bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defects in Protein Glycosylation Cause SHO1-Dependent Activation of a STE12 Signaling Pathway in Yeast
Authors: Cullen Paul J , Schultz Janet , Horecka Joe , Stevenson Brian J , Jigami Yoshifumi , Sprague George F 
Published: April 2021

Abstract
In haploid Saccharomyces cerevisiae, mating occurs by activation of the pheromone response pathway. A genetic selection for mutants that activate this pathway uncovered a class of mutants defective in cell wall integrity. Partial loss-of-function alleles of PGI1, PMI40, PSA1, DPM1, ALG1, MNN10, SPT14, and OCH1, genes required for mannose utilization and protein glycosylation, activated a pheromone-response-pathway-dependent reporter (FUS1) in cells lacking a basal signal (ste4). Pathway activation was suppressed by the addition of mannose to hexose isomerase mutants pgi1-101 and pmi40-101, which bypassed the requirement for mannose biosynthesis in these mutants. Pathway activation was also suppressed in dpm1-101 mutants by plasmids that contained RER2 or PSA1, which produce the substrates for Dpm1. Activation of FUS1 transcription in the mannose utilization/protein glycosylation mutants required some but not all proteins from three different signaling pathways: the pheromone response, invasive growth, and HOG pathways. We specifically suggest that a Sho1 → Ste20/Ste50 → Ste11 → Ste7 → Kss1 → Ste12 pathway is responsible for activation of FUS1 transcription in these mutants. Because loss of pheromone response pathway components leads to a synthetic growth defect in mannose utilization/protein glycosylation mutants, we suggest that the Sho1 → Ste12 pathway contributes to maintenance of cell wall integrity in vegetative cells.
The Saccharomyces cerevisiae RDN1 Locus Is Sequestered From Interchromosomal Meiotic Ectopic Recombination in a SIR2-Dependent Manner
Authors: Davis Edward S , Shafer Brenda K , Strathern Jeffrey N 
Published: April 2021

Abstract
Meiotic ectopic recombination occurs at similar frequencies among many sites in the yeast genome, suggesting that all loci are similarly accessible to homology searching. In contrast, we found that his3 sequences integrated in the RDN1 (rDNA) locus were unusually poor participants in meiotic recombination with his3 sequences at other sites. We show that the low rate of meiotic ectopic recombination resulted from the poor ability of RDN1::his3 to act as a donor sequence. SIR2 partially repressed interchromosomal meiotic ectopic recombination at RDN1, consistent with its role in regulating recombination, gene expression, and retrotransposition within RDN1. We propose that RDN1 is physically sequestered from meiotic homology searching mechanisms.
MPH1, A Yeast Gene Encoding a DEAH Protein, Plays a Role in Protection of the Genome From Spontaneous and Chemically Induced Damage
Authors: Scheller Jürgen , Schürer Anke , Rudolph Christian , Hettwer Stefan , Kramer Wilfried 
Published: April 2021

Abstract
We have characterized the MPH1 gene from Saccharomyces cerevisiae. mph1 mutants display a spontaneous mutator phenotype. Homologs were found in archaea and in the EST libraries of Drosophila, mouse, and man. Mph1 carries the signature motifs of the DEAH family of helicases. Selected motifs were shown to be necessary for MPH1 function by introducing missense mutations. Possible indirect effects on translation and splicing were excluded by demonstrating nuclear localization of the protein and splicing proficiency of the mutant. A mutation spectrum did not show any conspicuous deviations from wild type except for an underrepresentation of frameshift mutations. The mutator phenotype was dependent on REV3 and RAD6. The mutant was sensitive to MMS, EMS, 4-NQO, and camptothecin, but not to UV light and X rays. Epistasis analyses were carried out with representative mutants from various repair pathways (msh6, mag1, apn1, rad14, rad52, rad6, mms2, and rev3). No epistatic interactions were found, either for the spontaneous mutator phenotype or for MMS, EMS, and 4-NQO sensitivity. mph1 slightly increased the UV sensitivity of mms2, rad6, and rad14 mutants, but no effect on X-ray sensitivity was observed. These data suggest that MPH1 is not part of a hitherto known repair pathway. Possible functions are discussed.
Physical Map of a Conditionally Dispensable Chromosome in Nectria haematococca Mating Population VI and Location of Chromosome Breakpoints
Authors: Enkerli Jürg , Reed Heather , Briley Angela , Bhatt Garima , Covert Sarah F 
Published: April 2021

Abstract
Certain isolates of the plant pathogenic fungus Nectria haematococca mating population (MP) VI contain a 1.6-Mb conditionally dispensable (CD) chromosome carrying the phytoalexin detoxification genes MAK1 and PDA6-1. This chromosome is structurally unstable during sexual reproduction. As a first step in our analysis of the mechanisms underlying this chromosomal instability, hybridization between overlapping cosmid clones was used to construct a map of the MAK1 PDA6-1 chromosome. The map consists of 33 probes that are linked by 199 cosmid clones. The polymerase chain reaction and Southern analysis of N. haematococca MP VI DNA digested with infrequently cutting restriction enzymes were used to close gaps and order the hybridization-derived contigs. Hybridization to a probe extended from telomeric repeats was used to anchor the ends of the map to the actual chromosome ends. The resulting map is estimated to cover 95% of the MAK1 PDA6-1 chromosome and is composed of two ordered contigs. Thirty-eight percent of the clones in the minimal map are known to contain repeated DNA sequences. Three dispersed repeats were cloned during map construction; each is present in five to seven copies on the chromosome. The cosmid clones representing the map were probed with deleted forms of the CD chromosome and the results were integrated into the map. This allowed the identification of chromosome breakpoints and deletions.
Caenorhabditis elegans lin-13, a Member of the LIN-35 Rb Class of Genes Involved in Vulval Development, Encodes a Protein With Zinc Fingers and an LXCXE Motif
Authors: Meléndez Alicia , Greenwald Iva 
Published: April 2021

Abstract
The SynMuv genes appear to be involved in providing a signal that inhibits vulval precursor cells from adopting vulval fates in Caenorhabditis elegans. One group of SynMuv genes, termed class B, includes genes encoding proteins related to the tumor suppressor Rb and RbAp48, a protein that binds Rb. Here, we provide genetic evidence that lin-13 behaves as a class B SynMuv gene. We show that null alleles of lin-13 are temperature sensitive and maternally rescued, resulting in phenotypes ranging in severity from L2 arrest (when both maternal and zygotic activities are removed at 25°), to sterile Multivulva (when only zygotic activity is removed at 25°), to sterile non-Multivulva (when both maternal and zygotic activities are removed at 15°), to wild-type/class B SynMuv (when only zygotic activity is removed at 15°). We also show that LIN-13 is a nuclear protein that contains multiple zinc fingers and a motif, LXCXE, that has been implicated in Rb binding. These results together suggest a role for LIN-13 in Rb-mediated repression of vulval fates.
Long Microsatellite Alleles inDrosophila melanogasterHave a Downward Mutation Bias and Short Persistence Times, Which Cause Their Genome-Wide Underrepresentation
Authors: Harr Bettina , Schlötterer Christian 
Published: April 2021

AbstractMicrosatellites are short tandemly repeated DNA sequence motifs that are highly variable in most organisms. In contrast to mammals, long microsatellites (&gt;15 repeats) are extremely rare in the Drosophila melanogaster genome. To investigate this paucity of long microsatellites in Drosophila, we studied 19 loci with exceptionally long microsatellite alleles. Inter- and intraspecific analysis showed that long microsatellite alleles arose in D. melanogaster only very recently. This lack of old alleles with many repeats indicated that long microsatellite alleles have short persistence times. The size distribution of microsatellite mutations in mutation-accumulation lines suggests that long alleles have a mutation bias toward a reduction in the number of repeat units. This bias causes the short persistence times of long microsatellite alleles. We propose that species-specific, size-dependent mutation spectra of microsatellite alleles may provide a general mechanism to account for the observed differences in microsatellite length between species.
Genetic Analysis of Isometric Growth Control Mechanisms in the Zebrafish Caudal Fin
Authors: Iovine M Kathryn , Johnson Stephen L 
Published: April 2021

Abstract
The body and fins of the zebrafish grow rapidly as juveniles and slower as they reach maturation. Throughout their lives, the fins grow isometrically with respect to the body. Growth of individual fin rays is achieved by the distal addition of bony segments. We have investigated the genetic control of mechanisms that initiate new segments or control size of newly initiated segments. We find that both segment initiation and segment length are regulated during fin growth in wild-type fish. We examined the growth properties of lof and sof fin length mutants for effects on the number and length of fin ray segments. Fins of lof mutants continue to grow rapidly even after wild-type fin growth slows, resulting in positive allometric growth and additional fin ray segments. We suggest that lof mutants bypass mechanisms that limit segment initiation. Isometric growth is retained in sof mutants, resulting in shorter fins one-half the length of wild-type fins. The primary defect in sof mutants is that fin ray segments are shorter than wild-type segments, although segment number is also diminished. Double mutants for sof;lof reveal that segment length and segment number are controlled in different pathways. Our findings suggest that the lof gene product regulates segment initiation and the sof gene product regulates segment length.
Through a Glass, Darkly: Reflections of Mutation From lacI Transgenic Mice
Authors: Stuart Gregory R , Glickman Barry W 
Published: April 2021

Abstract
The study of mutational frequency (Mf) and specificity in aging Big Blue lacI transgenic mice provides a unique opportunity to determine mutation rates (MR) in vivo in different tissues. We found that MR are not static, but rather, vary with the age or developmental stage of the tissue. Although Mf increase more rapidly early in life, MR are actually lower in younger animals than in older animals. For example, we estimate that the changes in Mf are 4.9 × 10−8 and 1.1 × 10−8 mutations/base pair/month in the livers of younger mice (&lt;1.5 months old) and older mice (≥1.5 months old), respectively (a 4-fold decrease), and that the MR are 3.9 × 10−9 and 1.3 × 10−7 mutations/base pair/cell division, respectively (~30-fold increase). These data also permit an estimate of the MR of GC → AT transitions occurring at 5′-CpG-3′ (CpG) dinucleotide sequences. Subsequently, the contribution of these transitions to age-related demethylation of genomic DNA can be evaluated. Finally, to better understand the origin of observed Mf, we consider the contribution of various factors, including DNA damage and repair, by constructing a descriptive mutational model. We then apply this model to estimate the efficiency of repair of deaminated 5-methylcytosine nucleosides occurring at CpG dinucleotide sequences, as well as the influence of the Msh2−/− DNA repair defect on overall DNA repair efficiency in Big Blue mice. We conclude that even slight changes in DNA repair efficiency could lead to significant increases in mutation frequencies, potentially contributing significantly to human pathogenesis, including cancer.
Combined Analyses of Data From Quantitative Trait Loci Mapping Studies: Chromosome 4 Effects on Porcine Growth and Fatness
Authors: Walling Grant A , Visscher Peter M , Andersson Leif , Rothschild Max F , Wang Lizhen , Moser Gerhard , Groenen Martien A M , Bidanel Jean-Pierre , Cepica Stanislav , Archibald Alan L , Geldermann Hermann , de Koning Dirk J , Milan Denis , Haley Chris S 
Published: April 2021

Abstract
For many species several similar QTL mapping populations have been produced and analyzed independently. Joint analysis of such data could be used to increase power to detect QTL and evaluate population differences. In this study, data were collated on almost 3000 pigs from seven different F2 crosses between Western commercial breeds and either the European wild boar or the Chinese Meishan breed. Genotypes were available for 31 markers on chromosome 4 (on average 8.3 markers per population). Data from three traits common to all populations (birth weight, mean backfat depth at slaughter or end of test, and growth rate from birth to slaughter or end of test) were analyzed for individual populations and jointly. A QTL influencing birth weight was detected in one individual population and in the combined data, with no significant interaction of the QTL effect with population. A QTL affecting backfat that had a significantly greater effect in wild boar than in Meishan crosses was detected. Some evidence for a QTL affecting growth rate was detected in all populations, with no significant differences between populations. This study is the largest F2 QTL analysis achieved in a livestock species and demonstrates the potential of joint analysis.
The narrow sheath Duplicate Genes: Sectors of Dual Aneuploidy Reveal Ancestrally Conserved Gene Functions During Maize Leaf Development
Authors: Scanlon Michael J , Chen K David , McKnight Calvin C 
Published: April 2021

Abstract
The narrow sheath mutant of maize displays a leaf and plant stature phenotype controlled by the duplicate factor mutations narrow sheath1 and narrow sheath2. Mutant leaves fail to develop a lateral domain that includes the leaf margins. Genetic data are presented to show that the narrow sheath mutations map to duplicated chromosomal regions, reflecting an ancestral duplication of the maize genome. Genetic and cytogenetic evidence indicates that the original mutation at narrow sheath2 is associated with a chromosomal inversion on the long arm of chromosome 4. Meristematic sectors of dual aneuploidy were generated, producing plants genetically mosaic for NARROW SHEATH function. These mosaic plants exhibited characteristic half-plant phenotypes, in which leaves from one side of the plant were of nonmutant morphology and leaves from the opposite side were of narrow sheath mutant phenotype. The data suggest that the narrow sheath duplicate genes may perform ancestrally conserved, redundant functions in the development of a lateral domain in the maize leaf.
Cats as an Aid to Teaching Genetics
Authors: Christensen Alan C 
Published: April 2021

Abstract
I have used an exercise involving domestic cats in the General Genetics course at the University of Nebraska-Lincoln for the past 5 years. Using a coherent set of traits in an organism familiar to the students makes it easy to illustrate principles of transmission and population genetics. The one-semester course consists primarily of sophomores and juniors who have either taken a one-semester introductory biology course, a one-semester cell biology course, or have a strong high school biology background. The students are given a handout and asked to determine the genotype at seven unlinked loci of at least one cat. To fill out the form, the students have to grasp such concepts as dominance, incomplete dominance, temperature-sensitive mutations, epistatic interactions, sex linkage, and variable expressivity. Completing the form reinforces these concepts as they observe the cat's phenotype and fill in the genotype. I then analyze the collected data and use it in my lectures on population genetics to illustrate the Hardy-Weinberg equilibrium, calculate allele frequencies, and use statistics. This allows the students to look at population genetics in a very positive light and provides concrete examples of some often misunderstood principles.
Booms and Busts in Housing Market and Health Outcomes for Older Americans
Authors: Yue Dahai , Ponce Ninez A 
Published: April 2021

Abstract

Background and Objectives
The US housing market has experienced considerable fluctuations over the last decades. This study aimed to investigate the impacts of housing price dynamics on physical health, mental health, and health-related behaviors for older American outright owners, mortgaged owners, and renters.

Research Design and Methods
We drew longitudinal data from the 1992–2016 Health and Retirement Study and merged it to the 5-digit zip code–level Housing Price Index. The analytic sample comprised 34 182 persons and 174 759 person-year observations. We used a fixed-effects model to identify the health impacts of housing price dynamics separately for outright owners, mortgaged owners, and renters.

Results
A 100% increase in Housing Price Index was associated with a 2.81 and 3.50 percentage points (pp) increase in the probability of reporting excellent/very good/good health status for mortgage owners and renters, respectively. It was also related to a lower likelihood of obesity (1.82 pp) for outright owners and a lesser chance of obesity (2.85 pp) and smoking (3.03 pp) for renters. All of these relationships were statistically significant (p &lt; .05). Renters also experienced significantly decreased depression scores (−0.24), measured by the Center for Epidemiologic Studies—Depression scale, associated with the same housing price changes.

Discussion and Implications
Housing price dynamics have significant health impacts, and renters are more sensitive to fluctuations in the housing market. Our study rules out the wealth effect as the mechanism through which changes in housing prices affect older adults’ health. Our findings may inform policies to promote older adults’ health by investing in local area amenities and improving socioeconomic conditions.
Impact of gender on 10-year outcome after coronary artery bypass grafting
Authors: Barili Fabio , D’Errigo Paola , Rosato Stefano , Biancari Fausto , Forti Marco , Pagano Eva , Parolari Alessandro , Gellini Mara , Badoni Gabriella , Seccareccia Fulvia 
Published: April 2021

Abstract

OBJECTIVES
Our goal was to evaluate the impact of gender on the 10-year outcome of patients after isolated coronary artery bypass grafting (CABG) included in the Italian nationwide PRedictIng long-term Outcomes afteR Isolated coronary arTery bypass surgery (PRIORITY) study.

METHODS
The PRIORITY project was designed to evaluate the long-term outcomes of patients who underwent CABG and were included in 2 prospective multicentre cohort studies. The primary end point of this analysis was major adverse cardiac and cerebrovascular events. Baseline differences between the study groups were balanced with propensity score matching and inverse probability of treatment. Time to events was analysed using Cox regression and competing risk analysis.

RESULTS
The study population comprised 10 989 patients who underwent isolated CABG (women 19.6%). Propensity score matching produced 1898 well-balanced pairs. The hazard of major adverse cardiac and cerebrovascular event was higher in women compared to men [adjusted hazard ratio (HR) 1.13, 95% confidence interval (CI) 1.03–1.23; P = 0.009]. The incidence of major adverse cardiac and cerebrovascular event in women was significantly higher at 1 year (HR 1.31, 95% CI 1.11–1.55; P &lt; 0.001) and after 1 year (HR 1.11, 95% CI 1.00–1.24; P = 0.05). Mortality at 10 years in the matched groups was comparable (HR 1.04, 95% CI 0.93–1.16; P = 0.531). Women have significantly a higher 10-year risk of myocardial infarction (adjusted HR 1.40, 95% CI 1.17–1.68; P = 0.002) and percutaneous coronary intervention (adjusted HR 1.32, 95% CI 1.10–1.59; P = 0.003).

CONCLUSIONS
The present study documented an excess of non-fatal cardiac events after CABG among women despite comparable 10-year survival with men. These findings suggest that studies investigating measures of tertiary prevention are needed to decrease the risk of adverse cardiovascular events among women.
Deformation Principle and André motives of Projective Hyperkähler Manifolds
Authors: Soldatenkov Andrey 
Published: April 2021

Abstract
Let $X_1$ and $X_2$ be deformation equivalent projective hyperkähler manifolds. We prove that the André motive of $X_1$ is abelian if and only if the André motive of $X_2$ is abelian. Applying this to manifolds of $\mbox {K3}^{[n]}$, generalized Kummer and OG6 deformation types, we deduce that their André motives are abelian. As a consequence, we prove that all Hodge classes in arbitrary degree on such manifolds are absolute. We discuss applications to the Mumford–Tate conjecture, showing in particular that it holds for even degree cohomology of such manifolds.
Fifty Shades of Terrorist Credit-Taking: A Review of the Existing Scholarship on Terrorist Credit-Taking
Authors: Hansen Tanja Marie 
Published: April 2021

Abstract
The consistently low credit-taking rates, 16 percent in 2016 (Global Terrorism Database), continue to challenge the understanding of terrorism as “propaganda of the deed” twenty years after researchers initially pointed out the conundrum. While providing an overview and evaluation of the limited existing literature on credit-taking, this paper draws attention to three core problems in the current literature on terrorist credit-taking, which may have led the low credit-taking rates to appear more puzzling than is due. First, the available explanations struggle to find corroboration when empirically tested and many also show theoretical shortcomings with strong unspoken assumptions and unclear predictions of credit-taking behavior. Second, data structure and data availability unnecessarily narrow our academic understanding of credit-taking. Finally, theories focused on group characteristics such as religious motivation or state sponsorship suffer from severe issues of sample bias due to unintended selection on the dependent variable. The paper concludes with suggestions for future research less prone to the problematic issues identified in the article. A re-orientation toward a less restrictive and more fine-grained understanding of credit-taking is advised.
Continuous monitoring in COVID-19 care: a retrospective study in time of crisis
Authors: de Ree Roy , Willemsen Jorn , te Grotenhuis Gilbert , de Ree Rick , Kolkert Joé , Peppelman Malou 
Published: April 2021

Abstract

Background
A new monitoring system was implemented to support nursing staff and physicians on the COVID-19 ward. This system was designed to remotely monitor vital signs, to calculate an automated Early Warning Score, and to help identify patients at risk of deterioration.

Methods
Hospitalized patients who tested positive for SARS-CoV-2 were connected to 2 wireless sensors measuring vital signs. Patients were divided into 2 groups based on the occurrence of adverse events during hospitalization. Heart and respiratory rate were monitored continuously and an automated EWS was calculated every 5 minutes. Data were compared between groups.

Results
Prior to the occurrence of adverse events, significantly higher median heart and respiration rate and significantly lower median SPO2 values were observed. Mean and median automated EWS were significantly higher in patients with an adverse event.

Conclusion
Continuous monitoring systems might help to detect clinical deterioration in COVID-19 patients at an earlier stage.