bluuebunny/crossref_metadata_2025 huggingface dataset:
Water stress combined with sulfur deficiency in pea affects yield components but mitigates the effect of deficiency on seed globulin composition
Authors: Henriet Charlotte , Aimé Delphine , Térézol Morgane , Kilandamoko Anderson , Rossin Nadia , Combes-Soia Lucie , Labas Valerie , Serre Rémy-Félix , Prudent Marion , Kreplak Jonathan , Vernoud Vanessa , Gallardo Karine
Published: March 2019

Water stress and sulfur (S) deficiency are two constraints increasingly faced by crops due to climate change and low-input agricultural practices. To investigate their interaction in the grain legume pea (Pisum sativum), sulfate was depleted at the mid-vegetative stage and a moderate 9-d water stress period was imposed during the early reproductive phase. The combination of the stresses impeded reproductive processes in a synergistic manner, reducing seed weight and seed number, and inducing seed abortion, which highlighted the paramount importance of sulfur for maintaining seed yield components under water stress. On the other hand, the moderate water stress mitigated the negative effect of sulfur deficiency on the accumulation of S-rich globulins (11S) in seeds, probably due to a lower seed sink strength for nitrogen, enabling a readjustment of the ratio of S-poor (7S) to 11S globulins. Transcriptome analysis of developing seeds at the end of the combined stress period indicated that similar biological processes were regulated in response to sulfur deficiency and to the combined stress, but that the extent of the transcriptional regulation was greater under sulfur deficiency. Seeds from plants subjected to the combined stresses showed a specific up-regulation of a set of transcription factor and SUMO ligase genes, indicating the establishment of unique regulatory processes when sulfur deficiency is combined with water stress.
Spatial heterogeneity of the planktonic protistan community in a semi-closed eutrophic bay, China
Authors: Du Ping , Jiang Zhi B , Wang Yong M , Qian Peng , Hu Han J , Liao Yi B , Zhou Kong L , Zeng Jiang N , Chen Quan Z , Shou Lu , Zhang De M
Published: March 2019

We examined the planktonic protistan community in Xiangshan Bay during spring 2015 using 18S rDNA sequencing. We found significant spatial heterogeneity in α-diversity, β-diversity (Bray–Curtis and Jaccard indices) and the relative abundance of dominant taxa. The spatial heterogeneity of the protistan community was due more to variation in species (operational taxonomic units) than abundance, and the spatial variation in species was dominated by variation in rare biota. Salinity was the most important driver of spatial heterogeneity in the total community and the abundant subcommunity, but environmental factors could not explain the variation in the rare subcommunity. For α-diversity, spatial heterogeneity was mainly associated with the rare biota; α-diversity was positively correlated with water mass complexity but negatively correlated with temperature and nutrients. Of the dominant protistan phyla, the more abundant Cryptophyta, Chlorophyta and Haptophyta were correlated with lower salinity and higher nutrient concentrations, while the more abundant mixotrophs (e.g. Dinoflagellata and Protalveolata) were associated with lower nutrient concentration. Our study suggests that rare taxa are important for preserving the spatial heterogeneity of the protistan community, whose structural variation might be influenced by biotic interactions.
Comorbidity burden in axial spondyloarthritis: a cluster analysis
Authors: Zhao Sizheng Steven , Radner Helga , Siebert Stefan , Duffield Stephen J , Thong Daniel , Hughes David M , Moots Robert J , Solomon Daniel H , Goodson Nicola J
Published: March 2019

Objectives

To examine how comorbidities cluster in axial spondyloarthritis (axSpA) and whether these clusters are associated with quality of life, global health and other outcome measures.

Methods

We conducted a cross-sectional study of consecutive patients meeting ASAS criteria for axSpA in Liverpool, UK. Outcome measures included quality of life (EQ5D), global health and disease activity (BASDAI). We used hierarchical cluster analysis to group patients according to 38 pre-specified comorbidities. In multivariable linear models, the associations between distinct comorbidity clusters and each outcome measure were compared, using axSpA patients with no comorbidities as the reference group. Analyses were adjusted for age, gender, symptom duration, BMI, deprivation, NSAID-use and smoking.

Results

We studied 419 patients (69% male, mean age 46 years). 255 patients (61%) had at least one comorbidity, among whom the median number was 1 (range 1–6). Common comorbidities were hypertension (19%) and depression (16%). Of 15 clusters identified, the most prevalent clusters were hypertension-coronary heart disease and depression-anxiety. Compared with patients with no comorbidities, the fibromyalgia-irritable bowel syndrome cluster was associated with adverse patient-reported outcome measures; these patients reported 1.5-unit poorer global health (95%CI 0.01, 2.9), reduced quality of life (0.25-unit lower EQ5D; 95%CI −0.37, −0.12) and 1.8-unit higher BASDAI (95% CI 0.4, 3.3). Similar effect estimates were found for patients in the depression-anxiety cluster.

Conclusion

Comorbidity is common among axSpA patients. The two most common comorbidities were hypertension and depression. Patients in the depression-anxiety and fibromyalgia-IBS clusters reported poorer health and increased axSpA severity.
Magnetic Resonance Spectroscopy as a Non-invasive Method to Quantify Muscle Carnosine in Humans: a Comprehensive Validity Assessment
Authors: da Eira Silva Vinicius , de Salles Painelli Vitor , Shinjo Samuel Katsuyuki , Pereira Wagner Ribeiro , Cilli Eduardo Maffud , Sale Craig , Gualano Bruno , Otaduy Maria Concepción , Artioli Guilherme Giannini
Published: March 2019

Carnosine is a dipeptide abundantly found in human skeletal muscle, cardiac muscle and neuronal cells having numerous properties that confers performance enhancing effects, as well as a wide-range of potential therapeutic applications. A reliable and valid method for tissue carnosine quantification is crucial for advancing the knowledge on biological processes involved with carnosine metabolism. In this regard, proton magnetic resonance spectroscopy (1H-MRS) has been used as a non-invasive alternative to quantify carnosine in human skeletal muscle. However, carnosine quantification by 1H-MRS has some potential limitations that warrant a thorough experimental examination of its validity. The present investigation examined the reliability, accuracy and sensitivity for the determination of muscle carnosine in humans using in vitro and in vivo experiments and comparing it to reference method for carnosine quantification (high-performance liquid chromatography – HPLC). We used in vitro 1H-MRS to verify signal linearity and possible noise sources. Carnosine was determined in the m. gastrocnemius by 1H-MRS and HPLC to compare signal quality and convergent validity. 1H-MRS showed adequate discriminant validity, but limited reliability and poor agreement with a reference method. Low signal amplitude, low signal-to-noise ratio, and voxel repositioning are major sources of error.
Experimental introgression to evaluate the impact of sex specific traits onDrosophila melanogasterincipient speciation
Authors: Cortot Jérôme , Farine Jean-Pierre , Houot Benjamin , Everaerts Claude , Ferveur Jean-François
Published: March 2019

Sex specific traits are involved in speciation but it is difficult to determine whether their variation initiates or reinforces sexual isolation. In some insects, speciation depends of the rapid change of expression in desaturase genes coding for sex pheromones. Two closely related desaturase genes are involved inDrosophila melanogasterpheromonal communication:desat1affects both the production and the reception of sex pheromones whiledesat2is involved in their production in flies of Zimbabwe populations. There is a strong asymmetric sexual isolation between Zimbabwe populations and all other “Cosmopolitan” populations: Zimbabwe females rarely copulate with Cosmopolitan males whereas Zimbabwe males readily copulate with all females. All populations expressdesat1but only Zimbabwe strains show highdesat2expression. To evaluate the impact of sex pheromones, female receptivity anddesatexpression on the incipient speciation process between Zimbabwe and Cosmopolitan populations, we introgressed the Zimbabwe genome into a Cosmopolitan genome labelled with thewhitemutation, using a multi-generation procedure. The association between these sex-specific traits was determined during the procedure. The production of pheromones was largely dissociated between the sexes. The copulation frequency (but not latency) was highly correlated with the female—but not with the male—principal pheromones. We finally obtained two stablewhitelines showing Zimbabwe-like sex pheromones, copulation discrimination anddesatexpression. Our study indicates that the variation of sex pheromones and of mating discrimination depend of distinct—yet overlapping—sets of genes in each sex suggesting that their cumulated effects participate to reinforce the speciation process.
Mechanical, physical and chemical characterisation of mycelium-based composites with different types of lignocellulosic substrates
Authors: Elsacker Elise , Vandelook Simon , Brancart Joost , Peeters Eveline , Laet Lars De
Published: March 2019

The current physical goods economy produces materials by extracting finite valuable resources without taking their end of the life and environmental impact into account. Modernity leaves us with devasted landscapes of depleted resources, waste landfill, queries, oil platforms. At the time of the Anthropocene, the various effects the human role has on the constitution of the soils create an acceleration of material entropy. It is the terrestrial entanglement of fungal materials that we investigate in this paper by offering an alternative fabrication paradigm based on the growth of resources rather than on extraction. Unlike the latter, biologically augmented building materials can be grown by combining micro-organisms such as fungal mycelium with agricultural plant-based waste. In this study, we investigate the production process, the mechanical, hygrothermal and chemical properties of mycelium-based composites with different types of lignocellulosic reinforcement fibres combined with a white rot fungus, Trametes versicolor. Together, they form an interwoven three-dimensional filamentous network binding the feedstock into a lightweight material. The mycelium-based material is heat-killed after the growing process. This is the first study reporting the dry density, the Young’s modulus, the compressive stiffness, the stress-strain curves, the thermal conductivity, the water absorption rate and a complete FTIR analyse of mycelium-based composites by making use of a disclosed protocol with T. versicolor and five different type of fibres (hemp, flax, flax waste, softwood, straw) and fibre conditions (loose, chopped, dust, pre-compressed and tow). These experimental results show that mycelium-composites can fulfil the requirements of thermal insulation. The thermal conductivity and water absorption coefficient of the mycelium composites with flax, hemp, and straw have an overall good insulation behaviour in all the aspects compared to conventional unsustainable materials. The conducted tests reveal that the mechanical performances of the mycelium-based composites depend more on the fibre condition, size, and processing than on the chemical composition of the fibres.

Abstract Figure

Graphical abstract

Highlights

The type of fibre influences the colonisation of mycelium: samples containing flax, hemp, straw and flax-waste resulted in a well-developed composite

The type of fibre has a smaller influence on the compressive stiffness than the fibre processing and size.

Pre-compression and chopped fibres (particle size <5mm) improve the compressive mechanical properties of mycelium composites.

The thermal conductivity and water absorption coefficient of the mycelium composites with flax, hemp, and straw have an overall good insulation behaviour in all the aspects compared to conventional unsustainable materials.
A causal approach to understanding management factors, reproductive underperformance and reproductive infections in dairy cattle
Authors: Softic Adis , Asmare Kassahun , Granquist Erik Georg , Godfroid Jacques , Fejzic Nihad , Skjerve Eystein
Published: March 2019

The objective of this study was to investigate causal associations between cattle farms’ management practices and reproductive disorders (abortion, stillbirth, retention of placenta, metritis). Besides, direct causal associations between farms’ management and reproductive infections (Chlamydia abortus, Coxiella burnetii, and Neospora caninum), reproductive disorders and infections were also investigated in this study. As a secondary objective, constraints that affect the production in cattle farms were examined. The study was carried out in the north-western (Una-Sana), western (Canton 10) and central part (Central Bosnia Canton) of Bosnia and Herzegovina. A total of 201 farms were selected for participation. A semi-structured questionnaire-based interview was conducted among farmers/managers from January 1st to August 31st, 2015. The 40 questions were divided into three groups: socio-demographic, management, and information on reproductive performances in cattle. Supplementary questions were asked about the perceived primary constraints of the production.

A multivariable mixed-effects logistic regression was used to screen management factors for potential statistical influence. All investigated outcomes were associated with farms’ management. The final multivariable models were merged into a Structural Equation Model (SEM). The causal model was then specified graphically. The SEM model showed that herds that experienced abortions (OR=4.3) and stillbirth (OR=6.7) were associated with N. caninum seropositivity. Also, herds that experienced retention of placenta were strongly associated with the occurrence of metritis (OR=10.1). C. abortus and C. burnetii herd seropositivities were mainly associated with environmental factors and contact with potential intermediate hosts.

Our study demonstrated that management practices on dairy farms in Bosnia and Herzegovina contributed to the occurrence of severe reproductive outcomes and reproductive infections. N. caninum seems to be an infectious agent that substantially contributed to the reproductive underperformance. Further we demonstrate the need for using causal models in understanding complex relationships.
Approach for Semi-Automated Measurement of Fiber Diameter in Murine and Canine Skeletal Muscle
Authors: Stevens Courtney R. , Sledziona Michael , Moore Timothy P. , Dong Lynn , Cheetham Jonathan
Published: March 2019

Currently available software tools for automated segmentation and analysis of muscle cross-section images often perform poorly in cases of weak or non-uniform staining conditions. To address these issues, our group has developed the MyoSAT (Myofiber Segmentation and Analysis Tool) image-processing pipeline.

MyoSAT combines several unconventional approaches including advanced background leveling, Perona-Malik anisotropic diffusion filtering, and Steger’s line detection algorithm to aid in pre-processing and enhancement of the muscle image. Final segmentation is based upon marker-based watershed segmentation.

Validation tests using collagen V labeled murine and canine muscle tissue demonstrate that MyoSAT can determine mean muscle fiber diameter with an average accuracy of ~97%. The software has been tested to work on full muscle cross-sections and works well even under non-optimal staining conditions.

The MyoSAT software tool has been implemented as a macro for the freely available ImageJ software platform. This new segmentation tool allows scientists to efficiently analyze large muscle cross-sections for use in research studies and diagnostics.
Sterol-O acyltransferase 1 is inhibited by gga-miR-181a-5p and gga-miR-429-3p through the TGFβ pathway in endodermal epithelial cells of Japanese quail
Authors: Lin Han-Jen , Lin Chiao-Wei , Mersmann Harry J. , Ding Shih-Torng
Published: March 2019

Nutrients are utilized and re-constructed by endodermal epithelial cells (EECs) in yolk sac membranes in avian species. Sterol-O acyltransferase 1 (SOAT1) is the key enzyme to convert cholesterol to cholesteryl ester for delivery to growing embryos. During development, absorption of yolk is matched with significant changes of SOAT1 mRNA and enzyme activity. miRNAs regulate angiogenesis and metabolism during mammalian development. However, the involvement of miRNAs in lipid utilization during avian embryogenesis remains ambiguous.

Using a miRNA sequencing technique, we found several candidate miRNAs and confirmed expression patterns with real time PCR. They were selected for as candidates targeting the receptor (TGFβ receptor type 1, TGFBR1) that may regulate SOAT1. Similar to SOAT1 mRNA accumulation, the gga-miR-181a-5p expression was gradually elevated during development, but the concentration of gga-miR-429-3p was in the opposite direction. Transfection with gga-miR-181a-5p or gga-miR-429-3p inhibited TGFBR1 and SOAT1 in EECs. The 3’ untranslated region (3’UTR) of TGFBR1 was then confirmed to be one of the targets of gga-miR-181a-5p and gga-miR-429-3p. Taken together, expression of miRNAs during embryonic development regulates SOAT1 expression by inhibiting the 3’UTR of TGFBR1. This is indicative of possible regulation of avian yolk lipid utilization and modification of hatchability by changing miRNA expressions.
Assessing introgressive hybridization in roan antelope (Hippotragus equinus): Lessons from South Africa
Authors: van Wyk Anna M , Dalton Desiré L , Kotzé Antoinette , Grobler J. Paul , Mokgokong Prudent S. , Kropff Anna S , Vuuren Bettine Jansen van
Published: March 2019

Biological diversity is being lost at unprecedented rates, with admixture and introgression presenting major threats to species’ conservation. To this end, our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. A case in hand concerns roan antelope, one of Africa’s most iconic large mammal species. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the remaining bastions with increasing population sizes, there are a number of West African roan antelope populations on private farms, and concerns are that these animals hybridize with roan that naturally occur in the southern African region. We used a suite of 27 microsatellite markers to conduct admixture analysis. Our results unequivocally indicate evidence of hybridization, with our developed tests able to accurately identify F1, F2 and non-admixed individuals at threshold values ofqi= 0.20 andqi= 0.15, although further backcrosses were not always detectable. Our study is the first to confirm ongoing hybridization in this iconic African antelope, and we provide recommendations for the future conservation and management of this species.
An abscisic acid (ABA) homeostasis regulated by its production, catabolism and transport in peanut leaves in response to drought stress
Authors: Long Haitao , Zheng Zhao , Zhang Yajun , Xing Pengzhan , Wan Xiaorong , Zheng Yixiong , Li Ling
Published: March 2019

ABA is an important messenger that acts as the signaling mediator for regulating the adaptive response of plants to drought stress. Two production pathways,de novobiosynthesis and hydrolysis of glucose-conjugated ABA by β-glucosidase (BG), increase cellular ABA levels in plants. ABA catabolism via hydroxylation by 8’-hydroxylase (CYP707A), or conjugation by uridine diphosphate glucosyltransferase (UGT), decreases cellular ABA levels. The transport of ABA through ATP-binding cassette (ABC)-containing transporter proteins, members of ABC transporter G family (ABCG), across plasma membrane (PM) is another important pathway to regulate cellular ABA levels. In this study, based on our previously constructed transcriptome of peanut leaves in response to drought stress, fourteen candidate genes involved in ABA production (includingAhZEP,AhNCED1andAhNCED3,AhABA2,AhAAO1andAhAAO2,AhABA3,AhBG11andAhBG24), catabolism (includingAhCYP707A3,AhUGT71K1andAhUGT73B4) and transport (includingAhABCG22-1andAhABCG22-2), were identified homologously and phylogenetically, and further analyzed at the transcriptional level by real-time RT-PCR, simultaneously determining ABA levels in peanut leaves in response to drought. The high sequence identity and very similar subcellular localization of the proteins deduced from 14 identified genes involved in ABA production, catabolism and transport with the reported corresponding enzymes in databases suggest their similar roles in regulating cellular ABA levels. In response to drought stress, ABA accumulation levels in peanut leaves agree very well with the up-regulated expressions of ABA-producing genes (AhZEP,AhNCED1,AhAAO2,AhABA3,AhBG11andAhBG24) and PM-localized ABA importer genes (AhABCG22-1andAhABCG22-2), although the expression of ABA catabolic genes (AhCYP707A3andAhUGT71K1) was also up-regulated. It is likely that drought-responsive induction of catabolic genes helps not only to maintain ABA levels within a permissible range, but also to prepare the plant for degradation of ABA after removal of the stress. These results suggest that ABA homeostasis in peanut leaves in response to drought may be coordinated by a master regulatory circuit that involves production, catabolism, and as well as transport.
Revised subunit order of mammalian septin complexes explains their in vitro polymerization properties
Authors: Soroor Forooz , Kim Moshe S. , Palander Oliva , Balachandran Yadu , Collins Richard , Benlekbir Samir , Rubinstein John , Trimble William S.
Published: March 2019

Septins are conserved GTP-binding cytoskeletal proteins that polymerize into filaments by end-to-end joining of heterooligomeric complexes. In human cells, both hexamers and octamers exist, and crystallography studies predicted the order of the hexamers to be SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7, while octamers are thought to have the same core, but with SEPT9 at the ends. However, based on this septin organization, octamers and hexamers would not be expected to co-polymerize due to incompatible ends. Here we isolated hexamers and octamers of specific composition from human cells and show that hexamers and octamers polymerize individually and, surprisingly, with each other. Binding of Borg3 results in distinctive clustering of each filament type. Moreover, we show that the organization of hexameric and octameric complexes is inverted compared to its original prediction. This revised septin organization is congruent with the organization and behavior of yeast septins suggesting that their properties are more conserved than was previously thought.
Distinct matrix composition and mechanics in aged and estrogen-deficient mouse skin
Authors: Saville Charis R , Mallikarjun Venkatesh , Holmes David F , Emmerson Elaine , Derby Brian , Swift Joe , Sherratt Michael J , Hardman Matthew J
Published: March 2019

Hormone deficiency has been widely linked to accelerated tissue ageing, and increased incidence of chronic degenerative disease. Furthermore, age-associated hormonal dysregulation is thought to be a major contributing factor to the increased fragility of aged skin. The ageing process is driven by an aggregation of damage to cells and extracellular matrix, which can directly influence the mechanical properties of the tissue. Here we report on the correlation between mechanical properties and composition of skin from ovariectomised and aged mice, to assess the extent to which estrogen deprivation drives dermal ageing. We found that age and estrogen abrogation affected skin mechanical properties in contrasting ways: ageing led to increased tensile strength and stiffness while estrogen deprivation had the opposite effect. Mass spectrometry proteomics showed that the quantity of extractable fibrillar collagen-I decreased with ageing, but no change was observed in ovariectomised mice. This observation, in combination with measurements of tensile strength, was interpreted to reflect changes to the extent of extracellular matrix crosslinking, supported by a significant increase in the staining of advanced glycation endpoints in aged skin. Loss of mechanical strength in the skin following ovariectomy was consistent with a loss of elastic fibres. Other changes in extracellular matrix composition broadly correlated between aged and ovariectomised mice, confirming the important role of estrogen-related pathways in ageing. This study offers new insight into the relationship between tissue composition and mechanics, and suggests that the deleterious effects of intrinsic skin ageing are compounded by factors beyond hormonal dysregulation.
The Rab32/BLOC-3 dependent pathway mediates host- defence against different pathogens in human macrophages
Authors: Baldassarre Massimiliano , Solano-Collado Virtu , Balci Arda , Colamarino Rosa A. , Dambuza Ivy M , Reid Delyth M. , Wilson Heather M , Brown Gordon D , Mukhopadhyay Subhankar , Dougan Gordon , Spanò Stefania
Published: March 2019

Macrophages provide a first line of defence against microorganisms, and while some mechanisms to kill pathogens such as the oxidative burst are well described, others are still undefined or unknown. Here we report that the Rab32 GTPase and its guanine nucleotide exchange factor BLOC-3 are central components of a trafficking pathway that controls both bacterial and fungal intracellular pathogens. This broad host-defence mechanism is active in both human and murine macrophages and is independent of well known antimicrobial mechanisms such as the NADPH-dependent oxidative burst, production of nitric oxide and antimicrobial peptides. To survive in human macrophages, Salmonella Typhi actively counteracts the Rab32/BLOC-3 pathway through its Salmonella pathogenicity island-1-encoded type III secretion system. These findings demonstrate that the Rab32/BLOC-3 pathway is a novel and universal host-defence pathway and protects mammalian species from a wide range of intracellular pathogens.
NOD2 and TLR2 Signal via TBK1 and PI31 to Direct Cross-presentation and CD8 T Cell Responses
Authors: Corridoni Daniele , Shiraishi Seiji , Chapman Thomas , Steevels Tessa , Muraro Daniele , Thézénas Marie-Laëtitia , Prota Gennaro , Chen Ji-Li , Gileadi Uzi , Ternette Nicola , Cerundolo Vincenzo , Simmons Alison
Published: March 2019

NOD2 and TLR2 recognize components of bacterial cell wall peptidoglycan and direct defense against enteric pathogens. CD8+ T cells are important for immunity to such pathogens but how NOD2 and TLR2 induce antigen specific CD8+ T cell responses is unknown. Here, we define how these pattern recognition receptors (PRRs) signal in primary dendritic cells (DCs) to influence MHC class I antigen presentation. We show NOD2 and TLR2 phosphorylate PI31 via TBK1 following activation in DCs. PI31 interacts with TBK1 and Sec16A at endoplasmic reticulum exit sites (ERES), which positively regulates MHC class I peptide loading and immunoproteasome stability. Following NOD2 and TLR2 stimulation, depletion of PI31 or inhibition of TBK1 activity in vivo impairs DC cross-presentation and CD8+ T cell activation. DCs from Crohn’s patients expressing NOD2 polymorphisms show dysregulated cross-presentation and CD8+ T cell responses. Our findings reveal unidentified mechanisms that underlie CD8+ T cell responses to bacteria in health and in Crohn’s.
GCNA preserves genome integrity and fertility across species
Authors: Bhargava Varsha , Goldstein Courtney D. , Russell Logan , Xu Lin , Ahmed Murtaza , Li Wei , Casey Amanda , Servage Kelly , Kollipara Rahul , Picciarelli Zachary , Kittler Ralf , Yatsenko Alexander , Carmell Michelle , Orth Kim , Amatruda James F. , Yanowitz Judith L. , Buszczak Michael
Published: March 2019

The propagation of species depends on the ability of germ cells to protect their genome in the face of numerous exogenous and endogenous threats. While these cells employ a number of known repair pathways, specialized mechanisms that ensure high-fidelity replication, chromosome segregation, and repair of germ cell genomes remain incompletely understood. Here, we identify Germ Cell Nuclear Acidic Peptidase (GCNA) as a highly conserved regulator of genome stability in flies, worms, zebrafish, and humans. GCNA contains a long acidic intrinsically disordered region (IDR) and a protease-like SprT domain. In addition to chromosomal instability and replication stress, GCNA mutants accumulate DNA-protein crosslinks (DPCs). GCNA acts in parallel with a second SprT domain protein Spartan. Structural analysis reveals that while the SprT domain is needed to limit meiotic and replicative damage, most of GCNA’s function maps to its IDR. This work shows GCNA protects germ cells from various sources of damage, providing novel insights into conserved mechanisms that promote genome integrity across generations.

Highlights

GCNA ensures genomic stability in germ cells and early embryos across species

GCNA limits replication stress and DNA double stranded breaks

GCNA restricts DNA-Protein Crosslinks within germ cells and early embryos

The IDR and SprT domains of GCNA govern distinct aspects of genome integrity

Graphic Abstract
Reorientation and propulsion in fast-starting zebrafish larvae: an inverse dynamics analysis
Authors: Voesenek Cees J. , Pieters Remco P. M. , Muijres Florian T. , van Leeuwen Johan L.
Published: March 2019

Most fish species use fast starts to escape from predators. Zebrafish larvae perform effective fast starts immediately after hatching. They use a C-start, where the body curls into a C-shape, and then unfolds to accelerate. These escape responses need to fulfil a number of functional demands, under the constraints of the fluid environment and the larva’s body shape. Primarily, the larvae need to generate sufficient escape speed in a wide range of possible directions, in a short-enough time. In this study, we examined how the larvae meet these demands. We filmed fast starts of zebrafish larvae with a unique five-camera setup with high spatiotemporal resolution. From these videos, we reconstructed the three-dimensional swimming motion with an automated method and from these data calculated resultant hydrodynamic forces and, for the first time, 3D torques. We show that zebrafish larvae reorient mostly in the first stage of the start by producing a strong yaw torque, often without using the pectoral fins. This reorientation is expressed as the body angle, a measure that represents the rotation of the complete body, rather than the commonly used head angle. The fish accelerates its centre of mass mostly in stage 2 by generating a considerable force peak while the fish “unfolds”. The escape direction of the fish correlates strongly with the amount of body curvature in stage 1, while the escape speed correlates strongly with the duration of the start. This may allow the fish to independently control the direction and speed of the escape.

Summary statement

Fish larvae can independently adjust the direction and speed of their fast start escape response, a manoeuvre crucial for survival.
Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems
Authors: Luan Haoan , Gao Wei , Huang Shaowen , Tang Jiwei , Li Mingyue , Zhang Huaizhi , Chen Xinping
Published: March 2019

Soil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G− bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon–Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.
Genetic determinants of gut microbiota composition and bile acid profiles in mice
Authors: Kemis Julia H. , Linke Vanessa , Barrett Kelsey L. , Boehm Frederick J. , Traeger Lindsay L. , Keller Mark P. , Rabaglia Mary E. , Schueler Kathryn L. , Stapleton Donald S. , Gatti Daniel M. , Churchill Gary A. , Amador-Noguez Daniel , Russell Jason D. , Yandell Brian S. , Broman Karl W. , Coon Joshua J. , Attie Alan D. , Rey Federico E.
Published: March 2019

The microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for ∼22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL forTuricibacter sp.and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter,Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences inSlc10a2gene expression associated with the different strains influences levels of both traits and revealed novel interactions betweenTuricibacterand BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.

Author summary

Inter-individual variation in the composition of the intestinal microbiota can in part be attributed to host genetics. However, the specific genes and genetic variants underlying differences in the microbiota remain largely unknown. To address this, we profiled the fecal microbiota composition of 400 genetically distinct mice, for which genotypic data is available. We identified many loci of the mouse genome associated with changes in abundance of bacterial taxa. One of these loci is also associated with changes in the abundance of plasma bile acids—metabolites generated by the host that influence both microbiota composition and host physiology. Follow up validation experiments provide mechanistic insights linking host genetic differences, with changes in ileum gene expression, bile acid-bacteria interactions and bile acid homeostasis. Together, this work demonstrates how genetic approaches can be used to generate testable hypothesis to yield novel insight into how host genetics shape gut microbiota composition.
The Cdc14 phosphatase controls resolution of recombination intermediates and crossover formation during meiosis
Authors: Alonso-Ramos Paula , Álvarez-Melo David , Strouhalova Katerina , Pascual-Silva Carolina , Garside George B. , Arter Meret , Bermejo Teresa , Grigaitis Rokas , Wettstein Rahel , Fernández-Díaz Marta , Matos Joao , Geymonat Marco , San-Segundo Pedro A. , Carballo Jesús A.
Published: March 2019

Meiotic defects derived from incorrect DNA repair during gametogenesis can lead to mutations, aneuploidies and infertility. Coordinated resolution of meiotic recombination intermediates is required for crossover formation, ultimately necessary for accurate completion of both rounds of chromosome segregation. Numerous master kinases orchestrate the correct assembly and activity of the repair machinery. Although much less is known, reversal of phosphorylation events in meiosis must also be key to coordinate the timing and functionality of repair enzymes. Cdc14 is an evolutionarily conserved phosphatase required for the dephosphorylation of multiple CDK1 targets. Mutations that inactivate this phosphatase lead to meiotic failure, but until now it was unknown if Cdc14 plays a direct role in meiotic recombination. Here, we show that elimination of Cdc14 leads to severe defects in the processing and resolution of recombination intermediates, causing a drastic depletion of crossovers when other repair pathways are compromised. We also show that Cdc14 is required for correct activity and localization of the Holliday Junction resolvase Yen1/GEN1. We reveal that Cdc14 regulates Yen1 activity from meiosis I onwards, and this function is essential for crossover resolution in the absence of other repair pathways. We also demonstrate that Cdc14 and Yen1 are required to safeguard sister chromatid segregation during the second meiotic division, a late action that is independent of the earlier role in crossover formation. Thus, this work uncovers previously undescribed functions of Cdc14 in the regulation of meiotic recombination.
Electrospray Surface Charge Describes Protein Molecular Motion
Authors: Chalk Rod , Borkowska Oktawia , Azeez Kamal Abdul , Oerum Stephanie , Born Petra , Gileadi Opher , Burgess-Brown Nicola
Published: March 2019

The electrospray mass/charge distribution for a protein is an instantaneous measurement of surface areas during the transition from liquid to gas phase. Protonation is dependent upon surface area and surface area is related to protein folding under all conditions. M/z distributions for proteins and protein analogues all with different degrees of entropy were compared. Rigid dipeptide self-assemblies of any size possess a single m/z, whereas protein always displays multiple m/z distributions. Native proteins have narrow, defined m/z distributions, while denatured proteins and synthetic homopolypetides possess the widest possible m/z distributions. These observations are consistent with dynamic changes in surface area resulting from molecular motion.
A Bayesian method using sparse data to estimate penetrance of disease-associated genetic variants
Authors: Kroncke Brett M. , Smith Derek K. , Glazer Andrew M. , Roden Dan M. , Blume Jeffrey D.
Published: March 2019

Purpose

A major challenge in genomic medicine is how to best predict risk of disease from rare variants discovered in Mendelian disease genes but with limited phenotypic data. We have recently used Bayesian methods to show thatin vitrofunctional measurements and computational pathogenicity classification of variants in the cardiac geneSCN5Acorrelate with rare arrhythmia penetrance. We hypothesized that similar predictors could be used to impute variant-specific penetrance prior probabilities.

Methods

From a review of 756 publications, we developed a pattern mixture algorithm, based on a Bayesian Beta-Binomial model, to generateSCN5Avariant-specific penetrance priors for the heart arrhythmia Brugada syndrome (BrS).

Results

The resulting priors correlate with mean BrS penetrance posteriors (cross validated R2= 0.41).SCN5Avariant function and structural context provide the most information predictive of BrS penetrance. The resulting priors are interpretable as equivalent to the observation of affected and unaffected carriers.

Conclusions

Bayesian estimates of penetrance can efficiently integrate variant-specific data (e.g. functional, structural, and sequence) to accurately estimate disease risk attributable to individual variants. We suggest this formulation of penetrance is quantitative, probabilistic, and more precise than, but consistent with, discrete pathogenicity classification approaches.
In vivoglucose imaging in multiple model organisms with an engineered single-wavelength sensor
Authors: Keller Jacob P. , Marvin Jonathan S. , Lacin Haluk , Lemon William C. , Shea Jamien , Kim Soomin , Lee Richard T. , Koyama Minoru , Keller Philipp J. , Looger Loren L.
Published: March 2019

Glucose is arguably the most important molecule in metabolism, and its mismanagement underlies diseases of vast societal import, most notably diabetes. Although glucose-related metabolism has been the subject of intense study for over a century, tools to track glucose in living organisms with high spatio-temporal resolution are lacking. We describe the engineering of a family of genetically encoded glucose sensors with high signal-to-noise ratio, fast kinetics and affinities varying over four orders of magnitude (1 µM to 10 mM). The sensors allow rigorous mechanistic characterization of glucose transporters expressed in cultured cells with high spatial and temporal resolution. Imaging of neuron/glia co-cultures revealed ∼3-fold higher glucose changes in astrocytes versus neurons. In larvalDrosophilacentral nervous system explants, imaging of intracellular neuronal glucose suggested a novel rostro-caudal transport pathway in the ventral nerve cord neuropil, with paradoxically slower uptake into the peripheral cell bodies and brain lobes. In living zebrafish, expected glucose-related physiological sequelae of insulin and epinephrine treatments were directly visualized in real time. Additionally, spontaneous muscle twitches induced glucose uptake in muscle, and sensory- and pharmacological perturbations gave rise to large but enigmatic changes in the brain. These sensors will enable myriad experiments, most notably rapid, high-resolution imaging of glucose influx, efflux, and metabolism in behaving animals.
Noroviruses subvert the core stress granule component G3BP1 to promote viral VPg-dependent translation
Authors: Hosmillo Myra , Lu Jia , McAllaster Michael R. , Eaglesham James B. , Wang Xinjie , Emmott Edward , Domingues Patricia , Chaudhry Yasmin , Fitzmaurice Timothy J , Tung Matthew K.H. , Panas Marc , McInerney Gerald , Locker Nicholas , Willen Craig B. , Goodfellow Ian
Published: March 2019

Knowledge of the host factors required for norovirus replication has been hindered by the challenges associated with culturing human noroviruses. We have combined proteomic analysis of the viral translation and replication complexes with a CRISPR screen, to identify host factors required for norovirus infection. The core stress granule component G3BP1 was identified as a host factor essential for efficient human and murine norovirus infection, demonstrating a conserved function across theNorovirusgenus. Furthermore, we show that G3BP1 functions in the novel paradigm of viral VPg-dependent translation initiation, contributing to the assembly of translation complexes on the VPg-linked viral positive sense RNA genome by facilitating 40S recruitment. Our data suggest that G3BP1 functions by providing viral RNA a competitive advantage over capped cellular RNAs, uncovering a novel function for G3BP1 in the life cycle of positive sense RNA viruses and identifying the first host factor with pan-norovirus pro-viral activity.
Nuclear Genome Size is Positively Correlated with Mean LTR Insertion Date in Fern and Lycophyte Genomes
Authors: Baniaga Anthony E. , Barker Michael S.
Published: March 2019

Abstract

Nuclear genome size is highly variable in vascular plants. The composition of long terminal repeat retrotransposons (LTRs) is a chief mechanism of long term change in the amount of nuclear DNA. Compared to flowering plants, little is known about LTR dynamics in ferns and lycophytes. Drawing upon the availability of recently sequenced fern and lycophyte genomes we investigated these dynamics and placed them in the context of vascular plants. We found that similar to seed plants, mean LTR insertion dates were strongly correlated with haploid nuclear genome size. Fern and lycophyte species with small genomes such as those of the heterosporousSelaginellaand members of the Salviniaceae had recent mean LTR insertion dates, whereas species with large genomes such as homosporous ferns had old mean LTR insertion dates intermediate between angiosperms and gymnosperms. This pattern holds despite methylation and life history differences in ferns and lycophytes compared to seed plants, and our results are consistent with other patterns of structural variation in fern and lycophyte genomes.
Deciphering the ‘m6A code’ via quantitative profiling of m6A at single-nucleotide resolution
Authors: Garcia-Campos Miguel Angel , Edelheit Sarit , Toth Ursula , Shachar Ran , Nir Ronit , Lasman Lior , Brandis Alexander , Hanna Jacob H. , Rossmanith Walter , Schwartz Schraga
Published: March 2019

N6-methyladenosine (m6A) is the most abundant modification on mRNA, and is implicated in critical roles in development, physiology and disease. The ability to map m6A using immunoprecipitation-based approaches has played a critical role in dissecting m6A functions and mechanisms of action. Yet, these approaches are of limited specificity, unknown sensitivity, and unable to quantify m6A stoichiometry. These limitations have severely hampered our ability to unravel the factors determining where m6A will be deposited, to which levels (the ‘m6A code’), and to quantitatively profile m6A dynamics across biological systems. Here, we used the RNase MazF, which cleaves specifically at unmethylated RNA sites, to develop MASTER-seq for systematic quantitative profiling of m6A sites at 16-25% of all m6A sites at single nucleotide resolution. We established MASTER-seq for orthogonal validation andde novodetection of m6A sites, and for tracking of m6A dynamics in yeast gametogenesis and in early mammalian differentiation. We discover that antibody-based approaches severely underestimate the number of m6A sites, and that both the presence of m6A and its stoichiometry are ‘hard-coded’ via a simple and predictable code within the extended sequence composition at the methylation sites. This code accounts for ~50% of the variability in methylation levels across sites, allows excellentde novoprediction of methylation sites, and predicts methylation acquisition and loss across evolution. We anticipate that MASTER-seq will pave the path towards a more quantitative investigation of m6A biogenesis and regulation in a wide variety of systems, including diverse cell types, stimuli, subcellular components, and disease states.