bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bicaudal Cis required for the function of the follicular epithelium during oogenesis inRhodnius prolixus
Authors: Pascual Agustina , Vilardo Emiliano S. , Taibo Catalina , García Julia Sabio y , Pomar Rolando Rivera 
Published: February 2020

AbstractThe morphology and physiology of the oogenesis have been well studied in the vector of Chagas diseaseRhodnius prolixus. However, the molecular interactions that regulate the process of egg formation, key for the reproductive cycle of the vector, is still largely unknown. In order to understand the molecular and cellular basis of the oogenesis we examined the function of the geneBicaudal C(BicC) during oogenesis and early development ofR. prolixus. We show thatR. prolixus BicC(Rp-BicC) gene is expressed in the germarium, with cytoplasmic distribution, as well as in the follicular epithelium of the developing oocytes. RNAi silencing ofRp-BicCresulted in sterile females that lay few, small, non-viable eggs. The ovaries are reduced in size and show a disarray of the follicular epithelium. This indicates thatRp-BicChas a central role in the regulation of oogenesis. Although the follicular cells are able to form the chorion, the uptake of vitelline by the oocytes is compromised. We show evidence that the polarity of the follicular epithelium and the endocytic pathway, which is crucial for the proper yolk deposition, are affected. This study provides insights into the molecular mechanisms underlying oocyte development and show thatRp-BicCis important for de developenta of the egg and, therefore, a key player in the reproduction of this Chagas disease vector.Author summaryThe oogenesis is the process of egg formation. It is essential to guarantee transgenerational inheritance. It implies the differentiation of the gamete (oocyte) from a niche of stem cells in the germ line, the accumulation of yolk, and the formation of the chorion. These events are entangled in a regulated manner by the concerted communication between the different cell types that form the ovary. It is regulated by endogenous gene networks and linked to the physiological state of the insect by hormonal clues. This timely orchestrated process represents the interaction of gene networks. The genetic regulation behind the oogenesis is largely unknown inRhodnius prolixus. Here we identified a gene required for egg formation that interferes the uptake of the yolk by affecting the functional integrity of the follicular epithelium. Our results are of interest for a better understanding of a complex process essential for the survival of vector populations and provide knowledge to envisage and design new strategies for vector control.
Dynamic regulation of JAK-STAT signaling through the prolactin receptor predicted by computational modeling
Authors: Mortlock Ryland D. , Georgia Senta K. , Finley Stacey D. 
Published: February 2020

ABSTRACTIntroductionHormones signal through various receptors and cascades of biochemical reactions to expand beta cell mass during pregnancy. Harnessing this phenomenon to treat beta cell dysfunction requires quantitative understanding of the signaling at the molecular level. This study explores how different regulatory elements impact JAK-STAT signaling through the prolactin receptor in pancreatic beta cells.MethodsA mechanistic computational model was constructed to describe the key reactions and molecular species involved in JAK-STAT signaling in response to the hormone prolactin. The effect of including and excluding different regulatory modules in the model structure was explored through ensemble modeling. A Bayesian approach for likelihood estimation was used to parametrize the model to experimental data from the literature.ResultsReceptor upregulation, combined with either inhibition by SOCS proteins, receptor internalization, or both, was required to obtain STAT5 dynamics matching experimental results for INS-1 cells treated with prolactin. Multiple model structures could fit the experimental data, and key findings were conserved across model structures, including faster dimerization and nuclear import rates of STAT5B compared to STAT5A. The model was validated using experimental data from rat primary beta cells not used in parameter estimation. Probing the fitted, validated model revealed possible strategies to modulate STAT5 signaling.ConclusionsJAK-STAT signaling must be tightly controlled to obtain the biphasic response in STAT5 activation seen experimentally. Receptor up-regulation, combined with SOCS inhibition, receptor internalization, or both is required to match experimental data. Modulating reactions upstream in the signaling can enhance STAT5 activation to increase beta cell mass.
Autophagy is induced during plant grafting for wound healing
Authors: Kurotani Ken-ichi , Tabata Ryo , Kawakatsu Yaichi , Sugita Ryohei , Okayasu Koji , Tanoi Keitaro , Notaguchi Michitaka 
Published: February 2020

SummaryGrafting is an important technique in agriculture to obtain several good traits such as high disease tolerance and high yield by exchanging root system. However, the underlined cellular processes to compensate the wound damage and repair tissues were largely unknown.We analyzed two graft combinations: Nicotiana benthamiana (Nb) homograft as a compatible, wound repairing model and Nb heterograft with Arabidopsis thaliana (At) as an incompatible and more stressful model, which we recently identified as an exceptional maintainable interfamily grafting.In both graft combinations, nutrient loss was observed in gene expression after grafting, where the level of nutrient loss was more sever in heterografts. Transmission electron micrographs of Nb/At heterografts suggested that microautophagy was induced in cells near the graft boundary. In At seedling micrografting, the fluorescence of autophagy protein marker GFP-ATG8 was highly observed at graft junction especially in cambial region. In At atg2 mutant homografts, growth after grafting decreased compared with wild-type homografts. Moreover, when NbATG5 knocked-down Nb scion was grafted to At stock, the successful rate of grafting was significantly decreased.Altogether, these results suggest that component of autophagy is induced during grafting and has a role in wound healing.
Cytosine methylation dynamics during post-testicular sperm maturation in mammals
Authors: Galan Carolina , Serra Ryan W. , Sun Fengyun , Rinaldi Vera D. , Conine Colin C. , Rando Oliver J. 
Published: February 2020

ABSTRACTBeyond the haploid genome, mammalian sperm contribute a payload of epigenetic information which can modulate offspring phenotypes. Recent studies have shown that the small RNA payload of sperm undergoes extensive remodeling during post-testicular maturation in the epididymis. Intriguingly, epididymal maturation has also been linked to changes in the sperm methylome, suggesting that the epididymis might play a broader role in remodeling the sperm epigenome. Here, we build on prior studies of the maturing sperm methylation landscape, further characterizing the genome-wide methylation landscape in seven germ cell populations collected from throughout the male reproductive tract. Overall, we find very few changes in the cytosine methylation landscape between testicular germ cell populations and cauda epididymal sperm, demonstrating that the sperm methylome is largely stable throughout post-testicular maturation. Intriguingly, although our sequencing data suggested that caput epididymal sperm exhibit a highly unusual methylome, follow-up studies revealed that this resulted from contamination of caput sperm by extracellular DNA. Extracellular DNA formed web-like structures that ensnared sperm, was present only in the caput epididymis of virgin males, where it was associated with citrullinated histone H3 and presumably resulted from a PAD-driven genome decondensation process. Taken together, our data emphasize the stability of the cytosine methylation landscape in mammalian sperm, and identify a surprising but transient period during which immature sperm are associated with extracellular DNA.
Generating synthetic aging trajectories with a weighted network model using cross-sectional data
Authors: Farrell Spencer , Mitnitski Arnold , Rockwood Kenneth , Rutenberg Andrew 
Published: February 2020

ABSTRACTWe develop a computational model of human aging that generates individual health trajectories with a set of observed health attributes. Our model consists of a network of interacting health attributes that stochastically damage with age to form health deficits, leading to eventual mortality. We train and test the model for two different cross-sectional observational aging studies that include simple binarized clinical indicators of health. In both studies, we find that cohorts of simulated individuals generated from the model resemble the observed cross-sectional data in both health characteristics and mortality. We can generate large numbers of synthetic individual aging trajectories with our weighted network model. Predicted average health trajectories and survival probabilities agree well with the observed data.
Antibiotics affect migratory restlessness orientation
Authors: Werber Yuval , Natan Eviatar , Lavner Yizhar , Vortman Yoni 
Published: February 2020

AbstractMagnetoreception is a sense that allows the organism to perceive and act according to different parameters of the magnetic field. This magnetic sense plays a part in many fundamental processes in various living organisms. Much effort was expended in finding the ‘magnetic sensor’ in animals. While some experiments show a role of the ophthalmic nerve in magnetic sensing, others show that effects of light on processes in the retina are involved. According to these inconclusive and puzzling findings, the scientific community has yet to reach an agreement concerning the underlying mechanism behind animal magnetic sensing. Recently, the symbiotic magnetotaxis hypothesis has been forwarded as a mechanistic explanation for the phenomenon of animal magnetoreception. It suggests a symbiotic relationship between magnetotactic bacteria (MTB) and the navigating host. Here we show that in contrast to the control group, antibiotic treatment caused a lack of clear directionality in an Emlen funnel experiment. Accordingly, the antibiotics treatment group showed a significant increase in directional variance. This effect of antibiotics on behaviors associated with animal magnetic sensing is, to the best of our knowledge, the first experimental support of the symbiotic magnetotactic hypothesis.
Network efficiency predicts resilience to cognitive decline in elderly at risk for Alzheimer’s
Authors: Fischer Florian U. , Wolf Dominik , Fellgiebel Andreas ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: February 2020

AbstractTo determine whether white matter network efficiency (WMNE) may be a surrogate marker of the physiological basis of resilience to cognitive decline in elderly persons without dementia and age and AD-related cerebral pathology, we quantified WMNE from baseline MRI scans and investigated its association with longitudinal neuropsychological assessments independent of baseline amyloid, tau and white matter hyperintensity volume. 85 cognitively normal elderly subjects and patients with mild cognitive impairment (MCI) with baseline diffusion imaging, CSF specimens, AV45-PET and longitudinal cognitive assessments were included. WMNE was calculated from reconstructed cerebral white matter networks for each individual. Mixed linear effects models were estimated to investigate the association of higher resilience to cognitive decline with higher WMNE and the modulation of this association by increased cerebral amyloid, CSF tau or WMHV. For the majority of cognitive outcome measures, higher WMNE was associated with higher resilience to cognitive decline independently of pathology measures (beta: .074 – .098; p: .011 – .039). Additionally, WMNE was consistently associated with higher resilience to cognitive decline in subjects with higher cerebral amyloid burden (beta: .024 – .276; p: .000 – .036) and with lower CSF tau (beta: −.030 – −.074; p: .015 – .002) across all cognitive outcome measures. The results of this study indicate that WMNE in particular and possibly white matter organization in general may be worthy targets of investigation to provide measures quantifying a patient’s resilience to cognitive decline and thus provide an individual prognosis.
Coordinated Interaction: A model and test for globally signed epistasis in complex traits
Authors: Sheppard Brooke , Rappoport Nadav , Loh Po-Ru , Sanders Stephan J. , Dahl Andy , Zaitlen Noah 
Published: February 2020

AbstractInteractions between genetic variants – epistasis – is pervasive in model systems and can profoundly impact evolutionary adaption, population disease dynamics, genetic mapping, and precision medicine efforts. In this work we develop a model for structured polygenic epistasis, calledCoordinated Interaction(CI), and prove that several recent theories of genetic architecture fall under the formal umbrella of CI. Unlike standard polygenic epistasis models that assume interaction and main effects are independent, in the CI model, sets of SNPs broadly interact positively or negatively, on balance skewing the penetrance of main genetic effects. To test for the existence of CI we propose theeven-odd(EO) test and prove it is calibrated in a range of realistic biological models. Applying the EO test in the UK Biobank, we find evidence of CI in 14 of 26 traits spanning disease, anthropometric, and blood categories. Finally, we extend the EO test to tissue-specific enrichment and identify several plausible tissue-trait pairs. Overall, CI is a new dimension of genetic architecture that can capture structured, systemic interactions in complex human traits.
Activation of WNT signaling restores the facial deficits in a zebrafish with defects in cholesterol metabolism
Authors: Castro Victoria L. , Reyes-Nava Nayeli G. , Sanchez Brianna B. , Gonzalez Cesar G. , Quintana Anita M. 
Published: February 2020

AbstractBackgroundInborn errors of cholesterol metabolism occur as a result of mutations in the cholesterol synthesis pathway (CSP). Although mutations in the CSP cause a multiple congenital anomaly syndrome, craniofacial abnormalities are a hallmark phenotype associated with these disorders. Previous studies have established that mutation of the zebrafishhmgcs1gene (Vu57 allele), which encodes the first enzyme in the CSP, causes defects in craniofacial development and abnormal neural crest cell (NCC) differentiation. However, the molecular mechanisms by which the products of the CSP disrupt NCC differentiation are not completely known. Cholesterol is known to regulate the activity of WNT signaling, an established regulator of NCC differentiation. We hypothesized that defects in cholesterol synthesis reduce WNT signaling, consequently resulting in abnormal craniofacial development.MethodsTo test our hypothesis we performed a combination of pharmaceutical inhibition, gene expression assays, and targeted rescue experiments to understand the function of CSP and WNT signaling during craniofacial development.ResultsWe demonstrate reduced expression ofaxin2, a WNT downstream target gene in homozygous carriers of the Vu57 allele and in larvae treated with Ro-48-8071, which inhibits the synthesis of cholesterol. Moreover, activation of WNT signaling via treatment with a WNT agonist completely restored the craniofacial defects present in the Vu57 allele.ConclusionsCollectively, these data suggest interplay between the CSP and WNT signaling during craniofacial development.
The work of early childhood coaches in one US state
Authors: Hnasko Amy 
Published: February 2020

PurposeThis paper discusses the findings of a mixed-methods study of early childhood instructional coaches employed in state-funded preschool (aged three and four years) programs in the state of New Jersey (NJ) in the United States (US), highlighting a case study of one coach that provides an example of individual and organizational factors influencing the work.Design/methodology/approachAn online survey was distributed to all coaches (master teachers) in 35 districts' early childhood programs. Two master teachers were then studied for a period of five months. During that time, three structured interviews were conducted, focused observations occurred each month, and coach logs were collected.FindingsThe findings of the data analyses illuminated both individual (i.e., a coach's own professional development) and organizational (i.e., varying interpretations of role) factors that influenced the work of the early childhood coaches.Research limitations/implicationsThe data in this paper is limited to one US state's approach to early childhood coaching. The case study data examined is limited to the contexts of the specific participating districts and master teachers involved. It is suggested that future research be conducted on a nationwide pool of instructional coaches.Practical implicationsThe findings of this study highlight the role of the state in providing more guidance surrounding the primary responsibilities of the master teacher. It is suggested that further attention be placed on creating and sustaining a professional development network for the master teachers serving NJ's early childhood programs.Originality/valueAs one of the few statewide studies of instructional coaching in early childhood, this study provides insights into how policy is translated into practice.
Habitat‐specific effects of bark on wood decomposition: Influences of fragmentation, nitrogen concentration and microbial community composition
Authors: Jones Jennifer M. , Heath Katy D. , Ferrer Astrid , Dalling James W. 
Published: February 2020

Abstract

Identifying the drivers of decomposition is critical for understanding carbon cycling dynamics in forest ecosystems. Woody biomass is an important pool of carbon, composed of bark and underlying wood which vary in structure, nutrient concentrations and exposure to the environment. We hypothesized that higher nutrient concentrations in bark would speed the decomposition of underlying wood, and that this effect would be greater in streams, where nutrients are less available to decomposers than on land.

Replicate branches of three tree species, with and without bark, were placed in streams and on land in a lowland tropical forest in Panama. After 3 and 11 months of decomposition, we measured mass loss and nitrogen (N) concentrations and sequenced the fungal and bacterial communities of both wood and bark tissues.

While bark decomposed faster than the underlying wood and had higher N concentrations, bark presence slowed wood mass loss. Nitrogen concentration could account for interspecific variation in wood mass loss, but not bark mass loss. In contrast, bark mass loss, but not wood mass loss, was faster in streams than on land, suggesting fragmentation is more important for bark mass loss in streams. Differences in fungal and bacterial community composition between bark and wood substrates were significant but small.

Our results indicate that bark can slow wood decomposition instead of promoting it, and that at least for branch wood, the primary drivers of decomposition differ between bark and wood. Differences in the factors driving decomposition rate between bark and wood suggest that the contribution of bark to the decomposition of woody biomass may depend on habitat.

A free Plain Language Summary can be found within the Supporting Information of this article.
Transcriptional response of Emiliania huxleyi under changing nutrient environments in the North Pacific Subtropical Gyre
Authors: Alexander Harriet , Rouco Mónica , Haley Sheean T. , Dyhrman Sonya T. 
Published: February 2020

SummaryThe widespread coccolithophore Emiliania huxleyi is an abundant oceanic phytoplankton, impacting the global cycling of carbon through both photosynthesis and calcification. Here, we examined the transcriptional responses of populations of E. huxleyi in the North Pacific Subtropical Gyre to shifts in the nutrient environment. Using a metatranscriptomic approach, nutrient‐amended microcosm studies were used to track the global metabolism of E. huxleyi. The addition of nitrate led to significant changes in transcript abundance for gene pathways involved in nitrogen and phosphorus metabolism, with a decrease in the abundance of genes involved in the acquisition of nitrogen (e.g. N‐transporters) and an increase in the abundance of genes associated with phosphate acquisition (e.g. phosphatases). Simultaneously, after the addition of nitrate, genes associated with calcification and genes unique to the diploid life stages of E. huxleyi significantly increased. These results suggest that nitrogen is a major driver of the physiological ecology of E. huxleyi in this system and further suggest that the addition of nitrate drives shifts in the dominant life‐stage of the population. Together, these results underscore the importance of phenotypic plasticity to the success of E. huxleyi, a characteristic that likely underpins its ability to thrive across a variety of marine environments.
Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species
Authors: Barbanti Anna , Torrado Hector , Macpherson Enrique , Bargelloni Luca , Franch Rafaella , Carreras Carlos , Pascual Marta 
Published: February 2020

AbstractHigh‐throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b‐RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b‐RAD protocols on non‐model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b‐RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade‐off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b‐RAD protocols on non‐model organisms with different genome sizes, helping decision‐making for a reliable and cost‐effective genotyping.