bluuebunny/crossref_metadata_2025 huggingface dataset:
PRIMATE LIMB CONFORMATION: IMPLICATIONS FOR MECHANICAL ENERGY CONSERVATION*
Authors: Catalino Michael P.
Published: March 2021

In order to understand the energy implications of primate limb conformation, the biomechanics of swing phase and the vertical movements of limb center of gravity were examined in the arboreal rhesus macaque (Macaca mulatta) and the semi-terrestrial long-tailed macaque (Macaca fascicularis). The objective was to better understand the potential variation in locomotor adaptations in these two macaque species within different ecological environments. In particular, the objective of this study was to identify the implications that these movements have on the internal energy costs of locomotion. I show that the biomechanics of swing phase for these two species have important effects on their limb center of gravity, although they may have similar limb segment mass distributions. This study suggests that mechanical energy conservation during swing phase is important in mammalian locomotion.
Aggregated Mycobacterium tuberculosis enhances the inflammatory response
Authors: Rodel Hylton E. , Ferreira Isabella Markham , Ziegler Carly G.K , Ganga Yashica , Bernstein Mallory , Hwa Shi-Hsia , Nargan Kievershen , Lustig Gila , Kaplan Gilla , Noursadeghi Mahdad , Shalek Alex K. , Steyn Adrie , Sigal Alex
Published: March 2021

Mycobacterium tuberculosis (Mtb) readily aggregates in culture and Mtb aggregates in the lung were observed in experimental Mtb infection. However, the physiological consequences of Mtb aggregation are incompletely understood. Here we examined the human macrophage transcriptional response to aggregated Mtb relative to infection with non-aggregated single or multiple bacilli per host cell. Infection with aggregated Mtb led to an early upregulation of pro-inflammatory associated genes and enhanced TNFα signaling via the NFκB pathway. Both these pathways were significantly upregulated relative to infection with single bacilli, and TNFα signaling was also significantly elevated relative to infection with multiple non-aggregated Mtb. Secretion of TNFα and downstream cytokines were also enhanced. On a longer timescale, aggregate infection led to overall increased acidification per macrophage and a high proportion of death in these cells after aggregate phagocytosis. Host cell death did not occur when Mtb aggregates were heat killed despite such clumps being readily picked up. To validate that Mtb aggregates do occur in the human lung, we document Mtb aggregates surrounding a cavity in a human TB lesion. Aggregates may therefore be present in some lesions and elicit a stronger inflammatory response resulting in recruitment of additional phagocytes and their subsequent death, potentially leading to necrosis and transmission.
Mechanical influences onin silicotumor evolution
Authors: Rosenbauer Jakob , Berghoff Marco , Glazier James A. , Schug Alexander
Published: March 2021

Experimental insight and conceptual understanding of tumor growth are steadily growing and leading to new therapeutic interventions. Experiments and clinical studies are able to link single-cell properties to macroscopic tumor attributes. The development of cellular subpopulations in heterogeneous tumors can be understood as an evolutionary system with different cell types competing over both space and nutrients. However, to predict the growth trajectory and development of a tumor, fitness and trade-offs of cell properties in the context of the surroundings are required and often inaccessible. The optimum of the evolutionary trajectory provides a target for intervention, but can mostly not be identified. We propose that the optimal value of cellular properties is influenced by the tumor surrounding. Computational multiscale-modeling of tissue enables the observation of the trajectory of each cell while modeling the tumor surrounding. We model a 3D spheroid tumor and the fitness of individual cells and the evolutionary behavior of the tumor are quantified and linked to global parameters. Cell–cell adhesion and cell motility are two important mechanical properties for cell development and used as free parameters. Mechanical properties alone are able to drive the tumor towards low adhesion.We implement a dynamically changing nutrient surrounding representing the fluctuating blood-supply through blood vessel collapse and angiogenesis. We find that the evolutionary speed depends on the frequency of the fluctuations. We identify a frequency domain in which the evolutionary speed is significantly increased over a tumor with constant nutrient supply. The findings suggest that mechanically-induced fluctuations can accelerate tumor evolution.

Author summary

Limited space and nutrients together with competing cell types drive an evolutionary process inside tumors. This process selects for the fittest cell types and optimizes the growing behavior for its local surroundings. An expanding tumor exerts mechanical forces on its cells and its surroundings, leading to a fluctuating nutrient supply through collapsing blood vessels. Here, we observe the influence of a dynamically changing surrounding on the evolutionary behavior of heterogeneous tumors in a high-resolution computational model. We find that the evolutionary speed depends on the frequency of the fluctuations and a fitness advantage of low-adhesion cells.
Brain solute transport is more rapid in periarterial than perivenous spaces
Authors: Vinje Vegard , Bakker Erik NTP , Rognes Marie E
Published: March 2021

Background

Perivascular fluid flow, of cerebrospinal or interstitial fluid in spaces surrounding brain blood vessels, is recognized as a key component underlying brain transport and clearance. An important open question is how and to what extent differences in vessel type or geometry affect perivascular fluid flow and transport.

Methods

Using computational modelling in both idealized and image-based geometries, we study and compare fluid flow and solute transport in pial (surface) periarterial and perivenous spaces.

Results

Our findings demonstrate that differences in geometry between arterial and venous pial perivascular spaces (PVSs) lead to higher net CSF flow, more rapid tracer transport and earlier arrival times of injected tracers in periarterial spaces compared to perivenous spaces.

Conclusions

These findings can explain the experimentally observed rapid appearance of tracers around arteries, and the delayed appearance around veins without the need of a circulation through the parenchyma, but rather by direct transport along the PVSs.
The oxygen sensor Prolyl hydroxylase domain 2 regulates the in vivo suppressive capacity of regulatory T cells
Authors: Ajouaou Yousra , Azouz Abdulkader , Taquin Anaelle , Denanglaire Sebastien , Hussein Hind , Krayem Mohammad , Andris Fabienne , Moser Muriel , Goriely Stanislas , Leo Oberdan
Published: March 2021

The oxygen sensor PHD2 (prolyl hydroxylase domain 2) plays an important role in cell hypoxia adaptation by regulating the stability of HIF proteins (HIF1α and HIF2α) in numerous cell types including T lymphocytes. The role of oxygen sensor on immune cells, in particular on regulatory T cell (Treg) function, has not been fully elucidated. The purpose of our study was to evaluate the role of PHD2 in the regulation of Treg phenotype and function. We demonstrate herein that selective ablation of PHD2 expression in Treg (PHD2ΔTregmice) leads to a spontaneous systemic inflammatory syndrome, as evidenced by weight loss, development of a rectal prolapse, splenomegaly, shortening of the colon and elevated expression of IFN-γ in the mesenteric lymph nodes, intestine and spleen. PHD2 deficiency in Tregs led to an increased number of activated CD4 conventional T cells expressing a Th1-like effector phenotype. Concomitantly, the expression of innate-type cytokines such asIl1b,Il12a,Il12bandTnfawas found to be elevated in peripheral (gut) tissues and spleen. PHD2ΔTregmice also displayed an enhanced sensitivity to DSS-induced colitis and to toxoplasmosis, suggesting that PHD2-deficient Tregs did not efficiently control inflammatory response in vivo, in particular those characterized by IFN-γ production. Further analysis revealed that Treg dysregulation was largely prevented in PHD2-HIF2α (PHD2-HIF2αΔTregmice), but not in PHD2-HIF1α (PHD2-HIF1αΔTregmice) double KOs, suggesting an important and possibly selective role of the PHD2-HIF2α axis in the control of Treg function. Finally, the transcriptomic analysis of PHD2-deficient Tregs identified the STAT1 pathway as a target of the PHD2-HIF2α axis in regulatory T cell phenotype and in vivo function.
A comparison of rotation-based scores for gene set analysis
Authors: Caballe Mestres Adria , Berenguer Llergo Antonio , Stephan-Otto Attolini Camille
Published: March 2021

Gene-wise differential expression is usually the first major step in the statistical analysis of high-throughput data obtained from tech-niques such as microarrays or RNA-sequencing. The analysis at gene level is often complemented by the screening of the data in a broader biological context that considers as unit of analysis meaningful groups of genes that may have functions in certain biological processes.

Among the vast number of publications about gene set analysis, the rotation test for gene set analysis, also referred by roast, is a general sample randomization approach that maintains the integrity of the intra-gene set correlation structure in defining the null distribution of the test.

In this work we compare the performance of several enrichment score functions using such rotational approach for hypothesis testing. We find that computationally intensive measures based on Kolmogorov-Smirnov statistics fail to improve the rates of simpler measures of GSA like mean and maxmean scores. We also show the importance of ac-counting for the gene linear dependence structure of the testing set, which it is linked to the loss of effective signature size. In this regard, weighted statistics are introduced with the aim of maximizing the ef-fective signature size. These are found to out-power other usual scores in some simulations scenarios. The average of absolute values is found to be the most powerful score using both simulated and benchmarking data.

All tools are available in theroastgsaR package.
A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution
Authors: Debelius Justine W , Robeson Michael , Hugerth Luisa W. , Boulund Fredrik , Ye Weimin , Engstrand Lars
Published: March 2021

Motivation

Full length, high resolution 16s rRNA marker gene sequencing has been challenging historically. Short amplicons provide high accuracy reads with widely available equipment, at the cost of taxonomic resolution. One recent proposal has been to reconstruct multiple amplicons along the full-length marker gene, however no barcode-free computationally tractable approach for this is available. To address this gap, we present Sidle (SMURF Implementation Done to acceLerate Efficiency), an implementation of the Short MUltiple Reads Framework algorithm with a novel tree building approach to reconstruct rRNA genes from individually amplified regions.

Results

Using simulated and real data, we compared Sidle to two other approaches of leveraging multiple gene region data. We found that Sidle had the least bias in non-phylogenetic alpha diversity, feature-based measures of beta diversity, and the reconstruction of individual clades. With a curated database, Sidle also provided the most precise species-level resolution.

Availability and Implementation

Sidle is available under a BSD 3 license from https://github.com/jwdebelius/q2-sidle
Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers
Authors: Riahi Saleh , Lee Jae Hyeon , Wei Shuai , Cost Robert , Masiero Alessandro , Prades Catherine , Olfati-Saber Reza , Wendt Maria , Park Anna , Qiu Yu , Zhou Yanfeng
Published: March 2021

As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here we leverage our expertise in computational antibody engineering to rationally design/optimize three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R, and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS. Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody induced virus activation or enhancement, we applied NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.
Shining a light on Laurentian Great Lakes cisco (Coregonus artedi): how ice coverage may impact embryonic development
Authors: Stewart Taylor R. , Vinson Mark R. , Stockwell Jason D.
Published: March 2021

Changes in winter conditions, such as decreased ice coverage and duration, have been observed in the Laurentian Great Lakes for more than 20 years. Such changes have been hypothesized to be linked to lowCoregonusspp. survival to age-1 as most cisco (Coregonus artedi) populations are autumn spawners whose embryos incubate under ice throughout the winter. The quantity of light during winter is regulated by ice coverage, and light affects embryo survival and development in some teleosts. We experimentally evaluated how cisco embryos from lakes Superior and Ontario respond to three light treatments that represented day-light intensity under 0-10, 40-60, and 90-100% ice coverage. Embryonic response measures included two developmental factors (embryo survival and incubation period) and two morphological traits (length-at-hatch and yolk-sac volume). Embryo survival was highest at the medium light treatment and decreased at high and low treatments for both populations, suggesting cisco may be adapted to withstand some light exposure from inter-annual variability in ice coverage. Light intensity had no overall effect on length of incubation. Increasing light intensity decreased length-at-hatch in Lake Superior but had no effect in Lake Ontario. Yolk-sac volume was positively correlated with increasing light in Lake Superior and negatively correlated in Lake Ontario. Contrasting responses in embryo development between lakes suggests differences in populations’ response to light is flexible. Our results provide a step towards better understanding the high variability observed in coregonine recruitment and may help predict what the future of this species may look like under current climate trends.
Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues
Authors: Neurath Rachel A. , Pett-Ridge Jennifer , Chu-Jacoby Ilexis , Herman Donald , Whitman Thea , Nico Peter , Lipton Andrew S. , Kyle Jennifer , Tfaily Malak M. , Thompson Alison , Firestone Mary K.
Published: March 2021

1.

Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a13CO2labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon,13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a “transient fraction” of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids.

Synopsis

This study explores the interaction of rhizosphere carbon, minerals, and microbial influence on the fate of soil carbon.

TOC
Multiple origins of nematode-Wolbachiasymbiosis in supergroup F and convergent loss of bacterioferritin in filarialWolbachia
Authors: Sinha Amit , Li Zhiru , Poole Catherine B. , Ettwiller Laurence , Lima Nathália F. , Ferreira Marcelo U. , Fombad Fanny F. , Wanji Samuel , Carlow Clotilde K. S.
Published: March 2021

The intracellular endosymbiotic proteobacteriaWolbachiahave evolved across the phyla nematoda and arthropoda. InWolbachiaphylogeny, supergroup F is the only clade known so far with members from both arthropod and filarial nematode hosts and therefore can provide unique insights into their evolution and biology. In this study, 4 new supergroup FWolbachiagenomes have been assembled using a metagenomic assembly and binning approach,wMoz andwMpe from the human filarial parasitesMansonella ozzardiandMansonella perstans, andwOcae andwMoviF from the blue mason beeOsmia caerulescensand the sheep kedMelophagus ovinusrespectively. A comprehensive phylogenomic analysis revealed two independent origins of filarialWolbachiain supergroup F, most likely from ancestral arthropod hosts. The analysis also reveals that the switch from arthropod to filarial host is accompanied by a convergent pseudogenization and loss of the bacterioferritin gene, a phenomenon found to be shared by all filarialWolbachia, even those outside supergroup F. These observations indicate that differences in heme metabolism might be a key feature distinguishing filarial and arthropodWolbachia. The new genomes provide a valuable resource for further studies on symbiosis, evolution, and the discovery of new antibiotics to treat mansonellosis.

Significance statement

Wolbachiaare bacterial endosymbionts of medically important parasitic filarial nematodes and arthropods. The evolutionary history and biological roles ofWolbachiain these different hosts are not well understood. The supergroup F inWolbachiaphylogeny harbors members from both filarial and arthropod hosts, providing an unparalleled opportunity for genomic comparisons to uncover distinguishing characteristics. This study provides new genomes from filarial and arthropodWolbachiafrom this unique supergroup. Their phylogenomic analysis reveals multiple, independent transfers ofWolbachiafrom arthropod to filariae. Remarkably, these transfers were associated with a convergent loss of the bacterioferritin gene, a key regulator of heme metabolism. Heme supplementation is considered a critical component ofWolbachia- filaria symbiosis. We demonstrate bacterioferritin loss is a novel feature exclusive to filarialWolbachia.
Crotamine as a vehicle for non-viral gene delivery for Pompe disease
Authors: Martiniuk Frank , Mack Adra , Martiniuk Justin , Karpel Richard , Meinke Peter , Schoser Benedikt , Wu Feng , Tchou-Wong Kam-Meng
Published: March 2021

Genetic deficiency of lysosomal acid alpha glucosidase or acid maltase (GAA) results in Pompe disease (PD), encompassing at least five clinical subtypes of varying severity. The current approved enzyme replacement therapy (ERT) for PD is via IV infusion every 2 weeks of a recombinant human GAA (rhGAA) secreted by Chinese hamster ovary (CHO) cells (alglucosidase alfa/Myozyme, Sanofi/Genzyme). Although alglucosidase alfa has proven to be efficient in rescuing cardiac abnormalities and extending the life span of the infantile form, the response in skeletal muscle is variable. ERT usually begins when the patients are symptomatic and secondary problems are already present which are compounded by low alglucosidase alfa uptake, transient nature (every 2 weeks with a rapid return to defect levels), variable glycogen reduction, autophagic accumulation, immune response and high cost. A consensus at a recent US Acid Maltase Deficiency (AMD) conference suggested that a multi-pronged approach including gene therapy, diet, exercise, etc. must be evaluated for a successful treatment of PD. Compared to replication defective viruses, non-viral gene transfer offers fewer safety concerns and, if recent studies are validated, has a wider range of cells. In order for gene therapy (GT) to succeed, the gene of interest must be delivered into the affected cell and expressed to overcome the inherited deficiency. Cell penetrating peptides (CPPs) enter eukaryotic cells through an energy-independent mechanism and efficiently carry biologically active and therapeutic molecules into cells and localize in the cytoplasm or nucleus. CPPs are usually covalently linked to the cargo, including peptides and DNA. Crotamine (Cro) from the South American rattlesnake-Crotalus durrissus terrificusvenom, can bind electrostatically to plasmid DNA to deliver into cells, including muscle. We have assembled a bacterial expression vector for Cro and purified the recombinant Cro (rCro). Transient transfection in AMD fibroblasts andex vivoin whole blood from an adult Pompe patient with rCro complexed with the pcDNA3 xhGAAcDNA demonstrated increased GAA activity. In GAA knockout (KO) mice receiving a single injection of rCro complexed to pcDNA3 xhGAAcDNA intraperitoneally (IP), we found increased GAA activity in tissues after 48 hr. After 8 treatments-IP over 55 days, we found increased vertical hang-time activity, reduced glycogen deposition, increased GAA activity/hGAAplasmid in tissues and minimal immune-reaction to rCro. A subsequent study of 5 administrations every 2 to 3 weeks showed reverse of the clinical phenotypes by running wheel activity, Rotarod, grip-strength meter, open field mobility and T-maze. Tissue culture experiments in PD fibroblast, lymphoid and skeletal muscle cell lines showed increased GAA activity after rCro transient gene delivery.
The SARS-CoV-2 replication-transcription complex is a priority target for broad-spectrum pan-coronavirus drugs
Authors: Yazdani Setayesh , De Maio Nicola , Ding Yining , Shahani Vijay , Goldman Nick , Schapira Matthieu
Published: March 2021

In the absence of effective treatment, COVID-19 is likely to remain a global disease burden. Compounding this threat is the near certainty that novel coronaviruses with pandemic potential will emerge in years to come. Pan-coronavirus drugs – agents active against both SARS-CoV-2 and other coronaviruses – would address both threats. A strategy to develop such broad-spectrum inhibitors is to pharmacologically target binding sites on SARS-CoV-2 proteins that are highly conserved in other known coronaviruses, the assumption being that any selective pressure to keep a site conserved across past viruses will apply to future ones. Here, we systematically mapped druggable binding pockets on the experimental structure of fifteen SARS-CoV-2 proteins and analyzed their variation across twenty-seven α- and β-coronaviruses and across thousands of SARS-CoV-2 samples from COVID-19 patients. We find that the two most conserved druggable sites are a pocket overlapping the RNA binding site of the helicase nsp13, and the catalytic site of the RNA-dependent RNA polymerase nsp12, both components of the viral replication-transcription complex. We present the data on a public web portal (https://www.thesgc.org/SARSCoV2_pocketome/) where users can interactively navigate individual protein structures and view the genetic variability of drug binding pockets in 3D.
fMRIflows: a consortium of fully automatic univariate and multivariate fMRI processing pipelines
Authors: Notter Michael P. , Herholz Peer , Da Costa Sandra , Gulban Omer F. , Isik Ayse Ilkay , Gaglianese Anna , Murray Micah M.
Published: March 2021

How functional MRI (fMRI) data are analyzed depends on the researcher and the toolbox used. It is not uncommon that the processing pipeline is rewritten for each new dataset. Consequently, code transparency, quality control and objective analysis pipelines are important for improving reproducibility in neuroimaging studies. Toolboxes, such as Nipype and fMRIPrep, have documented the need for and interest in automated pre-processing analysis pipelines. Recent developments in data-driven models combined with high-resolution neuroimaging datasets have strengthened the need not only for a standardized preprocessing workflow but also for a reliable and comparable statistical pipeline. Here, we introduce fMRIflows: a consortium of fully automatic neuroimaging pipelines for fMRI analysis, which performs standard preprocessing, as well as 1st- and 2nd-level univariate and multivariate analyses. In addition to the standardized pre-processing pipelines, fMRIflows provides flexible temporal and spatial filtering to account for datasets with increasingly high temporal resolution and to help appropriately prepare data for advanced machine learning analyses, improving signal decoding accuracy and reliability. This paperfirstdescribes fMRIflows’ structure and functionality,thenexplains its infrastructure and access, andlastlyvalidates the toolbox by comparing it to other neuroimaging processing pipelines such as fMRIPrep, FSL and SPM. This validation was performed on three datasets with varying temporal sampling and acquisition parameters to prove its flexibility and robustness. fMRIflows is a fully automatic fMRI processing pipeline that uniquely offers univariate and multivariate single-subject and group analyses as well as pre-processing.
Genetic analysis of coronary artery disease using tree-based automated machine learning informed by biology-based feature selection
Authors: Manduchi Elisabetta , Le Trang T. , Fu Weixuan , Moore Jason H.
Published: March 2021

Machine Learning (ML) approaches are increasingly being used in biomedical applications. Important challenges of ML include choosing the right algorithm and tuning the parameters for optimal performance. Automated ML (AutoML) methods, such as Tree-based Pipeline Optimization Tool (TPOT), have been developed to take some of the guesswork out of ML thus making this technology available to users from more diverse backgrounds. The goals of this study were to assess applicability of TPOT to genomics and to identify combinations of single nucleotide polymorphisms (SNPs) associated with coronary artery disease (CAD), with a focus on genes with high likelihood of being good CAD drug targets. We leveraged public functional genomic resources to group SNPs into biologically meaningful sets to be selected by TPOT. We applied this strategy to data from the UK Biobank, detecting a strikingly recurrent signal stemming from a group of 28 SNPs. Importance analysis of these uncovered functional relevance of the top SNPs to genes whose association with CAD is supported in the literature and other resources. Furthermore, we employed game-theory based metrics to study SNP contributions to individual level TPOT predictions and discover distinct clusters of well-predicted CAD cases. The latter indicates a promising approach towards precision medicine.
Two promoters integrate multiple enhancer inputs to drive wild-typeknirpsexpression in theD. melanogasterembryo
Authors: Li Lily , Waymack Rachel , Elabd Mario , Wunderlich Zeba
Published: March 2021

Proper development depends on precise spatiotemporal gene expression patterns. Most genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that these multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of theknirpslocus in the earlyDrosophila melanogasterembryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical “sharp” developmental promoter, while the other resembles a “broad” promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter. By analyzing the dynamics of these reporters, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the specific combination of promoter and enhancer. Using locus-sized reporters, we discovered that even enhancers that show no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is both due to enhancer preference and a need for redundancy and that “broad” promoters with dispersed transcription start sites are common among developmental genes. Our results also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where many variables shape a gene’s overall expression pattern.
Cation and anion channelrhodopsins: Sequence motifs and taxonomic distribution
Authors: Govorunova Elena G. , Sineshchekov Oleg A. , Li Hai , Wang Yumei , Brown Leonid S. , Palmateer Alyssa , Melkonian Michael , Cheng Shifeng , Carpenter Eric , Patterson Jordan , Wong Gane K.-S. , Spudich John L.
Published: March 2021

Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as optogenetic tools to control cell membrane potential with light. We mined algal and other protist polynucleotide sequencing projects and metagenomic samples to identify 75 channelrhodopsin homologs from three channelrhodopsin families, including one revealed in dinoflagellates in this study. We carried out electrophysiological analysis of 33 natural channelrhodopsin variants from different phylogenetic lineages and 10 metagenomic homologs in search of sequence determinants of ion selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins. Our results show that association of a reduced number of glutamates near the conductance path with anion selectivity depends on a wider protein context, because prasinophyte homologs with the identical glutamate pattern as in cryptophyte ACRs are cation-selective. Desensitization is also broadly context-dependent, as in one branch of stramenopile ACRs and their metagenomic homologs its extent roughly correlates with phylogenetic relationship of their sequences. Regarding spectral tuning, two prasinophyte CCRs exhibit red-shifted spectra to 585 nm, although their retinal-binding pockets do not match those of previously known similarly red-shifted channelrhodopsins. In cryptophyte ACRs we identified three specific residue positions in the retinal-binding pocket that define the wavelength of their spectral maxima. Lastly, we found that dinoflagellate rhodopsins with a TCP motif in the third transmembrane helix and a metagenomic homolog exhibit channel activity.

IMPORTANCE

Channelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered as prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind. In this study we used manual and automated patch clamp recording of representative members of four channelrhodopsin families including a family that we report in this study in dinoflagellates. Our results contribute to a better understanding of molecular determinants of ionic selectivity, photocurrent desensitization, and spectral tuning in channelrhodopsins.
Impact of increased membrane realism on conformational sampling of proteins
Authors: Weigle Austin T. , Carr Matthew , Shukla Diwakar
Published: March 2021

The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) is heavily dependent on the lipid composition. While the field is pushing towards implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein function or if it matters over long timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma with more than 10 different lipid species membrane is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or -independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ~1 kcal/mol. The free energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.
Isolation and Characterization of Cross-Neutralizing Coronavirus Antibodies from COVID-19+ Subjects
Authors: Jennewein Madeleine F. , MacCamy Anna J. , Akins Nicholas R. , Feng Junli , Homad Leah J. , Hurlburt Nicholas K. , Seydoux Emily , Wan Yu-Hsin , Stuart Andrew B. , Edara Venkata Viswanadh , Floyd Katharine , Vanderheiden Abigail , Mascola John R. , Doria-Rose Nicole , Wang Lingshu , Yang Eun Sung , Chu Helen Y. , Torres Jonathan L. , Ozorowski Gabriel , Ward Andrew B. , Whaley Rachael E. , Cohen Kristen W. , Pancera Marie , McElrath M. Juliana , Englund Janet A. , Finzi Andrés , Suthar Mehul S. , McGuire Andrew T. , Stamatatos Leonidas
Published: March 2021

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterized 198 antibodies isolated from four COVID19+ subjects and identified 14 SARS-CoV-2 neutralizing antibodies. One targeted the NTD, one recognized an epitope in S2 and twelve bound the RBD. Three anti-RBD neutralizing antibodies cross-neutralized SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency rather than the antibody epitope specificity regulates thein vivoprotective potential of anti-SARS-CoV-2 antibodies. The anti-S2 antibody also neutralized SARS-CoV-1 and all four cross-neutralizing antibodies neutralized the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.
The proteome of remyelination is different from that of developmental myelination
Authors: de Faria Joana Paes , Azevedo Maria M. , Bausch-Fluck Damaris , Seixas Ana , Domingues Helena S. , Monteiro Maria A. , Pedrioli Patrick G.A. , Lopes Eduarda , Fernandes Rui , Zhao Chao , Franklin Robin J. M. , Wollscheid Bernd , Relvas Joao B. , Montani Laura
Published: March 2021

Loss of myelin underlies the pathology of several neurological disorders of diverse etiology. CNS remyelination by adult oligodendrocyte progenitor cells (OPCs) can occur but it differs from developmental myelination carried out by neonatal OPCs. We asked whether the myelin proteome of remyelinated regions is changed. We compared the myelin proteome formed during development to the remyelination proteome attained after lysolecithin-induced demyelination in the mouse spinal cord. Mass-spectrometry analysis of iTRAQ labelled myelin protein lysates showed that the proteome of remyelination is different from that of developmental myelination, leading to profound changes in myelin protein content. Aside from known mediators of oligodendrocyte differentiation, we found proteome alterations included modulators of metabolism, cell signaling and actin cytoskeleton dynamics. Downregulating one candidate (FSCN1/Fascin1) was sufficient to partially hamper oligodendrocytesin-vitro. In summary, we identify the difference in the proteome of remyelinating oligodendrocytes as a novel potential contributor to the pathophysiology of demyelinating disorders, thus providing new potential therapeutic targets for future studies.
B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies
Authors: Zhou Hao , Dcosta Belinda M. , Samanovic Marie I. , Mulligan Mark J. , Landau Nathaniel R. , Tada Takuya
Published: March 2021

DNA sequence analysis recently identified the novel SARS-CoV-2 variant B.1.526 that is spreading at an alarming rate in the New York City area. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein together with four novel point mutations and with an E484K or S477N mutation in the receptor binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. We report that convalescent sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer as compared to D614G. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody but the combination cocktail with REGN10987 was fully active. The findings suggest that current vaccines and therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of wide-spread vaccination.
A polyyne toxin produced by an antagonistic bacterium blinds and lyses a green microalga
Authors: Hotter Vivien , Zopf David , Kim Hak Joong , Silge Anja , Schmitt Michael , Aiyar Prasad , Fleck Johanna , Matthäus Christian , Hniopek Julian , Yan Qing , Loper Joyce , Sasso Severin , Hertweck Christian , Popp Jürgen , Mittag Maria
Published: March 2021

Microalgae are key contributors to global carbon fixation and the basis of many food webs. In nature, their growth is often supported or suppressed by other microorganisms. The bacteriumPseudomonas protegensPf-5 arrests the growth of the green algaChlamydomonas reinhardtii, deflagellates the alga by the cyclic lipopeptide orfamide A, and alters its morphology. Using a combination of Raman microspectroscopy, genome mining and mutational analysis, we discovered a novel polyyne toxin we name protegencin that is secreted byP. protegensand penetrates algal cells to destroy their primitive visual system, the eyespot. Together with secreted orfamide A, protegencin prevents the phototactic behavior ofC. reinhardtiineeded to perform optimal photosynthesis. A protegencin-deficient biosynthetic mutant ofP. protegensdoes not affect growth or eyespot carotenoids ofC. reinhardtii. Thus, protegencin acts in a direct and destructive way, and reveals at least a two-pronged molecular strategy used by algicidal bacteria.
RNA Pol IV has antagonistic parent-of-origin effects on Arabidopsis endosperm
Authors: Satyaki Prasad R.V. , Gehring Mary
Published: March 2021

Gene expression in endosperm – a seed tissue that mediates transfer of maternal resources to offspring – is under complex epigenetic control. We show here that plant-specific RNA Polymerase IV mediates parental control of endosperm gene expression. Pol IV is required for the production of small interfering RNAs that typically direct DNA methylation. We compared small RNAs, DNA methylation, and mRNAs inA. thalianaendosperm from reciprocal heterozygotes produced by crossing wild-type plants to Pol IV mutants. We find that maternally and paternally acting Pol IV have divergent effects on endosperm. Losses of maternal and paternal Pol IV impact sRNAs and DNA methylation at distinct genomic sites. Strikingly, maternally and paternally-acting Pol IV have antagonistic impacts on gene expression at some loci, divergently promoting or repressing endosperm gene expression. Antagonistic parent-of-origin effects have only rarely been described and are consistent with a gene regulatory system evolving under parental conflict.
Four-point dynamic leveling method for drilling platform application
Authors: Li Dongmin , Ma Guofang , Li Jia
Published: March 2021

Purpose

It is essential to level the drilling platform across which a drilling robot travels in a slant underground coal mine tunnel to ensure smooth operation of the drill rod. However, existing leveling methods do not provide dynamic performance under the drilling conditions of the underground coal mine. A four-point dynamic leveling algorithm is presented in this paper based on the platform attitude and support rod displacement (DLAAD). An experimental drilling robot demonstrates its dynamic leveling capability and ability to ensure smooth drill rod operations.

Design/methodology/approach

The attitude coordinate of the drilling robot is established according to its structure. A six-axis combined sensor is adopted to detect the platform attitude, thus revealing the three-axis Euler angles. The support rod displacement values are continuously detected by laser displacement sensors to obtain the displacement increment of each support rod as needed. The drilling robot is leveled according to the current support rod displacement and three-dimensional (3 D) attitude detected by the six-axis combined sensor dynamically.

Findings

Experimental results indicate that the DLAAD algorithm is correct and effectively levels the drilling platform dynamically. It can thus provide essential support in resolving drill rod sticking problems during actual underground coal mine drilling operations.

Practical implications

The DLAAD algorithm supports smooth drill rod operations in underground coal mines, which greatly enhances safety, reduces power consumption, and minimizes cost. The approach proposed here thus represents considerable benefits in terms of coal mine production and shows notable potential for application in similar fields.

Originality/value

The novel DLAAD algorithm and leveling control method are the key contributions of this work, they provide dynamical 3 D leveling and help to resolve drill rod sticking problems.
ELMOPP: an application of graph theory and machine learning to traffic light coordination
Authors: Sheriff Fareed
Published: March 2021

Purpose

This paper presents the Edge Load Management and Optimization through Pseudoflow Prediction (ELMOPP) algorithm, which aims to solve problems detailed in previous algorithms; through machine learning with nested long short-term memory (NLSTM) modules and graph theory, the algorithm attempts to predict the near future using past data and traffic patterns to inform its real-time decisions and better mitigate traffic by predicting future traffic flow based on past flow and using those predictions to both maximize present traffic flow and decrease future traffic congestion.

Design/methodology/approach

ELMOPP was tested against the ITLC and OAF traffic management algorithms using a simulation modeled after the one presented in the ITLC paper, a single-intersection simulation.

Findings

The collected data supports the conclusion that ELMOPP statistically significantly outperforms both algorithms in throughput rate, a measure of how many vehicles are able to exit inroads every second.

Originality/value

Furthermore, while ITLC and OAF require the use of GPS transponders and GPS, speed sensors and radio, respectively, ELMOPP only uses traffic light camera footage, something that is almost always readily available in contrast to GPS and speed sensors.
Consumer-led eco-development of food products: a case study to propose a framework
Authors: Thomas Chloé , Maître Isabelle , Symoneaux Ronan
Published: March 2021

Purpose

The purpose of this paper is to propose an agile methodology for the development of food products that has two key characteristics: (1) consumers are included as co-creators and (2) the assessment of environmental impacts plays a central role.

Design/methodology/approach

In collaboration with a French small-to-mid-size enterprise, a research-intervention approach was used to test the agile methodology designed, which features three iterative runs of food product development. In each run, prototypes were presented and modified with consumers during focus groups. Life cycle analysis assessed the relative environmental impacts of the prototypes. The research data from consumers were mainly qualitative.

Findings

The main result of this work is the implementation of a methodology to develop new food products in an efficient way by integrating consumers' insights and environmental concerns simultaneously. The method was successful in integrating consumers as co-creators and in drawing attention to the potential environmental effects of different prototypes for the decision-making process.

Research limitations/implications

The research is based on a single case study. Thus, generalisation to other companies is limited. The authors invite further research focussed on different types of companies. The methodology and the tools could be modified to suit a variety of contexts.

Originality/value

This work addresses the need for guidelines to integrate consumers and environmental considerations into the food development process by testing an agile methodology with a company. It contributes to the scope of sustainable and consumer-oriented food innovation management.