bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron can be microbially extracted from Lunar and Martian regolith simulants and 3D printed into tough structural materials
Authors: Castelein Sofie M. , Aarts Tom F. , Schleppi Juergen , Hendrikx Ruud , Böttger Amarante J. , Benz Dominik , Marechal Maude , Makaya Advenit , Brouns Stan J. , Schwentenwein Martin , Meyer Anne S. , Lehner Benjamin A.E.
Published: November 2020

In-situresource utilization (ISRU) is increasingly acknowledged as an essential requirement for the construction of sustainable extra-terrestrial colonies. Even with decreasing launch costs, the ultimate goal of establishing colonies must be the usage of resources found at the destination of interest. Typical approaches towards ISRU are often constrained by the mass and energy requirements of transporting processing machineries, such as rovers and massive reactors, and the vast amount of consumables needed. Application of self-reproducing bacteria for the extraction of resources is a promising approach to avoid these pitfalls. In this work, the bacteriumShewanella oneidensiswas used to reduce three different types of Lunar and Martian regolith simulants, allowing for the magnetic extraction of iron-rich materials. The quantity of bacterially extracted material was up to 5.8 times higher and the total iron concentration was up to 43.6% higher in comparison to untreated material. The materials were 3D printed into cylinders and the mechanical properties were tested, resulting in a 396 ± 115% improvement in compressive strength in the bacterially treated samples. This work demonstrates a proof of concept for the on-demand production of construction and replacement parts in space exploration.
Androgen responsiveness to simulated territorial intrusions inAllobates femoralismales: evidence supporting the challenge hypothesis in a territorial frog
Authors: Rodríguez Camilo , Fusani Leonida , Raboisson Gaëlle , Hödl Walter , Ringler Eva , Canoine Virginie
Published: November 2020

Territorial behaviour has been widely described across many animal taxa, where the acquisition and defence of a territory are critical for the fitness of an individual. Extensive evidence suggests that androgens (e.g. testosterone) are involved in the modulation of territorial behaviour in male vertebrates. Short-term increase of androgen following a territorial encounter appears to favour the outcome of a challenge. The “Challenge Hypothesis” proposed by Wingfield and colleagues outlines the existence of a positive feedback relationship between androgen and social challenges (e.g. territorial intrusions) in male vertebrates. Here we tested the challenge hypothesis in the highly territorial poison frog,Allobates femoralis, in its natural habitat by exposing males to simulated territorial intrusions in form of acoustic playbacks. We quantified repeatedly androgen concentrations of individual males via a non-invasive water-borne sampling approach. Our results show thatA. femoralismales exhibited a positive behavioural and androgenic response after being confronted to simulated territorial intrusions, providing support for the Challenge Hypothesis in a territorial frog.
Hematological parameters of high and low altitude Tibetan populations
Authors: Basak Nipa , Norboo Tsering , Mustak Mohammed S. , Thangaraj Kumarasamy
Published: November 2020

High altitude hypoxia is believed to be experienced at elevations more than 2500 meters. A few studies have shed light on the biochemical aspects of high altitude acclimatization that profoundly included the subjects sojourning to the high altitude from low altitude and observation of the transient changes. However, information regarding the difference between the adapted people in high altitude and their counterpart, who reside in the low altitude are lacking. To address that issue, we have measured various hematological parameters and level of serum erythropoietin (EPO) in Tibetan population, who are residing in both high and low altitudes. We observed significant difference (p value < 0.0001) between high and low altitude Tibetan, in various hematological parameters, including red blood cells (RBC) count, hematocrit (HCT) or packed cell volume (PCV), and hemoglobin concentration (Hb). In case of mean corpuscular volume (MCV), significant difference was observed only in females (p value < 0.0001). Mean corpuscular hemoglobin concentration (MCHC) was significantly different between both males and females, but age was a potential confounder. There was no significant difference in serum EPO level between these two groups, either in males or females, which might be due to blunted erythropoietin response in the Tibetan population. We have also analyzed correlation between serum EPO with Hb and serum EPO with HCT and found no significant correlation. In multiple regression analysis, low altitude and male-gender showed significant impact on both Hb and HCT. In conclusion, our study suggests significant perturbation of hematological parameters, when native high altitude populations migrated to low altitude and inhabited for a long period.
Sensitivity to Immune Checkpoint Blockade and Progression-Free Survival is associated with baseline CD8+T cell clone size and cytotoxicity
Authors: Watson RA , Tong O , Cooper R , Taylor CA , Sharma PK , Verge de Los Aires A , Mahé EA , Ruffieux H , Nassiri I , Middleton MR , Fairfax BP
Published: November 2020

Immune checkpoint blockers (ICB) exert their anti-cancer effects via CD8+T cells, although how responses vary over sub-populations and across clones is incompletely understood. We performed single-cell RNA-sequencing of CD8+T cells and their receptors pre- and post-ICB across eight patients, integrating results with bulk-sequencing data (n=209). We identify seven subsets with divergent responses to ICB, finding the effector cluster demonstrates the most pronounced changes. Likewise, transcriptomic response to ICB relates to clone size, with large clones demonstrating increased numbers of regulated genes of higher immunological pertinence. Cytotoxic effector clones were more likely to persist long-term following ICB and overlapped with public tumour-infiltrating lymphocyte clonotypes. Notably, pre-treatment CD8+cytotoxicity associated with progression-free survival, highlighting the importance of the baseline CD8+immune landscape in long-term response. This work further advances understanding of the molecular determinants of ICB response and assists in the search for peripheral prognostic biomarkers.

ONE SENTENCE SUMMARY

Using single-cell and bulk RNA sequencing we explore checkpoint immunotherapy activity on peripheral CD8+T cells in metastatic melanoma; demonstrating that cell subset and clone size determine gene expression responses to treatment, and that pre-treatment cytotoxicity and clonality of peripheral CD8+T cells is clinically prognostic.
Active Participation of Membrane Lipids in Inhibition of Multidrug Transporter P-Glycoprotein
Authors: Kapoor Karan , Pant Shashank , Tajkhorshid Emad
Published: November 2020

P-glycoprotein (Pgp) is a major efflux pump in humans, overexpressed in a variety of cancers and associated with the development of multi-drug resistance. Allosteric modulation by various ligands (e.g., transport substrates, inhibitors, and ATP) has been biochemically shown to directly influence structural dynamics, and thereby, the function of Pgp. However, the molecular details of such effects, particularly with respect to the role and involvement of the surrounding lipids, are not well established. Here, we employ all-atom molecular dynamics (MD) simulations to study the conformational landscape of Pgp in the presence of a high-affinity, third-generation inhibitor, tariquidar, in comparison to the nucleotide-free (APO) and the ATP-bound states, in order to characterize the mechanical effects of the inhibitor that might be of relevance to its blocking mechanism of Pgp. Simulations in a multi-component lipid bilayer show a dynamic equilibrium between open(er) and more closed inward-facing (IF) conformations in the APO state, with binding of ATP shifting the equilibrium towards conformations more prone to ATP hydrolysis and subsequent events in the transport cycle. In the presence of the inhibitor bound to the drug-binding pocket within the transmembrane domain (TMD), Pgp samples more open IF conformations, and the nucleotide binding domains (NBDs) become highly dynamic. Interestingly, and reproduced in multiple independent simulations, the inhibitor is observed to facilitate recruitment of lipid molecules into the Pgp lumen through the two proposed drug-entry portals, where the lipid head groups from the cytoplasmic leaflet penetrate into and, in some cases, translocate inside the TMD, while the lipid tails remain extended into the bulk lipid environment. These “wedge” lipids likely enhance the inhibitor-induced conformational restriction of the TMD leading to the differential modulation of coupling pathways observed with the NBDs downstream. We suggest a novel inhibitory mechanism for tariquidar, and potentially for related third-generation Pgp inhibitors, where lipids are seen to enhance the inhibitory role in the catalytic cycle of membrane transporters.
Evolutionary rates are correlated betweenBuchneraendosymbionts and mitochondrial genomes of their aphid hosts
Authors: Arab Daej A. , Lo Nathan
Published: November 2020

The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such a correlation between the mitochondrial genomes of cockroaches and the genome of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of bacterial endosymbionts,B. aphidicolaandSulcia mulleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses show a highly significant correlation of molecular rates between genomes ofBuchneraand mitochondrial genomes of their hosts. A similar correlation was detected betweenSulciaand their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.
Anti-CRISPR RNAs: designing universal riboregulators with deep learning of Csy4-mediated RNA processing
Authors: Guo Haotian , Song Xiaohu , Lindner Ariel B.
Published: November 2020

RNA-based regulation offers a promising alternative of protein-based transcriptional networks. However, designing synthetic riboregulators with desirable functionalities using arbitrary sequences remains challenging, due in part to insufficient exploration of RNA sequence-to-function landscapes. Here we report that CRISPR-Csy4 mediates a nearly all-or-none processing of precursor CRISPR RNAs (pre-crRNAs), by profiling Csy4 binding sites flanked by > 1 million random sequences. This represents an ideal sequence-to-function space for universal riboregulator designs. Lacking discernible sequence-structural commonality among processable pre-crRNAs, we trained a neural network for accurate classification (f1-score ≈ 0.93). Inspired by exhaustive probing of palindromic flanking sequences, we designed anti-CRISPR RNAs (acrRNAs) that suppress processing of pre-crRNAs via stem stacking. We validated machine-learning-guided designs with >30 functional pairs of acrRNAs and pre-crRNAs to achieve switch-like properties. This opens a wide range of plug-and-play applications tailored through pre-crRNA designs, and represents a programmable alternative to protein-based anti-CRISPRs.
The bone microenvironment invigorates metastatic seeds for further dissemination
Authors: Zhang Weijie , Bado Igor L. , Wang Hai , Singh Swarnima , Lo Hin-Ching , Niu Muchun , Xu Zhan , Liu Jun , Jiang Weiyu , Li Yi , Hu Jingyuan , Zhang Xiang H.-F.
Published: November 2020

Metastasis has been considered as the terminal step of tumor progression. However, recent clinical studies suggest that many metastases are seeded from other metastases, rather than primary tumors. Thus, some metastases can further spread, but the corresponding pre-clinical models are lacking. By using several approaches including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. Importantly, dissemination from the bone microenvironment appears to be more aggressive compared to that from mammary tumors and lung metastases. We further uncovered that this metastasis-promoting effect is independent from genetic selection, as single cell-derived cancer cell populations (SCPs) exhibited enhanced metastasis capacity after being extracted from the bone microenvironment. Taken together, our work revealed a previously unappreciated effect of the bone microenvironment on metastasis evolution, and suggested a stable reprogramming process that engenders cancer cells more metastatic.
Spatiotemporal sensitivity of embryonic heart specification to FGFR signaling inDrosophila
Authors: Yadav V. , Tolwinski N. , Saunders T. E.
Published: November 2020

Development of theDrosophilaembryonic mesoderm is controlled through both internal and external inputs to the mesoderm. One such factor is Heartless (Htl), a Fibroblast Growth Factor Receptor (FGFR) expressed in the mesoderm. Htl is involved in shaping the mesoderm at both early and later stages during embryogenesis. How Htl expression levels and timing of signaling affect mesoderm morphogenesis after spreading remains elusive. We have developed an optogenetic tool (Opto-htl) to control the activation of Htl signaling with precise spatiotemporal resolutionin vivo. We find that the embryo is most sensitive to Htl over-activation within a developmental window of ~4 hours ranging from late stage 10 until early stage 13, which corresponds to early stages of heart morphogenesis. Opto-htl restores heart cells inhtlmutants upon light activation, independent of its role in early mesoderm shaping events. We also successfully generated spatially distinct regions of Htl activity in the mesoderm using light-sheet microscopy. The developing tissue was unable to correct for the ensuing asymmetries in cell fate. Overall, Opto-htl is a powerful tool for studying spatiotemporal regulation of Htl signaling during embryogenesis.
Modelling species presence-only data with random forests
Authors: Valavi Roozbeh , Elith Jane , Lahoz-Monfort José J. , Guillera-Arroita Gurutzeta
Published: November 2020

The Random Forest (RF) algorithm is an ensemble of classification or regression trees, and is a widely used and high-performing machine learning technique. It is increasingly used for species distribution modelling (SDM). Many researchers use implementations of RF in the R programming language with default parameters to analyse species presence-only data together with background samples. However, there is good evidence that RF with default parameters does not perform well with such species “presence-background” data. This is often attributed to the typical disparity between the number of presence and background samples also known asclass imbalance, and several solutions have been proposed.

Here, we first set the context: the background sample should be large enough to represent all environments in the region. We then aim to understand the drivers of poor performance of RF with presence-background data, and explain, test and evaluate suggested solutions. Using simulated and real species data, we compare performance of default RF with other weighting and sampling approaches.

We show thatclass overlapis an important driver of poor performance, alongside class imbalance. The results demonstrate clear evidence of improvement in the performance of RFs when class imbalance is explicitly managed by sampling methods or when the overfitting commonly associated with overlapping classes is avoided by forcing shallow trees.

Presence-background data is a particular version of class imbalance in which class overlap is highly likely and extreme imbalance exists. Without compromising the environmental representativeness of the sampled background, we show several approaches to fitting RF that ameliorate the effects of imbalance and overlap, and allow excellent predictive performance. Understanding the problems of RF in presence-background data allows new insights into how best to fit models, and should guide future efforts to best deal with such data.
The HIV-1 provirus excised by a single CRISPR/Cas9 RNA guide persists in the host cell and may be reactivated
Authors: Lai Michele , Maori Eyal , Quaranta Paola , Matteoli Giulia , Maggi Fabrizio , Sgarbanti Marco , Crucitta Stefania , Pacini Simone , Turriziani Ombretta , Freer Giulia , Antonelli Guido , Heeney Jonathan L. , Pistello Mauro
Published: November 2020

Gene editing may be used to cut out the human immunodeficiency virus type-1 (HIV-1) provirus from the host cell genome and eradicate infection. Here, using cells acutely or latently infected by HIV and treated with long terminal repeat-targeting CRISPR/Cas9, we show that the excised HIV provirus persists for a few weeks and, by means of HIV Integrase, rearranges in circular molecules. Circularization and integration restore proviral transcriptional activity that is enhanced in the presence of exogenous Tat and Rev or tumor necrosis factor-α, respectively, in acutely or latently infected cells. Although confirming that gene editing is a powerful tool to eradicate HIV infection, this work highlights that, to achieve this goal, the provirus has to be cleaved in several pieces and the infected cells treated with antiviral therapy before and after editing.
Resurgence of a perinatal attraction for animate objects via thyroid hormone T3
Authors: Lorenzi Elena , Lemaire Bastien S. , Versace Elisabetta , Matsushima Toshiya , Vallortigara Giorgio
Published: November 2020

For inexperienced brains, some stimuli are more attractive than others. Human neonates and newly-hatched chicks preferentially orient towards face-like stimuli, biological motion, and objects changing speed. In chicks, this enhances exposure to social partners, and subsequent attachment trough filial imprinting. Early preferences are not steady. The preference for stimuli changing speed fades away after three days in chicks. To understand the physiological mechanisms underlying these transient responses, we tested whether the early preferences for objects changing speed can be promoted by thyroid hormone 3,5,3’-triiodothyronine (T3). This hormone determines the start of imprinting’s sensitive period. We found that the preference for objects changing speed can be re-established in female chicks treated with T3. Moreover, day-one chicks treated with an inhibitor of endogenous T3did not show any preference. These results suggest that the time windows of early predispositions and of high plasticity are controlled by the same molecular mechanisms.
Hexarelin exerts neuroprotective and antioxidant effects against hydrogen peroxide-induced toxicity through the modulation of MAPK and PI3K/Akt patways in Neuro-2A cells
Authors: Meanti Ramona , Rizzi Laura , Bresciani Elena , Molteni Laura , Locatelli Vittorio , Coco Silvia , Omeljaniuk Robert J. , Torsello Antonio
Published: November 2020

Hexarelin, a synthetic hexapeptide, protects cardiac and skeletal muscles by inhibiting apoptosis, bothin vitroandin vivo. Moreover, evidence suggests that hexarelin could have important neuroprotective bioactivity.

Oxidative stress and the generation of free radicals has been implicated in the etiologies of several neurodegenerative diseases, including amyotrophic lateral sclerosis, Parkinson’s disease, Alzheimer’s disease, Huntington’s disease and multiple sclerosis. In addition to direct oxidative stress, exogenous hydrogen peroxide (H2O2) can penetrate biological membranes and enhance the formation of other reactive oxygen species.

The aim of this study was to examine the inhibitory influence of hexarelin on H2O2-induced apoptosis in Neuro-2A cells, a mouse neuroblastoma cell line. Our results indicate that H2O2reduced the viability of Neuro-2A cells in a dose-related fashion. Furthermore, H2O2induced significant changes in the morphology of Neuro-2A cells, reflected in the formation of apoptotic cell bodies, and an increase of nitric oxide (NO) production. Hexarelin effectively antagonized H2O2oxidative damage to Neuro-2A cells as indicated by improved cell viability, normal morphology and reduced nitrite (NO2−) release. Hexarelin treatment of Neuro-2A cells also reduced mRNA levels of caspases−3 and −7 and those of the pro-apoptotic molecule Bax; by contrast, hexarelin treatment increased anti-apoptotic Bcl-2 mRNA levels. Hexarelin also reduced MAPKs phosphorylation induced by H2O2and concurrently increased p-Akt protein expression.

In conclusion, our results identify several neuroprotective and anti-apoptotic effects of hexarelin. These properties suggest that further investigation of hexarelin as a neuroprotective agent in an investigational and therapeutic context are merited.
BMSCs differentiated into neurons, astrocytes and oligodendrocytes alleviated the inflammation and demyelination of EAE mice models
Authors: Liu Guo-yi , Wu Yan , Kong Fan-yi , Ma Shu , Fu Li-yan , Geng Jia
Published: November 2020

Multiple sclerosis (MS) is a complex, progressive neuroinflammatory disease associated with autoimmunity. Currently, effective therapeutic strategy was poorly found in MS. Experimental autoimmune encephalomyelitis (EAE) is widely used to study the pathogenesis of MS. Previous studies have shown that bone marrow mesenchymal stem Cells (BMSCs) transplantation could treat EAE animal models, but the mechanism was divergent. Here, we systematically evaluated whether BMSCs can differentiate into neurons, astrocytes and oligodendrocytes to alleviate the symptoms of EAE mice. We used Immunofluorescence staining to detect MAP-2 neurons marker, GFAP astrocytes marker, and MBP oligodendrocytes marker expression to evaluate whether BMSCs can differentiate. The effect of BMSCs transplantation on inflammatory cell invasion and demyelination in EAE mice were detected by Hematoxylin-Eosin (H&E) and Luxol Fast Blue (LFB) staining. Inflammatory factors expression was detected by ELISA and RT-qPCR. Our results showed that BMSCs could be induced to differentiate into neuron cells, astrocytes and oligodendrocyte in vivo and in vitro. In addition, BMSCs transplant improved the survival rate and weight, and reduced neurological function scores and disease incidence of EAE mice. Moreover, BMSCs transplant alleviated the inflammation and demyelination of EAE mice. Finally, we found that BMSCs transplantation down-regulated the expression levels of pro-inflammatory factors TNF-α, IL-1β and IFN-γ, and up-regulated the expression levels of anti-inflammatory factors IL-10 and TGF-β. In conclusion, this study found that BMSCs could alleviate the inflammatory response and demyelination in EAE mice, which may be achieved by the differentiation of BMSCs into neurons, astrocytes and oligodendrocytes in EAE mice.
Social transmission of egg rejection in a cuckoo host
Authors: Yang Canchao , Feeney William E
Published: November 2020

Social learning can enable the rapid dissemination of behaviors throughout a population. Rejection of foreign eggs is a key defense in hosts of avian brood parasites; however, whether social cues can inform whether a host rejects an egg remains unknown. Here, we aimed to determine whether access to social information can influence egg rejection behavior in semi-colonial barn swallows (Hirundo rustica). By manipulating the social information available from a neighboring nest, we found that swallows that had access to social information (i.e. neighbor recently rejected an egg) were more likely to reject a foreign egg compared to those that did not have access to social information (i.e. neighbor did not reject an egg). This result provides the first empirical evidence that egg rejection behavior can solely be informed by social information, and in doing so highlights the dynamic nature of defenses that hosts can deploy against brood parasitism.
Incredible internal strains within a biogenic single crystal viewed by X-ray diffraction tomography
Authors: Seknazi Eva , Zaslansky Paul , Katsman Alex , Villanova Julie , Pokroy Boaz
Published: November 2020

The dorsal arm plates (DAPs) of theOphiocoma Wendtiibrittle star are highly functional single crystalline biominerals whose optimized structure and nanostructure enable them to fullfill mechanical and optical functions in the organism. Here, a large DAP bulk piece is characterized by means of synchrotron X-ray Diffraction Tomography (XRDT). This non-destructive crystallographic characterization revealed an astounding feature: the presence of very high compressive strains which relax when the mineral is cracked or grinded into a powder. Thus, previous destructive characterization techniques did not allow their detection. We attribute the compressive strains to the previously identified high-Mg calcite particles, which are coherently included and thereby compress the low-Mg calcite matrix. The measured slice contained both the bulk DAP sample as well as DAP powder. The data generated by the bulk piece could be separated from those by the powder, and the latter was used to calibrate and interprete the former. This study reveals yet another awe-inspiring feature of a biogenic structure, highlights the importance of non-destructive crystallographic characterization for biominerals, and exemplifies the potential of XRDT use in studying a single crystalline material, as well as the advantage of complementary measurement of bulk and powder for data calibration and interpretation.
Solving the sex ratio scandal inMelittobiawasps
Authors: Abe Jun , Iritani Ryosuke , Tsuchida Koji , Kamimura Yoshitaka , West Stuart A.
Published: November 2020

The scandalous sex ratio behaviour ofMelittobiawasps has long posed one of the greatest problems for the field of sex allocation. In contrast to the predictions of theory, and the behaviour of numerous other organisms, laboratory experiments have found thatMelittobiafemales do not produce less female-biased offspring sex ratios when more females lay eggs on a patch. We resolve this scandal, by showing that, in nature, females ofM. australicahave sophisticated sex ratio behaviour, where their strategy also depends upon whether they have dispersed from the patch where they emerged. When females have not dispersed, they will be laying eggs with close relatives, which keeps local mate competition high, even with multiple females, and so they are selected to produce consistently female-biased sex ratios. Laboratory experiments mimic these conditions. In contrast, when females disperse, they will be interacting with non-relatives, and so they adjust their sex ratio depending upon the number of females laying eggs. Consequently, females appear to use dispersal status as an indirect cue of relatedness, and whether they should adjust their sex ratio in response to the number of females laying eggs on the patch.
CAMP: a Convolutional Attention-based Neural Network for Multifaceted Peptide-protein Interaction Prediction
Authors: Lei Yipin , Li Shuya , Liu Ziyi , Wan Fangping , Tian Tingzhong , Li Shao , Zhao Dan , Zeng Jianyang
Published: November 2020

Peptide-protein interactions (PepPIs) are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. To facilitate the peptide drug discovery process, a number of computational methods have been developed to predict peptide-protein interactions. However, most of the existing prediction approaches heavily depend on high-resolution structure data. Although several deep-learning-based frameworks have been proposed to predict compound-protein interactions or protein-protein interactions, few of them are particularly designed to specifically predict peptide-protein interactions. In this paper, We present a sequence-basedConvolutionalAttention-based neural network forMultifaceted prediction ofPeptide-protein interactions, calledCAMP, including predicting binary peptide-protein interactions and corresponding binding residues in the peptides. We also construct a benchmark dataset containing high-quality peptide-protein interaction pairs with the corresponding peptide binding residues for model training and evaluation. CAMP incorporates convolution neural network architectures and attention mechanism to fully exploit informative sequence-based features, including secondary structures, physicochemical properties, intrinsic disorder features and position-specific scoring matrix of the protein. Systematical evaluation of our benchmark dataset demonstrates that CAMP outperforms the state-of-the-art baseline methods on binary peptide-protein interaction prediction. In addition, CAMP can successfully identify the binding residues involved non-covalent interactions for peptides. These results indicate that CAMP can serve as a useful tool in peptide-protein interaction prediction and peptide binding site identification, which can thus greatly facilitate the peptide drug discovery process. The source code of CAMP can be found inhttps://github.com/twopin/CAMP.
LOXL2 Mediates Airway Smooth Muscle Cell Matrix Stiffness and Drives Asthmatic Airway Remodelling
Authors: Ramis Jopeth , Middlewick Robert , Pappalardo Francesco , Cairns Jennifer T. , Stewart Iain D. , John Alison E. , Naveed Shams-un Nisa , Krishnan Ramaswamy , Miller Suzanne , Shaw Dominick E. , Brightling Christopher E. , Buttery Lee , Rose Felicity , Jenkins Gisli , Johnson Simon R. , Tatler Amanda L
Published: November 2020

Airway smooth muscle cells (ASM) are fundamental to asthma pathogenesis, influencing bronchoconstriction, airway hyper-responsiveness, and airway remodelling. Extracellular matrix (ECM) can influence tissue remodelling pathways, however, to date no study has investigated the effect of ASM ECM stiffness and crosslinking on the development of asthmatic airway remodelling. We hypothesised that TGFβ activation by ASM is influenced by ECM in asthma and sought to investigate the mechanisms involved.

This study combines in vitro and in vivo approaches: human ASM cells were used in vitro to investigate basal TGFβ activation and expression of ECM crosslinking enzymes. Human bronchial biopsies from asthmatic and non-asthmatic donors were used to confirm LOXL2 expression ASM. A chronic ovalbumin model of asthma was used to study the effect of LOXL2 inhibition on airway remodelling.

We found that ASM cells from asthmatics activated more TGFβ basally than non-asthmatic controls and that diseased cell-derived ECM influences levels of TGFβ activated. Our data demonstrate that the ECM crosslinking enzyme LOXL2 is increased in asthmatic ASM cells and in bronchial biopsies. Crucially, we show that LOXL2 inhibition reduces ECM stiffness and TGFβ activation in vitro, and can reduce subepithelial collagen deposition and ASM thickness, two features of airway remodelling, in an ovalbumin mouse model of asthma.

These data are the first to highlight a role for LOXL2 in the development of asthmatic airway remodelling and suggest that LOXL2 inhibition warrants further investigation as a potential therapy to reduce remodelling of the airways in severe asthma.
Self-organization and culture of Mesenchymal Stromal Cell spheroids in acoustic levitation
Authors: Jeger-Madiot Nathan , Arakelian Lousineh , Setterblad Niclas , Bruneval Patrick , Hoyos Mauricio , Larghero Jérôme , Aider Jean-Luc
Published: November 2020

In recent years, 3D cell culture models such as spheroid or organoid technologies have known important developments. Many studies have shown that 3D cultures exhibit better biomimetic properties compared to 2D cultures. These properties are important forin-vitromodeling systems, as well as forin-vivocell therapies and tissue engineering approaches. A reliable use of 3D cellular models still requires standardized protocols with well-controlled and reproducible parameters. To address this challenge, a robust and scaffold-free approach is proposed, which relies on multi-trap acoustic levitation. This technology is successfully applied to Mesenchymal Stromal Cells (MSCs) maintained in acoustic levitation over a 24-hour period. During the culture, MSCs spontaneously self-organized from cell sheets to cell spheroids with a characteristic time of about ten hours. Each acoustofluidic chip could contain up to 30 spheroids in acoustic levitation and four chips could be ran in parallel, leading to the production of 120 spheroids per experiment. Various biological characterizations showed that the cells inside the spheroids were viable, maintained the expression of their cell surface markers and had a higher differentiation capacity compared to standard 2D culture conditions. These results open the path to long-time cell culture in acoustic levitation of cell sheets or spheroids for any type of cells.
SeqStain using fluorescent-DNA conjugated antibodies allows efficient, multiplexed, spatialomic profiling of human and murine tissues
Authors: Rajagopalan Anugraha , Venkatesh Ishwarya , Aslam Rabail , Kirchenbuechler David , Khanna Shreyaa , Cimbaluk David , Gupta Vineet
Published: November 2020

Spatial organization of molecules and cells in complex tissue microenvironments provides essential cues during healthy growth and in disease. Novel techniques are needed for elucidation of their spatial relationships and architecture. Although a few multiplex immunofluorescence based techniques have been developed for visualization of the spatial relationships of various molecules in cells and tissues, there remains a significant need for newer methods that are rapid, easy to adapt and are gentle during the cyclic steps of fluorescence staining and de-staining. Here, we describe a novel, multiplex immunofluorescence imaging method, termed SeqStain, that uses fluorescent-DNA labelled antibodies for immunofluorescence staining of cells and tissues, and nuclease treatment for de-staining that allows selective enzymatic removal of the fluorescent signal. SeqStain can be used with primary antibodies, secondary antibodies and antibody fragments, such as Fabs, to efficiently analyse complex cells and tissues in multiple rounds of staining and de-staining. Additionally, incorporation of specific endonuclease restriction sites in antibody labels allows for selective removal of fluorescent signals, while retaining other signals that can serve as marks for subsequent analyses. The application of SeqStain on human kidney tissue provided spatialomic profile of the organization of >25 markers in the kidney, highlighting it as a versatile, easy to use and gentle new technique for spatialomic analyses of complex microenvironments.
Rapid evolution and horizontal gene transfer in the genome of a male-killingWolbachia
Authors: Hill Tom , Unckless Robert L. , Perlmutter Jessamyn I.
Published: November 2020

Wolbachiaare widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains ofWolbachiahave some striking effects on their hosts. In some cases, these symbionts manipulate host reproduction to increase the fitness of infected, transmitting females. Here we examine the genome and population genomics of a male-killingWolbachiastrain,wInn, that infectsDrosophila innubilamushroom-feeding flies. We comparedwInn to other closely-relatedWolbachiagenomes to understand the evolutionary dynamics of specific genes. ThewInn genome is similar in overall gene content towMel, but also contains many unique genes and repetitive elements that indicate distinct gene transfers betweenwInn and non-Drosophilahosts. We also find that genes in theWolbachiaprophage and Octomom regions are particularly rapidly evolving, including those putatively or empirically confirmed to be involved in host pathogenicity. Of the genes that rapidly evolve, many also show evidence of recent horizontal transfer amongWolbachiasymbiont genomes, suggesting frequent movement of rapidly evolving regions among individuals. These dynamics of rapid evolution and horizontal gene transfer across the genomes of severalWolbachiastrains and divergent host species may be important underlying factors inWolbachia’s global success as a symbiont.
Sex-specific plasticity and the nutritional geometry of insulin-signaling gene expression inDrosophila melanogaster
Authors: McDonald Jeanne M.C. , Nabili Pegah , Thorsen Lily , Jeon Sohee , Shingleton Alexander
Published: November 2020

1.

Background

Sexual-size dimorphism (SSD) is replete among animals, but while the selective pressures that drive the evolution of SSD have been well studied, the developmental mechanisms upon which these pressures act are poorly understood. Ours and others’ research has shown that SSD inDrosophilareflects elevated levels of nutritional plasticity in females versus males, such that SSD increases with dietary intake and body size, a phenomenon called sex-specific plasticity (SSP). Additional data indicate that while body size in both sexes responds to variation in protein level, only female body size is sensitive to variation in carbohydrate level. Here we explore whether these difference in sensitivity at the morphological level are reflected by differences in how the insulin/IGF-signaling (IIS) and TOR-signaling pathways respond to changes in carbohydrates and proteins in females versus males, using a nutritional geometry approach.

Results

The IIS-regulated transcripts of4E-BPandInRmost strongly correlated with body size in females and males respectively, but neither responded to carbohydrate level and so could not explain the sex-specific response to body size to dietary carbohydrate. Transcripts regulated by TOR-signaling did, however, respond to dietary carbohydrate in a sex-specific manner. In females, expression ofdILP5positively correlated with body size, while expression ofdILP2,3and8,was elevated on diets with a low concentration of both carbohydrate and protein. In contrast, we detected lower levels of dILP2 and 5 protein in the brains of females fed on low concentration diets. We could not detect any effect of diet ondILPexpression in males.

Conclusion

Although females and males show sex-specific transcriptional responses to changes in protein and carbohydrate, the patterns of expression do not support a simple model of the regulation of body-size SSP by either insulin-or TOR-signaling. The data also indicate a complex relationship between carbohydrate and protein level,dILPexpression and dILP peptide levels in the brain. In general, diet quality and sex both affect the transcriptional response to changes in diet quantity, and so should be considered in future studies that explore the effect of nutrition on body size.
Novel quaternary structures of the human prion protein globular domain
Authors: Bortot Leandro Oliveira , Rangel Victor Lopes , Pavlovici Francesca A. , Omari Kamel El , Wagner Armin , Brandao-Neto Jose , Talon Romain , von Delft Frank , Reidenbach Andrew G , Vallabh Sonia M , Minikel Eric Vallabh , Schreiber Stuart , Nonato Maria Cristina
Published: November 2020

Prion disease is caused by the misfolding of the cellular prion protein, PrPC, into a self-templating conformer, PrPSc. Nuclear magnetic resonance (NMR) and X-ray crystallography revealed the 3D structure of the globular domain of PrPC and the possibility of its dimerization via an interchain disulfide bridge that forms due to domain swap or by non-covalent association of two monomers. On the contrary, PrPSc is composed by a complex and heterogeneous ensemble of poorly defined conformations and quaternary arrangements that are related to different patterns of neurotoxicity. Targeting PrPC with molecules that stabilize the native conformation of its globular domain emerged as a promising approach to develop anti-prion therapies. One of the advantages of this approach is employing structure-based drug discovery methods to PrPC. Thus, it is essential to expand our structural knowledge about PrPC as much as possible to aid such drug discovery efforts. In this work, we report a crystallographic structure of the globular domain of human PrPC that shows a novel dimeric form and a novel oligomeric arrangement. We use molecular dynamics simulations to explore its structural dynamics and stability and discuss potential implications of these new quaternary structures to the conversion process.
New capabilities for enhancement of RMCProfile: instrumental profiles with arbitrary peak shapes for structural refinements using the reverse Monte Carlo method
Authors: Zhang Yuanpeng , Eremenko Maksim , Krayzman Victor , Tucker Matthew G. , Levin Igor
Published: November 2020

Reported here are the development and application of new capabilities in the RMCProfile software for structural refinements using the reverse Monte Carlo (RMC) method. An algorithm has been implemented to enable the use of arbitrary peak-shape functions in the modeling of Bragg diffraction patterns and instrumental resolution effects on total-scattering data. This capability eliminates the dependence of RMCProfile on preset functions, which are inadequate for data produced by some total-scattering instruments, e.g. NOMAD at the Spallation Neutron Source (SNS) at Oak Ridge, Tennessee, USA. The recently developed procedure for the instrument-resolution correction has been modified to improve its accuracy, which is critical for recovering nanoscale structure. The ability to measure fine details of local and nanoscale structures with high fidelity is required because such features are increasingly exploited in the design of materials with enhanced functional properties. The new methodology has been tested via RMC refinements of large-scale atomic configurations (distances up to 8 nm) for SrTiO3 using neutron total-scattering data collected on the Polaris and NOMAD time-of-flight powder diffractometers at the ISIS facility (Didcot, Oxfordshire, UK) and SNS, respectively. While the Polaris instrument is known to provide the high-quality data needed for RMC analysis, the similar and sound atomic configurations obtained from both instruments confirmed that the NOMAD data are also suitable for RMC refinements over a broad distance range.
High-pressure sapphire capillary cell for synchrotron single-crystal X-ray diffraction measurements to 1500 bar
Authors: McMonagle Charles J. , Allan David R. , Warren Mark R. , Kamenev Konstantin V. , Turner Gemma F. , Moggach Stephen A.
Published: November 2020

A new sapphire capillary pressure cell for single-crystal X-ray diffraction measurements at moderate pressures (200−1500 bar; 1 bar = 100 kPa) has been developed and optimized for use on beamline I19 at Diamond Light Source. The three-component cell permits optical centring of the crystal andin situpressure modification to a precision of 1 bar. Compression of hexamethylenetetramine and its deuterated analogue to 1000 bar was performed, showcasing the accuracy and precision of the measurements, and highlighting evidence of a geometric isotope effect.
Crystal structure of 2-[(naphthalen-2-yl)methyl]isothiouronium bromide
Authors: Eigner Václav
Published: November 2020

Herein we report the crystal structure of 2-[(naphthalen-2-yl)methyl]isothiouronium bromide, C12H13N2S+·Br−, which crystallizes in the monoclinicP21/ccentrosymmetric space group. The asymmetric unit contains one 2-[(naphthalen-2-yl)methyl]isothiouronium cation and one bromide anion. The methylene carbon lies in plane of the naphthalene core. In comparison with reference structures, elongation of C—S bonds as well as tilting of the isothiouronium group is observed. Given the ionic nature of the compound, the structure is held by charge-assisted N—H...Br hydrogen bonds, with a noteworthy contribution of dipole–dipole interactions, which form bilayers in the structure. The bilayers are held by the weak London forces.
Re-evaluating the risk costing agenda in PPP projects
Authors: Almarri Khalid , Boussabaine Halim
Published: November 2020

Purpose

The level at which risk is priced and the magnitude of risks transferred to the private sector will have a significant impact on the cost of the public–private partnership (PPP) deals as well as on the value for money analysis and on the section of the optimum investment options. The price of risk associated with PPP schemes is complex, dynamic and continuous throughout the concession agreement. Risk allocation needs to be re-evaluated to ensure the optimum outcome of the PPP contract.

Design/methodology/approach

This paper provides a coherent theoretical framework for dealing with scenarios of potential gain and loss from retaining or transferring risks.

Findings

The outcome indicates that using the proposed framework will provide innovative ways of deriving risk prices in PPP projects using several risk determinants strategies.

Practical implications

In costing risks, analysts have to take into consideration the balance between the cost of risk transfer and the cost of losses if risk is retained.

Originality/value

This paper contributes to the PPP literature and practice by proposing a framework which is consistent with a risk allocation approach in PPP projects, where the key proposition is that risk pricing can overload project debt leading to loss of value.
Exploring the career trajectories of Black male educators in p-12 education
Authors: Underwood Kimberly , Taylor Joy , Smith Donna , Roberts J. Medgar
Published: November 2020

Purpose

This paper aims to provide a critical examination of the career trajectories of Black male educators through the discussion of key issues relevant to the professional development and advancement of this population.

Design/methodology/approach

The authors approach this paper through the examination of literature related to Black male educators. The authors seek to provide insight into the status of Black male educators through a critical focus of scholarship in the three critical areas of Black male educator recruitment, retention and mobility.

Findings

This examination supports the need to generate sustainable initiatives to diversify our nation’s classrooms and create additional opportunities for Black male representation in school leadership positions. Effectively dismantling the entrenched hurdles many encounter within their teaching careers requires a concerted commitment by advocates, policymakers and school administrators at all levels. Additionally, there is a continued need for stakeholders to keep the diversification of P-12 schools as a key priority in current education reform strategies.

Social implications

This paper serves as an impetus to highlight the continued need for further exploration and consequential action to increase the numbers of Black males in the teaching profession.

Originality/value

This paper adds to the literature surrounding Black male educators by providing a holistic view of their career trajectories of Black male educators and shedding light on the need for ongoing efforts to diversify the P-12 teaching workforce.
A networked public: formal and relational approaches to the public sphere
Authors: Erikson Emily A.
Published: November 2020

Purpose

The purpose of this paper is to explore the potential for conceptualizing the public sphere through the tools of network analysis.

Design/methodology/approach

To do so, this paper combines comparative historical analysis of the early modern expansion of the public sphere with a review of relevant literature and logical exposition.

Findings

The paper develops several hypotheses about the potential of the approach and areas that may require advances in methodology and additional theoretical development.

Originality/value

The paper encourages the development and use of formal approaches for the analysis and conceptualization of the public sphere.