bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the impact of disruptions in lymphatic filariasis elimination programmes due to the outbreak of coronavirus disease (COVID-19) and possible mitigation strategies
Authors: Prada Joaquín M. , Stolk Wilma A. , Davis Emma L. , Touloupou Panayiota , Sharma Swarnali , Muñoz Johanna , Caja Rivera Rocio M. , Reimer Lisa J. , Michael Edwin , de Vlas Sake J , Hollingsworth T Déirdre
Published: November 2020

Background

In view of the current global COVID-19 pandemic, mass drug administration interventions for neglected tropical diseases, including lymphatic filariasis, have been halted. We used mathematical modelling to estimate the impact of delaying or cancelling treatment rounds and explore possible mitigation strategies.

Methods

We used three established lymphatic filariasis transmission models to simulate infection trends in settings with annual treatment rounds and programme delays in 2020 of 6, 12, 18 or 24 months. We then evaluated the impact of various mitigation strategies upon resuming activities.

Results

The delay in achieving the elimination goals is on average similar to the number of years the treatment rounds are missed. Enhanced interventions implemented for as little as one year can allow catch-up on the progress lost, and if maintained throughout the programme can lead to acceleration of up to 3 years.

Conclusions

In general, a short delay in the programme does not cause major delay in achieving the goals. Impact is strongest in high endemicity areas. Mitigation strategies such as biannual treatment or increased coverage are key to minimizing the impact of the disruption once the programme resumes; and lead to potential acceleration, should these enhanced strategies be maintained.
Ex vivoosteochondral test system with control over cartilage defect depth – a pilot study to investigate the effect of oxygen tension and chondrocyte-based treatments in chondral and full thickness defects in an organ model
Authors: Schwab Andrea , Buss Alexa , Pullig Oliver , Ehlicke Franziska
Published: November 2020

Objective

Cartilage defect treatment strategies are dependent on the lesion size and severity. Osteochondral explants models are a platform to test cartilage repair strategiesex vivo. Current models lack in mimicking the variety of clinically relevant defect scenarios. In this controlled laboratory study, an automated device (artificial tissue cutter, ARTcut®) was implemented to reproducible create cartilage defects with controlled depth. In a pilot study, the effect of cartilage defect depth and oxygen tension on cartilage repair was investigated.

Design

Osteochondral explants were isolated from porcine condyles. 4 mm chondral and full thickness defects were treated with either porcine chondrocytes (CHON) or co-culture of 20 % CHON and 80 % MSC (MIX) embedded in collagen hydrogel. Explants were cultured with tissue specific media (without TGF-β) under normoxia (20 % O2) and physiological hypoxia (2 % O2). After 28 days, immune-histological stainings (Collagen II and X, Aggrecan) were scored (modified Bern-score, 3 independent scorer) to quantitatively compare treatments outcome.

Results

ARTcut®represents a software-controlled device for creation of uniform cartilage defects. Comparing the scoring results of the MIX and the CHON treatment, a positive relation between oxygen tension and defect depth was observed. Low oxygen tension stimulated cartilaginous matrix deposition in MIX group in chondral defects and CHON treatment in full thickness defects.

Conclusion

ARTcut®has proved a powerful tool to create cartilage defects and thus opens a wide range of novel applications of the osteochondral model, including the relation between oxygen tension and defect depth on cartilage repair.
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
Authors: Song Hanbing , Weinstein Hannah N.W. , Allegakoen Paul , Wadsworth Marc H. , Xie Jamie , Yang Heiko , Feng Felix Y. , Carroll Peter R. , Wang Bruce , Cooperberg Matthew R. , Shalek Alex K. , Huang Franklin W.
Published: November 2020

Prostate cancer is the second most common malignancy in men worldwide and consists of a mixture of tumor and non-tumor cell types. To characterize the prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients. We identify a population of tumor-associated club cells that may act as progenitor cells and uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer.ERG- tumor cells, compared toERG+ cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids recapitulate tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues. Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.
Recurrent chromosomal imbalances provide selective advantage to human embryonic stem cells under enhanced replicative stress conditions
Authors: Mus Liselot M. , Van Haver Stéphane , Popovic Mina , Trypsteen Wim , Lefever Steve , Zeltner Nadja , Ogando Yudelca , Jacobs Eva Z. , Denecker Geertrui , Sanders Ellen , Van Neste Christophe , Vanhauwaert Suzanne , Decaesteker Bieke , Deforce Dieter , Van Nieuwerburgh Filip , Mestdagh Pieter , Vandesompele Jo , Menten Björn , De Preter Katleen , Studer Lorenz , Heindryckx Björn , Durinck Kaat , Roberts Stephen , Speleman Frank
Published: November 2020

Human embryonic stem cells (hESCs) and embryonal tumors share a number of common features including a compromised G1/S checkpoint. Consequently, these rapidly dividing hESCs and cancer cells undergo elevated levels of replicative stress which is known to induce genomic instability causing chromosomal imbalances. In this context, it is of interest that long-termin vitrocultured hESCs exhibit a remarkable high incidence of segmental DNA copy number gains, some of which are also highly recurrent in certain malignancies such as 17q gain (17q+). The selective advantage of DNA copy number changes in these cells has been attributed to several underlying processes including enhanced proliferation. We hypothesized that these recurrent chromosomal imbalances become rapidly embedded in the cultured hESCs through a replicative stress driven Darwinian selection process. To this end, we compared the effect of hydroxyurea induced replicative stress versus normal growth conditions in an equally-mixed cell population of isogenic euploid and 17q+ hESCs. We could show that 17q+ hESCs rapidly overtook normal hESCs. Our data suggest that recurrent chromosomal segmental gains provide a proliferative advantage to hESCs under increased replicative stress, a process that may also explain the highly recurrent nature of certain imbalances in cancer.
Molecular hallmarks of heterochronic parabiosis at single cell resolution
Authors: Pálovics Róbert , Keller Andreas , Schaum Nicholas , Tan Weilun , Fehlmann Tobias , Borja Michael , Webber James , McGeever Aaron , Bonanno Liana ,   The Tabula Muris Consortium, Pisco Angela Oliveira , Karkanias Jim , Neff Norma F. , Darmanis Spyros , Quake Stephen R. , Wyss-Coray Tony
Published: November 2020

Slowing or reversing biological ageing would have major implications for mitigating disease risk and maintaining vitality. While an increasing number of interventions show promise for rejuvenation, the effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. We performed single-cell RNA-sequencing on 13 organs to reveal cell type specific responses to young or aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, hematopoietic stem cells, hepatocytes, and endothelial cells from multiple tissues appear especially responsive. On the pathway level, young blood invokes novel gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. Intriguingly, we observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it. Altogether, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.
CoBRA: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis - from differential peak calling to pathway analysis
Authors: Qiu Xintao , Feit Avery S. , Feiglin Ariel , Xie Yingtian , Kesten Nikolas , Taing Len , Perkins Joseph , Zhou Ningxuan , Gu Shengqing , Li Yihao , Cejas Paloma , Jeselsohn Rinath , Brown Myles , Liu X. Shirley , Long Henry W.
Published: November 2020

ChIP-seq and ATAC-seq have become essential technologies used as effective methods of measuring protein-DNA interactions and chromatin accessibility. However, there is a need for a scalable and reproducible pipeline that incorporates correct normalization between samples, adjustment of copy number variations, and integration of new downstream analysis tools. Here we present CoBRA, a modularized computational workflow which quantifies ChIP and ATAC-seq peak regions and performs unsupervised and supervised analysis. CoBRA provides a comprehensive state-of-the-art ChIP and ATAC-seq analysis pipeline that is usable by scientists with limited computational experience. This enables researchers to gain rapid insight into protein-DNA interactions and chromatin accessibility through sample clustering, differential peak calling, motif enrichment, comparison of sites to a reference DB and pathway analysis.

Code availability:https://bitbucket.org/cfce/cobra
Implementing the precautionary approach into fisheries management: Making the case for probability-based harvest control rules
Authors: Mildenberger Tobias K. , Berg Casper W. , Kokkalis Alexandros , Hordyk Adrian R. , Wetzel Chantel , Jacobsen Nis S. , Punt André E. , Nielsen J. Rasmus
Published: November 2020

The precautionary approach to fisheries management advocates for risk-averse management strategies that include biological reference points as well as decision rules and account for scientific uncertainty. In this regard, two approaches have been recommended: (i) harvest control rules (HCRs) with threshold reference points to safeguard against low stock biomass, and (ii) theP* method, a ‘probability-based HCR’ that reduces the catch limit as a function of scientific uncertainty (i.e. process, model, and observation uncertainty). This study compares the effectiveness of these precautionary approaches in recovering over-exploited fish stocks with various life-history traits and under a wide range of levels of scientific uncertainty. We use management strategy evaluation based on a stochastic, age-based operating model with quarterly time steps and a stochastic surplus production model. The results show that the most effective HCR includes both a biomass threshold as well as theP* method, and leads to high and stable long-term yield with a decreased risk of low stock biomass. For highly dynamics stocks, management strategies that aim for higher biomass targets than the traditionally usedBMSYresult in higher long-term yield. This study makes the case for probability-based HCRs by demonstrating their benefit over deterministic HCRs and provides a list of recommendations regarding their definition and implementation.
Time-course in attractiveness of pheromone lure on the smaller tea tortrix moth: a generalized additive mixed model approach
Authors: Sudo Masaaki , Sato Yasushi , Yorozuya Hiroshi
Published: November 2020

Long-term pest insect monitoring in agriculture and forestry has advanced population ecology. However, the discontinuation of research materials such as pheromone lure products jeopardizes data collection continuity, which constrains the utilization of the industrial datasets in ecology. Three pheromone lures against the smaller tea tortrix mothAdoxophyes honmaiYasuda (Lepidoptera; Tortricidae) were available but one was recently discontinued. Hence, a statistical method is required to convert data among records of moths captured with different lures. We developed several generalized additive mixed models (GAMM) separating temporal fluctuation in the background male density during trapping and attenuation of lure attractiveness due to aging or air exposure after settlement. We collected multisite trap data over four moth generations. The lures in each of these were unsealed at different times before trap settlement. We used cross-validation to select the model with the best generalization performance. The preferred GAMM had nonlinear density fluctuation terms and lure attractiveness decreased exponentially after unsealing. The attenuation rates varied among lures. A light trap dataset near the pheromone traps was a candidate for a male density predictor. Nevertheless, there was only a weak correlation between trap yields, suggesting the difficulty of data conversion between the traps differing in attraction mechanisms.
Function and regulation of chloroplast peroxiredoxin IIE
Authors: Dreyer Anna , Treffon Patrick , Basiry Daniel , Jozefowicz Anna Maria , Matros Andrea , Mock Hans-Peter , Dietz Karl-Josef
Published: November 2020

Peroxiredoxins (PRX) are thiol peroxidases which are highly conserved throughout all biological kingdoms. Increasing evidence suggests that their high reactivity toward peroxides has a function not only in antioxidant defense but in particular in redox regulation of the cell. Peroxiredoxin IIE is one of three PRX types found in plastids and has previously been linked to pathogen defense and protection from protein nitration. However, its posttranslational regulation and its function in the chloroplast protein network remained to be explored. Using recombinant protein, it was shown that the peroxidatic Cys121 is subjected to multiple posttranslational modifications, namely disulfide formation, S-nitrosation, S-glutathionylation and hyperoxidation. Slightly oxidized glutathione fostered S-glutathionylation and inhibited activityin vitro. Immobilized recombinant PRX-IIE allowed trapping and subsequent identification of interaction partners by mass spectrometry. Interaction with the 14-3-3 ν protein was confirmedin vitroand was shown to be stimulated under oxidizing conditions. Interactions did not depend on phosphorylation as revealed by testing phospho-mimicry variants of PRX-IIE. Based on these data it is proposed that 14-3-3ν guides PRX-IIE to certain target proteins, possibly for redox regulation. These findings together with the other identified potential interaction partners of type II PRXs localized to plastids, mitochondria and cytosol provide a new perspective on the redox regulatory network of the cell.
Target-driven design of a coumarinyl chalcone scaffold based novel EF2 Kinase inhibitor suppresses breast cancer growthin vivo
Authors: Onder Ferah Comert , Kahraman Nermin , Atici Esen Bellur , Cagir Ali , Kandemir Hakan , Tatar Gizem , Tok Tugba Taskin , Karliga Bekir , Durdagi Serdar , Ay Mehmet , Ozpolat Bulent
Published: November 2020

Eukaryotic elongation factor 2 kinase (eEF-2K), an unusual alpha kinase, is involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is indicated as one of the critical drivers of breast cancer and associated with poor clinical prognosis, representing a potential molecular target. The crystal structure of eEF-2K is unknown and there is no potent and effective eEF-2K inhibitor reported for clinical applications. To meet this challenge, we designed and synthesized several generations of potential inhibitor compounds and performedin silicostudies. The effect of the inhibitors at the binding pocket of eEF-2K is analyzed after developing a 3D target model by homology modeling approaches using a domain of another α-kinase called myosin heavy-chain kinase A (MHCKA) that is closely resembling eEF-2K. Our results showed that compounds with coumarin-chalcone cores have a high predicted binding affinity for binding to eEF-2K. Followingin vitrostudies, we identified a compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and inhibited proliferation of various breast cancer cells with different features (BT20, MDA-MB-231, MDA-MB-436 and MCF-7) by induction of apoptosis while sparing normal cells.In vivosystemic administration of the the lead inhibitor encapsulated in single lipid-based nanoparticles twice a week significantly supressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice. In conclusion, our study provides the firstin vivoeffective small molecule eEF-2K inhibitor that may be used for molecularly targeted precison medicine strategies in breast cancer or other eEF-2K-dependent tumors.
Microbiota-root-shoot axis modulation by MYC2 favoursArabidopsisgrowth over defence under suboptimal light
Authors: Hou Shiji , Thiergart Thorsten , Vannier Nathan , Mesny Fantin , Ziegler Jörg , Pickel Brigitte , Hacquard Stéphane
Published: November 2020

Bidirectional root-shoot signalling is likely key in orchestrating stress responses and ensuring plant survival. Here we show thatArabidopsis thalianaresponses to microbial root commensals and light are interconnected along a microbiota-root-shoot axis. Microbiota and light manipulation experiments in a gnotobiotic system reveal that low photosynthetically active radiation (LP) perceived by leaves induce long-distance modulation of root bacterial, but not fungal or oomycetal communities. Reciprocally, bacterial root commensals and particularlyPseudomomasisolates are necessary for rescuing plant growth under LP. RNA-Seq, combined with leaf inoculation experiments with biotrophic and necrotrophic microbial pathogens indicate that microbiota-induced growth under LP coincides with transcriptional repression of immune responses, thereby increasing susceptibility to both pathogens. Inspection of a set ofA. thalianamutants demonstrates that orchestration of this light-dependent growth-defence trade-off requires the transcriptional regulator MYC2. Our work indicates that aboveground stress responses in plants can be governed by signals from microbial root commensals.
VTAM: A robust pipeline for validating metabarcoding data using internal controls
Authors: González Aitor , Dubut Vincent , Corse Emmanuel , Mekdad Reda , Dechatre Thomas , Meglécz Emese
Published: November 2020

Metabarcoding studies should be carefully designed to minimize false positives and false negative occurrences. The use of internal controls, replicates, and several overlapping markers is expected to improve the bioinformatics data analysis.

VTAM is a tool to perform all steps of data curation from raw fastq data to taxonomically assigned ASV (Amplicon Sequence Variant or simply variant) table. It addresses all known technical error types and includes other features rarely present in existing pipelines for validating metabarcoding data: Filtering parameters are obtained from internal control samples; cross-sample contamination and tag-jump are controlled; technical replicates are used to ensure repeatability; it handles data obtained from several overlapping markers.

Two datasets were analysed by VTAM and the results were compared to those obtained with a pipeline based on DADA2. The false positive occurrences in samples were considerably higher when curated by DADA2, which is likely due to the lack of control for tag-jump and cross-sample contamination.

VTAM is a robust tool to validate metabarcoding data and improve traceability, reproducibility, and comparability between runs and datasets.
Variant pathogenic prediction by locus variability, the importance of the last picture of evolution
Authors: Cabrera-Alarcon Jose Luis , Enriquez Jose Antonio , Martinez Jorge Garcia , Sánchez-Cabo Fátima
Published: November 2020

Accurate pathogenic detection for single nucleotide variants (SNVs) is a key problem to perform variant ranking in whole exome sequencing studies. Several in silico tools have been developed to identify deleterious variants. Locus variability, computed as Shannon entropy from gnomAD/helixMTdb variant allele frequencies can be used as pathogenic variants predictor. In this study we evaluate the use of Shannon entropy in non-coding mitochondrial DNA and also in coding regions with an additional selective pressure other than that imposed by the genetic code, as are splice-sites. To benchmark this functionality in non-coding mitochondrial variants, Shannon entropy was compared with HmtVar disease score, outperforming it in non-coding SNVs (AUCH=0.99 in ROC curve and PR-AUCH=1.00 in Precision-recall curve). In the same way, for splice-sites’ variants, Shannon entropy was compared against two state-of-the-art ensemble predictors ada score and rf score, matching their overall performance both in ROC curves (AUCH=0.95) and Precision-recall curves (PR-AUC=0.97). Therefore, locus variability could aid in variant ranking process for these specific types of SNVs.

Contact

jlcabreraa@cnic.es;fscabo@cnic.es
Epichloë festucaein mutualistic association withLolium perennesuppresses host apoplastic cysteine protease activity
Authors: Passarge Andrea , Demir Fatih , Green Kimberly , Depotter Jasper R.L. , Scott Barry , Huesgen Pitter F. , Doehlemann Gunther , Misas Villamil Johana C.
Published: November 2020

Plants secrete various defence-related proteins into the apoplast, including proteases. Papain-like cysteine proteases (PLCPs) are central components of the plant immune system. To overcome plant immunity and successfully colonise their hosts, several plant pathogens secrete effector proteins inhibiting plant PLCPs. We hypothesized that not only pathogens but also mutualistic microorganisms interfere with PLCP-meditated plant defences to maintain endophytic colonisation with their hosts.Epichloë festucaeforms mutualist associations with cool season grasses and produces a range of secondary metabolites that protect the host against herbivores. In this study, we performed a genome wide identification ofLolium perennePLCPs, analysed their evolutionary relationship and classified them into nine PLCP subfamilies. Using activity-based protein profiling, we identified four active PLCPs in the apoplast ofL. perenneleaves that are inhibited during endophyte interactions. We characterized theL. perennecystatin LpCys1 for its inhibitory capacity against ryegrass PLCPs. LpCys1 inhibits LpCP2, indicating that LpCys1 might play a role in the suppression of PLCP activity during the interaction withE. festucae. However, since the activity of otherL. perennePLCPs is not sensitive to LpCys1 we propose that additional inhibitors are involved in the suppression of apoplastic PLCPs duringE. festucaeinfection.
Cortical representation of touchin silico
Authors: Huang Chao , Zeldenrust Fleur , Celikel Tansu
Published: November 2020

With its six layers and ~12000 neurons, a cortical column is a complex network whose function is plausibly greater than the sum of its constituents’. Functional characterization of its network components will require going beyond the brute-force modulation of the neural activity of a small group of neurons. Here we introduce an open-source, biologically inspired, computationally efficient network model of the somatosensory cortex’s granular and supragranular layers after reconstructing the barrel cortex in soma resolution. Comparisons of the network activity to empirical observations showed that thein siliconetwork replicates the known properties of touch representations and whisker deprivation-induced changes in synaptic strength inducedin vivo. Simulations show that the history of the membrane potential acts as a spatial filter that determines the presynaptic population of neurons contributing to a post-synaptic action potential; this spatial filtering might be critical for synaptic integration of top-down and bottom-up information.
Designer Scaffolds for Interfacial Bioengineering
Authors: Hickey Ryan J. , Latour Maxime Leblanc , Harden James L. , Pelling Andrew E.
Published: November 2020

In regenerative medicine, the healing of the interfacial zone between tissues is a major challenge, yet approaches for studying the complex microenvironment of this interface remain lacking. Here, we study these complex living interfaces by manufacturing modular “blocks” of naturally porous decellularized plant-derived scaffolds with a computer numerical controlled mill. We demonstrate how each scaffold can be seeded with different cell types and easily assembled in a manner akin to LEGO™ bricks to create an engineered tissue interface (ETI). Cells migrate across the interface formed between an empty scaffold and a scaffold pre-seeded with cells. However, when both scaffolds contain cells, only a shallow cross-over zone of cell infiltration forms at the interface. As a proof-of-concept study, we use ETIs to investigate the interaction between lab grown bone and connective tissues. Consistent with the above, a cross-over zone of the two distinct cell types forms at the interface between scaffolds, otherwise the populations remain distinct. Finally, we demonstrate how ETIs are biocompatible in vivo, becoming vascularized and integrated into surrounding tissue after implantation. This work creates new tissue design avenues for understanding biological processes or the development of synthetic artificial tissues.
Improved 7 Tesla Transmit Field Homogeneity with Reduced Electromagnetic Power Deposition Using Coupled Tic Tac Toe Antennas
Authors: Santini Tales , Wood Sossena , Krishnamurthy Narayanan , Martins Tiago , Aizenstein Howard J. , Ibrahim Tamer S.
Published: November 2020

Recently cleared by the FDA, 7 Tesla (7T) MRI is a rapidly growing technology that can provide higher resolution and enhanced contrast in human MRI images. However, the increased operational frequency (~297 MHz) hinders its full potential since it causes inhomogeneities in the images and increases the power deposition in the tissues. This work describes the optimization of an innovative radiofrequency (RF) head coil coupled design, named Tic Tac Toe, currently used in large scale human MRI scanning at 7T; to date, this device was used in more than 1,300 patient/volunteer neuro 7T MRI scans. Electromagnetic simulations were performed for each of the coil’s antennas using the finite-difference time-domain method. Numerical optimizations were used to combine the calculated electromagnetic fields produced by these antennas, based on the superposition principle, and successfully produced homogeneous magnetic field distributions at low levels of power deposition in the tissues. The simulations were then successfully validated in-vivo using the Tic Tac Toe RF head coil system on a 7T MRI scanner.
First report in France ofCaenoplana decolorata, a recently described species of alien terrestrial flatworm (Platyhelminthes, Geoplanidae)
Authors: Justine Jean-Lou , Gey Delphine , Thévenot Jessica , Gouraud Clément , Winsor Leigh
Published: November 2020

Alien land flatworms (family Geoplanidae) are invading many countries in the world. Some can easily be identified by their morphology and colour pattern, but some are more cryptic and necessitate a molecular approach.Caenoplana decolorataMateos et al., 2020 was recently described, from specimens found in Spain, as a sibling species toC. coeruleaMoseley, 1877. We found that one specimen collected in Nantes, France in 2014 had a 100% identity of its COI sequence with one specimen of the original description ofC. decolorata, and thus we record here the species for the first time in France.
Rapid compensatory evolution can rescue low fitness symbioses following partner-switching
Authors: Sørensen Megan E S , Wood A Jamie , Cameron Duncan D , Brockhurst Michael A
Published: November 2020

Partner-switching plays an important role in the evolution of symbiosis, enabling local adaptation and recovery from the breakdown of symbiosis. Because of intergenomic epistasis, partner-switched symbioses may possess novel combinations of phenotypes but may also exhibit low fitness due to their lack of recent coevolutionary history. Here, we examine the structure and mechanisms of intergenomic epistasis in theParamecium-Chlorellasymbiosis and test if compensatory evolution can rescue initially low fitness partner-switched symbioses. Using partner-switch experiments coupled with metabolomics we show evidence for intergenomic epistasis wherein low fitness arose from mismatched photoprotection traits and the resulting light stress experienced by non-native symbionts when in high light environments. Experimental evolution under high light conditions revealed that an initially low fitness partner-switched non-native host-symbiont pairing rapidly adapted, gaining fitness equivalent to the native host symbiont pairing in less than 50 host generations. Compensatory evolution took two alternative routes: Either, hosts evolved higher symbiont loads to mitigate for their new algal symbiont’s poor performance, or the algal symbionts themselves evolved higher investment in photosynthesis and photoprotective traits to better mitigate light stress. These findings suggest that partner-switching combined with rapid compensatory evolution will enable the recovery and local adaptation of symbioses in response to changing environments.

Significance statement

Symbiosis enables the formation of new organisms through the merger of once independent species. Through symbiosis, species can acquire new functions, driving evolutionary innovation and underpinning important ecosystem processes. Symbioses that breakdown due to changing environmental conditions can reform by acquiring new symbionts in a process called partner-switching but may exhibit low fitness due to their lack of coadaptation. Using a microbial symbiosis between the single-celled eukaryoteParameciumand the green algaChlorellawe show that low fitness in partner-switched host-symbiont pairings arises from mismatched photoprotection traits. However, such low fitness partner-switched pairings can be rapidly rescued by adaptive evolution, regaining high fitness in less than 50 host generations. Partner-switching coupled with rapid compensatory evolution can enable symbioses to recover from breakdown.
Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk
Authors: Twigger Alecia-Jane , Engelbrecht Lisa K. , Bach Karsten , Schultz-Pernice Isabel , Petricca Stefania , Scheel Christina H. , Khaled Walid
Published: November 2020

Findings from epidemiological studies suggest that breast cancer risk is influenced by parity in an age-dependent manner. However, human mammary tissue remodelling that takes place during pregnancy and lactation remain little understood due to the challenge of acquiring samples. Here, we present an approach to overcome this using single-cell RNA sequencing to examine viable primary mammary epithelial cells isolated from human milk compared to resting, non-lactating breast tissue. Thereby, we determined that separate to breast tissue, human milk largely contains epithelial cells belonging to the luminal lineage, as well as immune cells. Our data reveal the presence of two distinct secretory luminal cell clusters in milk which highly express luminal progenitor signatures akin to non-lactating breast tissue luminal cells. Taking advantage of the fact that both the resting and lactating mammary gland contain a luminal compartment, we focussed on comparing these transcriptomes and identified differences in mammary cell function and metabolism between these maturation states. These findings provide the basis to dissect human luminal differentiation and milk biosynthesis pathways that in the future, may be interrogated to determine how parity influences luminal cell metabolism and breast cancer risk.
Influence of E/I balance and pruning in peri-personal space differences in schizophrenia: a computational approach
Authors: Paredes Renato , Ferri Francesca , Seriès Peggy
Published: November 2020

The encoding of the space close to the body, named peri-personal space (PPS), is thought to play a crucial role in the unusual experiences of the self observed in schizophrenia (SCZ). However, it is unclear why SCZ patients and high schizotypal (H-SPQ) individuals present a narrower PPS and why the boundaries of the PPS are more sharply defined in patients. We hypothesise that the unusual PPS representation observed in SCZ is caused by an imbalance of excitation and inhibition (E/I) in recurrent synapses of unisensory neurons or an impairment of bottom-up and top-down connectivity between unisensory and multisensory neurons. These hypotheses were tested computationally by manipulating the effects of E/I imbalance, feedback weights and synaptic density in the network. Using simulations we explored the effects of such impairments in the PPS representation generated by the network and fitted the model to behavioural data. We found that increased excitation of sensory neurons could account for the smaller PPS observed in SCZ and H-SPQ, whereas a decrease of synaptic density caused the sharp definition of the PPS observed in SCZ. We propose a novel conceptual model of PPS representation in the SCZ spectrum that can account for alterations in self-world demarcation, failures in tactile discrimination and symptoms observed in patients.
Selection of start codon during mRNA scanning in eukaryotic translation initiation
Authors: Basu Ipsita , Gorai Biswajit , Chandran Thyageshwar , Maiti Prabal K. , Hussain Tanweer
Published: November 2020

During translational initiation in eukaryotes, the small ribosomal subunit forms a 48S preinitiation complex (PIC) with initiation factors. The 48S PIC binds to the 5’ end of mRNA and inspects long untranslated region (UTR) for the presence of the start codon (AUG). Accurate and high speed of scanning 5’ UTR and subsequent selection of the correct start codon are crucial for protein synthesis. However, the conformational state of 48S PIC required for inspecting every codon is not clearly understood. Whether the scanning or open conformation of 48S PIC can accurately select the cognate start codon over near/non-cognate codons, or this discrimination is carried out only in the scanning-arrested or closed conformation of 48S PIC. Here, using atomistic molecular dynamics (MD) simulations and free energy calculations, we show that the scanning conformation of 48S PIC can reject all but 4 of the 63 non-AUG codons. Among nine near-cognate codons with a single mismatch, only codons with a first position mismatch (GUG, CUG and UUG) or a pyrimidine mismatch at the second position (ACG) are not discriminated by scanning state of 48S PIC. In contrast, any mismatch in the third position is rejected. Simulations runs in absence of one or more eukaryotic initiation factors (eIF1, eIF1+eIF1A, eIF2ɑ or eIF2β) from the system show critical role of eIF1 and eIF2ɑ in start codon selection. The structural analysis indicates that tRNAi dynamics at the widened P site of 48S open state drives codon selection. Further, a stable codon: anticodon interaction prepares the PIC to transit to the closed state. Overall, we provide insights into the selection of start codon during scanning and how the open conformation of 48S PIC can scan long 5’ UTRs with accuracy and high speed without the requirement of sampling the closed state for every codon.
Shore crabs reveal novel evolutionary attributes of the mushroom body
Authors: Strausfeld Nicholas James , Sayre Marcel Ethan
Published: November 2020

Neural organization of mushroom bodies is largely consistent across insects, whereas the ancestral ground pattern diverges broadly across crustacean lineages, resulting in successive loss of columns and the acquisition of domed centers retaining ancestral Hebbian-like networks and aminergic connections. We demonstrate here a major departure from this evolutionary trend in Brachyura, the most recent malacostracan lineage. Instead of occupying the rostral surface of the lateral protocerebrum, mushroom body calyces are buried deep within it, with their columns extending outwards to an expansive system of gyri on the brain’s surface. The organization amongst mushroom body neurons reaches extreme elaboration throughout its constituent neuropils. The calyces, columns, and especially the gyri show DC0 immunoreactivity, an indicator of extensive circuits involved in learning and memory.
Improved bioavailability of montelukast through a novel oral mucoadhesive film in humans and mice
Authors: Michael Johanna , de Sousa Diana Bessa , Conway Justin , Gonzales-Labrada Erick , Obeid Rodolphe , Tevini Julia , Felder Thomas , Hutter-Paier Birgit , Zerbe Horst , Paiement Nadine , Aigner Ludwig
Published: November 2020

The leukotriene receptor antagonist Montelukast (MTK) is an approved medication for the treatment of asthma and allergic rhinitis. The existing marketed tablet forms of MTK exhibit inconsistent uptake and bioavailability, which partially explains the presence of a significant proportion of MTK low- and non-responders in the population. Besides that, tablets are suboptimal formulations for patients suffering of dysphagia, for example seen in COVID-19 patients or in patients with neurodegenerative diseases such as Alzheimer’s Disease. The increasing interest in repurposing of MTK for the treatment of such patients and the need for an improved bioavailability triggered us to reformulate MTK. The aim was to develop a mucoadhesive MTK film with a good safety and improved pharmacological, i.e. improved bioavailability, profile in humans as well as in a mouse model of Alzheimer’s Disease.

We tested dissolution of the mucoadhesive film containing MTK in saliva buffer and assessed pharmacoexposure and −kinetics after acute and chronic oral application in mice. Furthermore, we performed a Phase I safety / bioavailability / pharmacokinetic analysis in healthy volunteers. The latter included a comparison with the marketed tablet form as well as a quantitative analysis of the MTK levels in the cerebrospinal fluid.

The novel MTK film demonstrated significantly improved bioavailability compared to the marketed tablet in the clinical phase 1a study in healthy humans. Furthermore, there were measurable amounts of MTK present in the cerebrospinal fluid (CSF) at the 3.0 and 7.0 hour time points post drug administration in humans. In mice, MTK was detected in serum and CSF after acute and chronic exposure in a dose-dependent manner.

The developed mucoadhesive film of MTK represents a promising alternative for the tablet delivery. The oral film might lower the non-responder rate in patients with asthma and might be an interesting product for repurposing of MTK in other diseases. As we demonstrate BBB penetrance in a preclinical model as well as in a clinical study, the oral film of MTK might find its use as a therapeutic for acute and chronic neurodegenerative diseases such as dementias and stroke.
Molecular Elucidation of Pancreatic Elastase Inhibition by Baicalein
Authors: Ghosh Debajeet , Bansode Sneha , Joshi Rakesh , Kolte Baban , Gacche Rajesh
Published: November 2020

The serine protease, elastase exists in various forms and plays diverse roles in the human body. Pharmacological inhibition of elastase has been investigated for its therapeutic role in managing conditions such as diabetes, pneumonia and arthritis. Sivelestat, a synthetic molecule, is the only elastase inhibitor to have been approved by any major drug regulatory authority (PMDA, in this case) – but still has failed to attain widespread clinical usage owing to its high price, cumbersome administration and obscure long-term safety profile. In order to find a relatively better-suited alternative, screening was conducted using plant flavonoids, which yielded Baicalein – a molecule that showed robust inhibition against Pancreatic Elastase inhibition (IC50: 3.53 μM). Other than having an IC50almost 1/5thof that of sivelestat’s, baicalein is also cheaper, safer and easier to administer. While Microscale thermophoresis validated baicalein-elastase interaction, enzyme-kinetic studies, molecular docking and molecular dynamic simulation revealed the mode of inhibition to be non-competitive. Baicalein exhibited binding to a distinct allosteric site on the enzyme. The current study demonstrates the elastase inhibition properties of baicalein in anin-vitroandin-silicoenvironment.
“Tracking the Rain Bird”: Modeling the monthly distribution of Pied cuckoo in India
Authors: Sarkar Debanjan , Tomar Bharti , Kumar R. Suresh , Saran Sameer , Talukdar Gautam
Published: November 2020

Pied cuckooClamator jacobinus(Boddart, 1783) is a migratory, brood-parasitic bird found in the African and Indian Subcontinent. Although the southern Indian population is presumably resident, the North Indian Population migrates from Africa to India during the summer. The arrival of the bird is linked to the onset of monsoon in India from scientific literature to folklore. It is known to make its appearance in central and northern India in the last week of May or early June, indicating the imminent arrival of the monsoon with its unmistakably loud metallic calls. There have been few attempts to compile relevant information on the species migration in the early 1900s and citizen science approach by Bird-count India; little information is available on how environmental factors might be affecting its migration. Here, we have used Maximum Entropy modeling to identify the monthly and seasonal distribution patterns and major bioclimatic factors that might be influencing the distribution of the species in India. We have used E-Bird citizen science platform data, seven bioclimatic variables, and monthly NDVI of respective months for building the models. The predicted output shows the species presence throughout the year in southern India. In contrast, in northern India, the distribution is dynamic, peaking in summers in the Month of May-June and no presence in winter. The influence of bioclimatic variables used in SDM varied monthly; Water vapor pressure was the primary contributing variable in the months prior to species arrival. In July, it was NDVI (Higher NDVI suggests abundance of food resources for the species). In August-September, Windspeed and water vapor pressure (Factors might be responsible for the departure of the species) have contributed highest. Our approach provides a more concise understanding of Pied cuckoo’s monthly distributions throughout India, which helps understand the complex seasonal shifts in the distribution of such migratory birds.
Liver environment-imposed constraints diversify movement strategies of liver-localized CD8 T cells
Authors: Rajakaruna Harshana , O’Connor James , Cockburn Ian A. , Ganusov Vitaly V.
Published: November 2020

Pathogen-specific CD8 T cells face the problem of finding rare cells that present their cognate antigen either in the lymph node or infected tissue. While quantitative details of T cell movement strategies in some tissues such lymph nodes or skin have been relatively well characterized, we still lack quantitative understanding of T cell movement in many other important tissues such as the spleen, lung, liver, and gut. Furthermore, how environmental constraints influence movement patterns of T cells in tissues remains incompletely characterized. Liver is one of the major organs in mice and humans and is the target site for many pathogens such as hepatitis B and C viruses in humans andPlasmodiumparasites in multiple mammalian species. We developed a protocol to generate stable numbers of liver-located CD8 T cells, used intravital microscopy to record movement patterns of CD8 T cells in livers of live mice, and analyzed these and previously published data using well-established statistical and computational methods. We show that in most of our experimentsPlasmodium-specific liver-localized CD8 T cells perform correlated random walks characterized by transiently superdiffusive displacement with persistence times of 10-15 min that exceed those observed for T cells in lymph nodes. Liver-localized CD8 T cells typically crawl on the lumenal side of liver sinusoids (i.e., are in the blood); simulating T cell movement in digital structures derived from the liver sinusoids illustrates that liver structure alone is sufficient to explain the relatively long superdiffusive displacement of T cells. In experiments when CD8 T cells in the liver poorly attach to the sinusoids (e.g., one week post immunization with radiation-attenuatedPlasmodiumsporozoites) T cells also undergo Levy flights – large displacements occurring due to cell deattaching from the endothelium, floating with the blood flow, and re-attaching at another location. Our analysis, thus, provides quantitative details of movement patterns of liver-localized CD8 T cells and illustrates how structural and physiological details of the tissue may impact T cell movement patterns.
Landscape analysis of escape variants identifies SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization
Authors: Liu Zhuoming , VanBlargan Laura A. , Bloyet Louis-Marie , Rothlauf Paul W. , Chen Rita E. , Stumpf Spencer , Zhao Haiyan , Errico John M. , Theel Elitza S. , Liebeskind Mariel J. , Alford Brynn , Buchser William J. , Ellebedy Ali H. , Fremont Daved H. , Diamond Michael S. , Whelan Sean P. J.
Published: November 2020

Although neutralizing antibodies against the SARS-CoV-2 spike (S) protein are a goal of COVID-19 vaccines and have received emergency use authorization as therapeutics, viral escape mutants could compromise their efficacy. To define the immune-selected mutational landscape in S protein, we used a VSV-eGFP-SARS-CoV-2-S chimeric virus and 19 neutralizing monoclonal antibodies (mAbs) against the receptor-binding domain (RBD) to generate 50 different escape mutants. The variants were mapped onto the RBD structure and evaluated for cross-resistance to mAbs and convalescent human sera. Each mAb had a unique resistance profile, although many shared residues within an epitope. Some variants (e.g., S477N) were resistant to neutralization by multiple mAbs, whereas others (e.g., E484K) escaped neutralization by convalescent sera, suggesting some humans induce a narrow repertoire of neutralizing antibodies. Comparing the antibody-mediated mutational landscape in S with sequence variation in circulating SARS-CoV-2, we define substitutions that may attenuate neutralizing immune responses in some humans.