bluuebunny/crossref_metadata_2025_split huggingface dataset:
Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia
Authors: Kerr Peter J. , Eden John-Sebastian , Di Giallonardo Francesca , Peacock David , Liu June , Strive Tanja , Read Andrew F. , Holmes Edward C. 
Published: November 2018

ABSTRACTMyxoma virus (MYXV) has been evolving in a novel host species – European rabbits – in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017 we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic break-down of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of non-synonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of theM005L/Rgene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in south-eastern Australia, followed by the partial recovery of populations. We therefore suggest that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV and altered the course of virus evolution.IMPORTANCEThe co-evolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural ‘experiments’ in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a break-down in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple non-synonymous and indel mutations. We suggest that this punctuated evolutionary event likely reflects a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
Global Quantitative Mapping of Enhancers in Rice Genome by STARR-seq
Authors: Sun Jialei , He Na , Niu Longjian , Huang Yingzhang , Shen Wei , Zhang Yuedong , Li Li , Hou Chunhui 
Published: November 2018

AbstractIdentification of enhancers has been a challenge in plants. STARR-seq measures enhancer activity of millions fragments in parallel. Here we present a global map of rice enhancers quantitatively determined using STARR-seq. Most enhancers are mapped within genes, especially at the 5’ untranslated regions (5’ UTR) and the coding sequences. Silent and low expressed genes in genomic regions enriched with transposable elements (TEs) are frequently found containing proximal enhancers. Analysis of enhancer epigenetic features at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and are lack of H3K4me1. Clustering enhancers by their epigenetic modifications revealed that about 40% of identified enhancers carry one or more epigenetic marks. Repressive H3K27me3 is frequently enriched with positive marks of H3K4m3 and/or H3K27ac, which together may bookmark poised enhancers. Intergenic enhancers were predicted based on the location of DHS relative to genes, which overlap poorly with functionally identified enhancers. In summary, enhancers were quantitatively identified by functional analysis in a model plant genome, which provides a valuable resource for further mechanistic studies in different biological contexts.
The concerted action of E2-2 and HEB is critical for early lymphoid specification
Authors: Bouderlique Thibault , Perez Lucia Peña , Kharazi Shabnam , Hils Miriam , Li Xiaoze , Krstic Aleksandra , De Paepe Ayla , Schachtrup Christian , Gustafsson Charlotte , Holmberg Dan , Schachtrup Kristina , Månsson Robert 
Published: November 2018

AbstractThe apparition of adaptive immunity inGnathostomatacorrelates with the expansion of the E-protein family to encompass E2-2, HEB and E2A. Within the family, E2-2 and HEB are more closely evolutionarily related but their concerted action in hematopoiesis remains to be explored. Here we show that the combined disruption of E2-2 and HEB results in failure to express the early lymphoid program in CLPs and a near complete block in B-cell development. In the thymus, ETPs were reduced and T-cell development perturbed, resulting in reduced CD4 T- and increased γδ T-cell numbers. In contrast, HSCs, erythro-myeloid progenitors and innate immune cells were unaffected showing that E2-2 and HEB are dispensable for the ancestral hematopoietic lineages. Taken together, this E-protein dependence suggests that the appearance of the fullGnathostomataE-protein repertoire was critical to reinforce the gene regulatory circuits that drove the emergence and expansion of the lineages constituting humoral immunity.
Subdivision of light signalling networks contributes to cellular partitioning of C4photosynthesis in maize
Authors: Hendron Ross-W. , Kelly Steven 
Published: November 2018

AbstractPlants coordinate the expression of genes required to conduct photosynthesis in response to growth and environmental changes. In species that conduct two-cell C4photosynthesis, the expression of photosynthesis genes is partitioned such that leaf mesophyll and vascular sheath cells accumulate different components of the photosynthetic pathway. The identity of the regulatory networks that facilitate this partitioning are unknown. Here we show that differences in light perception between mesophyll and bundle sheath cells facilitate differential regulation and accumulation of photosynthesis genes in the C4cropZea mays(maize). We show that transcripts encoding photoreceptors differentially accumulate in mesophyll and bundle sheath cells in a manner that is consistent with biophysical light filtration. We further show the blue light (but not red) is necessary and sufficient to activate photosystem II assembly in etiolated maize mesophyll cells, while both red and blue produce the same effect in C3Hordeum vulgare(barley). Finally, we demonstrate that changes in abundance of >20% of genes that differentially accumulate between mesophyll and bundle sheath cells can be recapitulated by spectrum specific deetiolation of maize seedlings. These findings provide evidence that subdivision of light signalling networks is a key component of cellular partitioning of C4photosynthesis in maize.
Enhanced cell-cell contact stability and decreased N-cadherin-mediated migration upon Fibroblast Growth Factor Receptor-N-cadherin cross-talk
Authors: Nguyen Thao , Duchesne Laurence , Sankara Narayana Gautham Hari Narayana , Boggetto Nicole , Fernig David D. , Murade Chandrashekhar Uttamrao , Ladoux Benoit , Mège René-Marc 
Published: November 2018

AbstractN-cadherin adhesion has been reported to enhance cancer and neuronal cell migration either by mediating actomyosin-based force transduction or initiating Fibroblast Growth Factor Receptor (FGFR)-dependent biochemical signalling. Here we show that FGFR1 reduces N-cadherin-mediated cell migration. Both proteins are co-stabilised at cell-cell contacts through direct interaction. As a consequence, cell adhesion is strengthened, limiting the migration of cells on N-cadherin. Both the inhibition of migration and the stabilisation of cell adhesions require the FGFR activity stimulated by N-cadherin engagement. FGFR1 stabilises N-cadherin at the cell membrane through a pathway involving Src and p120. Moreover, FGFR1 stimulates the anchoring of N-cadherin to actin. We found that the migratory behaviour of cells depends on an optimum balance between FGFR-regulated N-cadherin adhesion and actin dynamics. Based on these findings we propose a positive feedback loop between N-cadherin and FGFR at adhesion sites limiting N-cadherin-based single cell migration.
Murine bone properties and their relationship to gait during growth
Authors: Song Hyunggwi , Polk John D. , Kersh Mariana E. 
Published: November 2018

AbstractAllometric relationships have been queried over orders of mammals to understand how bone accommodates the mechanical demands associated with increasing mass. However, less attention has been given to the scaling of bone within a single lifetime. We aimed to determine if bone morphology and apparent density is related to (1) bending and compressive strength, and (2) gait dynamics. Longitudinal in vivo computed tomography and gait data were collected from female rats (n=5, age 8 - 20 weeks). Cross sectional properties and apparent density were measured at the diaphysis, distal, and proximal regions of the tibia and scaling exponents were calculated. Finite-element models were used to simulate four-point bending and axial compression using time-specific ground reaction forces (GRF) to calculate the mean strain energy density (SED) at the midshaft. Second moment of area at the diaphysis followed strain similarity based allometry, while bone area was positively allometric. The average SED at the diaphysis decreased, especially after the age of 10 weeks (R2=0.99), while it increased in compression (R2=0.96). The apparent density in all regions initially increased and converged by 11 weeks of age and this was correlated with changes in joint angle. The scaling analyses implies that rodent tibia is (re)modeled in order to sustain bending at the midshaft during growth. The finite element results and relatively constant density after 10 weeks of age indicate that structural parameters may be the primary determinant of bone strength in the growing rodent tibia. The correlations between bone properties and joint angles imply that the changes in posture may affect bone growth in specific regions.
First Report of Recurrent Genomic Selection with Real Data in Popcorn and Genetic Gain Increases
Authors: Schwantes Ismael Albino , do Amaral Antônio Teixeira , de Almeida Filho Janeo Eustáquio , Vivas Marcelo , Cabral Pablo Diego Silva , Guimarães Amanda Gonçalves , de Lima e Silva Fernando Higino , Santos Pedro Henrique Araújo Diniz , Pereira Messias Gonzaga , Viana Alexandre Pio , Pena Guilherme Ferreira , Ferreira Fernando Rafael Alves 
Published: November 2018

AbstractRecurrent Selection increases the frequencies of favorable alleles for economically important traits, which in the case of popcorn are popping expansion and grain yield. However, is time-consuming, since each selection cycle consists of three stages: progeny development and evaluation, and recombination of the best families. With the Recurrent Genomic Selection use, the time required for each selection cycle can be shortened, as it allows the evaluation and recombination phases to be performed simultaneously, reducing the time needed to complete one selection cycle to only one growing season. In this respect, the objective of this study was to determine the selection accuracy and genetic gains for different selection strategies: PhEN = estimates based exclusively on the phenotypic data of 98 plants; PhEN + GEN = estimates based exclusively on the phenotypic and genotypic data of 98 plants; and GEN = estimates based exclusively on SNP marker genotyping. The following traits were evaluated: 100-grain weight, ear height, grain yield, popping expansion, plant height, and popcorn volume. Field trials were carried out with 98 S1 progenies, at two locations, in an incomplete block design with three replications. The parents of these progenies were genotyped with a panel of ~ 21K SNPs. From the results based on the predictions by strategy GEN, at different selection intensities, the average annual genetic gain for the different traits was 29.1% and 25.2% higher than that by the strategies PhEN and GEN + PhEN for 98 selection candidates; 148.3% and 140.9% higher for 500; and 187.9% and 179.4% higher for 1,000 selection candidates, respectively. Therefore, recurrent genomic selection may result in a high genetic gain, provided that: i) phenotyping is accurate; ii) selection intensity is explored by genotyping several plants, increasing the number of selection candidates, and iii) genomic selection is used for early selection in recurrent selection.
Evidence of a noncoding transcript of theRIPK2gene overexpressed in head and neck tumor
Authors: Villagra Ulises M. M. , da Cunha Bianca R. , Polachini Giovana M. , Henrique Tiago , da Silva Carlos H. T. P. , Feitosa Olavo A. , Fukuyama Erica E. , López Rossana V. M. , Dias-Neto Emmanuel , Nunes Fabio D. , Severino Patricia , Tajara Eloiza H. 
Published: November 2018

ABSTRACTReceptor-interacting proteins are a family of serine/threonine kinases, which integrate extra and intracellular stress signals caused by different factors, including infections, inflammation and DNA damage. Receptor-interacting serine/threonine-protein kinase 2 (RIP-2) is a member of this family and an important component of the nuclear factor NF-kappa-B signaling pathway. The corresponding human geneRIPK2generates two transcripts by alternative splicing, the full-length and a short transcript. The short transcript has a truncated 5’ sequence, which results in a predicted isoform with a partial kinase domain but able to transduce signals through its caspase recruitment domain. In this study, the expression ofRIPK2was investigated in human tissue samples and, in order to determine if both transcripts are similarly regulated at the transcriptional level, cancer cell lines were submitted to temperature and acid stresses. We observed that both transcripts are expressed in all tissues analyzed, with higher expression of the short one in tumor samples, and they are differentially regulated following temperature stress. Despite transcription, no corresponding protein for the short transcript was detected in tissues and cell lines analyzed. We propose that the shorter transcript is a noncoding RNA and that its presence in the cell may play regulatory roles and affect inflammation and other biological processes related to the kinase activity of RIP-2.
Homeostatic Controllers Compensating for Growth and Perturbations
Authors: Ruoff Peter , Agafonov Oleg , Tveit Daniel M. , Thorsen Kristian , Drengstig Tormod 
Published: November 2018

AbstractCells and organisms have developed homeostatic mechanisms to maintain internal stabilities which protect them against a changing environment. How cellular growth and homeostasis interact is still not well understood, but of increasing interest to the synthetic and molecular biology community where molecular control circuits are sought and tried to maintain homeostasis that opposes the diluting effects of cell growth. In this paper we describe the performance of four negative feedback (inflow) controllers, which, for different observed growth laws (time-dependent increase in the cellular volume V) are able to compensate for various time-dependent removals of the controlled variable A. The four implementations of integral control are based on zero-order, first-order autocatalytic, second-order (antithetic), and derepressing inhibition kinetics. All controllers behave ideal in the sense that they for step-wise perturbations in V and A are able to drive the controlled variable precisely back to the controller’s theoretical set-point

The applied increase in cellular volume includes linear, exponential and saturating growth and reflect experimentally observed growth laws of single cell organisms and other cell types. During the increase in V, additional linear or exponential time-dependent perturbations which remove A are applied, and controllers are tested with respect to their ability to compensate for both the increase in volume V and the applied perturbations removing A. Our results show that the way how integral control is kinetically implemented and the structure of the negative feedback loop are essential determinants of a controller’s performance. The results provide a ranking between the four tested controller types. Considering exponential volume increases together with an exponentially increasing removal rate of A controllers based on derepression kinetics perform best, but break down when the control-inhibitor’s concentration gets too low. The first-order autocatalytic controller is able to defend time-dependent exponential growth and removals in A, but generally with a certain offset below its theoretical set-point

The controllers based on zero-order and second-order (antithetic) integral feedback can only manage linear increases in V and removals in A, in dependence of the controllers’ aggressiveness. Our results provide a theoretical basis what controller kinetics are needed in order to compensate for different growth laws.
Evaluating DNA methylation age on the Illumina’s methylationEPIC BeadChip
Authors: Radhika Dhingra , Kwee Lydia Coulter , Diaz-Sanchez David , Devlin Robert B. , Cascio Wayne , Haynes Carol , Hauser Elizabeth R. , Gregory Simon , Shah Svati , Kraus William , Olden Kenneth , Ward-Caviness Cavin K. 
Published: November 2018

AbstractDNA methylation age (DNAm age) has become a widely utilized epigenetic biomarker for the aging process. The Horvath method for determining DNAm age is perhaps the most widely utilized and validated DNA methylation age assessment measure. Horvath DNAm age is calculated based on methylation measurements at 353 loci which were present on Illumina’s 450k and 27k DNA methylation microarrays. With the increasing use of the more recently developed Illumina MethylationEPIC (850k) microarray, it is worth revisiting this widely used aging measure to evaluate differences in DNA methylation age estimation based on array design. Of the requisite 353 loci, 17 are missing from the current 850k microarray. Using 17 datasets with 27k, 450k, and/or 850k methylation data, we calculated and compared each sample’s epigenetic age estimated from all 353 loci required from the Horvath DNAm age calculator (full), and using only the 336 loci present on the 27k, 450k, and 850k arrays (reduced). In 450k/27k data, missing loci caused underestimation of epigenetic age when compared with the full clock. Underestimation of full epigenetic age grew from ages 0 to ~20, remaining stable thereafter (mean= −3.46 y, SD=1.13) years for individuals ≥20 years. Underestimation of DNAm age by the reduced 450k/27k data was similar to the underestimation observed in the 850k data indicating that array differences in DNAm age estimation are primarily driven by missing probes. Correlations between age and DNAm age were not dependent on missing probes or on array designs and consequently associations between DNAm age and outcomes such as sex remained the same independent of missing probes and probe design. In conclusion, DNAm age estimations are array dependent driven by missing probes between arrays. Though correlations and associations with DNAm age may remain the same, researchers should exercise caution when interpreting results based on absolute differences in DNAm age or when mixing samples assayed on different arrays.DisclaimerThis paper has been reviewed by the National Health and Environmental Effects Research Laboratory, U.S. EPA, and is approved for publication. Approval does not signify that the contents necessarily reflect the views and policies of the agency, nor does mention of trade names or commercial products constitute endorsement or recommendation for use. The authors declare they have no competing financial interests.
Diversification in the microlepidopteran genusMompha(Lepidoptera: Gelechioidea: Momphidae) is explained more by tissue specificity than host plant family
Authors: Bruzzese Daniel J. , Wagner David L. , Harrison Terry , Jogesh Tania , Overson Rick P. , Wickett Norman J. , Raguso Robert A. , Skogen Krissa A. 
Published: November 2018

AbstractInsect herbivores and their hostplants constitute much of Earth’s described diversity, but how these often-specialized associations evolve and generate biodiversity is still not fully understood. We combined detailed hostplant data and comparative phylogenetic analyses of the lepidopteran family Momphidae to explore how shifts in the use of hostplant resources, not just hostplant taxonomy, contribute to the diversification of phytophagous insect lineages. We generated two phylogenies primarily from momphid species in the nominate genus,MomphaHübner. A six-gene phylogeny was constructed with exemplars from Onagraceae hosts in western and southwestern USA and a cytochromecoxidase subunit 1 (COI) phylogeny utilized both our collected sequences and publicly available accessions from the Barcode of Life Data System. Coalescent-based analyses combined with morphological data revealed ca. 56 undescribedMomphaspecies-level taxa, many of which are hostplant specialists on southwestern USA Onagraceae. Our phylogenetic reconstructions identified four major momphid clades: 1) an Onagraceae flower- and fruit-feeding clade, 2) a Melastomataceae galling clade, 3) an Onagraceae and Rubiaceae leafmining clade, and 4) a heterogeneous clade associated with multiple hostplant families, plant tissues, and larval feeding modes. Ancestral trait reconstructions on the COI tree identified leafmining on Onagraceae as the ancestral state for Momphidae. Cophylogenetic analyses detected loose phylogenetic tracking of hostplant taxa. Our study finds that shifts along three hostplant resource axes (hostplant taxon, plant tissue type, and larval feeding mode) contributed to the evolutionary success and diversification ofMompha. More transitions between exploited host tissue types than between hostplant families indicated that exploited host tissue (without a change in host) played an unexpectedly large role in the diversification of these moths.