bluuebunny/crossref_metadata_2025 huggingface dataset:
Exportin Crm1 is important for Swi6 nucleocytoplasmic shuttling and MBF transcription activation inSaccharomyces cerevisiae
Authors: Belanger Kenneth D. , Yewdell William T. , Barber Matthew F. , Russo Amy N. , Pettit Mark A. , Damuth Emily K. , Hussain Naveen , Geier Susan J. , Belanger Karyn G.
Published: June 2020

The Swi6 protein acts as a transcription factor in budding yeast, functioning in two different heterodimeric complexes, SBF and MBF, that activate the expression of distinct but overlapping sets of genes. Swi6 undergoes regulated changes in nucleocytoplasmic localization throughout the cell cycle that correlate with changes in gene expression. While the process of Swi6 nuclear import is well understood, mechanisms underlying its nuclear export remain unclear. Here we investigate Swi6 nuclear export and its impact on Swi6 function. We show that the exportin Crm1, in addition to three other karyopherins previously shown to affect Swi6 localization, is important for Swi6 nuclear export and activity. A truncation of Swi6 that removes a putative Crm1 nuclear export signal results in the loss of changes in nucleocytoplasmic Swi6 localization that normally occur during progression through the cell cycle. Mutagenesis of the NES-like sequence or removal of Crm1 activity using leptomycin B results in a similar decrease in nuclear export as cells enter S-phase. Using two-hybrid analysis, we also show that Swi6 associates with Crm1in vivo. Alteration of the Crm1 NES in Swi6 results in a decrease in MBF-mediated gene expression, but does not affect expression of an SBF reporter, suggesting that export of Swi6 by Crm1 regulates a subset of Swi6 transcription activation activity. Finally, alteration of the Crm1 NES in Swi6 results in cells that are larger than wild type, but not to the extent of those with a complete Swi6 deletion. Expressing a Swi6 NES mutant in combination with a deletion of Msn5, an exportin involved in Swi6 nuclear export and specifically affecting SBF activation, further increases the large cell phenotype, but still not to the extent observed in a Swi6 deletion mutant. These data suggest that Swi6 has at least two different exportins, Crm1 and Msn5, each of which interacts with a distinct nuclear export signal and influences expression of a different subset of Swi6-controlled genes.

Summary Statement

Precise intracellular localization is important for the proper activity of proteins. Here we provide evidence that the Swi6 transcription factor important for cell cycle progression shuttles between the cell nucleus and cytoplasm, its nuclear export is important for its activity, and that it contains a nuclear export signal (NES) recognized by the Crm1 nuclear transport factor.
ATP-sensitive K+channels control the spontaneous firing of a glycinergic interneuron in the auditory brainstem
Authors: Strazza Paulo S. , de Siqueira Daniela V.F. , Benites Nikollas M. , Leão Ricardo M.
Published: June 2020

Cartwheel neurons from the dorsal cochlear nucleus (DCN) are glycinergic interneurons and the primary source of inhibition on the fusiform neurons, the principal excitatory neuron in the DCN. Most cartwheel neurons present spontaneous firing (activeneurons), producing a steady inhibitory tone on fusiform neurons. In contrast, a smaller fraction does not fire spontaneously (quietneurons). Additionally, hyperactivity of fusiform neurons is seen in animals with behavioral evidence of tinnitus. Due to its relevance in controlling the excitability of fusiform neurons, we investigated the ion channels responsible for the spontaneous firing of cartwheel neurons. We found that quiet neurons express an outward conductance not seen in active neurons, which generates a stable resting potential. This current was sensitive to tolbutamide, an ATP-sensitive potassium channel (KATP) antagonist. After its inhibition, quiet neurons start to fire spontaneously, while the behavior of active neurons was not affected. On the other hand, in active neurons, KATPagonist diazoxide activated a conductance similar to the KATPconductance of quiet neurons and stopped spontaneous firing. According to the effect of KATPchannels on CW neuron firing, glycinergic neurotransmission in DCN was increased by tolbutamide and decreased by diazoxide. Finally, slices incubated with the tinnitus-inducing agent sodium salicylate presented more quiet neurons expressing the KATPconductance, which increased the proportion of quiet neurons. Our results reveal an unexpected role of KATPchannels in controlling the spontaneous firing of neurons. Additionally, changes in KATPchannel activity of cartwheel neurons can be related to the DCN hyperactivity seen in tinnitus.
Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs
Authors: Kern David M. , Sorum Ben , Mali Sonali S. , Hoel Christopher M. , Sridharan Savitha , Remis Jonathan P. , Toso Daniel B. , Kotecha Abhay , Bautista Diana M. , Brohawn Stephen G.
Published: June 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3–6. 3a has been implicated in viral release7, inhibition of autophagy8, inflammasome activation9, and cell death10,11and its deletion reduces viral titer and morbidity in mice1, raising the possibility that 3a could be an effective vaccine or therapeutic target3,12. Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 Å resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca2+-permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multipleAlphacoronavirusandBetacoronaviruslineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases.
Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cell
Authors: Hérault Léonard , Poplineau Mathilde , Mazuel Adrien , Platet Nadine , Remy Élisabeth , Duprez Estelle
Published: June 2020

Hematopoietic stem cells (HSCs) are the guarantor of the proper functioning of hematopoiesis due to their incredible diversity of potential. During aging the heterogeneity of mouse HSCs evolves, which contributes to the deterioration of the immune system. Here we address the transcriptional plasticity of HSC upon aging at the single-cell resolution. Through the analysis of 15,000 young and aged transcriptomes, we reveal 15 clusters of HSCs unveiling rare and specific HSC abilities that change with age. Pseudotime ordering complemented with regulon analysis showed that the consecutive differentiation states of HSC are delayed upon aging. By analysing cell cycle at the single cell level we highlight an imbalance of cell cycle regulators of very immature aged HSC that may contribute to their accumulation in an undifferentiated state.

Our results therefore establish a reference map of young and old mouse HSC differentiation and reveal a potential mechanism that delay aged HSC differentiation.
First report of the sexual stage of the flax pathogenMycosphaerella linicolain France and its impact on pasmo epidemiology
Authors: Paumier Delphine , Bammé Blandine , Penaud Annette , Valade Romain , Suffert Frédéric
Published: June 2020

We performed a three-year field survey in France to characterize the dynamics of sexual reproduction inMycosphaerella linicola, the causal agent of pasmo, during the interepidemic period. Cohorts of fruiting bodies were sampled from linseed straw during the autumn and winter and carefully observed, focusing on pseudothecia, asci and ascospores. A sequence of experimental steps corresponding to Koch’s postulates confirmed in July 2014, for the first time in France and continental Europe, the widespread presence of the sexual stage ofM. linicolain plant host tissues. The developmental dynamics of pseudothecia on straw, expressed as the change over time in the percentage of mature pseudothecia, was similar in all three years. Pseudothecia appeared in late summer, with peak maturity reached in October. A temporal shift, thought to be due to early autumn rainfall, was highlighted in one of the three years. These observations suggest that sexual reproduction plays a significant role in the epidemiology of pasmo in France. A resurgence ofM. linicolainfections in spring flax is thought to have occurred in recent years, due to the increase in the area under flax. The presence of the sexual stage of this pathogen probably increased the quantitative impact of residues of winter linseed (used for oil) and flax straw (left on the soil for retting and used for fibers) as an interepidemic ‘brown bridge’. This case study highlights how certain parts of a disease cycle, in this case the sexual phase, can become crucial due to changes in production conditions.
Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors
Authors: Ding Pingtao , Sakai Toshiyuki , Shrestha Ram Krishna , Perez Nicolas Manosalva , Guo Wenbin , Ngou Bruno Pok Man , He Shengbo , Liu Chang , Feng Xiaoqi , Zhang Runxuan , Vandepoele Klaas , MacLean Dan , Jones Jonathan DG
Published: June 2020

Activation of cell Surface and Intracellular Receptor-Mediated Immunity (SRMI and IRMI) results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which SRMI and IRMI lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility; both SRMI and IRMI increase chromatin accessibility at induced defense genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by SRMI and IRMI, and by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanism between the two immune systems.
Nutritional status and fecundity are synchronised by muscular exopheresis
Authors: Turek Michał , Piechota Małgorzata , Banasiak Katarzyna , Shanmugam Nilesh , Macias Matylda , Śliwińska Małgorzata Alicja , Niklewicz Marta , Kowalski Konrad , Nowak Natalia , Chacińska Agnieszka , Pokrzywa Wojciech
Published: June 2020

Organismal functionality and reproduction depend on metabolic rewiring and balanced energy resources. However, the crosstalk between organismal homeostasis and fecundity, and the associated paracrine signaling mechanisms are still poorly understood. Using theCaenorhabditis eleganswe discovered that large extracellular vesicles termed exophers, attributed in neurons and cardiomyocytes to the removal of damaged subcellular components, are released by body wall muscles to support embryonic growth. We found that exopher formation (exopheresis) is a non-cell autonomous process regulated by egg formation in the uterus. Our data suggest that exophers serve as transporters for muscle-generated yolk proteins used for nourishing and improving the growth rate of the next generation. We propose that the primary role of muscular exopheresis is to stimulate the reproductive capacity, thereby influencing the adaptation of worm populations to the current environmental conditions.
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
Authors: Andújar C. , Creedy T. J. , Arribas P. , López H. , Salces-Castellano A. , Pérez-Delgado A. , Vogler A. P. , Emerson B. C.
Published: June 2020

Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of individuals in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets.metaMATErequires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mtDNA haplotypes) or non-authentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns.metaMATE(i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of non-authentic ASVs and the collateral effects on the removal of authentic ASVs. The output frommetaMATEfacilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in themetaMATEsoftware, available athttps://github.com/tjcreedy/metamate).
Comparative assessment of the effects of bumped kinase inhibitors on early zebrafish embryo development and pregnancy in mice
Authors: Anghel Nicoleta , Winzer Pablo A. , Imhof Dennis , Müller Joachim , Langa Javier , Rieder Jessica , Barrett Lynn K. , Vidadala Rama Subba Rao , Huang Wenlin , Choi Ryan , Hulverson Mathew A. , Whitman Grant R. , Arnold Samuel L. , Van Voorhis Wesley C. , Ojo Kayode K. , Maly Dustin J. , Fan Erkang , Hemphill Andrew
Published: June 2020

Bumped kinase inhibitors (BKIs) are effective against a variety of apicomplexan parasites. Fifteen BKIs with promisingin vitroefficacy againstNeospora caninumtachyzoites, low cytotoxicity in mammalian cells, and no toxic effects in non-pregnant BALB/c mice, were assessed in pregnant mice. Drugs were emulsified in corn oil and applied by gavage for 5 days. Five BKIs did not affect pregnancy, 5 BKIs exhibited 15-35% of neonatal mortality, and 5 compounds caused strong effects (infertility, abortion, stillbirth and pup mortality). Additionally, the impact of these compounds on zebrafish (Danio rerio) embryo development was assessed by exposing freshly fertilized eggs to 0.2-50μM of BKIs and microscopical monitoring of embryo development in a blinded manner during 4 days. We propose an algorithm that includes quantification of malformations and embryo deaths, and established a scoring system that allows to calculate an impact score (Si) that indicates at which concentrations BKIs visibly affect zebrafish embryo development. Comparison of the two models showed that for 9 compounds no clear correlation between Siand pregnancy outcome was visible. However, those 3 BKIs affecting zebrafish embryos only at high concentrations (40μM or higher) did not impair mouse pregnancy at all, and those 3 compounds that inhibited zebrafish embryo development already at 0.2μM showed detrimental effects in the pregnancy model. Thus, the zebrafish embryo development test has a limited predictive value to foresee pregnancy outcome in BKI-treated mice. We conclude, that maternal health-related factors such as cardiovascular, pharmacokinetic and/or bioavailability properties also contribute to BKI-pregnancy effects.
Novel mTORC1 inhibitors kill Glioblastoma stem cells
Authors: Sandoval Jose , Tomilov Alexey , Datta Sandipan , Allen Sonia , O’Donnell Robert , Angelastro James , Cortopassi Gino
Published: June 2020

Glioblastoma Multiforme (GBM) is an aggressive tumor of the brain, with an average post-diagnosis survival of 15 months. GBM stem cells (GBMSC) resist the standard-of-care therapy, temozolomide, and are considered a major contributor to tumor resistance. mTORC1 regulates cell proliferation and has been shown by others to have reduced activity in GBMSC. We recently identified a novel chemical series of human-safe piperazine-based brain-penetrant mTORC1-specific inhibitors. We assayed piperazine-mTOR binding strength by two biophysical measurements-- biolayer interferometry and field effect biosensing, and these confirmed each other and demonstrated a structure-activity relationship. Since mTORC1 is reduced in human GBMSC, and as mTORC1 inhibitors have been tested in previous GBM clinical trials, we tested the killing potency of the tightest-binding piperazines and observed these were potent GBMSC killers. GBMSCs are resistant to the standard-of-care temozolomide therapy--but temozolomide supplemented with tight-binding piperazine meclizine and flunarizine greatly enhanced GBMSC death over temozolomide alone. Lastly, we investigated IDH1-mutated GBMSC mutations that are known to affect mitochondrial and mTORC1 metabolism, the tight-binding Meclizine provoked ‘synthetic lethality’ in IDH1-mutant GBMSCs. These data tend to support a novel clinical strategy for GBM, i.e. the co-administration of meclizine or flunarizine as adjuvant therapy in the treatment of GBM, and IDH1-mutant GBM.
Life under quartz: Hypolithic mosses in the Mojave Desert
Authors: Ekwealor Jenna T. B. , Fisher Kirsten M.
Published: June 2020

Several species of dryland cyanobacteria are known to occur as hypoliths under semi-translucent rocks. In the Mojave Desert, these organisms find refuge from intense solar radiation under milky quartz where moisture persists for a longer period of time than in adjacent soil surface habitat. Desert mosses, which are extremely desiccation-tolerant, can also occur in these hypolithic spaces, though little is known about this unique moss microhabitat and how species composition compares to that of adjacent soil surface communities. To address this question, we deployed microclimate dataloggers and collected moss samples from under and adjacent to 18 milky quartz rocks (quartz mean center thickness 26 ± 15 mm) in a western high elevation Mojave Desert site. Light transmission through Mojave quartz rocks may be as low as 1.2%, and data from microclimate loggers deployed for five months support the hypothesis that quartz provides thermal buffering and higher relative humidity compared to the soil surface. Of the 53 samples collected from hypolith and surface microhabitats, 68% wereSyntrichia caninervis, the dominant bryophyte of the Mojave Desert biological soil crust.Tortula inermisaccounted for 28% of the samples and 4% wereBryum argenteum. In a comparison of moss community composition, we found thatS. caninerviswas more likely to be on the soil surface, though it was abundant in both microhabitats, whileT. inermiswas more restricted to hypoliths, perhaps due to protection from temperature extremes. In our study site, the differences between hypolithic and surface microhabitats enable niche partitioning betweenT. inermisandS. caninervis, enhancing alpha diversity. This work points to the need to thoroughly consider microhabitats when assessing bryophyte species diversity and modelling species distributions. This focus is particularly important in extreme environments, where mosses may find refuge from the prevailing macroclimatic conditions in microhabitats such as hypoliths.
Team flow is a unique brain state associated with enhanced information integration and neural synchrony
Authors: Shehata Mohammad , Cheng Miao , Leung Angus , Tsuchiya Naotsugu , Wu Daw-An , Tseng Chia-huei , Nakauchi Shigeki , Shimojo Shinsuke
Published: June 2020

Team flow occurs when a group of people reaches high task engagement while sharing a common goal as in sports teams and music bands. While team flow is a superior enjoyable experience to individuals experiencing flow or regular socialization, the neural basis for such superiority is still unclear. Here, we addressed this question utilizing a music rhythm task and electroencephalogram hyper-scanning. Experimental manipulations held the motor task constant while disrupted the hedonic musical correspondence to blocking flow or occluded the partner’s body and task feedback to block social interaction. The manipulations’ effectiveness was confirmed using psychometric ratings and an objective measure for the depth of flow experience through the inhibition of the auditory-evoked potential to a task-irrelevant stimulus. Spectral power analysis revealed higher beta/gamma power specific to team flow at the left temporal cortex. Causal interaction analysis revealed that the left temporal cortex receives information from areas encoding individual flow or socialization. The left temporal cortex was also significantly involved in integrated information at both the intra- and inter-brains levels. Moreover, team flow resulted in enhanced global inter-brain integrated information and neural synchrony. Thus, our report presents neural evidence that team flow results in a distinct brain state and suggests a neurocognitive mechanism by which the brain creates this unique experience.

Data Availability

All data and analysis codes used in the preparation of this article are available athttps://osf.io/3b4hp.
The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Authors: Cubuk Jasmine , Alston Jhullian J. , Incicco J. Jeremías , Singh Sukrit , Stuchell-Brereton Melissa D. , Ward Michael D. , Zimmerman Maxwell I. , Vithani Neha , Griffith Daniel , Wagoner Jason A. , Bowman Gregory R. , Hall Kathleen B. , Soranno Andrea , Holehouse Alex S.
Published: June 2020

The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
Membrane Insertion of MoS2Nanosheets: Fresh vs. Aged
Authors: Ye Rui , Song Wei , Gu Zonglin , Zhou Ruhong
Published: June 2020

Fresh two-dimensional (2D) molybdenum disulfide (MoS2) can absorb the hydrocarbon contamination from the ambient air and cause surface aging. Thus, understanding how the surface aging process of MoS2affects the interaction with biomolecules is crucial for its applications in the biomedical field. Here, we employed atomistic molecular dynamics simulations to investigate the interactions of fresh and aged MoS2nanosheets with POPE lipid membranes. Our results show that even though both the fresh and aged MoS2nanosheets are capable of spontaneous insertion into the POPE bilayer membrane, the fresh MoS2nanosheet displays significantly more robust interaction than the aged one. The potential mean force (PMF) calculations further confirm that the fresh MoS2nanosheet is more energetically favorable than the aged one in penetrating into the POPE lipid membranes, with the former having ~17 kJ/mol stronger binding affinity than the later. This work provides a deeper understanding of the surface-aging-dependent interaction of MoS2nanosheet with biomolecules, which might help the design of better MoS2-based nanodevices with appropriate surface properties.
Portieragives new clues on the evolutionary history of whiteflies
Authors: Santos-Garcia D. , Mestre-Rincon N. , Ouvrard D. , Zchori-Fein E. , Morin S.
Published: June 2020

Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. Their taxonomy is currently based on the morphology of nymphal stages that display phenotypic plasticity, which produces inconsistencies. To overcome this limitation, we developed a new phylogenetic framework that targets five genes ofCandidatusPortiera aleyrodidarum, the primary endosymbiont of whiteflies.Portieralineages have been co-diverging with whiteflies since their origin and therefore reflect their host evolutionary history. We also studied the origin of stability and instability inPortieragenomes by testing for the presence of two alternative gene rearrangements and the loss of a functional polymerase proofreading subunit (dnaQ), previously associated with genome instability. We present two phylogenetic reconstructions. One using the sequences of all five target genes from 22 whitefly species belonging to 17 genera. The second uses only two genes to include additional publishedPortierasequences of 21 whitefly species, increasing our sampling size to 42 species from 25 genera. The developed framework showed low signal saturation, specificity to whitefly samples, and efficiency in solving inter-genera relationships and standing inconsistencies in the current taxonomy of the superfamily. Genome instability was found to be present only in the Aleurolobini tribe containing theSinghiella, AleurolobusandBemisiagenera. This suggests thatPortieragenome instability likely arose in the Aleurolobini tribe’s common ancestor, around 70 Mya. We propose a link between the switch from multi-bacteriocyte to a single-bacteriocyte mode of inheritance in the Aleurolobini tribe and the appearance of genome instability inPortiera.
Conjugal DNA transfer in the maternally inherited symbiont of tsetse fliesSodalis glossinidius
Authors: Kendra Christopher G. , Keller Chelsea M. , Bruna Roberto E. , Pontes Mauricio H.
Published: June 2020

Stable associations between insects and bacterial species are widespread in nature. This is the case for many economically important insects, such as tsetse flies. Tsetse flies are the vectors ofTrypanosoma brucei, the etiological agent of African trypanosomiasis—a zoonotic disease that incurs a high socioeconomic cost in endemic regions. Populations of tsetse flies are often infected with the bacteriumSodalis glossinidius. Following infection,S. glossinidiusestablishes a chronic, stable association characterized by vertical (maternal) and horizontal (paternal) modes of transmission. Due to the stable nature of this association,S. glossinidiushas been long sought as a means for the implementation ofanti-Trypanosomaparatransgenesis in tsetse flies. However, the lack of tools for the genetic modification ofS. glossinidiushas hindered progress in this area. Here we establish thatS. glossinidiusis amenable to DNA uptake by conjugation. We show that conjugation can be used as a DNA delivery method to conduct forward and reverse genetic experiments in this bacterium. This study serves as an important step in the development of genetic tools forS. glossinidius. The methods highlighted here should guide the implementation of genetics for the study of the tsetse-Sodalisassociation and the evaluation ofS. glossinidius-based tsetse fly paratransgenesis strategies.

Importance

Tsetse flies are the insect vectors ofT. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost to a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacteriumS. glossinidiusto establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies allowingS. glossinidiusto spread and persist within populations. To this effect,S. glossinidiushas been considered as a potential expression platform to create flies which reduceT. bruceistasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation ofS. glossinidiushas remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulateS. glossinidiusfor future studies in reducing trypanosome transmission.
Reduced odor detection and hedonic changes in asymptomatic university students as SARS-CoV-2 emerged locally
Authors: Walsh-Messinger Julie , Kaouk Sahar , Manis Hannah , Kaye Rachel , Cecchi Guillermo , Meyer Pablo , Malaspina Dolores
Published: June 2020

Aerosol droplets have emerged as the primary mode of SARS-Cov-2 transmission and can be spread by infectious asymptomatic/pre-symptomatic persons rendering indicators of latent viral infection essential. Olfactory impairment is now a recognized symptom of COVID-19 and is rapidly becoming one of the most reliable indicators of the disease. We compared olfaction data from asymptomatic students, who were assessed as SARS-CoV-2 was unknowingly spreading locally, to students tested prior to the arrival of the virus. This study was naturalistic by design as testing occurred in the context of four research studies, all of which used the same inclusion/exclusion criteria and the same protocol to objectively assess odor detection, identification, and hedonics with physiological tests. Data from students (Cohort II; N=22) with probable SARS-CoV-2 exposure were compared to students tested just prior to local virus transmission (Cohort I; N=25), and a normative sample of students assessed over the previous four years (N=272). Students in Cohort II demonstrated significantly reduced odor detection sensitivity compared to students in Cohort I (t=2.60; P=.01; d=0.77; CI, 0.17, 1.36), with a distribution skewed towards reduced detection sensitivity (D=0.38; P=.005). Categorically, the exposed group was significantly more likely to have hyposmia (OR=7.74; CI, 3.1, 19.40), particularly the subgroup assessed in the final week before campus closure (OR=13.61; CI, 3.40, 35.66;). The exposed cohort also rated odors as less unpleasant (P<.001, CLES=0.77). A limitation of our study is that participants were not tested for COVID-19 as testing was unavailable in the area. Objective measures of olfaction may detect olfactory impairment in asymptomatic persons who are otherwise unaware of smell loss. The development of cost-effective, objective olfaction tests that could be self-administered regularly could aid in early detection of SARS-CoV-2 exposure, which is vital to combatting this pandemic.
In-depth virological assessment of kidney transplant recipients with COVID-19
Authors: Benotmane Ilies , Vargas Gabriela Gautier , Wendling Marie-Josée , Perrin Peggy , Velay Aurélie , Bassand Xavier , Bedo Dimitri , Baldacini Clement , Sagnard Mylene , Bozman Dogan-Firat , Chiesa Margaux Della , Solis Morgane , Gallais Floriane , Cognard Noëlle , Olagne Jerome , Delagreverie Héloïse , Gontard Louise , Panaget Baptiste , Marx David , Heibel Francoise , Braun Laura , Moulin Bruno , Caillard Sophie , Fafi-Kremer Samira
Published: June 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread widely, causing coronavirus disease 2019 (COVID-19) and significant mortality. However, data on viral loads and antibody kinetics in immunocompromised populations are lacking. We aimed to determine nasopharyngeal and plasma viral loads via RT-PCR and SARS-CoV-2 serology via ELISA and study their association with severe forms of COVID-19 and death in kidney transplant recipients. In this study we examined hospitalized kidney transplant recipients with non-severe (n = 21) and severe (n =19) COVID-19. SARS-CoV-2 nasopharyngeal and plasma viral load and serological response were evaluated based on outcomes and disease severity. Ten recipients (25%) displayed persistent viral shedding 30 days after symptom onset. The SARS-CoV-2 viral load of the upper respiratory tract was not associated with severe COVID-19, whereas the plasma viral load was associated with COVID-19 severity (p=0.0087) and mortality (p=0.024). All patients harbored antibodies the second week after symptom onset that persisted for two months. We conclude that plasma viral load is associated with COVID-19 morbidity and mortality, whereas nasopharyngeal viral load is not. SARS-CoV-2 shedding is prolonged in kidney transplant recipients and the humoral response to SARS-CoV-2 does not show significant impairment in this series of transplant recipients.
Safety-Critical Control of Active Interventions for COVID-19 Mitigation
Authors: Ames Aaron D. , Molnár Tamás G. , Singletary Andrew W. , Orosz Gábor
Published: June 2020

The world has recently undergone the most ambitious mitigation effort in a century1, consisting of wide-spread quarantines aimed at preventing the spread of COVID-192. The use of influential epidemiological models3–6 of COVID-19 helped to encourage decision makers to take drastic non-pharmaceutical interventions. Yet, inherent in these models are often assumptions that the active interventions are static, e.g., that social distancing is enforced until infections are minimized, which can lead to inaccurate predictions that are ever evolving as new data is assimilated. We present a methodology to dynamically guide the active intervention by shifting the focus from viewing epidemiological models as systems that evolve in autonomous fashion to control systems with an “input” that can be varied in time in order to change the evolution of the system. We show that a safety-critical control approach7 to COVID-19 mitigation gives active intervention policies that formally guarantee the safe evolution of compartmental epidemiological models. This perspective is applied to current US data on cases while taking into account reduction of mobility, and we find that it accurately describes the current trends when time delays8 associated with incubation and testing are incorporated. Optimal active intervention policies are synthesized to determine future mitigations necessary to bound infections, hospitalizations, and death, both at national and state levels. We therefore provide means in which to model and modulate active interventions with a view toward the phased reopenings that are currently beginning across the US and the world in a decentralized fashion. This framework can be converted into public policies, accounting for the fractured landscape of COVID-19 mitigation in a safety-critical fashion.
A novel comprehensive metric to assess COVID-19 testing outcomes: Effects of geography, government, and policy response
Authors: Kuster Anthony C. , Overgaard Hans J.
Published: June 2020

Testing and case identification are key strategies in controlling the COVID-19 pandemic. Contact tracing and isolation are only possible if cases have been identified. The effectiveness of testing must be tracked, but a single comprehensive metric is not available to assess testing effectiveness, and no timely estimates of case detection rate are available globally, making inter-country comparisons difficult. The purpose of this paper was to propose a single, comprehensive metric, called the COVID-19 Testing Index (CovTI) scaled from 0 to 100, that incorporated several testing metrics. The index was based on case-fatality rate, test positivity rate, active cases, and an estimate of the detection rate. It used parsimonious modeling to estimate the true total number of COVID-19 cases based on deaths, testing, health system capacity, and government transparency. Publicly reported data from 188 countries and territories were included in the index. Estimates of detection rates aligned with previous estimates in literature (R2=0.97). As of June 3, 2020, the states with the highest CovTI included Iceland, Australia, New Zealand, Hong Kong, and Thailand, and some island nations. Globally, CovTI increased from April 20 to June 3 but declined in ca. 10% of countries. Bivariate analyses showed the average in countries with open public testing policies (59.7, 95% CI 55.6-63.8) were significantly higher than countries with no testing policy (30.2, 95% CI 18.1-42.3) (p<0.0001). A multiple linear regression model assessed the association of independent grouping variables with CovTI. Open public testing and extensive contact tracing were shown to significantly increase CovTI, after adjusting for extrinsic factors, including geographic isolation and centralized forms of government. This tool may be useful for policymakers to assess testing effectiveness, inform decisions, and identify model countries. It may also serve as a tool for researchers in analyses by combining it with other databases.
Essential epidemiological parameters of COVID-19 for clinical and mathematical modeling purposes: a rapid review and meta-analysis
Authors: Fonfría Eva S. , Vigo María Isabel , García-García David , Herrador Zaida , Navarro Miriam , Bordehore Cesar
Published: June 2020

We present a literature review and meta-analysis of relevant epidemiological parameters (24 for adults, 7 for children) of COVID-19. Standardization of these parameters is key to performing valid clinical and mathematical modeling, as well as forecasts, helping us to improve our understanding about the characteristics and impact of the pandemic.
Health Implications of the Nutritional Status of Indian Adults
Authors: Chaurasia Aalok Ranjan
Published: June 2020

This paper analyses the nutritional status of around 630 thousand Indian adults aged 20-49 years on the basis of their body mass index (BMI) in the context of the implications for the health of adults. The analysis reveals that Indian adults can be divided into 15 mutually exclusive groups on the basis of their nutritional status and individual and household characteristics which has implications not only for health policy and planning but also for productivity and economic growth. The problem of under nourished adults appears to be quite challenging in the poor and the poorest adults of the country living in households without a toilet whereas the problem of over weight and obesity among adults has been found to be largely confined to rich and the richest adults living in the urban areas.
Transcriptional response of human articular chondrocytes treated with fibronectin fragments: anin vitromodel of the osteoarthritis phenotype
Authors: Reed Kathleen S. M. , Ulici Veronica , Kim Cheeho , Chubinskaya Susan , Loeser Richard F. , Phanstiel Douglas H.
Published: June 2020

Objective

Fibronectin is a matrix protein that is fragmented during cartilage degradation in osteoarthritis (OA). Treatment of chondrocytes with fibronectin fragments (FN-f) has been used to model OAin vitro, but the system has not been fully characterized. This study sought to define the transcriptional response of chondrocytes to FN-f, and directly compare it to responses traditionally observed in OA.

Design

Normal human femoral chondrocytes isolated from tissue donors were treated with either FN-f or PBS (control) for 3, 6, or 18 hours. RNA-seq libraries were compared between time-matched FN-f and control samples in order to identify changes in gene expression over time. Differentially expressed genes were compared to a published OA gene set and used for pathway, transcription factor motif, and kinome analysis.

Results

FN-f treatment resulted in 1,224 differentially expressed genes over the time course. Genes that are up- or downregulated in OA were significantly up- (p < 0.00001) or downregulated (p < 0.0004) in response to FN-f. Early response genes were involved in proinflammatory pathways and their promoters were enriched for NF-κB-related motifs, whereas many late response genes were involved in ferroptosis, and their promoters were enriched for Jun-related motifs. Highly upregulated kinases included CAMK1G, IRAK2, and the uncharacterized kinase DYRK3, while growth factor receptors TGFBR2 and FGFR2 were downregulated.

Conclusions

FN-f treatment of normal human articular chondrocytes recapitulated many key aspects of the OA chondrocyte phenotype. Thisin vitromodel is promising for future OA studies, especially considering its compatibility with genomics and genome-editing techniques.
Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR
Authors: Amos Sarah-Beth T. A. , Schwarz Thomas C. , Shi Jiye , Cossins Benjamin P. , Baker Terry S. , Taylor Richard J. , Konrat Robert , Sansom Mark S. P.
Published: June 2020

α-Synuclein is a presynaptic protein that binds to cell membranes and is linked to Parkinson’s disease (PD). Whilst the normal function of remains α-synuclein remains uncertain, it is thought that oligomerization of the protein on the cell membrane contributes to cell damage. Knowledge of how α-synuclein binds to lipid bilayers is therefore of great interest as a likely first step in the molecular pathophysiology of PD, and may provide insight of the phenotype of PD-promoting mutations. We use coarse-grained and atomistic simulations in conjunction with NMR and cross-linking mass spectrometry studies of α-synuclein bound to anionic lipid bilayers to reveal a break in the helical structure of the NAC region, which may give rise to subsequent oligomer formation. Coarse-grained simulations of α-synuclein show that the interhelical region leads recognition and binding to both POPG and mixed composition bilayers and identifies important protein-lipid contacts, including those in the region between the two helices in the folded structure. We extend these simulations with all-atom simulations of the initial binding event to reveal details of the time-progression of lipid binding. We present secondary structure analysis that reveals points of possible β-strand formation in the structure, and investigate intramolecular contacts with simulations and mass-spectrometry crosslinking. Additionally we show how Markov state models can be used to investigate possible conformational changes of membrane bound α-synuclein in the NAC region, and we extract representative structures. These structural insights will aid the design and development of novel therapeutic approaches.
The mitochondrial carrier SFXN1 is critical for Complex III integrity and cellular metabolism
Authors: Acoba Michelle Grace , Selen Alpergin Ebru S. , Renuse Santosh , Fernández-del-Río Lucía , Lu Ya-Wen , Clarke Catherine F. , Pandey Akhilesh , Wolfgang Michael J. , Claypool Steven M.
Published: June 2020

Mitochondrial carriers (MC) mediate the passage of small molecules across the inner mitochondrial membrane (IMM) enabling regulated crosstalk between compartmentalized reactions. Despite MCs representing the largest family of solute carriers in mammals, most have not been subjected to a comprehensive investigation, limiting our understanding of their metabolic contributions. Here, we functionally characterized SFXN1, a member of the non-canonical, sideroflexin MC family. We find that SFXN1, an integral membrane protein in the IMM with an uneven number of transmembrane domains, is a novel TIM22 substrate. SFXN1 deficiency specifically impairs Complex III (CIII) biogenesis, activity, and assembly, compromising coenzyme Q levels. This CIII dysfunction is independent of one-carbon metabolism, the known primary role for SFXN1 as a mitochondrial serine transporter. Instead, SFXN1 supports CIII function by participating in heme and central carbon metabolism. Our findings highlight the multiple ways that SFXN1-based amino acid transport impacts mitochondrial and cellular metabolic efficiency.
Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance
Authors: Dumonteil Eric , Herrera Claudia
Published: June 2020

The ongoing SARS-CoV-2 pandemic has triggered multiple efforts for serological tests and vaccine development. Most of these tests and vaccines are based on the Spike glycoprotein (S) or the Nucleocapsid (N) viral protein. Conservation of these antigens among viral strains is critical to ensure optimum diagnostic test performance and broad protective efficacy, respectively. We assessed N and S antigen diversity from 17,853 SARS-CoV-2 genome sequences and evaluated selection pressure. Up to 6-7 incipient phylogenetic clades were identified for both antigens, confirming early variants of the S antigen and identifying new ones. Significant diversifying selection was detected at multiple sites for both antigens. Some sequence variants have already spread in multiple regions, in spite of their low frequency. In conclusion, the N and S antigens of SARS-CoV-2 are well conserved antigens, but new clades are emerging and may need to be included in future diagnostic and vaccine formulations.
The role of trehalose 6-phosphate in shoot branching – local and non-local effects on axillary bud outgrowth in arabidopsis rosettes
Authors: Fichtner Franziska , Barbier Francois F. , Annunziata Maria G. , Feil Regina , Olas Justyna J. , Mueller-Roeber Bernd , Stitt Mark , Beveridge Christine A. , Lunn John E.
Published: June 2020

- Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood.

- We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds.

- TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous trehalose-6-phosphate phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression ofFLOWERING LOCUS T(FT)and up-regulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching inbranched1but not inftmutant backgrounds.

- These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT.
Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein
Authors: Toelzer Christine , Gupta Kapil , Yadav Sathish K.N. , Borucu Ufuk , Garzoni Frederic , Staufer Oskar , Capin Julien , Spatz Joachim , Fitzgerald Daniel , Berger Imre , Schaffitzel Christiane
Published: June 2020

COVID-19, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. Our cryo-EM structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains (RBDs) tightly and specifically bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The pocket also appears to be present in the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. Lipid metabolome remodeling is a key feature of coronavirus infection, with LA at its core. LA metabolic pathways are central to inflammation, immune modulation and membrane fluidity. Our structure directly links LA and S, setting the stage for interventions targeting LA binding and metabolic remodeling by SARS-CoV-2.

One Sentence Summary

A direct structural link between SARS-CoV-2 spike and linoleic acid, a key molecule in inflammation, immune modulation and membrane fluidity.