bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative definition of neurobehavior, vision, hearing and brain volumes in macaques congenitally exposed to Zika virus
Authors: Koenig Michelle R. , Razo Elaina , Mitzey Ann , Newman Christina M. , Dudley Dawn M. , Breitbach Meghan E. , Semler Matthew R. , Stewart Laurel M. , Weiler Andrea M. , Rybarczyk Sierra , Bach Kathryn M. , Mohns Mariel S. , Simmons Heather A. , Mejia Andres , Fritsch Michael , Dennis Maria , Teixeira Leandro B. C. , Schotzko Michele L. , Nork T. Michael , Rasmussen Carol A. , Katz Alex , Nair Veena , Hou Jiancheng , Hartman Amy , Hoeve James Ver , Kim Charlene , Schneider Mary L. , Ausderau Karla , Kohn Sarah , Jaeger Anna S. , Aliota Matthew T. , Hayes Jennifer M. , Schultz-Darken Nancy , Eickhoff Jens , Antony Kathleen M. , Noguchi Kevin , Zeng Xiankun , Permar Sallie , Prabhakaran Vivek , Capuano Saverio , Friedrich Thomas C. , Golos Thaddeus G. , O’Connor David H. , Mohr Emma L.
Published: August 2019

Congenital Zika virus (ZIKV) exposure results in a spectrum of disease ranging from severe birth defects to delayed onset neurodevelopmental deficits. ZIKV-related neuropathogenesis, predictors of birth defects, and neurodevelopmental deficits are not well defined in people. Here we assess the methodological and statistical feasibility of a congenital ZIKV exposure macaque model for identifying infant neurobehavior and brain abnormalities that may underlie neurodevelopmental deficits. We inoculated five pregnant macaques with ZIKV and mock-inoculated one macaque in the first trimester. Following birth, growth, ocular structure/function, brain structure, hearing, histopathology, and neurobehavior were quantitatively assessed during the first week of life. We identified the typical pregnancy outcomes of congenital ZIKV infection, with fetal demise and placental abnormalities. We estimated sample sizes needed to define differences between groups and demonstrated that future studies quantifying brain region volumes, retinal structure, hearing, and visual pathway function require a sample size of 14 animals per group (14 ZIKV, 14 control) to detect statistically significant differences in at least half of the infant exam parameters. Establishing the parameters for future studies of neurodevelopmental outcomes following congenital ZIKV exposure in macaques is essential for robust and rigorous experimental design.
An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion ofTrypanosoma brucei
Authors: Bandini Giulia , Damerow Sebastian , Güther Maria Lucia Sampaio , Guo Hongjie , Mehlert Angela , Beverley Stephen M. , Ferguson Michael A. J.
Published: August 2019

Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential inTrypanosoma brucei.Here we show that the single identifiableT. bruceifucosyltransferase (TbFUT1) is a GDP-Fuc: β-D-galactose α-1,2-fucosyltransferase with an apparent preference for a Galβ1,3GlcNAcβ1-O-R acceptor motif. Conditional null mutants ofTbFUT1demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion ofT. bruceiand found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, theTbFUT1gene was able to complement aLeishmania majormutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids.
A Fyn - specific biosensor reveals localized, pulsatile kinase activity and spatially regulated signaling crosstalk
Authors: Mukherjee Ananya , Singh Randhir , Udayan Sreeram , Biswas Sayan , Pothula Purushotham , Manmadhan Saumya , George Geen , Kumar Shilpa Dilip , Das Ranabir , Rao Balaji M. , Gulyani Akash
Published: August 2019

Cell behavior is controlled through spatio-temporally localized protein activity. Despite unique and often contradictory roles played by Src-family-kinases (SFKs) in regulating cell physiology, activity patterns of individual SFKs have remained elusive. Here, we report a biosensor for specifically visualizing active conformation of SFK-Fyn in live cells. We deployed combinatorial library screening to isolate a binding-protein (F29) targeting activated Fyn. Nuclear-magnetic-resonance (NMR) analysis provides the structural basis of F29 specificity for Fyn over homologous SFKs. Using F29, we engineered a sensitive, minimally-perturbing fluorescence-resonance-energy-transfer (FRET) biosensor (FynSensor) that reveals cellular Fyn activity to be spatially localized, pulsatile and sensitive to adhesion/integrin signaling. Strikingly, growth factor stimulation further enhanced Fyn activity in pre-activated intracellular zones. However, inhibition of focal-adhesion-kinase activity not only attenuates Fyn activity, but abolishes growth-factor modulation. FynSensorimaging uncovers spatially-organized, sensitized signaling clusters, direct crosstalk between integrin and growth-factor-signaling, and clarifies how compartmentalized Src-kinase activity may drive cell fate.
The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria
Authors: Wein Tanita , Dagan Tal
Published: August 2019

Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to genetic drift following population bottlenecks. We evolvedEscherichia colipopulations under three different population bottlenecks (small, medium, large) in two temperature regimes (37°C and 20°C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity in all bottleneck sizes, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of the evolvability in bacteria; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.
Modulation of β-catenin levels is critical for cranial neural crest patterning and dispersal into first pharyngeal arch
Authors: Javali Alok , Laxmanan Vairavan , Palakodeti Dasaradhi , Sambasivan Ramkumar
Published: August 2019

Vertebrate cranial neural crest cells (CNCC) are multipotent. Proximal to the source CNCC form the cranial ganglia. Distally, in the pharyngeal arches, they give rise to the craniofacial skeleton and connective tissues. Fate choices are made as CNCC pattern into distinct destination compartments. In spite of this importance, the mechanism patterning CNCC is poorly defined. Here, we report that a novel β-catenin-controlled switch in the cell arrangement is critical in patterning CNCC. In mouse embryos, at the first pharyngeal arch axial level, membrane β-catenin levels correlate with the extent of cell-cell adhesion and thus, with a collective or a dispersed state of CNCC. Using in vitro human neural crest model and chemical modulators of β-catenin levels, we show a requirement for down-modulating β-catenin for the collective-to-dispersed switch. Similarly, in β-catenin gain of function mutant mouse embryos, CNCC fail to disperse, which may underlie their failure to populate first pharyngeal arch. Thus, we show that β-catenin-mediated regulation of CNCC tissue architecture, a previously underappreciated mechanism, underlies the patterning of CNCC into fate-specific compartments.

Summary statement

The report shows a crucial step in cranial neural crest patterning. Neural crest cells invading the pharyngeal arches transition from a collective to a dispersed state. This transition in cell arrangement is dependent on membrane β-catenin levels.
Alcohol Drinking Exacerbates Neural and Behavioral Pathology in the 3xTg-AD Mouse Model of Alzheimer’s Disease
Authors: Hoffman Jessica L. , Faccidomo Sara , Kim Michelle , Taylor Seth M. , Agoglia Abigail E. , May Ashley M. , Smith Evan N. , Wong LC , Hodge Clyde W.
Published: August 2019

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that represents the most common cause of dementia in the United States. Although the link between alcohol use and AD has been studied, preclinical research has potential to elucidate neurobiological mechanisms that underlie this interaction. This study was designed to test the hypothesis that non-dependent alcohol drinking exacerbates the onset and magnitude of AD-like neural and behavioral pathology. We first evaluated the impact of voluntary 24-h, 2-bottle choice home-cage alcohol drinking on the prefrontal cortex and amygdala neuroproteome in C57BL/6J mice and found a striking association between alcohol drinking and AD-like pathology. Bioinformatics identified the AD-associated proteins MAPT (Tau), amyloid beta precursor protein (APP), and presenilin-1 (PSEN-1) as the main modulators of alcohol-sensitive protein networks that included AD-related proteins that regulate energy metabolism (ATP5D, HK1, AK1, PGAM1, CKB), cytoskeletal development (BASP1, CAP1, DPYSL2 [CRMP2], ALDOA, TUBA1A, CFL2, ACTG1), cellular/oxidative stress (HSPA5, HSPA8, ENO1, ENO2), and DNA regulation (PURA, YWHAZ). To address the impact of alcohol drinking on AD, studies were conducted using 3xTg-AD mice that express human MAPT, APP, and PSEN-1 transgenes and develop AD-like brain and behavioral pathology. 3xTg-AD and wildtype mice consumed alcohol or saccharin for 4 months. Behavioral tests were administered during a 1-month alcohol free period. Alcohol intake induced AD-like behavioral pathologies in 3xTg-AD mice including impaired spatial memory in the Morris Water Maze, diminished sensorimotor gating as measured by prepulse inhibition, and exacerbated conditioned fear. Multiplex immunoassay conducted on brain lysates showed that alcohol drinking upregulated primary markers of AD pathology in 3xTg-AD mice: Aβ 42/40 ratio in the lateral entorhinal and prefrontal cortex and total Tau expression in the lateral entorhinal cortex and amygdala at 1-month post alcohol exposure. Immunocytochemistry showed that alcohol use upregulated expression of pTau (Ser199/Ser202) in the hippocampus, which is consistent with late stage AD. According to the NIA-AA Research Framework, these results suggest that alcohol use is associated with Alzheimer’s pathology. Results also showed that alcohol use was associated with a general reduction in Akt/mTOR signaling via several phosphoproteins (IR, IRS1, IGF1R, PTEN, ERK, mTOR, p70S6K, RPS6) in multiple brain regions including hippocampus and entorhinal cortex. Dysregulation of Akt/mTOR phosphoproteins suggests alcohol may target this pathway in AD progression. These results suggest that nondependent alcohol drinking increases the onset and magnitude of AD-like neural and behavioral pathology in 3xTg-AD mice.
Intramolecular regulation of anillin during cytokinesis
Authors: Beaudet Daniel , Pham Nhat , Skaik Noha , Piekny Alisa
Published: August 2019

Cytokinesis occurs by the ingression of an actomyosin ring that cleaves a cell into two daughters. This process is tightly controlled to avoid aneuploidy, and we previously showed that active Ran coordinates ring positioning with chromatin. Active Ran is high around chromatin, and forms an inverse gradient to cargo-bound importins. We found that the ring component anillin contains an NLS that binds to importin and is required for its function. Anillin contains a RhoA-binding domain (RBD), which we revealed autoinhibits the adjacent NLS-containing C2 domain. Here, we show that active RhoA relieves inhibition of the C2 domain. Furthermore, FRAP experiments show that the NLS regulates anillin’s cortical properties, supporting feedback to the RBD. Indeed, mutations that disrupt the interface between the RBD and C2 domain disrupt anillin’s localization and function. Thus, active RhoA induces a conformational change that increases accessibility to the C2 domain, which is maintained by importin-binding for recruitment to the equatorial cortex.
Gram-positive and Gram-negative Bacteria Share Common Principles to Coordinate Growth and the Cell Cycle at the Single-cell Level
Authors: Sauls John T. , Cox Sarah E. , Do Quynh , Castillo Victoria , Ghulam-Jelani Zulfar , Jun Suckjoon
Published: August 2019

Bacillus subtilisandEscherichia coliare evolutionarily divergent model organisms that have elucidated fundamental differences between Gram-positive and Gram-negative bacteria, respectively. Despite their differences in cell cycle control at the molecular level, both organisms follow the same phenomenological principle for cell size homeostasis known as the adder. We thus asked to what extentB. subtilisandE. colishare common physiological principles in coordinating growth and the cell cycle. To answer this question, we measured physiological parameters ofB. subtilisunder various steady-state growth conditions with and without translation inhibition at both population and single-cell level. These experiments revealed core shared physiological principles betweenB. subtilisandE. coli. Specifically, we show that both organisms maintain an invariant cell size per replication origin at initiation, with and without growth inhibition, and even during nutrient shifts at the single-cell level. Furthermore, both organisms also inherit the same “hierarchy” of physiological parameters ranked by their coefficient of variation. Based on these findings, we suggest that the basic coordination principles between growth and the cell cycle in bacteria may have been established in the very early stages of evolution.
The influence of substrate concentration on the culturability of heterotrophic soil microbes isolated by high-throughput dilution-to-extinction cultivation
Authors: Bartelme Ryan P. , Custer Joy M. , Dupont Christopher L. , Espinoza Josh L. , Torralba Manolito , Khalili Banafshe , Carini Paul
Published: August 2019

The vast majority of microbes inhabiting oligotrophic shallow subsurface soil environments have not been isolated or studied under controlled laboratory conditions. In part, the challenges associated with isolating shallow subsurface microbes may persist because microbes in deeper soils are adapted to low nutrient availability or quality. Here we use high-throughput dilution-to-extinction culturing to isolate shallow subsurface microbes from a conifer forest in Arizona, USA. We hypothesized that the concentration of heterotrophic substrates in microbiological growth medium would affect which microbial taxa were culturable from these soils. To test this, we diluted extracted cells into one of two custom-designed defined growth media that differed only by a 100-fold difference in the concentration of amino acids and organic carbon. Across both media, we isolated a total of 133 pure cultures, all of which were classified as Actinobacteria or Alphaproteobacteria. The substrate availability dictated which actinobacterial phylotypes were culturable but had no significant effect on the culturability of Alphaproteobacteria. We isolated cultures that were representative of the most abundant phylotype in the soil microbial community (Bradyrhizobiumspp.) and representatives of five of the top 10 most abundantActinobacteriaphylotypes, includingNocardioidesspp.,Mycobacteriumspp., and several other phylogenetically-divergent lineages. Flow cytometry of nucleic acid-stained cells showed that cultures isolated on low-substrate medium had significantly lower nucleic-acid fluorescence than those isolated on high-substrate medium. These results show that dilution-to-extinction is an effective method to isolate abundant soil microbes and the concentration of substrates in culture medium influences the culturability of specific microbial lineages.

Importance

Isolating environmental microbes and studying their physiology under controlled conditions is an essential aspect of understanding their ecology. Subsurface ecosystems are typically nutrient-poor environments that harbor diverse microbial communities—the majority of which are thus far uncultured. In this study, we use modified high-throughput cultivation methods to isolate subsurface soil microbes. We show that a component of whether a microbe is culturable from subsurface soils is the concentration of growth substrates in the culture medium. Our results offer new insight into technical approaches and growth medium design that can be used to access the uncultured diversity of soil microbes.
Mutant GT198 in angiogenesis as a common origin of human prostate and bladder cancers
Authors: Zhang Liyong , Liu Yehai , Cheng Liang , Zhao Chengquan , Ko Lan
Published: August 2019

Prostate and bladder cancers are common cancers in men. It has been speculated that the high concomitant incidence of the two cancers is due to a potential shared cause underlying both cancers. In this report, we have identified a common cause of human prostate and bladder cancers as the mutant oncoprotein GT198 (PSMC3IP). GT198 is a DNA repair factor and a steroid hormone receptor coactivator. GT198 has been previously shown to be mutated in angiogenic pericyte stem cells in solid tumor microenvironment. GT198 is also a direct protein target of chemo drugs paclitaxel and doxorubicin. Here we show, the GT198 gene is mutated with protein overexpression in tumor stroma of human prostate and bladder cancers. Affected stromal cells include angiogenic blood vessel pericyte stem cells, and vascular smooth muscle cell lineages including myofibroblasts in prostate and smooth muscle cells in bladder. In prostate cancers, GT198+ tumor stromal cells are associated with early stages of cancer with lower Gleason scores. In bladder cancers, the presence of angiogenesis and GT198+ stroma are associated with better progression-free survival in docetaxel-treated patients. Together, our evidence suggests that angiogenic pericyte stem cells are initial lesions producing a mutant stroma carrying GT198 somatic mutations. Subsequently, mutant myofibroblasts promote adenocarcinomas in prostate and mutant smooth muscle cells promote urothelial carcinomas in bladder. Chemo drugs targeting to GT198 is more effective in early stages of cancers with GT198+ stromal cells. This study supports oncoprotein GT198 as a common cause and a drug target in human prostate and bladder cancers.
Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species,Yucca gloriosa
Authors: Heyduk Karolina , Ray Jeremy N. , Leebens-Mack Jim
Published: August 2019

Background and Aims

CAM photosynthesis is often considered to be a complex trait, requiring orchestration of leaf anatomy and physiology for optimal performance. But the observation of trait correlations is based largely on comparisons between C3and strong CAM species, resulting in a lack of understanding as to how such traits evolve and the level of intraspecific variability for CAM and associated traits.

Methods

To understand intraspecific variation for traits underlying CAM and how these traits might assemble over evolutionary time, we conducted detailed time course physiological screens and measured aspects of leaf anatomy in 24 genotypes of a C3+CAM hybrid species,Yucca gloriosa(Asparagaceae). Comparisons were made toY. gloriosasprogenitor species,Y. filamentosa(C3) andY. aloifolia(CAM).

Key results

Based on gas exchange and measurement of leaf acids,Y. gloriosaappears to use both C3and CAM, and varies across genotypes in the degree to which CAM can be upregulated under drought stress. While correlations between leaf anatomy and physiology exist when testing across all threeYuccaspecies, such correlations break down at the species level inY. gloriosa.

Conclusions

The variation in CAM upregulation inY. gloriosais a result of its relatively recent hybrid origin. The lack of trait correlations between anatomy and physiology withinY. gloriosaindicate that the evolution of CAM, at least initially, can proceed through a wide combination of traits, and more favorable combinations are eventually selected for in strong CAM plants.
Early Tetrapodomorph Biogeography: Controlling for Fossil Record Bias in Macroevolutionary Analyses
Authors: Gardner Jacob D. , Surya Kevin , Organ Chris L.
Published: August 2019

The fossil record provides direct empirical data for understanding macroevolutionary patterns and processes. Inherent biases in the fossil record are well known to confound analyses of this data. Sampling bias proxies have been used as covariates in regression models to test for such biases. Proxies, such as formation count, are associated with paleobiodiversity, but are insufficient for explaining species dispersal owing to a lack of geographic context. Here, we develop a sampling bias proxy that incorporates geographic information and test it with a case study on early tetrapodomorph biogeography. We use recently-developed Bayesian phylogeographic models and a new supertree of early tetrapodomorphs to estimate dispersal rates and ancestral habitat locations. We find strong evidence that geographic sampling bias explains supposed radiations in dispersal rate (potential adaptive radiations). Our study highlights the necessity of accounting for geographic sampling bias in macroevolutionary and phylogenetic analyses and provides an approach to test for its effect.
The critical role of mental imagery in human emotion: insights from Aphantasia
Authors: Wicken Marcus , Keogh Rebecca , Pearson Joel
Published: August 2019

One proposed function of imagery is to make thoughts more emotionally evocative through sensory simulations. Here we report a novel test of this theory utilizing a special population with no visual imagery: Aphantasia. After using multi-method verification of aphantasia, we show that this condition, but not the general population, is associated with a flat-line physiological response to frightening written, but not perceptual scenarios, supporting imagery’s critical role in emotion.
Isolation of an archaeon at the prokaryote-eukaryote interface
Authors: Imachi Hiroyuki , Nobu Masaru K. , Nakahara Nozomi , Morono Yuki , Ogawara Miyuki , Takaki Yoshihiro , Takano Yoshinori , Uematsu Katsuyuki , Ikuta Tetsuro , Ito Motoo , Matsui Yohei , Miyazaki Masayuki , Murata Kazuyoshi , Saito Yumi , Sakai Sanae , Song Chihong , Tasumi Eiji , Yamanaka Yuko , Yamaguchi Takashi , Kamagata Yoichi , Tamaki Hideyuki , Takai Ken
Published: August 2019

The origin of eukaryotes remains enigmatic. Current data suggests that eukaryotes may have risen from an archaeal lineage known as “Asgard archaea”. Despite the eukaryote-like genomic features found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear due to the lack of cultured representatives and corresponding physiological insight. Here we report the decade-long isolation of a Lokiarchaeota-related Asgard archaeon from deep marine sediment. The archaeon, “CandidatusPrometheoarchaeum syntrophicum strain MK-D1”, is an anaerobic, extremely slow-growing, small cocci (∼550 nm), that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexities have been proposed for Asgard archaea, the isolate has no visible organella-like structure.Ca. P. syntrophicum instead displays morphological complexity – unique long, and often, branching protrusions. Based on cultivation and genomics, we propose an “Entangle-Engulf-Enslave (E3) model” for eukaryogenesis through archaea-alphaproteobacteria symbiosis mediated by the physical complexities and metabolic dependency of the hosting archaeon.
Dynamics of Livestock-Associated Methicillin ResistantStaphylococcus aureusin pig farms networks: insight from mathematical modeling and French data
Authors: Bastard Jonathan , Andraud Mathieu , Chauvin Claire , Glaser Philippe , Opatowski Lulla , Temime Laura
Published: August 2019

Livestock-associated methicillin resistantStaphylococcus aureus(LA-MRSA) colonizes livestock animals worldwide, especially pigs and calves. Although frequently carried asymptomatically, LA-MRSA can cause severe infections in humans. It is therefore important to better understand LA-MRSA spreading dynamics within pig farms and over pig farms networks, and to compare different strategies of control and surveillance. For this purpose, we propose a stochastic meta-population model of LA-MRSA spread along the French pig-farm network (n=10,542 farms), combining within- and between-farms dynamics, based on detailed data on breeding practices and pig exchanges between holdings. We calibrate the model using French epidemiological data. We then identify farm-level factors associated with the spreading potential of LA-MRSA in the network. We also show that, assuming control measures applied in a limited (n=100) number of farms, targeting farms depending on their centrality in the network is the only way to significantly reduce LA-MRSA global prevalence. Finally, we investigate the scenario of emergence of a new LA-MRSA strain, and find that the farms with the highest indegree would be the best sentinels for a targeted surveillance of such a strain’s introduction.
Influence of Salt Stress on the flg22 Induced ROS Production in Arabidopsis Thaliana Leaves
Authors: Rashid Amrahov Nurlan , Janda Martin , Mahmud Mammadov Ziaddin , Valentová Olga , Burketová Lenka , Alekber Quliyev Akif
Published: August 2019

In their natural habitats, plants have to cope with multiple stress factors triggering respective response pathways, leading to mutual interference. Our work aimed to study the effect of salt stress in combination with immune response triggered by microbe-associated molecular pattern (MAMP) in Arabidopsis thaliana Col-0 plants. We measured ROS production after treatment with flg22 and the influence of concomitant salt stress (NaCl and Na2CO3).The maximum combined effect of NaCl solution and flg22 on ROS production was achieved at 6 mM salt, which was almost 2 times higher than the single effect of MAMP. A similar maximum combined effect with Na2CO3 was observed at 10 mM concentration. High concentration of NaCl and Na2CO3 was accompanied with declining of ROS production, which was completely inhibited at 150 mM of NaCl and at 50 mM of Na2CO3.The immediate and long term (24 h) effect of NaCl on leaf tissue of Arabidopsis thaliana showed that the impact of salt stress on flg22induced ROS production probably did not affect the genetic aspects of the tissue response, but was associated with ionic and osmotic stresses. Experiments with mannitol, KCl and CaCl2 allowed to conclude that the observed effect was due to the ionic stress of the salt rather than the osmotic one.
VHUT-cryo-FIB, a method to fabricate frozen-hydrated lamella of tissue specimen for in situ cryo-electron tomography
Authors: Zhang Jianguo , Zhang Danyang , Sun Lei , Ji Gang , Huang Xiaojun , Niu Tongxin , Sun Fei
Published: August 2019

ABSTACT

Cryo-electron tomography (cryo-ET) provides a promising technique to study high resolution structures of macromolecules in situ, opening a new era of structural biology. One major bottleneck of this technique is to prepare suitable cryo-lamellas of cell/tissue samples. The emergence of cryo-focused ion beam (cryo-FIB) milling technique provides a good solution of this bottleneck. However, there are still large limitations of using cryo-FIB to prepare cryo-lamella of tissue specimen because the thickness of tissue increases the difficulty of specimen freezing and cryo-FIB milling. Here we report a new workflow, VHUT-cryo-FIB (Vibratome - High pressure freezing - Ultramicrotome Trimming – cryo-FIB), aiming for efficient preparation of frozen hydrated tissue lamella for subsequent cryo-ET data collection. This workflow includes tissue slicing using vibratome, high pressure freezing, ultramicrotome cryo-trimming, cryo-FIB milling and the subsequent cryo-electron microscopy (cryo-EM). The modification of equipment in this workflow is highly eliminated. We developed two strategies with a special cryo-holder tip or carrier for loading cryo-lamella into side entry cryo-holder or Autoloader catridge. We tested this workflow using the tissue sample of rat skeleton muscle and spinach leaf and collected high quality cryo-ET tilt series, which enabled us to obtain an in situ structure of spinach ribosome by sub-tomogram averaging.
Using QSARs for predictions in drug delivery
Authors: Rivera-Delgado Edgardo , Xin Alison , von Recum Horst A.
Published: August 2019

Drug delivery research is an inherently empirical process, however high-throughput approaches could take advantage of understanding drug/material interactions such as from electrostatic, hydrophobic, or other non-covalent interactions between therapeutic molecules and a drug delivery polymer. Cyclodextrin polymers have been investigated for drug delivery specifically due to their capacity to exploit this affinity interaction to change the rate of drug release. Testing drug candidates; however, for affinity is time-consuming, making computational predictions more effective. One option, molecular "docking" programs, provide predictions of affinity, but lack reliability, as their accuracy with cyclodextrin remains unverified experimentally. Alternatively, quantitative structure-activity relationship models (QSARs), which analyze statistical relationships between molecular properties, appear more promising. Previously constructed QSARs for cyclodextrin are not publicly available, necessitating an openly accessible model. Around 600 experimental affinities between cyclodextrin and guest molecules were cleaned and imported from published research. The software PaDEL-Descriptor calculated over 1000 chemical descriptors for each molecule, which were then analyzed in R to create several QSARs with different statistical methods. These QSARs proved highly time efficient, calculating in minutes what docking programs would take hours to accomplish. Additionally, on test sets, QSARs reached R2values of around 0.7-0.8. The speed, accuracy, and accessibility of these QSARs improve evaluation of individual drugs and facilitate screening of large datasets for potential candidates in cyclodextrin affinity-based delivery systems. An app was built to rapidly access model predictions for end users using the "shiny" library in R. To demonstrate the usability for drug release planning, the QSAR predictions were coupled with a mechanistic model of diffusion within the app. Integrating new modules should provide an accessible approach to use other cheminformatic tools in the field of drug delivery.
Effects of Gamma Irradiation Against Mating Competitiveness of Male Culex quinquefasciatus (Diptera:Culicidae) in Laboratory
Authors: Ramadhani T , Hadi UK , Soviana S , Irawati Z , Rahayu A , Sunaryo  , Prastawa A , Mallongi A
Published: August 2019

Culex quinquefasciatus is the main vector of lymphatic filariasis in Pekalongan City. Sterile Insect Tehnique (SIT) could be complementary vector control for filariasis. The key success of the technique depend on the ability of laboratory-reared sterile males with the wild-type females.The aim of the research was to determine the mating competitiveness, the fecundity and the fertility of sterile male Culex quinquefasciatus. The pupae of Cx. quinquefasciatus were gamma irradiated at the doses of 60Gy, 70Gy, and 80Gy, while unirradiated pupae were prepared as control. The mosquitoes emerging from the irradiated pupae could mate with a normal female in the cages. It were observed for the mean female laying eggs, the fecundity, the fertility and the mating competitiveness. The data were analyzed by one way ANOVA. The result showed that the irradiated Cx. quinquefasciatus at the doses tested did not affect on the fecundity and the mating competitiveness, but the fertility was disturbed (sterile). A dose of 70 Gy was the optimum dose or a fertility rate of 1.8% (98.2% sterile), and the value of competitiveness (C index) was 0.568. Based on the result, the irradiated Cx. quinquefasciatus can be recommended for semifield application.
Trans-epithelial Fluid Pumping Performance of Renal Epithelial Cells and Mechanics of Cystic Expansion
Authors: Choudhury Mohammad Ikbal , Li Yizeng , Mistriotis Panagiotis , Dixon Eryn E. , Yang Jing , Maity Debonil , Walker Rebecca , Benson Morgen , Martin Leigha , Koroma Fatima , Qian Feng , Konstantopoulos Konstantinos , Woodward Owen M. , Sun Sean X.
Published: August 2019

Using a novel microfluidic platform to recapitulate fluid absorption activity of kidney cells, we report that renal epithelial cells can actively generate hydraulic pressure gradients across the epithelium. The fluidic flux declines with increasing hydraulic pressure until a stall pressure, at which the fluidic flux vanishes--in a manner similar to mechanical fluidic pumps. The developed pressure gradient translates to a force of 50-100 nanoNewtons per cell. For normal human kidney cells, the fluidic flux is from apical to basal, and the pressure is higher on the basal side. For human polycystic kidney disease (PKD) cells, the fluidic flux is reversed from basal to apical with a significantly higher stall pressure. Molecular studies and proteomic analysis reveal that renal epithelial cells are highly sensitive to hydraulic pressure gradients, developing different expression profiles and spatial arrangements of ion exchangers and the cytoskeleton in different pressure conditions. These results, together with data from osmotic and pharmacological perturbations of fluidic pumping, implicate mechanical force and hydraulic pressure as important variables during morphological changes in epithelial tubules, and provide further insights into pathophysiological mechanisms underlying the development of high luminal pressure within renal cysts.
Oxygen tension regulates lysosomal activation and receptor tyrosine kinase degradation
Authors: Hong Jaewoo , Wuest Todd R. , Min Yongfen , Lin P. Charles
Published: August 2019

Oxygen sensing is crucial for adaptation to variable habitats and physiological conditions. Low oxygen tension, or hypoxia, is a common feature of solid tumors and hypoxic tumors are often more aggressive and resistant to therapy. Here we show that, in mammalian tissue culture cells, hypoxia suppressed lysosomal acidification/activation and receptor tyrosine kinase (RTK) degradation. Hypoxia down-regulated mTORc1, reducing its ability to activate transcription factor EB (TFEB), a master regulator of v-ATPase, the lysosomal proton pump. Hypoxia prevented epidermal growth factor receptor (EGFR) degradation in tumor tissues, whereas activation of lysosomes enhanced tumor cell response to anti-EGFR treatment. Our results link oxygen tension and lysosomal activity, provide a molecular explanation of the malignant phenotype associated with hypoxic tumors, and suggest activation of lysosomes may provide therapeutic benefit in RTK-targeted cancer therapy.

One Sentence Summary

Hypoxia suppresses lysosomal activation and proteolysis.
ZIP-5/bZIP transcription factor regulation of folate metabolism is critical for aging axon regeneration
Authors: Lakhina Vanisha , McReynolds Melanie , Grimes Daniel T. , Rabinowitz Joshua D. , Burdine Rebecca D. , Murphy Coleen T.
Published: August 2019

Aging is associated with reduced capacity for tissue repair, perhaps the most critical of which is a decline in the ability of aged neurons to recover after injury. Identifying factors that improve the regenerative ability of aging neurons is a prerequisite for therapy design and remains an enormous challenge, yet many of the genes that play a role in regeneration of youthful axons do not regulate axon regeneration in older animals2,9, highlighting the need to identify aging-specific regeneration mechanisms. Previously, we found that increased DAF-16/FOXO activity enhances the regenerative ability of mechanosensory axons in aged animals9. Here we show that DAF-16/FOXO mediates its pro-regenerative effects by upregulating folate metabolism genes via the ZIP-5 bZIP transcription factor. Remarkably, dietary folic acid supplementation improves the regeneration of aging C. elegans axons. Enzymes regulating folate metabolism are also up-regulated in regenerating zebrafish fins, and we show that dietary folic acid supplementation post-amputation enhances fin regrowth in aging zebrafish. Our results demonstrate that boosting folate metabolism is a conserved and non-invasive approach to increase the regenerative capacity of aging neurons and tissues. Given that lower folate status has been linked with reduced cognition in the elderly17, maintaining optimal folate metabolism may be a general strategy to achieve healthy brain aging.
Case-based modeling: fostering expertise development and small group learning
Authors: Lyons Paul , Bandura Randall P.
Published: August 2019

Purpose

This paper aims to present a detailed explication of a learner-centered instructional approach for adults labeled case-based modeling (CBM). The approach is an example of integrative pedagogy aimed at expertise development and is an extension of other instructional approaches, namely, problem-based learning (PBL) and case-based learning (CBL).

Design/methodology/approach

The design of the paper contains several integrated components to include: an explanation of the needs and characteristics of the adult learner, comparisons of CBM with both PBL and CBL, a complete theory grounding of the method, a detailed expression of the entire CBM method (phases and steps) for explanation and replication purposes, linkages of CBM with performance, and an empirical test of the CBM method with a sample of employees.

Findings

First, the CBM method is an extension of the well-researched methods of CBL and PBL. The script preparation and implementation phases of CBM easily could be appended to either CBL or PBL. Second, the empirical test of the CBM method demonstrates that it may be a positive, efficient tool for education/training with employees, although no significant differences were found in work performance comparisons of CBM-trained employees with traditionally trained employees.

Research limitations/implications

The empirical examination has some limitations to include: relatively small sample sizes, lack of demonstration of clear linkage between measures of training performance and measures of job performance, and variations in working conditions of participants.

Originality/value

The CBM approach offers to HR practitioners and persons involved with training an efficient yet comprehensive method. The method makes use of script development for the implementation of various interventions, which stimulate performance improvement and development of expertise.
What does healthy eating mean? Australian teachers’ perceptions of healthy eating in secondary school curricula
Authors: Boddy Gail , Booth Alison , Worsley Anthony
Published: August 2019

Purpose

Teachers disseminate food knowledge and skills in secondary school curricula that provide essential skills for a healthy life. The purpose of this paper is to explore Australian secondary school teachers’ views of healthy eating and their sources of information in planning their food, nutrition and health curriculum.

Design/methodology/approach

Secondary school teachers’ perceptions were explored through semi-structured, in-depth interviews that were de-identified and transcribed verbatim. Codes were ascribed to sections of the transcripts and throughout the process of inductive thematic analysis. The teachers’ responses were grouped into five main themes: approaches to teaching healthy eating, sources of food and nutrition information, curriculum planning, teaching goals and teacher career influences.

Findings

The teachers were clear about the aims and importance of teaching healthy eating in an experiential curriculum. They reported that teaching healthy eating assists the health and well--being of adolescents and their families. The effectiveness of current teaching in Australian secondary schools may be compromised by the positioning of food, nutrition and health topics in two separate curriculum areas: technologies and health and physical education, and competing school priorities and resources that limit the students’ exposures to food curricula. The teachers sourced food information from online websites, popular culture and social media. Their knowledge and views of healthy eating appeared to be associated with their interests, life experiences, education and employment histories.

Practical implications

These findings can assist with health promotion and education policy development. They can assist the design of healthy eating curriculum approaches for secondary schools and professional development courses for teachers, which will foster healthy food habits for adolescents, and their families in the future.

Originality/value

Secondary school teacher perceptions of the place of healthy eating in food, and nutrition curricula have been under examined.
Large eddy simulation of an axial pump with coupled flow rate calculation using the sharp interface immersed boundary method
Authors: Haji Mohammadi Mohammad , Brinkerhoff Joshua R.
Published: August 2019

Purpose

Turbomachinery, including pumps, are mainly designed to extract/produce energy from/to the flow. A major challenge in the numerical simulation of turbomachinery is the inlet flow rate, which is routinely treated as a known boundary condition for simulation purposes but is properly a dependent output of the solution. As a consequence, the results from numerical simulations may be erroneous due to the incorrect specification of the discharge flow rate. Moreover, the transient behavior of the pumps in their initial states of startup and final states of shutoff phases has not been studied numerically. This paper aims to develop a coupled procedure for calculating the transient inlet flow rate as a part of the solution via application of the control volume method for linear momentum. Large eddy simulation of a four-blade axial hydraulic pump is carried out to calculate the forces at every time step. The sharp interface immersed boundary method is used to resolve the flow around the complex geometry of the propeller, stator and the pipe casing. The effect of the spurious pressure fluctuations, inherent in the sharp interface immersed boundary method, is damped by local time-averaging of the forces. The developed code is validated by comparing the steady-state volumetric flow rate with the experimental data provided by the pump manufacturer. The instantaneous and time-averaged flow fields are also studied to reveal the flow pattern and turbulence characteristics in the pump flow field.

Design/methodology/approach

The authors use control volume analysis for linear momentum to simulate the discharge rate as part of the solution in a large eddy simulation of an axial hydraulic pump. The linear momentum balance equation is used to update the inlet flow rate. The sharp interface immersed boundary method with dynamic Smagorinsky sub-grid stress model and a proper wall model is used.

Findings

The steady-state volumetric flow rate has been computed and validated by comparing to the flow rate specified by the manufacturer at the simulation conditions, which shows a promising result. The instantaneous and time averaged flow fields are also studied to reveal the flow pattern and turbulence characteristics in the pump flow field.

Originality/value

An approach is proposed for computing the volumetric flow rate as a coupled part of the flow solution, enabling the simulation of turbomachinery at all phases, including the startup/shutdown phase. To the best of the authors’ knowledge, this is the first large eddy simulation of a hydraulic pump to calculate the transient inlet flow rate as a part of the solution rather than specifying it as a fixed boundary condition. The method serves as a numerical framework for simulating problems incorporating complex shapes with moving/stationary parts at all regimes including the transient start-up and shut-down phases.
Evaluation of MWCNT/ethylene glycol nanofluid flow in a parabolic trough collector with glass-glass absorber tube
Authors: Kasaeian Ab , Daneshazarian Reza , Pourfayaz Fathollah , Babaei Sahar , Sheikhpour Mojgan , Nakhjavani Shima
Published: August 2019

Purpose

Because of its increased absorptance in fluid and reduced heat loss, direct absorption nanofluid (DANF) is receiving intense interest as an efficient way to harvest solar energy. This work aims to investigate, for the first time, the application of DANF in parabolic trough collectors (PTC), a promising collector for solar thermal systems.

Design/methodology/approach

A representative flow and heat transfer study of different fluids in a straight tube is conducted, and the basic energy equation and radiative transfer equations are numerically solved to obtain the fluid temperature distribution and energy conversion efficiency. Ethylene glycol (EG) and different concentrations of (i.e., 0.1-0.6 per cent) multi-wall carbon nanotubes (MWCNT) in EG are used as sample fluids. Four cases are studied for a traditional PTC (i.e., using metal tube) and a direct absorption PTC (i.e., using transparent tube) including a bare tube, a tube with an air-filled glass envelope and a tube with vacuumed glass envelop. The numerical results are verified by an experimental study using a copper-glass absorber tube, which reveals the good potential of DANFs.

Findings

Compared with a conventional PTC, using DANF shows an increase of 8.6 per cent and 6.5 K, respectively, in thermal efficiency and outlet temperature difference at a volume fraction (0.5 per cent) of nanoparticles. The results also show that the improvement in solar efficiency increases with increasing particle concentrations, and the vacuum insulated case has the highest efficiency.

Originality/value

In all previous studies, an important section was missing as the effect of photons on the direct solar absorption trough collector, which is considered in this study. This paper proposes a new concept of using direct solar absorption nanofluids for concentrated solar collectors and analyzes the performance of both absorptance and transmittance efficiency considerations. To reveal the potential of the new concept, an analytical model based on energy balance is developed, and two case studies are performed.