bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of low temperature and cold-acclimation on photoinhibition and singlet oxygen production in four natural accessions ofArabidopsis
Authors: Mattila Heta , Mishra Kumud B. , Kuusisto Iiris , Mishra Anamika , Novotná Kateřina , Šebela David , Tyystjärvi Esa 
Published: September 2019

AbstractTo understand the effects of low temperature and cold-acclimation on reactive oxygen species and photoinhibition of photosystem II (PSII), light-induced inactivation of PSII was measured at 22 and 4 °C from fourArabidopsis thalianaaccessions (Rschew, Tenela, Columbia-0 and Coimbra) grown under optimal conditions. Photoinhibition was also measured at 4 °C from plants cold-acclimated at 4 °C for two weeks. Measurements were done in the absence and presence of lincomycin that blocks PSII repair, and PSII activity was assayed with the ratio of variable to maximum chlorophyllafluorescence (FV/FM) and with light-saturated rate of oxygen evolution using a quinone acceptor. Of the non-acclimated accessions, Rschew was the most tolerant to photoinhibition and Coimbra the least; the rate constants of photoinhibition of the most sensitive accession were 1.3-1.9 times as high as those of the tolerant ones. The damaging reaction of photoinhibition in non-acclimated plants was slower or equal at 4 °C than at 22 °C. The rate constants of photoinhibition of cold-acclimated plants, at 4 °C, were 0.55 to 1.25 times as high as those of non-acclimated plants; the protective effect of cold-acclimation on photoinhibition was consistent in Columbia-0 and Coimbra whereas Rschew and Tenela were either slightly more tolerant or susceptible, depending on the method used to assay photoinhibition. Production of singlet oxygen, measured from thylakoid membranes isolated from non-acclimated and cold-acclimated plants, did not decrease due to cold-acclimation, nor did singlet oxygen production correlate with the rate of photoinhibition or with flavonol contents of the leaves.
Intraflagellar transport complex B proteins regulate the Hippo effector Yap1 during cardiogenesis
Authors: Peralta Marina , Jerabkova Katerina , Lucchesi Tommaso , Lopez Laia Ortiz , Vitre Benjamin , Han Dong , Guillemot Laurent , Dingare Chaitanya , Sumara Izabela , Mercader Nadia , Lecaudey Virginie , Delaval Benedicte , Meilhac Sigolène M. , Vermot Julien 
Published: September 2019

AbstractCilia and the intraflagellar transport (IFT) proteins involved in ciliogenesis are associated with congenital heart diseases (CHD). However, the molecular links between cilia, IFT proteins and cardiogenesis are yet to be established. Using a combination of biochemistry, genetics, and live imaging methods, we show that IFT complex B proteins (Ift88, Ift54 and Ift20) modulate the Hippo pathway effector YAP1 in zebrafish and mouse. We demonstrate that this interaction is key to restrict the formation of the proepicardium and the myocardium.In celluloexperiments suggest that IFT88 and IFT20 interact with YAP1 in the cytoplasm and functionally modulates its activity, identifying a molecular link between cilia related proteins and the Hippo pathway. Taken together, our results highlight a novel role for IFT complex B proteins during cardiogenesis and shed light on an unexpected mechanism of action for ciliary proteins in YAP1 regulation. These findings provide mechanistic insights into a non-canonical role for cilia related proteins during cardiogenesis.
Gonadotropes in medaka grow long extensions with varicosity-like swellings, projecting towards each other and blood vessels
Authors: Grønlien Heidi Kristine , Fontaine Romain , Hodne Kjetil , Tysseng Isabelle , Ager-Wick Eirill , Weltzien Finn-Arne , Haug Trude Marie 
Published: September 2019

AbstractAccumulating evidence in the scientific literature indicates that some pituitary cell types are organized in complex networks. Previous observations have indicated that this may also be the case in medaka (Oryzias latipes), where long cellular extensions with varicosity-like swellings are formed by luteinizing hormone (Lh)-producing gonadotropes expressing green fluorescent protein. In this study, immunofluorescence of intact pituitaries reveal that Lh beta polypeptides are mainly located in the varicosity-like swellings and at the extremity of the extensions. Some extensions approach nearby Lh-producing cells, and other extensions are in close contact with blood vessels. To investigate whether these extensions may contribute to network formation, we followed their development using confocal and fluorescent microscopy on primary cultures. During the first two days in culture, the extensions initiated the formation of homotypic cellular networks and clustering. The extensions were classified as either major or minor. Major extensions were several cell diameters long, dependent on microtubules, and displaying varicosity-like swellings at regular intervals. Minor extensions typically protruded from the major, were significantly shorter and thinner, and dependent on actin. The swellings were dependent on both microtubules and actin. Flash photolysis of caged Ca2+showed that the signal was propagated along the major extensions, intensifying in each swelling, indicating a continuous structure. However, the Ca2+signal did not transfer to the next cell in the network, but was transferred between cells merged at their somas. In summary, Lh-producing gonadotropes in medaka display a complex cellular structure of extensions, possibly linked to communication with blood vessels and/or other gonadotrope cells.
Cytoprotective effects of (E)-N-(2-(3, 5-dimethoxystyryl) phenyl) furan-2-carboxamide (BK3C231) against 4-nitroquinoline 1-oxide-induced damage in CCD-18Co human colon fibroblast cells
Authors: Tan Huan Huan , Thomas Noel F. , Inayat-Hussain Salmaan H. , Chan Kok Meng 
Published: September 2019

AbstractStilbenes are a group of chemicals characterized with the presence of 1,2-diphenylethylene. Previously, our group has demonstrated that synthesized (E)-N-(2-(3, 5-dimethoxystyryl) phenyl) furan-2-carboxamide (BK3C231) possesses potential chemopreventive activity specifically inducing NAD(P)H:quinone oxidoreductase 1 (NQO1) protein expression and activity. In this study, the cytoprotective effects of BK3C231 on cellular DNA and mitochondria were investigated in normal human colon fibroblast, CCD-18Co cells. The cells were pretreated with BK3C231 prior to exposure to the carcinogen 4-nitroquinoline 1-oxide (4NQO). BK3C231 was able to inhibit 4NQO-induced cytotoxicity. Cells treated with 4NQO alone caused high level of DNA and mitochondrial damages. However, pretreatment with BK3C231 protected against these damages by reducing DNA strand breaks and micronucleus formation as well as decreasing losses of mitochondrial membrane potential (ΔΨm) and cardiolipin. Interestingly, our study has demonstrated that nitrosative stress instead of oxidative stress was involved in 4NQO-induced DNA and mitochondrial damages. Inhibition of 4NQO-induced nitrosative stress by BK3C231 was observed through a decrease in nitric oxide (NO) level and an increase in glutathione (GSH) level. These new findings elucidate the chemopreventive potential of BK3C231 specifically its cytoprotective effects in human colon fibroblast CCD-18Co cell model.
How do dairy farmers wish their future farm?
Authors: Dalcq Anne-Catherine , Dogot Thomas , Beckers Yves , Brostaux Yves , Froidmont Eric , Vanwindekens Frédéric , Soyeurt Hélène 
Published: September 2019

AbstractDairy farming systems are evolving. This study presents dairy producers’ perceptions of their ideal future farm (IFF) to ensure revenue and attempts to determine the reasons for this choice, the environmental aspects related to this choice, the proximity between the current farm and the IFF and the requirements for reaching this IFF. Just before the end of the European milk quota, a total of 245 dairy producers answered a survey about the characteristics of their IFF and other socio-environmental-economic information. A multiple correspondence analysis (MCA) was carried out using seven characteristics of IFF (intensive vs. extensive, specialised vs. diversified, strongly vs. weakly based on new technologies, managed by a group of managers vs. an independent farmer, employed vs. familial workforce, local vs. global market, standard vs. quality-differentiated production). Based on the main contributors to the second dimension of MCA, this axis was defined as an IFF gradient between the local-based extensive (LBE) producers (26%) and the global-based intensive (GBI) producers (46%). The differences of IFF gradient between modalities of qualitative variables were estimated using generalised linear models. Pearson correlations were calculated between the scores on the IFF gradient and quantitative variables. Finally, frequencies for IFF characteristic and the corresponding characteristic for the current situation were calculated to determine the percentages of “unhappy” producers. Some reasons for the choice of IFF by the producers have been highlighted in this study. Environmental initiatives were more valued by LBE than GBI producers. Low similarity was observed between the current farm situation of the respondents and their IFF choice. LBE and GBI producers differed significantly regarding domains of formation (technical and bureaucratic vs transformation and diversification respectively) and paths of formation (non-market vs. market respectively). Two kinds of farming systems were considered by dairy producers and some socioeconomic and environmental components differed between them.
Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma
Authors: Hervás-Marín David , Higgins Faatiemah , Sanmartín Onofre , López-Guerrero Jose Antonio , Bañó M. Carmen , Igual J. Carlos , Quilis Inma , Sandoval Juan 
Published: September 2019

ABSTRACTCutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. Although most cSCCs have good prognosis, a subgroup of high-risk cSCC has a higher frequency of recurrence and mortality. Therefore, the identification of molecular risk factors associated with this aggressive subtype is of major interest. In this work we carried out a global-scale approach to investigate the DNA-methylation profile in patients at different stages, from premalignant actinic keratosis to low-risk invasive and high-risk non-metastatic and metastatic cSCC. The results showed massive non-sequential changes in DNA-methylome and identified a minimal methylation signature that discriminates between stages. Importantly, a direct comparison of low-risk and high-risk stages revealed epigenetic traits characteristic of high-risk tumours. Finally, a prognostic prediction model in cSCC patients identified a methylation signature able to predict the overall survival of patients. Thus, the analysis of DNA-methylation in cSCC revealed changes during the evolution of the disease through the different stages that can be of great value not only in the diagnosis but also in the prognosis of the disease.
A Human Accelerated Region participates in early human forebrain patterning and expansion
Authors: Acosta Sandra , Sidhaye Jaydeep , Fiore Luciano , Rollan Isabel , Iacono Giovanni , Misharin Alexander V. , Takata Nozomu , Sikora Martin , Joshi Nikita , Xu Beisi , Willerslev Eske , Heyn Holger , Manzanares Miguel , Knoblich Juergen A. , Oliver Guillermo 
Published: September 2019

AbstractThe expansion of the mammalian brain is associated with specific developmental processes; however, not much is known about how evolutionary changes participated in the acquisition of human brain traits during early developmental stages. Here we investigated whether enhancers active during the phylotypic stage show human-specific genomic divergence which could contribute to the evolutionary expansion of the forebrain. Notably, we identified an active enhancer containing a human accelerated region (HAR) located in the Chromosome 14q12, a region enriched with neurodevelopmental genes, such as Foxg1, Nkx2.1 and Nova1. Reporter analysis revealed that the human variant is active in the forebrain in transgenic mice and that it has stronger enhancer activity than the mouse or chimpanzee versions. Humanization of the mouse enhancer variant in transgenic mice and in mouse organoids resulted in an expansion of Foxg1 expressing domains in the forebrain early neural progenitors with a bias towards dorsal identities. Overall, our results suggest that human-specific mutations in critical regulatory elements controlling early brain development impact the expansion and patterning of the forebrain.
Generalized differential equation compartmental models of infectious disease transmission
Authors: Greenhalgh Scott , Rozins Carly 
Published: September 2019

AbstractFor decades, mathematical models of disease transmission have provided researchers and public health officials with critical insights into the progression, control, and prevention of disease spread. Of these models, one of most fundamental is the SIR differential equation model. However, this ubiquitous model has one significant and rarely acknowledged shortcoming: it is unable to account for a disease’s true infectious period distribution. As the misspecification of such a biological characteristic is known to significantly affect model behavior, there is a need to develop new modeling approaches that capture such information. Therefore, we illustrate an innovative take on compartmental models, derived from their general formulation as systems of nonlinear Volterra integral equations, to capture a broader range of infectious period distributions, yet maintain the desirable formulation as systems of differential equations. Our work illustrates a compartmental model that captures any Erlang distributed duration of infection with only 3 differential equations, instead of the typical inflated model sizes required by differential equation compartmental models, and a compartmental model that capture any mean, standard deviation, skewness, and kurtosis of an infectious period distribution with merely 4 differential equations. The significance of our work is that it opens up a new class of easy-to-use compartmental models to predict disease outbreaks that does not require a complete overhaul of existing theory, and thus provides a starting point for multiple research avenues of investigation under the contexts of mathematics, public health, and evolutionary biology.
Monocyte reconstitution and gut microbiota composition after hematopoietic stem cell transplantation
Authors: Morjaria Sejal , Zhang Allen W. , Kim Sohn , Peled Jonathan U. , Becattini Simone , Littmann Eric R. , Pamer Eric. G. , Perales Miguel-Angel , Abt Michael C. 
Published: September 2019

BackgroundMonocytes are an essential cellular component of the innate immune system that support the host’s effectivenss to combat a range of infectious pathogens. Hemopoietic cell transplantation (HCT) results in transient monocyte depletion, but the factors that regulate recovery of monocyte populations are not fully understood. In this study, we investigated whether the composition of the gastrointestinal microbiota is associated with the recovery of monocyte homeostasis after HCT.MethodsWe performed a single-center, prospective, pilot study of 18 recipients of either autologous or allogeneic HCT. Serial blood and stool samples were collected from each patient during their HCT hospitalization. Analysis of the gut microbiota was done using 16S rRNA gene sequencing and flow cytometric analysis was used to characterize the phenotypic composition of monocyte populations.ResultsDynamic fluctuations in monocyte reconstitution occurred after HCT and large differences were observed in monocyte frequency among patients over time. Recovery of absolute monocyte counts and monocyte subsets showed significant variability across the heterogeneous transplant types and conditioning intensities; no relationship to the microbiota composition was observed in this small cohort.ConclusionA relationship between the microbiota composition and monocyte homeostasis could not be firmly established in this pilot study.
Anatomical tool in the identification of ploids in maize seedlings and potential use in initial stage of double haploides obtainment process
Authors: Pires Raquel M. O. , Souza Genaina A. , Vilela Danielle R. , Santos Heloisa O. , C.Vasconcellos Renato C. , Von Pinho Édila V. R. 
Published: September 2019

AbstractStudies that optimize the haploid technique in the removal of maize lines are necessary. Between the stages that mostly requires attention and it is directly related to the success of the technology is the correctly separation of induced haploids and diploids. Morphological markers are commonly used but have strong influence of the environment, and laboratory methods have been developed and may be more efficient. Thus, the objective was to study the use of the anatomical analysis tool, through the analysis of young maize leaf for use as the indirect markers in the identification of ploidys. The hybrids were crossed with the KEMS haploid inducer. The seeds crossed, were selected according to the R-navajo marker and submitted to two different protocols of chromosome duplication. Plants that survived to the duplication protocols were acclimated in greenhouse and then transferred to the field. After the self-polinization of the DH0 plants, the DH1 seeds were taken to the field, divided into treatments according to the parentals and duplication protocols. At the vegetative stage V4 of the plants, leaf tissue samples were collected to the evaluation of the amount of DNA and identification of ploidys and anatomical analysis. The nuclear DNA review of each sample was performed for the comparison in histograms of the position of G1 peak to the G1 peak of the internal or external reference standard. A high accuracy came to validate an anatomical tool, through the variables studied in this work, as a marker in the differentiation of ploidis in maize plants, and it can be used in selection programs. The anatomy made in some letters is a non-destructible technique and, together with a flow cytometry technique, can be used as an indirect method in haploid cutting programs at the initial stage of the identification of seedlings.
Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk
Authors: Jacinta-Fernandes Ana , Xavier Joana M. , Magno Ramiro , Lage Joel G. , Maia Ana-Teresa 
Published: September 2019

ABSTRACTMost breast cancer (BC) risk-associated variants (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting miRNA genes and/or miRNA-binding. To test this we adapted two miRNA-binding prediction algorithms — TargetScan and miRanda — to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant (P ≤ 5 × 10−8) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3’UTRs of putative miRNA target genes were predicted to alter miRNA∷mRNA pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and re-inforce the role of miRNA mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.
Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation
Authors: Dimchev Georgi , Amiri Behnam , Humphries Ashley C. , Schaks Matthias , Dimchev Vanessa , Stradal Theresia E.B. , Faix Jan , Krause Matthias , Way Michael , Falcke Martin , Rottner Klemens 
Published: September 2019

ABSTRACTEfficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex (WRC), an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.Summary statementWe describe how genetic ablation of the prominent actin- and VASP-binding protein lamellipodin combined with software-aided protrusion analysis uncovers mechanistic insights into its cellular function during cell migration.
Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis
Authors: Ludikhuize M.C. , Meerlo M. , Gallego M. Pages , Julià M. Burgaya , Nguyen N.T.B. , Brombacher E. C. , Paik J.H. , Burgering B.M. T. , Rodriguez Colman M.J. 
Published: September 2019

SummaryDifferential signalling of the WNT and Notch pathways regulates proliferation and differentiation of Lgr5+crypt-based columnar cells (CBCs) into all cell lineages of the intestine. We have recently shown that high mitochondrial activity in CBCs is key in maintaining stem cell function. Interestingly, while high mitochondrial activity drives CBCs, it is reduced in the adjacent secretory Paneth cells (PCs). This observation implies that during differentiation towards PCs, CBCs undergo a metabolic rewiring involving downregulation of mitochondrial number and activity, through a hitherto unknown mechanism. Here we demonstrate, using intestinal organoids that FoxO transcription factors and Notch signalling functionally interact in determining CBC cell fate. In agreement with the organoid data, combinedFoxo1and3deletion in mice increases PC number in the intestine. Importantly, we show that FOXO and Notch signalling converge onto regulation of mitochondrial fission, which in turn provokes stem cell differentiation into the secretory types; Goblet cells and PCs. Finally, mapping intestinal stem cell differentiation based on pseudotime computation of scRNA-seq data further supports the role of FOXO, Notch and mitochondria in determining secretory differentiation. This shows that mitochondria is not only a discriminatory hallmark of CBCs and PCs, but that its status actively determines lineage commitment during differentiation. Together, our work describes a new signalling-metabolic axis in stem cell differentiation and highlights the importance of mitochondria in determining cell fate.