bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Platelet Lysate as Alternative of Fetal Bovine Serum for Enhanced Human in vitro Bone Resorption and Remodeling
Authors: de Wildt Bregje W.M. , Ito Keita , Hofmann Sandra 
Published: April 2022

AbstractTo study human physiological and pathological bone remodeling while addressing the principle of replacement, reduction and refinement of animal experiments (3Rs), human in vitro bone remodeling models are being developed. Despite increasing safety-, scientific-, and ethical concerns, fetal bovine serum (FBS), a nutritional medium supplement, is still routinely used in these models. To comply with the 3Rs and to improve the reproducibility of such in vitro models, xenogeneic-free medium supplements should be investigated. Human platelet lysate (hPL) might be a good alternative as it has been shown to accelerate osteogenic differentiation of mesenchymal stromal cells (MSCs) and improve subsequent mineralization. However, for a human in vitro bone model, hPL should also be able to adequately support osteoclastic differentiation and subsequent bone resorption. In addition, optimizing co-culture medium conditions in mono-cultures might lead to unequal stimulation of co-cultured cells. Here, we compared supplementation with 10% FBS vs. 10%, 5%, and 2.5% hPL for osteoclast formation and resorption by human monocytes (MCs) in mono-culture and in co-culture with (osteogenically stimulated) human MSCs. Our results indicate that the supplementation of hPL can lead to a less donor-dependent and more homogeneous osteoclastic differentiation of MCs when compared to supplementation with 10% FBS. In co-cultures, osteoclastic differentiation and resorption in the 10% FBS group was almost completely inhibited by MSCs, while the supplementation with hPL still allowed for resorption, mostly at low concentrations. The addition of hPL to osteogenically stimulated MSC mono- and MC-MSC co-cultures resulted in osteogenic differentiation and bone-like matrix formation, mostly at high concentrations. Therefore, we conclude that hPL could support both osteoclastic differentiation of human MCs and osteogenic differentiation of human MSCs in mono- and in co-culture, and that this can be balanced by the hPL concentration. Thus, the use of hPL could limit the need for FBS, which is currently commonly accepted for in vitro bone remodeling models.
Dispersal and Plant Arrangement Condition the Timing and Magnitude of Coffee Rust Infection
Authors: Van Cauwelaert Emilio Mora , González Cecilia González , Boyer Denis , Forooshani Zachary Hajian , Vandermeer John , Benítez Mariana 
Published: April 2022

AbstractOne central issue in coffee-leaf rust (Hemileia vastatrix) epidemiology is to understand what determines the intensity and the timing of yearly infections in coffee plantations. However, most experimental and theoretical studies report infection as an average at the plot level, obscuring the role of potentially key factors like rust dispersal or the planting pattern. Here, we first review the rust epidemic patterns of different sites, which reveal large variability in the duration and magnitude of the different epidemiologic phases. We then present a spatially explicit and parametrised model, where the host population is subdivided into discrete patches linked through spore dispersal, modelled as simple diffusion. With this model, we study the role of the planting arrangement, the dispersal intensity and plant-level variables on the maximum average tree infection (MATI) and its timing. Our results suggest that the epidemic timeline can be divided into two phases: a time lag and a growth phaseper se. The model shows that the combination of the dispersal magnitude and plant aggregation modifies the MATI and the time to MATI, mainly by preventing some plants from reaching their maximum peak during the epidemic. It also affects the epidemic curves, which can have a stepped, or a rather smooth pattern in plots with otherwise similar conditions. The initial rust infection modulates the time lag before the epidemic and the infected leaf-fall rate drastically changes the MATI. These findings highlight the importance of explicitly considering the spatial aspects of coffee agroecosystems when measuring and managing rust infection, and help us to further understand the spatio-temporal dynamics of ecological systems in general.
The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats
Authors: Munro Daniel , Wang Tengfei , Chitre Apurva S , Polesskaya Oksana , Ehsan Nava , Gao Jianjun , Gusev Alexander , Solberg Woods Leah C , Saba Laura M , Chen Hao , Palmer Abraham A , Mohammadi Pejman 
Published: April 2022

AbstractHeterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21,392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
Mathematical Modeling of Rhesus Cytomegalovirus (RhCMV) Placental Transmission in Seronegative Rhesus Macaques
Authors: Gong Yishu , Moström Matilda , Otero Claire , Valencia Sarah , Kaur Amitinder , Permar Sallie R. , Chan Cliburn 
Published: April 2022

AbstractApproximately 1 in 200 infants is born with congenital cytomegalovirus (CMV), making it the most common congenital infection. About 1 in 5 congenitally-infected babies will suffer long-term sequelae, including sensorineural deafness, intellectual disability, and epilepsy. CMV infection is highly species-dependent, and the Rhesus CMV (RhCMV) infection of rhesus monkey fetuses is the only animal model that replicates essential features of congenital CMV infection in humans, including placental transmission, fetal disease, and fetal loss. To better understand the determinants and dynamics of congenital CMV transmission, we developed a mathematical model for placental transmission, comprising of maternal, placental, and fetal compartments using parameters from literature and experimental data from RhCMV seronegative rhesus macaques inoculated with RhCMV at 7.7-9.0 weeks of pregnancy. The model was then used to study the effect of the timing of inoculation, maternal immune suppression, and hyper-immune globulin infusion on the risk of placental transmission in the context of primary and reactivated chronic maternal CMV infection.Author summaryCongenital cytomegalovirus (CMV) is the most common congenital infection in humans. Congenial CMV affects 1 in 200 infants, and can result in sensorineural deafness, intellectual disability, epilepsy, and death. The Rhesus CMV (RhCMV) model is the only animal model that replicates essential features of congenital CMV infection and fetal sequelae in humans and provides a critical experimental system to develop mechanistic insight. We propose a novel mathematical model for CMV transmission that integrates viral dynamics in the maternal, placental, and fetal compartments. We calibrate the model using data from RhCMV transmission experiments and show that the model can recapitulate experimental observations of primary versus reactivated chronic CMV infection in pregnancy, primary infection at different stages in pregnancy, and infection in the presence of varying degrees of immune suppression and hyper-immune globulin infusion. Our in-silico model provides a means to rapidly explore mechanistic hypotheses for the physical, viral, and immune determinants of CMV transmission to complement and support expensive and difficult experiments on non-human primates.
Genome-wide analysis reveals PhoP regulates pathogenicity in Riemerella anatipestifer
Authors: Zhang Yang , Wang Ying , Zhang Yanhao , Jia Xiangchao , Li Chenxi , Zhou Zutao , Hu Sishun , Li Zili 
Published: April 2022

AbstractDuck infectious serositis, also known as the Riemerella anatipestifer disease infects domestic ducks, geese, turkeys, and wild birds. However, the regulatory mechanism of its pathogenicity remains unclear. The phoP/phoR two-component system was first reported in gram-negative bacteria in our previous research and was demonstrated to be involved in virulence and gene expression. Here, the DNA-affinity-purified sequencing (DAP-seq) was applied to further explore the regulation of phoP/phoR to pathogenicity in R. anatipestifer. A conserved motif was identified in the upstream of 583 candidate target genes which were directly regulated by phoP. To further confirm the genes which are regulated by phoP/phoR, phoR and phoP, the single-gene deletion strains were constructed. The results of transcriptome analysis using next-generation RNA sequencing showed 136 differential expression genes (DEGs) between ΔphoP and RA-YM, and 183 DEGs between ΔphoR and WT. The candidate target genes of PhoP were further identified by combining transcriptome analysis and DAP-seq. The results of DAP-seq and RNA-seq of ΔphoP in combination revealed that the main direct regulons of PhoP are located on the membrane and PhoP is involved in regulating aerotolerance. Using the in vivo duck model, the pathogenicity of ΔphoP or ΔphoR was significantly lower than that of the WT. Together, our findings provided a perception about the direct regulation of PhoP and suggested that phoP/phoR is essential for the pathogenicity of R. anatipestifer, and phoP/phoR is related to the aerotolerance of R. anatipestifer. The gene deletion strains are expected to be the candidate live vaccine strains of R. anatipestifer which can be used as ideal genetic engineering vector strains for the expression of foreign antigens.Author summaryRiemerella anatipestifer is a severe pathogen in the poultry industry with high mortality in ducks and geese mainly due to acute septicemia and infectious polyserositis. A two-component system phoP/phoR was previously characterized in R. anatipestifer, and the phoP/phoR TCS was reported for the first time in Gram-negative bacteria. A deleted phoP/phoR in R. anatipestifer has been reported to almost lose its pathogenicity in ducklings. However, the mechanism of phoP/phoR regulating the virulence of R. anatipestifer had not been explored in detail. This study has utilized DAP-seq to explore the DNA-binding sites of PhoP as a response regulator in the global genome. Furthermore, the phoP and phoR were deleted separately and the transcriptomics of the corresponding gene-deleted strains was analyzed. A series of directly regulated genes of phoP/phoR TCS were determined in combination. The duckling model revealed both PhoP and PhoR as essential virulence-related factors of R. anatipestifer.
Myeloid hypoxia-inducible factor HIF1A provides cardio-protection during ischemia and reperfusion via induction of netrin-1
Authors: Heck-Swain Ka Lin , Li Jiwen , Ruan Wei , Yuan Xiaoyi , Wang Yanyu , Koeppen Michael , Eltzschig Holger K. 
Published: April 2022

AbstractThe transcription factor hypoxia-inducible factor HIF1A elicitics cardioprotection from ischemia and reperfusion injury. Here, we investigated tissue-specific pathways that are critical for HIF1A-elicited tissue protection. Initial studies showed that mice with induced global deletion of Hif1a (Hif1aloxP/loxP UbiquitinCre+) have exaggerated myocardial injury during in situ ischemia and reperfusion. Surprisingly, this phenotype was mirrored only in mice with myeloid-specific Hif1a deletion (Hif1aloxP/loxP LysM Cre+). In contrast, mice with myocardial specific (Hif1aloxP/loxP Myosin Cre+), or vascular Hif1a deletion (Hif1aloxP/loxP VEcadherin Cre+) experienced similar injury levels as controls. Subsequent studies using adoptive transfer of Hif1a-deficient polymorphonuclear neutrophils (PMNs) prior to myocardial injury demonstrated increased reperfusion injury. In contrast, adoptive transfer of PMNS treated ex-vivo with the HIF stabilizer dimethyloxalylglycine (DMOG) was associated with attenuated myocardial injury. Moreover, cardioprotection mediated by DMOG was abolished in Hif1aloxP/loxP LysM Cre+ mice, but not in Hif2aloxP/loxP LysM Cre+ mice. Finally, studies of PMN-dependent HIF1A target genes implicated the neuronal guidance molecule netrin-1 in mediating the cardioprotective effects of myeloid HIF1A. Taken together, the present studies identified a functional role for myeloid-expressed HIF1A in providing cardio-protection during ischemia and reperfusion injury, which - at least in part - is mediated by the induction of neuronal guidance molecule netrin-1 in neutrophils.
Natural and human-mediated drivers of microevolution in Neotropical palms: a historical genomics approach
Authors: Brousseau Louise , Santoni Sylvain , Weber Audrey , Odonne Guillaume 
Published: April 2022

AbstractMicroevolution in Amazonia has been far less documented than in temperate regions and still constitutes a major knowledge gap. Moreover, the actual influence of pre-Columbian societies through the Holocene remains unclear, although it could provide interesting insights on the relationship between natural and human-mediated evolutionary processes in driving microevolution.Because they are widespread and traditionally managed since pre-Columbian times, Neotropical palms are choice models to investigate the drivers of microevolution in Amazonia. In this study, we carried out a preliminary exploration of the genomic diversity in two pairs of congeneric palm species in French Guiana (Astrocaryumspp. andOenocarpusspp.).We built upon an original sampling design, taking into account both regional climate variations and local-scale pre-Columbian occupation, and designed a new target capture kit of 20,000 molecular probes scattered across exonic regions of more than 5,000 nuclear genes in Arecoïdeae (“ARECO5000+”). Hundreds of palm libraries were sequenced through Illumina sequencing, providing a unique – high-coverage – genomic dataset in these non-model species.We explored patterns of genomic diversity and differentiation within and across populations, bringing state-of-the-art knowledge about the roles of climate adaptation and pre-Columbian domestication. By documenting original cases of “incipient” domestication, these pioneer results open new avenues toward a better understanding of microevolution in Amazonia and of the impact of pre-Columbian societies on present-day biodiversity patterns.
Targeting RNA:Protein Interactions with an Integrative Approach Leads to the Identification of Potent YB-1 Inhibitors
Authors: El Hage Krystel , Babault Nicolas , Maciejak Olek , Desforges Bénédicte , Craveur Pierrick , Steiner Emilie , Rengifo-Gonzalez Juan Carlos , Henrie Hélène , Clément Marie-Jeanne , Joshi Vandana , Bouhss Ahmed , Wang Liya , Bauvais Cyril , Pastré David 
Published: April 2022

AbstractRNA-binding proteins are promising targets for developing new molecules of therapeutic interest. Nevertheless, targeting RNA:Protein interfaces is hampered by the lack of methods able to detect these interactions in cells while being amenable to High Content Screening. Here, we adapt the microtubule bench assay to score small molecules targeting interactions of endogenous mRNA with a specific protein in cells and demonstrate its robustness by targeting YB-1 (YBX-1 gene), a mRNA-binding protein involved in cancer progression and resistance to chemotherapy. The implementation of an integrative approach led to the identification of 22 hits validated by NMR and MD simulations of which 11 were found to significantly interfere with the binding of mRNA to YB-1 in cells at low micromolar concentrations. One of our leads is P1, an FDA-approved PARP-1 inhibitor. This work shows the potential of our integrative approach and paves the way for the development of RNA:Protein Interaction inhibitors.
Salt stress alters the spectrum of de novo mutation available to selection during experimental adaptation of Chlamydomonas reinhardtii
Authors: Hasan Ahmed R. , Lachapelle Josianne , El-Shawa Sara A. , Potjewyd Roman , Ford Scott A. , Ness Rob W. 
Published: April 2022

AbstractThe genetic basis of adaptation is driven not only by selection, but also by the spectrum of available mutations. Given that the rate of mutation is not uniformly distributed across the genome and varies depending on the environment, understanding the signatures of selection across the genome is aided by first establishing what the expectations of genetic change are from mutation. To determine the interaction between salt stress, selection, and mutation across the genome, we compared the rates and patterns of mutation observed in a selection experiment for salt tolerance in Chlamydomonas reinhardtii to those observed in mutation accumulation experiments with and without salt exposure. We found that salt stress led to an increased rate of indel mutations, but that many of these mutations were removed under selection. Finally, lines adapted to salt also showed excess clustering of mutations in the genome and the co-expression network, suggesting a role for positive selection in retaining mutations in particular compartments of the genome during the evolution of salt tolerance. Our study shows that characterizing mutation rates and spectra expected under stress helps disentangle the effects of environment and selection during adaptation.
On demand nanoliter sampling probe for collection of brain fluid
Authors: Teixidor Joan , Novello Salvatore , Ortiz Daniel , Menin Laure , Lashuel Hilal A. , Bertsch Arnaud , Renaud Philippe 
Published: April 2022

ABSTRACTContinuous fluidic sampling systems allow collection of brain biomarkers in vivo. Here, we propose a new sampling paradigm, Droplet on Demand (DoD), implemented in a microfabricated neural probe. It allows sampling droplets loaded with molecules from the brain extracellular fluid punctually, without the long transient equilibration periods typical of continuous methods. It uses an accurate fluidic sequence and correct operation is verified by the embedded electrodes. As a proof of concept, we demonstrated the application of this novel approach in vitro and in vivo, to collect glucose in the brain of mice, with a temporal resolution of 1-2 minutes and without transient regime. Absolute quantification of the glucose level in the samples was performed by direct infusion nanoelectrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS). By adjusting the diffusion time and the perfusion volume of DoD, the fraction of molecules recovered in the samples can be tuned to mirror the tissue concentration at accurate points in time. This makes quantification of biomarkers in the brain possible within acute experiments of only 20 to 120 minutes. DoD provides a complementary tool to continuous microdialysis and push-pull sampling probes. The advances allowed by DoD will benefit quantitative molecular studies in the brain, namely for molecules involved in volume transmission or for protein aggregates that form in neurodegenerative diseases over long periods.Abstract Figure
Immobilised enzyme cascade for targeted glycosylation
Authors: Makrydaki Elli , Donini Roberto , Krueger Anja , Royle Kate , Moya-Ramirez Ignacio , Kuntz Douglas A. , Rose David R. , Haslam Stuart M. , Polizzi Karen , Kontoravdi Cleo 
Published: April 2022

AbstractGlycosylation is a critical post-translational modification of proteins, improving properties such as folding, half-life and functionality. However, glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. Here we describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro. This novel proof-of-concept system is enabled by immobilised enzymes produced with a “one-step immobilisation/purification” method to express, biotinylate in vivo and immobilise glycosyltransferases. The immobilised enzymes are used in a reaction cascade mimicking a human-like N-linked glycosylation pathway where promiscuity naturally exists. The enzyme cascade is applied to free glycans, and a monomeric Fc domain expressed in glycoengineered Pichia pastoris, yielding near homogeneous glycoforms (>95% conversion). Finally, immobilised β-1,4 galactosyltransferase is used to enhance the galactosylation profile of three different IgGs yielding 80.2 – 96.3 % terminal galactosylation. Enzyme recycling was further demonstrated for 7 cycles, with a combined reaction time greater than 140 hours. The novel SUGAR-TARGET platform is easy to implement, modular and reusable, and therefore can lead to the development of homogeneous glycan structures for functional and clinical evaluation. The use of immobilised enzymes enables the economical modification of cell-based material supporting applications at a large industrial scale.
SIQ: easy quantitative measurement of mutation profiles in sequencing data
Authors: van Schendel Robin , Schimmel Joost , Tijsterman Marcel 
Published: April 2022

ABSTRACTEstablishing mutational outcomes after genome editing is of increasing importance with the advent of highly efficient genome-targeting tools. Next-generation sequencing (NGS) has become a vital method to investigate the extent of mutagenesis at specific target sites. Thus, robust and simple-to-use software that enables researchers to retrieve mutation profiles from NGS data is needed. Here, we present Sequence Interrogation and Quantification (SIQ), a tool that can analyse sequence data of any targeted experiment (e.g. CRISPR, I-SceI, TALENs) with a focus on event classification such as deletions, single-nucleotide variations, (templated) insertions and tandem duplications. SIQ results can be directly analysed and visualized via SIQPlotteR, an interactive web tool that we made freely available. Using novel and insightful tornado plot visualizations as outputs we illustrate that SIQ readily identifies differences in mutational signatures obtained from various DNA-repair deficient genetic backgrounds. SIQ greatly facilitates the interpretation of complex sequence data by establishing mutational profiles at specific loci and is, to our knowledge, the first tool that can analyse Sanger sequence data as well as short and long-read NGS data (e.g. Illumina and PacBio).