bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drebrin attenuates atherosclerosis by limiting smooth muscle cell transdifferentiation
Authors: Wu Jiao-Hui , Zhang Lisheng , Nepliouev Igor , Brian Leigh , Huang Taiqin , Snow Kamie P , Schickling Brandon M , Hauser Elizabeth R , Miller Francis J , Freedman Neil J , Stiber Jonathan A 
Published: April 2021

Abstract

Aims
The F-actin-binding protein Drebrin inhibits smooth muscle cell (SMC) migration, proliferation, and pro-inflammatory signalling. Therefore, we tested the hypothesis that Drebrin constrains atherosclerosis.

Methods and results
SM22-Cre+/Dbnflox/flox/Ldlr−/− (SMC-Dbn−/−/Ldlr−/−) and control mice (SM22-Cre+/Ldlr−/−, Dbnflox/flox/Ldlr−/−, and Ldlr−/−) were fed a western diet for 14–20 weeks. Brachiocephalic arteries of SMC-Dbn −/−/Ldlr−/− mice exhibited 1.5- or 1.8-fold greater cross-sectional lesion area than control mice at 14 or 20 weeks, respectively. Aortic atherosclerotic lesion surface area was 1.2-fold greater in SMC-Dbn−/−/Ldlr−/− mice. SMC-Dbn−/−/Ldlr−/− lesions comprised necrotic cores that were two-fold greater in size than those of control mice. Consistent with their bigger necrotic core size, lesions in SMC-Dbn−/− arteries also showed more transdifferentiation of SMCs to macrophage-like cells: 1.5- to 2.5-fold greater, assessed with BODIPY or with CD68, respectively. In vitro data were concordant: Dbn−/− SMCs had 1.7-fold higher levels of KLF4 and transdifferentiated to macrophage-like cells more readily than Dbnflox/flox SMCs upon cholesterol loading, as evidenced by greater up-regulation of CD68 and galectin-3. Adenovirally mediated Drebrin rescue produced equivalent levels of macrophage-like transdifferentiation in Dbn−/− and Dbnflox/flox SMCs. During early atherogenesis, SMC-Dbn−/−/Ldlr−/− aortas demonstrated 1.6-fold higher levels of reactive oxygen species than control mouse aortas. The 1.8-fold higher levels of Nox1 in Dbn−/− SMCs were reduced to WT levels with KLF4 silencing. Inhibition of Nox1 chemically or with siRNA produced equivalent levels of macrophage-like transdifferentiation in Dbn−/− and Dbnflox/flox SMCs.

Conclusion
We conclude that SMC Drebrin limits atherosclerosis by constraining SMC Nox1 activity and SMC transdifferentiation to macrophage-like cells.
Transcriptomic Signatures of Ageing Vary in Solitary and Social Forms of an Orchid Bee
Authors: Séguret Alice , Stolle Eckart , Fleites-Ayil Fernando A , Quezada-Euán José Javier G , Hartfelder Klaus , Meusemann Karen , Harrison Mark C , Soro Antonella , Paxton Robert J 
Published: April 2021

AbstractEusocial insect queens are remarkable in their ability to maximize both fecundity and longevity, thus escaping the typical trade-off between these two traits. Several mechanisms have been proposed to underlie the remolding of the trade-off, such as reshaping of the juvenile hormone (JH) pathway, or caste-specific susceptibility to oxidative stress. However, it remains a challenge to disentangle the molecular mechanisms underlying the remolding of the trade-off in eusocial insects from caste-specific physiological attributes that have subsequently arisen. The socially polymorphic orchid bee Euglossa viridissima represents an excellent model to address the role of sociality per se in longevity as it allows direct comparisons of solitary and social individuals within a common genetic background. We investigated gene expression and JH levels in young and old bees from both solitary and social nests. We found 902 genes to be differentially expressed with age in solitary females, including genes involved in oxidative stress, versus only 100 genes in social dominant females, and 13 genes in subordinate females. A weighted gene coexpression network analysis further highlights pathways related to ageing in this species, including the target of rapamycin pathway. Eleven genes involved in translation, apoptosis, and DNA repair show concurrent age-related expression changes in solitary but not in social females, representing potential differences based on social status. JH titers did not vary with age or social status. Our results represent an important step in understanding the proximate mechanisms underlying the remodeling of the fecundity/longevity trade-off that accompanies the evolutionary transition from solitary life to eusociality.
The Codon Usage Code for Cotranslational Folding of Viral Capsids
Authors: Pintó Rosa M , Bosch Albert 
Published: April 2021

Abstract
Codon bias is common to all organisms and is the result of mutation, drift, and selection. Selection for the efficiency and accuracy of translation is well recognized as a factor shaping the codon usage. In contrast, fewer studies report the control of the rate of translation as an additional selective pressure influencing the codon usage of an organism. Experimental molecular evolution using RNA virus populations is a powerful tool for the identification of mechanisms underlying the codon bias. Indeed, the role of deoptimized codons on the cotranslational folding has been proven in the capsids of two fecal-orally transmitted picornaviruses, poliovirus, and the hepatitis A virus, emphasizing the role of the frequency of codons in determining the phenotype. However, most studies on virus codon usage rely only on computational analyses, and experimental studies should be encouraged to clearly define the role of selection on codon evolution.
Chromosomal-Level Reference Genome of the Neotropical Tree Jacaranda mimosifolia D. Don
Authors: Wang Mingcheng , Zhang Lei , Wang Zhiqiang 
Published: April 2021

Abstract
Jacaranda mimosifolia D. Don is a deciduous tree widely cultivated in the tropics and subtropics of the world. It is famous for its beautiful blue flowers and pinnate compound leaves. In addition, this tree has great potential in environmental monitoring, soil quality improvement, and medicinal applications. However, a genome resource for J. mimosifolia has not been reported to date. In this study, we constructed a chromosome-level genome assembly of J. mimosifolia using PacBio sequencing, Illumina sequencing, and Hi-C technology. The final genome assembly was ∼707.32 Mb in size, 688.76 Mb (97.36%) of which could be grouped into 18 pseudochromosomes, with contig and scaffold N50 values of 16.77 and 39.98 Mb, respectively. A total of 30,507 protein-coding genes were predicted, 95.17% of which could be functionally annotated. Phylogenetic analysis among 12 plant species confirmed the close genetic relationship between J. mimosifolia and Handroanthus impetiginosus. Gene family clustering revealed 481 unique, 103 significantly expanded, and 16 significantly contracted gene families in the J. mimosifolia genome. This chromosome-level genome assembly of J. mimosifolia will provide a valuable genomic resource for elucidating the genetic bases of the morphological characteristics, adaption evolution, and active compounds biosynthesis of J. mimosifolia.
A Targeted Gene Knockout in Drosophila
Authors: Rong Yikang S , Golic Kent G 
Published: April 2021

Abstract
We previously described a method for targeted homologous recombination at the yellow gene of Drosophila melanogaster. Because only a single gene was targeted, further work was required to show whether the method could be extended to become generally useful for gene modification in Drosophila. We have now used this method to produce a knockout of the autosomal pugilist gene by homologous recombination between the endogenous locus and a 2.5-kb DNA fragment. This was accomplished solely by tracking the altered genetic linkage of an arbitrary marker gene as the targeting DNA moved from chromosome X or 2 to chromosome 3. The results indicate that this method of homologous recombination is likely to be generally useful for Drosophila gene targeting.
A Simple Formula Useful for Positional Cloning
Authors: Durrett Richard T , Chen Kai-Yi , Tanksley Steven D 
Published: April 2021

Abstract
We derive a formula for the distribution of the length T of the recombination interval containing a target gene and using N gametes in a region where R kilobases correspond to 1 cM. The formula can be used to calculate the number of meiotic events required to narrow a target gene down to a specific interval size and hence should be useful for planning positional cloning experiments. The predictions of this formula agree well with the results from a number of published experiments in Arabidopsis.
Investigating the Probability of Sign Inconsistency in the Regression Coefficients of Markers Flanking Quantitative Trait Loci
Authors: Hwang J T Gene , Nettleton Dan 
Published: April 2021

Abstract
Estimates of the locations and effects of quantitative trait loci (QTL) can be obtained by regressing phenotype on marker genotype. Under certain basic conditions, the signs of regression coefficients flanking QTL must be the same. There is no guarantee, however, that the signs of the regression coefficient estimates will be the same. We use sign inconsistency to describe the situation in which there is disagreement between the signs of the estimated regression coefficients flanking QTL. The presence of sign inconsistency can undermine the effectiveness of QTL mapping strategies that presume intervals whose markers have regression coefficient estimates of differing sign to be devoid of QTL. This article investigates the likelihood of sign inconsistency under various conditions. We derive an analytic expression for the approximate probability of sign inconsistency in the single-QTL case. We also examine sign inconsistency probabilities when multiple QTL are present through simulation. We have discovered that the probability of sign inconsistency can be unacceptably high, even when the conditions for QTL detection are otherwise quite favorable.
Host Genotype Determines Cytoplasmic Incompatibility Type in the Haplodiploid Genus Nasonia
Authors: Bordenstein Seth R , Uy Julieanne J , Werren John H 
Published: April 2021

AbstractIn haplodiploid species, Wolbachia-induced cytoplasmic incompatibility (CI) can be expressed in one of two ways: as a “conversion” of diploid fertilized eggs into haploid males or as embryonic mortality. Here we describe CI-type variation within the parasitic wasp genus Nasonia and genetically analyze the basis of this variation. We reach four main conclusions: (i) CI is expressed primarily as conversion in N. vitripennis, but as embryonic mortality in the sibling species N. giraulti and N. longicornis; (ii) the difference in CI type between N. giraulti (mortality) and N. vitripennis (conversion) is determined by host nuclear genotype rather than by Wolbachia differences; (iii) N. vitripennis “conversion genes” are recessive in hybrid females; and (iv) a difference in CI level between the sibling species N. giraulti and N. longicornis is due to the different Wolbachia infections in the species rather than to the host genotype. These results show that host nuclear genes can influence the type of CI present in a species. On the basis of these findings, we propose a model for how different CI types evolve in haplodiploids due to selection on nuclear genes modifying CI.
Experimental Prediction of the Evolution of Cefepime Resistance From the CMY-2 AmpC β-Lactamase
Authors: Barlow Miriam , Hall Barry G 
Published: April 2021

Abstract
Understanding of the evolutionary histories of many genes has not yet allowed us to predict the evolutionary potential of those genes. Intuition suggests that current biochemical activity of gene products should be a good predictor of the potential to evolve related activities; however, we have little evidence to support that intuition. Here we use our in vitro evolution method to evaluate biochemical activity as a predictor of future evolutionary potential. Neither the class C Citrobacter freundii CMY-2 AmpC β-lactamase nor the class A TEM-1 β-lactamase confer resistance to the β-lactam antibiotic cefepime, nor do any of the naturally occurring alleles descended from them. However, the CMY-2 AmpC enzyme and some alleles descended from TEM-1 confer high-level resistance to the structurally similar ceftazidime. On the basis of the comparison of TEM-1 and CMY-2, we asked whether biochemical activity is a good predictor of the evolutionary potential of an enzyme. If it is, then CMY-2 should be more able than the TEMs to evolve the ability to confer higher levels of cefepime resistance. Although we generated CMY-2 evolvants that conferred increased cefepime resistance, we did not recover any CMY-2 evolvants that conferred resistance levels as high as the best cefepime-resistant TEM alleles.
Ectopic Expression of Inhibitors of Protein Phosphatase Type 1 (PP1) Can Be Used to Analyze Roles of PP1 in Drosophila Development
Authors: Bennett Daimark , Szöőr Balázs , Gross Sascha , Vereshchagina Natalia , Alphey Luke 
Published: April 2021

Abstract
We have identified two proteins that bind with high specificity to type 1 serine/threonine protein phosphatase (PP1) and have exploited their inhibitory properties to develop an efficient and flexible strategy for conditional inactivation of PP1 in vivo. We show that modest overexpression of Drosophila homologs of I-2 and NIPP1 (I-2Dm and NIPP1Dm) reduces the level of PP1 activity and phenotypically resembles known PP1 mutants. These phenotypes, which include lethality, abnormal mitotic figures, and defects in muscle development, are suppressed by coexpression of PP1, indicating that the effect is due specifically to loss of PP1 activity. Reactivation of I-2Dm:PP1c complexes suggests that inhibition of PP1 activity in vivo does not result in a compensating increase in synthesis of active PP1. PP1 mutants enhance the wing overgrowth phenotype caused by ectopic expression of the type II TGFβ superfamily signaling receptor Punt. Using I-2Dm, which has a less severe effect than NIPP1Dm, we show that lowering the level of PP1 activity specifically in cells overexpressing Punt is sufficient for wing overgrowth and that the interaction between PP1 and Punt requires the type I receptor Thick-veins (Tkv) but is not strongly sensitive to the level of the ligand, Decapentaplegic (Dpp), nor to that of the other type I receptors. This is consistent with a role for PP1 in antagonizing Punt by preventing phosphorylation of Tkv. These studies demonstrate that inhibitors of PP1 can be used in a tissue- and developmental-specific manner to examine the developmental roles of PP1.
Sry Expression Level and Protein Isoform Differences Play a Role in Abnormal Testis Development in C57BL/6J Mice Carrying Certain Sry Alleles
Authors: Albrecht Kenneth H , Young Maureen , Washburn Linda L , Eicher Eva M 
Published: April 2021

Abstract
Transfer of certain Mus domesticus-derived Y chromosomes (SryDOM alleles, e.g., SryPOS and SryAKR) onto the C57BL/6J (B6) mouse strain causes abnormal gonad development due to an aberrant interaction between the SryDOM allele and the B6-derived autosomal (tda) genes. For example, B6 XYPOS fetuses develop ovaries and ovotestes and B6 XYAKR fetuses have delayed testis cord development. To test whether abnormal testis development is caused by insufficient SryDOM expression, two approaches were used. First, gonad development and relative Sry expression levels were examined in fetal gonads from two strains of B6 mice that contained a single M. domesticus-derived and a single M. musculus-derived Sry allele (B6-YPOS,RIII and B6-YAKR,RIII). In both cases, presence of the M. musculus SryRIII allele corrected abnormal testis development. On the B6 background, SryPOS was expressed at about half the level of SryRIII whereas SryAKR and SryRIII were equally expressed. On an F1 hybrid background, both SryPOS and SryRIII expression increased, but SryPOS expression increased to a greater extent. Second, sexual development and Sry expression levels were determined in XX mice carrying a transgene expressing SryPOS controlled by POS-derived or MUS-derived regulatory regions. In both cases one B6 transgenic line was recovered in which XX transgenic mice developed only testicular tissue but cord development was delayed despite normal Sry transcriptional initiation and overexpression. For three transgenes where B6 XX transgenic mice developed as females, hermaphrodites, or males, the percentage of XX transgenic males increased on an F1 background. For the one transgene examined, Sry expression increased on an F1 background. These results support a model in which delayed testis development is caused by the presence of particular DOM SRY protein isoforms and this, combined with insufficient Sry expression, causes sex reversal. These results also indicate that at least one tda gene regulates Sry expression, possibly by directly binding to Sry regulatory regions.
A Bacterial Artificial Chromosome Contig Spanning the Major Domestication Locus Q in Wheat and Identification of a Candidate Gene
Authors: Faris Justin D , Fellers John P , Brooks Steven A , Gill Bikram S 
Published: April 2021

Abstract
The Q locus played a major role in the domestication of wheat because it confers the free-threshing character and influences many other agronomically important traits. We constructed a physical contig spanning the Q locus using a Triticum monococcum BAC library. Three chromosome walking steps were performed by complete sequencing of BACs and identification of low-copy markers through similarity searches of database sequences. The BAC contig spans a physical distance of ∼300 kb corresponding to a genetic distance of 0.9 cM. The physical map of T. monococcum had perfect colinearity with the genetic map of wheat chromosome arm 5AL. Recombination data in conjunction with analysis of fast neutron deletions confirmed that the contig spanned the Q locus. The Q gene was narrowed to a 100-kb segment, which contains an APETALA2 (AP2)-like gene that cosegregates with Q. AP2 is known to play a major role in controlling floral homeotic gene expression and thus is an excellent candidate for Q.
Comparison of a Brassica oleracea Genetic Map With the Genome of Arabidopsis thaliana
Authors: Lukens Lewis , Zou Fei , Lydiate Derek , Parkin Isobel , Osborn Tom 
Published: April 2021

Abstract
Brassica oleracea is closely related to the model plant, Arabidopsis thaliana. Despite this relationship, it has been difficult to both identify the most closely related segments between the genomes and determine the degree of genome replication within B. oleracea relative to A. thaliana. These difficulties have arisen in part because both species have replicated genomes, and the criteria used to identify orthologous regions between the genomes are often ambiguous. In this report, we compare the positions of sequenced Brassica loci with a known position on a B. oleracea genetic map to the positions of their putative orthologs within the A. thaliana genome. We use explicit criteria to distinguish orthologous from paralogous loci. In addition, we develop a conservative algorithm to identify collinear loci between the genomes and a permutation test to evaluate the significance of these regions. The algorithm identified 34 significant A. thaliana regions that are collinear with &gt;28% of the B. oleracea genetic map. These regions have a mean of 3.3 markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Our findings are consistent with the hypothesis that the B. oleracea genome has been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.
Mathematical Issues Arising From the Directed Mutation Controversy
Authors: Zheng Qi 
Published: April 2021

Abstract
During the past 14 years or so a large body of new evidence that supposedly supports the directed mutation hypothesis has accumulated. Interpretation of some of the evidence depends on mathematical reasoning, which can be subtler than it appears at first sight. This article attempts to clarify some of the mathematical issues arising from the directed mutation controversy, thereby offering alternative interpretations of some of the evidence.
Effects of Population Structure and Admixture on Exact Tests for Association Between Loci
Authors: Law B , Buckleton J S , Triggs C M , Weir B S 
Published: April 2021

Abstract
The probability of multilocus genotype counts conditional on allelic counts and on allelic independence provides a test statistic for independence within and between loci. As the number of loci increases and each sampled genotype becomes unique, the conditional probability becomes a function of total heterozygosity. In that case, it does not address between-locus dependence directly but only indirectly through detection of the Wahlund effect. Moreover, the test will reject the hypothesis of allelic independence only for small values of heterozygosity. Low heterozygosity is expected for population subdivision but not for population admixture. The test may therefore be inappropriate for admixed populations. If individuals with parents in two different populations are always considered to belong to one of the populations, then heterozygosity is increased in that population and the exact test should not be used for sparse data sets from that population. If such a case is suspected, then alternative testing strategies are suggested.
Multiple Roles for Saccharomyces cerevisiae Histone H2A in Telomere Position Effect, Spt Phenotypes and Double-Strand-Break Repair
Authors: Wyatt Holly R , Liaw Hungjiun , Green George R , Lustig Arthur J 
Published: April 2021

Abstract
Telomere position effects on transcription (TPE, or telomeric silencing) are nucleated by association of nonhistone silencing factors with the telomere and propagated in subtelomeric regions through association of silencing factors with the specifically modified histones H3 and H4. However, the function of histone H2A in TPE is unknown. We found that deletion of either the amino or the carboxyltails of H2A substantially reduces TPE. We identified four H2A modification sites necessary for wild-type efficiency of TPE. These “hta1tpe” alleles also act as suppressors of a δ insertion allele of LYS2, suggesting shared elements of chromatin structure at both loci. Interestingly, we observed combinatorial effects of allele pairs, suggesting both interdependent acetylation and deacetylation events in the amino-terminal tail and a regulatory circuit between multiple phosphorylated residues in the carboxyl-terminal tail. Decreases in silencing and viability are observed in most hta1tpe alleles after treatment with low and high concentrations, respectively, of bleomycin, which forms double-strand breaks (DSBs). In the absence of the DSB and telomere-binding protein yKu70, the bleomycin sensitivity of hta1tpe alleles is further enhanced. We also provide data suggesting the presence of a yKu-dependent histone H2A function in TPE. These data indicate that the amino- and carboxyl-terminal tails of H2A are essential for wild-type levels of yKu-mediated TPE and DSB repair.