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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 73 records · Page 4Linked to original sources
bioRxiv2017

Human occipital bone sexual dimorphism in an Archiac period archaeological population

PREPRINT NOTESThis paper was submitted for publication the International Journal of Osteoarchaeology in August of 2003. The paper was rejected roughly a year later due to scope and collection issues. I revisited the paper in 2007 with an eye to updating and resubmitting with additional data but the project was triaged from the publication pipeline due to the work involved relative to other projects more relevant to my research interests at the time. The current preprint paper contains updated references on occipital bone sexual dimorphism--all limited to the condylar region rather than the full suite of variation in the region.\n\nI am posting this to the preprint server to contribute the findings to the larger scientific community in the hopes that I might have time to revisit the paper as a student project. A more rigorous study would need to expand the sample either to a study collection that has remains with known sex (either verified via molecular sexing techniques or using a modern study collection) or additional comparative collections from hunter-gatherer populations. If a student is interested in taking up the topic and assuming lead authorship on a co-authored paper, Id be happy to collaborate and see this piece through the publication pipeline.\n\nABSTRACTThis paper presents the results of a comprehensive study of sexual dimorphism in the human occipital region of the skull using the remains of 39 prehistoric adults from the prehistoric Windover (6,000-8,000 BP). The results of a discriminant analysis classified 64% of the individuals correctly (using osteologically identified sex). Sexual dimorphism in this population may not be prevalent due to environmental stress.

physiology↗
bioRxiv2020

ROS-triggered AMPK de-SUMOylation promotes Warburg effect in hepatocellular carcinoma cells

The authors have withdrawn this manuscript as they no longer stand by the conclusions. As found in previous literature review, the regulation effect and mechanism of reactive oxygen species (ROS) on the metabolism and proliferation of tumor cells are very complex. The preliminary results in the preprint may be just one front of "ROS-AMPK-tumor cell metabolism". After further experiments, the effects of different ROS concentrations on the metabolism of tumor cells as the cell passage increased were not completely consistent with the results shared in the preprint, so the author decided to withdraw the data in this preprint. The author do not wish this version to be cited as reference for this study. Subsequent investigators should carefully evaluate the consistency of the role of ROS stimulation in cell studies in vitro.

cancer biology↗
bioRxiv2020

Exploring the evolution and adaptive role of mosaic aneuploidy in a clonal Leishmania donovani population using high throughput single-cell genome sequencing

Maintenance of stable ploidy over continuous mitotic events is a paradigm for most higher eukaryotes. Defects in chromosome segregation and/or replication can lead to aneuploidy, a condition often considered deleterious. However, in Leishmania, a Protozoan parasite, aneuploidy is a constitutive feature, where variations of somies represent a mechanism of gene expression adaptation, possibly impacting phenotypes. Strikingly, clonal Leishmania populations display cell-to-cell somy variation, a phenomenon named mosaic aneuploidy (MA). However, until recently, no method was available for the determination of the complete karyotype of single Leishmania parasites. To overcome this limitation, we used here for the first time a high-throughput single-cell genomic sequencing (SCGS) method to estimate individual karyotypes of 1560 promastigote cells in a clonal population of Leishmania donovani. We identified 128 different karyotypes, of which 4 were dominant. A network analysis revealed that most karyotypes are linked to each other by changes in copy number of a single chromosome and allowed us to propose a hypothesis of MA evolution. Moreover, aneuploidy patterns that were previously described by Bulk Genome Sequencing as emerging during first contact of promastigotes populations with different drugs are already pre-existing in single karyotypes in the SCGS data, suggesting a (pre-)adaptive role of MA. Additionally, the degree of somy variation was chromosome-specific. The SCGS also revealed a small fraction of cells where one or more chromosomes were nullisomic. Together, these results demonstrate the power of SCGS to resolve sub-clonal karyotype heterogeneity in Leishmania and pave the way for understanding the role of MA in these parasites adaptability. Update: 25th May 2021A revision of the present preprint was released in BioRxiv on 11th May 2021 (https://www.biorxiv.org/content/10.1101/2021.05.11.443577v2). In the new version, we included two extra samples in our single-cell genome sequencing (SCGS) analysis - the BPK081 cl8 clone (a nearly euploid strain), and a population consisting of a mixture of four L. donovani strains which was used as control for high levels of mosaicism in aneuploidy and for estimation of doublets. We also upgraded the bioinformatics pipeline to determine single-cell karyotypes and performed new fluorescence in situ hybridization (FISH) analysis. The new findings observed especially in the BPK081 cl8 led to a reformulation of the text, a new hypothesis for the evolution of mosaicism and a general restructuring of the article. Therefore, the present preprint is obsolete. Please refer to the new preprint entitled "High throughput single cell genome sequencing gives insights in the generation and evolution of mosaic aneuploidy in Leishmania donovani" for more information.

genomics↗
bioRxiv2021

High throughput single-cell genome sequencing gives insights into the generation andevolution of mosaic aneuploidy in Leishmania donovani

Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might have important evolutionary and functional implications but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two Leishmania clonal populations representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations. MA usually affected a defined subset of chromosomes, of which some display an enrichment in snoRNA genes which could represent an adaptative benefit to the amplification of these chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies. Note to the BioRxiv communityThe present preprint is a revision of an older preprint posted on 06th March 2020 on BioRxiv (https://www.biorxiv.org/content/10.1101/2020.03.05.976233v1). Here we included two extra samples in our single-cell genome sequencing (SCGS) analysis - the BPK081 cl8 clone (a nearly euploid strain) and a population consisting of a mixture of four L. donovani strains which was used as control for high levels of mosaicism in aneuploidy and for estimation of doublets. We also upgraded the bioinformatics pipeline to determine single-cell karyotypes and performed new fluorescence in situ hybridization (FISH) analysis. The new findings observed especially in the BPK081 cl8 led to a reformulation of the text, a new hypothesis for the evolution of mosaicism and a general restructuring of the article. Therefore, the older preprint is obsolete.

genomics↗
bioRxiv2021

SimpleForest - a comprehensive tool for 3d reconstruction of trees from forest plot point clouds

The here-on presented SimpleForest is written in C++ and published under GPL v3. As input data SimpleForest utilizes forestry scenes recorded as terrestrial laser scan clouds. SimpleForest provides a fully automated pipeline to model the ground as a digital terrain model, then segment the vegetation and finally build quantitative structure models of trees (QSMs) consisting of up to thousands of topologically ordered cylinders. These QSMs allow us to calculate traditional forestry metrics such as diameter at breast height, but also volume and other structural metrics that are hard to measure in the field. Our volume evaluation on three data sets with destructive volumes show high prediction qualities with concordance correlation coefficient CCC [Formula] of 0.91 (0.87), 0.94 (0.92) and 0.97 (0.93) for each data set respectively. We combine two common assumptions in plant modeling "The sum of cross sectional areas after a branch junction equals the one before the branch junction" (Pipe Model Theory) and "Twigs are self-similar" (West, Brown and Enquist model). As even sized twigs correspond to even sized cross sectional areas for twigs we define the Reverse Pipe Radius Branchorder (RPRB) as the square root of the number of supported twigs. The prediction model radius = B0 * RPRB relies only on correct topological information and can be used to detect and correct overestimated cylinders. In QSM building the necessity to handle overestimated cylinders is well known. The RPRB correction performs better with a CCC [Formula] of 0.97 (0.93) than former published ones 0.80 (0.88) and 0.86 (0.85) in our validation. We encourage forest ecologists to analyze output parameters such as the GrowthVolume published in earlier works, but also other parameters such as the GrowthLength, VesselVolume and RPRB which we define in this manuscript. Upload statementSelf-uploaded pre-print for peer-review submitted manuscript. The manuscript was submitted on 26th of July 2021 to Plos Computational Biology: I, Jan Hackenberg uploaded this manuscript because the automated journal upload was rejected for the following reason: Thank you for considering posting your manuscript "SimpleForest - a comprehensive tool for 3d reconstruction of tree from forest plot point clouds." as a preprint. Your manuscript does not meet bioRxivs criteria and therefore we will not be sending it for posting as a preprint. For more information about our checks, see link. We have noted that it contains material that is potentially subject to copyright. In particular, screenshot in Figure 1. Preprints posted to bioRxiv following submission to PLOS journals are done so under the CC BY license. To avoid a potential breach of the copyright that applies to the material listed above, we are unable to make the manuscript publicly available. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/454344v1_fig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@1094b17org.highwire.dtl.DTLVardef@120d7a3org.highwire.dtl.DTLVardef@12d2fbcorg.highwire.dtl.DTLVardef@1990a4d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Submission system screenshot. C_FIG Please note that this decision does not affect the editorial process at PLOS Computational Biology. Your manuscript is being separately assessed with regards to sending for peer review. From section Abstract on, the pdf you see is same as submitted one.

plant biology↗
bioRxiv2021

MKK6 deficiency promotes cardiac dysfunction through MKK3-p38γ/δ-mTOR hyperactivation

Stress-activated p38 kinases control a plethora of functions and their dysregulation has been linked to development of steatosis, obesity, immune disorders and cancer. Therefore, they have been identified as potential targets for novel therapeutic strategies. There are four p38 family members (p38, p38{beta}, p38{gamma}, and p38{delta}) that are activated by MKK3 and MKK6. Here we demonstrate that lack of MKK6 reduces the life span in mice. Longitudinal study of cardiac function in Mkk6-/- mice showed that young mice have cardiac hypertrophy which progresses to cardiac dilatation and fibrosis with age. Mechanistically, lack of MKK6 blunts p38 activation while causing MKK3-p38{gamma}/{delta} hyperphosphorylation and increased mTOR signaling, resulting in cardiac hypertrophy. Cardiac hypertrophy in Mkk6-/- mice is reverted by knocking out either p38{gamma} or p38{delta}, or by inhibiting mTOR pathway with rapamycin. In conclusion, we have identified a key role for the MKK3/6-p38{gamma}/{delta} pathway in the development of cardiac hypertrophy, which has important implications for the clinical use of p38 inhibitors in the long-term treatment since they might result in cardiotoxicity. eLifes Review ProcesseLife works to improve the process of peer review so that it more effectively conveys the assessment of expert reviewers to authors, readers and other interested parties. In the future we envision a system in which research is first published as a preprint and the outputs of peer review are the primary way research is assessed, rather than journal title. Our editorial process produces two outputs: i) an assessment by peers designed to be posted alongside a preprint for the benefit of the readers; ii) detailed feedback on the manuscript for the authors, including requests for revisions and suggestions for improvement. Therefore we want to change how we construct and write peer reviews to make them useful to both authors and readers in a way that better reflects the work you put into reading and thinking about a paper. eLife reviews now have three parts: O_LIAn evaluation summary (in two or three sentences) that captures the major conclusions of the review in a concise manner, accessible to a wide audience. C_LIO_LIA public review that details the strengths and weaknesses of the manuscript before you, and discusses whether the authors claims and conclusions are justified by their data. C_LIO_LIA set of private recommendations for the authors that outline how you think the science and its presentation could be strengthened. C_LI All three sections will be used as the basis for an eLife publishing decision, which will, as always, be made after a consultation among the reviewers and editor. Each of the public reviews will be published (anonymously) alongside the preprint, together with a response from the authors if they choose. In the case of papers we reject after review, the authors can choose to delay posting until their paper has been published elsewhere. If this is your first time going through this new process, we ask that you take some time to read our Reviewer Guide, which discusses how we see each section will be used, what it should contain, and what we hope it accomplishes. And we remind you that, with the shift of reviews from private correspondence to public discourse, it is more important than ever that reviews are written in a clear and constructive manner appropriate for a public audience and mindful of the impact language choices might have on the authors.

molecular biology↗
bioRxiv2022

Changing word meanings in biomedical literature reveal pandemics and new technologies

While we often think of words as having a fixed meaning that we use to describe a changing world, words are also dynamic and changing. Scientific research can also be remarkably fast-moving, with new concepts or approaches rapidly gaining mind share. We examined scientific writing, both preprint and pre-publication peer-reviewed text, to identify terms that have changed and examine their use. One particular challenge that we faced was that the shift from closed to open access publishing meant that the size of available corpora changed by over an order of magnitude in the last two decades. We developed an approach to evaluate semantic shift by accounting for both intra- and inter-year variability using multiple integrated models. Using this strategy and examining year-by-year changes revealed thousands of change points in both corpora. We found change points for tokens including cas9, pandemic, and sars among many others. The consistent change-points between pre-publication peer-reviewed and preprinted text were largely related to the COVID-19 pandemic. We developed a web app for exploration (https://greenelab.github.io/word-lapse/) that enables users to investigate individual terms. To our knowledge, this analysis is the first to examine semantic shift in biomedical preprints and pre-publication peer-reviewed text, and it lays the foundation for future work to examine how terms acquire new meaning and the extent to which that process is encouraged or discouraged by peer review.

scientific communication and education↗
bioRxiv2022

Label free autofluorescence imaging permits comprehensive and simultaneous assignment of cell type identity and reveals the existence of airway secretory cell associated antigen passages (SAPs).

The specific functional properties of a tissue are distributed amongst its component cell types. The various cells act coherently, as an ensemble, in order to execute a properly orchestrated physiologic response. Thus, modern approaches to dissect physiologic mechanism would benefit from an ability to identify specific cell types in live tissues and image them in real time. Current techniques require the use of fluorescent genetic reporters that are not only cumbersome, but which only allow the simultaneous study of 2 or 3 cell types. We report a non-invasive imaging modality that capitalizes on the endogenous autofluorescence signatures of the metabolic cofactors NAD(P)H and FAD. By marrying morphological characteristics with autofluorescence signatures, all seven of the airway epithelial cell types can be distinguished simultaneously in real time. Furthermore, we find that this methodology for direct cell type specific identification avoid potential pitfalls with the use of ostensibly cell type-specific markers that can be altered by clinically relevant physiologic stimuli. Finally, we utilize this methodology to interrogate real-time physiology using a clinically relevant model of cholinergic stimulation and identify dynamic secretory cell associated antigen passages (SAPs) that are highly reminiscent of previously reported goblet cell associated antigen passages (GAPs) in the intestine. eLifes Review ProcesseLife works to improve the process of peer review so that it more effectively conveys the assessment of expert reviewers to authors, readers and other interested parties. In the future we envision a system in which research is first published as a preprint and the outputs of peer review are the primary way research is assessed, rather than journal title. Our editorial process produces two outputs: i) an assessment by peers designed to be posted alongside a preprint for the benefit of the readers; i) detailed feedback on the manuscript for the authors, including requests for revisions and suggestions for improvement. Therefore we want to change how we construct and write peer reviews to make themuseful to both authors and readers in a way that better reflects the work you put into reading and thinking about a paper. eLife reviews now have three parts: O_LIAn evaluation summary (in two or three sentences) that captures the major conclusions of the review in a concise manner, accessible to a wide audience. C_LIO_LIA public review that details the strengths and weaknesses of the manuscript before you, and discusses whether the authors claims and conclusions are justified by their data. C_LIO_LIA set of private recommendations for the authors that outline how you think the science and its presentation could be strengthened. C_LI All three sections will be used as the basis for an eLife publishing decision, which will, as always, be made after a consultation among the reviewers and editor. Each of the public reviews will be published (anonymously) alongside the preprint, together with a response from the authors if they choose. In the case of papers we reject after review, the authors can choose to delay posting until their paper has been published elsewhere. If this is your first time going through this new process, we ask that you take some time to read our Reviewer Guide, which discusses how we see each section will be used, what it should contain, and what we hope it accomplishes. And we remind you that, with the shift of reviews from private correspondence to public discourse, it is more important than ever that reviews are written in a clear and constructive manner appropriate for a public audience and mindful of the impact language choices might have on the authors.

cell biology↗
bioRxiv2023

Relict duck-billed dinosaurs survived into the last age of the dinosaurs in subantarctic Chile

In the dusk of the dinosaur era, the advanced duck-billed dinosaurs (Family Hadrosauridae) are thought to have outcompeted other herbivores, making ecosystems less diverse and more vulnerable to the Cretaceous-Paleogene asteroid impact. They were also among the first terrestrial organisms to disperse from North America into South America. Here, we present the first new species of subantarctic duck-billed dinosaur, CPAP 3054, of early Maastrichtian age in Magallanes, Chile. Surprisingly, unlike duckbills further north in Patagonia, CPAP 3054 is not an advanced duckbill, but descends from North American forms that were transitional to Hadrosauridae, diverging shortly before the origin of this family. In North America, these forms were replaced by hadrosaurids in the late Campanian. The survival into the Maastrichtian of a pre-hadrosaurid lineage suggests the ancestors of CPAP 3054 arrived earlier in South America than the hadrosaurids, reaching further south before the Cretaceous-Paleogene mass extinction, where they avoided competition from hadrosaurids. Additional noteThis work contains a new biological name. New names in preprints are not considered available by the ICZN. To avoid ambiguity, the new biological name is not included in this preprint, and the holotype specimen number CPAP 3054 is used as a placeholder. Paratypes described in this preprint are also used in the diagnosis.

paleontology↗
bioRxiv2018

Predator odor increases glutamatergic synaptic transmission in the prelimbic cortex via corticotropin-releasing factor receptor 1 signaling

The authors have withdrawn their manuscript because the University of North Carolina at Chapel Hill conducted a research misconduct proceeding and concluded that research misconduct occurred involving results presented in this preprint. Hence, the results and conclusions of the preprint article are no longer reliable. The published version of this preprint (Neuropsychopharmacology, doi: 10.1038/s41386-018-0279-2) is being retracted as well. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

neuroscience↗
bioRxiv2019

Bioinformatic analysis of brain-specific miRNAs for identification of candidate traumatic brain injury blood biomarkers.

BackgroundDetection of brain-specific miRNAs in the peripheral blood could serve as a surrogate marker of traumatic brain injury (TBI). Here, we systematically identified brain-enriched miRNAs, and tested their utility for use as TBI biomarkers in the acute phase of care. MethodsPublically-available microarray data generated from 31 postmortem human tissues was used to rank 1,364 miRNAs in terms of their degree of brain-specific expression. Levels of the top five ranked miRNAs were then prospectively measured in serum samples collected from 10 TBI patients at hospital admission, as well as from 10 controls. ResultsThe top five miRNAs identified in our analysis (miR-137, miR-219a-5p, miR-128-3p, miR-124-3p, and miR-138-5p) exhibited 31 to 74-fold higher expression in brain relative to other tissues. Furthermore, their levels were elevated in serum from TBI patients compared to controls, and were collectively able to discriminate between groups with 90% sensitivity and 80% specificity. Subsequent informatic pathway analysis revealed that their target transcripts were significantly enriched for components of signaling pathways which are active in peripheral organs such as the heart. ConclusionsThe five candidate miRNAs identified in this study have promise as blood biomarkers of TBI, and could also be molecular contributors to systemic physiologic changes commonly observed post-injury. A FINAL PEER REVIEWED VERSION OF THIS ARTICLE HAS BEEN PUBLISHED IN BRAIN INJURY AT THE FOLLOWING DOI: 10.1080/02699052.2020.1764102 There are some notable differences between the analysis presented in this preprint and our final peer-reviewed article. There was a single tissue sample originating from spinal cord that we had classified as a non-brain tissue in our original analysis outlined in this preprint. Because the composition of spinal cord and brain are highly similar in terms of gene expression, classifying this sample as a non-brain tissue dramatically reduced the levels of brain enrichment observed in the analysis. Because brain and spinal cord are molecularly highly similar, but technically distinct anatomical structures, we simply decided to exclude this sample from our final analysis published in Brain Injury to avoid confounds. The top 5 miRNAs identified in our original analysis still fell within the top 7 of this final analysis. In addition, the final analysis identified two additional miRNAs which could be candidate biomarkers based on levels of brain enrichment. The final article published in Brain Injury also reports an additional confirmatory tissue specificity analysis performed in a second independent dataset, as well as additional analysis examining the brain specificity of several notable previously proposed miRNA TBI biomarkers, which is not described in this preprint.

neuroscience↗
bioRxiv2026

APEX1 Protects Cardiomyocytes Against Oxidative Stress by Regulating p53 Protein Stability

Withdrawal statementThe authors have withdrawn this manuscript because the preprint was uploaded to bioRxiv before all co-authors had been fully informed and had provided their explicit consent to make the manuscript publicly available as a preprint. Following internal discussions, the authors have reached a consensus that they do not wish this version to be publicly available. We therefore kindly request that this preprint be withdrawn on the bioRxiv platform. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗
bioRxiv2017

Polygenic Adaptation has Impacted Multiple Anthropometric Traits

Our understanding of the genetic basis of human adaptation is biased toward loci of large pheno-typic effect. Genome wide association studies (GWAS) now enable the study of genetic adaptation in polygenic phenotypes. We test for polygenic adaptation among 187 world-wide human populations using polygenic scores constructed from GWAS of 34 complex traits. We identify signals of polygenic adaptation for anthropometric traits including height, infant head circumference (IHC), hip circumference and waist-to-hip ratio (WHR). Analysis of ancient DNA samples indicates that a north-south cline of height within Europe and and a west-east cline across Eurasia can be traced to selection for increased height in two late Pleistocene hunter gatherer populations living in western and west-central Eurasia. Our observation that IHC and WHR follow a latitudinal cline in Western Eurasia support the role of natural selection driving Bergmanns Rule in humans, consistent with thermoregulatory adaptation in response to latitudinal temperature variation.\n\nAuthors Note on Failure to ReplicateAfter this preprint was posted, the UK Biobank dataset was released, providing a new and open GWAS resource. When attempting to replicate the height selection results from this preprint using GWAS data from the UK Biobank, we discovered that we could not. In subsequent analyses, we determined that both the GIANT consortium height GWAS data, as well as another dataset that was used for replication, were impacted by stratification issues that created or at a minimum substantially inflated the height selection signals reported here. The results of this second investigation, written together with additional coauthors, have now been published (https://elifesciences.org/articles/39725 along with another paper by a separate group of authors, showing similar issues https://elifesciences.org/articles/39702). A preliminary investigation shows that the other non-height based results may suffer from similar issues. We stand by the theory and statistical methods reported in this paper, and the paper can be cited for these results. However, we have shown that the data on which the major empirical results were based are not sound, and so should be treated with caution until replicated.

evolutionary biology↗
bioRxiv2020

Tracking age differences in neural distinctiveness across representational levels

The authors have withdrawn the preprint due to two errors in the analyses: The first error was a failure to account for three dummy volumes (TR = 2s) collected at the beginning of each experimental run. The second error was a coding error related to the definition of the category-selective clusters. Since correcting for these errors drastically altered the results and conclusions of this paper, the authors have withdrawn the preprint and retracted the published paper. More information as well as a report comparing original and corrected results can be found on https://osf.io/t8dpv/. If you have any questions please contact the corresponding author (sander@mpib-berlin.mpg.de).

neuroscience↗
bioRxiv2020

Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities

The current CoVid-19 crisis is revealing the strengths and the weaknesses of the worlds capacity to respond to a global health crisis. A critical weakness has resulted from the excessive centralization of the current biomanufacturing capacities, a matter of great concern, if not a source of nationalistic tensions. On the positive side, scientific data and information have been shared at an unprecedented speed fuelled by the preprint phenomena, and this has considerably strengthened our ability to develop new technology-based solutions. In this work we explore how, in a context of rapid exchange of scientific information, plant biofactories can serve as a rapid and easily adaptable solution for local manufacturing of bioreagents, more specifically recombinant antibodies. For this purpose, we tested our ability to produce, in the framework of an academic lab and in a matter of weeks, milligram amounts of six different recombinant monoclonal antibodies against SARS-CoV-2 in Nicotiana benthamiana. For the design of the antibodies we took advantage, among other data sources, of the DNA sequence information made rapidly available by other groups in preprint publications. mAbs were all engineered as single-chain fragments fused to a human gamma Fc and transiently expressed using a viral vector. In parallel, we also produced the recombinant SARS-CoV-2 N protein and its Receptor Binding Domain (RBD) in planta and used them to test the binding specificity of the recombinant mAbs. Finally, for two of the antibodies we assayed a simple scale-up production protocol based on the extraction of apoplastic fluid. Our results indicate that gram amounts of anti-SARS-CoV-2 antibodies could be easily produced in little more than 6 weeks in repurposed greenhouses with little infrastructure requirements using N. benthamiana as production platform. Similar procedures could be easily deployed to produce diagnostic reagents and, eventually, could be adapted for rapid therapeutic responses.

synthetic biology↗
bioRxiv2021

Four new species of Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis

African cichlids are model systems for evolutionary studies and for host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Here, we sampled five locations in southern Lake Victoria, the youngest of the African Great Lakes. We surveyed gillinfecting monogeneans from 18 cichlid species belonging to the Lake Victoria radiation superflock and two cichlid species representing two older and distantly related lineages. We found one species of Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Cichlidogyrus (Dactylogyridae, Monogenea). Four species are herein described: Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Another species is reported but not formally described (because of few specimens and morphological similarity with C. furu n. sp.). Two other species are redescribed: Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the other hooks, highlighting the need to re-evaluate the current classification system of haptoral configurations that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis and C. nyanza n. sp. suggest that these are closely related to other congeners that infect haplochromines. We also found morphological indications that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonized by two cichlid tribes (Haplochromini and Oreochromini). DisclaimerThis preprint is disclaimed for purposes of Zoological Nomenclature in accordance with the International Code of Zoological Nomenclature, Fourth Edition Articles 8.2 and 8.3 (ICZN 1999). No new names or nomenclatural changes are available from statements in this preprint. Resume - Quatre especes nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites dhaplochromine (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives quils ont subies, les cichlides africain sont des systemes modeles pour etudier levolution, mais aussi les relations hotes/parasites, car ils hebergent de nombreuses especes de Monogenes parasites qui presentent une specificite etroite vis-a-vis de leurs hotes. Dans ce travail, nous avons echantillonne cinq localites dans le Sud du lac Victoria, le plus jeune des grands lacs dAfrique de lEst. Nous avons examine les Monogenes presents sur les branchies de 18 especes de Cichlides appartenant a la radiation adaptative << superflock >> du lac Victoria et de deux especes representant deux lignees anciennes et non etroitement apparentees. Nous avons trouve une espece de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept especes de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre especes nouvelles sont decrites dans le present travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalee mais non decrite formellement (trop peux dindividus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redecrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos resultats confirment que la faune des Monogenes des Cichlides du lac Victoria fait preuve dune richesse specifique et dune specificite moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V etant nettement plus longue que les autres, il faudra reconsiderer le systeme de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considere que tous les crochets (III a VII) ont la meme taille. Quelques caracteristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient etre la preuve dune ascendance commune avec des congeneres presents chez dautres Haplochromines. De meme, certains caracteres indiqueraient que des representants des Cichlidogyrus ont colonise les Haplochromines du lac Victoria, ou leurs ancetres, au moins a deux reprises, ce qui est coherent avec une colonisation du lac par deux lignees de cichlides distinctes (Haplochromini and Oreochromini).

zoology↗
bioRxiv2021

Meta-Research: Citation needed? Wikipedia and the COVID-19 pandemic

BackgroundWith the COVID-19 pandemics outbreak, millions flocked to Wikipedia for updated information. Amid growing concerns regarding an "infodemic", ensuring the quality of information is a crucial vector of public health. Investigating if and how Wikipedia remained up to date and in line with science is key to formulating strategies to counter misinformation. Using citation analyses, we asked: which sources informed Wikipedias COVID-19-related articles before and during the pandemics first wave (January-May 2020). ResultsWe found that coronavirus-related articles referenced trusted media sources and high-quality academic research. Moreover, despite a surge in COVID-19 preprints, Wikipedia had a clear preference for open-access studies published in respected journals and made little use of preprints. Building a timeline of English COVID-19 articles from 2001-2020 revealed a nuanced trade-off between quality and timeliness. It further showed how preexisting articles on key topics related to the virus created a framework for integrating new knowledge. Supported by a rigid sourcing policy, this "scientific infrastructure" facilitated contextualization and regulated the influx of new information. Lastly, we constructed a network of DOI-Wikipedia articles, which showed the shifting landscape of pandemic-related knowledge on Wikipedia and how academic citations create a web of shared knowledge supporting topics like COVID-19 vaccine development. ConclusionsUnderstanding how scientific research interacts with the digital knowledge-sphere during the pandemic provides insight into how Wikipedia can facilitate access to science. It also reveals how, aided by what we term its "citizen encyclopedists", it successfully fended off COVID-19 disinformation and how this unique model may be deployed in other contexts.

scientific communication and education↗