bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue
Authors: Mubemba Benjamin , Gogarten Jan F. , Schuenemann Verena J. , Düx Ariane , Lang Alexander , Nowak Kathrin , Pléh Kamilla , Reiter Ella , Ulrich Markus , Agbor Anthony , Brazzola Gregory , Deschner Tobias , Dieguez Paula , Granjon Anne-Céline , Jones Sorrel , Junker Jessica , Wessling Erin , Arandjelovic Mimi , Kuehl Hjalmar , Wittig Roman M. , Leendertz Fabian H. , Calvignac-Spencer Sébastien
Published: October 2020

Many non-human primate species in sub-Saharan Africa are infected with

Treponema pallidum

subsp.

pertenue

, the bacterium causing yaws in humans. In humans, yaws is often characterized by lesions of the extremities and face, while

T. pallidum

subsp.

pallidum

causes venereal syphilis and is typically characterized by primary lesions on the genital, anal or oral mucosae. It remains unclear whether other

T. pallidum

subspecies found in humans also occur in non-human primates and how the genomic diversity of non-human primate

T. pallidum

subsp.

pertenue

lineages is distributed across hosts and space. We observed orofacial and genital lesions in sooty mangabeys (Cercocebus atys) in Taï National Park, Côte d’Ivoire and collected swabs and biopsies from symptomatic animals. We also collected non-human primate bones from 8 species in Taï National Park and 16 species from 11 other sites across sub-Saharan Africa. Samples were screened for

T. pallidum

DNA using polymerase chain reactions (PCRs) and we used in-solution hybridization capture to sequence

T. pallidum

genomes. We generated three nearly complete

T. pallidum

genomes from biopsies and swabs and detected treponemal DNA in bones of six non-human primate species in five countries, allowing us to reconstruct three partial genomes. Phylogenomic analyses revealed that both orofacial and genital lesions in sooty mangabeys from Taï National Park were caused by

T. pallidum

subsp.

pertenue

. We showed that

T. pallidum

subsp.

pertenue

has infected non-human primates in Taï National Park for at least 28 years and has been present in two non-human primate species that had not been described as

T. pallidum

subsp.

pertenue

hosts in this ecosystem, western chimpanzees (Pan troglodytes verus) and western red colobus (Piliocolobus badius), complementing clinical evidence that started accumulating in Taï National Park in 2014. More broadly, simian

T. pallidum

subsp.

pertenue

strains did not form monophyletic clades based on host species or the symptoms caused, but rather clustered based on geography. Geographical clustering of

T. pallidum

subsp.

pertenue

genomes might be compatible with cross-species transmission of

T. pallidum

subsp.

pertenue

within ecosystems or environmental exposure, leading to the acquisition of closely related strains. Finally, we found no evidence for mutations that confer antimicrobial resistance.
Protective Effects of STI-2020 Antibody Delivered Post-Infection by the Intranasal or Intravenous Route in a Syrian Golden Hamster COVID-19 Model
Authors: Fu Yanwen , Maruyama Junki , Singh Alok , Lim Reyna , Ledesma Arthur , Lee Daniel , Rivero-Nava Laura , Ko Jamie , Rivera Ianne , Sattler Rachel A. , Manning John T. , Kerwin Lisa , Zhou Heyue , Brunswick Mark , Bresson Damien , Ji Henry , Paessler Slobodan , Allen Robert D.
Published: October 2020

We have previously reported that the SARS-CoV-2 neutralizing antibody, STI-2020, potently inhibits cytopathic effects of infection by genetically diverse clinical SARS-CoV-2 pandemic isolates in vitro, and has demonstrated efficacy in a hamster model of COVID-19 when administered by the intravenous route immediately following infection. We now have extended our in vivo studies of STI-2020 to include disease treatment efficacy, profiling of biodistribution of STI-2020 in mice when antibody is delivered intranasally (IN) or intravenously (IV), as well as pharmacokinetics in mice following IN antibody administration. Importantly, SARS-CoV-2-infected hamsters were treated with STI-2020 using these routes, and treatment effects on severity and duration of COVID-19-like disease in this model were evaluated. In SARS-CoV-2 infected hamsters, treatment with STI-2020 12 hours post-infection using the IN route led to a decrease in severity of clinical disease signs and a more robust recovery during 9 days of infection as compared to animals treated with an isotype control antibody. Treatment via the IV route using the same dose and timing regimen resulted in a decrease in the average number of consecutive days that infected animals experienced weight loss, shortening the duration of disease and allowing recovery to begin more rapidly in STI-2020 treated animals. Following IN administration in mice, STI-2020 was detected within 10 minutes in both lung tissue and lung lavage. The half-life of STI-2020 in lung tissue is approximately 25 hours. We are currently investigating the minimum effective dose of IN-delivered STI-2020 in the hamster model as well as establishing the relative benefit of delivering neutralizing antibodies by both IV and IN routes.
GDV1 C-terminal truncation of 39 amino acids disrupts sexual commitment inPlasmodium falciparum
Authors: Tibúrcio Marta , Hitz Eva , Niederwieser Igor , Kelly Gavin , Davies Heledd , Doerig Christian , Billker Oliver , Voss Till S. , Treeck Moritz
Published: October 2020

Malaria is a mosquito-borne disease caused by apicomplexan parasites of the genusPlasmodium.Completion of the parasite’s life cycle depends on the transmission of sexual stages, the gametocytes, from an infected human host to the mosquito vector. Sexual commitment occurs in only a small fraction of asexual blood stage parasites and is initiated by external cues. The gametocyte development protein 1 (GDV1) has been described as a key facilitator to trigger sexual commitment. GDV1 interacts with the silencing factor heterochromatin protein 1 (HP1), leading to its dissociation from heterochromatic DNA at the genomic locus encoding AP2-G, the master transcription factor of gametocytogenesis. How this process is regulated is not known. In this study we have addressed the role of protein kinases implicated in gametocyte development. From a pool of available protein kinase KO lines, we identified two kinase knockout lines which fail to produce gametocytes. However, independent genetic verification revealed that both kinases are not required for gametocytogenesis but both lines harbour the same mutation that leads to a truncation in the extreme C-terminus of GDV1. Introduction of the identified nonsense mutation into the genome of wild type parasite lines replicates the observed phenotype. Using a GDV1 overexpression line we show that the truncation in the GDV1 C-terminus does neither interfere with the nuclear import of GDV1 nor its interaction with HP1in vitro, but appears important to sustain GDV1 protein levels and thereby sexual commitment.

Importance

Transmission of malaria causingPlasmodiumspecies by mosquitos requires the parasite to change from a continuously growing asexual parasite form growing in the blood, to a sexually differentiated form, the gametocyte. Only a small subset of asexual parasites differentiates into gametocytes that are taken up by the mosquito. Transmission represents a bottleneck in the lifecycle of the parasite, so a molecular understanding of the events that lead to stage conversion may identify novel intervention points. Here we screened a subset of kinases we hypothesized to play a role in this process. While we did not identify kinases required for sexual conversion, we identified a mutation in the C-terminus of the Gametocyte Development 1 protein (GDV1), which abrogates sexual development. The mutation destabilises the protein but not its interaction with its cognate binding partner HP1. This suggest an important role for the GDV1 C-terminus beyond trafficking and protein stability.
Real-Time Multi-Angle Projection Imaging of Biological Dynamics
Authors: Chang Bo-Jui , Sapoznik Etai , Pohlkamp Theresa , Terrones Tamara S. , Welf Erik S. , Manton James D. , Roudot Philippe , Hake Kayley , Whitehead Lachlan , York Andrew G. , Dean Kevin M. , Fiolka Reto
Published: October 2020

We introduce a cost-effective and easily implemented scan unit which enables any camera-based microscope to perform projection imaging from diverse viewing angles. We demonstrate this capability on Lattice Light-Sheet and Oblique Plane Microscopy by rapidly delivering projection images with an uncompromised lateral resolution and high optical contrast. By imaging the sample from one or multiple perspectives, our method enables visualization of rapid biological processes, real time stereoscopic imaging as well as three-dimensional particle localization throughout a cellular volume from just two images. Furthermore, because our projection imaging technique provides intuitive three-dimensional renderings in real-time, it improves microscope usability, allows users to more-readily optimize instrument performance and identify biological phenomena of interest on-the-fly, while also reducing data overhead by a factor of >100. We leverage our rapid projection method to image cancer cell morpho-dynamics and calcium signaling in cultured neurons, to perform three-dimensional localization of genetically encoded nanoparticles, as well as to image orthogonal views of an embryonic Zebrafish heart simultaneously.
How many and which species to plant? A multi-trait-based approach to select species to restore ecosystem services
Authors: Tsujii Paula Kiyomi , Coutinho André Ganem , Medina Anderson M. , Kraft Nathan J. B. , Gonzalez-Melo Andres , Higuchi Pedro , Müller Sandra Cristina , Niinemets Ülo , Pillar Valério D. , Sosinski Enio E. , Carlucci Marcos B.
Published: October 2020

It has been increasingly argued that ecological restoration should focus more on targeting ecosystem services than on species composition of reference ecosystems. In this sense, the role that species play on community assembly and functioning through their functional traits is very relevant, because effect traits mediate ecosystem processes, ultimately resulting in provision of ecosystem services. One major challenge in ecological restoration is to know which species to use that will deliver the target ecosystem services. We developed an algorithm to select the minimum set of species that maximize the functional richness (FRic) and the functional redundancy (FR) of the restored community, a proxy for the provision of multiple ecosystem services and the resilience of the system to environmental changes, respectively. For this, we simulated the restoration of 24 riparian woody communities of the Brazilian Cerrado. Using the species pool of each original local community, we ran restoration simulations for gradually increasing species richness until reaching the total species richness of the original local community. We computed FRic and FR for each simulated restoration community using the traits specific leaf area, maximum plant height and seed mass. Our simulation results indicate that multiple ecosystem services could be restored with an average of 66% of the species of the original community. Moreover, an average of 59% of the species would be needed to restore communities resilient to environmental changes. Our approach contributes to solving one of the major challenges of ecological restoration, which is defining how many and which species should be used to achieve functional targets. We believe this approach can help in projects of restoration by enabling restoration practitioners to select minimum alternative sets of species that optimize the provision of multiple ecosystem services in a resilient restored ecosystem.
Synteny-based genome assembly for 16 species ofHeliconiusbutterflies, and an assessment of structural variation across the genus
Authors: Seixas Fernando A. , Edelman Nathaniel B. , Mallet James
Published: October 2020

Heliconiusbutterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species,Heliconius melpomeneandH. erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16Heliconiusspecies. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (H. hecale,H. elevatusandH. pardalinus) differences in genome size are mainly driven by a few restricted repetitive regions. Genes within these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on non-synonymous changes, and increased expression, all of which suggest that the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two majorHeliconiusclades. We infer that one of these inversions was transferred by introgression between the lineages leading to theerato/saraandburneyi/dorisclades. These reference-guided assemblies represent a major improvement inHeliconiusgenomic resources that should aid further genetic and evolutionary studies in this genus.
Metabolic flux signatures of the ER unfolded protein responsein vivoreveal decreased hepaticde novolipogenesis and mobilization of lipids from adipose tissue to liver
Authors: Schneider Catherine P. , Peng Lucy , Yuen Samuel , Chang Michael , Karapetyan Rozalina , Nyangau Edna , Mohammed Hussein , Palacios Hector , Ziari Naveed , Joe Larry K. , Frakes Ashley E. , Dillin Andrew , Hellerstein Marc K.
Published: October 2020

The unfolded protein response in the endoplasmic reticulum (UPRER) is involved in a number of metabolic diseases, including non-alcoholic fatty liver disease. Here, we characterize the UPRERinduced metabolic changes in mouse liver throughin vivometabolic labeling and mass spectrometric analysis of proteome and lipid fluxes. We induced ER stressin vivovia tunicamycin treatment and measured rates of proteome-wide protein synthesis,de novolipogenesis and cholesterol synthesis serially over a three-day period, thereby generating a metabolic “signature” of the UPRERover time. Synthesis of most proteins was suppressed under ER stress conditions, including proteins involved in lipogenesis, consistent with reducedde novolipogenesis at 48 and 72 hours. Electron microscopy revealed striking morphological changes to ER and H&E staining showed lipid droplet enriched livers under ER stress. Pre-labeling of adipose tissue prior to ER stress induction revealed mobilization of lipids from adipose to the liver. Interestingly, the source of these lipids was uptake of free fatty acids, not whole triglycerides or phospholipids from lipoproteins, as demonstrated by replacement of the triglyceride-glycerol moiety in liver concurrently with increased incorporation of labeled palmitate from adipose. We also induced ER stress by a high-fat diet and observed similar metabolic flux signatures, suggesting that this mechanism may play a role in the progression of fatty liver disease. This flux-based approach provides a powerful tool to identify novel regulators of ER stress and potential targets for pharmacological intervention.
Sex-biasedZRSR2mutations in myeloid malignancies impair plasmacytoid dendritic cell activation and apoptosis
Authors: Togami Katsuhiro , Chung Sun Sook , Madan Vikas , Kenyon Christopher M. , Cabal-Hierro Lucia , Taylor Justin , Kim Sunhee S. , Griffin Gabriel K. , Ghandi Mahmoud , Li Jia , Li Yvonne Y. , Angelot-Delettre Fanny , Biichle Sabeha , Seiler Michael , Buonamici Silvia , Lovitch Scott B. , Louissaint Abner , Morgan Elizabeth A. , Jardin Fabrice , Piccaluga Pier Paolo , Weinstock David M. , Hammerman Peter S. , Yang Henry , Konopleva Marina , Pemmaraju Naveen , Garnache-Ottou Francine , Abdel-Wahab Omar , Koeffler H. Phillip , Lane Andrew A.
Published: October 2020

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive leukemia of plasmacytoid dendritic cells (pDCs). BPDCN occurs at least three times more frequently in men than women, but the reasons for this sex bias are unknown. Here, studying genomics of primary BPDCN and modeling disease-associated mutations, we link acquired alterations in RNA splicing to abnormal pDC development and inflammatory response through Toll-like receptors. Loss-of-function mutations inZRSR2,an X chromosome gene encoding a splicing factor, are enriched in BPDCN and nearly all mutations occur in males.ZRSR2mutation impairs pDC activation and apoptosis after inflammatory stimuli, associated with intron retention and inability to upregulate the transcription factor IRF7. In vivo, BPDCN-associated mutations promote pDC expansion and signatures of decreased activation. These data support a model in which male-biased mutations in hematopoietic progenitors alter pDC function and confer protection from apoptosis, which may impair immunity and predispose to leukemic transformation.

STATEMENT OF SIGNIFICANCE

Sex bias in cancer is well recognized but the underlying mechanisms are incompletely defined. We connect X chromosome mutations inZRSR2to an extremely male-predominant leukemia. Aberrant RNA splicing induced byZRSR2mutation impairs dendritic cell inflammatory signaling, interferon production, and apoptosis, revealing a sex- and lineage-related tumor suppressor pathway.
SurfStamp: 3D Printer Compatible Molecular Surface Representation
Authors: Oda Toshiyuki
Published: October 2020

SurfStamp is an application that is used to generate textures for surface models of proteins. The textures contain information about surface residues and the information is drawn directly on the 3D object of the models. This approach is more intuitive than the labeling functions that most three-dimensional (3D) structure viewers use to show residue information. Therefore, the use of this application enables researchers, readers, or audiences to easily determine which residues are contributing the surface they are focusing on.

Availability

The application is provided under the open-source Apache License Version 2.0 (http://www.apache.org/licenses/LICENSE-2.0). The application and source code are available fromhttps://github.com/yamule/SurfStamp-public/releases. The application is also available as a plugin for the recent versions of PyMOL (Schrodinger, 2015,https://github.com/schrodinger/pymol-open-source) fromhttps://github.com/yamule/SurfStamp-pymol-plugin.
Nonsense mediated decay and a novel protein Period-2 regulatecasein kinase Iin an opposing manner to control circadian period inNeurospora crassa
Authors: Kelliher Christina M. , Lambreghts Randy , Xiang Qijun , Baker Christopher L. , Loros Jennifer J. , Dunlap Jay C.
Published: October 2020

Circadian clocks in fungi and animals are driven by a functionally conserved transcription-translation feedback loop. InNeurospora crassa, negative feedback is executed by a complex of Frequency (FRQ), FRQ-interacting RNA helicase (FRH), and Casein Kinase I (CKI), which inhibits the activity of the clock’s positive arm, the White Collar Complex (WCC). Here, we show that theperiod-2gene, whose mutation is characterized by recessive inheritance of a long 26-hour period phenotype, encodes an RNA-binding protein that stabilizes theck-1atranscript, resulting in CKI protein levels sufficient for normal rhythmicity. Moreover, by examining the molecular basis for the short circadian period ofperiod-6mutants, we uncovered a strong influence of the Nonsense Mediated Decay pathway on CKI levels. The finding that circadian period defects in two classically-derivedNeurosporaclock mutants each arise from disruption ofck-1aregulation is consistent with circadian period being exquisitely sensitive to levels ofcasein kinase I.
Purinergic P2Y1 and P2Y2/4 receptors elicit distinct Ca2+signaling patterns in hepatocytes via differential feedback regulation by Protein Kinase C
Authors: Corrêa-Velloso Juliana C. , Bartlett Paula J. , Brumer Robert , Gaspers Lawrence , Ulrich Henning , Thomas Andrew P.
Published: October 2020

Extracellular nucleotides are key regulators of liver physiology. In primary rat hepatocytes, P2Y1 receptor (P2Y1R) activation by ADP generates cytosolic calcium ([Ca2+]c) oscillations with narrow spikes, whereas P2Y2/4R activation by UTP led to more complex broad [Ca2+]coscillations. Both [Ca2+]coscillation signatures were observed with the common agonist ATP. Inhibition of Gαqsignaling with YM-254890 abolished ATP-induced [Ca2+]coscillations, indicating that they depend on inositol 1,4,5-trisphosphate (IP3), and are not mediated by P2X receptors. The narrow P2Y1-linked [Ca2+]cspikes and the broad P2Y2/4-linked [Ca2+]cspikes are shaped by differential and complex PKC-mediated feedback mechanisms. Downregulation of PKC broadened both ADP- and UTP-induced [Ca2+]coscillations, with a more pronounced effect on the former. PKC downregulation also selectively elicited a more robust response to ADP stimulation, enhancing oscillatory and sustained [Ca2+]cresponses. Acute PKC modulation confirmed the importance of the negative PKC feedback regulation of P2Y1R-linked [Ca2+]csignals; such that PKC activation decreased [Ca2+]coscillation frequency and PKC inhibition increased [Ca2+]cspike width. However, both PKC activation and inhibition decreased the spike width of P2Y2/4R-induced [Ca2+]coscillations, suggesting that multiple opposing PKC feedback mechanisms shape P2Y2/4R responses. Significantly, plasma membrane Ca2+entry was required for negative PKC feedback on P2Y1R-linked [Ca2+]coscillations, whereas P2Y2/4R-linked [Ca2+]coscillations were less sensitive to negative regulation by PKC and independent of Ca2+influx. Thus, differential feedback regulation by PKC gives rise to receptor-specific [Ca2+]coscillation profiles, which can encode the diverse physiological and pathophysiological responses to distinct agonists that all act through the IP3signaling cascade.
Epitope profiling reveals binding signatures of SARS-CoV-2 immune response and cross-reactivity with endemic HCoVs
Authors: Stoddard Caitlin I. , Galloway Jared , Chu Helen Y. , Shipley Mackenzie M. , Itell Hannah L. , Wolf Caitlin R. , Logue Jennifer K. , Magedson Ariana , Sung Kevin , Garrett Meghan , Crawford Katharine H.D. , Laserson Uri , Matsen Frederick A. , Overbaugh Julie
Published: October 2020

A major goal of current SARS-CoV-2 vaccine efforts is to elicit antibody responses that confer protection. Mapping the epitope targets of the SARS-CoV-2 antibody response is critical for innovative vaccine design, diagnostics, and development of therapeutics. Here, we developed a phage display library to map antibody binding sites at high resolution within the complete viral proteomes of all human-infecting coronaviruses in patients with mild or moderate/severe COVID-19. The dominant immune responses to SARS-CoV-2 were targeted to regions spanning the Spike protein, Nucleocapsid, and ORF1ab. Some epitopes were identified in the majority of samples while others were rare, and we found variation in the number of epitopes targeted by different individuals. We also identified a set of cross-reactive sequences that were bound by antibodies in SARS-CoV-2 unexposed individuals. Finally, we uncovered a subset of enriched epitopes from commonly circulating human coronaviruses with significant homology to highly reactive SARS-CoV-2 sequences.
Transcriptomic profiling of fibropapillomatosis in green sea turtles (Chelonia mydas) from South Texas
Authors: Blackburn Nicholas B. , Leandro Ana Cristina , Nahvi Nina , Devlin Mariana A. , Leandro Marcelo , Escobedo Ignacio Martinez , Peralta Juan M. , George Jeff , Stacy Brian A. , deMaar Thomas W. , Blangero John , Keniry Megan , Curran Joanne E
Published: October 2020

Sea turtle fibropapillomatosis (FP) is a tumor promoting disease that is one of several threats globally to endangered sea turtle populations. The prevalence of FP is highest in green sea turtle (Chelonia mydas) populations, and historically has shown considerable temporal growth. FP tumors can significantly affect the ability of turtles to forage for food and avoid predation and can grow to debilitating sizes. In the current study, based in South Texas, we have applied transcriptome sequencing to FP tumors and healthy control tissue to study the gene expression profiles of FP. By identifying differentially expressed turtle genes in FP, and matching these genes to their closest human ortholog we draw on the wealth of human based knowledge, specifically human cancer, to identify new insights into the biology of sea turtle FP. We show that several genes aberrantly expressed in FP tumors have known tumor promoting biology in humans, includingCTHRC1andNLRC5, and provide support that disruption of the Wnt signaling pathway is a feature of FP. Further, we profiled the expression of current targets of immune checkpoint inhibitors from human oncology in FP tumors and identified potential candidates for future studies.
KCC2 is required for the survival of mature neurons but not for their development
Authors: Kontou Georgina , Ng Josephine , Cardarelli Ross Andrew , Howden Jack , Choi Catherine , Ren Qiu , Kittler Josef , Brandon Nicholas , Moss Stephen J. , Smalley Joshua L.
Published: October 2020

The K+/Cl– co-transporter KCC2 (SLC12A5) allows mature neurons in the CNS to maintain low intracellular Cl−levels that are critical in mediating fast hyperpolarizing synaptic inhibition via type A γ-aminobutyric acid receptors GABAARs. In accordance with this, compromised KCC2 activity results in seizures but whether such deficits directly contribute to the subsequent changes in neuronal viability that lead to epileptogenesis, remains to be assessed. Canonical hyperpolarizing GABAAR currents develop postnatally which reflect a progressive increase in KCC2 expression levels and activity. To investigate the role that KCC2 plays in regulating neuronal viability and architecture we have conditionally ablated KCC2 expression in developing and mature neurons. Decreasing KCC2 expression resulted in the rapid activation of the extrinsic apoptotic pathway, in mature hippocampal neurons. Intriguingly, direct pharmacological inhibition of KCC2 in mature neurons resulted in the rapid activation of the extrinsic apoptotic pathway. In contrast, ablating KCC2 expression in immature neurons had no discernable effects on their subsequent development, arborization or dendritic structure. However ablating KCC2 expression in immature neurons was sufficient to prevent the subsequent postnatal development of hyperpolarizing GABAAR currents. Collectively, our results demonstrate that KCC2 plays a critical role in neuronal survival by limiting apoptosis, and mature neurons are highly sensitive to loss of KCC2 function. In contrast KCC2 appears to play a minimal role in mediating neuronal development or architecture.
Multiple Mechanisms Underlie State-Independent Inhibitory Effects of Norfluoxetine on TREK-2 K2P Channels
Authors: Proks Peter , Schewe Marcus , Conrad Linus J. , Rao Shanlin , Rathje Kristin , Rödström Karin E. J. , Carpenter Elisabeth P. , Baukrowitz Thomas , Tucker Stephen J
Published: October 2020

The TREK subfamily of Two-Pore Domain (K2P) K+channels are inhibited by fluoxetine and its metabolite, norfluoxetine (NFx). Although not the principal targets of this antidepressant, TREK channel inhibition by NFx has provided important insights into the conformational changes associated with channel gating and highlighted the role of the selectivity filter in this process. But despite the availability of TREK-2 crystal structures with NFx bound, the precise mechanisms underlying NFx inhibition remain elusive. NFx has previously been proposed to be a state-dependent inhibitor, but its binding site suggests many possible ways in which this positively charged drug might inhibit channel activity. Here we show that NFx exerts multiple effects on single channel behavior that influence both the open and closed states of the channel, and that the channel can become highly activated by 2-APB whilst remaining in the down conformation. We also show that that the inhibitory effects of NFx are unrelated to its positive charge, but can be influenced by agonists such as ML335 which alter filter stability, as well as by an intrinsic voltage-dependent gating process within the filter. NFx therefore not only inhibits channel activity by altering the equilibrium between up and down conformations, but can also directly influence filter gating. These results provide further insight into the complex allosteric mechanisms that modulate filter-gating in TREK K2P channels and highlight the different ways that filter gating can be regulated to permit polymodal regulation.
LncRNAPAINTis Associated with Aggressive Prostate Cancer and Dysregulation of Slug and Related Genes
Authors: Hasan Md Faqrul , Ganapathy Kavya , Sun Jiao , Ayman Khatib , Andl Thomas , Saulakova Julia N. , Coppola Domenico , Zhang Wei , Chakrabarti Ratna
Published: October 2020

Long non-coding RNAs (lncRNAs) play regulatory roles in cellular processes and their aberrant expression may drive cancer progression. Here we report the function of a lncRNAPAINT(Prostate Cancer Associated Intergenic Non-Coding Transcript) in promoting prostate cancer (PCa) progression. Upregulation ofPAINTwas noted in advanced stage and metastatic PCa. Inhibition ofPAINTdecreased cell proliferation, S-phase progression, increased expression of apoptotic markers, and improved sensitivity to docetaxel and Aurora kinase inhibitor VX-680. Inhibition ofPAINTdecreased cell migration and reduced expression of Slug and Vimentin. Ectopic expression ofPAINTsuppressed E-cadherin, increased S-phase progression and cell migration.PAINTexpression in PCa cells induced larger colony formation and higher expression of mesenchymal markers. Transcriptome analysis followed by qRT-PCR validation showed differentially expressed genes involved in epithelial mesenchymal transition (EMT), apoptosis and drug resistance inPAINT-expressing cells. Our study establishes an oncogenic function ofPAINTin PCa.
Modeling the Opening SARS-CoV-2 Spike: an Investigation of its Dynamic Electro-Geometric Properties
Authors: Kucherova Anna , Strango Selma , Sukenik Shahar , Theillard Maxime
Published: October 2020

The recent COVID-19 pandemic has brought about a surge of crowd-sourced initiatives aimed at simulating the proteins of the SARS-CoV-2 virus. A bottleneck currently exists in translating these simulations into tangible predictions that can be leveraged for pharmacological studies. Here we report on extensive electrostatic calculations done on an exascale simulation of the opening of the SARS-CoV-2 spike protein, performed by the Folding@home initiative. We compute the electric potential as the solution of the non-linear Poisson-Boltzmann equation using a parallel sharp numerical solver. The inherent multiple length scales present in the geometry and solution are reproduced using highly adaptive Octree grids. We analyze our results focusing on the electro-geometric properties of the receptor-binding domain and its vicinity. This work paves the way for a new class of hybrid computational and data-enabled approaches, where molecular dynamics simulations are combined with continuum modeling to produce high-fidelity computational measurements serving as a basis for protein bio-mechanism investigations.
Reconstructing genomes of carbon monoxide oxidisers in volcanic deposits including members of the class Ktedonobacteria
Authors: Hernández Marcela , Vera-Gargallo Blanca , Calabi-Floody Marcela , King Gary M , Conrad Ralf , Tebbe Christoph C.
Published: October 2020

Microorganisms can potentially colonize volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form IcoxLoperon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase andhypgenes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilize H2and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth.
Disentangling metacommunity processes using multiple metrics in space and time
Authors: Guzman Laura Melissa , Thompson Patrick L. , Viana Duarte S , Vanschoenwinkel Bram , Horváth Zsófia , Ptacnik Robert , Jeliazkov Alienor , Gascón Stéphanie , Lemmens Pieter , Anton-Pardo Maria , Langenheder Silke , De Meester Luc , Chase Jonathan M.
Published: October 2020

Metacommunity ecology has focused on using observational and analytical approaches to disentangle the role of critical assembly processes, such as dispersal limitation and environmental filtering. Many methods have been proposed for this purpose, most notably multivariate analyses of species abundance and its association with variation in spatial and environmental conditions. These approaches tend to focus on few emergent properties of metacommunities and have largely ignored temporal community dynamics. By doing so, these are limited in their ability to differentiate metacommunity dynamics. Here, we develop a Virtual ecologist’ approach to evaluate critical metacommunity assembly processes based on a number of summary statistics of community structure across space and time. Specifically, we first simulate metacommunities emphasizing three main processes that underlie metacommunity dynamics (density-independent responses to abiotic conditions, density-dependent biotic interactions, and dispersal). We then calculate a number of commonly used summary statistics of community structure in space and time, and use random forests to evaluate their utility for understanding the strength of these three processes. We found that: (i) time series are necessary to disentangle metacommunity processes, (ii) each of the three studied processes is distinguished with different descriptors, (iii) each summary statistic is differently sensitive to temporal and spatial sampling effort. Some of the most useful statistics include the coefficient of variation of abundances through time and metrics that incorporate variation in the relative abundances (evenness) of species. Surprisingly, we found that when we only used a single snapshot of community variation in space, the most commonly used approaches based on variation partitioning were largely uninformative regarding assembly processes, particularly, variation in dispersal. We conclude that a combination of methods and summary statistics will be necessary to understand the processes that underlie metacommunity assembly through space and time.
Molecular and morphological analyses clarify species delimitation and reveal a newBetulaspecies in sectionCostatae
Authors: Wang Luwei , Ding Junyi , Borrell James S. , McAllister Hugh A. , Wang Feifei , Liu Lu , Wang Nian
Published: October 2020

Background and Aims

Delineating closely related and morphologically similar species with overlapping ranges can be difficult. Here, we use sectionCostatae(genusBetula) as a model to resolve species and subspecies boundaries in four morphologically similar trees:Betula ashburneri, Betula costata, Betula ermaniiandBetula utilis(including ssp.utilis,and diploid and tetraploid races of ssp.albosinensis).

Methods

We genotyped 298 individuals (20-80 per species) from 38 populations at 15 microsatellite markers and a subset of 34 individuals from 21 populations using restriction-site associated DNA sequencing (RAD-seq). Morphometric analysis was conducted to characterise leaf variation for a subset of 89 individuals.

Key Results

Molecular analyses and leaf morphology found little differentiation betweenB. ashburneri,diploidB. utilisssp.albosinensisand some samples ofB. utilisssp.utilissuggesting that these should be treated as a single species. By contrast, tetraploidBetula utilisssp.albosinensiswas divided into two groups with group I genetically similar toB. utilisssp.utilisbased on SNPs and group II, a very distinct cluster, which we propose as a new species, namely,Betula buggsii. Phylogenomic analysis based on 2,285,620 SNPs show a well-supported monophyletic clade ofB. buggsii,forming a sister with a well-supported clade ofB. ashburneri,diploidB. albosinensisand some samples ofB. utilisssp.utilis. Morphologically,Betula buggsiiis characterised by elongated lenticels and a distinct pattern of bark peeling.Betula buggsiiis geographically restricted to the Qinling-Daba Mountains.

Conclusions

Our study reveals six genetically distinguishable species:B. ashburneri, B. buggsii, B. costata, B. utilisssp.utilis,B. utilisssp.albosinensisandB. ermanii. Our research demonstrates an integrative approach in delimitating species using morphological and genetic samples from their nearly entire distributions. Analyses based on subsets of species’ distributions may lead to erroneous species or subspecies delineation.
Genomic diversity and antimicrobial resistance among non-typhoidalSalmonellaassociated with human disease in The Gambia
Authors: Darboe Saffiatou , Bradbury Richard S. , Phelan Jody , Kanteh Abdoulie , Muhammad Abdul-Khalie , Worwui Archibald , Yang Shangxin , Nwakanma Davis , Perez-Sepulveda Blanca , Kariuki Samuel , Kwambana-Adams Brenda , Antonio Martin
Published: October 2020

Non-typhoidalSalmonellaassociated with multidrug resistance cause invasive disease in sub-Saharan African. Specific lineages of serovarsS. Typhimurium andS. Enteritidis are implicated. We characterised the genomic diversity of 100 clinical Non-typhoidalSalmonellacollected from 93 patients in 2001 from the eastern and 2006 to 2018 in the western regions of The Gambia respectively. Phenotypic susceptibility applied Kirby Baur disk diffusion and whole genome sequencing utilized Illumina platforms. The predominant serovars wereS.Typhimurium ST19 (31/100) andS.Enteritidis ST11 (18/100) restricted to invasive disease with the notable absence ofS.Typhimurium ST313. Phylogenetic analysis performed in the context of 495 African strains from the European Nucleotide Archive confirmed the presence of theS. Enteritidis virulent epidemic invasive multidrug resistant West African clade. Multidrug resistance including chloramphenicol and azithromycin has emerged among the West AfricanS.Enteritidis clade 7/9 (78%) with potential for spread, thus having important implications for patient management warranting systematic surveillance and epidemiologic investigations to inform control.

Data summary

Sequences are deposited in the NCBI sequence reads archive (SRA) under BioProject ID:PRJEB38968. The genomic assemblies are available for download from the European Nucleotide Archive (ENA):http://www.ebi.ac.uk/ena/data/view/. Accession numbers SAMEA6991082 to SAME6991180
BMPR-2 gates activity-dependent stabilization of dendrites during mitral cell remodeling
Authors: Aihara Shuhei , Fujimoto Satoshi , Sakaguchi Richi , Imai Takeshi
Published: October 2020

Developing neurons initially form excessive neurites and then remodel them based on molecular cues and neuronal activity. Developing mitral cells in the olfactory bulb initially extend multiple primary dendrites. They then stabilize single primary dendrites, while eliminating others. However, the mechanisms underlying the selective dendrite remodeling remain elusive. Using CRISPR/Cas9-based knockout screening combined within uteroelectroporation, we identified BMPR-2 as a key regulator for the selective dendrite stabilization.Bmpr2knockout and its rescue experiments show that BMPR-2 inhibits LIMK without ligands and thereby facilitates dendrite destabilization. In contrast, the overexpression of antagonists and agonists indicate that ligand-bound BMPR-2 stabilizes dendrites, most likely by releasing LIMK. Using genetic and FRET imaging experiments, we also demonstrate that free LIMK is activated by NMDARs via Rac1, facilitating dendrite stabilization through F-actin formation. Thus, the selective stabilization of mitral cell dendrites is ensured by concomitant inputs of BMP ligands and neuronal activity.
Highly Divergent Neuropeptide - non-coding RNA regulatory networks underpin variant host-finding behaviours inSteinernemaspecies infective juveniles
Authors: Warnock Neil D. , Atcheson Erwan , McCoy Ciaran , Dalzell Johnathan J.
Published: October 2020

We conducted a transcriptomic and small RNA analysis of infective juveniles (IJs) from three behaviourally distinctSteinernemaspecies. Substantial variation was found in the expression of shared gene orthologues, revealing gene expression signatures that correlate with behavioural states. 97% of predicted microRNAs are novel to each species. Surprisingly, our data provide evidence that isoform variation can effectively convert protein-coding neuropeptide genes into non-coding transcripts, which may represent a new family of long non-coding RNAs. These data suggest that differences in neuropeptide gene expression, isoform variation, and small RNA interactions could contribute to behavioural differences within theSteinernemagenus.
Differential patterns of gyral and sulcal morphological changes during normal aging process
Authors: Lin Hsin-Yu , Huang Chu-Chung , Chou Kun-Hsien , Yang Albert C. , Lo Chun-Yi Zac , Tsai Shih-Jen , Lin Ching-Po
Published: October 2020

The cerebral cortex is a highly convoluted structure with distinct morphologic features, namely the gyri and sulci, which are associated with the functional segregation or integration in the human brain. During the lifespan, the brain atrophy that is accompanied by cognitive decline is a well-accepted aging phenotype. However, the detailed patterns of cortical folding change during aging, especially the changing trajectories of gyri and sulci, which is essential to brain functioning, remain unclear. In this study, we investigated the morphology of the gyral and sulcal regions from pial and white matter surfaces using MR imaging data of 417 healthy participants across the lifespan (21-92y). To elucidate the age-related changes in the cortical pattern, we fitted cortical thickness and intrinsic curvature of gyri and sulci using the quadratic model to evaluate their trajectories during normal aging. Our findings show that comparing to gyri, the sulcal thinning is the most prominent pattern during the aging process, and the gyrification of pial and white matter surfaces were also affected differently, which implies the vulnerability of functional segregation during aging. Taken together, we propose a morphological model of aging that may provide a framework for understanding the mechanisms underlying the gray matter degeneration.
Punctuated loci on chromosome IV determine natural variation in Orsay virus susceptibility ofCaenorhabditis elegansstrains Bristol N2 and Hawaiian CB4856
Authors: Sterken Mark G. , van Sluijs Lisa , Wang Yiru A. , Ritmahan Wannisa , Gultom Mitra L. , Riksen Joost A.G. , Volkers Rita J.M. , Snoek L. Basten , Pijlman Gorben P. , Kammenga Jan E.
Published: October 2020

Host-pathogen interactions play a major role in evolutionary selection and shape natural genetic variation. The genetically distinctCaenorhabditis elegansstrains, Bristol N2 and Hawaiian CB4856, are differentially susceptible to the Orsay virus (OrV). Here we report the dissection of the genetic architecture of susceptibility to OrV infection. We compare OrV infection in the relatively resistant wild-type CB4856 strain to the more susceptible canonical N2 strain. To gain insight into the genetic architecture of viral susceptibility, 52 fully sequenced recombinant inbred lines (CB4856 x N2 RILs) were exposed to OrV. This led to the identification of two loci on chromosome IV associated with OrV resistance. To verify the two loci and gain additional insight into the genetic architecture controlling virus infection, introgression lines (ILs) that together cover chromosome IV, were exposed to OrV. Of the 27 ILs used, 17 had an CB4856 introgression in an N2 background and 10 had an N2 introgression in a CB4856 background. Infection of the ILs confirmed and fine-mapped the locus underlying variation in OrV susceptibility and we found that a single nucleotide polymorphism incul-6contributes to the difference in OrV susceptibility between N2 and CB4856. An allele swap experiment showed the strain CB4856 became more susceptible by having an N2cul-6allele, although having the CB4856cul-6allele did not increase resistance in N2. Additionally, we found that multiple strains with non-overlapping introgressions showed a distinct infection phenotype from the parental strain, indicating that there are punctuated locations on chromosome IV determining OrV susceptibility. Thus, our findings reveal the genetic complexity of OrV susceptibility inC. elegansand suggest that viral susceptibility is governed by multiple genes.
Irradiated mesenchymal stromal cells induce genetic instability in human CD34+ cells
Authors: Kohl Vanessa , Drews Oliver , Costina Victor , Bierbaum Miriam , Jawhar Ahmed , Roehl Henning , Weiss Christel , Brendel Susanne , Kleiner Helga , Flach Johanna , Spiess Birgit , Seifarth Wolfgang , Nowak Daniel , Hofmann Wolf-Karsten , Fabarius Alice , Popp Henning D.
Published: October 2020

Radiation-induced bystander effects (RIBE) in human hematopoietic stem and progenitor cells may initiate myeloid neoplasms (MN). Here, the occurrence of RIBE caused by genotoxic signaling from irradiated human mesenchymal stromal cells (MSC) on human bone marrow CD34+ cells was investigated. For this purpose, healthy MSC were irradiated in order to generate conditioned medium containing potential genotoxic signaling factors. Afterwards, healthy CD34+ cells from the same donors were grown in conditioned medium and RIBE were analyzed. Increased DNA damage and chromosomal instability were detected in CD34+ cells grown in MSC conditioned medium when compared to CD34+ cells grown in control medium. Furthermore, reactive oxygen species and distinct proteome alterations, e.g., heat-shock protein GRP78, that might be secreted into the extracellular medium, were identified as potential RIBE mediators. In summary, our data provide evidence that irradiated MSC induce genetic instability in human CD34+ cells potentially resulting in the initiation of MN. Furthermore, the identification of key bystander signals, such as GRP78, may lay the framework for the development of next-generation anti-leukemic drugs.