and the error rate of maintenance methylation. From the equations, an equilibrium is reached such that the proportion of sites which are newly methylated equals the proportion of sites which become demethylated in a cell generation. This equilibrium is empirically determined as the level of maintenance methylation. We then chose reasonable values for the parameters using maize and mice as model species. In general, if the genome is either hypermethylated or hypomethylated it will approach the equilibrium level of maintenance methylation asymptotically over time; events occurring just once per life cycle to suppress methylation can maintain a relatively hypomethylated state. Although the equations developed are used here as framework for evaluating events in the whole genome, they can also be used to evaluate the rates of methylation and demethylation in specific sites over time.
Isolation and characterization of omnipotent suppressors in the yeast Saccharomyces cerevisiae.
Authors: Wakem L P , Sherman F
Published: January 2021

Approximately 290 omnipotent suppressors, which enhance translational misreading, were isolated in strains of the yeast Saccharomyces cerevisiae containing the psi+ extrachromosomal determinant. The suppressors could be assigned to 8 classes by their pattern of suppression of five nutritional markers. The suppressors were further distinguished by differences in growth on paromomycin medium, hypertonic medium, low temperatures (10 degrees), nonfermentable carbon sources, alpha-aminoadipic acid medium, and by their dominance and recessiveness. Genetic analysis of 12 representative suppressors resulted in the assignment of these suppressors to 6 different loci, including the three previously described loci SUP35 (chromosome IV), SUP45 (chromosome II) and SUP46 (chromosome II), as well as three new loci SUP42 (chromosome IV), SUP43 (chromosome XV) and SUP44 (chromosome VII). Suppressors belonging to the same locus had a wide range of different phenotypes. Differences between alleles of the same locus and similarities between alleles of different loci suggest that the omnipotent suppressors encode proteins that effect different functions and that altered forms of each of the proteins can effect the same function.
Genetic and molecular analysis of the SOE1 gene: a tRNA(3Glu) missense suppressor of yeast cdc8 mutations.
Authors: Su J Y , Belmont L , Sclafani R A
Published: January 2021

The CDC8 gene of Saccharomyces cerevisiae encodes deoxythymidylate (dTMP) kinase and is required for nuclear and mitochondrial DNA replication in both the mitotic and meiotic cell cycles. All cdc8 temperature-sensitive mutants are partially defective in meiotic and mitochondrial functions at the permissive temperature. In a study of revertants of temperature-sensitive cdc8 mutants, the SOE201 and SOE1 mutants were isolated. The SOE201 mutant is a disome of chromosome X to which the cdc8 gene maps. Using the chromosome X aneuploids to vary cdc8 gene dosage, we demonstrate that different levels of dTMP kinase activity are required for mitotic, meiotic or mitochondrial DNA replication. The SOE1 mutant contains a dominant suppressor that suppresses five different cdc8 alleles but does not suppress a complete cdc8 deletion. The SOE1 gene is located less than 1.5 cM from the CYH2 gene on chromosome VII and is adjacent to the TSM437-CYH2 region, with the gene order being SOE1-TSM437-CYH2. SOE1 is an inefficient suppressor that can neither suppress the cdc8 hypomorphic phenotype nor restore dTMP kinase activity in vitro. SOE1 is a single C to T mutation in the anticodon of a tRNA(3Glu) gene and thereby, produces a missense suppressor tRNA capable of recognizing AAA lysine codons. We propose that the resultant lysine to glutamate change stabilizes thermo-labile dTMP kinase molecules in the cell.
Genetic analysis of defecation in Caenorhabditis elegans.
Authors: Thomas J H
Published: January 2021

Defecation in the nematode Caenorhabditis elegans is achieved by a cyclical stereotyped motor program. The first step in each cycle is contraction of a set of posterior body muscles (pBoc), followed by contraction of a set of anterior body muscles (aBoc), and finally contraction of specialized anal muscles that open the anus and expel intestinal contents (Exp). By testing existing behavioral mutants and screening for new mutants that become constipated due to defects in defecation, I have identified 18 genes that are involved in defecation. Mutations in 16 of these genes affect specific parts of the motor program: mutations in two genes specifically affect the pBoc step; mutations in four genes affect the aBoc step; mutations in four genes affect the Exp step; and mutations in six genes affect both aBoc and Exp. Mutations in two other genes affect the defecation cycle period but have a normal motor program. Sensory inputs that regulate the cycle timing in the wild type are also described. On the basis of the phenotypes of the defecation mutants and of double mutants, I suggest a formal genetic pathway for the control of the defecation motor program.
Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci.
Authors: Takahata N , Nei M
Published: January 2021

To explain the long-term persistence of polymorphic alleles (trans-specific polymorphism) at the major histocompatibility complex (MHC) loci in rodents and primates, a computer simulation study was conducted about the coalescence time of different alleles sampled under various forms of selection. At the same time, average heterozygosity, the number of alleles in a sample, and the rate of codon substitution were examined to explain the mechanism of maintenance of polymorphism at the MHC loci. The results obtained are as follows. (1) The coalescence time for neutral alleles is too short to explain the trans-specific polymorphism at the MHC loci. (2) Under overdominant selection, the coalescence time can be tens of millions of years, depending on the parameter values used. The average heterozygosity and the number of alleles observed are also high enough to explain MHC polymorphism. (3) The pathogen adaptation model proposed by Snell is incapable of explaining MHC polymorphism, since the coalescence time for this model is too short and the expected heterozygosity and the expected number of alleles are too small. (4) From the mathematical point of view, the minority advantage model of frequency-dependent selection is capable of explaining a high degree of polymorphism and trans-specific polymorphism. (5) The molecular mimicry hypothesis also gives a sufficiently long coalescence time when the mutation rate is low in the host but very high in the parasite. However, the expected heterozygosity and the expected number of alleles tend to be too small. (6) Consideration of the molecular mechanism of the function of MHC molecules and other biological observations suggest that the most important factor for the maintenance of MHC polymorphism is overdominant selection. However, some experiments are necessary to distinguish between the overdominance and frequency-dependent selection hypotheses.
Context effects in the formation of deletions in Escherichia coli.
Authors: Kazic T , Berg D E
Published: January 2021

We have examined the frequency with which identical deletions are formed in different chromosomal contexts. A panel of six mutant bla genes containing palindrome/direct repeat structures were moved from pBR322 to three locations: at lambda att, at chromosomal lac, and at F'lac. Deletion of the palindromes and one of the direct repeats results in reversion to Ampr. The frequency of deletion for all alleles declines beyond the reduction in copy number when they are moved from the multicopy plasmid environment to a single-copy chromosome. The magnitude of the declines varies in an allele-specific and location-specific manner. Our data support the hypothesis that context can influence the frequency of mutation independent of the immediate DNA sequence.
Transvection in the Drosophila Ultrabithorax gene: a Cbx1 mutant allele induces ectopic expression of a normal allele in trans.
Authors: Castelli-Gair J E , Micol J L , García-Bellido A
Published: January 2021

In wild-type Drosophila melanogaster larvae, the Ultrabithorax (Ubx) gene is expressed in the haltere imaginal discs but not in the majority of cells of the wing imaginal discs. Ectopic expression of the Ubx gene in wing discs can be elicited by the presence of Contrabithorax (Cbx) gain-of-function alleles of the Ubx gene or by loss-of-function mutations in Polycomb (Pc) or in other trans-regulatory genes which behave as repressors of Ubx gene activity. Several Ubx loss-of-function alleles cause the absence of detectable Ubx proteins (UBX) or the presence of truncated UBX lacking the homeodomain. We have compared adult wing phenotypes with larval wing disc UBX patterns in genotypes involving double mutant chromosomes carrying in cis one of those Ubx mutations and the Cbx1 mutation. We show that such double mutant genes are (1) active in the same cells in which the single mutant Cbx1 is expressed, although they are unable to yield functional proteins, and (2) able to induce ectopic expression of a normal homologous Ubx allele in a part of the cells in which the single mutant Cbx1 is active. That induction is conditional upon pairing of the homologous chromosomes (the phenomenon known as transvection), and it is not mediated by UBX. Depletion of Pc gene products by Pc3 mutation strongly enhances the induction phenomenon, as shown by (1) the increase of the number of wing disc cells in which induction of the homologous allele is detectable, and (2) the induction of not only a paired normal allele but also an unpaired one.
DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing.
Authors: Shattuck-Eidens D M , Bell R N , Neuhausen S L , Helentjaris T
Published: January 2021

While compiling genetic linkage maps in several plant species based upon restriction fragment length polymorphisms (RFLPs), it was noted that the incidence of polymorphism differs among species. The basis of this disparity was investigated in this study by examining the nucleotide sequence at homologous loci among distinct cultivars within two species which exhibit considerably different levels of RFLPs. Using the polymerase chain reaction, homologous regions from different cultivars were first amplified and the nucleotide sequence of the products were determined. Four genomic regions of seven maize cultivars and three genomic regions of eight melon cultivars were examined to compare the respective levels of sequence variation between the two species. Levels of variation for both base substitutions and insertions/deletions varied widely among the maize sequences and between maize and melon for base substitutions. Estimates of theta (a measure of polymorphism) ranged from 0 to 0.002 in melon and from 0.006 to 0.040 for base substitutions and from 0.002 to 0.023 for insertions/deletions in maize. Critical value tests and chi-squared tests suggested that in maize the underlying processes generating and maintaining neutral mutations differ among the regions. The results not only suggest that several mechanisms are necessary to explain the variation seen in these two species, but also point to some basic dissimilarities in the organization and maintenance of the genomes of different plant species.
Relationship between migration and DNA polymorphism in a local population.
Authors: Tajima F
Published: January 2021

The expected amount of DNA polymorphism, measured in terms of the number of nucleotide differences between the two DNA sequences randomly sampled from subpopulations, was studied by using the stepping-stone model and the finite island model, under the assumption that the migration rate is not the same among different subpopulations. The results obtained indicate that the expected amount of DNA polymorphism in the subpopulation with lower migration rate is smaller than that of higher migration rate. This suggests that marginal populations tend to have lower level of DNA polymorphism than central populations if the migration rate in the marginal populations is lower than that of the central populations.