bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissecting errors made in response to externally- and internally-driven visual tasks in the common marmosets and humans
Authors: Amly Wajd , Chen Chih-Yang , Onoe Hirotaka , Isa Tadashi
Published: August 2021

Various visual paradigms in oculomotor research have been used for studying the neural processes of eye movement, cognitive control, attention and neurological disorders. However, we usually analyse data collected from humans or over-trained non-human primates (NHPs), focusing only on successful trials, whereas error trials are usually excluded. These errors may repetitively show up in diseases, but their interpretation would be difficult due to the absence of records taken from healthy controls. In the current study, we aimed to analyse both correctly and incorrectly performed trials in both marmosets and humans. We trained marmosets to perform the gap saccade task and the oculomotor delayed response task. We also collected data from human subjects who performed identical tasks. We categorised error trials into three different groups, based on the time when an incorrect response occurred. We also interpreted possible causes by analysing saccade reaction time, saccade landing position and task history. Despite the rareness of human error, we found that marmosets and humans showed remarkably similar behaviour in error and success. We also found that successful saccades in the gap saccade task had always the highest peak velocity in both species, reflecting faster sensorimotor processing for correct responses. Our results suggest that marmosets and humans might share similar neural processing for successful and unsuccessful oculomotor behaviour, making them a suitable model for studying human behaviour. More importantly, analysing error trials in sync with successful ones will provide further insights into the cognitive and sensorimotor processes.

NEW AND NOTEWORTHY

This is the first detailed report focusing on analysing both error and successful trials in oculomotor tasks. We proposed nomenclatures and a generalizable way of grouping and analysing error trials. Our results also indicate that marmosets can be a promising experimental candidate for oculomotor research because they replicate the saccade properties of error and success seen in humans. This will help set the baseline measurements to study brain disorders using NHP and understand the neural mechanisms from a different perspective.
BiomeHorizon: visualizing microbiome time series data in R
Authors: Fink Isaac , Abdill Richard J. , Blekhman Ran , Grieneisen Laura
Published: August 2021

A key aspect of microbiome research is analysis of longitudinal dynamics using time series data. A method to visualize both the proportional and absolute change in the abundance of multiple taxa across multiple subjects over time is needed. We developed BiomeHorizon, an open-source R package that visualizes longitudinal compositional microbiome data using horizon plots.

Availability and Implementation

BiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and released under the MIT license. A guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/. The guide also provides code to reproduce all plots in this manuscript.

Contact

lgrienei@umn.edu, blekhman@umn.edu, iafink@uchicago.edu

Supplementary information

None
Exploiting flow cytometry for the unbiased quantification of protein inclusions inCaenorhabditis elegans
Authors: Claesson Kristian , Chew Yee Lian , Ecroyd Heath
Published: August 2021

The aggregation of proteins into inclusions or plaques is a prominent hallmark of a diverse range of pathologies including neurodegenerative diseases. The quantification of such inclusions inCaenorhabditis elegansmodels of aggregation is usually achieved by fluorescence microscopy or other techniques involving biochemical fractionation of worm lysates. Here, we describe a simple and rapid flow cytometry-based approach that allows fluorescently-tagged inclusions to be enumerated in whole worm lysate in a quantitative and unbiased fashion. We demonstrate that this technique is applicable to multipleC. elegansmodels of aggregation and importantly, can be used to monitor the dynamics of inclusion formation in response to heat shock and during aging. This includes the characterisation of physicochemical properties of inclusions, such as their size, which may reveal how aggregate formation is distinct in different tissues or at different stages of pathology or aging. This new method can be used as a powerful technique for the medium- to high-throughput quantification of inclusions in future studies of genetic or chemical modulators of aggregation inC. elegans.
AZD7442 demonstrates prophylactic and therapeutic efficacy in non-human primates and extended half-life in humans
Authors: Loo Yueh-Ming , McTamney Patrick M. , Arends Rosalinda H. , Gasser Robert A. , Abram Michael E. , Aksyuk Anastasia , Diallo Seme , Flores Daniel J. , Kelly Elizabeth J. , Ren Kuishu , Roque Richard , Rosenthal Kim , Streicher Katie , Tuffy Kevin M. , Bond Nicholas J. , Cornwell Owen , Bouquet Jerome , Cheng Lily I. , Dunyak James , Huang Yue , Rosenbaum Anton I. , Andersen Hanne , Carnahan Robert H. , Crowe James E. , Kuehne Ana I. , Herbert Andrew S. , Dye John M. , Bright Helen , Kallewaard Nicole L. , Pangalos Menelas N. , Esser Mark T.
Published: August 2021

Despite the success of SARS-CoV-2 vaccines, there remains a need for more prevention and treatment options for individuals remaining at risk of COVID-19. Monoclonal antibodies (mAbs) against the viral spike protein have potential to both prevent and treat COVID-19, and reduce the risk of severe disease and death. Here, we describe AZD7442, a combination of two mAbs, AZD8895 (tixagevimab) and AZD1061 (cilgavimab), that simultaneously bind to distinct non-overlapping epitopes on the spike protein receptor binding domain to potently neutralize SARS-CoV-2. Initially isolated from individuals with prior SARS-CoV-2 infection, the two mAbs were designed to extend their half-lives and abrogate effector functions. The AZD7442 mAbs individually prevent the spike protein from binding to angiotensin-converting enzyme 2 receptor, blocking virus cell entry. Together, these two mAbs create a higher barrier to viral escape and a wider breadth of coverage, neutralizing all known SARS-CoV-2 variants of concern. In a non-human primate model of SARS-CoV-2 infection, prophylactic AZD7442 administration prevented infection, while therapeutic administration accelerated virus clearance from lung. In an ongoing Phase I study in healthy participants (NCT04507256), 300 mg intramuscular AZD7442 provided SARS-CoV-2 serum geometric mean neutralizing titers >10-fold above those of convalescent sera for ≥3 months, which remained 3-fold above those of convalescent sera 9 months post-AZD7442 administration. Approximately 1–2% of serum AZD7442 levels were detected in nasal mucosa, a site of SARS-CoV-2 infection. Extrapolation of the time course of serum AZD7442 concentrations suggests AZD7442 may provide up to 12 months of protection and benefit individuals at high-risk of COVID-19.
Single-cell transcriptomic atlas of individuals receiving inactivated COVID-19 vaccines reveals distinct immunological responses between vaccine and natural SARS-CoV-2 infection
Authors: Wang Yi , Wang Xiaoxia , Luu Laurence Don Wai , Li Jieqiong , Cui Xiaodai , Yao Hailan , Zhang Xin , Chen Shaojin , Fu Jin , Wang Licheng , Wang Chongzhen , Yuan Rui , Cai Qingguo , Huang Xiaolan , Huang Junfei , Xu Wenjian , Li Shijun , Zhu Xiong , Tai Jun
Published: August 2021

To control the ongoing COVID-19 pandemic, CoronaVac (Sinovac), an inactivated vaccine, has been granted emergency use authorization by many countries. However, the underlying mechanisms of the inactivated COVID-19 vaccine-induced immune response remain unclear, and little is known about its features compared to SARS-CoV-2 infection. Here, we implemented single-cell RNA sequencing (scRNA-seq) to profile longitudinally collected PBMCs (peripheral blood mononuclear cells) in six individuals immunized with CoronaVac and compared these to the profiles of COVID-19 infected patients from a Single Cell Consortium. Both inactivated vaccines and SARS-CoV-2 infection drove changes in immune cell type proportions, caused B cell activation and differentiation, and induced the expression of genes associated with antibody production in the plasma. The inactivated vaccine and SARS-COV-2 infection also caused alterations in peripheral immune activity such as interferon response, inflammatory cytokine expression, innate immune cell apoptosis and migration, effector T cell exhaustion and cytotoxicity, however, the magnitude of change was greater in COVID-19 patients, especially those with severe disease, than in immunized individuals. Further analyses revealed a distinct peripheral immune cell phenotype associated with CoronaVac immunization (HLA class II upregulation and IL21R upregulation in naïve B cells) versus SARS-CoV-2 infection (HLA class II downregulation and IL21R downregulation in naïve B cells severe disease). There were also differences in the expression of important genes associated with proinflammatory cytokines and thrombosis. In conclusion, this study provides a single-cell atlas of the systemic immune response to CoronaVac immunization and reveals distinct immune responses between inactivated vaccines and SARS-CoV-2 infection.
Total Infectomes Characterization of Respiratory Infections in pre-COVID-19 Wuhan, China
Authors: Shi Mang , Zhao Su , Yu Bin , Wu Wei-Chen , Hu Yi , Tian Jun-Hua , Yin Wen , Ni Fang , Hu Hong-Ling , Geng Shuang , Tan Li , Peng Ying , Song Zhi-Gang , Wang Wen , Chen Yan-Mei , Holmes Edward C. , Zhang Yong-Zhen
Published: August 2021

At the end of 2019 Wuhan witnessed an outbreak of “atypical pneumonia” that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus - SARS-CoV-2. Herein, to provide a snapshot of the pathogens in pneumonia-associated respiratory samples from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid samples from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their “total infectome”, including viruses, bacteria and fungi. Consequently, we identified 37 pathogen species, comprising 15 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (12.8%). However, SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen –Chlamydia psittaci. Samples from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of individual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more diverse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016-2017.
A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding
Authors: van Rengs Willem M. J. , Schmidt Maximilian H.-W. , Effgen Sieglinde , Wang Yazhong , Zaidan Mohd Waznul Adly Mohd , Huettel Bruno , Schouten Henk J. , Usadel Björn , Underwood Charles J.
Published: August 2021

The assembly and scaffolding of plant crop genomes facilitates the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of Tobacco Mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all twelve chromosomes were represented as twelve contiguous sequences (N50=68.5 Mbp). The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps and HiC for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1 Mbp region of the S. peruvianum genome during tomato breeding. We show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near complete genome sequences.
Recurrent Integration of Human Papillomavirus Genomes at Transcriptional Regulatory Hubs
Authors: Warburton Alix , Markowitz Tovah E. , Katz Joshua P. , Pipas James M. , McBride Alison A.
Published: August 2021

Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy, or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation, and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here, we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites, but often only one “driver” site that expressed viral RNA. Since common fragile sites and active enhancer elements are cell-type specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites, and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration “hotspots” that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters, and accidental integration could promote viral oncogene expression and carcinogenesis.
Recognition of natural objects in the archerfish
Authors: Volotsky Svetlana , Ben-Shahar Ohad , Donchin Opher , Segev Ronen
Published: August 2021

Recognition of individual objects and their categorization is a complex computational task. Nevertheless, visual systems are able to perform this task in a rapid and accurate manner. Humans and other animals can efficiently recognize objects despite countless variations in their projection on the retina due to different viewing angles, distance, illumination conditions, and other parameters. Numerous studies conducted in mammals have associated the recognition process with cortical activity. Although the ability to recognize objects is not limited to mammals and has been well-documented in other vertebrates that lack a cortex, the mechanism remains elusive. To address this gap, we explored object recognition in the archerfish, which lack a fully developed cortex. Archerfish hunt by shooting a jet of water at aerial targets. We leveraged this unique skill to monitor visual behavior in archerfish by presenting fish with a set of images on a computer screen above the water tank and observing the behavioral response. This methodology served to characterize the ability of the archerfish to perform ecologically relevant recognition of natural objects. We found that archerfish can recognize an individual object presented under different conditions and that they can also categorize novel objects into known categories. Manipulating features of these objects revealed that the fish were more sensitive to object contours than texture and that a small number of features was sufficient for categorization. Our findings suggest the existence of a complex visual process in the archerfish visual system that enables object recognition and categorization.
On co-activation pattern analysis and non-stationarity of resting brain activity
Authors: Matsui Teppei , Pham Trung Quang , Jimura Koji , Chikazoe Junichi
Published: August 2021

The non-stationarity of resting-state brain activity has received increasing attention in recent years. Functional connectivity (FC) analysis with short sliding windows and coactivation pattern (CAP) analysis are two widely used methods for assessing the dynamic characteristics of brain activity observed with functional magnetic resonance imaging (fMRI). However, the statistical nature of the dynamics captured by these techniques needs to be verified. In this study, we found that the results of CAP analysis were similar for real fMRI data and simulated stationary data with matching covariance structures and spectral contents. We also found that, for both the real and simulated data, CAPs were clustered into spatially heterogeneous modules. Moreover, for each of the modules in the real data, a spatially similar module was found in the simulated data. The present results suggest that care needs to be taken when interpreting observations drawn from CAP analysis as it does not necessarily reflect non-stationarity or a mixture of states in resting brain activity.

Highlights

CAP was conducted for real fMRI data and a stationary null model.

The results of CAP analysis were similar for the real and simulated data.

Similar results for real and simulated data in both ROI- and voxel-based analyses.

Results of CAP analysis may not reflect non-stationarity of resting brain activity.
Translation of MT-ATP6 pathogenic variants reveals distinct regulatory consequences from the co-translational quality control of mitochondrial protein synthesis
Authors: Ng Kah Ying , Richter Uwe , Jackson Christopher B. , Seneca Sara , Battersby Brendan J.
Published: August 2021

Pathogenic variants that disrupt human mitochondrial protein synthesis are associated with a clinically heterogenous group of diseases. Despite an impairment in oxidative phosphorylation being a common phenotype, the underlying molecular pathogenesis is more complex than simply a bioenergetic deficiency. Currently, we have limited mechanistic understanding on the scope by which a primary defect in mitochondrial protein synthesis contributes to organelle dysfunction. Since the proteins encoded in the mitochondrial genome are hydrophobic and need co-translational insertion into a lipid bilayer, responsive quality control mechanisms are required to resolve aberrations that arise with the synthesis of truncated and misfolded proteins. Here, we show that defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex. Using pathogenic MT-ATP6 variants, we then reveal discrete steps in this quality control mechanism and the differential functional consequences to mitochondrial gene expression. The inherent ability of a given cell type to recognize and resolve impairments in mitochondrial protein synthesis may in part contribute at the molecular level to the wide clinical spectrum of these disorders.
Apelin signaling dependent endocardial protrusions promote cardiac trabeculation in zebrafish
Authors: Qi Jialing , Rittershaus Annegret , Priya Rashmi , Mansingh Shivani , Stainier Didier Y.R. , Helker Christian S.M.
Published: August 2021

During cardiac development, endocardial cells (EdCs) produce growth factors to promote myocardial morphogenesis and growth. In particular, EdCs produce Neuregulin which is required for ventricular cardiomyocytes (CMs) to seed the multicellular ridges known as trabeculae. Defects in Neuregulin signaling, or in endocardial sprouting towards CMs, cause hypotrabeculation. However, the mechanisms underlying endocardial sprouting remain largely unknown. Here, we first show by live imaging in zebrafish embryos that EdCs interact with CMs via dynamic membrane protrusions. After touching CMs, these protrusions remain in close contact with their target despite the vigorous cardiac contractions. Loss of the CM-derived peptide Apelin, or of the Apelin receptor, which is expressed in EdCs, leads to reduced endocardial sprouting and hypotrabeculation. Mechanistically, Neuregulin signaling requires endocardial protrusions to activate extracellular signal-regulated kinase (Erk) signaling in CMs and trigger their delamination. Altogether, these data show that Apelin signaling dependent endocardial protrusions modulate CM behavior during trabeculation.
Influenza A virus (H1N1) infection induces microglia activation and temporal dysbalance in glutamatergic synaptic transmission
Authors: Düsedau Henning Peter , Steffen Johannes , Figueiredo Caio Andreeta , Boehme Julia Désirée , Schultz Kristin , Erck Christian , Korte Martin , Faber-Zuschratter Heidi , Smalla Karl-Heinz , Dieterich Daniela , Kröger Andrea , Bruder Dunja , Dunay Ildiko Rita
Published: August 2021

3.

Influenza A virus (IAV) causes respiratory tract disease and is responsible for seasonal and reoccurring epidemics affecting all age groups. Next to typical disease symptoms such as fever and fatigue, IAV infection has been associated with behavioral alterations presumably contributing to the development of major depression. Previous experiments using IAV/H1N1 infection models have shown impaired hippocampal neuronal morphology and cognitive abilities, but the underlying pathways have not been fully described. In this study, we demonstrate that infection with a low dose non-neurotrophic H1N1 strain of IAV causes ample peripheral immune response followed by a temporary blood-brain-barrier disturbance. Although histological examination did not reveal obvious pathological processes in the brains of IAV-infected mice, detailed multidimensional flow cytometric characterization of immune cells uncovered subtle alterations in the activation status of microglia cells. More specifically, we detected an altered expression pattern of major histocompatibility complex class I and II, CD80, and F4/80 accompanied by elevated mRNA levels of CD36, CD68, C1QA, and C3, suggesting evolved synaptic pruning. To closer evaluate how these profound changes affect synaptic balance, we established a highly sensitive multiplex flow cytometry-based approach called Flow Synaptometry. The introduction of this novel technique enabled us to simultaneously quantify the abundance of pre- and postsynapses from distinct brain regions. Our data reveal a significant reduction of VGLUT1 in excitatory presynaptic terminals in the Cortex and Hippocampus, identifying a subtle dysbalance in glutamatergic synapse transmission upon H1N1 infection in mice. In conclusion, our results highlight the consequences of systemic IAV-triggered inflammation on the central nervous system and the induction and progression of neuronal alterations.
A novel effective live-attenuated human metapneumovirus vaccine candidate produced in the serum-free suspension DuckCelt®-T17 cell platform
Authors: Chupin Caroline , Pizzorno Andrés , Traversier Aurélien , Brun Pauline , Ogonczyk-Makowska Daniela , Padey Blandine , Milesi Cédrine , Dulière Victoria , Laurent Emilie , Julien Thomas , Galloux Marie , Lina Bruno , Eléouët Jean-François , Moreau Karen , Hamelin Marie-Eve , Terrier Olivier , Boivin Guy , Dubois Julia , Rosa-Calatrava Manuel
Published: August 2021

Human metapneumovirus (HMPV) is a major pediatric respiratory pathogen for which there is currently no specific treatment or licensed vaccine. Different strategies have been evaluated to prevent this infection, including the use of live-attenuated vaccines (LAVs). However, further development of LAV approaches is often hampered by the lack of highly efficient and scalable cell-based production systems that support worldwide vaccine production. In this context, avian cell lines cultivated in suspension are currently competing with traditional cell platforms used for viral vaccine manufacturing. We investigated whether the DuckCelt®-T17 avian cell line (Vaxxel) we previously described as an efficient production system for several influenza strains could also be used to produce a new HMPV LAV candidate (Metavac®), an engineered SH gene-deleted mutant of the A1/C-85473 strain of HMPV. To that end, we characterized the operational parameters of multiplicity of infection (MOI), cell density, and trypsin addition to achieve optimal production of the LAV Metavac® in the DuckCelt®-T17 cell line platform. We demonstrated that the DuckCelt®-T17 cell line is permissive and is well adapted to the production of the wild-type A1/C-85473 HMPV and the Metavac® vaccine candidate. Moreover, our results confirmed that the LAV candidate produced in DuckCelt®-T17 cells conserves its advantageous replication properties in LLC-MK2 and 3D-reconstituted human airway epithelium models, as well as its capacity to induce efficient neutralizing antibodies in a mouse model. Our results suggest that the DuckCelt®-T17 avian cell line is a very promising platform for scalable in-suspension serum-free production of the HMPV-based LAV candidate Metavac®.
Exploring the conformational landscape and stability of Aurora A using ion-mobility mass spectrometry and molecular modelling
Authors: Tomlinson Lauren J. , Batchelor Matthew , Sarsby Joscelyn , Byrne Dominic P. , Brownridge Philip , Bayliss Richard , Eyers Patrick A. , Eyers Claire E.
Published: August 2021

Protein kinase inhibitors are proving highly effective in helping treat a number of non-communicable diseases driven by aberrant kinase signaling. They are also extremely valuable as chemical tools to help delineate cellular roles of kinase signaling complexes. The binding of small molecule inhibitors induces conformational effects on kinase dynamics; evaluating the effect of such interactions can assist in developing specific inhibitors and is deemed imperative to understand both inhibition and resistance mechanisms. Using gas-phase ion mobility-mass spectrometry (IM-MS) we characterized changes in the conformational landscape and stability of the protein kinase Aurora A (Aur A) driven by binding of the physiological activator TPX2 or small molecule inhibition. Aided by molecular modeling, we establish three major conformations: one highly-populated compact conformer similar to that observed in most crystal structures, a second highly-populated conformer possessing a more open structure that is infrequently found in crystal structures, and an additional low-abundance conformer not currently represented in the protein databank. Comparison of active (phosphorylated) and inactive (non-phosphorylated) forms of Aur A revealed that the active enzyme has different conformer weightings and is less stable than the inactive enzyme. Notably, inhibitor binding shifts conformer balance towards the more compact configurations adopted by the unbound enzyme, with both IM-MS and modelling revealing inhibitor-mediated stabilisation of active Aur A. These data highlight the power of IM-MS in combination with molecular dynamics simulations to probe and compare protein kinase structural dynamics that arise due to differences in activity and as a result of compound binding.
NetRAX: Accurate and Fast Maximum Likelihood Phylogenetic Network Inference⋆
Authors: Lutteropp Sarah , Scornavacca Céline , Kozlov Alexey M. , Morel Benoit , Stamatakis Alexandros
Published: August 2021

Phylogenetic networks are used to represent non-treelike evolutionary scenarios. Current, actively developed approaches for phylogenetic network inference jointly account for non-treelike evolution and incomplete lineage sorting (ILS). Unfortunately, this induces a very high computational complexity. Hence, current tools can only analyze small data sets.

We present NetRAX, a tool for maximum likelihood inference of phylogenetic networks in the absence of incomplete lineage sorting. Our tool leverages state-of-the-art methods for efficiently computing the phylogenetic likelihood function on trees, and extends them to phylogenetic networks via the notion of “displayed trees”. NetRAX can infer maximum likelihood phylogenetic networks from partitioned multiple sequence alignments and returns the inferred networks in Extended Newick format.

On simulated data, our results show a very low relative difference in BIC score and a near-zero unrooted softwired cluster distance to the true, simulated networks. With NetRAX, a network inference on a partitioned alignment with 8, 000 sites, 30 taxa, and 3 reticulations completes within a few minutes on a standard laptop.

Our implementation is available under the GNU General Public License v3.0 at https://github.com/lutteropp/NetRAX.
The beneficial role ofCandida intermediaandSaccharomyces boulardiiyeasts on the immune response of mice vaccinated with a SARS-CoV-2 experimental vaccine
Authors: Piraine Renan Eugênio Araujo , Conrad Neida Lucia , Gonçalves Vitória Sequeira , Ramos Jeferson Vidart , Leite Fábio Pereira Leivas
Published: August 2021

Non-Saccharomycesyeasts emerge as possible new probiotics with a beneficial effect equal to or greater than the reference probiotic yeast,Saccharomyces boulardii. In this work, we evaluated the immunomodulation effect caused byCandida intermediain mice vaccinated with inactivated SARS-CoV-2. We conducted preliminary tests using murine macrophages (RAW 264.7) stimulated with viable and heat-killed yeast cells, culture supernatant, and DNA, using qPCR to detect the mRNA transcription. Next, mice were supplemented withC. intermediabefore each dose of the SARS-CoV-2 vaccine, and then antibody production was measured by ELISA. The probiotic strainS. boulardiiCNCM I-745 was used as a control. We also explored the differences in fecal microbiomes between the non-supplemented and supplemented groups. Live cells ofC. intermediaincreased the transcription ofIL-4,IL-13, andSTAT3by macrophages RAW 264.7, while heat-killed cells up-regulatedTNFαandBcl6, and the culture supernatant positively impactedTLR2transcription. Concanavalin, zymosan, and lipopolysaccharide were used to stimulate splenocytes fromC. intermedia-supplemented animals, which showed increased transcription ofTNFα,IFNγ,IL-4,Bcl6, andSTAT3. Sera from these animals showed enhanced levels of anti-SARS-CoV-2 IgG, as well as IgG1 and IgM isotypes, and sIgA in fecal samples. The microbiome of theC. intermedia-supplemented group showed a higher abundance ofBacteroidesspp. andClostridiumspp., impacting the Bacteroidetes/Firmicutes balance. We concluded thatC. intermediaandS. boulardiicould stimulate and impact the gene expression of cells important for innate immunity, influence the composition of the gastrointestinal microbiome, and primarily boost the humoral response after vaccination.

Statements and Declarations Funding

The present work was carried out with the support of Conselho Nacional de Desenvolvimento Científico (CNPq, Brazil), grant number 150538/2021-9.
Theory of branching morphogenesis by local interactions and global guidance
Authors: Uçar Mehmet Can , Kamenev Dmitrii , Sunadome Kazunori , Fachet Dominik , Lallemend François , Adameyko Igor , Hadjab Saida , Hannezo Edouard
Published: August 2021

Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales.
The male and female gonad transcriptome of the edible sea urchin, Paracentrotus lividus: identification of sex-related and lipid biosynthesis genes
Authors: Machado André M. , Fernández-Boo Sergio , Nande Manuel , Pinto Rui , Costas Benjamin , Castro L. Filipe C.
Published: August 2021

Paracentrotus lividus is the most abundant, distributed and desirable echinoid species in Europe. Although, economically important, this species has scarce genomic resources available. Here, we produced and comprehensively characterized the male and female gonad transcriptome of P. lividus. The P. lividus transcriptome assembly has 53,865 transcripts, an N50 transcript length of 1,842 bp and an estimated gene completeness of 97.4% and 95.6% in Eukaryota and Metazoa BUSCO databases, respectively. Differential gene expression analyses yielded a total of 3371 and 3351 up regulated genes in P. lividus male and female gonad tissues, respectively. Additionally, we analysed and validated a catalogue of pivotal transcripts involved in sexual development and determination (206 transcripts) as well as in biosynthesis and storage of lipids (119 transcripts) in male and female specimens. This study provides a valuable transcriptomic resource and will contribute for the future conservation of the species as well as the exploitation in aquaculture settings.

Highlights

Assembly of a reference transcriptome of Paracentrotus lividus gonads.

Differential gene expression between males and female gonads of Paracentrotus lividus.

Identification and validation of pivotal genes involved in biosynthesis and storage of lipids.
Loss of Secretory Pathway Ca2+ ATPase (SPCA1) Impairs Insulin Secretion and Reduces Autophagy in the Pancreatic Islet
Authors: Bone Robert N. , Tong Xin , Weaver Staci A. , Muralidharan Charanya , Krishnan Preethi , Kono Tatsuyoshi , Evans-Molina Carmella
Published: August 2021

The β cell Golgi apparatus serves as a significant store of intracellular Ca2+ and an important site of proinsulin maturation. However, the contribution of Golgi Ca2+ to diabetes pathophysiology is unknown. The Golgi primarily utilizes the Secretory Pathway Ca2+ ATPase (SPCA1) to maintain intraluminal Ca2+ stores, and loss of SPCA1 has been linked to impaired Golgi function in other cell types. Here, we demonstrated that SPCA1 expression is decreased in islets from diabetic mice and human organ donors with type 2 diabetes, suggesting SPCA1 may impact diabetes development. INS-1 β cells lacking SPCA1 (SPCA1KO) showed reduced intraluminal Golgi Ca2+ levels, reduced glucose-stimulated insulin secretion (GSIS), and increased insulin content. Islets from SPCA1 haploinsufficient mice (SPCA1+/-) exhibited reduced GSIS, altered glucose-induced Ca2+ oscillations, and altered insulin granule maturation. Autophagy can regulate granule homeostasis, therefore we induced autophagy with Torin1 and found that SPCA1KO cells and SPCA1+/- islets had reduced levels of the autophagosome marker LC3-II. Furthermore, SPCA1KO LC3-II were unchanged after blocking autophagy initiation or autophagolysosome fusion and acidification. Thus, we concluded that β cell SPCA1 plays an important role in the maintenance of Golgi Ca2+ homeostasis and reduced Golgi Ca2+ impairs autophagy initiation and may impact insulin granule homeostasis.
Relationship between COVID-19 infection and neurodegeneration: Computational insight into interactions between the SARS-CoV-2 spike protein and the monoamine oxidase enzymes
Authors: Hok Lucija , Rimac Hrvoje , Mavri Janez , Vianello Robert
Published: August 2021

Although COVID-19 has been primarily associated with pneumonia, recent data show that its causative agent, the SARS-CoV-2 coronavirus, can infect many vital organs beyond the lungs, including the heart, kidneys and the brain. The literature agrees that COVID-19 is likely to have long-term mental health effects on infected individuals, which signifies a need to understand the role of the virus in the pathophysiology of brain disorders that is currently unknown and widely debated. Our docking and molecular dynamic simulations show that the affinity of the spike protein from the wild type (WT) and the South African B.1.351 (SA) variant towards the MAO enzymes is comparable to that for its ACE2 receptor. This allows for the WT/SA…MAO complex formation, which changes MAO affinities for their neurotransmitter substrates, thus consequently impacting the rates of their metabolic conversion and misbalancing their levels. Knowing that this fine regulation is strongly linked with the etiology of various brain pathologies, these results are the first to highlight the possibility that the interference with the brain MAO catalytic activity is responsible for the increased neurodegenerative illnesses following a COVID-19 infection, thus placing a neurobiological link between these two conditions in the spotlight. Since the obtained insight suggests that a more contagious SA variant causes even larger disturbances, and with new and more problematic strains likely emerging in the near future, we firmly advise that the presented prospect of the SARS-CoV-2 induced neurological complications should not be ignored, but rather requires further clinical investigations to achieve an early diagnosis and timely therapeutic interventions.

TABLE OF CONTENTS ENTRY

Docking and molecular dynamic simulations highlight the possibility that the interference with the brain monoamine oxidase (MAO) catalytic activity is responsible for the increased neurodegenerative illnesses following a COVID-19 infection.
Songbird subthalamic neurons signal song timing and error and project to dopaminergic midbrain
Authors: Das Anindita , Goldberg Jesse H.
Published: August 2021

Skill learning requires motor output to be evaluated against internal performance benchmarks. In songbirds, ventral tegmental area (VTA) dopamine neurons (DA) signal performance errors important for learning, but it remains unclear which brain regions project VTA and how these inputs may implement the sensorimotor comparisons necessary for error computation. Here we find that the songbird subthalamic nucleus (STN) projects to VTA and that STN microstimulation can excite VTA neurons. We also discover that STN receives inputs from auditory cortical and ventral pallidal brain regions previously implicated in song evaluation. In the first neural recordings from songbird STN, we discover that the activity of most STN neurons is associated with body movements and not singing, but a small fraction of neurons exhibits precise song timing and performance error signals consistent with performance evaluation. Together our results implicate the STN-VTA projection as an evolutionarily conserved pathway important for motor learning and expand the territories of songbird brain associated with song learning.

New & Noteworthy

Songbird subthalamic (STN) neurons exhibit song-timing and performance error signals and are interconnected with auditory pallium, ventral pallidum and ventral tegmental area, three areas important for song learning.
CryoEM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition
Authors: Shaban Nadine M. , Yan Rui , Shi Ke , Moraes Sofia N. , Cheng Adam Z. , Carpenter Michael A. , McLellan Jason S. , Yu Zhiheng , Harris Reuben S.
Published: August 2021

Viruses use a plethora of mechanisms to evade immune responses. A new example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000 Å2binding surface comprised of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. An atomic understanding of this novel pathogen-host interaction may contribute to the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B.

One-Sentence Summary

These studies show how a conserved viral nucleotide metabolism protein is repurposed to inhibit a potent antiviral factor.
Unraveling Phylogenetic Relationships, Reticulate Evolution, and Genome Composition of Polyploid Plant Complexes by Rad-Seq and Hyb-Seq
Authors: Karbstein Kevin , Tomasello Salvatore , Hodač Ladislav , Wagner Natascha , Marinček Pia , Barke Birthe Hilkka , Pätzold Claudia , Hörandl Elvira
Published: August 2021

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3–5 supported polyploid groups, each containing sexual progenitor species. In total, analyses revealed four diploid sexual progenitors and a one unknown, probably extinct progenitor, contributing to the genome composition of R. auricomus polyploids. Phylogenetic network, structure, and SNP-origin analyses based on RAD-Seq loci and phased nuclear genes completed by plastid data demonstrated predominantly allopolyploid origins, each involving 2–3 different diploid sexual subgenomes. Allotetraploid genomes were characterized by subgenome dominance and large proportions of interspecific, non-hybrid SNPs, indicating an enormous degree of post-origin evolution (i.e., Mendelian segregation of the diploid hybrid generations, back-crossings, and gene flow due to facultative sexuality of apomicts), but only low proportions of lineage-specific SNPs. The R. auricomus model system is the first large European polyploid species complex studied with reduced representation OMICS data. Our bioinformatic pipeline underlines the importance of combining different approaches and datasets to successfully unveil how reticulate evolution and post-origin processes shape the diversity of polyploid plant complexes.
Trick or Treat? Pollinator attraction inVanilla pompona(Orchidaceae)
Authors: Watteyn Charlotte , Scaccabarozzi Daniela , Muys Bart , Van Der Schueren Nele , Van Meerbeek Koenraad , Guizar Amador Maria F. , Ackerman James D. , Cedeño Fonseca Marco V. , Chinchilla Alvarado Isler F. , Reubens Bert , Pillco Huarcaya Ruthmery , Cozzolino Salvatore , Karremans Adam P.
Published: August 2021

Natural pollination of species belonging to the pantropical orchid genusVanillaremains poorly understood. Based on sporadic records, euglossine bees have been observed visiting flowers of NeotropicalVanillaspecies. Our research aimed at better understanding the pollinator attraction mechanism of the Neotropical speciesVanilla pompona, a crop wild relative with valuable traits for vanilla crop improvement programs. Using video footage, we identified floral visitors and examined their behavior. The flowers ofV. pomponaattractedEulaema cingulatamales, which distinctively displayed two behaviors: floral scent collection and nectar search; with the latter leading to pollen removal. Morphological measurements of floral and visitor traits showed that otherEulaemaspecies may also act as potential pollinators. Additionally, we recorded natural fruit set in three populations and over a period of two years, tested for nectar presence and analyzed floral fragrances through gas chromatography - mass spectrometry. We observed a low natural fruit set (2.42%) and did not detect nectar. Twenty floral volatile compounds were identified, with the dominant compound trans-carvone oxide previously found to attractEulaema cingulatamales. We hypothesize a dual attraction ofEulaema cingulatamales toV. pomponaflowers, based on floral fragrance reward as the primary long-distance attraction, and food deception for successful pollen removal. Further research confirming this hypothesis is recommended to develop appropriate conservation policies forVanillacrop wild relatives, which are the primary reserves of this crop’s genetic variation.