bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recommendations to address uncertainties in environmental risk assessment using toxicokinetics-toxicodynamics models
Authors: Baudrot Virgile , Charles Sandrine 
Published: June 2018

ABSTRACTProviding reliable environmental quality standards (EQSs) is a challenging issue in environmental risk assessment (ERA). These EQSs are derived from toxicity endpoints estimated from dose-response models to identify and characterize the environmental hazard of chemical compounds such as those released by human activities. These toxicity endpoints include the classicalx% effect/lethal concentrations at a specific timet(EC/LC(x,t)) and the new multiplication factors applied to environmental exposure profiles leading tox% effect reduction at a specific timet(MF(x,t), or denotedLP(x,t) by the EFSA). However, classical dose-response models used to estimate toxicity endpoints have some weaknesses, such as their dependency on observation time points, which are likely to differ between species (e.g., experiment duration). Furthermore, real-world exposure profiles are rarely constant over time, which makes the use of classical dose-response models difficult and compromises the derivation ofMF(x,t). When dealing with survival or immobility toxicity test data, these issues can be overcome with the use of the general unified threshold model of survival (GUTS), a toxicokinetics-toxicodynamics (TKTD) model that provides an explicit framework to analyse both time- and concentration-dependent data sets as well as obtain a mechanistic derivation ofEC/LC(x,t) andMF(x,t) regardless of x and at any time t of interest. In addition, the assessment of a risk is inherently built upon probability distributions, such that the next critical step for ERA is to characterize the uncertainties of toxicity endpoints and, consequently, those of EQSs. With this perspective, we investigated the use of a Bayesian framework to obtain the uncertainties from the calibration process and to propagate them to model predictions, includingLC(x,t) andMF(x,t) derivations. We also explored the mathematical properties ofLC(x,t) andMF(x,t) as well as the impact of different experimental designs to provide some recommendations for a robust derivation of toxicity endpoints leading to reliable EQSs: avoid computingLC(x,t) andMF(x,t) for extremexvalues (0 or 100%), where uncertainty is maximal; computeMF(x,t) after a long period of time to take depuration time into account and test survival under few correlated and uncorrelated pulses of the contaminant in terms of depuration.
Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes
Authors: Chen Min , Lin Jer-Young , Hur Jungim , Pelletier Julie M. , Baden Russell , Pellegrini Matteo , Harada John J. , Goldberg Robert B. 
Published: June 2018

AbstractThe precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.SignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.
The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungusCryptococcus neoformans.
Authors: Caza Mélissa , Hu Guanggan , Neilson Eric David , Cho Minsu , Jung Won Hee , Kronstad James W. 
Published: June 2018

ABSTRACTThe battle for iron between invading microorganisms and mammalian hosts is a pivotal determinant of the outcome of infection. The pathogenic fungus,Cryptococcus neoformans, employs multiple mechanisms to compete for iron during cryptococcosis, a disease primarily of immunocompromised hosts. In this study, we examined the role of endocytic trafficking in iron uptake by characterizing a mutant defective in the Sec1/Munc18 (SM) protein Vps45. This protein is known to regulate the machinery for vesicle trafficking and fusion via interactions with SNARE proteins. As expected, avps45deletion mutant was impaired in endocytosis and showed sensitivity to trafficking inhibitors. The mutant also showed poor growth on iron-limited media and a defect in transporting the Cfo1 ferroxidase of the high-affinity iron uptake system from the plasma membrane to the vacuole. Remarkably, we made the novel observation that Vps45 also contributes to mitochondrial function in that a Vps45-Gfp fusion protein associated with mitotracker, and avps45mutant showed enhanced sensitivity to inhibitors of electron transport complexes as well as changes in mitochondrial membrane potential. Consistent with mitochondrial function, thevps45mutant was impaired in calcium homeostasis. To assess the relevance of these defects for virulence, we examined cell surface properties of thevps45mutant and found increased sensitivity to agents that challenge cell wall integrity and antifungal drugs. A change in cell wall properties was consistent with our observation of altered capsule polysaccharide attachment, and with attenuated virulence in a mouse model of cryptococcosis. Overall, our studies reveal a novel role for Vps45-mediated trafficking for iron uptake, mitochondrial function and virulence.
A Genome-Wide Association Study Reveals a Novel Regulator of Ovule Number and Fertility inArabidopsis thaliana
Authors: Yuan Jing , Kessler Sharon A. 
Published: June 2018

AbstractOvules contain the female gametophytes which are fertilized during pollination to initiate seed development. Thus, the number of ovules that are produced during flower development is an important determinant of seed crop yield and plant fitness. Mutants with pleiotropic effects on development often alter the number of ovules, but specific regulators of ovule number have been difficult to identify in traditional mutant screens. We used natural variation in Arabidopsis accessions to identify new genes involved in the regulation of ovule number. The ovule numbers per flower of 189 Arabidopsis accessions were determined and found to have broad phenotypic variation that ranged from 39 ovules to 84 ovules per pistil. Genome-Wide Association tests revealed several genomic regions that are associated with ovule number. T-DNA insertion lines in candidate genes from the most significantly associated loci were screened for ovule number phenotypes. TheNEW ENHANCER of ROOT DWARFISM (NERD1)gene was found to have pleiotropic effects on plant fertility that include regulation of ovule number and both male and female gametophyte development. Overexpression of NERD1 increased ovule number per fruit in a background-dependent manner and more than doubled the total number of flowers produced in all backgrounds tested, indicating that manipulation of NERD1 levels can be used to increase plant productivity.Author SummaryOvules are the precursors of seeds in flowering plants. Each ovule contains an egg cell and a central cell that fuse with two sperm cells during double fertilization to generate seeds containing an embryo and endosperm. The number of ovules produced during flower development determines the maximum number of seeds that can be produced by a flower. In this paper, we used natural variation inArabidopsis thalianaaccessions to identify regions of the genome that are associated with ovule number. Polymorphisms in the plant-specific NERD1 gene on chromosome 3 were significantly associated with ovule number. Mutant and overexpression analyses revealed thatNERD1is a positive regulator of ovule number, lateral branching, and flower number in Arabidopsis. Manipulation of NERD1 expression levels could potentially be used to increase yield in crop plants.
EnsembleCNV: An ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data
Authors: Zhang Zhongyang , Cheng Haoxiang , Hong Xiumei , Narzo Antonio F. Di , Franzen Oscar , Peng Shouneng , Ruusalepp Arno , Kovacic Jason C. , Bjorkegren Johan LM , Wang Xiaobin , Hao Ke 
Published: June 2018

ABSTRACTThe associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose a novel ensemble learning framework, ensembleCNV, to detect and genotype CNVs using single nucleotide polymorphism (SNP) array data. EnsembleCNV a) identifies and eliminates batch effects at raw data level; b) assembles individual CNV calls into CNV regions (CNVRs) from multiple existing callers with complementary strengths by a heuristic algorithm; c) re-genotypes each CNVR with local likelihood model adjusted by global information across multiple CNVRs; d) refines CNVR boundaries by local correlation structure in copy number intensities; e) provides direct CNV genotyping accompanied with confidence score, directly accessible for downstream quality control and association analysis. Benchmarked on two large datasets, ensembleCNV outperformed competing methods and achieved a high call rate (93.3%) and reproducibility (98.6%), while concurrently achieving high sensitivity by capturing 85% of common CNVs documented in the 1000 Genomes Project. Given this CNV call rate and accuracy, which are comparable to SNP genotyping, we suggest ensembleCNV holds significant promise for performing genome-wide CNV association studies and investigating how CNVs predispose to human diseases.
Using human sequencing to guide craniofacial research
Authors: Liegel Ryan P. , Finnerty Erin , Ward Lauren , DiStasio Andrew , Hufnagel Robert B. , Saal Howard M. , Prows Cynthia A. , Stottmann Rolf 
Published: June 2018

ABSTRACTA recent convergence of technological innovations has re-energized the ability to apply genetics to research in human craniofacial development. Next-generation exome and whole genome sequencing have dropped in price significantly making it relatively trivial to sequence and analyze patients and families with congenital craniofacial anomalies. A concurrent revolution in genome editing with the use of the CRISPR-Cas9 system enables the rapid generation of animal models, including mouse, which can precisely recapitulate human variants. Here we summarize the choices currently available to the research community. We illustrate this approach with the study of a family with a novel craniofacial syndrome with dominant inheritance pattern. The genomic analysis suggest a causal variant in AMOTL1 which we modeled in mice. We also made a novel deletion allele of Amotl1. Our results indicate that Amotl1 is not required in the mouse for survival to weaning. Mice carrying the variant identified in the human sequencing studies, however, do not survive to weaning in normal ratios. The cause of death is not understood for these mice complicating our conclusions about the pathogenicity in the index patient. Thus, we highlight some of the powerful opportunities and confounding factors confronting current craniofacial genetic research.
Stoichiometry and Mobility Switching of a Morphogenetic Protein in Live Differentiating Cells
Authors: Wollman Adam J. M. , Muchová Katarína , Chromiková Zuzana , Wilkinson Anthony J. , Barák Imrich , Leake Mark C. 
Published: June 2018

AbstractSpore formation following asymmetric cell division in Bacillus subtilis offers a model system to study development, morphogenesis and signal transduction in more complex organisms. Extensive biochemical and genetic details of its sporulation factors are known, however, the molecular mechanisms by which asymmetry is generated remain unclear. A crucial membrane phosphatase, SpoIIE, couples gene regulation to morphology changes, but how it performs different functions dependent on cell stage is unknown. We addressed this puzzle using high-speed single-molecule fluorescence microscopy on live B. subtilis expressing genomically encoded SpoIIE fluorescent protein fusions during sporulation. Copy number analysis indicated a few tens of SpoIIE at sporulation onset increasing to 400-600 molecules per cell following asymmetric cell division with up to 30% greater proportion in the forespore, corresponding to a concentration enhancement in the smaller forespore sufficient for differential dephosphorylation of an anti-sigma factor antagonist and activation of the forespore specific transcription factor, σF. Step-wise photobleach analysis indicates that SpoIIE forms tetramers capable of reversible oligomerisation to form clusters correlated with stage-specific functions. Specifically, low mobility SpoIIE clusters which initially localize to the asymmetric septum are released as mobile SpoIIE clusters around the forespore when phosphatase activity is manifested. SpoIIE is subsequently recaptured at the septum in a SpoIIQ-dependent manner. After mother cell engulfment of the forespore, SpoIIE is released as a mix of higher mobility clusters and tetramers. Our findings suggest that additional information captured in the changing state of multimerization and mobility enable one protein to perform different roles at different cell stages.Significance/impactCertain bacteria undergo sporulation involving cells dividing asymmetrically. A crucial protein SpoIIE facilitates this morphological asymmetry and directly links it to asymmetry in gene expression. Here, we used specialized light microscopy, capable of observing single molecules, plus biophysics, genetics and biochemical tools, to monitor SpoIIE in single living bacteria in real time, allowing us to count how many molecules are present in different cell regions, and how mobile they are. We find that SpoIIE clusters and moves depending on development stages, indicating that it has different roles depending on other binding proteins and their cellular locations. Our results suggest that changes in molecular stoichiometry and mobility may be used as switches in more complex cell processes.
Evidence that recurrent Group A streptococcus tonsillitis is an immunosusceptibility disease involving antibody deficiency and aberrant Tfh cells
Authors: Dan Jennifer M. , Havenar-Daughton Colin , Kendric Kayla , Kaushik Kirti , Rosales Sandy L. , Anderson Erika , LaRock Christopher , Vijayanand Pandurangan , Seumois Gregory , Layfield David , Cutress Ramsey , Ottensmier Christian , Lindestam Arlehamn Cecilia , Sette Alessandro , Nizet Victor , Bothwell Marcella , Brigger Matthew , Crotty Shane 
Published: June 2018

One Sentence SummaryRecurrent tonsillitis is a multifactorial disease associated with an aberrant tonsillar germinal center response to Group A Streptococcus.ABSTRACTRecurrent Group A Streptococcus (GAS) tonsillitis (RT) is a common indication for pediatric tonsillectomy. ‘Strep throat’ is highly prevalent among children; yet, it is unknown why some children develop RT. To gain insights into this classic childhood disease, we performed phenotypic, genotypic, and functional studies on pediatric GAS RT and non-RT tonsils. We observed significantly smaller germinal centers in GAS RT tonsils, and underrepresentation of GAS-specific germinal center follicular helper (GC Tfh) CD4+T cells. RT children exhibited reduced antibody responses to GAS virulence factor SpeA. Risk and protective HLA Class II alleles for RT were identified. Finally, SpeA induced granzyme B+GC Tfh cells in RT tonsils that had capacity to kill B cells. Together, these observations suggest that RT susceptibility can occur due to genetic differences that can result in aberrant GC Tfh cells and poor antibody responses to GAS SpeA.
Malaria and Burkitt’s Lymphoma: An In Silico Analysis of Gene Expression Links between Malaria and Burkitt’s Lymphoma and Potential Anticancer Activity of Artemisinin Derivatives
Authors: Elsayed Inas , Amin Mutaz , Abdel Hamid Muzamil Mahdi , Wang Xiaosheng , Rizig Mie 
Published: June 2018

AbstractBackgroundBurkitt’s lymphoma (BL) is an aggressive form of B-cell non-Hodgkin lymphoma. Endemic subtype of the disease showed a remarkable statistical and epidemiological association with malaria infection. Despite the numerous studies performed to explain this association; molecular mechanisms underlie such coincidence still remain unclear. Dissecting molecular mechanisms which link Malaria infection and Burkitt’s lymphoma can provide insights about reported anticancer action of certain antimalarial drugs, namely artemisinin derivatives.MethodsHere we applied an integrative approach to investigate for potential links between malaria infection and endemic Burkitt’s lymphoma regarding their gene expression, and further explore common molecular mechanisms through which artemisinin compounds might act in endemic Burkitt’s lymphoma. Using gene expression data of malaria (Plasmodium falciparum infected erythroblasts) and endemic Burkitt’s lymphoma from Gene Expression Omnibus database, expression patterns in the two conditions were examined through clustering analysis using Self Organizing Maps, and then by significance testing of differentially expressed genes in each condition followed by Functional annotation using Gene Ontology clustering and Pathways analysis.ResultsClustering analysis identified a significant overlap between the expression patterns in endemic Burkitt’s lymphoma and Plasmodium falciparum infected cells. Four out of the 12 identified clusters contained genes with similar expression patterns in both conditions. Differential expression analysis identified 1689 genes as significantly differentially expressed in endemic Burkitt’s lymphoma and 405 in malaria. Those genes were found to be related to important Gene Ontology terms and pathways. Interestingly 65% of the identified pathways in Malaria were overlapped with those identified in endemic Burkitt’s lymphoma. Several of these pathways reported to be related to actions of artemisinin derivatives.ConclusionOur In-silico analysis showed a significant molecular convergence between endemic Burkitt’s lymphoma and malaria. A number of 43pathways which demonstrated enrichment in tumour were shared with Plasmodium falciparum infected erythrocytes. Such pathways represent potential targets for antimalarial drugs to exert therapeutic effects in such malignancy.
Incomplete penetrance for isolated congenital asplenia in humans with mutations in translated and untranslated RPSA exons
Authors: Bolze Alexandre , Boisson Bertrand , Bosch Barbara , Antipenko Alexander , Bouaziz Matthieu , Sackstein Paul , Chaker-Margot Malik , Barlogis Vincent , Briggs Tracy , Colino Elena , Elmore Aurora C. , Fischer Alain , Genel Ferah , Hewlett Angela , Jedidi Maher , Kelecic Jadranka , Krüger Renate , Ku Cheng-Lung , Kumararatne Dinakantha , Loughlin Sam , Lefevre-Utile Alain , Mahlaoui Nizar , Markus Susanne , Garcia Juan-Miguel , Nizon Mathilde , Oleastro Matias , Pac Malgorzata , Picard Capucine , Pollard Andrew J. , Rodriguez-Gallego Carlos , Thomas Caroline , Von Bernuth Horst , Worth Austen , Meyts Isabelle , Risolino Maurizio , Selleri Licia , Puel Anne , Klinge Sebastian , Abel Laurent , Casanova Jean-Laurent 
Published: June 2018

AbstractIsolated congenital asplenia (ICA) is the only known human developmental defect exclusively affecting a lymphoid organ. In 2013, we showed that private deleterious mutations in the protein-coding region of RPSA, encoding ribosomal protein SA, caused ICA by haploinsufficiency with complete penetrance. We reported seven heterozygous protein-coding mutations in 8 of the 23 kindreds studied, including 6 of the 8 multiplex kindreds. We have since enrolled 33 new kindreds, 5 of which are multiplex. We describe here eleven new heterozygous ICA-causing RPSA protein-coding mutations, and the first two mutations in the 5’-UTR of this gene, which disrupt mRNA splicing. Overall, 40 of the 73 ICA patients (55%) and 23 of the 56 kindreds (41%) carry mutations located in translated or untranslated exons of RPSA. Eleven of the 43 kindreds affected by sporadic disease (26%) carry RPSA mutations, whereas 12 of the 13 multiplex kindreds (92%) carry RPSA mutations. We also report that six of eighteen (33%) protein-coding mutations and the two (100%) 5’-UTR mutations display incomplete penetrance. Three mutations were identified in 2 independent kindreds, due to a hotspot or a founder effect. Lastly, RPSA ICA-causing mutations were demonstrated to be de novo in 7 of the 23 probands. Mutations in RPSA exons can affect the translated or untranslated regions and can underlie ICA with complete or incomplete penetrance.