bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extragenic suppressors of Schizosaccharomyces pombe rad9 mutations uncouple radioresistance and hydroxyurea sensitivity from cell cycle checkpoint control.
Authors: Lieberman H B 
Published: April 2021

Abstract
Schizosaccharomyces pombe cells that contain a mutation within rad9 are sensitive to ionizing radiation, UV light and hydroxyurea, relative to wild-type strains. In addition, the mutants are moderately hypomutable by UV and unable to delay initiation of mitosis after treatment with radiation or hydroxyurea. Three radioresistant derivatives of rad9::ura4 cells were isolated, and each contained a single unique extragenic suppressor responsible for the acquired resistance. The suppressor loci also conferred radioresistance upon cells containing rad9-192, which differs from rad9+ by a single base pair change. The suppressors additionally enhanced the radioresistance of cells containing rad3-136, a mutation that leads to phenotypes similar to those mediated by rad9::ura4. None of the derivatives of rad9::ura4 cells recovered the ability to delay cycling in G2 after exposure to ionizing radiation or UV light. All three suppressor derivatives, relative to the parental rad9::ura4 strain, also exhibited a moderate increase in resistance to the DNA replication inhibitor hydroxyurea without gaining the ability to stop progression into mitosis despite the inhibition of DNA synthesis. Results are discussed in terms of models to explain the putative role of rad9 and the suppressor genes in promoting radioresistance and mediating checkpoint controls responsive to DNA damage or incomplete DNA replication.
Genetic analysis of the colicin V secretion pathway.
Authors: Zhang L H , Fath M J , Mahanty H K , Tai P C , Kolter R 
Published: April 2021

Abstract
Colicin V (ColV) is peptide antibiotic secreted by Escherichia coli through a dedicated exporter composed of three proteins, CvaA, CvaB, and TolC. ColV secretion is independent of the E. coli general secretory pathway (Sec) but requires an N-terminal export signal specific for the CvaAB/TolC exporter. ColV secretion was characterized using genetic and biochemical methods. When the ColV N-terminal extension is replaced with the OmpA signal sequence, the Sec system can localize ColV to the periplasm. Periplasmic ColV is lethal to cells lacking the ColV immunity protein, Cvi. Based on this result, a genetic assay was designed to monitor for the presence of periplasmic ColV during normal CvaAB/TolC mediated secretion. Results indicate that low levels of ColV may be present in the periplasm during secretion. Precursor and mature ColV were also characterized from the wild-type system and in various exporter mutant backgrounds using immunoprecipitation. ColV processing is rapid in wild-type cells, and CvaA and CvaB are critical for processing to occur. In contrast, processing occurs normally, albeit more slowly, in a TolC mutant.
5 S rRNA is involved in fidelity of translational reading frame.
Authors: Dinman J D , Wickner R B 
Published: April 2021

Abstract
Chromosomal mutants (maintenance of frame = mof) in which the efficiency of -1 ribosomal frameshifting is increased can be isolated using constructs in which lacZ expression is dependent upon a -1 shift of reading frame. We isolate a new mof mutation, mof9, in Saccharomyces cerevisiae and show that it is complemented by both single and multi-copy 5 S rDNA clones. Two independent insertion mutations in the rDNA locus (rDNA::LEU2 and rDNA::URA3) also display the Mof- phenotype and are also complemented by single and multi-copy 5 S rDNA clones. Mutant 5 S rRNAs expressed from a plasmid as 20-50% of total 5 S rRNA in a wild-type host also induced the Mof- phenotype. The increase in frameshifting is greatest when the lacZ reporter gene is expressed on a high copy, episomal vector. No differences were found in 5 S rRNA copy number or electrophoretic mobilities in mof9 strains. Both mof9 and rDNA::LEU2 increase the efficiency of +1 frameshifting as well but have no effect on readthrough of UAG or UAA termination codons, indicating that not all translational specificity is affected. These data suggest a role for 5 S rRNA in the maintenance of frame in translation.
Functional Interaction of CCR4-NOT Proteins With TATAA-Binding Protein (TBP) and Its Associated Factors in Yeast
Authors: Badarinarayana Vasudeo , Chiang Yueh-Chin , Denis Clyde L 
Published: April 2021

Abstract
The CCR4-NOT transcriptional regulatory complex affects expression of a number of genes both positively and negatively. We report here that components of the CCR4-NOT complex functionally and physically interact with TBP and TBP-associated factors. First, mutations in CCR4-NOT components suppressed the his4-912δ insertion in a manner similar to that observed for the defective TBP allele spt15-122. Second, using modified HIS3 promoter derivatives containing specific mutations within the TATA sequence, we found that the NOT proteins were general repressors that disrupt TBP function irrespective of the DNA sequence. Third, increasing the dosage of NOT1 specifically inhibited the ability of spt15-122 to suppress the his4-912δ insertion but did not affect the Spt− phenotype of spt3 or spt10 at this locus. Fourth, spt3, spt8, and spt15-21 alleles (all involved in affecting interaction of SPT3 with TBP) suppressed ccr4 and caf1 defects. Finally, we show that NOT2 and NOT5 can be immunoprecipitated by TBP. NOT5 was subsequently shown to associate with TBP and TAFs and this association was dependent on the integrity of TFIID. These genetic and physical interactions indicate that one role of the CCR4-NOT proteins is to inhibit functional TBP-DNA interactions, perhaps by interacting with and modulating the function of TFIID.
Genetic Analyses ofSchizosaccharomyces pombe dna2+ Reveal That Dna2 Plays an Essential Role in Okazaki Fragment Metabolism
Authors: Kang Ho-Young , Choi Eunjoo , Bae Sung-Ho , Lee Kyoung-Hwa , Gim Byung-Soo , Kim Hee-Dai , Park Chankyu , MacNeill Stuart A , Seo Yeon-Soo 
Published: April 2021

AbstractIn this report, we investigated the phenotypes caused by temperature-sensitive (ts) mutant alleles of dna2+ of Schizosaccharomyces pombe, a homologue of DNA2 of budding yeast, in an attempt to further define its function in vivo with respect to lagging-strand synthesis during the S-phase of the cell cycle. At the restrictive temperature, dna2 (ts) cells arrested at late S-phase but were unaffected in bulk DNA synthesis. Moreover, they exhibited aberrant mitosis when combined with checkpoint mutations, in keeping with a role for Dna2 in Okazaki fragment maturation. Similarly, spores in which dna2+ was disrupted duplicated their DNA content during germination and also arrested at late S-phase. Inactivation of dna2+ led to chromosome fragmentation strikingly similar to that seen when cdc17+, the DNA ligase I gene, is inactivated. The temperature-dependent lethality of dna2 (ts) mutants was suppressed by overexpression of genes encoding subunits of polymerase δ (cdc1+ and cdc27+), DNA ligase I (cdc17+), and Fen-1 (rad2+). Each of these gene products plays a role in the elongation or maturation of Okazaki fragments. Moreover, they all interacted with S. pombe Dna2 in a yeast two-hybrid assay, albeit to different extents. On the basis of these results, we conclude that dna2+ plays a direct role in the Okazaki fragment elongation and maturation. We propose that dna2+ acts as a central protein to form a complex with other proteins required to coordinate the multienzyme process for Okazaki fragment elongation and maturation.
Joint Effects of Natural Selection and Recombination on Gene Flow Between Drosophila ananassae Populations
Authors: Chen Ying , Marsh Brenda J , Stephan Wolfgang 
Published: April 2021

Abstract
We estimated DNA sequence variation in a 5.7-kb fragment of the furrowed (fw) gene region within and between four populations of Drosophila ananassae; fw is located in a chromosomal region of very low recombination. We analyzed gene flow between these four populations along a latitudinal transect on the Indian subcontinent: two populations from southern, subtropical areas (Hyderabad, India, and Sri Lanka) and two from more temperate zones in the north (Nepal and Burma). Furthermore, we compared the pattern of differentiation at fw with published data from Om(1D), a gene located in a region of normal recombination. While differentiation at Om(1D) shows an isolation-by-distance effect, at fw the pattern of differentiation is quite different such that the frequencies of single nucleotide polymorphisms are homogenized over extended geographic regions (i.e., among the two populations of the northern species range from Burma and Nepal as well as among the two southern populations from India and Sri Lanka), but strongly differentiated between the northern and southern populations. To examine these differences in the patterns of variation and differentiation between the Om(1D) and fw gene regions, we determine the critical values of our previously proposed test of the background selection hypothesis (henceforth called FST test). Using these results, we show that the pattern of differentiation at fw may be inconsistent with the background selection model. The data depart from this model in a direction that is compatible with the occurrence of recent selective sweeps in the northern as well as southern populations.
Chromosomal Position Effects Reveal Different cis-Acting Requirements for rDNA Transcription and Sex Chromosome Pairing in Drosophila melanogaster
Authors: Briscoe Albert , Tomkiel John E 
Published: April 2021

Abstract
In Drosophila melanogaster, the rDNA loci function in ribosome biogenesis and nucleolar formation and also as sex chromosome pairing sites in male meiosis. These activities are not dependent on the heterochromatic location of the rDNA, because euchromatic transgenes are competent to form nucleoli and restore pairing to rDNA-deficient X chromosomes. These transgene studies, however, do not address requirements for the function of the endogenous rDNA loci within the heterochromatin. Here we describe two chromosome rearrangements that disrupt rDNA functions. Both rearrangements are translocations that cause an extreme bobbed visible phenotype and XY nondisjunction and meiotic drive in males. However, neither rearrangement interacts with a specific Y chromosome, Ymal+, that induces male sterility in combination with rDNA deletions. Molecular studies show that the translocations are not associated with gross rearrangements of the rDNA repeat arrays. Rather, suppression of the bobbed phenotypes by Y heterochromatin suggests that decreased rDNA function is caused by a chromosomal position effect. While both translocations affect rDNA transcription, only one disrupts meiotic XY pairing, indicating that there are different cis-acting requirements for rDNA transcription and rDNA-mediated meiotic pairing.
Nucleotide Polymorphism at the RpII215 Gene in Drosophila subobscura: Weak Selection on Synonymous Mutations
Authors: Llopart Ana , Aguadé Montserrat 
Published: April 2021

Abstract
Nucleotide variation in an 8.1-kb fragment encompassing the RpII215 gene, which encodes the largest subunit of the RNA polymerase II complex, is analyzed in a sample of 11 chromosomes from a natural population of Drosophila subobscura. No amino acid polymorphism was detected among the 157 segregating sites. The observed numbers of preferred and unpreferred derived synonymous mutations can be explained by neutral mutational processes. In contrast, preferred mutations segregate at significantly higher frequency than unpreferred mutations, suggesting the action of natural selection. The polymorphism to divergence ratio is different for preferred and unpreferred changes, in agreement with their beneficial and deleterious effects on fitness, respectively. Preferred and unpreferred codons are nonrandomly distributed in the RpII215 gene, leading to a heterogeneous distribution of polymorphic to fixed synonymous differences across this coding region. This intragenic variation of the polymorphism/divergence ratio cannot be explained by different patterns of gene expression, mutation, or recombination rates, and therefore it indicates that selection coefficients for synonymous mutations can vary extensively across a coding region. The application of nucleotide composition stationarity tests in coding and flanking noncoding regions, assumed to behave neutrally, allows the detection of the action of natural selection when stationarity holds in the noncoding region.
Cellular Consequences in the Brain and Liver of Age-Specific Selection for Rate of Development in Mice
Authors: Atchley William R , Wei Rong , Crenshaw Pamela 
Published: April 2021

AbstractChanges in cell number (hyperplasia) and cell size (hypertrophy) in the brain and liver are described for mice subjected to 24 generations of age-specific restricted index selection for rate of development in body weight. One selection treatment (E) altered rate of development between birth and 10 days of age, another treatment (L) involved changes in rate of development between 28 and 56 days of age, while a third control treatment (C) involved random selection. Each selection treatment was replicated three times. These age-specific selection treatments focused on intervals during ontogeny when different developmental processes (hypertrophy or hyperplasia) were more predominant in the control of growth. Significant changes in brain and liver weight occurred at both 28 and 70 days of age. Early selection (E) generated significant changes in the number of cells in the brain while later selection (L) had no effect since the brain had stopped growth before selection was initiated. For the liver, early and late selection produced significant effects on both cell number and cell size. These results describe the dynamic and multidimensional aspects of selection in terms of its ability to alter different cellular and developmental components of complex morphological traits.
Bayesian Mapping of Quantitative Trait Loci for Complex Binary Traits
Authors: Yi Nengjun , Xu Shizhong 
Published: April 2021

Abstract
A complex binary trait is a character that has a dichotomous expression but with a polygenic genetic background. Mapping quantitative trait loci (QTL) for such traits is difficult because of the discrete nature and the reduced variation in the phenotypic distribution. Bayesian statistics are proved to be a powerful tool for solving complicated genetic problems, such as multiple QTL with nonadditive effects, and have been successfully applied to QTL mapping for continuous traits. In this study, we show that Bayesian statistics are particularly useful for mapping QTL for complex binary traits. We model the binary trait under the classical threshold model of quantitative genetics. The Bayesian mapping statistics are developed on the basis of the idea of data augmentation. This treatment allows an easy way to generate the value of a hypothetical underlying variable (called the liability) and a threshold, which in turn allow the use of existing Bayesian statistics. The reversible jump Markov chain Monte Carlo algorithm is used to simulate the posterior samples of all unknowns, including the number of QTL, the locations and effects of identified QTL, genotypes of each individual at both the QTL and markers, and eventually the liability of each individual. The Bayesian mapping ends with an estimation of the joint posterior distribution of the number of QTL and the locations and effects of the identified QTL. Utilities of the method are demonstrated using a simulated outbred full-sib family. A computer program written in FORTRAN language is freely available on request.
Multipoint Mapping of Viability and Segregation Distorting Loci Using Molecular Markers
Authors: Vogl Claus , Xu Shizhong 
Published: April 2021

Abstract
In line-crossing experiments, deviations from Mendelian segregation ratios are usually observed for some markers. We hypothesize that these deviations are caused by one or more segregation-distorting loci (SDL) linked to the markers. We develop both a maximum-likelihood (ML) method and a Bayesian method to map SDL using molecular markers. The ML mapping is implemented via an EM algorithm and the Bayesian method is performed via the Markov chain Monte Carlo (MCMC). The Bayesian mapping is computationally more intensive than the ML mapping but can handle more complicated models such as multiple SDL and variable number of SDL. Both methods are applied to a set of simulated data and real data from a cross of two Scots pine trees.
Zygotic Associations and Multilocus Statistics in a Nonequilibrium Diploid Population
Authors: Yang Rong-Cai 
Published: April 2021

AbstractThe usual approach to characterizing and estimating multilocus associations in a diploid population assumes that the population is in Hardy-Weinberg equilibrium. The purpose of this study is to develop a set of summary statistics that can be used to characterize and estimate the multilocus associations in a nonequilibrium population. The concept of “zygotic associations” is first expanded to facilitate the development. The summary statistics are calculated using the distribution of a random variable, the number of heterozygous loci (K) found in diploid individuals in the population. In particular, the variance of K consists of single-locus and multilocus components with the latter being the sum of zygotic associations between pairs of loci. Simulation results show that the multilocus associations in the variance of K are detectable in a sample of moderate size (≥30) when the sum of all pairwise zygotic associations is greater than zero and when gene frequency is intermediate. The method presented here is a generalization of the well-known development for the Hardy-Weinberg equilibrium population and thus may be of more general use in elucidating the multilocus organizations in nonequilibrium and equilibrium populations.
A Unique Academic–Government Collaboration Yields First Report of Detailed Habitat Description for Haemaphysalis longicornis (Ixodida: Ixodidae) in Madison County, KY
Authors: Vogt J T , Allen B D , Paulsen D , Trout Fryxell R T 
Published: April 2021

Abstract
Haemaphysalis longicornis Neumann, Asian longhorned tick, was collected in Madison County, Kentucky, United States as part of an ongoing collaborative-tick surveillance project. This is the first collection of this invasive tick that includes ancillary data on habitat and landscape features derived from the USDA Forest Service, Forest Inventory and Analysis program.
HDAC9 exacerbates myocardial infarction via inactivating Nrf2 pathways
Authors: Liu Fan , Di Yali , Ma Wei , Kang Xiaoli , Li Xia , Ji Zheng 
Published: April 2021

Abstract

Objectives
Myocardial infarction (MI) is the leading cause of death worldwide. Histone deacetylases (HDACs) collectively participate in the initiation and progression of heart diseases, including MI. This study aimed to investigate the roles of histone deacetylase 9 (HDAC9) in the development of MI.

Methods
In vivo and in vitro assays were conducted to determine the effects of HDAC9 on heart function and MI. qRT-PCR was applied to determine the mRNA level. Western blot was performed for protein expression. Immunofluorescence was applied to detect the fluorescence tensity of Myog and Myod. CCK-8, flow cytometry and transwell assays were carried out for function analysis.

Key findings
HDAC9 was upregulated in MI models in vivo and in vitro. Downregulated HDAC9 modulated the changes in left ventricle ejection fraction (LVEF), left ventricle fractional shortening (LVFS) and left ventricular end-diastolic diameter (LVEDD) and left ventricular end-systolic diameter (LVESD). Moreover, HDAC9 knockdown activated NFE2-related factor 2 (Nrf2)/Keap1/HO-1 pathways. Additionally, HDAC9/Nrf2 axis modulated the proliferation, apoptosis and myogenesis of cardiomyocytes.

Conclusions
Taken together, HDAC9 knockout induced the activation of Nrf2 and protected heart from MI injury. Thus, the HDAC9/Nrf2 axis can be a novel marker for the treatment of MI.
Slow control and monitoring system at the JSNS2
Authors: Park J S , Ajimura S , Botran M , Choi J H , Choi J W , Cheoun M K , Dodo T , Furuta H , Goh J , Harada M , Hasegawa S , Hino Y , Hiraiwa T , Jang H I , Jang J S , Jang M C , Jeon H , Jeon S , Joo K K , Jordan J R , Jung D E , Kang S K , Kasugai Y , Kawasaki T , Kim E J , Kim J Y , Kim S B , Kim W , Konno T , Lee D H , Lee S , Lim I T , Marzec E , Maruyama T , Meigo S , Monjushiro S , Moon D H , Nakano T , Niiyama M , Nishikawa K , Nomachi M , Pac M Y , Peeters S J M , Ray H , Roellinghoff G , Rott C , Sakai K , Sakamoto S , Shima T , Shin C D , Spitz J , Stancu I , Sugaya Y , Suekane F , Suzuya K , Taira M , Ujiie R , Yeh M , Yeo I S , Yoo C , Yu I , Zohaib A 
Published: April 2021

Abstract
The Sterile Neutrino Search at the J-PARC Spallation Neutron Source (JSNS$^2$) experiment aims to search for sterile neutrino oscillations using a neutrino beam from muon decays at rest. The JSNS$^2$ detector contains 17 tons of 0.1$\%$ gadolinium (Gd) loaded liquid scintillator (LS) as a neutrino target. Detector construction was completed in the spring of 2020. A slow control and monitoring system (SCMS) was implemented for reliable control and quick monitoring of the detector operational status and environmental conditions. It issues an alarm if any of the monitored parameters exceed a preset acceptable range. The SCMS monitors the high voltage of the photomultiplier tubes, the LS level in the detector, possible LS overflow and leakage, the temperature and air pressure in the detector, the humidity of the experimental hall, and the LS flow rate during filling and extraction. An initial 10 days of data-taking with a neutrino beam was done following a successful commissioning of the detector and SCMS in 2020 June. In this paper, we present a description of the assembly and installation of the SCMS and its performance.
Prevalence and Risk Factors for Intraductal Papillary Mucinous Neoplasm in Patients With Chronic Kidney Disease
Authors: Shah Rushikesh , Mulki Ramzi , Lamm Vladimir , Kapil Neil , Patel Vaishali , Chawla Saurabh , Cai Qiang , Willingham Field F. , Keilin Steven 
Published: April 2021

Objectives
The exact prevalence for intraductal papillary mucinous neoplasm (IPMN) in patients with chronic kidney disease (CKD) remains unknown. In this single-center case-control study, we aimed to study the prevalence and risk factors for IPMN in patients with CKD.

Methods
We performed a retrospective case-control study comparing patients with and without CKD who had magnetic resonance imaging of the abdomen performed between January 2018 and December 2018. Patient demographic, clinical, and imaging metrics were extracted from chart review. The prevalence of IPMN was compared between the 2 groups.

Results
A total of 800 patient charts were reviewed. There were 400 patients with CKD compared with an age-matched control group of 400 patients without CKD. The total prevalence of IPMN in patients with CKD was 13.7% (55/400) compared with 7.8% (29/400; P = 0.002) in non-CKD patients. The prevalence of diabetes mellitus was significantly higher in the CKD group (41% vs 14%, P = 0.0001). The percentage of patients consuming alcohol was significantly higher in the non-CKD group (23% vs 35%, P = 0.002).

Conclusions
Patients with CKD have a significantly higher prevalence of IPMN compared with non-CKD patients. Larger population-based studies are needed to confirm these findings.