bluuebunny/crossref_metadata_2025 huggingface dataset:
Jiella sonneratiae sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia apetala
Authors: Chen Ming-Sheng , Yi Hai-Bo , Huang Zi-Hao , Yan Xiao-Rui , Chen Xiao-Hui , Ma Xiao , Zheng Zhou-Qing , Tuo Li
Published: March 2022

A new endophytic bacterium, designated strain MQZ13P-4T was isolated from Sonneratia apetala collected from Maowei sea Mangrove Nature Reserve in Guangxi Zhuang Autonomous Region, PR China. The 16S rRNA gene sequence similarity between strain MQZ13P-4T and its closest phylogenetic neighbour

Jiella endophytica

CBS5Q-3T was 97.9 %. Phylogenetic analyses using 16S rRNA gene sequences and whole-genome sequences showed that strain MQZ13P-4T formed a distinct lineage with

Jiella endophytica

CBS5Q-3T,

Jiella pacifica

40Bstr34T and

Jiella aquimaris

JCM 30119T. The draft genome of strain MQZ13P-4T was 5 153 243 bp in size and its DNA G+C content was 68.1 mol%. Comparative genome analysis revealed that the average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values among strain MQZ13P-4T and other related species were below the cut-off levels of 95, 70 and 95.5 %, respectively. The cell-wall peptidoglycan of strain MQZ13P-4T contained meso-diaminopimelic acid as the diagnostic diamino acid. The respiratory quinone was Q-10. The major cellular fatty acid was C18 : 1
 ω7c. The polar lipids comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. Strain MQZ13P-4T had a typical chemical compositions of fatty acids, lipids, quinones and diagnostic diamino acid for

Jiella

species, but could be distinguished from known species of the genus

Jiella

. Based on polyphasic evidence, strain MQZ13P-4T represents novel species of the genus

Jiella

, for which the name Jiella sonneratiae sp. nov. is proposed. The type strain is MQZ13P-4T (=CGMCC 1.18727T=JCM 34333T).
Mass Homicide by Firearm in Canada: Effects of Legislation
Authors: Langmann Caillin
Published: March 2022

Canada implemented a series of laws regulating firearms including background checks and licensing, references, psychological questionnaires, prohibition of paramilitary style rifles, and magazine capacity restrictions in order to decrease the incidences and deaths from mass shootings. The associated effects of these laws were examined over the years 1974 to 2020.

A model was constructed using difference-in-differences analysis of firearms and non-firearms mass homicide incidences and death rates. Mass homicides were defined as a homicide due to one event involving three or more deaths.

Incidence rates of mass homicide by firearm were found to be 0.11 (95%CI 0.08, 0.14) per million compared to a non-firearm mass homicide rate of 0.12 (95% CI 0.10, 0.15) per million. Mass homicide death rates by firearm were found to be 0.39 (95% CI 0.29, 0.49) per million compared to a non-firearm mass homicide rate of 0.47 (95% CI 0.34, 0.61) per million. Overall, there is a gradual declining trend in the incidence of mass homicide by firearm (IRR 0.97 (95% CI 0.96, 0.98)) and by non-firearm (IRR 0.97 (95% CI 0.97, 0.98)). The decline in mass homicide death rate by firearm and non-firearm is IRR 0.96 (95% CI 0.95, 0.97), and IRR 0.97 (95% CI 0.96, 0.98) respectively.

No associated decrease in mass homicide incidence rates or death rates with firearms legislation was found after the implementation of background checks and prohibition of full auto firearms in 1980, by the implementation of references and psychological questionnaires in 1994, by the restriction of magazine capacity in 1994, the prohibition of paramilitary rifles in 1994, or licensing in 2001.
Lagrangian Formalism in Biology: I. Standard Lagrangians and their Role in Population Dynamics
Authors: Pham D.T. , Musielak Z.E.
Published: March 2022

The Lagrangian formalism is developed for the population dynamics of interacting species that are described by several well-known models. The formalism is based on standard Lagrangians, which represent differences between the physical kinetic and potential energy-like terms. A method to derive these Lagrangians is presented and applied to selected theoretical models of the population dynamics. The role of the derived Lagrangians and the energy-like terms in the population dynamics is investigated and discussed. It is suggested that the obtained standard Lagrangians can be used to identify physical similarities between different population models.
Cell type profiling in salamanders identifies innovations in vertebrate forebrain evolution
Authors: Woych Jamie , Gurrola Alonso Ortega , Deryckere Astrid , Jaeger Eliza C. B. , Gumnit Elias , Merello Gianluca , Gu Jiacheng , Araus Alberto Joven , Leigh Nicholas D. , Yun Maximina , Simon András , Tosches Maria Antonietta
Published: March 2022

The evolution of advanced cognition in vertebrates is associated with two independent innovations in the forebrain: the six-layered neocortex in mammals and the dorsal ventricular ridge (DVR) in sauropsids (reptiles and birds). How these novelties arose in vertebrate ancestors remains unclear. To reconstruct forebrain evolution in tetrapods, we built a cell type atlas of the telencephalon of the salamander Pleurodeles waltl. Our molecular, developmental, and connectivity data indicate that parts of the sauropsid DVR trace back to tetrapod ancestors. In contrast, the salamander dorsal pallium is devoid of cellular and molecular characteristics of the mammalian neocortex, yet shares similarities with entorhinal cortex and subiculum. Our findings chart the series of innovations that resulted in the emergence of the sauropsid DVR, and the mammalian six-layered neocortex.
Digitizing the coral reef: machine learning of underwater spectral images enables dense taxonomic mapping of benthic habitats
Authors: Schürholz Daniel , Chennu Arjun
Published: March 2022

Coral reefs are the most biodiverse marine ecosystems, and host a wide range of taxonomic diversity in a complex spatial habitat structure. Existing coral reef survey methods struggle to accurately capture the taxonomic detail within the complex spatial structure of benthic communities.

We propose a workflow to leverage underwater hyperspectral transects and two machine learning algorithms to produce dense habitat maps of 1150 m2 of reefs across the Curaçao coastline. Our multi-method workflow labelled all 500+ million pixels with one of 43 classes at taxonomic family, genus or species level for corals, algae, sponges, or to substrate labels such as sediment, turf algae and cyanobacterial mats.

With low annotation effort (2% pixels) and no external data, our workflow enables accurate (Fbeta 87%) survey-scale mapping, with unprecedented thematic and spatial detail. Our assessments of the composition and configuration of the benthic communities of 23 transect showed high consistency.

Digitizing the reef habitat structure enables validation and novel analysis of pattern and scale in coral reef ecology. Our dense habitat maps reveal the inadequacies of point sampling methods to accurately describe reef benthic communities.
The Modular µSiM: a Mass Produced, Rapidly Assembled, and Reconfigurable Platform for the Study of Barrier Tissue ModelsIn Vitro
Authors: McCloskey Molly C. , Kasap Pelin , Ahmad S. Danial , Su Shiuan-Haur , Chen Kaihua , Mansouri Mehran , Ramesh Natalie , Nishihara Hideaki , Belyaev Yury , Abhyankar Vinay V. , Begolo Stefano , Singer Benjamin H. , Webb Kevin F. , Kurabayashi Katsuo , Flax Jonathan , Waugh Richard E. , Engelhardt Britta , McGrath James L.
Published: March 2022

Advancedin vitrotissue chip models can reduce and replace animal experimentation and may eventually support ‘on-chip’ clinical trials. To realize this potential, however, tissue chip platforms must be both mass-produced and reconfigurable to allow for customized design. To address these unmet needs, we introduce an extension of our µSiM (microdevice featuring asilicon-nitridemembrane) platform. ThemodularµSiM (m-µSiM) uses mass-produced components to enable rapid assembly and reconfiguration by laboratories without knowledge of microfabrication. We demonstrate the utility of the m-µSiM by establishing an hiPSC-derived blood-brain barrier (BBB) in bioengineering and non-engineering, brain barriers focused laboratories. We develop and validatein situand sampling-based assays of small molecule diffusion as a measure of barrier function. BBB properties show excellent interlaboratory agreement and match expectations from literature, validating the m-µSiM as a platform for barrier models and demonstrating successful dissemination of components and protocols. We then demonstrate the ability to quickly reconfigure the m-µSiM for co-culture and immune cell transmigration studies through addition of accessories and/or quick exchange of components. Because the development of modified components and accessories is easily achieved, custom designs of the m-µSiM should be accessible to any laboratory desiring a barrier-style tissue chip platform.
The Modular μSiM Reconfigured: Integration of Microfluidic Capabilities to Study in vitro Barrier Tissue Models under Flow
Authors: Mansouri Mehran , Ahmed Adeel , Ahmad S. Danial , McCloskey Molly C. , Joshi Indranil M. , Gaborski Thomas R. , Waugh Richard E. , McGrath James L. , Day Steven W. , Abhyankar Vinay V.
Published: March 2022

Microfluidic approaches to study tissue barriers have emerged to address the lack of fluid flow in conventional “open-well” Transwell™-like devices. However, microfluidic techniques have not achieved widespread usage in bioscience laboratories because they are not fully compatible with traditional, tried-and-true experimental protocols. To advance barrier tissue research, there is a need for a platform that combines the advantages of both conventional open-well and microfluidic systems. Here, we develop a plug-and-play flow module to add on-demand microfluidic capabilities to amodularmicrofluidic system featuring asiliconmembrane “m-μSiM” as an open-well device with live-cell imaging capabilities. The magnetic latching assembly of our design enables bi-directional reconfiguration between open-well and fluidic modes. This design feature allows users to conduct an experiment in an open-well format with established protocols and then add or remove microfluidic capabilities as desired. Our work also provides an experimentally-validated flow model to help select desired flow conditions based on the experimental needs. As a proof-of-concept, we demonstrate flow-induced alignment of endothelial cells and visualize different phases of neutrophil transmigration across an endothelial monolayer under flow. We anticipate that our reconfigurable design will be adopted by both engineering and bioscience laboratories due to the compatibility with standard open-well protocols and the simple flow addition capabilities.
Canonical Wnt Signaling and the Regulation of Divergent Mesenchymal Fgf8 expression in Axolotl Limb Development and Regeneration
Authors: Glotzer Giacomo L. , Tardivo Pietro , Tanaka Elly M.
Published: March 2022

The expression of Fibroblast growth factors (Fgf) ligands in a specialized epithelial compartment, the Apical Ectodermal Ridge (AER), is a conserved feature of limb development across vertebrate species. In vertebrates, Fgf 4, 8, 9, and 17 are all expressed in the AER. An exception to this paradigm is the salamander (axolotl) developing and regenerating limb, where key Fgf ligands are expressed in the mesenchyme. The mesenchymal expression of Amex.Fgf8 in axolotl has been suggested to be critical for regeneration. To date, there is little knowledge regarding what controls Amex.Fgf8 expression in the axolotl limb mesenchyme. A large body of mouse and chick studies have defined a set of transcription factors and canonical Wnt signaling as the main regulators of epidermal Fgf8 expression in these organisms. In this study, we address the hypothesis that alterations to one or more of these components during evolution has resulted in mesenchymal Amex.Fgf8 expression in the axolotl. To sensitively quantify gene expression with spatial precision, we combined optical clearing of whole-mount axolotl limb tissue with single molecule fluorescent in situ hybridization and a semi-automated quantification pipeline. Several candidate upstream components were found expressed in the axolotl ectoderm, indicating that they are not direct regulators of Amex.Fgf8 expression. We found that Amex.Wnt3a is expressed in axolotl limb epidermis, similarly to chicken and mouse. However, unlike in amniotes, Wnt target genes are activated preferentially in limb mesenchyme rather than in epidermis. Inhibition and activation of Wnt signaling results in downregulation and upregulation of mesenchymal Amex.Fgf8 expression respectively. These results implicate a shift in tissue responsiveness to canonical Wnt signaling from epidermis to mesenchyme as one step contributing to the unique mesenchymal Amex.Fgf8 expression seen in the axolotl.
On whole-genome demography of world’s ethnic groups and individual genomic identity
Authors: Kim Byung-Ju , Choi JaeJin , Kim Sung-Hou
Published: March 2022

All current categorizations of human population, such as ethnicity, ancestry and race, are based on various selections and combinations ofsubjectively-and/orqualitatively-defined characteristics, such as ancestral lineage/location, cultural/societal norm, language, skin color and other phenotypes and traits perceived by the members within or from outside of the categorized group. Yet, such categorization has been broadly used also in the fields of human genetics, health sciences and medical practices (e.g.,1,2,3), where the observed health characteristics are objectively and quantitatively definable, but the population categorization is not yet available. Here we show the feasibility of deriving a whole-genome-based categorization that is objectively definable and quantitatively measurable. We observe that: (a) the world’s ethnic populations form about 14 genomic groups (GGs); (b) each GG consists of multiple ethnic groups (EGs); and (c) at an individual level, approximately 99.8%, on average, of the whole genome contents are identical between anytwo individualsregardless of their GGs or EGs.
The pre-Bötzinger complex is necessary for the expression of post-inspiration
Authors: Dhingra Rishi R. , Furuya Werner I. , Dutschmann Mathias
Published: March 2022

The mammalian three-phase respiratory motor pattern of inspiration, post-inspiration and expiration is expressed in spinal and cranial motor nerve activities. This pattern is generated by a hierarchical brainstem-wide pre-motor network. However, the local rhythmogenic circuit of the pre-Bötzinger complex (pre-BötC) was established as the ‘noeud vitale’ necessary and sufficient to initiate inspiration. In present study, we tested the effect of unilateral and bilateral inactivation of the pre-BötC (microinjection of the GABAA receptor agonist isoguvacine 10 mM, 50 nl) on respiratory motor activities in an in situ perfused brainstem preparation of rat. As expected, bilateral inactivation of the pre-BötC triggered cessation of phrenic (PNA), hypoglossal (HNA) and vagal (VNA) nerve activities for 15-20 min. Partial recovery from bilateral isoguvacine injection was characterized by erratic activity in all recorded motor nerves reminiscent to patterns observed after disturbed excitatory-inhibitory balance within the local pre-BötC circuit. Surprisingly, ipsilateral isoguvacine injections into the pre-BötC triggered transient (6-8 min) cessation of inspiratory and post-inspiratory VNA (p<0.001) and suppressed inspiratory HNA by -70 ± 15% (p<0.01), while inspiratory PNA burst frequency increased by 46 ± 30% (p<0.01). Taken together, these observations confirm the role of the pre-BötC as the ‘noeud vitale’ of the mammalian respiratory network in situ and highlight a significant role for the pre-BötC in the expression of vagal post-inspiratory and inspiratory activity.
Comprehensive profiling of antibody responses to the human anellome using programmable phage display
Authors: Venkataraman Thiagarajan , Swaminathan Harish , Arze Cesar A. , Jacobo Sarah M. , Bhattacharyya Agamoni , David Tyler , Nawandar Dhananjay M. , Delagrave Simon , Mani Vinidhra , Yozwiak Nathan L. , Larman H. Benjamin
Published: March 2022

Viruses belonging to the diverse Anelloviridae family represent a major constituent of the commensal human virome. Aside from their widespread prevalence and persistence in humans and their absence of detectable pathologic associations, little is known about the immunobiology of the human anellome. In this study, we employed the Phage ImmunoPrecipitation Sequencing (PhlP-Seq) assay for comprehensive analyses of antibody binding to 56 amino acid long anellovirus peptides. We designed and constructed a large and diverse “AnelloScan” T7 phage library comprising more than 32,000 non-redundant peptides representing the ORF1, ORF2, ORF3 and TTV-derived apoptosis-inducing protein (TAIP) sequences of more than 800 human anelloviruses (spanning three genera). We used this library to profile the antibody reactivities of serum samples from 156 subjects. The vast majority of anellovirus peptides were not reactive in any of the subjects tested (n=~28,000; ~85% of the library). Antibody reactive peptides were largely restricted to the C-terminal region of the putative capsid protein, ORF1. To characterize antibody responses to newly acquired anellovirus infections, we screened a longitudinal cohort of matched blood-transfusion donors and recipients. Most transmitted anelloviruses did not elicit detectable antibody reactivity in the recipient (29 out of a total of 40 transmitted anelloviruses) and the remainder demonstrated delayed reactivity (~100-150 days after transfusion). This study represents the first large-scale epitope-level serological survey of the antibody response to the human anellome.

Graphical Abstract
Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing
Authors: Kaimal Jayasankar Mohanakrishnan , Tampere Marianna , Le Trang H. , Axelsson Ulrika , Xu Hao , Axelsson Hanna , Bäckström Anna , Marabita Francesco , Moussaud-Lamodière Elisabeth , Njenda Duncan , Sepulveda Carolina Oses , Oyuang Wei , Seashore-Ludlow Brinton , Vernersson Caroline , Mirazimi Ali , Lundberg Emma , Östling Päivi , Stadler Charlotte
Published: March 2022

The COVID-19 pandemic has resulted in millions of deaths and affected socioeconomic structure worldwide and the search for new antivirals and treatments are still ongoing. In the search for new drug target and to increase our understanding of the disease, we used large scale immunofluorescence to explore the host cell response to SARS-CoV-2 infection. Among the 602 host proteins studied in this host response screen, changes in abundance and subcellular localization were observed for 97 proteins, with 45 proteins showing increased abundance and 10 reduced abundances. 20 proteins displayed changed localization upon infection and an additional 22 proteins displayed altered abundance and localization, together contributing to diverse reshuffling of the host cell protein landscape. We then selected existing and approved small-molecule drugs (n =123) against our identified host response proteins and identified 3 compounds - elesclomol, crizotinib and rimcazole, that significantly reduced antiviral activity. Our study introduces a novel, targeted and systematic approach based on host protein profiling, to identify new targets for drug repurposing. The dataset of ∼75,000 immunofluorescence images from this study are published as a resource available for further studies.
Transcriptional dynamics of colorectal cancer risk associated variation at 11q23.1 are correlated with tuft cell abundance and marker expression in silico
Authors: Harris Bradley T. , Rajasekaran Vidya , Blackmur James P. , O’Callaghan Alan , Donnelly Kevin , Timofeeva Maria , Vaughan-Shaw Peter G. , Din Farhat V. N. , Dunlop Malcolm G. , Farrington Susan M.
Published: March 2022

Colorectal cancer (CRC) is characterised by heritable risk that is not well understood. Heritable, genetic variation at 11q23.1 is associated with increased colorectal cancer (CRC) risk, demonstrating eQTL effects on 3 cis- and 23 trans-eQTL targets. We sought to determine the relationship between 11q23.1 cis- and trans-eQTL target expression and test for potential cell-specificity. scRNAseq from 32,361 healthy colonic epithelial cells was aggregated and subject to weighted gene co-expression network analysis (WGCNA). One module (blue) included 19 trans-eQTL targets and was correlated with C11orf53 expression only. Following unsupervised clustering of single cells, the expression of 19 trans-eQTL targets was greatest and most variable in cluster number 11, which transcriptionally resembled tuft cells. 14 trans-eQTL targets were found to demarcate this cluster, 11 of which were corroborated in a second dataset. Intra-cluster WGCNA and module preservation analysis then identified twelve 11q23.1 trans-eQTL targets to comprise a network that was specific to cluster 11. Finally, linear modelling and differential abundance testing showed 11q23.1 trans-eQTL target expression was predictive of cluster 11 abundance. Our findings suggest 11q23.1 trans-eQTL targets comprise a C11orf53-related network that is likely tuft cell-specific and reduced expression of these genes correlates with reduced tuft cell abundance in silico.
Large scale in vivo acquisition, segmentation, and 3D reconstruction of cortical vasculature using open-source functional ultrasound imaging platform
Authors: Strumane Anoek , Lambert Théo , Aelterman Jan , Babin Danilo , Philips Wilfried , Montaldo Gabriel , Brunner Clément , Urban Alan
Published: March 2022

The brain is composed of a dense and ramified vascular network comprising various sizes of arteries, veins, and capillaries. One way to assess the risk of cerebrovascular pathologies is to use computational models to predict the physiological effects of a reduction of blood supply and correlate these responses with observations of brain damage. Therefore, it is crucial to establish a detailed 3D organization of the brain vasculature, which could be used to develop more accurate in silico models. For this purpose, we have adapted our open-access functional ultrasound imaging platform previously designed for recording brain-wide activity that is now capable of fast and reproducible acquisition, segmentation, and reconstruction of the cortical vasculature. For the first time, it allows us to digitize the cortical vasculature in awake rodents with a ∼100 µm3 spatial resolution. Contrary to most available strategies, our approach can be performed in vivo within minutes. Moreover, it is easy to implement since it neither requires exogenous contrast agents nor long post-processing time. Hence, we performed a cortex-wide reconstruction of the vasculature and its quantitative analysis, including i) classification of descending arteries versus ascending veins in more than 1500 vessels/animal, ii) quick estimation of their length. Importantly, we confirmed the relevance of our approach in a model of cortical stroke, which enables quick visualization of the ischemic lesion. This development contributes to extending the capabilities of ultrasound neuroimaging to understand better cerebrovascular pathologies such as stroke, vascular cognitive impairment, and brain tumors and is highly scalable for the clinic.
Development of a new 3D tracking system for multiple marmosets under free-moving conditions
Authors: Yurimoto Terumi , Kumita Wakako , Sato Kenya , Kikuchi Rika , Shibuki Yusuke , Hashimoto Rino , Kamioka Michiko , Hayasegawa Yumi , Yamazaki Eiko , Kurotaki Yoko , Goda Norio , Kitakami Junichi , Fujita Tatsuya , Inoue Takashi , Sasaki Erika
Published: March 2022

Assessment of social interactions and behavioral changes in nonhuman primates is useful for understanding brain function changes during life events and pathogenesis of neurological diseases. The common marmoset (Callithrix jacchus), that lives in a nuclear family like humans, is a useful model, but long-term automated behavioral observation of multiple animals has not been achieved. Here, we developed aFullMonitoring andAnimal Identification (FulMAI) system for long-term detection of three-dimensional (3D) trajectories of each individual in multiple marmosets under free-moving conditions by combining video tracking, Light Detection And Ranging, and deep learning. Using this system, identification of each animal was more than 97% accurate. Location preferences and inter-individual distance could be calculated, and deep learning could detect grooming behavior. The FulMAI system allows us to analyze the natural behavior of individuals in a family over their lifetime and understand how behavior changes due to life events together with other data.
Validation of DeepLabCut as a tool for markerless 3D pose estimation
Authors: Kosourikhina Veronika , Kavanagh Diarmuid , Richardson Michael J. , Kaplan David M.
Published: March 2022

Deep learning-based approaches to markerless 3D pose estimation have taken neuroscience by storm. Yet many of these tools remain unvalidated. Here, we report on the validation of one increasingly popular tool (DeepLabCut) against simultaneous measurements obtained from a reference measurement system (Fastrak) with well-known performance characteristics. Our results confirm close (mm range) agreement between the two, indicating that deep learning-based approaches can be used by the research community with confidence.
A mosaic-type trimeric RBD-based COVID-19 vaccine candidate induces potent neutralization against Omicron and other SARS-CoV-2 variants
Authors: Zhang Jing , Han Zi Bo , Liang Yu , Zhang Xue Feng , Jin Yu Qin , Du Li Fang , Shao Shuai , Wang Hui , Hou Jun Wei , Xu Ke , Lei Ze Hua , Liu Zhao Ming , Zhang Jin , Hou Ya Nan , Liu Ning , Shen Fu Jie , Wu Jin Juan , Zheng Xiang , Li Xin Yu , Li Xin , Huang Wei Jin , Wu Gui Zhen , Su Ji Guo , Li Qi Ming
Published: March 2022

Large-scale populations in the world have been vaccinated with COVID-19 vaccines, however, breakthrough infections of SARS-CoV-2 are still growing rapidly due to the emergence of immune-evasive variants, especially Omicron. It is urgent to develop effective broad-spectrum vaccines to better control the pandemic of these variants. Here, we present a mosaic-type trimeric form of spike receptor-binding domain (mos-tri-RBD) as a broad-spectrum vaccine candidate, which carries the key mutations from Omicron and other circulating variants. Tests in rats showed that the designed mos-tri-RBD, whether used alone or as a booster shot, elicited potent cross-neutralizing antibodies against not only Omicron but also other immune-evasive variants. Neutralizing antibody titers induced by mos-tri-RBD were substantially higher than those elicited by homo-tri-RBD (containing homologous RBDs from prototype strain) or the inactivated vaccine BBIBP-CorV. Our study indicates that mos-tri-RBD is highly immunogenic, which may serve as a broad-spectrum vaccine candidate in combating SARS-CoV-2 variants including Omicron.
CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses
Authors: Jalloh Sallieu , Olejnik Judith , Berrigan Jacob , Nisa Annuurun , Suder Ellen L , Akiyama Hisashi , Lei Maohua , Tyagi Sanjay , Bushkin Yuri , Mühlberger Elke , Gummuluru Suryaram
Published: March 2022

Exacerbated and persistent innate immune response marked by pro-inflammatory cytokine expression is thought to be a major driver of chronic COVID-19 pathology. Although macrophages are not the primary target cells of SARS-CoV-2 infection in humans, viral RNA and antigens in activated monocytes and macrophages have been detected in post-mortem samples, and dysfunctional monocytes and macrophages have been hypothesized to contribute to a protracted hyper-inflammatory state in COVID-19 patients. In this study, we demonstrate that CD169, a myeloid cell specific I-type lectin, facilitated ACE2-independent SARS-CoV-2 fusion and entry in macrophages. CD169- mediated SARS-CoV-2 entry in macrophages resulted in expression of viral genomic and sub-genomic (sg) RNAs with minimal viral protein expression and no infectious viral particle release, suggesting a post-entry restriction of the SARS-CoV-2 replication cycle. Intriguingly this post-entry replication block was alleviated by exogenous ACE2 expression in macrophages. Restricted expression of viral gRNA and sgRNA in CD169+macrophages elicited a pro-inflammatory cytokine expression (TNFα, IL-6 and IL-1β) in a RIG-I, MDA-5 and MAVS-dependent manner, which was suppressed by remdesivir pre- treatment. These findings suggest thatde novoexpression of SARS-CoV-2 RNA in macrophages contributes to the pro-inflammatory cytokine signature and that blocking CD169-mediated ACE2 independent infection and subsequent activation of macrophages by viral RNA might alleviate COVID-19-associated hyperinflammatory response.

Author Summary

Over-exuberant production of pro-inflammatory cytokine expression by macrophages has been hypothesized to contribute to severity of COVID-19 disease. Molecular mechanisms that contribute to macrophage-intrinsic immune activation during SARS- CoV-2 infection are not fully understood. Here we show that CD169, a macrophage- specific sialic-acid binding lectin, facilitates abortive SARS-CoV-2 infection of macrophages that results in innate immune sensing of viral replication intermediates and production of proinflammatory responses. We identify an ACE2-independent, CD169- mediated endosomal viral entry mechanism that results in cytoplasmic delivery of viral capsids and initiation of virus replication, but absence of infectious viral production. Restricted viral replication in CD169+macrophages and detection of viral genomic and sub-genomic RNAs by cytoplasmic RIG-I-like receptor family members, RIG-I and MDA5, and initiation of downstream signaling via the adaptor protein MAVS, was required for innate immune activation. These studies uncover mechanisms important for initiation of innate immune sensing of SARS-CoV-2 infection in macrophages, persistent activation of which might contribute to severe COVID-19 pathophysiology.
Sex differences in allometry for mouse phenotypic traits indicate that females are not scaled males
Authors: Wilson Laura A. B. , Zajitschek Susanne R. K. , Lagisz Malgorzata , Mason Jeremy , Haselimashhadi Hamed , Nakagawa Shinichi
Published: March 2022

Sex differences in the lifetime risk and expression of disease are well-known. Preclinical research targeted at improving treatment, increasing health span, and reducing the financial burden of health care, has mostly been conducted on male animals and cells. The extent to which sex differences in phenotypic traits are explained by sex differences in body weight remains unclear. We quantify sex differences in the allometric relationship between trait value and body weight for 375 phenotypic traits in male and female mice, recorded in >2.1 million measurements from the International Mouse Phenotyping Consortium. We find sex differences in allometric parameters (slope, intercept, residual SD) are common (76% traits). Body weight differences do not explain all sex differences in trait values but scaling by weight may be useful for some traits. Our results support a trait-specific patterning of sex differences in phenotypic traits, promoting case-specific approaches to drug dosage scaled by body weight.
DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations
Authors: Hu Jing , Gao Jie , Fang Xiaomin , Liu Zijing , Wang Fan , Huang Weili , wu Hua , Zhao Guodong
Published: March 2022

Drug combination therapies are superior to monotherapy for cancer treatment in many ways when addressing tumor heterogeneity issue. For wet-lab experiment, screening out novel synergistic drug pairs is challenging due to the enormous searching space of possible drug pairs. Thus, computational methods have been developed to predict drug pairs with potential synergistic function. Notwithstanding the success of current models, the power of generalization to other datasets as wells as understanding of mechanism for chemical-chemical interaction or chemical-sample interaction are lack of study, hindering current algorithms from real application. In this paper, we proposed a deep neural model termed DTSyn (Dual Transformer model for drug pair Synergy prediction) based on multi-head attention mechanism to identify novel drug combinations. We designed a fine-granularity transformer for capturing chemical substructure-gene and gene-gene associations and a coarse-granularity transformer for extracting chemical-chemical and chemical-cell line interactions. DTSyn achieves highest Receiver operating characteristic area under curve (ROC AUC) of 0.73, 0.78. 0.82 and 0.81 on four different cross validation tasks, outperforming all competing methods. Further, DTSyn achieved best True Positive Rate (TPR) over five independent datasets. The ablation study showed that both transformer blocks contributed to the performance of DTSyn. In addition, DTSyn can extract interactions among chemicals and cell lines, which may represent the mechanisms of drug action. Thus, we envision our model a valuable tool to prioritize synergistic drug pairs by utilizing chemicals and transcriptome data.
Membrane compartmentalization of Ect2/Cyk4/Mklp1 and NuMA/dynein/dynactin is essential for cleavage furrow formation during anaphase
Authors: Sana Shrividya , Rajeevan Ashwathi , Kotak Sachin
Published: March 2022

In animal cells, spindle elongation during anaphase is temporally coupled with cleavage furrow formation. Spindle elongation during anaphase is regulated by NuMA/dynein/dynactin complexes that occupy the polar region of the cell membrane and are excluded from the equatorial membrane. How NuMA/dynein/dynactin are excluded from the equatorial membrane and the biological significance of this exclusion remains unknown. Here, we show that the centralspindlin (Cyk4/Mklp1) and its interacting partner RhoGEF Ect2 are required for NuMA/dynein/dynactin exclusion from the equatorial cell membrane. The Ect2-based (Ect2/Cyk4/Mklp1) and NuMA-based (NuMA/dynein/dynactin) complexes occupy mutually exclusive membrane surfaces during anaphase. The equatorial membrane enrichment of Ect2-based complexes is essential for NuMA/dynein/dynactin exclusion and proper spindle elongation. Conversely, NuMA-based complexes at the polar region of the cell membrane ensure spatially confined localization of Ect2-based complexes and thus RhoA. Overall, our work establishes that membrane compartmentalization of NuMA-based and Ect2-based complexes at the two distinct cell surfaces restricts dynein/dynactin and RhoA for coordinating spindle elongation with cleavage furrow formation.
Structural basis of actin filament assembly and aging
Authors: Oosterheert Wout , Klink Björn U , Belyy Alexander , Pospich Sabrina , Raunser Stefan
Published: March 2022

The dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state. It remains unclear how F-actin hydrolyzes ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here, we present cryo-EM structures of F-actin in all nucleotide states, polymerized in the presence of Mg2+ or Ca2+, at resolutions (∼2.2 Å) that allow for the visualization of hundreds of water molecules. The structures reveal that the G- to F-actin transition induces the relocation of water molecules in the nucleotide binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (Pi) is closed in all structures, indicating that the F-actin conformation that allows for Pi release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and Pi release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of waters in the nucleotide binding pocket explain why Ca2+-actin exhibits slower polymerization rates than Mg2+-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications.
Mechano-redox control of Mac-1 de-adhesion from ICAM-1 by protein disulfide isomerase promotes directional movement of neutrophils under flow
Authors: Dupuy Alexander , Santamaría Camilo Aponte , Yeheskel Adva , Gräter Frauke , Hogg Philip J. , Passam Freda H. , Chiu Joyce
Published: March 2022

Macrophage-1 antigen or Mac-1 (CD11b/CD18, αMβ2) is a leukocyte integrin essential for firm adhesion of neutrophils, lymphocytes and monocytes against flow when recruited to the endothelium. To migrate to the site of inflammation, leukocytes require coordinated adhesion and de-adhesion for directional movement. The vascular thiol isomerase, protein disulfide isomerase (PDI), was found by fluorescence microscopy to colocalize with high affinity Mac-1 at the trailing edge of stimulated neutrophils when adhered to ICAM-1 under fluid shear. From differential cysteine alkylation and mass spectrometry studies, PDI cleaves two allosteric disulfide bonds, C169-C176 and C224-C264, in the βI domain of the β2 subunit, and in mutagenesis and cell transfection studies, cleavage of the C224-C264 disulfide bond was shown to selectively control Mac-1 dis-engagement from ICAM-1 under fluid shear. Molecular dynamics simulations and binding of conformation-specific antibodies reveal that cleavage of the C224-C264 bond induces conformational change and mechanical stress in the βI domain that allosterically alters exposure of an αI domain epitope and shifts Mac-1 to a lower affinity state. From studies of neutrophil adherence to ICAM-1 under fluid shear, these molecular events promote neutrophil motility in the direction of flow at high shear stress. In summary, shear-dependent PDI cleavage of neutrophil Mac-1 C224-C264 disulfide bond triggers Mac-1 de-adherence from ICAM-1 at the trailing edge of the cell and enables directional movement of neutrophils during inflammation.
Phylogenomics Illuminates the Evolutionary History of Wild Silkmoths in Space and Time (Lepidoptera: Saturniidae)
Authors: Rougerie Rodolphe , Cruaud Astrid , Arnal Pierre , Ballesteros-Mejia Liliana , Condamine Fabien L. , Decaëns Thibaud , Elias Marianne , Gey Delphine , Hebert Paul D. N. , Kitching Ian J. , Lavergne Sébastien , Lopez-Vaamonde Carlos , Murienne Jérôme , Cuenot Yves , Nidelet Sabine , Rasplus Jean-Yves
Published: March 2022

Abstract

Wild silkmoths (Saturniidae) are one of the most emblematic and most studied families of moths. Yet, the absence of a robust phylogenetic framework based on a comprehensive taxonomic sampling impedes our understanding of their evolutionary history. We analyzed 1,024 ultraconserved elements (UCEs) and their flanking regions to infer the relationships among 338 species of Saturniidae representing all described subfamilies, tribes, and genera. We investigated systematic biases in genomic data and performed dating and historical biogeographic analyses to reconstruct the evolutionary history of wild silkmoths in space and time. Using Gene Genealogy Interrogation, we showed that saturation of nucleotide sequence data blurred our understanding of early divergences and first biogeographic events. Our analyses support a Neotropical origin of saturniids, shortly after the Cretaceous-Paleogene extinction event (ca64.0 [stem] - 52.0 [crown] Ma), and two independent colonization events of the Old World during the Eocene, presumably through the Bering Land Bridge. Early divergences strongly shaped the distribution of extant subfamilies as they showed very limited mobility across biogeographical regions, except for Saturniinae, a subfamily now present on all continents but Antarctica. Overall, our results provide a framework for in-depth investigations into the spatial and temporal dynamics of all saturniid lineages and for the integration of their evolutionary history into further global studies of biodiversity and conservation. Rather unexpectedly for a taxonomically well-known family such as Saturniidae, the proper alignment of taxonomic divisions and ranks with our phylogenetic results leads us to propose substantial rearrangements of the family classification, including the description of one new subfamily and two new tribes.
Reanalysis of double EphA3 knockin maps in mouse suggests that stochasticity in topographic map formation acts within the retinal cell population rather than between competing mechanisms at the colliculus
Authors: Willshaw David J , Gale Nicholas M
Published: March 2022

It has been suggested that stochasticity can act in the formation of topographically ordered maps in the visual system through the opposing chemoaffinity and neural activity forces acting on the innervating nerve fibres being held in an unstable equilibrium. Evidence comes from the Islet2-EphA3 knockin mouse, in which approximately 50% of the retinal ganglion cells, distributed across the retina, acquire the EphA3 receptor, thus having an enhanced density of EphA which specifies retinotopic order along one axis of the retinocollicular map. Sampling EphA3 knockin maps in heterozygotes at different positions along the mediolateral extent of the colliculus had found single 1D maps (as in wild-types), double maps (as in homozygous knockins) or both single and double maps. We constructed full 2D maps from the same dataset. We found either single maps or maps where the visual field projects rostrally, with a part-projection more caudally to form a double map, the extent and location of this duplication varying considerably. Contrary to previous analyses, there was no strict demarcation between heterozygous and homozygous maps. These maps were replicated in a computational model where, as the level of EphA3 was increased, there was a smooth transition from single to double maps. Our results suggest that the diversity in these retinotopic maps has its origin in a variability over the retina in the effective amount of EphA3, such as through variability in gene expression or the proportion of EphA3+ retinal ganglion cells, rather than the result of competing mechanisms acting at the colliculus.

Significance statement

Analysis by others of visuocollicular maps in EphA3 knockin mice indicated stochasticity in the development of nerve connections. Here a proportion of the retinal ganglion cells have the chemoaffinity ligand EphA3. Sampling the heterozygous map revealed either a single map (as in wildtypes), a double map (as in homozygotes) or a mixture, suggesting an unstable balance between competing chemoaffinity and neural activity forces. We constructed full 2D maps from the same dataset. We found a diversity of double maps in both genotypes, with no demarcation between heterozygote and homozygote, replicated in a computational model where the level of EphA3 varies between animals. We suggest that any stochasticity acts at the level of the retina rather than downstream at the colliculus.
Lack of universal mutational biases in a fungal phylum
Authors: Zheng Qianhui , Steenwyk Jacob L. , Rokas Antonis
Published: March 2022

Mutations fuel the diversity of life forms on earth through changes of nucleotides in DNA sequence. Patterns of mutations are biased; for example, mutational biases toward adenine and thymine have been previously noted in bacteria and biases for transitions over transversions are observed in diverse groups of organisms. However, the mutational biases in fungi, whose genomes vary widely in their GC content, remain poorly understood. Here, we characterized patterns of single nucleotide polymorphisms among 537 strains from 30 species and four classes from Ascomycota, the most species-rich fungal phylum. We found that mutational biases vary across Ascomycota; for example, some species in the class Saccharomycetes, in particular the bipolar budding yeast Hanseniaspora uvarum and the emerging pathogen Candida auris, show strong mutational bias toward A|T substitutions whereas the black mold Stachybotrys chartarum in the class Sordariomycetes shows substantial mutational bias toward G|C substitutions. Examination of GC content and GC equilibrium content, a measure that represents the GC content under selective neutrality and accounts for rates of G|C > A|T and A|T > G|C substitutions, revealed that fungal species vary in how their genome nucleotide composition is affected by neutral processes, mutational biases, and external evolutionary forces, such as selection. Whereas genome nucleotide composition is consistent with neutral expectations and is mainly driven by mutational bias in some species (e.g., Zymoseptoria tritici), the composition of others is influenced by both mutational bias and selection (e.g., H. uvarum and S. chartarum). These results highlight the variation of patterns of mutations across a fungal phylum and suggest that both neutral and selective processes shape the nucleotide composition of fungal genomes.
Effects of low intensity pulsed ultrasound stimulation on metabolic lipolysis of adipocytes
Authors: Kim Sangnam , Yoon Sangpil
Published: March 2022

Obesity is closely related to several metabolic diseases along with abnormal increase in fat cells. Reducing size and number of fat cells, a procedure known as lipolysis, may be used to prevent obesity as a potential therapy, which also requires fundamental understanding of the mechanisms of lipolysis at molecular level upon different types of stimulations. Here, we used low intensity pulsed ultrasound (LIPUS) stimulation to investigate underlying mechanisms of the activation of lipolysis and autophagy related genes and signaling pathways of adipocytes differentiated from 3T3-L1 cells. LIPUS with the center frequency of 2 MHz was applied for 10 minutes per day for three days. After LIPUS stimulation, quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blot were used to determine the regulation of lipolytic factors such as adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), and monoacylglycerol lipase (MGL). At RNA level, all three factors were upregulated while only MGL was upregulated at protein level, which presents slightly different activation pattern of lipolysis compared to widely used chemical stimulation. These results demonstrate that LIPUS stimulation can promote the lipolytic capacity of adipocytes in the differentiated state. The differences between transcriptional genes and metabolites were analyzed by transcript analysis and metabolomic profiling experiments. Cellular RNA-sequencing (RNA-Seq) showed an increase in lipolysis and immune-related genes and autophagy related genes after LIPUS stimulation. This study may provide an important experimental basis for the clinical applications and a fundamental understanding of the mechanisms of lipolysis using LIPUS stimulation.
Boquila: NGS read simulator to eliminate read nucleotide bias in sequence analysis
Authors: Akkose Umit , Adebali Ogun
Published: March 2022

Sequence content is heterogeneous throughout genomes. Therefore, Genome-wide NGS reads biased towards specific nucleotide profiles are affected by the genome-wide heterogeneous nucleotide distribution. Boquila generates sequences that mimic the nucleotide profile of true reads, which can be used to correct the nucleotide-based bias of genome-wide distribution of NGS reads. Boquila can be configured to generate reads from only specified regions of the reference genome. It also allows the use of input DNA sequencing to correct the bias due to the copy number variations in the genome. Boquila uses standard file formats for input and output data, and it can be easily integrated into any workflow for high-throughput sequencing applications.