bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of surface topography and taper mismatch on head-stem modular junction contact mechanics during assembly in modern total hip replacement
Authors: Gustafson Jonathan A. , Mell Steven P. , Levine Brett , Pourzal Robin , Lundberg Hannah J. 
Published: January 2022

AbstractImplant failure due to fretting corrosion at the head-stem modular junction is an increasing problem in modular total hip arthroplasty. The effect of varying microgroove topography on modular junction contact mechanics has not been well characterized. The aim of this work was to employ a novel, microgrooved finite element (FEA) model of the hip taper interface and assess the role of microgroove geometry and taper mismatch angle on the modular junction mechanics during assembly. A two-dimensional, axisymmetric FEA model was created using a modern 12/14 taper design of a CoCrMo femoral head taper and Ti6Al4V stem taper. Microgrooves were modelled at the contacting interface of the tapers and varied based on height and spacing measurements obtained from a repository of measured retrievals. Additionally, taper angular mismatch between the head and stem was varied to simulate proximal- and distal-locked engagement. Forty simulations were conducted to parametrically evaluate the effects of microgroove surface topography and angular mismatch on predicted contact area, contact pressure, and equivalent plastic strain. Multiple linear regression analysis was highly significant (p < 0.001; R2> 0.74) for all outcome variables. The regression analysis identified microgroove geometry on the head taper to have the greatest influence on modular junction contact mechanics. Additionally, there was a significant second order relationship between both peak contact pressure (p < 0.001) and plastic strain (p < 0.001) with taper mismatch angle. These modeling techniques will be used to identify the implant parameters that maximize taper interference strength via large in-silico parametric studies.
Additive genetic effects in interacting species jointly determine the outcome of caterpillar herbivory
Authors: Gompert Zachariah , Saley Tara , Philbin Casey , Yoon Su’ad A. , Perry Eva , Sneck Michelle E. , Harrison Joshua G. , Buerkle C. Alex , Fordyce James A. , Nice Chris C. , Dodson Craig , Lebeis Sarah L. , Lucas Lauren K. , Forister Matthew L. 
Published: January 2022

AbstractPlant-insect interactions are common and important in basic and applied biology. Trait and genetic variation can affect the outcome and evolution of these interactions, but the relative contributions of plant and insect genetic variation and how these interact remain unclear and are rarely subject to assessment in the same experimental context. Here we address this knowledge gap using a recent host range expansion onto alfalfa by the Melissa blue butterfly. Common garden rearing experiments and genomic data show that caterpillar performance depends on plant and insect genetic variation, with insect genetics contributing to performance earlier in development and plant genetics later. Our models of performance based on caterpillar genetics retained predictive power when applied to a second common garden. Much of the plant genetic effect could be explained by heritable variation in plant phytochemicals, especially saponins, peptides, and phosphatidyl cholines, providing a mechanistic understanding of variation in the species interaction. We find evidence of polygenic, mostly additive effects within and between species, with consistent effects of plant genotype on growth and development across multiple butterfly species. Our results inform theories of plant-insect coevolution and the evolution of diet breadth in herbivorous insects and other host-specific parasites.Teaser summaryThe combined, additive effects of plant and insect genetic variation explain Melissa blue caterpillar growth and development on alfalfa plants.
A quantitative, genome-wide analysis inDrosophilareveals transposable elements’ influence on gene expression is species-specific
Authors: Fablet Marie , Salces-Ortiz Judit , Jacquet Angelo , Menezes Bianca F. , Dechaud Corentin , Veber Philippe , Rebollo Rita , Vieira Cristina 
Published: January 2022

AbstractTransposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of severalDrosophila melanogasterandDrosophila simulanswild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes inD. simulanscompared toD. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes inD. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark inD. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.Significance StatementTransposable elements (TEs) are parasitic DNA sequences that are widespread components of all genomes. In this study, we combined genomic, transcriptomic and epigenomic high-throughput data produced from ovarian samples ofDrosophila melanogasterandDrosophila simulanswild-type strains, in order to finely quantify the genome-wide influence of TE insertions on gene expression. Our results uncover contrasted patterns depending on the strain, which may have evolutionary impacts.
Parallels of quantum superposition in ecological models: from counterintuitive patterns to eco-evolutionary interpretations of cryptic species
Authors: Angeler David G. , Fried-Petersen Hannah B. 
Published: January 2022

AbstractSuperposition, i.e. the ability of a particle (electron, photon) to occur in different states or positions simultaneously, is a hallmark in the subatomic world of quantum mechanics but non-sensical from the perspective of macro-systems such as ecosystems and other complex systems of people and nature. Using time series and spatial analysis of bird, phytoplankton and benthic invertebrate communities, this paper shows that superposition can occur analogously in redundancy analysis (RDA), a form of canonical ordination frequently used by ecologists. Specifically, we used correlation analysis to show that species can be associated simultaneously with different orthogonal axes in RDA models, a pattern reminiscent of superposition. We discuss this counterintuitive result in relation to the statistical and mathematical features of RDA and the recognized limitations with current traditional species concepts based on vegetative morphology. We suggest that such “quantum weirdness” is reconcilable with classical ecosystems logic when the focus of research shifts from morphological species to cryptic species that consist of genetically and ecologically differentiated subpopulations. We support our argument with theoretical discussions of eco-evolutionary interpretations that should become testable once suitable data are available.
Metabolic resource overlap impacts on the competition of phyllosphere bacteria
Authors: Schlechter Rudolf O. , Kear Evan J. , Bernach Michał , Remus Daniela M. , Remus-Emsermann Mitja N. P. 
Published: January 2022

ABSTRACTThe phyllosphere is densely colonised by rich microbial communities, despite sparse and heterogeneously distributed resources. The limitation of resources is expected to drive bacterial competition resulting in exclusion or coexistence based on fitness differences and resource overlap between individual colonisers. We studied the impact of resource competition by determining the effects of different bacterial colonisers on the growth of the model epiphytePantoea eucalypti299R (Pe299R). Resource overlap was predicted based on genome-scale metabolic modelling. By combining results of metabolic modelling and pairwise competitions in theArabidopsis thalianaphyllosphere andin vitro, we found that ten resources sufficed to explain fitness of Pe299R. An effect of both resource overlap and phylogenetic relationships was found on competition outcomesin vitroas well as in the phyllosphere. However, effects of resource competition were much weaker in the phyllosphere when compared toin vitroexperiments. When investigating growth dynamics and reproductive success at the single-cell resolution, resource overlap and phylogenetic relationships are only weakly correlated with epiphytic Pe299R reproductive success, indicating that the leaf’s spatial heterogeneity mitigates resource competition. Although the correlation is weak, the presence of competitors led to the development of Pe299R subpopulations that experienced different life histories and cell divisions. Surprisingly, in somein plantacompetitions, Pe299R benefitted from the presence of epiphytes despite high resource overlap to the competitor strain suggesting other factors having stronger effects than resource competition. This study provides fundamental insights into how bacterial communities are shaped in heterogeneous environments and provides a framework to predict competition outcomes.
Trophic ecology of deep-sea megafauna in the ultra-oligotrophic Southeastern Mediterranean Sea
Authors: Guy-Haim Tamar , Stern Nir , Sisma-Ventura Guy 
Published: January 2022

ABSTRACTThe trophic ecology of fourteen species of bathybenthic and bathypelagic fishes and six species of bathybenthic decapod crustaceans from the continental slope and rise of the Southeastern Mediterranean Sea (SEMS) was examined using stable isotope analysis. Mean δ13C values among fish species varied by more than 4.0‰, from −20.85‰ (Macroramphosus scolopax) to −16.57‰ (Conger conger and Centrophorus granulosus), and increased as a function of depth (200 - 1400 m). Mean δ13C values of the crustaceans showed smaller variation, between −16.38‰ (Polycheles typhlops) and −18.50‰ (Aristeus antennatus). This suggests a shift from pelagic to regenerated benthic carbon sources with depth. Benthic carbon regeneration is further supported by the low benthic-pelagic POM-δ13C values, averaging −24.7 ± 1.2‰, and the mixing model results, presenting very low contribution of epipelagic POM to the bathyal fauna. Mean δ15N values of fish and crustacean species ranged 7.91 ± 0.36‰ to 11.36 ± 0.39‰ and 6.15 ± 0.31‰ to 7.69 ± 0.37‰, respectively, resulting in trophic position estimates, occupying the third and the fourth trophic levels. Thus, despite the proximity to the more productive areas of the shallow shelf, low number of trophic levels (TL~1.0) and narrow isotopic niche breadths (SEAc <1) were observed for bathybenthic crustaceans (TL = 3.62 ± 0.22) and bathypelagic fishes (TL = 4.33 ± 0.34) in the study area – probably due to the ultra-oligotrophic state of the SEMS resulting in limited carbon sources. Our results, which provide the first trophic description of deep-sea megafauna in the SEMS, offer insight into the carbon sources and food web structure of deep-sea ecosystems in oligotrophic marginal seas, and can be further used in ecological modeling and support the sustainable management of marine resources in the deep Levantine Sea.
A new demethylase gene OsDML4 involved in high temperature induced floury endosperm formation in rice (Oryza sativa L.)
Authors: Yan Yan , Li Chao , Liu Zhen , Zhuang Jun-Jie , Kong Jia-Rui , Yang Zhen-Kun , Yu Jie , Alam Mohammad Shah , Ruan Cheng-Cheng , Zhang Heng-Mu , Xu Jian-Hong 
Published: January 2022

AbstractHigh temperature (HT) can affect the accumulation of seed storage materials and cause adverse effects on the yield and quality in rice. DNA methylation plays an important role in plant growth and development. However, the temperature and DNA methylation interaction on rice seed development has not been studied yet. Here, we identified a new demethylase gene OsDML4 and discovered its function on cytosine demethylation to affect the endosperm formation during the grain filling. Knockout of OsDML4 induced floury endosperm only under HT, which resulted from dramatically reduced the transcription and accumulation of glutelins and 16-kDa prolamin. The expression of two important transcription factors RISBZ1 and RPBF was significantly declined in the osdml4 mutants. The absence of OsDML4 also caused adverse effects on the formation of protein bodies (PBs), the number of PB-II was greatly decreased and incomplete PB-II with empty space and abnormally shaped PB-II were observed in the osdml4 mutants. Whole-genome bisulfite sequencing analysis of seeds at 15 days after pollination revealed much higher global methylation levels of CG, CHG and CHH contexts in the osdml4 mutants compared to wild type (WT). Moreover, the methylation status of RISBZ1 promoter was hypermethylated but RPBF promoter was nearly unchanged. No significant difference was detected between WT and the osdml4 mutants under room temperature. In conclusion, our study demonstrates a novel OsDML4-mediated epigenetic regulatory mechanism involving in the formation of floury endosperm, which will provide a new perspective in regulating endosperm development and the accumulation of SSPs in rice.
Using Survey Data to Estimate the Impact of the Omicron Variant on Vaccine Efficacy against COVID-19 Infection
Authors: Rufino Jesús , Baquero Carlos , Frey Davide , Glorioso Christin A. , Ortega Antonio , Reščič Nina , Roberts Julian Charles , Lillo Rosa E. , Menezes Raquel , Champati Jaya Prakash , Anta Antonio Fernádez 
Published: January 2022

AbstractData collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID, are used to evaluate the impact of the Omicron variant (in South Africa and other countries) on the prevalence of COVID-19 among unvaccinated and vaccinated population, in general and discriminating by the number of doses. In South Africa, we observe that the prevalence of COVID-19 in December (with strong presence of Omicron) among the unvaccinated population is comparable to the prevalence during the previous wave (in August-September), in which Delta was the variant with the largest presence. However, among vaccinated, the prevalence of COVID-19 in December is much higher than in the previous wave. In fact, a significant reduction of the vaccine efficacy is observed from August-September to December. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses, and from 0.51 to 0.09 for those vaccinated with one dose. The study is then extended to other countries in which Omicron has been detected, comparing the situation in October (before Omicron) with that of December. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around −0.6 between the measured prevalence of Omicron and the vaccine efficacy.
Reconstitution of an active human CENP-E motor
Authors: Craske Benjamin , Legal Thibault , Welburn Julie P.I. 
Published: January 2022

AbstractCENP-E is a large kinesin motor protein which plays pivotal roles in mitosis by facilitating chromosome capture, alignment and promoting microtubule flux in the spindle. So far, it has not been possible to obtain active human CENP-E to study its molecular properties. Xenopus CENP-E motor has been characterised in vitro and is used as a model motor, however its protein sequence differs significantly from human CENP-E. Here, we characterise human CENP-E motility in vitro. Full-length CENP-E exhibits an increase in run length and longer residency times on microtubules when compared to CENP-E motor truncations, indicating that the C-terminal microtubule binding site enhances the processivity when the full-length motor is active. In contrast to constitutively active human CENP-E truncations, full-length human CENP-E has a reduced microtubule landing rate in vitro, suggesting that the non-motor coiled coil regions self-regulate motor activity. Together, we demonstrate that human CENP-E is a processive motor, providing a useful tool to study the mechanistic basis for how human CENP-E drives chromosome congression and spindle organisation during human cell division.
CRISPR-Cas systems in Fusobacterium: An untapped genetic frontier
Authors: Umaña Ariana , Slade Daniel J. 
Published: January 2022

ABSTRACTFusobacterium nucleatum has recently received significant attention for its strong connection with the acceleration and gravity of multiple cancers (e.g., colorectal, pancreatic, esophageal). However, our understanding of the molecular mechanisms that drive infection by this ‘oncomicrobe’ have been hindered by a lack of universal genetic tools. Herein we report a global bioinformatic identification and characterization of multiple Fusobacterium CRISPR-Cas adaptive immune systems including Cas13c, and detailed report of the proteins, spacer/repeat loci, trans- activating CRISPR RNA (tracrRNA), and CRISPR RNA (cRNA) from a Type II-A CRISPR-Cas9 system. Since most Fusobacterium are currently genetically intractable, this CRISPR-Cas bioinformatic roadmap could be used to build new genome editing and transcriptional tuning tools to characterize an increasingly important genus of human opportunistic-pathogens connected to the onset, progression, and severity of cancer.
Genomes of the extinct Sicilian wolf reveal a complex history of isolation and admixture with ancient dogs
Authors: Ciucani Marta Maria , Ramos-Madrigal Jazmín , Hernández-Alonso Germán , Carmagnini Alberto , Aninta Sabhrina Gita , Scharff-Olsen Camilla Hjorth , Lanigan Liam Thomas , Fracasso Ilaria , Clausen Cecilie G. , Aspi Jouni , Kojola Ilpo , Baltrūnaitė Laima , Balčiauskas Linas , Moore Jane , Åkesson Mikael , Saarma Urmas , Hindrikson Maris , Hulva Pavel , Bolfíková Barbora Černá , Nowak Carsten , Godinho Raquel , Smith Steve , Paule Ladislav , Nowak Sabina , Mysłajek Robert W. , Brutto Sabrina Lo , Ciucci Paolo , Boitani Luigi , Vernesi Cristiano , Stenøien Hans K. , Smith Oliver , Frantz Laurent , Rossi Lorenzo , Angelici Francesco Maria , Cilli Elisabetta , Sinding Mikkel-Holger S. , Gilbert M. Thomas P. , Gopalakrishnan Shyam 
Published: January 2022

SummaryThe Sicilian wolf represented the only population of wolves living on a Mediterranean island until the first half of the twentieth century (1930s-1960s)1–7. Previous studies hypothesised that they remained isolated from mainland wolves from the end of the Last Glacial Maximum (LGM)8,9, until human persecutions led them to extinction1–7.There are only seven known Sicilian wolf specimens from the 19th and 20th century preserved in museums in Italy and recent morphometric analyses assigned them to the new subspeciesCanis lupus cristaldii10. To better understand the origins of the Sicilian wolf, and its relationship to other wolf populations, we sequenced four whole genomes (3.8×-11.6×) and five mitogenomes. We investigated the relationship between Sicilian wolves and other modern breeds to identify potential admixture. Furthermore, considering that the last land-bridge between Sicily and Italy disappeared after the LGM11, around 17 kya, we explored the possibility that the Sicilian wolf retained ancestry from ancient wolf and dog lineages. Additionally, we explored whether the long-term isolation might have affected the genomic diversity, inbreeding levels and genetic load of the Sicilian wolf.Our findings show that the Sicilian wolves shared most ancestry with the modern Italian wolf population but are better modelled as admixed with European dog breeds, and shared traces of Eneolithic and Bronze age European dogs. We also find signatures of severe inbreeding and low genomic diversity at population and individual levels due to long-term isolation and drift, suggesting also low effective population size.
Virus-assisted directed evolution of enhanced suppressor tRNAs in mammalian cells
Authors: Kelemen Rachel E. , Jewel Delilah , Huang Rachel L. , Zhu Zeyu , Cao Xiaofu , Pasha Muhammad , Anthony Jon , van Opijnen Tim , Chatterjee Abhishek 
Published: January 2022

AbstractSite-specific incorporation of unnatural amino acids (Uaas) in living cells relies on engineered aminoacyl-tRNA synthetase/tRNA pairs borrowed from a distant domain of life. Such heterologous suppressor tRNAs often show poor intrinsic activity, presumably due to the failure to optimally interact with a non-native translation system. This limitation can be addressed in E. coli using directed evolution. However, no suitable selection system is currently available to do the same in mammalian cells. Here we report virus-assisted directed evolution of tRNAs (VADER) in mammalian cells, which employs a double-sieve selection scheme to facilitate single-step enrichment of active-yet-orthogonal tRNA mutants from naïve libraries. Using VADER, we developed improved mutants of M. mazei pyrrolysyl-tRNA, the most popular Uaa mutagenesis platform in eukaryotes. We also show that the higher activity of the most efficient mutants is specific for mammalian cells, alluding to an improved interaction with the unique mammalian translation system.
Credit constraints and the survival and growth of beginning farms
Authors: Key Nigel 
Published: January 2022

PurposeCredit may help farmers survive and grow by helping farm households cope with farm or off-farm income variation and by allowing farmers to adopt more efficient production technologies and take advantage of scale economies. This study estimates how credit constraints affect the survival and growth of beginning farms and explores how this effect varies depending on the age of the farm operator.Design/methodology/approachFarms businesses are classified as credit constrained using a measure of repayment capacity: the interest expense ratio (interest expenses relative to gross income). Linked data from consecutive Agricultural Censuses are used to track individual farms over time.FindingsResults show that beginning farms with a high interest expense ratio take on less new debt over the subsequent five years. These credit-constrained farms were found to have lower five-year survival and growth rates than similar unconstrained farms. The negative effect of being constrained on growth is greater for farms with operators younger than 40 years old.Practical implicationsThe finding that credit constraints impede the growth and survival of beginning farms supports a rationale for targeted loan programs designed to help beginning farmers. Results suggest that some of the benefits from these programs will be greater for farms with younger operators.Originality/valueThis study is the first to estimate the effect of credit constraints on the survival and growth of farm businesses. The expansive farm-level panel dataset, which includes almost all beginning farmers in the US, allows for precise coefficient estimates while controlling for numerous farm and operator characteristics.