bluuebunny/crossref_metadata_2025 huggingface dataset:
A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility
Authors: Stamps Blake W. , Lyon Wanda J. , Irvin Adam P. , Kelley-Loughnane Nancy , Goodson Michael S.
Published: July 2020

Traveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.
Proteolytic cleavage ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1 modifies its allosteric regulation
Authors: Rojas Bruno E. , Hartman Matías D. , Figueroa Carlos M. , Iglesias Alberto A.
Published: July 2020

Phosphoenolpyruvate carboxykinase (PEPCK) plays a crucial role in gluconeogenesis. In this work, we analyze the proteolysis ofArabidopsis thalianaPEPCK1 (AthPEPCK1) in germinating seedlings. We found that expression ofAthPEPCK1 peaks at 24-48 hours post-imbibition. Concomitantly, we observed shorter versions ofAthPEPCK1, putatively generated by metacaspase-9 (AthMC9). To study the impact ofAthMC9 cleavage on the kinetic and regulatory properties ofAthPEPCK1, we produced truncated mutants based on the reportedAthMC9 cleavage sites. The Δ19 and Δ101 truncated mutants ofAthPEPCK1 showed similar kinetic parameters and the same quaternary structure than the WT. However, activation by malate and inhibition by glucose 6-phosphate were abolished in the Δ101 mutant. We propose that proteolysis ofAthPEPCK1 in germinating seedlings operates as a mechanism to adapt the sensitivity to allosteric regulation during the sink-to-source transition.

Highlight

This paper describes the effects of the N-terminal proteolytic cleavage on the kinetic and regulatory properties ofArabidopsis thalianaphosphoenolpyruvate carboxykinase-1.
The molecular taxonomy of primate amygdala via single-nucleus RNA-sequencing analysis
Authors: Zhang Lei , Cheng Yanyong , Wu Shihao , Lu Yufeng , Xue Zhenyu , Chen Dai , Zhang Bo , Qiu Zilong , Jiang Hong
Published: July 2020

Amygdala is the central brain region governing emotional responses of mammals. However, the detailed molecular taxonomy of amygdala in higher mammals such as primates is still absent. Here we present the molecular taxonomy of amygdala in rhesus monkeys by single-cell RNA sequencing analysis. We found that there are five major cell types in primate amygdala, glutamatergic neurons, GABAergic neurons, astroglia, oligodendrocytes and oligodendrocyte progenitor cells (OPCs). Glutamatergic neurons in the primate amygdala exhibits a great diversity comparing to them in the rodent amygdala. In particular, GABAergic neurons in primate amygdala appeared to be quite unique and contain different cellular composition as them in rodent amygdala. The astroglia in primate amygdala contains two more subtypes comparing to astroglia in rodent amygdala. Taken together, although the evolutionary conservation, the molecular taxonomy study of primate amygdala provides critical insights for understanding the cellular architecture of the primate brain.
How does an ectodomain of membrane-associated proteins stand upright and exert robust signal?
Authors: Lankipalli Swetha , Ramagopal Udupi A.
Published: July 2020

Even after decades of research, a comprehensive mechanism that elucidates the underpinnings of signaling through the cell membrane is still elusive. Here, we address a simple question- “how does the ectodomain of a membrane-associated protein consisting of multiple domains and connected by flexible linkers stand ‘upright’ on the membrane?”. Our analysis based on large amount of available structural and functional data, looking for a pattern of association of these molecules in the crystal structures and with the concept that ‘random things seldom repeat’ lead to a surprisingly interesting and consistent observation that (1) the weakcis-interaction mediated symmetric oligomerization of signaling molecules not only support their ‘upright’ orientation but often bury their ligand-binding surface to avoid spurious signaling (2) the linkers connecting the domains are probably not flexible as presumed. This analysis provides a model for pre-liganded receptor supramolecular organization that resolves some of the mysteries unanswered by hypothesis such as ‘lipid-rafts’ and ‘fence and pickets. With CD4, pMHCII, CD2 and TNFR1 as examples, we show that the observedcis-association of molecules also correlate well with their functional role. Further, our analysis reconciles the long-standing controversies related to these molecules and appear to be generic enough to be applied to other signaling molecules.
Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds
Authors: Di Muri C. , Handley L.L. , Bean C.W. , Li J. , Peirson G. , Sellers G.S. , Walsh K. , Watson H.V. , Winfield I.J. , Hänfling B.
Published: July 2020

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the growth of DNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems remains a major challenge. Few studies have examined the association between eDNA metabarcoding data and biomass inferred by whole-organism sampling, mesocosms or mock communities, and the interpretation of sequencing reads as a measure of biomass or number of organisms is largely disputed.

Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of fish abundance in holding ponds with known fish biomass and number of individuals.

eDNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used.

This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management.
Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture
Authors: Christakis Christos A. , Daskalogiannis Georgia , Chatzakis Anastasia , Markakis Emmanouil A. , Sagia Angeliki , Rizzo Giulio Flavio , Catara Vittoria , Lagkouvardos Ilias , Studholme David J. , Sarris Panagiotis F.
Published: July 2020

Halophytes have evolved several strategies to survive in saline environments; however, additional support from their associated microbiota could help combat adverse conditions. Endophytic communities of halophytes may be different than those in other plants because salinity acts as an environmental filter. At the same time, they may contribute to the host’s adaptation to adverse environmental conditions and can improve host tolerance against various biotic and abiotic stresses, which may be of importance in modern and sustainable agriculture.

In this study the culturable endophytic bacteria of three halophytic speciesCakile maritima,Matthiola tricuspidataandCrithmum maritimumwere isolated and identified. Endophytic bacteria were isolated from roots and leaves of the sampled plants. Significant differences were observed in bacterial species abundance among different plant species and tissue from which the isolates were obtained. In total, 115 strains were identified by analysis of complete 16S rDNA sequences, while the majority of these isolates were derived from the root samples.

The strains were evaluated for their ability to: 1) growin-vitroin high levels of NaCl; 2) inhibit the growth of the economically important plant pathogenic fungusVerticillium dahliae in vitroandin planta, the human pathogenic fungusAspergillus fumigatus in vitro, as well as, the economically important plant bacterial pathogensRalstonia solanacearumandClavibacter michiganensis in vitro; 3) provide salt tolerancein planta; 4) provide growth promoting effectin planta.

Additionally, the genomes of twelve selected isolates, exhibiting interesting features, were sequenced and analysed. Three novel bacterial species were identified that belong to the genusPseudomonas(two strains) andArthrobacter(one strain).

The outcome of our study is the proof-of-concept that the crop wild relatives (CWR) halophytic microbiome could potentially serve as a source of beneficial microorganisms that could be used (as unique species or as artificial communities) as Bio-Inoculants, for the enhancement of plant growth and stress tolerance in crops, including the high-salinity stress.

This is very important in the era of ecosystem degradation and climate change, where the maximizing microbial functions in agroecosystems could be a prerequisite for the future of global sustainable agriculture. Globally, there is a strong need for the identification and bio-banking of novel beneficial endophytic microbes with as many desirable characters, for the development of a new environmentally friendly global strategy in food production that will be based in the sustainable agriculture with low chemical inputs and a low environmental impact.
Heterodimeric insecticidal peptide provides new insights into the molecular and functional diversity of ant venoms
Authors: Touchard Axel , Mendel Helen C. , Boulogne Isabelle , Herzig Volker , Emidio Nayara Braga , King Glenn F. , Triquigneaux Mathilde , Jaquillard Lucie , Béroud Rémy , De Waard Michel , Delalande Olivier , Dejean Alain , Muttenthaler Markus , Duplais Christophe
Published: July 2020

Ants use venom for predation, defence and communication, however, the molecular diversity, function and potential applications of ant venom remains understudied compared to other venomous lineages such as arachnids, snakes and cone snails. In this work, we used a multidisciplinary approach that encompassed field work, proteomics, sequencing, chemical synthesis, structural analysis, molecular modelling, stability studies, and a series ofin vitroandin vivobioassays to investigate the molecular diversity of the venom of the AmazonianPseudomyrmex penetratorants. We isolated a potent insecticidal heterodimeric peptide Δ-pseudomyrmecitoxin-Pp1a (Δ-PSDTX-Pp1a) composed of a 27-residue long A-chain and a 33-residue long B-chain crosslinked by two disulfide bonds in an antiparallel orientation. We chemically synthesised Δ-PSDTX-Pp1a, its corresponding parallel AA and BB homodimers, and its monomeric chains and demonstrated that Δ-PSDTX-Pp1a had the most potent insecticidal effects in blow fly assays (LD50= 3 nM). Molecular modelling and circular dichroism studies revealed strong alpha-helical features, indicating its cytotoxic effects could derive from membrane disruption, which was further supported by insect cell calcium assays. The native heterodimer was also substantially more stable against proteolytic degradation (t1/2=13 h) than its homodimers or monomers (t1/2<20 min), indicating an evolutionary advantage of the more complex structure. The proteomic analysis ofPseudomyrmex penetratorvenom and in-depth characterisation of Δ-PSDTX-Pp1a provide novel insights in the structural complexity of ant venom, and further exemplifies how nature exploits disulfide-bond formation and dimerization to gain an evolutionary advantageviaimproved stability; a concept that is also highly relevant for the design and development of peptide therapeutics, molecular probes and bioinsecticides.
Functional dispersion of wetland birds, invertebrates and plants more strongly influenced by hydroperiod than each other
Authors: Daniel Jody , Rooney Rebecca C
Published: July 2020

The relative role of biological and abiotic filters on the assembly of co-occurring taxa is widely debated. While some authors point to biological interactions (e.g., competition) as the stronger driver of ecological selection, others assert that abiotic conditions are more important because they filter species at the regional level. Because communities influenced by a dominant abiotic filter, (e.g., Prairie Pothole Region (PPR) wetlands, each varying in ponded water permanence), often have strong cross-taxon relationships, we can study these communities to better understand the relative influence of abiotic vs biotic filters on community structure. Using functional dispersion as our measure of communities, we test six alternate hypotheses about the relative importance of various pathways representing influence of biological and permanence filters on birds, aquatic macroinvertebrates and wetland plants in the northwest PPR using structural equation modeling. We aimed to understand whether: 1) ponded water permanence alone explained functional dispersion; 2) the influence of permanence on functional dispersion was direct or mediated; and 3) abiotic filtering by permanence was stronger than biotic filtering by co-occurring taxa. The best model suggests that there is a direct influence of permanence on the functional dispersion of each taxonomic group and that both bird and macroinvertebrate functional dispersion are causally related to plant functional dispersion, though for invertebrates the influence of plants is much less than that of permanence. Thus, the relative importance of wetland permanence and the functional dispersion of co-occurring taxa depends on which taxon is considered in PPR wetlands.
The influence of liver fluke infection on production in sheep and cattle: a meta-analysis
Authors: Hayward Adam D. , Skuce Philip J. , McNeilly Tom N.
Published: July 2020

Liver flukes (Fasciolaspp) are important parasites of sheep and cattle across the world, causing significant damage to animal health and productivity due to both acute and chronic infection. Many comprehensive reviews have discussed the results of decades of research into the impact of fluke infection on livestock performance traits such as weight gain and milk production. While fluke are considered to be important, there have been no attempts to collate previous research in a quantitative manner, and nor has there been an attempt to determine why some studies find substantial effects of fluke while others conclude that effects of fluke on animal performance are negligible. In this study, we used meta-analysis to provide quantitative estimates of the impact of liver fluke on animal performance, and to identify elements of study design that influence the conclusions of such studies. A literature search provided 233 comparisons of performance in “fluke-infected” and “uninfected” animals. We standardized these data as log response ratios and calculated effect size variances in order to weight studies by their sample size and accuracy of their estimates. We performed multi-level meta-analysis to estimate effects of fluke infection in five traits: daily weight gain (N = 77); live weight (N = 47); carcass weight (N = 84); total weight gain (N = 18) and milk production (N = 6). There were significant negative effects of fluke infection on daily weight gain, live weight and carcass weight (9%, 6% and 0.6% reductions in performance, respectively), but not total weight gain or milk production. We then used mixed-effects meta-analysis to estimate the impact of moderator variables, including host, fluke, and study design factors, on study outcomes. We found that, in general, studies that gave experimental infections found generally larger effects of fluke than observational or drug studies; younger animals were more likely to suffer the effects of fluke infection on daily weight gain; and that effects on live weight increased across the course of an experiment. Our results provide the first quantitative estimate of the importance of liver fluke on performance across studies and highlight the elements of study design that can influence conclusions. Furthermore, our literature search revealed areas of research into liver fluke that could be the subject of greater effort, and types of study that could form the basis of future meta-analyses.
Physical activity and aerobic fitness show different associations with brain processes underlying anticipatory selective visuospatial attention in adolescents
Authors: Hernández Doris , Heinilä Erkka , Muotka Joona , Ruotsalainen Ilona , Lapinkero Hanna-Maija , Syväoja Heidi , Tammelin Tuija H. , Parviainen Tiina
Published: July 2020

Underlying brain processes of exercise-related benefits on executive functions and the specific contribution of physical activity vs. aerobic fitness are poorly understood, especially during adolescence. We explored whether and how physical activity and aerobic fitness are associated with selective attention and the oscillatory dynamics induced by an anticipatory spatial cue. Further, we studied whether the link between physical exercise level and cognitive control in adolescents is mediated by the task-related oscillatory activity. Magnetoencephalographic alpha oscillations during a modified Posner’s cueing paradigm were measured in 59 adolescents (37 females and 22 males, 12 to 17 years). Accelerometer-measured physical activity and aerobic fitness (20-m shuttle run test) were used to divide the sample into higher and lower performing groups. The interhemispheric alpha asymmetry during selective attention was larger in the high than in the low physical activity group, but there was no difference between the high and low aerobic fitness groups. Exploratory mediation analysis suggested that anticipatory interhemispheric asymmetry mediates the association between physical activity status and drift rate in the selective attention task. Higher physical activity was related to increased cue-induced asymmetry, which in turn was associated with less efficient processing of information. Behaviorally, higher physically active males showed stronger dependence on the cue while higher fit females showed more efficient processing of information. Our findings suggest that physical activity may be associated with a neural marker of anticipatory attention in adolescents. These findings have implications for understanding the varying results on the association between physical activity and attention in adolescents.

HIGHLIGHTS

Physical activity and aerobic fitness link differently with attention in adolescents.

Higher physical activity relates with stronger cue-induced oscillatory asymmetry.

Brain hemispheric interaction mediates the link between physical activity and attention.
Single-Molecule Micromanipulation Studies of Methylated DNA
Authors: Zaichuk T. , Marko J. F.
Published: July 2020

Cytosine methylated at the 5-carbon position is the most widely studied reversible DNA modification. Prior findings indicate that methylation can alter mechanical properties. However, those findings were qualitative and sometimes contradictory, leaving many aspects unclear. By applying single-molecule magnetic force spectroscopy techniques allowing for direct manipulation and dynamic observation of DNA mechanics and mechanically driven strand separation, we investigated how CpG and non-CpG cytosine methylation affects DNA micromechanical properties. We quantitatively characterized DNA stiffness using persistence length measurements from force-extension curves in the nanoscale length regime and demonstrated that cytosine methylation results in increased DNA flexibility (i.e., decreased persistence length). In addition, we observed the preferential formation of plectonemes over unwound single-stranded “bubbles” of DNA, under physiologically relevant stretching forces and supercoiling densities. The stiffness and high structural stability of methylated DNA is likely to have significant consequences on the recruitment of proteins recognizing cytosine methylation and DNA packaging.

Statement of Significance

Despite countless structural and functional studies of DNA methylation, a key epigenetic mark in higher organisms, research towards the understanding of DNA intrinsic structural properties in the context of methylation layout representing different epigenetic landscapes is still in its initial stage. We utilize single molecule spectroscopy to analyze the effect of sparse symmetric and asymmetric 5-mC modification on the mechanical stability of long double-stranded DNA. Our findings establish that at physiologically relevant forces and supercoiling densities increased DNA flexibility of non-CpG methylated DNA translates to the high structural stability.
Exosomes are predominantly loaded with mRNA transcript encoding cytoplasmic proteins and exclude mRNA transcript encoding nuclear proteins
Authors: Haque Shabirul , Vaiselbuh Sarah R.
Published: July 2020

Exosomes are nanovesicles (∼30-150 nm diameters) released via an endocytic pathway in almost all mammalian cell types. Exosomes are composed of a lipid bilayer membrane that encloses RNA, miRNA, proteins and DNA. This manuscript unravels how exosome cargo is collected by a highly precise process delineating two separate mRNA transcript entities encoding cytoplasmic and nuclear proteins separately.

Ultracentrifuge isolated exosomes were directly converted into cDNA (Exo-cDNA), by a method developed in our laboratory. Cellular RNA was extracted from each cell line and cDNA was prepared (Cell-cDNA). We amplified mRNA transcripts translatingcytoplasmicproteins CD10 and CXCR4 and mRNA transcripts translatingnuclearproteins such as proliferating cell nuclear antigen (PCNA), CREB-BP, activation induced cytidine deaminase (AID), and terminal deoxynucleotidyl transferase (TdT). We amplified all four different mRNA transcripts (PCNA, CREB-BP, AID, and TdT) fromcellularcDNA but none fromexosomalcDNA (Exo-cDNA). These findings suggest that exosomes carry mRNA transcripts encodingcytoplasmicproteins only but mRNA transcripts encodingnuclearproteins could not be detected. This important observation could prove to be crucial for the exosome research community since it sheds light on one of the limitations relating to the use of exosomes as biomarkers in cancer biology and other diseases.

Graphical Abstract
Disease-Linked Super-Trafficking of a Mutant Potassium Channel
Authors: Huang Hui , Chamness Laura M. , Vanoye Carlos G. , Kuenze Georg , Meiler Jens , George Alfred L. , Schlebach Jonathan P. , Sanders Charles R.
Published: July 2020

Gain-of-function (GOF) mutations in the KCNQ1 voltage-gated potassium channel can induce cardiac arrhythmia. We tested whether any of the known GOF disease mutations in KCNQ1 act by increasing the amount of KCNQ1 that reaches the cell surface—“super-trafficking”. We found that levels of R231C KCNQ1 in the plasma membrane are 5-fold higher than wild type KCNQ1. This arises from both enhanced translocon-mediated membrane integration of the S4 voltage-sensor helix and an energetic linkage of C231 with the V129 and F166 side chains. Whole-cell electrophysiology recordings confirmed that R231C KCNQ1 in complex with KCNE1 is constitutively active, but also revealed the single channel activity of this mutant to be only 20% that of WT. The GOF phenotype associated with R231C therefore reflects the net effects of super-trafficking, reduced single channel activity, and constitutive channel activation. These investigations document membrane protein super-trafficking as a contributing mechanism to human disease.
Structural and functional analysis of female sex hormones against SARS-Cov2 cell entry
Authors: Aguilar-Pineda Jorge Alberto , Albaghdadi Mazen , Jiang Wanlin , Lopez Karin J. Vera , Del-Carpio Gonzalo Davila , Valdez Badhin Gómez , Lindsay Mark E. , Malhotra Rajeev , Lino Cardenas Christian L.
Published: July 2020

Emerging evidence suggests that males are more susceptible to severe infection by the SARS-CoV-2 virus than females. A variety of mechanisms may underlie the observed gender-related disparities including differences in sex hormones. However, the precise mechanisms by which female sex hormones may provide protection against SARS-CoV-2 infectivity remains unknown. Here we report new insights into the molecular basis of the interactions between the SARS-CoV-2 spike (S) protein and the human ACE2 receptor. We further observed that glycosylation of the ACE2 receptor enhances SARS-CoV-2 infectivity. Importantly estrogens can disrupt glycan-glycan interactions and glycan-protein interactions between the human ACE2 and the SARS-CoV2 thereby blocking its entry into cells. In a mouse model, estrogens reduced ACE2 glycosylation and thereby alveolar uptake of the SARS-CoV-2 spike protein. These results shed light on a putative mechanism whereby female sex hormones may provide protection from developing severe infection and could inform the development of future therapies against COVID-19.
High-Pressure NMR Reveals Volume and Compressibility Differences Between Two Stably Folded Protein Conformations
Authors: Xu Xingjian , Gagné Donald , Aramini James M. , Gardner Kevin H.
Published: July 2020

Proteins often interconvert between different conformations in ways critical to their function. While manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic beta-strand slip as it switches between two stably-folded conformations. Coupling high pressure and biomolecular NMR, we obtained the first quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wildtype equivalent, and the interconversion proceeds through a chiefly-unfolded intermediate state. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.
Dissection of the corticotroph transcriptome in a mouse model of glucocorticoid-induced suppression of the HPA axis
Authors: Romanò N , Duncan PJ , McClafferty H , Nolan O , Ding Q , Homer NZ , Le Tissier P , Walker BR , Shipston MJ , Chambers TJG
Published: July 2020

Glucocorticoids (GC) are prescribed for periods >3 months to 1-3% of the UK population; 10-50% of these patients develop hypothalamus-pituitary-adrenal (HPA) axis suppression, which may last over 6 months and is associated with morbidity and mortality. Recovery of higher nodes of the axis is necessary for recovery of adrenal function. We developed a mouse model of Dexamethasone (DEX)-induced HPA axis dysfunction in order to further explore recovery in the pituitary. Adult male C57BL6/J or those crossed withPomc-eGFP mice were randomly assigned to receive DEX (~0.4 mg/kg bodyweight/day) or vehicle via drinking water for 4 weeks following which treatment was withdrawn. Tissues were harvested at 0, 1, and 4 weeks following withdrawal of treatment. Corticotrophs were isolated fromPomc-eGFP pituitaries using FACS, and RNA extracted for RNA-seq. DEX treatment suppressed corticosterone production, which remained partially suppressed at least 1 week following DEX withdrawal. In the adrenal, at time 0,Hsd3b2, Cyp11a1, andMc2rmRNA levels were significantly reduced, withMc2randCyp11a1remaining reduced 1 week following DEX withdrawal. The corticotroph transcriptome was modified by DEX treatment with some differences between groups persisting 4 weeks following withdrawal. No genes supressed by DEX exhibited ongoing attenuation 1 and 4 weeks following withdrawal, whilst only 2 genes were upregulated and remained so following withdrawal. A pattern of rebound at 1 and 4 weeks was observed in 14 genes that increased following suppression, and 6 genes that were reduced by DEX and then increased. Chronic GC treatment may induce persistent changes in the pituitary that may influence future response to GC treatment or stress.
Intrinsically disordered protein ensembles shape evolutionary rates revealing conformational patterns
Authors: Palopoli Nicolas , Marchetti Julia , Monzon Alexander M. , Zea Diego J. , Tosatto Silvio C.E. , Fornasari Maria S. , Parisi Gustavo
Published: July 2020

Intrinsically disordered proteins (IDPs) lack stable tertiary structure under physiological conditions. The unique composition and complex dynamical behaviour of IDPs make them a challenge for structural biology and molecular evolution studies. Using NMR ensembles, we found that IDPs evolve under a strong site-specific evolutionary rate heterogeneity, mainly originated by different constraints derived from their inter-residue contacts. Evolutionary rate profiles correlate with the experimentally observed conformational diversity of the protein, allowing the description of different conformational patterns possibly related to their structure-function relationships. The correlation between evolutionary rates and contact information improves when structural information is taken not from any individual conformer or the whole ensemble, but from combining a limited number of conformers. Our results suggest that residue contacts in disordered regions constrain evolutionary rates to conserve the dynamic behaviour of the ensemble and that evolutionary rates can be used as a proxy for the conformational diversity of IDPs.

Significance Statement

Intrinsically disordered proteins (IDPs) challenge the structure-function relationship paradigm. In this work we found that individual sites of IDPs evolve under a strong rate heterogeneity, mainly due to the structural constraints imposed by contacts between their residues. This can be better explained if the contacts are taken from selected subsets of their alternative native conformations, rather than from individual conformations or the whole native ensemble. From an evolutionary point of view, this result indicates that experimentally-based ensembles are redundant. We also observed that the evolutionary rates follow the structural variability between conformers, unveiling conformational preferences. Our results set the stage for establishing novel evolutionary-based methods to study IDP ensembles.
Gut Phageome Analysis Reveals Disease-Specific Hallmarks in Childhood Obesity
Authors: Bikel Shirley , López-Leal Gamaliel , Cornejo-Granados Fernanda , Gallardo-Becerra Luigui , Sánchez Filiberto , Equihua-Medina Edgar , Ochoa-Romo Juan Pablo , López-Contreras Blanca Estela , Canizales-Quinteros Samuel , Leyva Adrian Ochoa
Published: July 2020

Changes in the composition of the human gut microbiome are recognized to have a significant association with obesity and metabolic syndrome. Mexico leads worldwide childhood-obesity rankings representing an epidemic problem for public health. To this date, it is still unclear how the gut phageome, the bacteriophage component of the virome, influences childhood obesity and obesity with metabolic syndrome. We characterized the gut phageome of 28 school-age children with healthy normal-weight (NW), obese (O), and obese with metabolic syndrome (OMS) profiles, using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. Viromes derived from VLPs were mainly dominated by Caudovirales, and only Inoviridae family was significantly increased in obesity. The three groups showed a similar number of VLPs, while a significant increase in phage richness and diversity was found in obesity groups compared NW. Few phage contigs dominated the phageome composition in NW, being increased in obesity groups. Interestingly, the majority of the phageome was shared among all individuals, establishing a core and common phageome, which abundances correlated with anthropometric and biochemical traits and bacteria previously associated with obesity and metabolic syndrome. We also established a healthy core phageome shared in >80% of NW samples, with a decreased prevalence in the O and OMS groups. Our data support that changes in the gut phageome may contribute to obesity and metabolic syndrome development via bacterial dysbiosis. We consider the phageome characterization provides the basis for novel diagnostic and therapeutic strategies for managing obesity and preventing metabolic syndrome development in obese children through potential phage manipulation. To the best of our knowledge, this study represents the most in-depth sequenced dataset of human bacteriophages, demonstrating for the first time that alterations of the gut phageome characterize obesity.
Nanoscale curvature promotes high yield spontaneous formation of cell-mimetic giant vesicles
Authors: Pazzi Joseph , Subramaniam Anand Bala
Published: July 2020

To date, surface-assisted assembly of cell-like giant vesicles use planar surfaces and require the application of electric fields or dissolved molecules to obtain adequate yields. Here, we present the use of nanoscale surface curvature and hydrophilic surface chemistry to promote the high yield assembly of GUVs. We show that assembly on surfaces composed of entangled hydrophilic nanocellulose fibers results in an unprecedented 100,000-fold reduction in costs while increasing yields compared to extant techniques. Quantitative measurements of yields provide mechanistic insight on the effect of nanoscale curvature and the effect of surface chemistry. We present a thermodynamic ‘budding and merging’, BNM, model that unifies observations of assembly. The BNM model considers the change in free energy by balancing elastic, adhesion, and membrane edge energies in the formation of surface-attached spherical buds. Due to curvature and the hydrophilicity of cellulose, energetically unfavorable formation of buds on planar and spherical surfaces becomes favorable (spontaneous) on surfaces composed of cylindrical cellulose nanofibers.

TOC Graphic
MafF is an antiviral host factor that suppresses transcription from Hepatitis B Virus core promoter
Authors: Ibrahim Marwa K. , Abdelhafez Tawfeek H. , Takeuchi Junko S. , Wakae Kosho , Sugiyama Masaya , Tsuge Masataka , Ito Masahiko , Watashi Koichi , Kassas Mohamed El , Kato Takanobu , Murayama Asako , Suzuki Tetsuro , Chayama Kazuaki , Shimotohno Kunitada , Muramatsu Masamichi , Aly Hussein H. , Wakita Takaji
Published: July 2020

Hepatitis B Virus (HBV) is a stealth virus that exhibits only minimal induction of the interferon system that is required for both innate and adaptive immune responses. However, 90% of acutely infected adults can clear the virus, suggesting the presence of additional mechanisms that facilitate viral clearance. Herein, we report that Maf bZIP transcription factor F (MafF) promotes host defense against infection with HBV. Using siRNA library and an HBV/NL reporter virus, we screened to identify anti-HBV host factors. Our data showed that silencing ofMafFled to a 6-fold increase in luciferase activity after HBV/NL infection. Overexpression of MafF reduced HBV core promoter transcriptional activity, which was relieved upon mutating the putative MafF binding region. Loss of MafF expression by CRISPR/CAS9 (in HepG2-hNTCP-C4 cells) or siRNA silencing (in primary hepatocytes [PXB]), induced HBV core and HBV pregenomic RNA (pgRNA) levels, respectively, after HBV infection. MafF physically binds to HBV core promoter and competitively inhibits HNF-4α binding to an overlapping sequence in HBV enhancer II sequence (EnhII) as seen by ChIP analysis. MafF expression was induced by IL-1β/TNF-α treatment in both HepG2 and PXB cells, in an NF-κB-dependent manner. Consistently,MafFexpression levels were significantly enhanced and positively correlated with the levels of these cytokines in patients with chronic HBV infection, especially in the immune clearance phase.

Importance

HBV is a leading cause of chronic liver diseases, infecting about 250 million people worldwide. HBV has developed strategies to escape interferon-dependent innate immune responses. Hence, the identification of other anti-HBV mechanisms is important for understanding HBV pathogenesis, and developing anti-HBV strategies. MafF was shown to suppress transcription from HBV core promoter, leading to a significant suppression of HBV life cycle. Furthermore, MafF expression was induced in chronic HBV patients and in primary human hepatocytes (PXB). This induction correlated with the levels of inflammatory cytokines (IL-1β and TNF-α). These data suggest that the induction of MafF contributes to the host’s antiviral defense by suppressing transcription from selected viral promoters. Our data shed light on a novel role for MafF as anti-HBV host restriction factor.
Application of CRISPR/Cas9 nuclease in amphioxus genome editing
Authors: Su Liuru , Shi Chenggang , Huang Xin , Wang Yiquan , Li Guang
Published: July 2020

The cephalochordate amphioxus is a promising animal model for studying the origin of vertebrate due to its key phylogenetic position among chordates. Although transcription activator-like effector nucleases (TALENs) has been adopted in amphioxus genome editing, its labor intensive construction of the TALEN proteins limits its usage in many laboratories. We here report an application of the CRISPR/Cas9 system, a more amenable genome editing method, in this group of animals. Our data show that while co-injection ofCas9mRNAs and sgRNAs into amphioxus unfertilized eggs causes no detectable mutations at targeted loci, injections ofCas9mRNAs and sgRNAs at two cell stage, or of Cas9 protein and sgRNAs before fertilization can executes efficient disruptions of targeted genes. Among the nine tested sgRNAs (targeting five genes) co-injected with Cas9 protein, seven introduced mutations at efficiency ranging from 18.4% to 90% and four caused specific phenotypes in the injected embryos. We also demonstrate that monomerization of sgRNAs via thermal treatment or integration of sgRNAs into a longer backbone could increase mutation efficacies. Our study will not only promote application of genome editing method in amphioxus research, but also provide valuable experiences for other organisms in which the CRISPR/Cas9 system has not been successfully applied.
CX3CR1 Engagement by Respiratory Syncytial Virus Leads to Induction of Nucleolin and Dysregulation of Cilia-related Genes
Authors: Anderson Christopher S. , Chirkova Tatiana , Slaunwhite Christopher G. , Qiu Xing , Walsh Edward E. , Anderson Larry J. , Mariani Thomas J.
Published: July 2020

Respiratory syncytial virus (RSV) contains a conserved CX3C motif on the ectodomain of the G-protein. The motif has been indicated as facilitating attachment of the virus to the host initiating infection via the human CX3CR1 receptor. The natural CX3CR1 ligand, CX3CL1, has been shown to induce signaling pathways resulting in transcriptional changes in the host cells. We hypothesize that binding of RSV to CX3CR1 via CX3C leads to transcriptional changes in host epithelial cells. Using transcriptomic analysis, the effect of CX3CR1 engagement by RSV was investigated. Normal human bronchial epithelial (NHBE) cells were infected with RSV virus containing either wildtype G-protein, or a mutant virus containing a CX4C mutation in the G-protein. RNA sequencing was performed on mock and 4-days-post-infected cultures. NHBE cultures were also treated with purified recombinant wild-type A2 G-protein. Here we report that RSV infection resulted in significant changes in the levels 766 transcripts. Many nuclear associated proteins were upregulated in the WT group, including Nucleolin. Alternatively, cilia-associated genes, including CC2D2A and CFAP221 (PCDP1), were downregulated. The addition of recombinant G-protein to the culture lead to the suppression of cilia-related genes while also inducing Nucleolin. Mutation of the CX3C motif (CX4C) reversed these effects on transcription decreasing nucleolin induction and lessening the suppression of cilia-related transcripts in culture. Furthermore, immunohistochemical staining demonstrated decreases in in ciliated cells and altered morphology. Therefore, it appears that engagement of CX3CR1 leads to induction of genes necessary for RSV entry as well as dysregulation of genes associated with cilia function.

Importance

Respiratory Syncytial Virus (RSV) has an enormous impact on infants and the elderly including increased fatality rates and potential for causing lifelong lung problems. Humans become infected with RSV through the inhalation of viral particles exhaled from an infected individual. These virus particles contain specific proteins that the virus uses to attach to human ciliated lung epithelial cells, initiating infection. Two viral proteins, G-protein and F-protein, have been shown to bind to human CX3CR1and Nucleolin, respectively. Here we show that the G-protein induces Nucleolin and suppresses gene transcripts specific to ciliated cells. Furthermore, we show that mutation of the CX3C-motif on the G-protein, CX4C, reverses these transcriptional changes.
A Murine Model for Enhancement ofStreptococcus pneumoniaePathogenicity Upon Viral Infection and Advanced Age
Authors: Joma Basma H. , Siwapornchai Nalat , Vanguri Vijay K. , Shrestha Anishma , Roggensack Sara E. , Davidson Bruce A. , Tai Albert K. , Hakansson Anders P. , Meydani Simin N. , Leong John M. , Ghanem Elsa N. Bou
Published: July 2020

Streptococcus pneumoniae(pneumococcus) resides asymptomatically in the nasopharynx but can progress from benign colonizer to lethal pulmonary or systemic pathogen. Both viral infection and aging are risk factors for serious pneumococcal infections. Previous work established a murine model that featured the movement of pneumococcus from the nasopharynx to the lung upon nasopharyngeal inoculation with influenza A virus (IAV) but did not fully recapitulate the severe disease associated with human co-infection. We built upon this model by first establishing pneumococcal nasopharyngeal colonization, then inoculating both the nasopharynx and lungs with IAV. In young (2 months) mice, co-infection triggered bacterial dispersal from the nasopharynx into the lungs, pulmonary inflammation, disease and mortality in a fraction of mice. In old mice (20-22 months), co-infection resulted in earlier and more severe disease. Aging was not associated with greater bacterial burdens but rather with more rapid pulmonary inflammation and damage. Both aging and IAV infection led to inefficient bacterial killing by neutrophilsex vivo. Conversely, aging and pneumococcal colonization also blunted IFN-α production and increased pulmonary IAV burden. Thus, in this multistep model, IAV promotes pneumococcal pathogenicity by modifying bacterial behavior in the nasopharynx, diminishing neutrophil function, and enhancing bacterial growth in the lung, while pneumococci increase IAV burden likely by compromising a key antiviral response. Thus, this model provides a means to elucidate factors, such as age and co-infection, that promote the evolution ofS. pneumoniaefrom asymptomatic colonizer to invasive pathogen, as well as to investigate consequences of this transition on antiviral defense.
The mecca of Cold War scholarship: Hong Kong as the intellectual hub to reveal China to the World
Authors: Lan Kenneth
Published: July 2020

Purpose

This writing reveals Hong Kong’s role as the center of China research. Before Reform and Opening in 1979, the British colony was the only place in the world where all international China experts stopped over and obtained the latest and the most accurate accounts of PRC.

Design/methodology/approach

The paper analyzes how Hong Kong serves as the intellectual mecca through examining the lives of China scholars amid building up their international profiles. What prompted them to join the China field? How were their lives like in the British crown colony? This paper also unveils the roles of the two research institutions played on Communist China studies: University Services Center (USC) and Union Research Institute (URI). In addition to relying on archival correspondences, personal interviews were also conducted in the last two years.

Findings

Despite being the mecca of PRC research, Hong Kong was not the first destination for most aspiring China scholars from the West. Most of these Western scholars did not even plan to devote their whole working lives to the study of China. Through luck, draft avoidance and generous grants from Ford and Carnegie Foundations, these young men and women became internationally iconic figures of East Asian research. To complete their Ph.D. theses and subsequent China-related projects, Hong Kong was a “must-go” destination for them. Under the full protection of the Union Jack, these scholars enjoyed the freedom to speak, write, research and publish. God blessed Hong Kong with such a unique political status amid the Cold War.

Originality/value

155 Argyle Street was the Art Deco compound where Red China experts produced most groundbreaking scholarships. It was not only a two-story structure where they acquired their first-hand resources but a platform where any China-related topics were discussed openly under the auspices of British colonial rule of law. Despite claiming themselves as apolitical, both USC and URI were products of US containment policy against communism. Even so, the colonial government never prohibited the two’s operations. Through this paper, readers will also discover how young men and women became inspired into a career in China studies.
Addressing mentor wellbeing in practicum placement mentoring relationships in initial teacher education
Authors: Gillett-Swan Jenna , Grant-Smith Deanna
Published: July 2020

Purpose

University-affiliated mentors serve as liaisons between schools and pre-service teachers during practicum placements, offering academic, administrative and relational support. In the context of academic workload intensification, increasing student numbers and the need to respond to issues as they occur in time-pressured environments, the wellbeing of mentors can become compromised. Mentor wellbeing is explored, highlighting corollary impacts of threats to pre-service teacher wellbeing on those who support them.

Design/methodology/approach

A descriptive single case-study explored mentor lived experiences of wellbeing during the pre-service teacher practicum placement and mentoring process. Semi-structured interviews were conducted with mentors supervising pre-service teacher professional experience placements. Adopting a shadowed data approach, mentors shared their own experiences and reflected on the experiences of others. Data was analysed using thematic content analysis.

Findings

Mentor and pre-service teacher wellbeing experiences exhibited similar wellbeing indicators, including personal and professional stress, workload strains and ethical dilemmas. Many mentors felt invisible in terms of supports for their own self-care as the focus was on meeting practicum stakeholder and student support needs rather than their own wellbeing.

Originality/value

Changes to professional experience practices must consider potential impacts on pre-service teachers, in-school supervisors and the university-affiliated mentors as the wellbeing of each is potentially impacted the wellbeing of others in this professional experience triad. Increasing emphasis on work-integrated learning experiences across multiple disciplines invites future comparison and contrast of wellbeing experiences.