bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Oh make thy selfe with holy mourning blacke”: Aspects of Drama and Performance in John Donne’sHoly Sonnet“Oh My Black Soule”
Authors: Zirker Angelika 
Published: October 2016

AbstractThis article provides a close reading of John Donne’sHoly Sonnet“Oh My Black Soule” with regard to its dramatic and performative qualities. The opening line of the poem contains an allusion to the morality playEveryman; moreover, in this sonnet, the speaker addresses his soul as if he were on a stage; and, in the end, he finds a resolution to the inner conflict that is being described in the course of the poem. Drama is thus significant in three ways: the speaker witnesses a drama of the soul, which is summoned, and reacts to it; he takes part in the drama and its performance as the speaker of a soliloquy; and a drama (in the sense of conflict) goes on within himself. The sonnet is the enactment of a drama of salvation and an expression of the innermost fears and prayers of the speaker who, eventually, finds a resolution and comes to a happy ending. While these three dimensions are all equally linked to the dramatic and performative qualities of this poem, the focus will be on the second aspect and the question how theHoly Sonnetmay add to our understanding of the soliloquy, the communicative form which became most popular on the stage at the time John Donne wrote this poem.
Skeletal Muscle Contraction Time and Tone Decrease After 8 Weeks of Plyometric Training
Authors: Zubac Damir , Šimunič Boštjan 
Published: October 2016

Abstract
Zubac, D and Šimunič, B. Skeletal muscle contraction time and tone decrease after 8 weeks of plyometric training. J Strength Cond Res 31(6): 1610–1619, 2017—The aim of the study was to examine whether an improvement in jumping performance after 8 weeks of plyometric training (PT) runs in parallel with changes in lower-limb skeletal muscle contractile properties. Using noninvasive tensiomyography (TMG), we assessed contraction time (Tc) and the maximal amplitude of radial displacement (Dm) in 20 subjects (50% men; age 22.4 ± 4.7 years of age), randomly divided in PT group (N = 10; PLYO) and a control group (N = 10; CTRL). The PLYO performed 8 weeks of PT. Tensiomyography was measured in 5 leg skeletal muscles: vastus lateralis (VL), biceps femoris (BF), tibialis anterior (TA), gastrocnemius medialis (GM), and gastrocnemius lateralis (GL). Additionally, we evaluated countermovement jump (CMJ) height improvement on a ground force plate. Assessments were repeated before and after PT. After 8 weeks of PT, CMJ height increased by 12.2% in PLYO (p = 0.015), but not in CRTL. Contraction time, which is related to myosin heavy-chain type 1 (MHC-1) proportion, decreased in VL (−8.7%; p < 0.001), BF (−26.7%; p = 0.032), TA (−32.9%; p = 0.004), and GL (−25.8%; p = 0.044), but not in GM (−8.1%; p = 0.158). The estimated VL MHC-1 proportion decreased by −8.2% (p = 0.041). The maximal amplitude of radial displacement, inversely related to muscle tone, decreased in BF (−26.5%; p = 0.032), GM (−14.9%; p = 0.017), GL (−31.5%; p = 0.017), but not in TA (−16.8%; p = 0.113) and VL (−6.0%; p = 0.654). After PT, jumping performance increased, which was paralleled by decreased Tc and decreased muscle tone. Additionally, adaptations to contractile properties were muscle specific, which is important for future studies. It seems that adjustments were dose dependent, being higher in muscles with lower habitual load.
Effect of Lower-Body Resistance Training on Upper-Body Strength Adaptation in Trained Men
Authors: Bartolomei Sandro , Hoffman Jay R. , Stout Jeffrey R. , Merni Franco 
Published: October 2016

Abstract
Bartolomei, S, Hoffman, JR, Stout, JR, and Merni, F. Effect of lower-body resistance training on upper-body strength adaptation in trained men. J Strength Cond Res 32(1): 13–18, 2018—The aim of this study was to examine the effect of 2 different lower-body strength training schemes on upper-body adaptations to resistance training. Twenty resistance-trained men (4.25 ± 1.6 years of experience) were randomly assigned to either a high intensity (HI; n = 9; age = 24.9 ± 2.9 years; body mass = 88.7 ± 17.2 kg; height = 177.0 ± 5.6 cm) or a mixed high volume and HI resistance training program (MP; n = 11; age = 26.0 ± 4.7 years; body mass = 82.8 ± 9.1 kg; height = 177.54 ± 5.9 cm). High-intensity group followed a HI training for both upper and lower body (4–5 reps at 88%–90% of 1 repetition maximum (1RM)), whereas the MP group performed high-volume training sessions focused on muscle hypertrophy for lower body (10–12 reps at 65%–70% of 1-RM) and a HI protocol for the upper body. Maximal strength and power testing occurred before and after the 6-week training program. Analysis of covariance was used to compare performance measures between the groups. Greater increases in MP groups compared with HI groups were observed for bench press 1RM (p = 0.007), bench press power at 50% of 1RM (p = 0.011), and for arm muscle area (p = 0.046). Significant difference between the 2 groups at posttest were also observed for fat mass (p = 0.009). Results indicated that training programs focused on lower-body muscle hypertrophy and maximal strength for upper body can stimulate greater strength and power gains in the upper body compared with HI resistance training programs for both the upper and lower body.
Retrotransposon Proliferation Coincident with the Evolution of Dioecy inAsparagus
Authors: Harkess Alex , Mercati Francesco , Abbate Loredana , McKain Michael , Pires J Chris , Sala Tea , Sunseri Francesco , Falavigna Agostino , Leebens-Mack Jim 
Published: October 2016

AbstractCurrent phylogenetic sampling reveals that dioecy and an XY sex chromosome pair evolved once, or possibly twice, in the genus Asparagus. Although there appear to be some lineage-specific polyploidization events, the base chromosome number of 2n = 2× = 20 is relatively conserved across the Asparagus genus. Regardless, dioecious species tend to have larger genomes than hermaphroditic species. Here, we test whether this genome size expansion in dioecious species is related to a polyploidization and subsequent chromosome fusion, or to retrotransposon proliferation in dioecious species. We first estimate genome sizes, or use published values, for four hermaphrodites and four dioecious species distributed across the phylogeny, and show that dioecious species typically have larger genomes than hermaphroditic species. Utilizing a phylogenomic approach, we find no evidence for ancient polyploidization contributing to increased genome sizes of sampled dioecious species. We do find support for an ancient whole genome duplication (WGD) event predating the diversification of the Asparagus genus. Repetitive DNA content of the four hermaphroditic and four dioecious species was characterized based on randomly sampled whole genome shotgun sequencing, and common elements were annotated. Across our broad phylogenetic sampling, Ty-1 Copia retroelements, in particular, have undergone a marked proliferation in dioecious species. In the absence of a detectable WGD event, retrotransposon proliferation is the most likely explanation for the precipitous increase in genome size in dioecious Asparagus species.
Genetic Analysis and QTL Detection on Fiber Traits Using Two Recombinant Inbred Lines and Their Backcross Populations in Upland Cotton
Authors: Shang Lianguang , Wang Yumei , Wang Xiaocui , Liu Fang , Abduweli Abdugheni , Cai Shihu , Li Yuhua , Ma Lingling , Wang Kunbo , Hua Jinping 
Published: October 2016

AbstractCotton fiber, a raw natural fiber material, is widely used in the textile industry. Understanding the genetic mechanism of fiber traits is helpful for fiber quality improvement. In the present study, the genetic basis of fiber quality traits was explored using two recombinant inbred lines (RILs) and corresponding backcross (BC) populations under multiple environments in Upland cotton based on marker analysis. In backcross populations, no significant correlation was observed between marker heterozygosity and fiber quality performance and it suggested that heterozygosity was not always necessarily advantageous for the high fiber quality. In two hybrids, 111 quantitative trait loci (QTL) for fiber quality were detected using composite interval mapping, in which 62 new stable QTL were simultaneously identified in more than one environment or population. QTL detected at the single-locus level mainly showed additive effect. In addition, a total of 286 digenic interactions (E-QTL) and their environmental interactions [QTL × environment interactions (QEs)] were detected for fiber quality traits by inclusive composite interval mapping. QE effects should be considered in molecular marker-assisted selection breeding. On average, the E-QTL explained a larger proportion of the phenotypic variation than the main-effect QTL did. It is concluded that the additive effect of single-locus and epistasis with few detectable main effects play an important role in controlling fiber quality traits in Upland cotton.
Tandem Duplication Events in the Expansion of the Small Heat Shock Protein Gene Family inSolanum lycopersicum(cv. Heinz 1706)
Authors: Krsticevic Flavia J , Arce Débora P , Ezpeleta Joaquín , Tapia Elizabeth 
Published: October 2016

AbstractIn plants, fruit maturation and oxidative stress can induce small heat shock protein (sHSP) synthesis to maintain cellular homeostasis. Although the tomato reference genome was published in 2012, the actual number and functionality of sHSP genes remain unknown. Using a transcriptomic (RNA-seq) and evolutionary genomic approach, putative sHSP genes in the Solanum lycopersicum (cv. Heinz 1706) genome were investigated. A sHSP gene family of 33 members was established. Remarkably, roughly half of the members of this family can be explained by nine independent tandem duplication events that determined, evolutionarily, their functional fates. Within a mitochondrial class subfamily, only one duplicated member, Solyc08g078700, retained its ancestral chaperone function, while the others, Solyc08g078710 and Solyc08g078720, likely degenerated under neutrality and lack ancestral chaperone function. Functional conservation occurred within a cytosolic class I subfamily, whose four members, Solyc06g076570, Solyc06g076560, Solyc06g076540, and Solyc06g076520, support ∼57% of the total sHSP RNAm in the red ripe fruit. Subfunctionalization occurred within a new subfamily, whose two members, Solyc04g082720 and Solyc04g082740, show heterogeneous differential expression profiles during fruit ripening. These findings, involving the birth/death of some genes or the preferential/plastic expression of some others during fruit ripening, highlight the importance of tandem duplication events in the expansion of the sHSP gene family in the tomato genome. Despite its evolutionary diversity, the sHSP gene family in the tomato genome seems to be endowed with a core set of four homeostasis genes: Solyc05g014280, Solyc03g082420, Solyc11g020330, and Solyc06g076560, which appear to provide a baseline protection during both fruit ripening and heat shock stress in different tomato tissues.
Divergent DNA Methylation Provides Insights into the Evolution of Duplicate Genes in Zebrafish
Authors: Zhong Zaixuan , Du Kang , Yu Qian , Zhang Yong E , He Shunping 
Published: October 2016

AbstractThe evolutionary mechanism, fate and function of duplicate genes in various taxa have been widely studied; however, the mechanism underlying the maintenance and divergence of duplicate genes in Danio rerio remains largely unexplored. Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. In this study, by analyzing bisulfite sequencing (BS-seq) and RNA-seq datasets from public data, we demonstrated that DNA methylation played a critical role in duplicate gene evolution in zebrafish. Initially, we found promoter methylation of duplicate genes generally decreased with evolutionary time as measured by synonymous substitution rate between paralogous duplicates (Ks). Importantly, promoter methylation of duplicate genes was negatively correlated with gene expression. Interestingly, for 665 duplicate gene pairs, one gene was consistently promoter methylated, while the other was unmethylated across nine different datasets we studied. Moreover, one motif enriched in promoter methylated duplicate genes tended to be bound by the transcription repression factor FOXD3, whereas a motif enriched in the promoter unmethylated sequences interacted with the transcription activator Sp1, indicating a complex interaction between the genomic environment and epigenome. Besides, body-methylated genes showed longer length than body-unmethylated genes. Overall, our results suggest that DNA methylation is highly important in the differential expression and evolution of duplicate genes in zebrafish.
Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates inSaccharomyces cerevisiae
Authors: Neymotin Benjamin , Ettorre Victoria , Gresham David 
Published: October 2016

AbstractDegradation of mRNA contributes to variation in transcript abundance. Studies of individual mRNAs have shown that both cis and trans factors affect mRNA degradation rates. However, the factors underlying transcriptome-wide variation in mRNA degradation rates are poorly understood. We investigated the contribution of different transcript properties to transcriptome-wide degradation rate variation in the budding yeast, Saccharomyces cerevisiae, using multiple regression analysis. We find that multiple transcript properties are significantly associated with variation in mRNA degradation rates, and that a model incorporating these properties explains ∼50% of the genome-wide variance. Predictors of mRNA degradation rates include transcript length, ribosome density, biased codon usage, and GC content of the third position in codons. To experimentally validate these factors, we studied individual transcripts expressed from identical promoters. We find that decreasing ribosome density by mutating the first translational start site of a transcript increases its degradation rate. Using coding sequence variants of green fluorescent protein (GFP) that differ only at synonymous sites, we show that increased GC content of the third position of codons results in decreased rates of mRNA degradation. Thus, in steady-state conditions, a large fraction of genome-wide variation in mRNA degradation rates is determined by inherent properties of transcripts, many of which are related to translation, rather than specific regulatory mechanisms.
Simple and Efficient Targeting of Multiple Genes Through CRISPR-Cas9 in Physcomitrella patens
Authors: Lopez-Obando Mauricio , Hoffmann Beate , Géry Carine , Guyon-Debast Anouchka , Téoulé Evelyne , Rameau Catherine , Bonhomme Sandrine , Nogué Fabien 
Published: October 2016

Abstract
Powerful genome editing technologies are needed for efficient gene function analysis. The CRISPR-Cas9 system has been adapted as an efficient gene-knock-out technology in a variety of species. However, in a number of situations, knocking out or modifying a single gene is not sufficient; this is particularly true for genes belonging to a common family, or for genes showing redundant functions. Like many plants, the model organism Physcomitrella patens has experienced multiple events of polyploidization during evolution that has resulted in a number of families of duplicated genes. Here, we report a robust CRISPR-Cas9 system, based on the codelivery of a CAS9 expressing cassette, multiple sgRNA vectors, and a cassette for transient transformation selection, for gene knock-out in multiple gene families. We demonstrate that CRISPR-Cas9-mediated targeting of five different genes allows the selection of a quintuple mutant, and all possible subcombinations of mutants, in one experiment, with no mutations detected in potential off-target sequences. Furthermore, we confirmed the observation that the presence of repeats in the vicinity of the cutting region favors deletion due to the alternative end joining pathway, for which induced frameshift mutations can be potentially predicted. Because the number of multiple gene families in Physcomitrella is substantial, this tool opens new perspectives to study the role of expanded gene families in the colonization of land by plants.
Sequential Turnovers of Sex Chromosomes in African Clawed Frogs (Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination
Authors: Furman Benjamin L S , Evans Ben J 
Published: October 2016

Abstract
Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here, we extend these discoveries by demonstrating that yet another sex determination system exists in Xenopus, specifically in the species Xenopus borealis. This system evolved recently in an ancestor of X. borealis that had the same sex determination system as X. laevis, a system which itself is newly evolved. Strikingly, the genomic region carrying the sex determination factor in X. borealis is homologous to that of therian mammals, including humans. Our results offer insights into how the genetic underpinnings of conserved phenotypes evolve, and suggest an important role for cooption of genetic building blocks with conserved developmental roles.
The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-Zygotic Transition
Authors: Luo Hua , Li Xiao , Claycomb Julie M , Lipshitz Howard D 
Published: October 2016

Abstract
Metazoan embryos undergo a maternal-to-zygotic transition (MZT) during which maternal gene products are eliminated and the zygotic genome becomes transcriptionally active. During this process, RNA-binding proteins (RBPs) and the microRNA-induced silencing complex (miRISC) target maternal mRNAs for degradation. In Drosophila, the Smaug (SMG), Brain tumor (BRAT), and Pumilio (PUM) RBPs bind to and direct the degradation of largely distinct subsets of maternal mRNAs. SMG has also been shown to be required for zygotic synthesis of mRNAs and several members of the miR-309 family of microRNAs (miRNAs) during the MZT. Here, we have carried out global analysis of small RNAs both in wild-type and in smg mutants. Our results show that 85% of all miRNA species encoded by the genome are present during the MZT. Whereas loss of SMG has no detectable effect on Piwi-interacting RNAs (piRNAs) or small interfering RNAs (siRNAs), zygotic production of more than 70 species of miRNAs fails or is delayed in smg mutants. SMG is also required for the synthesis and stability of a key miRISC component, Argonaute 1 (AGO1), but plays no role in accumulation of the Argonaute family proteins associated with piRNAs or siRNAs. In smg mutants, maternal mRNAs that are predicted targets of the SMG-dependent zygotic miRNAs fail to be cleared. BRAT and PUM share target mRNAs with these miRNAs but not with SMG itself. We hypothesize that SMG controls the MZT, not only through direct targeting of a subset of maternal mRNAs for degradation but, indirectly, through production and function of miRNAs and miRISC, which act together with BRAT and/or PUM to control clearance of a distinct subset of maternal mRNAs.
Main Effect QTL with Dominance Determines Heterosis for Dynamic Plant Height in Upland Cotton
Authors: Shang Lianguang , Ma Lingling , Wang Yumei , Su Ying , Wang Xiaocui , Li Yuhua , Abduweli Abdugheni , Cai Shihu , Liu Fang , Wang Kunbo , Hua Jinping 
Published: October 2016

AbstractPlant height, which shows dynamic development and heterosis, is a major trait affecting plant architecture and has an indirect influence on economic yield related to biological yield in cotton. In the present study, we carried out dynamic analysis for plant height and its heterosis by quantitative trait loci (QTL) mapping at multiple developmental stages using two recombinant inbred lines (RILs) and their backcross progeny. At the single-locus level, 47 QTL were identified at five developmental stages in two hybrids. In backcross populations, QTL identified at an early stage mainly showed partial effects and QTL detected at a later stage mostly displayed overdominance effects. At the two-locus level, we found that main effect QTL played a more important role than epistatic QTL in the expression of heterosis in backcross populations. Therefore, this study implies that the genetic basis of plant height heterosis shows dynamic character and main effect QTL with dominance determines heterosis for plant height in Upland cotton.
Determinants in the LIN-12/Notch Intracellular Domain That Govern Its Activity and Stability DuringCaenorhabditis elegansVulval Development
Authors: Deng Yuting , Greenwald Iva 
Published: October 2016

AbstractUpon ligand binding, the LIN-12/Notch intracellular domain is released from its transmembrane tether to function in a nuclear complex that activates transcription of target genes. During Caenorhabditis elegans vulval development, LIN-12/Notch is activated by ligand in two of six multipotential vulval precursor cells (VPCs), specifying the “secondary vulval fate” and descendants that contribute to the vulva. If LIN-12 is ectopically activated in other VPCs, they also adopt the secondary fate, dividing to produce extra vulval cells, resulting in a “Multivulva” phenotype. Here, we identify determinants in the LIN-12 intracellular domain [“LIN-12(intra)”] that govern its activity and stability during C. elegans vulval development; we assayed activity of mutant forms based on their ability to cause a Multivulva phenotype and stability using a GFP tag to visualize their accumulation. Our analysis has revealed that, while the ubiquitin ligase SEL-10/Fbw7 promotes LIN-12(intra) downregulation in VPCs, there is a distinct mechanism for downregulation of LIN-12(intra) in VPC descendants. Our analysis also revealed that LIN-12(intra) must be in the nuclear complex to be regulated appropriately in VPCs and their descendants, and that the structure or conformation of the carboxy-terminal region influences stability as well. Although activity and stability are generally well-correlated, exceptions where they are uncoupled suggest that there may be roles for the carboxy-terminal region and sel-10 that are independent of their roles in regulating LIN-12(intra) stability.