bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Adhesion and Substrate Elasticity on Neutrophil Extracellular Trap Formation
Authors: Erpenbeck Luise , Gruhn Antonia Luise , Kudryasheva Galina , Günay Gökhan , Meyer Daniel , Neubert Elsa , Grandke Julia , Schön Michael P. , Rehfeldt Florian , Kruss Sebastian
Published: January 2019

Neutrophils are the most abundant type of white blood cells. Upon stimulation, they are able to decondense and release their chromatin as neutrophil extracellular traps (NETs). This process (NETosis) is part of immune defense mechanisms but also plays an important role in many chronic and inflammatory diseases such as atherosclerosis, rheumatoid arthritis, diabetes and cancer. For this reason, much effort has been invested into understanding biochemical signaling pathways in NETosis. However, the impact of the mechanical micro-environment and adhesion on NETosis is not well understood.

Here, we studied how adhesion and especially substrate elasticity affect NETosis. We employed polyacrylamide (PAA) gels with distinctly defined elasticities (Young’s modulus E) within the physiologically relevant range from 1 kPa to 128 kPa and coated the gels with integrin ligands (collagen I, fibrinogen). Neutrophils were cultured on these substrates and stimulated with potent inducers of NETosis: phorbol 12-myristate 13-acetate (PMA) and lipopolysaccharide (LPS). Interestingly, PMA-induced NETosis was neither affected by substrate elasticity nor by different integrin ligands. In contrast, for LPS stimulation, NETosis rates increased with increasing substrate elasticity (E > 20 kPa). LPS-induced NETosis increased with increasing cell contact area, while PMA-induced NETosis did not require adhesion at all. Furthermore, inhibition of phosphatidylinositide 3 kinase (PI3K), which is involved in adhesion signaling, completely abolished LPS-induced NETosis but only slightly decreased PMA-induced NETosis.

In summary, we show that LPS-induced NETosis depends on adhesion and substrate elasticity while PMA-induced NETosis is completely independent of adhesion.
Removal of a subset of non-essential genes fully attenuates a highly virulentMycoplasmastrain
Authors: Jores Joerg , Ma Li , Ssajjakambwe Paul , Schieck Elise , Liljander Anne , Chandran Suchismita , Stoffel Michael , Cippa Valentina , Arfi Yonathan , Asad-Garcia Nacyra , Falquet Laurent , Sirand-Pugnet Pascal , Blanchard Alain , Lartigue Carole , Posthaus Horst , Labroussaa Fabien , Vashee Sanjay
Published: January 2019

Mycoplasmas are the smallest free-living organisms and cause a number of economically important diseases affecting humans, animals, insects and plants. Here, we demonstrate that highly virulentMycoplasma mycoidessubspeciescapri(Mmc) can be fully attenuatedviatargeted deletion of non-essential genes encoding, among others, potential virulence traits. Five genomic regions, representing approximately ten percent of the originalMmcgenome, were successively deleted usingSaccharomyces cerevisiaeas an engineering platform. Specifically, a total of 68 genes out of the 432 genes verified to be individually nonessential in the JCVI-Syn3.0 minimal cell, were excised from the genome.In vitrocharacterization showed that this mutant was similar to its parental strain in terms of its doubling time, even though ten percent of the genome content were removed. A novelin vivochallenge model in goats revealed that the wild-type parental strain caused marked necrotizing inflammation at the site of inoculation, septicemia and all animals reaching endpoint criteria within seven days after experimental infection. This is in contrast to the mutant strain, which caused no clinical signs nor pathomorphological lesions. These results highlight, for the first time, the rational design, construction and complete attenuation of aMycoplasmastrain via synthetic genomics tools. Trait addition using the yeast-based genome engineering platform and subsequentin vitroorin vivotrials employing theMycoplasmachassis will allow us to dissect the role of individual candidateMycoplasmavirulence factors and lead the way for the development of an attenuated designer vaccine.

IMPORTANCE

Members of theMycoplasma mycoidescluster cause important animal plaques in Africa and Asia, which impact animal welfare, provision of food and the life of thousands of small-scale farmers. We applied synthetic biology tools toMycoplasma mycoidesin order to design and create a fully attenuatedMycoplasmastrain that was subsequently confirmedin vivousing a novel caprine infection model. This is the first time that aMycoplasmamutant developed by applying synthetic biology tools has been testedin vivoto pin point candidate virulence traits. The mutant strain is similar to “apathogenicE. coliK12” strains that boosted the research on host-pathogen interactions for the genusEscherichiaand other bacterial genera.
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma
Authors: Carow Berit , Hauling Thomas , Qian Xiaoyan , Kramnik Igor , Nilsson Mats , Rottenberg Martin E
Published: January 2019

Granulomas are the pathological hallmark of Tuberculosis (TB), and the niche in which bacilli can either grow and disseminate or the immunological microenvironment in which host cells interact to prevent bacterial dissemination. Here, after in situ sequencing, thirty-four immune transcripts in lung sections fromMycobacterium tuberculosis-infected mice were aligned to the tissue morphology at cellular resolution, allowing the analysis of local immune interactions in the granuloma.

Co-localizing transcript networks at <10 μm in C57BL/6 mouse granulomas increased in complexity with time after infection. B-cell clusters developed late after infection. Transcripts from activated macrophages were enriched at subcellular distances fromM. tuberculosis. Encapsulated C3HeB/FeJ granulomas showed necrotic centers with transcripts associated with immunosuppression (foxp3, il10), while those in the granuloma rims associated with activated T cells and macrophages. Highly diverse networks with common interactors were observed in similar lesions.

Thus, different immune landscapes ofM. tuberculosisgranulomas depending on the time after infection, the histopathological features of the lesion and the proximity to bacteria were here defined.
Identification of multiple kinetic populations of DNA-binding proteins in live cells
Authors: Ho Han N. , Zalami Daniel , Köhler Jürgen , van Oijen Antoine M. , Ghodke Harshad
Published: January 2019

Understanding how multi-protein complexes function in cells requires detailed quantitative understanding of their association and dissociation kinetics. Analysis of the heterogeneity of binding lifetimes enables interrogation of the various intermediate states formed during the reaction. Single-molecule fluorescence imaging permits the measurement of reaction kinetics inside living organisms with minimal perturbation. However, poor photo-physical properties of fluorescent probes limit the dynamic range and accuracy of measurements of off rates in live cells. Time-lapse single-molecule fluorescence imaging can partially overcome the limits of photobleaching, however, limitations of this technique remain uncharacterized. Here, we present a structured analysis of which timescales are most accessible using the time-lapse imaging approach and explore uncertainties in determining kinetic sub-populations. We demonstrate the effect of shot noise on the precision of the measurements, as well as the resolution and dynamic range limits that are inherent to the method. Our work provides a convenient implementation to determine theoretical errors from measurements and to support interpretation of experimental data.

STATEMENT OF SIGNIFICANCE

Measuring lifetimes of interactions between DNA-binding proteins and their substrates is important for understanding how they function in cells. In principle, time-lapse imaging of fluorescently-tagged proteins using single-molecule methods can be used to identify multiple sub-populations of DNA-binding proteins and determine binding lifetimes lasting for several tens of minutes. Despite this potential, currently available guidelines for the selection of binding models are unreliable, and the practical implementation of this approach is limited. Here, using experimental and simulated data we identify the minimum size of the dataset required to resolve multiple populations reliably and measure binding lifetimes with desired accuracy. This work serves to provide a guide to data collection, and measurement of DNA-binding lifetimes from single-molecule time-lapse imaging data.
SpliceV: Analysis and publication quality printing of linear and circular RNA splicing, expression and regulation
Authors: Ungerleider Nathan , Flemington Erik
Published: January 2019

In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited. Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward-and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript. SpliceV is compatible with both Python 2.7 and 3+, and is distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.
Integration of gut microbiome, host biomarkers, and urine metabolome data reveals networks of interactions associated with distinct clinical phenotypes
Authors: Li Rui-Jun , Jie Zhu-Ye , Feng Qiang , Fang Rui-Ling , Li Fei , Gao Yuan , Xia Hui-Hua , Zhong Huan-Zi , Tong Bin , Xu Jia-Yu , Madsen Lise , Liu Chun-Lei , Xu Zhen-Guo , Wang Jian , Yang Huan-Ming , Xu Xun , Hou Yong , Brix Susanne , Kristiansen Karsten , Yu RXin-Lei , Jia Hui-Jue , He Kun-Lun
Published: January 2019

Background

Comprehensive analyses of multi-omics data may provide insights into interactions between different biological layers in relation to distinct clinical features. Here we integrated data on the gut microbiota, blood parameters and urine metabolites of treatment-naive individuals presenting a wide range of metabolic disease phenotypes to delineate clinically meaningful associations.

Results

Trans-omics correlation networks revealed that candidate gut microbial biomarkers and urine metabolite features covaried with distinct clinical phenotypes. Integration of the gut microbiome, the urine metabolome and the phenome revealed that variations in one of these three systems correlated with changes in the other two. Of specific note in relation to clinical parameters of liver function, we identified Eubacterium eligens, Faecalibacterium prausnitzii and Ruminococcus lactaris to be associated with a healthy liver function, whereas Clostridium bolteae, Tyzzerella nexills, Ruminococcus gnavus, Blautia hansenii, and Atopobium parvulum were associated with blood biomarkers for liver diseases. Variations in these microbiota features paralleled changes in specific urine metabolites. Network modeling yielded two core clusters including one large gut microbe-urine metabolite close-knit cluster and one triangular cluster composed of a gut microbe-blood-urine network, demonstrating close inter-system crosstalk especially between the gut microbiome and the urine metabolome.

Conclusions

Distinct clinical phenotypes are manifested in both the gut microbiome and the urine metabolome, and inter-domain connectivity takes the form of high-dimensional networks. Such networks may further our understanding of complex biological systems, and may provide a basis for identifying biomarkers for diseases.
Cyclin F-Chk1 synthetic lethality mediated by E2F1 degradation
Authors: Burdova Kamila , Yang Hongbin , Faedda Roberta , Hume Samuel , Ebner Daniel , Kessler Benedikt M , Vendrell Iolanda , Drewry David H , Wells Carrow I , Hatch Stephanie B , D’Angiolella Vincenzo
Published: January 2019

Cyclins are central engines of cell cycle progression when partnered with Cyclin Dependent Kinases (CDKs). Among the different cyclins controlling cell cycle progression, cyclin F does not partner with a CDK, but forms an E3 ubiquitin ligase, assembling through the F-box domain, an Skp1-Cul1-F-box (SCF) module. Although multiple substrates of cyclin F have been identified the vulnerabilities of cells lacking cyclin F are not known. Thus, we assessed viability of cells lacking cyclin F upon challenging cells with more than 200 kinase inhibitors. The screen revealed a striking synthetic lethality between Chk1 inhibition and cyclin F loss. Chk1 inhibition in cells lacking cyclin F leads to DNA replication catastrophe. The DNA replication catastrophe depends on the accumulation of E2F1 in cyclin F depleted cells. We observe that SCFcyclin F promotes E2F1 degradation after Chk1 inhibitors in a CDK dependent manner. Thus, Cyclin F restricts E2F1 activity during cell cycle and upon checkpoint inhibition to prevent DNA replication stress. Our findings pave the way for patient selection in the clinical use of checkpoint inhibitors.
A pseudo-meiotic centrosomal function of TEX12 in cancer
Authors: Sandhu S , Salmon LJ , Hunter JE , Wilson CL , Perkins ND , Hunter N , Davies OR , McClurg UL
Published: January 2019

Cell division by meiosis involves an extraordinary chromosome choreography including pairing, synapsis and crossing over between homologous chromosomes1, 2. The many meiosis-specific genes involved in these processes also constitute a latent toolbox of chromosome remodelling and recombination factors that may be exploited through aberrant expression in cancer3, 4. Here, we report that TEX12, a structural protein involved in meiotic chromosome synapsis5–7, is aberrantly expressed in human cancers, with high TEX12 levels correlating with poor prognosis. We find that TEX12 knock-down causes proliferative failure in multiple cancer cell lines, and confirm its role in the early stages of oncogenesis through murine cancer models. Remarkably, somatically expressed TEX12 localises to centrosomes, leading to altered centrosome number and structure, features associated with cancer development. Further, we identify TEX12 in meiotic centrin-rich bodies, likely precursors of the mitotic centrosome, suggesting that this may represent an additional cellular function of TEX12 in meiosis that has been previously overlooked. Thus, we propose that an otherwise meiotic function of TEX12 in centrosome duplication is responsible for promoting oncogenesis and cellular proliferation in cancer, which may be targeted for novel cancer therapeutics and diagnostics.
Modulation of tonotopic ventral MGB is behaviorally relevant for speech recognition
Authors: Mihai Paul Glad , Moerel Michelle , de Martino Federico , Trampel Robert , Kiebel Stefan , von Kriegstein Katharina
Published: January 2019

Sensory thalami are central sensory pathway stations for information processing. Their role for human cognition and perception, however, remains unclear. Recent evidence suggests a specific involvement of the sensory thalami in speech recognition. In particular, the auditory thalamus (medial geniculate body, MGB) response is modulated by speech recognition tasks and the amount of this task-dependent modulation is associated with speech recognition abilities. Here we tested the specific hypothesis that this behaviorally relevant modulation is present in the MGB subsection that corresponds to the primary auditory pathway (i.e., the ventral MGB [vMGB]). We used ultra-high field 7T fMRI to identify the vMGB, and found a significant positive correlation between the amount of task-dependent modulation and the speech recognition performance across participants within left vMGB, but not within the other MGB subsections. These results imply that modulation of thalamic driving input to the auditory cortex facilitates speech recognition.
Personalized Tumor Growth Prediction with Multiscale Tumor Modeling
Authors: Unsal Serbulent , Acar Aybar , Itik Mehmet , Kabatas Ayse , Gedikli Oznur , Ozdemir Feyyaz , Turhan Kemal
Published: January 2019

Background

Cancer is one of the most complex phenomena in biology and medicine. Extensive attempts have been made to work around this complexity. In this study, we try to take a selective approach; not modeling each particular facet in detail but rather only the pertinent and essential parts of the tumor system are simulated and followed by optimization, revealing specific traits. This leads us to a pellucid personalized model which is noteworthy as it closely approximates existing experimental results.

Method

For years, research has focused on modeling tumor growth but not many studies have put forward a framework for the personalization of models. In the present study, a hybrid modeling approach which consists of cellular automata for discrete cell state representation and diffusion equations to calculate distribution of relevant substances in the tumor micro-environment is favored. Moreover, naive Bayesian decision making with weighted stochastic equations and a Bayesian network to model the temporal order of mutations is presented. The model is personalized according to the evidence using Markov Chain Monte Carlo. Ultimately, this way of thinking about tumor modeling leads us to a vascular multi-scale model of tumor growth.

Results

To validate the tumor model, a data set belonging to the A549 cell line is used. The data represents the growth of a tumor for 30 days. We optimize the coefficients of the stochastic decision making equations using first half of the timeline. Then we predict next 15 days of growth without any other supervision. Results are promising with their low error margin and simulated growth data is in line with laboratory results.

Conclusion

There are many subsystems which have an effect in the growth of a tumor. A detailed model which includes all of them is currently virtually impossible to implement. We have therefore focused on a system that only includes fundamental components in this study, and have evaluated its predictions. We propose novel probability functions to obtain a personalized model and estimate the individual importance (weights) of each with parameter optimization. Our approach of using simulated annealing for parameter estimation and the subsequent validation of the prediction with in-vitro tumor growth data are, to our knowledge, unique in the literature.
Spatial single-cell profiling of intracellular metabolomesin situ
Authors: Rappez Luca , Stadler Mira , Triana Sergio , Phapale Prasad , Heikenwalder Mathias , Alexandrov Theodore
Published: January 2019

The recently unveiled extent of cellular heterogeneity demands for single-cell investigations of intracellular metabolomes to reveal their roles in intracellular processes, molecular microenvironment and cell-cell interactions. To address this, we developed SpaceM, a method forin situspatial single-cell metabolomics of cell monolayers which detects >100 metabolites in >10000 individual cells together with fluorescence and morpho-spatial cellular features. We discovered that the intracellular metabolomes of co-cultured human HeLa cells and mouse NIH3T3 fibroblasts predict the cell type with 90.4% accuracy and revealed a short-distance metabolic intermixing between HeLa and NIH3T3. We characterized lipid classes composing lipid droplets in steatotic differentiated human hepatocytes, and discovered a preferential accumulation of long-chain phospholipids, a co-regulation of oleic and linoleic acids, and an association of phosphatidylinositol monophosphate with high cell-cell contact. SpaceM provides single-cell metabolic, phenotypic, and spatial information and enables spatio-molecular investigations of intracellular metabolomes in a variety of cellular models.
Chemically-defined induction of a primitive endoderm and epiblast-like niche supports post-implantation progression from blastoids
Authors: Vrij Erik J. , Scholte op Reimer Yvonne S. , Frias Aldeguer Javier , Misteli Guerreiro Isabel , Kind Jop , Koo Bon-Kyoung , van Blitterswijk Clemens A. , Rivron Nicolas C.
Published: January 2019

The early mammalian conceptus (blastocyst) contains two supporting extraembryonic tissues - the trophectoderm and the primitive endoderm (PrE) - that encase and guide the epiblast (Epi) to eventually form the all body. Modifications of the conceptus exposed key genes regulating these tissues co-development. However, the combinations of signalling pathways underlying the interplay of PrE and Epi remains elusive. Stem cell-based models including embryoid bodies and blastoids can be generated in large numbers and subjected to high-content screens. Here, we use combinatorial screens of proteins, GPCR ligands and small molecules to rapidly (72 hours) and efficiently (80%) guide embryoid bodies to form a three-dimensional PrE-/Epiblast-like niche in chemically-defined conditions (gel-free, serum-free). This bipotent niche spontaneously progresses, without growth factors, to form a pro-amniotic cavity surrounded by a polarized Epi covered with parietal and visceral endoderm-like cells. In blastoids, these molecules enhance the ratio and number of Gata6+/Nanog+ cells and promote the survival, expansion and morphogenesis of a post-implantation-like Epiin vitro. Altogether, modelling early development in chemically-defined conditions delineates the pathways sufficient to form a functional PrE/Epiblast niche that fuels post-implantation development.
Variation inMelitaea cinxiagut microbiota is phylogenetically highly structured but only mildly driven by host plant microbiota, sex or parasitism
Authors: Minard G. , Tikhonov G , Ovaskainen O. , Saastamoinen M.
Published: January 2019

Originality-Significance Statement

The factors contributing to the assembly of microbiota in animals are extremely complex, and thus a comprehensive understanding of the mechanisms shaping host-associated microbial communities in natural ecosystems requires extensive ecological studies and appropriate statistical methods. In this study, we investigated the bacterial microbiota associated with the caterpillars of the Glanville fritillary (Melitaea cinxia), which is a long-term-studied ecological model system. We assessed the structure of variation in both occurrence and abundance of gut microbial communities of individuals collected in the wild with joint-species modelling, with the aim to relate the microbial community structure with multiple potentially impacting covariates: host plant microbiota and metabolites, hosts’ sex, potential parasitoid infection, and family structure. These covariates exhibited substantial correlation with multiple microbial taxa’s occurrences, which correlations were consistent for phylogenetically related groups of taxa, but varied across the whole microbial community; on the contrary, only few correlations were found with taxa’s abundances. The dominating co-occurrence pattern of microbiota assembly, which effectively split caterpillar individuals into two distinct groups, was, however, unrelated to any of the considered covariates.

Understanding of what ecological factors shape intraspecific variation of insect microbiota is still relatively poor. In Lepidopteran caterpillars, microbiota is assumed to be mainly composed of transient bacterial symbionts acquired from the host plant. We sampled Glanville fritillary (Melitaea cinxia) caterpillars from natural populations to describe the microbiome and to identify potential factors that determine the structure of the microbial community, including the sex of the host, the impact of parasitoid infection, and the possible link between host plant and caterpillar microbiota. Our results demonstrate high variability of microbiota composition even among caterpillars that shared the same host plant individual. The observed variation in microbiota composition is partially attributed to the measured properties of the host or its plant microbial and chemical composition, and is aligned with microbial phylogenetic structure, with related taxa exhibiting similar patterns. However, the prevailing part of the observed variation was not associated with any of the assessed characteristics, although it followed a pronounced segregation structure: in some caterpillars the microbial communities were dominated by several related Enterobacteriaceae taxa, while in others these taxa were absent. Our results challenge previous findings that the host plant properties are the major drivers of microbiota communities of insect herbivores.
BCR analysis of single-sorted, putative IgE+memory B cells in food allergy:an ephemeral existence?
Authors: Jiménez-Saiz Rodrigo , Ellenbogen Yosef , Bruton Kelly , Spill Paul , Sommer Doron D. , Lima Hermenio , Waserman Susan , Patil Sarita U. , Shreffler Wayne G. , Jordana Manel
Published: January 2019

Immunoglobulin (Ig) E is the critical effector molecule in allergic reactions. Consequently, research efforts to understand the biology of IgE-expressing cells is of paramount importance. In particular, the role of IgE+memory B cells (MBCs) in the perpetuation of allergic reactivity has been the subject of intense research. Studies in mice have convincingly established that IgE+B cells are rare and transient and, therefore, an unlikely candidate to maintain allergic disease. In contrast, IgE+MBCs have been detected by flow cytometry in the sputum and peripheral blood of humans and have been proposed as a clinical marker of allergic disease. We established a method to genetically validate, at the single-cell level, the putative IgE+MBCs identified by flow cytometry from humans. We, then used this information to develop an enhanced flow cytometry protocol that more accurately identifiesbona fideIgE+MBCs. We found that IgE+MBCs were detected in some patients with atopic dermatitis, but at a frequency that was ~100 times lower than previously reported. We also found that IgE+MBCs were undetectable in PBMCs from peanut allergic patients. These findings provide tools to identifybona fideIgE+MBCs, demonstrate their extreme rarity in circulation and are consistent with the lack of a central role for IgE+MBCs in the maintenance of allergic sensitivity.

One Sentence Summary

The frequency of IgE+MBCs in the peripheral circulation of humans is orders of magnitude lower than previously reported and comparable between allergic and healthy donors, which cautions about the clinical utility of their assessment.
Oxidative Stress and Biomarker Responses in the Atlantic Halibut After Long Term Exposure to Elevated CO2and a Range of Temperatures
Authors: Carney Almroth B , Bresolin de Souza K , Jönsson E , Sturve J
Published: January 2019

Oceans are warming and pH levels are decreasing as a consequence of increasing levels of dissolved CO2concentrations. The CO2emissions are predicted to be produce in greater and faster changes in the ocean than any other event in geological and historical records over the past 300 million years. Marine organisms will need to respond to multiple stressors but the potential consequences of global change-related effects in fish are not fully understood. Since fish are affected by many biotic and abiotic environmental variables, including temperature and CO2fluctuations, it is critical to investigate how these variables may affect physiological and biochemical processes. We investigated the effects of elevated CO2levels (pH of 8.0, which served as a control, or 7.6, which is predicted for the year 2100) combined with exposure to different temperatures (5, 10, 12, 14, 16, and 18 °C) in the Atlantic halibut (Hippoglossus hippoglossus) during a three month experiment. We assessed effects on antioxidant and cholinesterase enzymes (AChE and BChE), and CYP1A enzyme activities (EROD). The treatments resulted in oxidative stress, and damage was evident in the form of protein carbonyls which were consistently higher in the elevated CO2-treated fish at all temperatures. Analyses of antioxidant enzymes did not show the same results, suggesting that the exposure to elevated CO2increased ROS formation but not defences. The antioxidant defence system was insufficient, and the resulting oxidative damage could impact physiological function of the halibut on a cellular level.
A free-running oscillator times and executes centriole biogenesis
Authors: Aydogan Mustafa G. , Steinacker Thomas L. , Mofatteh Mohammad , Gartenmann Lisa , Wainman Alan , Saurya Saroj , Conduit Paul T. , Zhou Felix Y. , Boemo Michael A. , Raff Jordan W.
Published: January 2019

The accurate timing of organelle biogenesis and the precise regulation of organelle size are crucial for cell physiology. Centriole biogenesis initiates exclusively in S-phase, when a daughter centriole emerges from the side of a pre-existing mother and grows until it reaches its mother’s size. This process is regulated by Polo-like kinase 4 (Plk4), which is recruited to centrioles in oscillatory waves in flies and human cells1,2. The nature and function of Plk4 oscillations is, however, unknown. Here we discover that Plk4 forms an adaptive oscillator at the base of the growing centriole, whose function is to time and set the duration of centriole biogenesis inDrosophilaembryos. We demonstrate that the Plk4 oscillator is free-running of, but is entrained and calibrated by, the core Cdk/Cyclin cell-cycle oscillator, explaining how centrioles can duplicate independently of the cell cycle3–5. Mathematical modelling and further experiments indicate that the Plk4 oscillator is generated by a time-delayed negative-feedback loop in which Plk4 recruitment to, and dissociation from, the centriole is monitored via changes in the affinity-state of its centriolar receptor, Asterless. We postulate that such organelle-specific autonomous oscillators could regulate the timing and execution of organelle biogenesis more generally.
Rigid Foot Soles Improve Balance in Beam Walking
Authors: Huber Meghan E. , Chiovetto Enrico , Giese Martin , Sternad Dagmar
Published: January 2019

Maintaining balance while walking on a narrow beam is a challenging motor task. This is presumably because the foot’s ability to exert torque on the support surface is limited by the beam width. Still, the feet serve as a critical interface between the body and the external environment, and it is unclear how the mechanical properties of the feet affect balance. Here we examined how restricting the degrees of freedom of the feet influenced balance behavior during beam walking. We recorded whole-body joint kinematics of subjects with varying skill levels as they walked on a narrow beam with and without wearing flat, rigid soles on their feet. We computed changes in whole-body motion and angular momentum across these conditions. Results showed that wearing rigid soles improved balance in the beam walking task, but that practice with rigid soles did not affect or transfer to task performance with bare feet. The absence of any after-effect suggested that the improved balance from constraining the foot was the result of a mechanical effect rather than a change in neural strategy. Though wearing rigid soles can be used to assist balance, there appear to be limited training or rehabilitation benefits from wearing rigid soles.
Sedentary behavior, physical inactivity and body composition in relation to idiopathic infertility among men and women
Authors: Aude-Marie Foucaut , Céline Faure , Chantal Julia , Sébastien Czernichow , Rachel Levy , Charlotte Dupont ,   the ALIFERT collaborative group
Published: January 2019

Background

Physical activity and sedentary behavior has inconsistent effects on fertility. High body mass index is associated with infertility but to our knowledge, very few studies have explored body composition in association to fertility.

Objective

To assess the association between physical inactivity, sedentary behavior, body composition and idiopathic infertility in French men and women.

Design

We conducted a case-control multicentric observational study. 159 infertile (79 men and 80 women) and 143 fertile (72 men and 71 women) were recorded in four fertility centers.

Main Outcome Measures

Participants completed self-administered questionnaires on sociodemographic and lifestyle characteristics, dietary intake, physical activity and sedentary behavior. Anthropometrics were measured, and bioelectrical impedance analysis was used to estimate body composition. Multivariable logistic regression was used to analyze the association of fertility with PA level and sedentary behavior.

Results

In men, being physically inactive (Odd ratio [OR] 2.20; 95% confidence interval [CI], 1.06, 4.58) and having fat mass greater than the reference values for their age (OR 2.83; 95%CI, 1.31, 6.10) were positively associated with infertility. Sedentary behavior and fat-free mass were not related to infertility in men. In women, sedentary behavior (OR 3.61; 95%CI, 1.58, 8.24), high body fat (OR 3.16; 95%CI, 1.36, 7.37) and low fat-free mass (OR 2.65; 95%CI, 1.10, 6.37) were associated with infertility. PA level was not associated with fertility in women.

Conclusions

This study suggests that sedentary behavior and physical inactivity would represent two independent risk factors associated with fertility. The various elements that make up physical activity (frequency, intensity, time, and type of exercise) and the interrupting time spent sitting should be considered. Body composition variation should be explored further in relation to the biological pathways involved in idiopathic infertility. Moreover, the improvement of lifestyle factors should be considered in infertility treatment.
High innate preference for black substrate in the chive gnat,Bradysia odoriphaga(Diptera: Sciaridae)
Authors: An Lina , Fan Fan , Lunau Klaus , Li Mengyao , Yang Xiaofan , Wei Guoshu
Published: January 2019

The chive gnat,Bradysia odoriphaga, is a notorious pest ofAlliumspecies in China. Colour trapping is an established method for monitoring and controlling ofBradysiaspecies. In order to clarify the effect of colour preference ofB. odoriphagafor the egg-laying substrate, multiple-choice tests were employed to assess the spontaneous response of the chive gnat to different colour hues and brightness levels under different intensities of white illumination and two spectrally different illuminations. Given the choice among four colours differing in hue under different intensities of white illumination and two spectrally different illuminations, chive gnat adults visited preferably the black substrate, a lesser extent to brown and green substrates, and the least extent to orange substrate irrespective of illumination. Given the choice among four levels of brightness under the same illumination conditions as those in the previous experiment (different intensities of white illumination and two spectrally different illuminations), chive gnats preferred black substrate over dark grey, and these over light grey and white substrates. Meanwhile, both virgin and copulated adults significantly preferred black over other colour hues and brightness. Based on our results, we conclude that the chive gnat adults significantly prefer black substrates irrespective of colour hues and brightness. This behaviour does not alter due to ambient light condition changes. No difference observed between choices of female and male adults. Our results provide new insight for understanding the colour choice behaviour in chive gnat and pave a way to improve monitoring and control of chive gnats and management.

Summary statement

Chive gnat (Bradysia odoriphaga) innately prefer to move to black substrate irrespective of colour hues and brightness. This behaviour maintained the ambient lights change.
Bacterial Diversity in Feces of Wild Bald Eagles, Turkey Vultures and Common Ravens from the Pacific Northwest Coast, U.S.A
Authors: Crespo Rocio , Dowd Scot E , Varland Daniel E. , Ford Scott , Hamer Thomas E.
Published: January 2019

Birds harbor diverse microorganisms in their guts, which collectively fulfill important roles in providing their hosts with nutrition and protection from pathogens. Although numerous studies have investigated the presence of certain pathogenic bacteria in the feces of wild birds, only a few have attempted to investigate the microbiota of the gut. This study analyzed the avian bacteria present in the cloaca of avian scavengers captured on coastal beaches of Washington and Oregon between 2013 and 2015: 10 turkey vultures (Cathartes aura), 9 bald eagles (Haliaeetus leucocephalus), and 2 common ravens (Corvus corax). We used illumina sequencing based on the V4 region of the 16s gene was to characterize the bacterial diversity. Our investigation revealed phylum-level differences in the microbiome of turkey vultures, compared with bald eagles and common ravens. Substantial microbiome differences were found between bald eagles and ravens below the phylum level. Although little is known about the possible relations among these microorganisms, our analyses provides the first integrated look at the composition of the avian microbiota and serves as a foundation for future studies in this area.
Multi-locus characterization and phylogenetic inference of Leishmania spp. in snakes from Northwest China
Authors: Chen Han , Li Jiao , Zhang Junrong , He Jinlei , Zhang Jianhui , Zheng Zhiwan , Chen Dali , Chen Jianping
Published: January 2019

Background

Leishmaniasis caused by protozoan parasite Leishmania is a neglected disease which is endemic in the northwest of China. Reptiles were considered to be the potential reservoir hosts for mammalian Leishmaniasis, and Leishmania had been detected in lizards from the epidemic area in the northwest of China. To date, few studies are focused on the natural infection of snakes with Leishmania.

Methods

In this study, 15 snakes captured from 10 endemic foci in the northwest of China were detected Leishmania spp. on the base of mitochondrial cytochrome b, heat shock protein 70 gene and ribosomal internal transcribed spacer 1 regions, and identified with phylogenetic and network analyses.

Result

In total, Leishmania gene was found in 7 snakes. The phylogenetic inference trees and network analysis suggests that the species identification was confirmed as Leishmania donovani, Leishmania turanica and Leishmania sp.

Conclusion

Our work is the first time to investigate the natural Leishmania spp. infection of snakes in the northwest of China. Mammalian Leishmania was discovered in snakes and the reptilian Leishmania was closely related to the clinical strains both prompt the importance of snakes in the disease cycle. To indicate the epidemiological involvement of snakes, a wide sample size in epidemic area and the pathogenic features of reptilian Leishmania promastigotes are recommended in the future research.
Molecular regulation of peripheral B cells and their progeny in immunity
Authors: Boothby Mark R. , Hodges Emily , Thomas James W.
Published: January 2019

Mature B lymphocytes are crucial components of adaptive immunity, a system essential for the evolutionary fitness of mammals. Adaptive lymphocyte function requires an initially naïve cell to proliferate extensively and its progeny to have the capacity to assume a variety of fates. These include either terminal differentiation (the long-lived plasma cell) or metastable transcriptional reprogramming (germinal center and memory B cells). In this review, we focus principally on the regulation of differentiation and functional diversification of the “B2” subset. An overview is combined with an account of more recent advances, including initial work on mechanisms that eliminate DNA methylation and potential links between intracellular metabolites and chromatin editing.
Saturation Mutagenesis by Codon Cassette Insertion
Authors: Forloni Matteo , Liu Alex Y. , Wajapeyee Narendra
Published: January 2019

Saturation mutagenesis by cassette insertion introduces a library of site-specific changes into a specific DNA sequence within a target gene and is especially useful for analyzing the effect of specific residues on the structure and function of a protein. In this protocol, a set of 11 universal oligodeoxyribonucleotide cassettes is used to generate mutations. The major advantage of this method is that a single set of mutagenic codon cassettes can be used to insert codons encoding all possible amino acids at any predetermined site within a gene. Each of the 11 cassettes contains two recognition sequences for SapI, a restriction enzyme that cleaves outside of its recognition sequence. The recognition sequences for SapI are arranged in opposite orientations and are separated by a central spacer. At the end of each cassette is a 3-bp direct repeat, positioned such that the sites of SapI cleavage bracket each repeat. Cleavage by SapI will result in the generation of three base-cohesive single-stranded ends on the end of the cassette. These three base-cohesive single-stranded ends can then be ligated together to regenerate the original 3-bp direct repeat, while excising the central spacer. It is this 3-bp repeat sequence that is ultimately incorporated into the template. By substituting the 3-bp direct repeats in the universal cassette with other sequences, one can essentially generate all possible amino acid substitutions.
Purification of Antibodies: Diethylaminoethyl (DEAE) Chromatography
Authors: Fishman Jordan B. , Berg Eric A.
Published: January 2019

Because IgG from most species (other than rodents) tends to have an isoelectric point around neutral, two approaches can be used when separating IgG using diethylaminoethyl (DEAE) resins. When serum containing antibodies is applied to DEAE at a slightly acidic pH, the IgG flows through the column while most other serum proteins bind to the DEAE. This method is best performed using a batch method. The DEAE beads can be kept in a disposable syringe containing a polypropylene frit, a glass reactor containing a coarse-sintered glass frit, or other suitable vessel. If the antibody solution is adjusted to a basic pH of 8–8.5, then IgG binds to the DEAE resin. After washing the column, the antibody is eluted by adding a buffer of increasing ionic strength to the column. Prepacked columns of many sizes are available for the isolation of antibodies by DEAE chromatography. Alternatively, DEAE medium can be swelled or prepped according to the manufacturer's instructions and a column can be poured when needed.
Performance improvement of helicopter rotors through blade redesigning
Authors: Stalewski Wienczyslaw , Zalewski Wieslaw
Published: January 2019

Purpose

The purpose of this paper is to determine dependencies between a rotor-blade shape and a rotor performance as well as to search for optimal shapes of blades dedicated for helicopter main and tail rotors.

Design/methodology/approach

The research is conducted based on computational methodology, using the parametric-design approach. The developed parametric model takes into account several typical blade-shape parameters. The rotor aerodynamic characteristics are evaluated using the unsteady Reynolds-averaged Navier–Stokes solver. Flow effects caused by rotating blades are modelled based on both simplified approach and truly 3D simulations.

Findings

The computational studies have shown that the helicopter-rotor performance may be significantly improved even through relatively simple aerodynamic redesigning of its blades. The research results confirm high potential of the developed methodology of rotor-blade optimisation. Developed families of helicopter-rotor-blade airfoils are competitive compared to the best airfoils cited in literature. The finally designed rotors, compared to the baselines, for the same driving power, are characterised by 5 and 32% higher thrust, in case of main and tail rotor, respectively.

Practical implications

The developed and implemented methodology of parametric design and optimisation of helicopter-rotor blades may be used in future studies on performance improvement of rotorcraft rotors. Some of presented results concern the redesigning of main and tail rotors of existing helicopters. These results may be used directly in modernisation processes of these helicopters.

Originality/value

The presented study is original in relation to the developed methodology of optimisation of helicopter-rotor blades, families of modern helicopter airfoils and innovative solutions in rotor-blade-design area.
Experimental investigation of plasma vortex generator in flow control
Authors: Ghayour Alireza , Mani Mahmoud
Published: January 2019

Purpose

The purpose of this paper is to compare the effects of two different configurations of plasma streamwise vortex generators (PSVG), including comb-type and mesh-type in controlling flow. This is demonstrated on the NACA 0012 airfoil.

Design/methodology/approach

The investigations have been done experimentally at the various electric and aerodynamic conditions. The surface oil flow visualization method has been used to the better understanding of the flow physics and the interaction of the oncoming flow passing over the airfoil and the vortex generated by comb-type PSVG.

Findings

This paper demonstrates the potential capabilities of the mesh-type and comb-type PSVGs in controlling flow in unsteady operation. It was found that the vortex generated by the mesh-type PSVG in unsteady operation was an order of magnitude stronger than comb-type PSVG. The flow visualisation technic proved that only a part of the plasma actuator is effective in the condition that the actuator is installed only on a portion of the upper surface of the airfoil.

Originality/value

This paper experimentally confirms the capabilities of the mesh-type PSVG unsteady operation in compare with comb-type PSVG in controlling flow, whereby recommends using mesh-type PSVG in the leading edge in front of comb-type PSVG on the entire wingspan to prevent the stall.