bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disruption of the kringle 1 domain of prothrombin leads to late onset mortality in zebrafish
Authors: Grzegorski Steven J. , Hu Zhilian , Liu Yang , Yu Xinge , Ferguson Allison C. , Madarati Hasam , Friedmann Alexander P. , Reyon Deepak , Kim Paul Y. , Kretz Colin A. , Joung J. Keith , Shavit Jordan A. 
Published: March 2019

AbstractThe ability to prevent blood loss in response to injury is a critical, evolutionarily conserved function of all vertebrates. Prothrombin (F2) contributes to both primary and secondary hemostasis through the activation of platelets and the conversion of soluble fibrinogen to insoluble fibrin, respectively. Complete prothrombin deficiency has never been observed in humans and is incompatible with life in mice, limiting the ability to understand the entirety of prothrombin’sin vivofunctions. We have previously demonstrated the ability of zebrafish to tolerate loss of both pro- and anticoagulant factors that are embryonic lethal in mammals, making them an ideal model for the study of prothrombin deficiency. Using genome editing with TALENs, we have generated a null allele in zebrafishf2. Homozygous mutant embryos develop normally into early adulthood, but demonstrate eventual complete mortality with the majority of fish succumbing to internal hemorrhage by 2 months of age. We show that despite the extended survival, the mutants are unable to form occlusive thrombi in both the venous and arterial systems as early as 3-5 days of life, and we were able to phenocopy this early hemostatic defect using direct oral anticoagulants. When the equivalent mutation was engineered into the homologous residues of human prothrombin, there were severe reductions in secretion and activation, suggesting a possible role for kringle 1 in thrombin maturation, and the possibility that the F1.2 fragment has a functional role in exerting the procoagulant effects of thrombin. Together, our data demonstrate the conserved function of thrombin in zebrafish, as well as the requirement for kringle 1 for biosynthesis and activation by prothrombinase. Understanding how zebrafish are able to develop normally and survive into early adulthood without prothrombin will provide important insight into its pleiotropic functions as well as the management of patients with bleeding disorders.Key PointsDisruption of the kringle 1 domain of prothrombin leads to severe impairment of biosynthesis, activation, and activityProthrombin deficiency is compatible with normal development in zebrafish but leads to inability to form clots followed by early mortality
Facilitation and inhibition of firing activity and N-methyl-D-aspartate-evoked responses of CA1 hippocampal pyramidal cells by alpha7 nicotinic acetylcholine receptor selective compounds in vivo
Authors: Bali Zsolt Kristóf , Nagy Lili Veronika , Budai Dénes , Hernádi István 
Published: March 2019

AbstractAlpha7 nicotinic acetylcholine receptors (nAChRs) are promising novel targets for the treatment of neurocognitive disorders. Although the cognitive enhancer potential of alpha7 nAChR agonists and positive allosteric modulators (PAMs) has been confirmed in several preclinical animal models, there are only sparse in vivo electrophysiological data on their effects on the firing activity and excitability of neurons. The present study investigated and compared local effects of alpha7 nAChR agonist PHA-543613 and PAMs PNU-120596 and NS-1738 on the spontaneous and N-methyl-D-aspartate-evoked (NMDA-evoked) firing rate of rat CA1 hippocampal pyramidal cells, in vivo. Furthermore, effects of alpha7 nAChR antagonist methyllycaconitine (MLA) and GABA were also tested. Results showed substantially different effects of the alpha7 nAChR agonist and PAMs. While PNU-120596 and NS-1738 predominantly and significantly increased both spontaneous and NMDA-evoked firing rate of the neurons, application of PHA-543613 resulted in almost equal distribution of facilitatory and inhibitory effects. The increase of the NMDA-evoked firing rate exerted by NS-1738 was superadditive over the sum of the single effects of NMDA and NS-1738. The simultaneous application of alpha7 nAChR agonist PHA-543613 and PAM NS-1738 resulted in additive increase of both spontaneous and NMDA-evoked firing rate. However, NS-1738 counteracted inhibitory effects of PHA-543613 in 5 out of 6 neurons, resulting in a synergistic potentiation of their firing responses to NMDA. Our results suggest that alpha7 nAChR PAMs increase neuronal excitability more potently than agonists, while the remarkable occurrence of inhibitory effects of PHA-543613 (possibly originating from receptor desensitization) implies that agonists may exert neuroprotective effects.
How pirate phage interferes with helper phage: Comparison of the two distinct strategies
Authors: Mitarai Namiko 
Published: March 2019

AbstractPirate phages use the structural proteins encoded by unrelated helper phages to propagate. The best-studied example is the pirate P4 and helper P2 of coliphages, and it has been known that theStaphylococcus aureuspathogenicity islands (SaPIs) that can encode virulence factors act as pirate phages, too. When alone in the host, the pirate phages act as a prophage, but when the helper phage gene is also in the same host cell, the pirate phage has ability to exploit the helper phages structural proteins to produce pirate phage particles and spread, interfering with the helper phage production. The known helper phages in these systems are temperate phages. Interestingly, the interference of the pirate phage to the helper phage occurs in a different manner between the SaPI-helper system and the P4-P2 system. SaPIs cannot lyse a helper lysogen upon infection, while when a helper phage lyse a SaPI lysogen, most of the phage particles produced are the SaPI particles. On the contrary, in the P4-P2 system, a pirate phage P4 can lyse a helper P2 lysogen to produce mostly the P4 particles, while when P2 phage lyses a P4 lysogen, most of the produced phages are the P2 particles. Here, the consequences of these different strategies in the pirate and helper phage spreading among uninfected host is analyzed by using mathematical models. It is found that SaPI’s strategy interferes with the helper phage spreading significantly more than the P4’s strategy, because SaPI interferes with the helper phage’s main reproduction step, while P4 interferes only by forcing the helper lysogens to lyse. However, the interference is found to be weaker in the spatially structured environment than in the well-mixed environment. This is because, in the spatial setting, the system tends to self-organize so that the helper phages take over the front of propagation due to the need of helper phage for the pirate phage spreading.Competing interestsThe author declares no competing interest.
Pax9is required for cardiovascular development and interacts withTbx1in the pharyngeal endoderm to control 4thpharyngeal arch artery morphogenesis
Authors: Phillips Helen M. , Stothard Catherine A. , Shaikh Qureshi Wasay Mohiuddin , Kousa Anastasia I. , Alberto Briones-Leon J. , Khasawneh Ramada R. , Sanders Rachel , Mazzotta Silvia , Dodds Rebecca , Seidel Kerstin , Bates Timothy , Nakatomi Mitsushiro , Cockell Simon J. , Schneider Jürgen E. , Mohun Timothy J. , Maehr René , Kist Ralf , Peters Heiko , Bamforth Simon D. 
Published: March 2019

AbstractDevelopmental defects affecting the heart and aortic arch arteries are a key phenotype observed in DiGeorge syndrome patients and are caused by a microdeletion on chromosome 22q11. Heterozygosity ofTBX1, one of the deleted genes, is expressed throughout the pharyngeal arches and is considered a key component for the arch artery defects.Pax9is expressed in the pharyngeal endoderm and is downregulated inTbx1mutant mice. We show here thatPax9deficient mice are born with complex cardiovascular malformations affecting the outflow tract and aortic arch arteries with failure of the 3rdand 4thpharyngeal arch arteries to form correctly. Transcriptome analysis indicated thatPax9andTbx1may function together, and mice double heterozygous forTbx1/Pax9presented with a significantly increased incidence of interrupted aortic arch when compared toTbx1heterozygous mice. Using a novelPax9Creallele we demonstrated that the site of thisTbx1-Pax9genetic interaction is in the pharyngeal endoderm, therefore revealing that aTbx1/Pax9-controlled signalling mechanism emanating from the pharyngeal endoderm is required for critical tissue interactions during normal morphogenesis of the pharyngeal arch artery system.Summary statementPax9is required for outflow tract and aortic arch development, and functions together withTbx1in the pharyngeal endoderm for 4tharch artery formation.
Dynamic changes in innate immune and T cell function and composition at the nasal mucosa across the human lifespan
Authors: Reiné Jesús , Carniel Beatriz F. , Solórzano Carla , Mitsi Elena , Pojar Sherin , Nikolaou Elissavet , German Esther L. , Hyder-Wright Angela D. , Hill Helen , Hales Caz , Brown Lynsey , Horsley Victoria , Hughes Lisa , Zaidi Seher , Connor Victoria , Morton Ben , Collins Andrea M. , Rylance Jamie , Adler Hugh , McNamara Paul S. , Ferreira Daniela M. , Jochems Simon P. 
Published: March 2019

AbstractThe very young and very old are at increased risk of serious infections, including pneumonia. This may relate to changes in the immune system as young children have limited immunological memory, while immunosenescence, inflammaging and a decreased pool of naïve immune cells are described with advanced age. How the immune system changes with age at mucosal surfaces, from where infections frequently develop, is not very clear as access to human tissue samples is limited. Therefore, we aimed to assess the composition and activation state of the immune system at the human mucosa. Here, we profiled nasal immune cells from 207 individuals between 1 to 80 years old using flow cytometry. Neutrophil and monocyte functionality were measured using whole blood assays. Levels of thirty nasal cytokines were measured from nasal lining fluid. Nasopharyngeal colonization by Streptococcus pneumoniae was assessed using classical microbiology and associated with immune responses. We found that young children have a striking paucity of granulocytes at the nasal mucosa compared to adults. In addition, T cell numbers at the nasal mucosa decreased progressively with age and were almost absent in older adults. While nasopharyngeal colonization by Streptococcus pneumoniae was associated with elevated levels of inflammation it had a limited effect on nasal immune composition, including levels of monocytes and neutrophils. These results show that the immune system at the nasal mucosal surface changes drastically with age and provides explanations for the increased susceptibility to infections in young and old age.Significance statementHow the immune system changes with age is an intensive area of research, but has been primarily studied in blood. However, blood poorly reflects the immune system at the mucosa, from where infections develop. This manuscript provides a first characterization of how the composition and function of the immune system in the upper respiratory tract changes with age, providing explanations for increased susceptibility to infection in the very young and old. Furthermore, by linking mucosal and systemic measurements with pneumococcal colonization, we observed that reduced monocyte and neutrophil responses associate with the increased burden of pneumococcal colonization in children. This study highlights the need to study the immune system also at other mucosal sites in the context of aging.
Prenatal diagnosis of HNF1B-associated renal cysts: Need to differentiate intragenic variants from 17q12 microdeletion syndrome?
Authors: Vasileiou Georgia , Hoyer Juliane , Thiel Christian T. , Schaefer Jan , Zapke Maren , Krumbiegel Mandy , Kraus Cornelia , Zweier Markus , Uebe Steffen , Ekici Arif B. , Schneider Michael , Wiesener Michael , Rauch Anita , Faschingbauer Florian , Reis André , Zweier Christiane , Popp Bernt 
Published: March 2019

ABSTRACTObjectiveLarge deletions of chromosome 17q12 (17q12DS) or intragenic variants in HNF1B are associated with variable developmental, endocrine and renal anomalies, often already noted prenatally as hyperechogenic/cystic kidneys. Here, we describe pre- and postnatal phenotypes of seven individuals with HNF1B aberrations and compare their clinical and genetic data to previous studies.MethodsPrenatal sequencing and postnatal chromosomal microarray analysis was performed in seven individuals with renal and/or neurodevelopmental phenotypes. We evaluated HNF1B-related clinical features from 82 studies and reclassified 192 reported intragenic HNF1B variants.ResultsIn a prenatal case, we identified a novel in-frame deletion p.(Gly239del) within the HNF1B DNA binding domain, a mutational hotspot as demonstrated by spatial clustering analysis and high computational prediction scores. The six postnatally diagnosed individuals harbored 17q12 microdeletions of varying size. Literature screening revealed highly variable reporting of HNF1B-associated clinical traits. Overall, developmental delay was more frequent in 17q12DS carriers, although both mutation groups showed a high phenotypic heterogeneity. The reclassification of all previously reported intragenic HNF1B variants provided an up-to-date overview of the mutational spectrum.ConclusionsWe highlight the value of prenatal HNF1B screening in renal developmental diseases. Standardized clinical reporting and systematic classification of HNF1B variants is necessary for a more accurate risk quantification of pre- and postnatal clinical features, improving genetic counseling and prenatal decision-making.
Midgut barriers prevent the replication and dissemination of the yellow fever vaccine inAedes aegypti
Authors: Danet Lucie , Beauclair Guillaume , Berthet Michèle , Moratorio Gonzalo , Gracias Ségolène , Tangy Frédéric , Choumet Valérie , Jouvenet Nolwenn 
Published: March 2019

AbstractBackgroundTo be transmitted to vertebrate hostsviathe saliva of their vectors, arthropod-borne viruses have to cross several barriers in the mosquito body, including the midgut infection and escape barriers. Yellow fever virus (YFV) belongs to the genusFlavivirus, which includes human viruses transmitted byAedesmosquitoes, such as Dengue and Zika viruses. The live-attenuated YFV-17D vaccine has been used safely and efficiently on a large scale since the end of World War II. Early studies have shown, using viral titration from salivary glands of infected mosquitoes, that YFV-17D can infectAedes aegyptimidgut, but does not disseminate to other tissues.Methodology/Principal FindingsHere, we re-visited this issue using a panel of techniques, such as RT-qPCR, Western blot, immunofluorescence and titration assays. We showed that YFV-17D replication was not efficient inAedes aegyptimidgut, as compared to the clinical isolate YFV-Dakar. Viruses that replicated in the midgut failed to disseminate to secondary organs. When injected into the thorax of mosquitoes, viruses succeeded in replicating into midgut-associated tissues, suggesting that, during natural infection, the block for YFV-17D replication occurs at the basal membrane of the midgut. Our NGS analysis revealed that YFV-Dakar genome exhibited a greater diversity than the vaccine strain; a trait that may contribute to its ability to infect and disseminate efficiently inAe. aegypti.Conclusions/SignificanceThe two barriers associated withAe. aegyptimidgut prevent YFV-17D replication. Our study contributes to our basic understanding of vector–pathogen interactions and may also aid in the development of non-transmissible live virus vaccines.Author summaryMost flaviviruses, including yellow fever virus (YFV), are transmitted between hosts by mosquito bites. The yellow fever vaccine (YFV-17D) is one of the safest and most effective live virus vaccine ever developed. It is also used as a platform for engineering vaccines against other health-threatening flaviviruses, such as Japanese encephalitis, West Nile, Dengue and Zika viruses. We studied here the replication and dissemination of YFV-17D in mosquitoes. Our data showed that YFV-17D replicates poorly in mosquito midgut and is unable to disseminate to secondary organs, as compare to a YFV clinical isolate. Our study contributes to our basic understanding of the interactions between viruses and their vectors, which is key for conceiving new approaches in inhibiting virus transmission and designing non-transmissible live virus vaccines.
Microvasculopathy And Soft Tissue Calcification In Mice Are Governed by Fetuin-A, Pyrophosphate And Magnesium
Authors: Babler Anne , Schmitz Carlo , Büscher Andrea , Herrmann Marietta , Gremse Felix , Gorgels Theo , Floege Jürgen , Jahnen-Dechent Willi 
Published: March 2019

AbstractObjectiveCalcifications can disrupt organ function in the cardiovascular system and the kidney, and are particularly common in patients with chronic kidney disease (CKD). Fetuin-A deficient mice maintained against the genetic background DBA/2 exhibit particularly severe soft tissue calcifications, while fetuin-A deficient C57BL/6 mice remain healthy. We employed molecular genetic analysis to identify risk factors of calcification in fetuin-A deficient mice. We sought to identify pharmaceutical therapeutic target that could be influenced by dietary of parenteral supplementation.Approach and ResultsWe studied the progeny of an intercross of fetuin-A deficient DBA/2 and C57BL/6 mice to identify candidate risk genes involved in calcification. We determined that a hypomorphic mutation of theAbcc6gene, a liver ATP transporter supplying systemic pyrophosphate, and failure to regulate the TRPM6 magnesium transporter in kidney were associated with severity of calcification. Calcification prone fetuin-A deficient mice were alternatively treated with dietary phosphate restriction, magnesium supplementation, or by parenteral administration of fetuin-A or pyrophosphate. All treatments markedly reduced soft tissue calcification, demonstrated by computed tomography, histology and tissue calcium measurement.ConclusionsWe show that pathological ectopic calcification in fetuin-A deficient DBA/2 mice is caused by a compound deficiency of three major extracellular and systemic inhibitors of calcification, namely fetuin-A, pyrophosphate, and magnesium. All three of these are individually known to contribute to stabilize protein-mineral complexes and thus inhibit mineral precipitation from extracellular fluid. We show for the first time a compound triple deficiency that can be treated by simple dietary or parenteral supplementation. This is of special importance in patients with advanced CKD, who commonly exhibit reduced serum fetuin-A, pyrophosphate and magnesium levels.Subject CodesAnimal Models of Human Disease, Fibrosis, Inflammation, Proteomics, Peripheral Vascular Disease
Quantifying and understanding well-to-well contamination in microbiome research
Authors: Minich Jeremiah J , Sanders Jon G , Amir Amnon , Humphrey Greg , Gilbert Jack , Knight Rob 
Published: March 2019

AbstractMicrobial sequences inferred as belonging to one sample may not have originated from that sample. Such contamination may arise from laboratory or reagent sources or from physical exchange between samples. This study seeks to rigorously assess the behavior of this often-neglected between-sample contamination. Using unique bacteria each assigned a particular well in a plate, we assess the frequency at which sequences from each source appears in other wells. We evaluate the effects of different DNA extraction methods performed in two labs using a consistent plate layout including blanks, low biomass, and high biomass samples. Well-to-well contamination occurred primarily during DNA extraction, and to a lesser extent in library preparation, while barcode leakage was negligible. Labs differed in the levels of contamination. DNA extraction methods differed in their occurrences and levels of well-to-well contamination, with robotic methods having more well-to-well contamination while manual methods having higher background contaminants. Well-to-well contamination was observed to occur primarily in neighboring samples, with rare events up to 10 wells apart. The effect of well-to-well was greatest in samples with lower biomass, and negatively impacted metrics of alpha and beta diversity. Our work emphasizes that sample contamination is a combination of crosstalk from nearby wells and background contaminants. To reduce well-to-well effects, samples should be randomized across plates, and samples of similar biomass processed together. Researchers should evaluate well-to-well contamination in study design and avoid removal of taxa or OTUs appearing in negative controls, as many will be microbes from other samples rather than reagent contaminants.ImportanceMicrobiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements including use of controls for validating accurate portrayals of microbial communities. In this study, we describe a previously undocumented form of contamination, well-to-well contamination and show that contamination primarily occurs during DNA extraction rather than PCR, is highest in plate-based methods as compared to single tube extraction, and occurs in higher frequency in low biomass samples. This finding has profound importance on the field as many current techniques to ‘decontaminate’ a dataset simply relies on an assumption that microbial reads found in blanks are contaminants from ‘outside’ namely the reagents or consumables.
Ultra-widefield fluorescein angiography findings in patients with multiple retinal holes
Authors: Baek Jiwon , Jung Byungju , Kwon Hyunggu , Jeon Sohee 
Published: March 2019

PurposeTo evaluate the ultra-widefield fluorescein angiography (UWFA) findings in patients with multiple retinal holes.MethodsSeventy-five eyes, each with more than two retinal holes, underwent a comprehensive ophthalmologic examination, including UWFA, along with 77 age-matched control eyes with no retinal holes. The UWFA was scored according to a system suggested by the Angiography Scoring for Uveitis Working Group (ASUWG). UWFA findings from the patients with retinal holes were compared with those of the control group without retinal holes. Factors associated with a high ASUWG score were also evaluated.ResultsPatients with multiple retinal holes showed a significantly higher prevalence of retinal vascular staining/leakage, capillary leakage at the posterior pole, and capillary leakage at the periphery when compared to the control group (p<0.001, for each of them). Univariate analysis revealed that logMAR BCVA (r=0.271, p=0.027), spherical equivalent (r= −0.275, p=0.021), and number of retinal holes (r=0.271, p=0.027) were associated with a higher ASUWG score. After adjustments for age, gender, and logMAR BCVA, multivariate regression analysis revealed that the spherical equivalent was independently associated with a higher ASUWG score (r2=0.161, p=0.001).ConclusionsPatients with multiple retinal holes showed profound peripheral vascular leakages on UWFA findings, suggesting the presence of chronic retinal traction induced by equatorial scleral elongation.