bluuebunny/crossref_metadata_2025 huggingface dataset:
Measuring biodiversity from DNA in the air
Authors: Clare Elizabeth L. , Economou Chloe K. , Bennett Frances J. , Dyer Caitlin E. , Adams Katherine , McRobie Benjamin , Drinkwater Rosie , Littlefair Joanne E.
Published: July 2021

Impacts of the biodiversity crisis far exceed our ability to monitor changes in terrestrial ecosystems. Environmental DNA has revolutionized aquatic biomonitoring, permitting remote population and diversity assessments. Here we demonstrate that DNA from terrestrial animals can now be collected from the air under natural conditions, a ground-breaking advance for terrestrial biomonitoring. Using air samples from a zoological park, where species are spatially confined and unique compared to native fauna, we show that DNA in air can be used to identify the captive species and their potential interactions with local taxa. Air samples contained DNA from 25 species of mammal and bird including 17 known (and distinct) terrestrial zoo species. We also identified food items from air sampled in enclosures and detected four taxa native to the local area, including the Eurasian hedgehog, endangered in the UK, and the muntjac deer, a locally established invasive species. Our data provide evidence that airDNA is concentrated around recently inhabited areas (e.g., indoor enclosures) but that there is dispersal away from the source suggesting an ecology to airDNA movement which highlights the potential for airDNA sampling at distance. Our data clearly demonstrate the profound potential of air as a source of DNA for global terrestrial biomonitoring and ecological analysis.

Significance Statement

The global decline in biodiversity requires rapid non-invasive biomonitoring tools applicable at a global scale. In this study we collect environmental DNA from mammals and birds from air samples collected in a natural setting. Using only air, we identified 25 species of mammal and bird known to be in the area. Our dataset detected species at risk of local extinction and several confirmed predator-prey interactions. This approach will revolutionize terrestrial biodiversity surveys.
Single-Molecule Manipulation of Macromolecules on Membranes Using High-Resolution Optical Tweezers
Authors: Wang Yukun , Jin Huaizhou , Zhang Yongli
Published: July 2021

Despite their wide applications into soluble macromolecules, optical tweezers have rarely been used to characterize dynamics of membrane proteins, mainly due to lack of model membranes compatible with optical trapping. Here, we found that optical tweezers can stably trap giant unilamellar vesicles (GUVs) containing iodixanol with controlled membrane tension, which can potentially serve as a model membrane to study dynamics of membranes, membrane proteins, or their interactions. We also observed that small unilamellar vesicles (SUVs) are rigid enough to resist large pulling force and offer potential advantages to pull membrane proteins. To demonstrate the use of both model membranes, we pulled membrane tethers from the trapped GUVs and measured the folding or binding dynamics of a single DNA hairpin or synaptotagmin-1 C2 domain attached to the GUV or SUV with high spatiotemporal resolution. Our methodologies facilitate single-molecule manipulation studies of membranes or membrane proteins using optical tweezers.
Decellularized Normal and Tumor Extracellular Matrix as Scaffold for Cancer Organoid Cultures of Colorectal Peritoneal Metastases
Authors: Varinelli Luca , Guaglio Marcello , Brich Silvia , Zanutto Susanna , Belfiore Antonino , Zanardi Federica , Iannelli Fabio , Oldani Amanda , Costa Elisa , Chighizola Matteo , Lorenc Ewelina , Minardi Simone P. , Fortuzzi Stefano , Filugelli Martina , Garzone Giovanna , Pisati Federica , Vecchi Manuela , Pruneri Giancarlo , Shigeki Kusamura , Baratti Dario , Cattaneo Laura , Parazzoli Dario , Podestà Alessandro , Milione Massimo , Deraco Marcello , Pierotti Marco A. , Gariboldi Manuela
Published: July 2021

Peritoneal metastases (PM) from colorectal cancer (CRC) are associated with poor survival. The extracellular matrix (ECM) plays a fundamental role in modulating the homing of CRC metastases to the peritoneum. The mechanisms underlying the interactions between metastatic cells and the ECM, however, remain poorly understood and the number ofin vitromodels available for the study of the peritoneal metastatic process is limited. Here, we show that decellularized ECM of the peritoneal cavity allows the growth of organoids obtained from PM, favoring the development of three-dimensional nodules that maintain the characteristics ofin vivoPM. Organoids preferentially grow on scaffolds obtained from neoplastic peritoneum, which are characterized by greater stiffness than normal scaffolds. A gene expression analysis of organoids grown on different substrates reflected faithfully the clinical and biological characteristics of the organoids. An impact of the ECM on the response to standard chemotherapy treatment for PM was also observed.

Significance

Evidence of the value of ex vivo 3D models obtained by combining patient-derived extracellular matrices depleted of cellular components and organoids to mimic the metastatic niche, to be used as a tool to develop new therapeutic strategies in a biologically relevant context, to personalize treatments and increase their efficacy.
Variant calling tool evaluation for variable size indel calling from next generation whole genome and targeted sequencing data
Authors: Wang Ning , Lysenkov Vladislav , Orte Katri , Kairisto Veli , Aakko Juhani , Khan Sofia , Elo Laura L.
Published: July 2021

Insertions and deletions (indels) in human genomes are associated with a wide range of phenotypes, including various clinical disorders. High-throughput, next generation sequencing (NGS) technologies enable detection of short genetic variants, such as single nucleotide variants (SNVs) and indels. However, the variant calling accuracy for indels remains considerably lower than for SNVs. Here we present a comparative study of the performance of variant calling tools on indel calling, evaluated with a wide repertoire of NGS datasets. While there is no single optimal tool to suit all circumstances, our results demonstrate that the choice of variant calling tool greatly impacts the precision and recall of indel calling. Furthermore, to reliably detect indels, it is essential to choose NGS technologies that offer a long read length and high coverage, coupled with specific variant calling tools.

Author summary

The development of next generation sequencing (NGS) technologies and computational algorithms enabled large scale, simultaneous detection of wide range of genetic variants, such as single nucleotide variants as well as insertions and deletions (indels), which may confer potential clinical significance. Recently, many studies have been conducted to evaluate variant calling tools on indel calling. However, the optimal indel size range for different variant calling tools remain unclear. A good benchmarking dataset for indel calling evaluation should contain biologically representative high-confident indels with a wide size range and preferably come from various sequencing settings. In this article, we created a semi-simulated whole genome sequencing dataset where the sequencing data was computationally generated. The indels in the semi-simulated genome were incorporated from a real human sample to represent biologically realistic indels and to avoid inclusion of variants due to potential technical sequencing errors. Furthermore, we used three real-world NGS datasets generated by whole genome or targeted sequencing to further evaluate our candidate tools. Our results demonstrated that variant calling tools varies greatly in calling different sizes of indels. Deletion calling and insertion calling also showed differences among the tools. The sequencing settings in coverage and read length also had a great impact on indel calling. Our results suggest that the accurate indel calling was dependent on the combination of a variant calling tool, indel size range and sequencing settings.
How Axon and Dendrite Branching Are Governed by Time, Energy, and Spatial Constraints
Authors: Desai-Chowdhry Paheli , Brummer Alexander , Savage Van
Published: July 2021

Neurons are connected by complex branching processes - axons and dendrites - that collectively process information for organisms to respond to their environment. Classifying neurons according to differences in structure or function is a fundamental part of neuroscience. Here, by constructing new biophysical theory and testing against our empirical measures of branching structure, we establish a correspondence between neuron structure and function as mediated by principles such as time or power minimization for information processing as well as spatial constraints for forming connections. Specifically, based on these principles, we use undetermined Lagrange multipliers to predict scaling ratios for axon and dendrite sizes across branching levels. We test our predictions for radius and length scale factors against those extracted from neuronal images, measured for cell types and species that range from insects to whales. Notably, our findings reveal that the branching of axons and peripheral nervous system neurons is mainly determined by time minimization, while dendritic branching is mainly determined by power minimization. Further comparison of different dendritic cell types reveals that Purkinje cell dendrite branching is constrained by material costs while motoneuron dendrite branching is constrained by conduction time delay over a range of species. Our model also predicts a quarter-power scaling relationship between conduction time delay and species body size, which is supported by experimental data and may help explain the emergence of hemispheric specialization in larger animals as a means to offset longer time delays.

Author summary

Neurons are the basic building blocks of the nervous system, responsible for information processing and communication in animals. They consist of a centralized cell body and two types of processes - axons and dendrites - that connect to one another. Previous studies of the differences among neuron cell types have focused on comparisons of either structure or function separately, without considering combined effects. Based on theory for structure of and flow through biological resource distribution networks, we develop a new model that relates neuron structure to function. We find that differences in structure between axons and dendrites as well as between dendrites of different cell types can be related to differences in function and associated evolutionary pressures. Moreover, using our mathematical model, we find that the conduction time delay of electrical signals systematically varies with species body size - neurons in larger species have longer delays - providing a possible explanation for hemispheric specialization in larger animals.
MFmap: A semi-supervised generative model matching cell lines to tumours and cancer subtypes
Authors: Zhang Xiaoxiao , Kschischo Maik
Published: July 2021

Translating in vitro results from experiments with cancer cell lines to clinical applications requires the selection of appropriate cell line models. Here we present MFmap (model fidelity map), a machine learning model to simultaneously predict the cancer subtype of a cell line and its similarity to an individual tumour sample. The MFmap is a semi-supervised generative model, which compresses high dimensional gene expression, copy number variation and mutation data into cancer subtype informed low dimensional latent representations. The accuracy (test set F1 score > 90%) of the MFmap subtype prediction is validated in ten different cancer datasets. We use breast cancer and glioblastoma cohorts as examples to show how subtype specific drug sensitivity can be translated to individual tumour samples. The low dimensional latent representations extracted by MFmap explain known and novel subtype specific features and enable the analysis of cell-state transformations between different subtypes. From a methodological perspective, we report that MFmap is a semi-supervised method which simultaneously achieves good generative and predictive performance and thus opens opportunities in other areas of computational biology.

Author summary

Cancer researchers perform experiments with cell lines to better understand the biology of cancer and to develop new anti-cancer treatments. A prerequisite to translate promising results from these in vitro experiments to clinical applications is to use the most appropriate cell line for a given tumour or cancer subtype. We present MFmap (model fidelity map), a deep learning technique to integrate cancer genomic data from patients with cell line data. The MFmap neural network compresses complex genomic features from thousands of genes into a small set of features called latent representations. This makes cell line and tumour data comparable and allows cancer researchers to select the best cell line which closely resembles a specific type of tumours or even an individual tumour. By classifying cancer cell lines into subtypes, MFmap offers a new possibility to predict the effect of therapeutic compounds in a particular tumour subtype. For the example of an aggressive brain tumour we demonstrate that MFmap can be used to study cell-state transformations during the disease course. In addition, MFmap is a promising machine learning method with potential applications in many other areas of biology and medicine.
Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin
Authors: Colabardini Ana Cristina , Wang Fang , Dong Zhiqiang , Pardeshi Lakhansing , Rocha Marina Campos , Costa Jonas Henrique , dos Reis Thaila Fernanda , Brown Alec , Jaber Qais Z. , Fridman Micha , Fill Taicia , Rokas Antonis , Malavazi Iran , Wong Koon Ho , Goldman Gustavo Henrique
Published: July 2021

Aspergillus fumigatus is the main causative agent of invasive pulmonary aspergillosis (IPA), a severe disease that affects immunosuppressed patients worldwide. The fungistatic drug caspofungin is the second line therapy against IPA but has increasingly been used against clinical strains that are resistant to azoles, the first line antifungal therapy. In high concentrations, caspofungin induces a tolerance phenotype with partial reestablishment of fungal growth called caspofungin paradoxical effect (CPE), resulting from a change in the composition of the cell wall. An increasing number of studies has shown that different isolates of A. fumigatus exhibit phenotypic heterogeneity, including heterogeneity in their CPE response. To gain insights into the underlying molecular mechanisms of CPE response heterogeneity, we analyzed the transcriptomes of two A. fumigatus reference strains, Af293 and CEA17, exposed to low and high caspofungin concentrations. We found that there is a core transcriptional response that involves genes related to cell wall remodeling processes, mitochondrial function, transmembrane transport, and amino acid and ergosterol metabolism, and a variable response related to secondary metabolite (SM) biosynthesis and iron homeostasis. Specifically, we show here that the overexpression of a SM pathway that works as an iron chelator extinguishes the CPE in both backgrounds, whereas iron depletion is detrimental for the CPE in Af293 but not in CEA17. We next investigated the function of the transcription factor CrzA, whose deletion was previously shown to result in heterogeneity in the CPE response of the Af293 and CEA17 strains. We found that CrzA constitutively binds to and modulates the expression of several genes related to processes involved in caspofungin tolerance, and that crzA deletion differentially impacts the SM production and growth of Af293 and CEA17. As opposed to the ΔcrzACEA17 mutant, the ΔcrzAAf293 mutant fails to activate cell wall remodeling genes upon caspofungin exposure, which most likely severely affects its macrostructure and extinguishes its CPE. This work describes how heterogeneity in the response to an antifungal agent between A. fumigatus strains stems from heterogeneity in the function of a transcription factor and its downstream target genes.
Supervised generative design of regulatory DNA for gene expression control
Authors: Zrimec Jan , Fu Xiaozhi , Muhammad Azam Sheikh , Skrekas Christos , Jauniskis Vykintas , Speicher Nora K. , Börlin Christoph S. , Verendel Vilhelm , Chehreghani Morteza Haghir , Dubhashi Devdatt , Siewers Verena , David Florian , Nielsen Jens , Zelezniak Aleksej
Published: July 2021

In order to control gene expression, regulatory DNA variants are commonly designed using random synthetic approaches with mutagenesis and screening. This however limits the size of the designed DNA to span merely a part of a single regulatory region, whereas the whole gene regulatory structure including the coding and adjacent non-coding regions is involved in controlling gene expression. Here, we prototype a deep neural network strategy that models whole gene regulatory structures and generatesde novofunctional regulatory DNA with prespecified expression levels. By learning directly from natural genomic data, without the need for large synthetic DNA libraries, our ExpressionGAN can traverse the whole sequence-expression landscape to produce sequence variants with target mRNA levels as well as natural-like properties, including over 30% dissimilarity to any natural sequence. We experimentally demonstrate that this generative strategy is more efficient than a mutational one when using purely natural genomic data, as 57% of the newly-generated highly-expressed sequences surpass the expression levels of natural controls. We foresee this as a lucrative strategy to expand our knowledge of gene expression regulation as well as increase expression control in any desired organism for synthetic biology and metabolic engineering applications.
Nuclear hormone receptors promote gut and glia detoxifying enzyme induction and protect C. elegans from the mold P. brevicompactum
Authors: Wallace Sean W. , Lizzappi Malcolm C. , Hur Hong , Liang Yupu , Shaham Shai
Published: July 2021

Animals encounter microorganisms in their habitats, adapting physiology and behavior accordingly. The nematode Caenorhabditis elegans is found in microbe-rich environments; however, its responses to fungi are not extensively studied. Here we describe interactions of C. elegans and Penicillium brevicompactum, an ecologically-relevant mold. Transcriptome studies reveal that co-culture upregulates stress-response genes, including xenobiotic metabolizing enzymes (XMEs), in C. elegans intestine and AMsh glial cells. The nuclear hormone receptors (NHR) NHR-45 and NHR-156 are key induction regulators, and mutants that cannot induce XMEs in the intestine when exposed to P. brevicompactum experience mitochondrial stress and exhibit developmental defects. Different C. elegans wild isolates harbor sequence polymorphisms in nhr-156, resulting in phenotypic diversity in AMsh glia responses to microbe exposure. We propose that P. brevicompactum mitochondria-targeting mycotoxins are deactivated by intestinal detoxification, allowing tolerance to moldy environments. Our studies support the idea that C. elegans NHR gene expansion/diversification underlies adaptation to microbial environments.
NOBIAS: Analyzing anomalous diffusion in single-molecule tracks with nonparametric Bayesian inference
Authors: Chen Ziyuan , Geffroy Laurent , Biteen Julie S.
Published: July 2021

Single particle tracking (SPT) enables the investigation of biomolecular dynamics at a high temporal and spatial resolution in living cells, and the analysis of these SPT datasets can reveal biochemical interactions and mechanisms. Still, how to make the best use of these tracking data for a broad set of experimental conditions remains an analysis challenge in the field. Here, we develop a new SPT analysis framework: NOBIAS (NOnparametric Bayesian Inference for Anomalous Diffusion in Single-Molecule Tracking), which applies nonparametric Bayesian statistics and deep learning approaches to thoroughly analyze SPT datasets. In particular, NOBIAS handles complicated live-cell SPT data for which: the number of diffusive states is unknown, mixtures of different diffusive populations may exist within single trajectories, symmetry cannot be assumed between the x and y directions, and anomalous diffusion is possible. NOBIAS provides the number of diffusive states without manual supervision, it quantifies the dynamics and relative populations of each diffusive state, it provides the transition probabilities between states, and it assesses the anomalous diffusion behavior for each state. We validate the performance of NOBIAS with simulated datasets and apply it to the diffusion of single outer-membrane proteins in Bacteroides thetaiotaomicron. Furthermore, we compare NOBIAS with other SPT analysis methods and find that, in addition to these advantages, NOBIAS is robust and has high computational efficiency and is particularly advantageous due to its ability to treat experimental trajectories with asymmetry and anomalous diffusion.
Synaptic decline precedes dopaminergic neuronal loss in human midbrain organoids harboring a triplication of the SNCA gene
Authors: Modamio Jennifer , Saraiva Claudia , Giro Gemma Gomez , Nickels Sarah Louise , Jarazo Javier , Antony Paul , Barbuti Peter , Hadler Rashi , Jäger Christian , Krüger Rejko , Glaab Enrico , Schwamborn Jens Christian
Published: July 2021

1.

Increased levels of the protein alpha-synuclein (α-syn) are associated with the development of neurodegenerative diseases like Parkinson’s disease (PD). In physiological conditions, α-syn modulates synaptic plasticity, neurogenesis and neuronal survival. However, its pathogenic accumulation and aggregation results in toxicity and neurodegeneration.

Here, we used a PD patient specific midbrain organoid model derived from induced pluripotent stem cells harboring a triplication in the SNCA gene to study PD-associated phenotypes. The model recapitulates the two main hallmarks of PD, which are α-syn aggregation and loss of dopaminergic neurons. Additionally, impairments in astrocyte differentiation were detected. Transcriptomics data indicate that synaptic function is impaired in PD specific midbrain organoids. This is further confirmed by alterations in synapse number and electrophysiological activity. We found that synaptic decline precedes neurodegeneration. Finally, this study substantiates that patient specific midbrain organoids allow a personalized phenotyping, which make them an interesting tool for precision medicine and drug discovery.
SARS-Cov-2 Spike binding to ACE2 is stronger and longer ranged due to glycan interaction
Authors: Huang Yihan , Harris Bradley S. , Minami Shiaki A. , Jung Seongwon , Shah Priya S. , Nandi Somen , McDonald Karen A. , Faller Roland
Published: July 2021

Highly detailed steered Molecular Dynamics simulations are performed on differently glycosylated receptor binding domains of the SARS-CoV-2 spike protein. The binding strength and the binding range increases with glycosylation. The interaction energy rises very quickly with pulling the proteins apart and only slowly drops at larger distances. We see a catch slip type behavior where interactions during pulling break and are taken over by new interactions forming. The dominant interaction mode are hydrogen bonds but Lennard-Jones and electrostatic interactions are relevant as well.

Statement of Significance

Glycosylation of the receptor binding domain of the Spike protein of SARS-CoV-2 as well as the ACE2 receptor leads to stronger and longer ranged binding interactions between the proteins. Particularly, at shorter distances the interactions are between residues of the proteins themselves whereas at larger distances these interactions are mediated by the glycans.

Abstract Figure
Evolving social behaviour through selection of single-cell adhesion in Dictyostelium discoideum
Authors: Adiba Sandrine , Forget Mathieu , De Monte Silvia
Published: July 2021

The social amoeba Dictyostelium discoideum commonly forms chimeric fruiting bodies. Genetic variants that produce a higher proportion of spores are predicted to undercut multicellular organization unless cooperators assort positively. Cell adhesion is considered a primary factor driving such assortment, but evolution of adhesion has not been experimentally connected to changes in social performance. We modified by experimental evolution the efficiency of individual cells in attaching to a surface. Surprisingly, evolution appears to have produced social cooperators irrespective of whether stronger or weaker adhesion was selected. Quantification of reproductive success, cell-cell adhesion and developmental patterns, however, revealed two distinct social behaviours, as captured when the classical metric for social success is generalized by considering clonal spore production. Our work shows that cell mechanical interactions can constrain evolution of development and sociality in chimeras, and that elucidation of proximate mechanisms is necessary in order to understand the ultimate emergence of multicellular organization.
Gut microbiota-based vaccination engages innate immunity to improve blood glucose control in obese mice
Authors: Duggan Brittany M. , Tamrakar Akhilesh K. , Barra Nicole G. , Anhê Fernando F. , Paniccia Gabriella , Wallace Jessica G. , Stacey Hannah D. , Miller Matthew S. , Sloboda Deborah M. , Schertzer Jonathan D.
Published: July 2021

Obesity and diabetes increase circulating levels of microbial components derived from the gut microbiota. Individual bacterial factors (i.e., postbiotics) can have opposing effects on metabolic inflammation and blood glucose control. We tested the net effect of gut bacterial extracts on blood glucose using a microbiota-based vaccination strategy in mice. Male and female mice had improved insulin sensitivity and blood glucose control five weeks after a single subcutaneous injection of a specific dose of a bacterial extract obtained from the luminal contents of the proximal gut. Injection of mice with proximal gut extracts from germ-free mice revealed that bacteria were required for a microbiota-based vaccination to improve blood glucose control. Vaccination ofNod1−/−,Nod2−/−, andRipk2−/−mice showed that each of these innate immune proteins was required for bacterial extract injection to improve blood glucose control. A microbiota-based vaccination promoted a proximal gut immunoglobulin-G (IgG) response directed against bacterial extract antigens, where subcutaneous injection of mice with the luminal contents of the ileum elicited a bacterial extract-specific IgG response that is compartmentalized to the ileum of vaccinated mice. A microbiota-based vaccination was associated with an altered the microbiota composition in the ileum and colon of mice. Lean mice required a single injection of proximal gut bacterial extracts, but high fat diet (HFD)-fed, obese mice required prime-boost bacterial extract injections for improvements in blood glucose control. These data show that, upon subversion of the gut barrier, vaccination with proximal gut bacterial extracts engages innate immunity to promote long-lasting improvements in blood glucose control in a dose-dependent manner.
Hyperbolic trade-off: the importance of balancing trial and subject sample sizes in neuroimaging
Authors: Chen Gang , Pine Daniel S. , Brotman Melissa A. , Smith Ashley R. , Cox Robert W. , Taylor Paul A. , Haller Simone P.
Published: July 2021

Here we investigate the crucial role of trials in task-based neuroimaging from the perspectives of statistical efficiency and condition-level generalizability. Big data initiatives have gained popularity for leveraging a large sample of subjects to study a wide range of effect magnitudes in the brain. On the other hand, most taskbased FMRI designs feature a relatively small number of subjects, so that resulting parameter estimates may be associated with compromised precision. Nevertheless, little attention has been given to another important dimension of experimental design, which can equally boost a study’s statistical efficiency: the trial sample size. The common practice of condition-level modeling implicitly assumes no cross-trial variability. Here, we systematically explore the different factors that impact effect uncertainty, drawing on evidence from hierarchical modeling, simulations and an FMRI dataset of 42 subjects who completed a large number of trials of cognitive control task. We find that, due to the hyperbolic relationship between trial and subject sample sizes and the presence of relatively large cross-trial variability, 1) trial sample size has nearly the same impact as subject sample size on statistical efficiency; 2) increasing both the number of trials and subjects improves statistical efficiency more effectively than focusing on subjects alone; 3) trial sample size can be leveraged alongside subject sample size to improve the cost-effectiveness of an experimental design; 4) for small trial sample sizes, trial-level modeling, rather than condition-level modeling through summary statistics, may be necessary to accurately assess the standard error of an effect estimate. We close by making practical suggestions for improving experimental designs across neuroimaging and behavioral studies.
On the Apportionment of Archaic Human Diversity
Authors: Witt Kelsey E. , Villanea Fernando , Loughran Elle , Huerta-Sanchez Emilia
Published: July 2021

The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives, and the impact of natural selection on archaic segments of the human genome. Resolving these interactions can be difficult, as archaic variants in modern populations have also been shaped by genetic drift, bottlenecks, and gene flow. Here, we investigate the apportionment of archaic variation in Eurasian populations. We find that archaic genome coverage at the individual- and population-level present unique patterns in modern human population: South Asians have an elevated count of population-unique archaic SNPs, and Europeans and East Asians have a higher degree of archaic SNP sharing, indicating that population demography and archaic admixture events had distinct effects in these populations. We confirm previous observations that East Asians have more Neanderthal ancestry than Europeans at an individual level, but surprisingly Europeans have more Neandertal ancestry at a population level. In comparing these results to our simulated models, we conclude that these patterns likely reflect a complex series of interactions between modern humans and archaic populations.
Epigenetic modulation of selected immune response genes and altered functions of T lymphocytes and macrophages collectively contribute to autoimmune diabetes protection
Authors: Jayaraman Sundararajan , Arianas Maria , Jayaraman Arathi
Published: July 2021

We have previously demonstrated that treatment of female NOD mice with the histone deacetylase inhibitor Trichostatin A (TSA) bestowed irreversible protection against autoimmune diabetes. Herein we show that drug treatment diminished the infiltration of the pancreas with CD4+ and CD8+ T cells and Ly-6C+ monocytes. Significantly, TSA administration selectively repressed the expression of a set of genes exaggerated during diabetes and constitutively expressed primarily in the spleen and rarely in the pancreas. These genes encode lymphokines, macrophage-associated determinants, and transcription factors. Although the copy numbers of many histone deacetylases increased during diabetes in the spleen and pancreas, only those upregulated in the spleen were rendered sensitive to repression by TSA treatment. The T lymphocytes derived from drug-treated donors displayed diminished diabetogenic potential following transfer into immunodeficient NOD.scid mice. In the immunocompromised recipients, diabetes caused by the transfer of activated T lymphocytes from untreated diabetic mice was hampered by the co-transfer of highly purified splenic Ly-6C+ macrophages from drug-treated mice. However, the transfer of Ly-6C+ macrophages from drug-treated mice failed to block ongoing diabetes in wild-type NOD mice. These data demonstrate that the modified gene expression and functional alteration of T lymphocytes and macrophages collectively contribute to diabetes protection afforded by the histone modifier in female NOD mice.
TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting multiple endogenous signaling pathways
Authors: Funa Nina Sofi , de Lichtenberg Kristian Honnens , Skjøtt Hansen Maria , van Cuyl Kuylenstierna Jonas , Jensen Kim Bak , Miao Yi , Garcia K. Christopher , Serup Palle
Published: July 2021

Genetic differences between pluripotent stem cell lines causes variable activity of extra-cellular signaling pathways, which limits the reproducibility of directed differentiation protocols. Here we used human embryonic stem cells (hESCs) to interrogate how exogenously provided factors modulate endogenous signaling events during specification of foregut endoderm lineages. We find that TGF-β1 activates anOTX2/LHX1gene regulatory network that promotes anterior fate by antagonizing endogenous Wnt signaling. In contrast to Porcupine inhibition, the effects of TGF-β1 cannot be reversed by exogenous Wnt ligands, suggesting that induction of SHISA proteins and intracellular accumulation of Fzd receptors make TGF-β1 treated cells refractory to Wnt signaling. Subsequently, TGF-β1-mediated inhibition of Bmp- and Wnt-signaling suppresses liver- and promotes pancreas fate. However, pancreas differentiation is delayed by TGF-β1-induced CYP26A1 expression and inhibition of RA signaling. Our study thus identifies multiple mechanisms of crosstalk between major developmental signaling pathways during foregut patterning.
Innate immune pathways act synergistically to constrain RNA virus evolution inDrosophila melanogaster
Authors: Mongelli Vanesa , Lequime Sebastian , Kousathanas Athanasios , Gausson Valérie , Blanc Hervé , Quintana-Murci Lluis , Elena Santiago F. , Saleh Maria-Carla
Published: July 2021

Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, usingD. melanogasteras model host and its natural pathogen Drosophila C virus (DCV). We first isogenized eight fly genotypes generating animals defective for RNAi, Imd and Toll innate immune pathways and also pathogen sensing and gut renewal pathways. Wild-type or mutant flies were then orally infected and DCV was serially passaged ten times. Viral population diversity was studied after each viral passage by high-throughput sequencing, and infection phenotypes were assessed at the beginning and at the end of the passaging scheme. We found that the absence of any of the various immune pathways studied increased viral genetic diversity and attenuated the viruses. Strikingly, these effects were observed in both host factors with antiviral properties and host factors with antibacterial properties. Together, our results indicate that the innate immunity system as a whole, and not specific antiviral defense pathways in isolation, generally constrains viral diversity and evolution.
Structure of Infective Getah Virus at 2.8 Å-resolution Determined by Cryo-EM
Authors: Wang Aojie , Zhou Feng , Liu Congcong , Gao Dongsheng , Qi Ruxi , Yin Yiheng , Liu Sheng , Gao Yuanzhu , Fu Lutang , Xia Yinhe , Xu Yawei , Wang Chuanqing , Liu Zheng
Published: July 2021

Getah virus (GETV), a member of genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% of healthy people, there are no reports of clinical symptom associated with GETV. The biological and pathological properties of GETV are largely unknown. Here, we present the structure of infective GETV at a resolution of 2.8 Å with the capsid protein and the envelope glycoproteins E1 and E2. We have identified numerous glycosylation and S-acylation sites in E1 and E2. The surface-exposed glycans revealed their impact on the viral immune evasion and host cell invasion. The S-acylation sites involve in stabilizing the transmembrane assembly. In addition, a cholesterol and a phospholipid molecule are observed in a transmembrane hydrophobic pocket, together with two more cholesterols surrounding the pocket. The structural information will assist structure-based antiviral and vaccine design.
Plasmin-mediated cleavage of EphA4 at central amygdala inhibitory synapses controls anxiety
Authors: Mucha Mariusz , Labrador-Ramos Alberto , Attwood Benjamin K. , Bajor Malgorzata , Kolenchery Jaison B. , Skrzypiec Anna E. , Brambilla Valentina , Magnowska Marta , Figiel Izabela , Swiatek Michal , Wiktorowska Lucja , Shah Rahul S. , Pijet Barbara , Sakai Yusuke , Nagai Nobuo , Klejman Agata , Wlodarczyk Jakub , Kaczmarek Leszek , Przewlocki Ryszard , Pawlak Robert
Published: July 2021

Severe stress can trigger complex behavioural changes such as high anxiety (1). Inhibitory GABA-ergic interneurons in the lateral division of the central amygdala (CEl) control anxiety through feedforward inhibition of their target cells in the medial division (CEm) (2, 3). In particular, PKCδ-positive (PKCδ+) interneurons in CEl are critical elements of the neuronal circuitry of fear and anxiety (3–5), but the molecular mechanisms they employ are poorly understood. Here, we show that, during stress, GABA-ergic synapses of amygdala PKCδ+interneurons are regulated by a serine protease plasmin. On stress, plasmin cleaves the extracellular portion of the tyrosine kinase receptor EphA4 triggering its dissociation from gephyrin, a postsynaptic GABA-receptor anchoring protein. Dynamic EphA4/gephyrin interaction leads to modification of dendritic spine morphology and synaptic GABA-receptor expression profile. Consistent with the critical role for the plasmin/EphA4/gephyrin signalling axis in anxiogenesis, viral delivery of plasmin-resistant (prEphA4) form of EphA4 into the central amygdala prevents the development of stress-induced anxiety in mice, while the delivery of plasmin-truncated EphA4 (tEphA4) dramatically enhances this effect. Thus, our studies identify a novel, critical molecular cascade regulating GABA-ergic signalling in the central amygdala synapses that allows bidirectional switching of animal behaviour from high to low anxiety states.
An oligosaccharide analog exhibited antifungal activity by misleading cell wall organization via targeting PHR transglucosidases
Authors: Li Ruilian , Zhu Limeng , Liu Dongdong , Wang Wenjing , Zhang Chen , Jiao Siming , Wei Jinhua , Ren Lishi , Zhang Yuchen , Gou Xun , Yuan Xianghua , Wang Zhuo A. , Du Yuguang
Published: July 2021

The fungal cell wall is an ideal target for the design of antifungal drugs. In this study we used an analog of cell wall polymer, a highly deacetylated long-chain chitosan oligosaccharide (HCOS), to test its effect against pathogenicCandidastrains. Results showed that HCOS was successfully incorporated into the dynamic cell wall organization process and exhibited an apparent antifungal activity against both plankton and mature fungal biofilm, by impairing the cell wall integrity. Unexpectedly, mechanistic studies suggested that HCOS exerts its activity by interfering with family members of PHR β-(1,3)-glucanosyl transferases and affecting the connection and assembly of cell wall polysaccharides. Furthermore, HCOS showed great synergistic activity with different fungicides againstCandidacells, especially those in biofilm. These findings indicated HCOS has a great potential as an antifungal drug or drug synergist and proposed a novel antifungal strategy with structure-specific oligosaccharides mimicking cell wall polysaccharide fragments.

IMPORTANCE

Fungal infections have always been a puzzle in clinical medicine. Only a few antifungal drugs are available for medical usage and the widespread use of antifungal drugs increased the incidence of drug resistance. It is an urgent need for the development of novel treatment strategies against fungal infections. In this study, we proposed a novel strategy targeting to fungal cell wall againstC. albicans.To our knowledge, it is the first study to show a cell wall polysaccharide fragment analog integrate into and interfere with the fungal cell wall, indicating a novel antifungal strategy using structure-specific oligosaccharides mimicking cell wall polysaccharide fragments.
Membrane thickness, lipid phase and sterol type are determining factors in the permeability of membranes to small solutes
Authors: Frallicciardi Jacopo , Melcr Josef , Siginou Pareskevi , Marrink Siewert J. , Poolman Bert
Published: July 2021

Cell membranes provide a selective semi-permeable barrier to the passive transport of molecules. This property differs greatly between organisms. While the cytoplasmic membrane of bacterial cells is highly permeable for weak acids and glycerol, yeasts can maintain large concentration gradients. Here we show that such differences can arise from the physical state of the plasma membrane. By combining stopped-flow kinetic measurements with molecular dynamics simulations, we performed a systematic analysis of the permeability through synthetic lipid membranes to obtain detailed molecular insight into the permeation mechanisms. While membrane thickness is an important parameter for the permeability through fluid membranes, the largest differences occur when the membranes transit from the liquid-disordered to liquid-ordered and/or to gel state. By comparing our results with in vivo measurements from yeast, we conclude that the yeast membrane exists in a highly ordered and rigid state, which is comparable to synthetic saturated DPPC-sterol membranes.
Climatic niche pre-adaptation in mainland Europe facilitated the colonization of Madeira by ivies (Hedera L., Araliaceae)
Authors: Alonso Alejandro , Gallego-Narbón Angélica , de la Iglesia Marina Coca , Monjas David , Medina Nagore G. , Fernández-Mazuecos Mario , Valcárcel Virginia
Published: July 2021

Background and aims

The way plants cope with biotic and abiotic selective pressures determines their success in the colonization of remote oceanic islands, which ultimately depends on the phylogenetic constrains and ecological response of the lineage. In this study we aim to evaluate the relative role of geographical and ecological forces in the origin and evolution of the Madeiran ivy (H. maderensis).

Methods

To determine the phylogenetic placement of H. maderensis within the western polyploid clade of Hedera (three species), we analysed 40 populations (92 individuals) using genotyping-by-sequencing and including H. helix as outgroup. Climatic niche differences among the four study species were evaluated using a database with 706 records representing the entire species ranges. To test species responses to climate, a set of 19 vegetative and regenerative functional traits were examined for 70 populations (335 individuals).

Key results

Phylogenomic results revealed a nested pattern with H. maderensis embedded within H. iberica. Gradual niche differentiation from the coldest and most continental populations of H. iberica to the warm and stable coastal population sister to H. maderensis parallels the geographical pattern observed in the phylogeny. Similarity in adaptive traits is observed for H. maderensis and H. iberica. The two species show leaves with higher SLA, lower LDMC and thickness and smaller fruits than those of H. hibernica.

Conclusions

Acquisition of the Macaronesian climatic niche and the associated functional syndrome in mainland European ivies (small fruits, leaves high SLA, and low LDMD and thickness) was a key step in the colonization of Madeira by the H. iberica/H. maderensis lineage, which points to climatic pre-adaptation as a driver of island colonization (dispersal and establishment). Once in Madeira, speciation was driven by geographical isolation, while ecological processes are regarded as secondary forces with a putative impact in the lack of further in situ diversification.
Genome-wide characterization of the MLO gene family in Cannabis sativa reveals two genes as strong candidates for powdery mildew susceptibility
Authors: Pépin Noémi , Hebert Francois Olivier , Joly David L.
Published: July 2021

Cannabis sativa is increasingly being grown around the world for medicinal, industrial, and recreational purposes. As in all cultivated plants, cannabis is exposed to a wide range of pathogens, including powdery mildew (PM). This fungal disease stresses cannabis plants and reduces flower bud quality, resulting in significant economic losses for licensed producers. The Mildew Locus O (MLO) gene family encodes plant-specific proteins distributed among conserved clades, of which clades IV and V are known to be involved in susceptibility to PM in monocots and dicots, respectively. In several studies, the inactivation of those genes resulted in durable resistance to the disease. In this study, we identified and characterized the MLO gene family members in five different cannabis genomes. Fifteen Cannabis sativa MLO (CsMLO) genes were manually curated in cannabis, with numbers varying between 14, 17, 19, 18, and 18 for CBDRx, Jamaican Lion female, Jamaican Lion male, Purple Kush, and Finola, respectively (when considering paralogs and incomplete genes). Further analysis of the CsMLO genes and their deduced protein sequences revealed that many characteristics of the gene family, such as the presence of 7 transmembrane domains, the MLO functional domain, and particular amino acid positions, were present and well conserved. Phylogenetic analysis of the MLO protein sequences from all five cannabis genomes and other plant species indicated seven distinct clades (I through VII), as reported in other crops. Expression analysis revealed that the CsMLOs from clade V, CsMLO1 and CsMLO4, were significantly upregulated following Golovinomyces ambrosiae infection, providing preliminary evidence that they could be involved in PM susceptibility. Finally, the examination of variation within CsMLO1 and CsMLO4 in 32 cannabis cultivars revealed several amino acid changes, which could affect their function. Altogether, cannabis MLO genes were identified and characterized, among which candidates potentially involved in PM susceptibility were noted. The results of this study will lay the foundation for further investigations, such as the functional characterization of clade V MLOs as well as the potential impact of the amino acid changes reported. Those will be useful for breeding purposes in order to develop resistant cultivars.