bluuebunny/crossref_metadata_2025 huggingface dataset:
Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States
Authors: Davis Jessica T. , Chinazzi Matteo , Perra Nicola , Mu Kunpeng , Piontti Ana Pastore y , Ajelli Marco , Dean Natalie E. , Gioannini Corrado , Litvinova Maria , Merler Stefano , Rossi Luca , Sun Kaiyuan , Xiong Xinyue , Halloran M. Elizabeth , Longini Ira M. , Viboud Cécile , Vespignani Alessandro
Published: March 2021

Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment of the COVID-19 pandemic in Europe and the United States (US). The model is calibrated on international case introductions at the early stage of the pandemic. We find that widespread community transmission of SARS-CoV-2 was likely in several areas of Europe and the US by January 2020, and estimate that by early March, only 1 − 3 in 100 SARS-CoV-2 infections were detected by surveillance systems. Modeling results indicate international travel as the key driver of the introduction of SARS-CoV-2 with possible importation and transmission events as early as December, 2019. We characterize the resulting heterogeneous spatio-temporal spread of SARS-CoV-2 and the burden of the first COVID-19 wave (February-July 2020). We estimate infection attack rates ranging from 0.78%-15.2% in the US and 0.19%-13.2% in Europe. The spatial modeling of SARS-CoV-2 introductions and spreading provides insights into the design of innovative, model-driven surveillance systems and preparedness plans that have a broader initial capacity and indication for testing.
Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages
Authors: Gupta Anushka , Shamsi Farnaz , Altemos Nicolas , Dorlhiac Gabriel F. , Cypess Aaron M. , White Andrew P. , Patti Mary Elizabeth , Tseng Yu-Hua , Streets Aaron
Published: March 2021

Single-cell RNA-sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue where collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nuclei extraction is often much more efficient and therefore single-nuclei RNA-sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We demonstrate that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, and how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we demonstrate successful integration of scRNA-seq and snRNA-seq datasets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for characterization of cellular diversity in the adipose tissue.
Histological analysis of implantation embryos in large Japanese field mouse (Apodemus speciosus) and estimation of developmental stage
Authors: Imai Hiroyuki , Kano Kiyoshi , Kusakabe Ken Takeshi
Published: March 2021

The large Japanese field mice (Apodemus speciosus) are small rodent specie endemic to Japan. The genetic characteristics ofA. speciosusis different chromosome numbers within one species. Furthermore,A. speciosusis used for research in radiation and genetics. In this present study, a pregnantA. speciosuswas obtained, and histochemical analysis of the implanted embryos was performed and compared with developmental stages of the mouse. Although there were some differences, the structures of the implanted embryos including the primitive streak and placenta ofA. speciosuswere similar to that of the mouse. Our study will be important report in the construction of a developmental atlas ofA. speciosus.
Duox generated reactive oxygen species activate ATR/Chk1 to induce G2 arrest in Drosophila tracheoblasts
Authors: Kizhedathu Amrutha , Chhajed Piyush , Yeramala Lahari , Basu Deblina Sain , Mukherjee Tina , Vinothkumar Kutti R. , Guha Arjun
Published: March 2021

Progenitors of the thoracic tracheal system of adult Drosophila (tracheoblasts) arrest in G2 during larval life and rekindle a mitotic program subsequently. G2 arrest is dependent on ATR-dependent phosphorylation of Chk1 that is actuated in the absence of detectable DNA damage. We are interested in the mechanisms that activate ATR/Chk1 (Kizhedathu et al., 2018, 2020). Here we report that levels of reactive oxygen species (ROS) are high in arrested tracheoblasts and decrease upon mitotic re-entry. High ROS is dependent on expression of Duox, an H2O2 generating-Dual Oxidase. ROS quenching by overexpression of Superoxide Dismutase 1, or by knockdown of Duox, abolishes Chk1 phosphorylation and results in precocious proliferation. Tracheae deficient in Duox, or deficient in both Duox and regulators of DNA damage-dependent ATR/Chk1 activation (Claspin/ATRIP/TOPBP1), can induce phosphorylation of Chk1 in response to micromolar concentrations of H2O2 in minutes. The findings presented reveal that H2O2 activates ATR/Chk1 in tracheoblasts by a non-canonical, potentially direct, mechanism.
Mitogenomic analyses provide further evidence for multiple miniaturization events during the evolution of Seychelles caecilian amphibians
Authors: Gwilt Annie J. , Streicher Jeffrey W. , Maddock Simon T.
Published: March 2021

Whole mitochondrial genomes have been helpful in estimating phylogenetic relationships in many organismal groups, including caecilian amphibians. Despite the increasing ease of obtaining mitochondrial genome sequences from high-throughput sequencing, several species of caecilian lack this important molecular resource. As part of a targeted-sequence capture project of nuclear ultraconserved elements for a small but substantially diverse radiation of caecilian amphibians found on the granitic Seychelles, we examined off-target sequences to determine if we captured enough mitochondrial fragments to reconstruct mitogenomes. We reconstructed (near-)complete mitogenomes for six of the eight species of Seychelles caecilians and completed 14 independent phylogenetic analyses (Bayesian inference and maximum likelihood) on different mitochondrial datasets assembled using different alignment techniques. As with other studies, we were unable to fully resolve internal phylogenetic relationships of the group. However, we found strong support in most analyses that a recently described miniaturized species,Hypogeophis pti, and another similarly-sized miniaturized species,H. brevisare not sister taxa. Our study suggests that miniature species of caecilians likely evolved at least twice on the Seychelles and highlights the need to revise genus-level taxonomy of Seychelles caecilians while providing further evidence that off-target sequences often contain enough mitochondrial fragments to reconstruct mitogenomes.
Base editing using CRISPR/Cas9 inDrosophila
Authors: Marr Elizabeth , Potter Christopher J.
Published: March 2021

Cas9 and a guide RNA function to target specific genomic loci for generation of a double stranded break. Catalytic dead versions of Cas9 (dCas9) no longer cause double stranded breaks and instead can serve as molecular scaffolds to target additional enzymatic proteins to specific genomic loci. To generate mutations in selected genomic residues, dCas9 can be used for genomic base editing by fusing a cytidine deaminase to induce C>T (or G>A) mutations at targeted sites. Here, we test base editing inDrosophilaby expressing a transgenicDrosophilabase editor (DBE2, based on the mammalian BE2) which consists of a fusion protein of cytidine deaminase, dCas9, and uracil glycosylase inhibitor. We utilized transgenic lines expressing gRNAs along with pan-tissue expression of theDrosophilaBase Editor (Actin5C-DBE2) and found high rates of base editing at multiple targeted loci in the 20 bp target sequence. Highest rates of conversion of C>T were found in positions 3-9 of the gRNA targeted site, with conversion reaching nearly 100% of targeted DNA is somatic tissues. The simultaneous use of two gRNA targeting a genomic region spaced ∼50 bps apart led to mutations between the two gRNA targets, implicating a method to broaden the available sites accessible to targeting. These results indicate base editing is efficient inDrosophila, and could be used to induce point mutations at select loci.
Hyperbolic disc embedding of functional human brain connectomes using resting state fMRI
Authors: Whi Wonseok , Ha Seunggyun , Kang Hyejin , Lee Dong Soo
Published: March 2021

The brain presents a real complex network of modular, small-world, and hierarchical nature, which are features of non-Euclidean geometry. Using resting-state functional magnetic resonance imaging (rs-fMRI), we constructed a scale-free binary graph for each subject, using internodal time-series correlation of regions-of-interest (ROIs) as a proximity measure. The resulted network could be embedded onto manifolds of various curvature and dimensions. While maintaining the fidelity of embedding (low distortion, high mean average precision), functional brain networks were found to be best represented in the hyperbolic disc. Usingmodel, we reduced the dimension of the network into 2-D hyperbolic space and were able to efficiently visualize the internodal connections of the brain, preserving proximity as distances and angles on the hyperbolic discs. Each individual disc revealed decentralized nature of information flow and anatomic relevance. Using the hyperbolic distance on themodel, we could detect the anomaly of network in autistic spectrum disorder (ASD) subjects. This procedure of embedding grants us a reliable new framework for studying functional brain networks and the possibility of detecting anomalies of the network in the hyperbolic disc on an individual scale.
Pellaea zygophylla, a new combination for a distinctive & well-known but neglected fern
Authors: Alexander Patrick J.
Published: March 2021

Pellaea ovatais a widespread species, sexual diploid in Texas &northeastern Mexico but an apogamous triploid in northwestern Mexico, south to northern Argentina, &on Hispaniola. The type belongs to the southern, apogamous triploid form. Although these two forms have been discussed repeatedly in the literature, morphological distinctions between them have been overlooked and they have not been recognized taxonomically. However, they are distinct.Pellaea ovatas.s. has puberulent rachides & costae; pinnae usually 2-pinnate with a well-defined main axis &pinnules borne singly; fertile pinnules ovate, cordate basally &rounded apically. The sexual diploid form has rachides &costae glabrous; pinnae pseudo-dichotomously branched &pinnules usually paired; fertile pinnules narrowly rounded-trapeziform, obliquely truncate to cordate basally &truncate apically. Riddell named the sexual diploid formPteris zygophylla, from which I give it the new combinationPellaea zygophylla.
TOWARDS QUANTITATIVE FORECASTING OF SPECIES YIELDS WITH INCOMPLETE INFORMATION ON MODEL PARAMETERS
Authors: Fort Hugo
Published: March 2021

Predicting both the absolute and the relative abundance of species in a spatial patch is of paramount interest in areas like, agriculture, ecology and environmental science.

The linear Lotka-Volterra generalized equations (LLVGE) serve for describing the dynamics of communities of species connected by negative as well as positive interspecific interactions.

Here we particularize these LLVGE to the case of single trophic ecological communities, like mixtures of plants, withS>2 species. Thus, by estimating the LLVGE parameters from the yields in monoculture and biculture experiments, the LLVGE are able to produce decently accurate predictions for species yields.

However, a common situation we face is that we don’t know all the parameters appearing in the LLVGE. Indeed, for large values ofS, only a fraction of the experiments necessary for estimating the model parameters is commonly carried out. We then analyze which quantitative predictions are possible with an incomplete knowledge of the parameters.
Copper intoxication in group BStreptococcustriggers transcriptional activation of thecopoperon that contributes to enhanced virulence during acute infection
Authors: Sullivan Matthew J. , Goh Kelvin G. K. , Gosling Dean , Katupitiya Lahiru , Ulett Glen C.
Published: March 2021

Bacteria can utilize Copper (Cu) as a trace element to support cellular processes; however, excess Cu can intoxicate bacteria. Here, we characterize thecopoperon in group B streptococcus (GBS), and establish its role in evasion of Cu intoxication and the response to Cu stress on virulence. Growth of GBS mutants deficient in either thecopACu exporter, or thecopYrepressor, were severely compromised in Cu-stress conditions. GBS survival of Cu stress reflected a mechanism of CopY de-repression of the CopA efflux system. However, neither mutant was attenuated for intracellular survival in macrophages. Analysis of global transcriptional responses to Cu by RNA-sequencing revealed a stress signature encompassing homeostasis of multiple metals. Genes induced by Cu stress included putative metal transporters for manganese import, whereas a system for iron export was repressed. In addition,copApromoted the ability of GBS to colonize the blood, liver and spleen of mice following disseminated infection. Together, these findings show that GBScopAmediates resistance to Cu intoxication, via regulation by the Cu-sensing transcriptional repressor,copY. Cu stress responses in GBS reflect a transcriptional signature that heightens virulence and represents an important part of the bacteria’s ability to survive in different environments.

Importance

Understanding how bacteria manage cellular levels of metal ions, such as copper, helps to explain how microbial cells can survive in different stressful environments. We show how the opportunistic pathogen group B Streptococcus (GBS) achieves homeostasis of intracellular copper through the activities of the genes that comprise the cop operon, and describe how this helps GBS survive in stressful environments, including in the mammalian host during systemic disseminated infection.
IL-18 and Lower Risk for Lung Cancer: Triangulated Evidence from Germline Predictions, Pre-Diagnostic Measurements, and Tumor Expression
Authors: Smith-Byrne Karl , Chen Yan , Kachuri Linda , Kapoor Pooja M. , Guida Florence , Zahed Hana , Alcala Karine , Amos Christopher , Atkins Joshua , Bodinier Barbara , Ferreiro-Iglesia Aida , Hung Rayjean J. , Johansson Mikael , Koh Woon-Puay , Kyrø Cecilie , Langhammer Arnulf , Pietzner Maik , Sala Núria , Sandanger Torkjel M. , Travis Ruth C. , Tsilidis Kostas , Yuan Jian-Min , Robbins Hilary , Brennan Paul , McKay James , Johansson Mattias , Mälarstig Anders
Published: March 2021

Lung cancer remains the most common cause of cancer death globally. Dysregulation of immune response and inflammatory signaling is known to play an important role in lung tumorigenesis, but the causal drivers of this process have yet to be elucidated. To identify circulating inflammatory and immune-related proteins that influence risk for lung cancer we related genetically predicted plasma levels for 85 inflammation and immune proteins with susceptibility to lung cancer. Mendelian randomization (MR) analyses in 29,266 cases and 56,450 controls identified a candidate causal marker, IL-18, which conferred lower risk of lung cancer (OR per standard deviation increase: 0.85 [95% CI: 0.79-0.92]), in particular for adenocarcinoma (OR: 0.80 [95% CI: 0.72-0.89]). We subsequently validated this association using polygenic IL-18 predictions in the UK Biobank (HR highest vs. lowest quartile: 0.83 [95% CI: 0.72-0.95]) and using pre-diagnostic blood concentrations of IL-18 in 732 cases and 732 controls after controlling for the inhibitory role of IL-18BP (OR highest vs. lowest quartile: 0. 63 [95% CI: 0. 41-0.91]). Genetic colocalization suggested that IL-18 may act on lung cancer risk locally via lung tissue expression, and joint MR and tumor microenvironment analyses highlight CD8 T cells and NK cells as potential mediators. In addition to risk, IL-18 expression in adenocarcinoma tumor tissue was found to be associated with all-cause mortality in 480 TCGA samples after controlling for IL-18BP (HR per SD: 0.87 [95% CI: 0.78, 0.98]), which is in line with recent studies showing anti-tumor effects of IL-18. Our comprehensive genomic triangulation study thus highlights the potential for IL-18 as an aetiological biomarker and targetable for immune-oncology therapies.
Immunoinformatic approach to design a vaccine against SARS-COV-2 membrane glycoprotein
Authors: Ravindran Radhika , Gunasekaran Shoba , Easwaran Murugesh , Lulu Sajitha , Unni P. Ambili , Vino S. , Doble Mukesh
Published: March 2021

SARS-COV-2 is a pandemic virus causing COVID-19 disease which affects lungs and upper respiratory tract leading to progressive increase in the death rate worldwide. Currently, there are more than 123 million cases and over 2.71 million confirmed death caused by this virus. In this study, by utilizing an immunoinformatic approach, multiepitope-based vaccine is designed from the membrane protein which plays a vital role in the virion assembly of the novel-CoV. A total of 19 MHC class- I binders with HLA-A and HLA-B alleles have been selected with NetMHC pan EL 4.0 method from IEDB MHC-I prediction server. Four epitopes candidates from M-protein were selected based on the antigenicity, stability, immunogenicity, Ramachandran plot and scores with 100 % was taken for docking analysis with alleles HLA-A (PDB ID: 1B0R) and HLA-B (PDB ID: 3C9N) using ClusPro server. Among the four epitopes, the epitope FVLAAVYRI has the least binding energy and forms electrostatic, hydrogen and hydrophobic interactions with HLA-A (−932.8 Kcal/mol) and HLA-B (−860.7 Kcal/mol) which induce the T-cell response. Each HLA-A and HLA-B complex in the system environment achieves stable backbone configuration between 45-100 ns of MD simulation. This study reports a potent antigenic and immunogenic profile of FVLAAVYRI epitope from M-protein and furtherin vitroandin vivovalidation is needed for its adaptive use as vaccine against COVID-19.
A simple micropreparative gel electrophoresis technique for purification of proteins, nucleic acids, and bioconjugates
Authors: Sajjadi Sayyed Hashem , Wu Shang-Jung , Zubkovs Vitalijs , Ahmadzadeh Hossein , Goharshadi Elaheh K. , Boghossian Ardemis A.
Published: March 2021

The biochemical and biomedical fields hinge on the ability to effectively separate and purify biological macromolecules. Though this need is largely addressed with a variety of chromatographic and electrophoretic purification techniques, such techniques are usually laborious, time-consuming, and often require complex and costly instalments that are inaccessible to most laboratories. In this work, we introduce a simple micro-preparative (MP) method based on polyacrylamide gel electrophoresis (PAGE) to purify biological samples containing proteins, nucleic acids, and complex bioconjugates. Using a conventional vertical slab system, we demonstrate the extraction of purified DNA, proteins, and DNA-protein bioconjugates from their respective mixtures using MP-PAGE. We apply this system to recover DNA from a ladder mixture with yields of up to 90%, compared to the 58% yield obtained using specialized commercial devices. We also demonstrate the purification of folded enhanced yellow fluorescence protein (EYFP) from crude cell extract with 90% purity, comparable to purities achieved using a two-step size exclusion and immobilized metal-ion affinity chromatography purification procedure. Finally, we demonstrate the successful isolation of an EYFP-DNA bioconjugate sample that otherwise could not be processed using the two-step chromatography procedure. MP-PAGE thus offers a rapid and versatile means of purifying a variety of biomolecules without the need for specialized equipment.
Recurrent chromosomal translocations in sarcomas create a mega-complex that mislocalizes NuA4/TIP60 to Polycomb target loci
Authors: Sudarshan Deepthi , Avvakumov Nikita , Lalonde Marie-Eve , Alerasool Nader , Joly-Beauparlant Charles , Jacquet Karine , Mameri Amel , Lambert Jean-Philippe , Rousseau Justine , Lachance Catherine , Paquet Eric , Herrmann Lara , Setty Samarth Thonta , Loehr Jeremy , Bernardini Marcus Q. , Rouzbahman Marjan , Gingras Anne-Claude , Coulombe Benoit , Droit Arnaud , Taipale Mikko , Doyon Yannick , Côté Jacques
Published: March 2021

Chromosomal translocations frequently promote carcinogenesis by producing gain-of-function fusion proteins. Recent studies have identified highly recurrent chromosomal translocations in patients with Endometrial Stromal Sarcomas (ESS) and Ossifying FibroMyxoid Tumors (OFMT) leading to an in-frame fusion of PHF1 (PCL1) to six different subunits of the NuA4/TIP60 complex. While NuA4/TIP60 is a co-activator that acetylates chromatin and loads the H2A.Z histone variant, PHF1 is part of the Polycomb repressive complex 2 (PRC2) linked to transcriptional repression of key developmental genes through methylation of histone H3 on lysine 27. In this study, we characterize the fusion protein produced by theEPC1-PHF1translocation. The chimeric protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically- associating domain including part of theHOXDcluster. This is linked to aberrant gene expression, most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1, implicated with a PRC2 component in the most frequent translocation in ESS,JAZF1-SUZ12, is a potent transcription activator that physically associates with NuA4/TIP60, its fusion creating similar outcomes asEPC1-PHF1. Importantly, the specific increased expression of PRC2 targets/HOXgenes was also confirmed with ESS patient samples. Altogether, these results indicate that most chromosomal translocations linked to these sarcomas employ the same molecular oncogenic mechanism through a physical merge of NuA4/TIP60 and PRC2 complexes leading to mislocalization of histone marks and aberrant polycomb target gene expression.
Massive loss of transcription factors and the initial diversification of placental mammals
Authors: Zhao Xin-Wei , Wu Jiaqi , Kishino Hirohisa
Published: March 2021

As one of the most successful categories of organisms, mammals occupy a variety of niches on earth as a result of macroevolution. Transcription factors (TFs), the basic regulators of gene expression, may also evolve during mammalian phenotypic diversification and macroevolution. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that mammals experienced an upsurge in TF losses around 100 million years ago and also near the K–Pg boundary, thus implying a relationship with the divergence of placental animals. From approximately 100 million years ago to the present, losses dominated TF events without a significant change in TF gains. To quantify the effects of this TF pruning on mammalian macroevolution, we analyzed rates of molecular evolution and expression profiles of regulated target genes. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes, suggesting increased functional constraints. Furthermore, an association study revealed that massive TF losses are significantly positively correlated with solitary behavior, nocturnality, reproductive-seasonality and insectivory life history traits, possibly through rewiring of regulatory networks.
Green Fluorescent Carbon Dots as Targeting Probes for LED-Dependent Bacterial Killing
Authors: Samphire Jenny , Takebayashi Yuiko , Hill Stephen A. , Hill Nicholas , Heesom Kate J. , Lewis Philip A. , Alibhai Dominic , Bragginton Eilis C. , Dorh Josephine , Dorh Neciah , Spencer James , Galan M. Carmen
Published: March 2021

The emergence of antimicrobial resistance represents a significant health and economic challenge worldwide. The slow pace of antibacterial discovery necessitates strategies for optimal use of existing agents, including effective diagnostics able to drive informed prescribing; and development of alternative therapeutic strategies that go beyond traditional small-molecule approaches. Thus, the development of novel probes able to target bacteria for detection and killing, and that can pave the way to effective theranostic strategies, is of great importance. Here we demonstrate that metal-free green-emitting fluorescent carbon dots (FCDs) synthesized from glucosamine HCl andm-phenylenediamine, and featuring 2,5-deoxyfructosazine on a robust amorphous core, can label both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa) bacterial pathogens within 10 minutes of exposure. Moreover, effective killing of Gram-positive and -negative bacteria can be induced by combining FCD treatment with irradiation by LED light in the visible range. Cell-based, electron microscopy and Tandem Mass Tag (TMT) proteomic experiments indicate that FCD administration in combination with LED exposure gives rise to local heating, ROS production, and membrane- and DNA-damage, suggesting multiple routes to FCD-mediated bacterial killing. Our data identify FCDs as materials that combine facile synthesis from low-cost precursors with labelling and light-dependent killing of clinically important bacterial species, and that thus warrant further exploration as the potential bases for novel theranostics.
Sex differences in concentrations of HMGB1 and numbers of pigmented monocytes in infants with malaria
Authors: Kanoi Bernard N. , Egwang Thomas G.
Published: March 2021

Females generally mount more robust innate and adaptive immune responses and demonstrate a higher rate of morbidity, and prevalence of autoimmune diseases by comparison with males. In malaria, females demonstrate higher concentrations of antibodies and rates of severe adverse events and mortality following natural infections and malaria vaccination. Although monocytes/macrophages play a crucial role in disease and protection in malaria, no studies have investigated sex differences in their functions in production of proinflammatory cytokines and chemokines in malaria-infected subjects. Here, we show significant sex differences in serum concentrations of HMGB1, a non-histone chromatin-associated protein, and numbers of pigmented monocytes, which are both markers of severe malaria, in infants <5 years old from a malaria endemic region in Northern Uganda. Female infants with clinical malaria had significantly higher HMGB1 concentrations than male infants, and female infants with asymptomatic malaria had significantly lower numbers of pigmented monocytes than male infants with asymptomatic malaria. There was (1) a significant correlation between HMGB1 concentrations and pigmented monocyte numbers in female but not male infants; and (2) a significant correlation between HMGB1 concentrations and parasite densities in female but not male infants. These findings suggest that female infants with clinical malaria might be at a greater risk of morbidity characterized by higher serum HMGB1 levels.
Higher phage virulence accelerates the evolution of host resistance
Authors: Wendling Carolin C. , Lange Janina , Liesegang Heiko , Sieber Michael , Pöhlein Anja , Bunk Boyke , Rajkov Jelena , Goehlich Henry , Roth Olivia , Brockhurst Michael A.
Published: March 2021

Parasites and pathogens vary strikingly in their virulence and the resulting selection they impose on their hosts. While the evolution of different virulence levels is well studied, the evolution of host resistance in response to different virulence levels is less understood and as of now mainly based on observations and theoretical predictions with few experimental tests. Increased virulence can increase selection for host resistance evolution if resistance costs are outweighed by the benefits of avoiding infection. To test this, we experimentally evolved the bacteriumVibrio alginolyticusin the presence of two variants of the filamentous phage, VALGΦ8, that differ in their virulence. The bacterial host exhibited two alternative defence strategies against future phage infection: (1) super infection exclusion (SIE) whereby phage-infected cells were immune to subsequent infection at a cost of reduced growth, and (2) surface receptor mutations (SRM) in genes encoding the MSHA type-IV pilus providing resistance to infection by preventing phage attachment. While SIE emerged rapidly against both phages, SRM evolved faster against the high virulence compared to the low virulence phage. Using a mathematical model of our system we show that increasing virulence strengthens selection for SRM due to the higher costs of infection suffered by SIE immune hosts. In both the experiments and the model, higher levels of SRM in the host population drove more rapid phage extinction. Thus, by accelerating the evolution of host resistance, more virulent phages caused shorter epidemics.
A Statistical Model for Describing and Simulating Microbial Community Profiles
Authors: Ma Siyuan , Ren Boyu , Mallick Himel , Moon Yo Sup , Schwager Emma , Maharjan Sagun , Tickle Timothy L. , Lu Yiren , Carmody Rachel N. , Franzosa Eric A. , Janson Lucas , Huttenhower Curtis
Published: March 2021

Many methods have been developed for statistical analysis of microbial community profiles, but due to the complex nature of typical microbiome measurements (e.g. sparsity, zero-inflation, nonindependence, and compositionality) and of the associated underlying biology, it is difficult to compare or evaluate such methods within a single systematic framework. To address this challenge, we developed SparseDOSSA (Sparse Data Observations for the Simulation of Synthetic Abundances): a statistical model of microbial ecological population structure, which can be used to parameterize real-world microbial community profiles and to simulate new, realistic profiles of known structure for methods evaluation. Specifically, SparseDOSSA’s model captures marginal microbial feature abundances as a zero-inflated log-normal distribution, with additional model components for absolute cell counts and the sequence read generation process, microbemicrobe, and microbe-environment interactions. Together, these allow fully known covariance structure between synthetic features (i.e. “taxa”) or between features and “phenotypes” to be simulated for method benchmarking. Here, we demonstrate SparseDOSSA’s performance for 1) accurately modeling human-associated microbial population profiles; 2) generating synthetic communities with controlled population and ecological structures; 3) spiking-in true positive synthetic associations to benchmark analysis methods; and 4) recapitulating an end-to-end mouse microbiome feeding experiment. Together, these represent the most common analysis types in assessment of real microbial community environmental and epidemiological statistics, thus demonstrating SparseDOSSA’s utility as a general-purpose aid for modeling communities and evaluating quantitative methods. An open-source implementation is available athttp://huttenhower.sph.harvard.edu/sparsedossa2.
Effect of aMonascussp. red yeast rice extract on germination of bacterial spores
Authors: Marketa Husakova , Michaela Plechata , Barbora Branska , Petra Patakova
Published: March 2021

The pink-red colour of traditional sausages (cured meat) is the result of nitrite addition and the formation of nitrosomyoglobin. However, the pleasant colour of processed meat products is a side effect of nitrite addition while the main anticipated goal is to suppress the germination of clostridial spores. The fungusMonascusis known as a producer of oligoketide pigments, which are used in Asian countries, especially in China, for colouring foods, including meat products. Although, different biological activities ofMonascuspigments have been tested and confirmed in many studies, their effect on germination of bacterial spores has never been investigated. This study is focused on testing the activity of red yeast rice (RYR) extract, containing monascin, rubropunctatin, rubropunctamine complexes and monascuspiloin as the main pigments, on germination ofClostridiumandBacillusspores. It was found that addition of nitrite alone, at the permitted concentration, had no effect on spore germination. However, the combined effects of nitrite with NaCl, tested after addition of pickling salt, was efficient in inhibiting the germination ofC. beijerinckiispores but had no effect onB. subtilisspores. In contrast, total suppression ofC. beijerinckiispore germination was reached after addition of RYR extract to the medium at a concentration of 2 % v/v. ForB. subtilis, total inhibition of spore germination was observed only after addition of 4 % v/v RYR extract to the medium containing 1.3% w/w NaCl.
Comparison of SARS-CoV-2 VOC 202012/01 (UK variant) and D614G variant transmission by different routes in Syrian hamsters
Authors: Mohandas Sreelekshmy , Yadav Pragya D , Nyayanit Dimpal , Shete-Aich Anita , Sarkale Prasad , Hundekar Supriya , Kumar Sanjay , Lole Kavita
Published: March 2021

Many SARS-CoV-2 variants of concern has been reported recently which were linked to increased transmission. In our earlier study on virus shedding using VOC 202012/01(UK variant) and D614G variant in hamster model, we observed significantly higher viral RNA shedding through nasal wash in case of UK variant. Hence, we compared the transmission of both the UK and D614G variant by various routes in Syrian hamsters to understand whether the high viral RNA shedding could enhance the transmission efficiency of the variant. The current study demonstrated comparable transmission efficiency of both UK and D614G variants of SARS-CoV-2 in Syrian hamsters.
In vivo photocontrol of microtubule dynamics and integrity, migration and mitosis, by the potent GFP-imaging-compatible photoswitchable reagents SBTubA4P and SBTub2M
Authors: Gao Li , Meiring Joyce C.M. , Varady Adam , Ruider Iris E. , Heise Constanze , Wranik Maximilian , Velasco Cecilia D. , Taylor Jennifer A. , Terni Beatrice , Standfuss Jörg , Cabernard Clemens C. , Llobet Artur , Steinmetz Michel O. , Bausch Andreas R. , Distel Martin , Thorn-Seshold Julia , Akhmanova Anna , Thorn-Seshold Oliver
Published: March 2021

Photoswitchable reagents to modulate microtubule stability and dynamics are an exciting tool approach towards micron- and millisecond-scale control over endogenous cytoskeleton-dependent processes. When these reagents are globally administered yet locally photoactivated in 2D cell culture, they can exert precise biological control that would have great potential forin vivotranslation across a variety of research fields and for all eukaryotes. However, photopharmacology’s reliance on the azobenzene photoswitch scaffold has been accompanied by a failure to translate this temporally- and cellularly-resolved control to 3D models or toin vivoapplications in multi-organ animals, which we attribute substantially to the metabolic liabilities of azobenzenes.

Here, we optimised the potency and solubility of metabolically stable, druglike colchicinoid microtubule inhibitors based instead on the styrylbenzothiazole (SBT) photoswitch scaffold, that are non-responsive to the major fluorescent protein imaging channels and so enable multiplexed imaging studies. We applied these reagents to 3D systems (organoids, tissue explants) and classic model organisms (zebrafish, clawed frog) with one- and two-protein imaging experiments. We successfully used systemic treatment plus spatiotemporally-localised illuminationsin vivoto photocontrol microtubule dynamics, network architecture, and microtubule-dependent processes in these systems with cellular precision and second-level resolution. These nanomolar,in vivo-capable photoswitchable reagents can prove a game-changer for high-precision cytoskeleton research in cargo transport, cell motility, cell division and development. More broadly, their straightforward design can also inspire the development of similarly capable optical reagents for a range of protein targets, so bringing generalin vivophotopharmacology one step closer to productive realisation.
Thriving of hyperthermophilic microbial communities from a deep-sea sulfidic hydrothermal chimney under electrolithoautotrophic conditions with nitrate as electron acceptor
Authors: Pillot G. , Davidson S. , Shintu L. , Tanet L. , Combet-Blanc Y. , Godfroy A. , Bonin P. , Liebgott P.-P.
Published: March 2021

Recent studies have shown the presence of an abiotic electrical current across the walls of deep-sea hydrothermal chimneys, allowing the growth of electroautotrophic microbial communities. To understand the role of the different phylogenetic groups and metabolisms involved, this study focused on an electrotrophic enrichment, with nitrate as electron acceptor. The biofilm density, the community composition, the organic products released, and the electrical consumption were monitored by FISH confocal microscopy, qPCR, Metabarcoding, MNR and potentiostat measurements. A statistic analysis by PCA showed the correlation between the different parameters in 3 distinct temporal phases. TheArchaeoglobaleshave been shown to play a key role in the development of the community, as first colonizers and producing pyruvate, therefor used as organic source for heterotrophs. SomeThermococcalesshowed the ability to perform electrofermentation of this pyruvate into acetate and H2. Finally, through subcultures of the community, we showed the development of a larger biodiversity over time. This observed phenomenon could explain the biodiversity development in hydrothermal context where energy sources are transient and unstable.
Unsaturated fatty acids augment protein transport via the SecA:SecYEG translocon
Authors: Kamel Michael , Löwe Maryna , Schott-Verdugo Stephan , Gohlke Holger , Kedrov Alexej
Published: March 2021

The translocon SecYEG forms the primary protein-conducting channel in the cytoplasmic membrane of bacteria, and the associated ATPase SecA provides the energy for the transport of secretory and cell envelope protein precursors. The translocation requires negative charge at the lipid membrane surface, but its dependence on the properties of the membrane hydrophobic core is not known. Here, we demonstrate that SecA:SecYEG-mediated protein transport is immensely stimulated by unsaturated fatty acids (UFAs). Furthermore, UFA-rich tetraoleoyl-cardiolipin, but not bis(palmitoyloleoyl)-cardiolipin, facilitate the translocation via the monomeric translocon. Biophysical analysis and molecular dynamics simulations show that UFAs determine the loosely packed membrane interface, where the N-terminal amphipathic helix of SecA docks. While UFAs do not affect the translocon folding, they promote SecA binding to the membrane, and the effect is enhanced manifold at elevated ionic strength. Tight SecA:lipid interactions convert into the augmented translocation. As bacterial cells actively change their membrane composition in response to their habitat, the modulation of SecA:SecYEG activity via the fatty acids may be crucial for protein secretion over a broad range of environmental conditions.
The RNA sensor MDA5 detects SARS-CoV-2 infection
Authors: Sampaio Natalia G. , Chauveau Lise , Hertzog Jonny , Bridgeman Anne , Fowler Gerissa , Moonen Jurgen P. , Dupont Maeva , Russell Rebecca A. , Noerenberg Marko , Rehwinkel Jan
Published: March 2021

Human cells respond to infection by SARS-CoV-2, the virus that causes COVID-19, by producing cytokines including type I and III interferons (IFNs) and proinflammatory factors such as IL6 and TNF. IFNs can limit SARS-CoV-2 replication but cytokine imbalance contributes to severe COVID-19. We studied how cells detect SARS-CoV-2 infection. We report that the cytosolic RNA sensor MDA5 was required for type I and III IFN induction in the lung cancer cell line Calu-3 upon SARS-CoV-2 infection. Type I and III IFN induction further required MAVS and IRF3. In contrast, induction of IL6 and TNF was independent of the MDA5-MAVS-IRF3 axis in this setting. We further found that SARS-CoV-2 infection inhibited the ability of cells to respond to IFNs. In sum, we identified MDA5 as a cellular sensor for SARS-CoV-2 infection that induced type I and III IFNs.
Genetic Variant in 3’ Untranslated Region of the MousePycardGene Regulates Inflammasome Activity
Authors: Ritchey Brian , Hai Qimin , Han Juying , Barnard John , Smith Jonathan D.
Published: March 2021

Quantitative trait locus mapping for interleukin-1β release after inflammasome priming and activation was performed on bone marrow-derived macrophages (BMDM) from an AKRxDBA/2 strain intercross. The strongest associated locus mapped very close to thePycardgene on chromosome 7, which codes for the inflammasome adaptor protein apoptosis-associated speck-like protein containing a CARD (ASC). The DBA/2 and AKRPycardgenes only differ at single nucleotide polymorphism (SNP) in their 3’ untranslated region (UTR). DBA/2 vs. AKR BMDM had increased levels ofPycardmRNA expression and ASC protein, and increased inflammasome speck formation, which was associated with increasedPycardmRNA stability without an increased transcription rate. CRIPSR/Cas9 gene editing was performed on DBA/2 embryonic stem cells to change thePycard3’UTR SNP from the DBA/2 to the AKR allele. This single base change significantly reducedPycardexpression and inflammasome activity after cells were differentiated into macrophages due to reducedPycardmRNA stability.
Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles
Authors: Sitarska Ewa , Almeida Silvia Dias , Beckwith Marianne Sandvold , Stopp Julian , Schwab Yannick , Sixt Michael , Kreshuk Anna , Erzberger Anna , Diz-Muñoz Alba
Published: March 2021

Cell migration is a hallmark out-of-equilibrium process in biology. In addition to persistent self-propelled motion, many cells display remarkable adaptive behaviors when they navigate complex environments within the body. Combining theory and experiments, we identify a curvature-sensing mechanism underlying obstacle avoidance in immune-like cells. The genetic perturbation of this machinery leads to a reduced capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. We propose that the active polymerization of the actin cytoskeleton at the advancing edge of migrating cells is locally inhibited by the curvature-sensitive BAR protein Snx33 in regions with inward plasma membrane curvature. This coupling between actin and membrane dynamics leads to a mechanochemical instability that generates complex protrusive patterns at the cellular front. Adaptive motility thus arises from two simultaneous curvature-dependent effects, i) the specific reduction of propulsion in regions where external objects deform the plasma membrane and ii) the intrinsic patterning capacity due to the membrane-actin coupling that promotes spontaneous changes in the cell’s protrusions. Our results show how cells utilize actin- and plasma membrane biophysics to sense their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment.
Structures ofBdellovibrio bacteriovorusphosphoglucose isomerase reveal novel rigidity in the active site of a selected subset of enzymes upon substrate binding
Authors: Meek R.W. , Cadby I.T. , Lovering A.L.
Published: March 2021

Glycolysis and gluconeogenesis are central pathways of metabolism across all domains of life. A prominent enzyme in these pathways is phosphoglucose isomerase (PGI) which mediates the interconversion of glucose-6-phosphate and fructose-6-phosphate (F6P). The predatory bacteriumBdellovibrio bacteriovorusleads a complex lifecycle, switching between intraperiplasmic replicative and extracellular “hunter” attack-phase stages. Passage through this complex lifecycle involves different metabolic states. Here we present the unliganded and substrate bound structures of theBdellovibrio bacteriovorusPGI, solved to 1.74Å and 1.67 Å, respectively. These structures reveal that an induced-fit conformational change within the active site is not a pre-requisite for the binding of substrates in some PGIs. Crucially, we suggest a phenylalanine residue, conserved across most PGI enzymes but substituted for a glycine inBdellovibrioand other select organisms, is central to the induced-fit mode of substrate recognition for PGIs. This enzyme also represents the smallest conventional PGI characterised to date and likely represents the minimal requirements for a functional PGI.
Development and Validation of Fluorescently Labeled, Functional Type I Collagen Molecules
Authors: Siadat Seyed Mohammad , Susilo Monica E. , Paten Jeffrey A. , Silverman Alexandra A. , DiMarzio Charles A. , Ruberti Jeffrey W.
Published: March 2021

While de novo collagen fibril formation is well-studied, there are few investigations into the growth and remodeling of extant fibrils, where molecular collagen incorporation into and erosion from the fibril surface must delicately balance during fibril growth and remodeling. Observing molecule/fibril interactions is difficult, requiring the tracking of molecular dynamics while, at the same time, minimizing the effect of the observation on fibril structure and assembly. To address the observation-interference problem, exogenous collagen molecules are tagged with small fluorophores and the fibrillogenesis kinetics of labeled collagen molecules as well as the structure and network morphology of assembled fibrils are quantified for the first time. While excessive labeling significantly disturbs fibrillogenesis kinetics and network morphology of assembled fibrils, adding less than ~1.2 labels preserves them. Applications of the functional, labeled collagen probe are demonstrated in both cellular and acellular systems. The functional, labelled collagen associates strongly with native fibrils and when added to an in vitro model of corneal stromal development, is endocytosed rapidly by cells and is translocated into synthesized matrix networks within 24 hours.