bluuebunny/crossref_metadata_2025 huggingface dataset:
How Efficacious Must a COVID-19 Coronavirus Vaccine be to Prevent or Stop an Epidemic by Itself
Authors: Bartsch Sarah M. , O’Shea Kelly J. , Ferguson Marie C. , Bottazzi Maria Elena , Cox Sarah N. , Strych Ulrich , McKinnell James A. , Wedlock Patrick T. , Siegmund Sheryl S. , Hotez Peter J. , Lee Bruce Y.
Published: May 2020

Background

Given the continuing coronavirus disease 2019 (COVID-19) pandemic and much of the U.S. implementing social distancing due to the lack of alternatives, there has been a push to develop a vaccine to eliminate the need for social distancing.

Methods

In 2020, we developed a computational model of the U.S. simulating the spread of COVID-19 coronavirus and vaccination.

Results

Simulation experiments revealed that when vaccine efficacy exceeded 70%, coverage exceeded 60%, and vaccination occurred on day 1, the attack rate dropped to 22% with daily cases not exceeding 3.2 million (reproductive rate, R0, 2.5). When R0 was 3.5, the attack rate dropped to 41% with daily cases not exceeding 14.4 million. Increasing coverage to 75% when vaccination occurred by day 90 resulted in 5% attack rate and daily cases not exceeding 258,029when R0 was 2.5 and a 26% attack rate and maximum daily cases of 22.6 million when R0 was 3.5. When vaccination did not occur until day 180, coverage (i.e., those vaccinated plus those otherwise immune) had to reach 100%. A vaccine with an efficacy between 40% and 70% could still obviate the need for other measures under certain circumstances such as much higher, and in some cases, potentially unachievable, vaccination coverages.

Conclusion

Our study found that to either prevent or largely extinguish an epidemic without any other measures (e.g., social distancing), the vaccine has to have an efficacy of at least 70%.
Mendelian randomization analysis to characterize causal association between coronary artery disease and COVID-19
Authors: Wu Lang , Zhu Jingjing , Wu Chong
Published: May 2020

Observational studies have suggested that having coronary artery disease increases the risk of Coronavirus disease 2019 (COVID-19) susceptibility and severity, but it remains unclear if this association is causal. Inferring causation is critical to facilitate the development of appropriate policies and/or individual decisions to reduce the incidence and burden of COVID-19. We applied Two-sample Mendelian randomization analysis and found that genetically predicted CAD was significantly associated with higher risk of COVID-19: the odds ratio was 1.29 (95% confidence interval 1.11 to 1.49; P = 0.001) per unit higher log odds of having CAD.
Intracortical Microstimulation Elicits Human Fingertip Sensations
Authors: Fifer Matthew S , McMullen David P , Thomas Tessy M , Osborn Luke E , Nickl Robert W , Candrea Daniel N , Pohlmeyer Eric A , Thompson Margaret C , Anaya Manuel , Schellekens Wouter , Ramsey Nick F , Bensmaia Sliman J , Anderson William S , Wester Brock A , Crone Nathan E , Celnik Pablo A , Cantarero Gabriela L , Tenore Francesco V
Published: May 2020

The restoration of cutaneous sensation to fingers and fingertips is critical to achieving dexterous prosthesis control for individuals with sensorimotor dysfunction. However, localized and reproducible fingertip sensations in humans have not been reported via intracortical microstimulation (ICMS) in humans. Here, we show that ICMS in a human participant was capable of eliciting percepts in 7 fingers spanning both hands, including 6 fingertip regions (i.e., 3 on each hand). Median percept size was estimated to include 1.40 finger or palmar segments (e.g., one segment being a fingertip or the section of upper palm below a finger). This was corroborated with a more sensitive manual marking technique where median percept size corresponded to roughly 120% of a fingertip segment. Percepts showed high intra-day consistency, including high performance (99%) on a blinded finger discrimination task. Across days, there was more variability in percepts, with 75.8% of trials containing the modal finger or palm region for the stimulated electrode. These results suggest that ICMS can enable the delivery of localized fingertip sensations during object manipulation by neuroprostheses.
Escape of TLR5 Recognition byLeptospira spp: A Rationale for Atypical Endoflagella
Authors: Holzapfel Marion , Bonhomme Delphine , Cagliero Julie , Vernel-Pauillac Frédérique , d’Andon Martine Fanton , Bortolussi Sophia , Fiette Laurence , Goarant Cyrille , Wunder Elsio A. , Picardeau Mathieu , Ko Albert I. , Werling Dirk , Matsui Mariko , Boneca Ivo G. , Werts Catherine
Published: May 2020

Leptospira interrogansare invasive bacteria responsible for leptospirosis, a worldwide zoonosis. They possess two periplasmic endoflagella that allow their motility.L. interrogansare stealth pathogens that escape the innate immune responses of the NOD-like receptors NOD1/2, and the human Toll-like receptor (TLR)4, sensing peptidoglycan and lipopolysaccharide (LPS), respectively. TLR5 is another receptor of bacterial cell wall components, recognizing flagellin subunits.

To study the contribution of TLR5 in the host defense against leptospires, we infected WT and TLR5 deficient mice with pathogenicL. interrogansand tracked the infection byin vivolive imaging of bioluminescent bacteria or by q-PCR. We did not identify any protective or inflammatory role of murine TLR5 to control pathogenicLeptospira. Likewise, subsequentin vitroexperiments showed that infections with different live strains ofL. interrogansandL. biflexadid not trigger TLR5. However, unexpectedly, heat-killed bacteria stimulated human and bovine TLR5, although barely mouse TLR5. Abolition of TLR5 recognition required extensive boiling time of the bacteria or proteinase K treatment, showing an unusual high stability of the leptospiral flagellins. Interestingly, using antimicrobial peptides to destabilize live leptospires, we detected some TLR5 activity, suggesting that TLR5 could participate in the fight against leptospires in humans or cattle. Using differentLeptospirastrains with mutations in flagellin proteins, we further showed that neither FlaAs nor Fcps participated in the recognition by TLR5, suggesting a role for the FlaBs. These have structural homology toSalmonellaFliC, and conserved residues important for TLR5 activation, as shown byin silicoanalyses. Accordingly, we found that leptospires regulate the expression of FlaB mRNA according to the growth phasein vitro, and that infection withL. interrogansin hamsters and in mice downregulated the expression of the FlaBs but not the FlaAs subunits.

Altogether, in contrast to different bacteria that modify their flagellin sequences to escape TLR5 recognition, our study suggests that the peculiar central localization and stability of the FlaB monomers in the periplasmic endoflagella, associated with the downregulation of FlaB subunits in hosts, constitute an efficient strategy of leptospires to escape TLR5 recognition and the immune response.
MRI-BASED DEEP LEARNING METHOD FOR DETERMINING METHYLATION STATUS OF THE O6-METHYLGUANINE–DNA METHYLTRANSFERASE PROMOTER OUTPERFORMS TISSUE BASED METHODS IN BRAIN GLIOMAS
Authors: Bangalore Yogananda Chandan Ganesh , Shah Bhavya R. , Nalawade Sahil S. , Murugesan Gowtham K. , Yu Frank F. , Pinho Marco C. , Wagner Benjamin C. , Mickey Bruce , Patel Toral R. , Fei Baowei , Madhuranthakam Ananth J. , Maldjian Joseph A.
Published: May 2020

PURPOSE

Methylation of the O6-Methylguanine-DNA Methyltransferase (MGMT) promoter results in epigenetic silencing of the MGMT enzyme and confers an improved prognosis and treatment response in gliomas. The purpose of this study was to develop a deep-learning network for determining the methylation status of the MGMT Promoter in gliomas using T2-w magnetic resonance images only.

METHODS

Brain MRI and corresponding genomic information were obtained for 247 subjects from The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA). 163 subjects had a methylated MGMT promoter. A T2-w image only network (MGMT-net) was developed to determine MGMT promoter methylation status and simultaneous single label tumor segmentation. The network was trained using 3D-Dense-UNets. Three-fold cross-validation was performed to generalize the networks’ performance. Dice-scores were computed to determine tumor segmentation accuracy.

RESULTS

MGMT-net demonstrated a mean cross validation accuracy of 94.73% across the 3 folds (95.12%, 93.98%, and 95.12%, standard dev=0.66) in predicting MGMT methylation status with a sensitivity and specificity of 96.31% ±0.04 and 91.66% ±2.06, respectively and a mean AUC of 0.93 ±0.01. The whole tumor segmentation mean Dice-score was 0.82 ± 0.008.

CONCLUSION

We demonstrate high classification accuracy in predicting the methylation status of the MGMT promoter using only T2-w MR images that surpasses the sensitivity, specificity, and accuracy of invasive histological methods such as pyrosequencing, methylation-specific PCR, and immunofluorescence methods. This represents an important milestone toward using MRI to predict glioma histology, prognosis, and response to treatment.
Phylogenetic analysis of migration, differentiation, and class switching in B cells
Authors: Hoehn Kenneth B. , Pybus Oliver G. , Kleinstein Steven H.
Published: May 2020

B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subsets, and switching between functional isotypes. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. To address this, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We use simulations to demonstrate the effectiveness of this approach. We then use this framework to infer patterns of cellular differentiation and isotype switching from high throughput BCR sequence datasets obtained from patients in a study of HIV infection and a study of food allergy. These methods are implemented in the R packagedowser, available athttps://bitbucket.org/kleinstein/dowser.

Author summary

B cells produce high affinity antibodies through an evolutionary process of mutation and selection during adaptive immune responses. Migration between tissues, differentiation to cellular subtypes, and switching between different antibody isotypes can be important factors in shaping the role B cells play in response to infection, autoimmune disease, and allergies. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. Here, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. Using simulations, we confirm the effectiveness of our approach, as well as identify some caveats. We further use these summary statistics to investigate patterns of cellular differentiation in three HIV patients, and patterns of isotype switching in an individual with food allergies. Our methods are released in the R packagedowser:https://bitbucket.org/kleinstein/dowser.
A high-quality genome assembly and annotation of the gray mangrove,Avicennia marina
Authors: Friis Guillermo , Vizueta Joel , Nelson David R. , Khraiwesh Basel , Qudeimat Enas , Salehi-Ashtiani Kourosh , Ortega Alejandra , Marshell Alyssa , Duarte Carlos M. , Burt John A.
Published: May 2020

The gray mangrove [Avicennia marina(Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome ofA. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188 bp long genome. The largest 32 scaffolds (22.4 Mb to 10.5 Mb) accounted for 98 % of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4 Kb to 1 Kb). We annotated 23,331 protein-coding genes using tissue-specific RNA-seq data, from which 13,312 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 92.3% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FSTsurvey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation, and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. OurA. marinagenomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.
PP2ARts1antagonizes Rck2-mediated hyperosmotic stress signaling in yeast
Authors: Hollenstein D. , Veis J. , Romanov N. , Gérecová G. , Ogris E. , Hartl M. , Ammerer G. , Reiter W.
Published: May 2020

InSaccharomyces cerevisiaeimpairment of protein phosphatase PP2ARts1leads to temperature and hyperosmotic stress sensitivity, yet the underlying mechanism and the scope of action of the phosphatase in the stress response remain elusive. Using quantitative mass spectrometry-based approaches we have identified a set of putative substrate proteins that show both, hyperosmotic stress- and PP2ARts1-dependent changes in their phosphorylation pattern. A comparative analysis with published MS-shotgun data revealed that the phosphorylation status of many of these sites is regulated by the MAPKAP kinase Rck2, suggesting a node of regulation. Detailed gel mobility shift assays and protein-protein interaction analysis strongly suggest that Rck2 activity is directly regulated by PP2ARts1via a SLiM B56-family interaction motif, uncovering a previously unknown mechanism of how PP2A influences the response to hyperosmotic stress in Yeast.
The ubiquitin ligase Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles
Authors: Fajner Valentina , Giavazzi Fabio , Sala Simona , Oldani Amanda , Martini Emanuele , Napoletano Francesco , Parazzoli Dario , Cerbino Roberto , Maspero Elena , Vaccari Thomas , Polo Simona
Published: May 2020

Specialised ribonucleoprotein (RNP) granules are a hallmark of germ cells. Among their main function is the spatial and temporal modulation of the activity of specific mRNA transcripts that allow specification of primary embryonic axes. While RNPs composition and role are well established, their regulation is poorly defined. Here, we demonstrate that Hecw, a newly identifiedDrosophilaubiquitin ligase, is a key modulator of RNPs in oogenesis. Loss of Hecw activity results in the formation of enlarged granules that transition from a liquid to a gel-like state. At the molecular level, Hecw depletion leads to reduced ubiquitination and activity of the translational repressor Fmrp, resulting in premature Orb expression/recruitment in nurse cells. In addition to defective oogenesis, flies lacking Hecw show neurodegenerative traits with premature aging and climbing defects due to neuronal loss that are linked to RNPs condensation. Our findings reveal an unprecedented function of ubiquitin in modulating RNP fluidity and activity.
Herpes Simplex Virus type 1 neuronal infection triggers disassembly of key structural components of dendritic spines
Authors: Acuña-Hinrichsen Francisca , Covarrubias-Pinto Adriana , Ishizuka Yuta , Stolzenbach Maria Francisca , Martin Carolina , Salazar Paula , Castro Maite A. , Bramham Clive , Otth Carola
Published: May 2020

Herpes simplex virus type 1 (HSV-1) is a widespread neurotropic virus. The primary infection in facial epithelium leads to retrograde axonal transport to the central nervous system (CNS) where it establishes latency. Under stressful conditions, the virus reactivates, and new progeny is transported anterogradely to the primary site of infection. In late stages of neuronal infection, axonal damage is known to occur. However, the impact of HSV-1 infection on morphology and functional integrity at earlier stages of infection in neuronal dendrites is unknown. Previously, we demonstrated that acute HSV-1 infection in neuronal cell lines selectively enhances the expression of Arc protein - a major regulator of long-term synaptic plasticity and memory consolidation, known for being a protein-interaction hub in the postsynaptic dendritic compartment. Thus, HSV-1 induced Arc may alter the functionality of the infected neurons having an impact on dendritic spine dynamics. In this study we demonstrated that HSV-1 infection causes structural disassembly and functional deregulation in cultured cortical neurons, through protein homeostasis alteration with intracellular accumulation of Arc, and decreased expression of spine scaffolding-like proteins such as PSD-95, Drebrin and CaMKIIβ. Our findings reveal progressive deleterious effects of HSV-1 infection on excitatory neuronal synapse function and dendritic morphology, supporting the thesis of the infectious origin of neurodegenerative processes.
Dynamin-2 regulates synaptic podosome maturation to facilitate neuromuscular junction development
Authors: Lin Shan-Shan , Hsieh Tsung-Lin , Liou Gunn-Guang , Li Tsai-Ning , Lin Hsin-Chieh , Chang Chiung-Wen , Wu Hsiang-Yi , Yao Chi-Kuang , Liu Ya-Wen
Published: May 2020

Neuromuscular junctions (NMJs) govern rapid and efficient neuronal communication with muscle cells, which relies on the proper architecture of specialized postsynaptic compartments. However, the intrinsic mechanism in muscle cells contributing to elaborate NMJ development has been unclear. In this study, we reveal that the GTPase dynamin-2 (Dyn2), best-known for catalyzing synaptic vesicle endocytosis at the presynaptic membrane, is also involved in postsynaptic morphogenesis. We demonstrate that Dyn2 is enriched in the postsynaptic membrane of muscle cells and is involved in the maturation of neurotransmitter receptor clusters via its actin bundling ability. Dyn2 functions as a molecular girdle to regulate synaptic podosome turnover and promote morphogenesis of the postsynaptic apparatus. InDrosophilaNMJs, Dyn2 is required to organize the postsynaptic actin cytoskeleton and to mediate its electrophysiological activities. Mechanistically, the actin binding, self-assembly, GTP hydrolysis ability, and Y597 phosphorylation of Dyn2 all regulate its actin bundling activity. Together, our study uncovers a role for Dyn2 in cytoskeleton remodeling and organization at the postsynaptic membrane of NMJs.
Large ribosomal subunit, eIF5B, Met-tRNAiMetand mRNA cooperate to complete accurate initiation
Authors: Wang Jinfan , Wang Jing , Shin Byung-Sik , Dever Thomas E. , Puglisi Joseph D. , Fernández Israel S.
Published: May 2020

Recognition of a start codon by the first aminoacyl-tRNA (Met-tRNAiMet) determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of Met-tRNAiMeton the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determined the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMetimmediately before transition into elongation. The structure uncovered an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.

One sentence summary

CryoEM structure of a naturally long-lived translation initiation intermediate with Met-tRNAiMetand eIF5B post GTP hydrolysis.
PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix
Authors: Kay Emily J , Paterson Karla , Domingo Carla Riero , Sumpton David , Daebritz Henry , Tardito Saverio , Boldrini Claudia , Hernandez-Fernaud Juan R , Athineos Dimitris , Dhayade Sandeep , Stepanova Ekaterina , Gjerga Enio , Neilson Lisa J , Lilla Sergio , Hedley Ann , Koulouras Grigorios , McGregor Grace , Jamieson Craig , Johnson Radia Marie , Park Morag , Kirschner Kristina , Miller Crispin , Kamphorst Jurre J , Loayza-Puch Fabricio , Saez-Rodriguez Julio , Mazzone Massimiliano , Blyth Karen , Zagnoni Michele , Zanivan Sara
Published: May 2020

TElevated production of collagen-rich extracellular matrix (ECM) is a hallmark of cancer associated fibroblasts (CAFs) and a central driver of cancer aggressiveness. How to target ECM production to oppose cancer is yet unclear, since targeting CAFs has been shown to restrain but also promote cancer progression. Metabolic rewiring is a hallmark of CAFs. Here we find that proline, which is a highly abundant amino acid in collagen proteins, is newly synthesised from glutamine to make tumour collagen in breast cancer xenografts, and that its production is elevated in breast cancer CAFs. PYCR1 is the rate-limiting enzyme for proline synthesis and is highly expressed in the tumour stroma of breast cancer patients and in CAFs. Reducing PYCR1 levels in CAFs is sufficient to reduce tumour collagen production, tumour growth and metastatic spread in vivo and cancer cell proliferation in vitro. PYCR1 and COL1A1 are overexpressed in patients with invasive ductal carcinoma with poor prognosis. Both collagen and glutamine-derived proline synthesis in CAFs are enhanced by increased pyruvate dehydrogenase-derived acetyl-CoA levels, via gene expression regulation through the epigenetic regulator histone acetyl transferase EP300. Altogether, our work unveils unprecedented roles of CAF metabolism to support pro-tumorigenic collagen production. PYCR1 is a recognised cancer cell vulnerability and potential target for therapy, hence, our work provides evidence that targeting PYCR1 in tumours may have the additional benefit of halting the production of pro-tumorigenic ECM.
Stagewise identification of significantly mutated and dysregulated gene clusters in major molecular classes of breast invasive carcinoma
Authors: Agarwal Shivangi , Naik Sanoj , Kumari Pratima , Mishra Sandip K. , Adhya Amit K. , Kashaw Sushil K. , Dixit Anshuman
Published: May 2020

Breast invasive carcinoma (BRCA) is most malignant and leading cause of death in women. The efforts are ongoing for improvement in early detection, prevention and treatment. Therefore, identification of biomarkers/candidate genes has become very important. The current work includes comprehensive analysis of RNA-sequencing data of 1097 BRCA samples and 114 normal adjacent tissues to identify dysregulated genes in major molecular classes of BRCA in various clinical stages. Huge number of dysregulated genes were found, some were stage-specific, and others were common. The pathways as interferon signaling, tryptophan degradation III, granulocyte adhesion & diapedesis and catecholamine biosynthesis were found in ER/PR+/HER-2- (p-value<0.010), pathways as RAR activation, adipogenesis, role of JAK1, JAK2 in interferon signaling, TGF-ß and STAT3 signaling (p-value<0.014) intricated in ER/PR-/HER-2+ and pathways as IL-1/IL-8 signaling, TNFR1/TNFR2 signaling, TWEAK and relaxin signaling (p-value<0.005) were found in triple negative breast cancer. The genes were clustered based on their mutation profile which revealed nine mutated clusters, some of which were known to be involved in well-known cancer signalling pathways while others were less characterized. Each cluster was analyzed in detail which led us to discover genes viz. NLGN3, MAML2, TTN, SYNE1, ANK2 as candidates in BRCA. The genes were found to be involved in important processes as chemotaxis, axon guidance, notch binding, cell-adhesion-molecule binding etc. They are central genes in the protein-protein-interaction network indicating they can have important regulatory roles. The qRT-PCR and western blot confirmed our findings in breast cancer cell-lines. Further, immunohistochemistry corroborated the results in ~100 tissue samples. The genes can be used as biomarker in BRCA.
Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast
Authors: Muraszko Jakub , Argunhan Bilge , Ito Kentaro , Baranowska Gabriela , Barg-Wojas Anna , Kramarz Karol , Kurokawa Yumiko , Iwasaki Hiroshi , Dziadkowiec Dorota
Published: May 2020

Rad51 is the key protein in homologous recombination DNA repair and has important roles during DNA replication. Auxiliary factors regulate Rad51 activity to facilitate productive, and prevent inappropriate, recombination that could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in counteracting Rad51 activity, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 activity in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 activity. Additionally, we demonstrate that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
Stop codon readthrough of a POU transcription factor regulates steroidogenesis and developmental transitions
Authors: Zhao Yunpo , Lindberg Bo Gustav , Esfahani Shiva Seyedoleslami , Tang Xiongzhuo , Piazza Stefano , Engström Ylva
Published: May 2020

Translational stop codon readthrough generates C-terminally extended protein isoforms. While evidence mounts of readthrough as a global phenomenon, proofs of its functional consequences are scarce. We show that readthrough of the mRNA for theDrosophilaPOU/Oct transcription factor Drifter occurs at a high rate and in a spatiotemporal mannerin vivo, reaching above 50% in the prothoracic gland. Phylogenetic analyses suggested that readthrough ofdrifteris conserved among Dipterans, with C-terminal extensions harboring intrinsically disordered regions, and amino acids streches implied in transcriptional activation. The C-terminally extended Drifter isoform is required for maintaining normal levels of the growth hormone ecdysone through regulation of its biosynthetic genes, acting in synergy with the transcription factor Molting defective. A 14-bp deletion that abolished readthrough, caused prolonged larval development and delayed metamorphosis. This study provides a striking example of alternative genetic decoding that feeds into the progression from one life cycle stage to another.
UDP-Glucose 6-Dehydrogenase Knockout Impairs Migration and Decreasesin vivoMetastatic Ability of Breast Cancer Cells
Authors: Teoh Shao Thing , Ogrodzinski Martin P. , Lunt Sophia Y.
Published: May 2020

Dysregulated metabolism is a hallmark of cancer that supports tumor growth and metastasis. One understudied aspect of cancer metabolism is altered nucleotide sugar biosynthesis, which drives aberrant cell surface glycosylation known to support various aspects of cancer cell behavior including migration and signaling. We examined clinical association of nucleotide sugar pathway gene expression and found thatUGDH, encoding UDP-glucose 6-dehydrogenase which catalyzes production of UDP-glucuronate, is associated with worse breast cancer patient survival. Knocking out the mouse homologUgdhin highly-metastatic 6DT1 breast cancer cells impaired migration ability without affectingin vitroproliferation. Further,Ugdh-KOresulted in significantly decreased metastatic capacityin vivowhen the cells were orthotopically injected in syngeneic mice. Our experiments show that UDP-glucuronate biosynthesis is critical for metastasis in a mouse model of breast cancer.
Interactions between the microbiome and mating influence the female’s transcriptional profile inDrosophila melanogaster
Authors: Delbare Sofie Y. N. , Ahmed-Braimah Yasir H. , Wolfner Mariana F. , Clark Andrew G.
Published: May 2020

Drosophila melanogasterfemales undergo a variety of post-mating changes that influence their activity, feeding behavior, metabolism, egg production and gene expression. These changes are induced either by mating itself or by sperm or seminal fluid proteins. In addition, studies have shown that axenic females—those lacking a microbiome—have altered fecundity compared to females with a microbiome, and that the microbiome of the female’s mate can influence reproductive success. However, the extent to which post-mating changes in transcript abundance are affected by microbiome state is not well-characterized. Here we investigated fecundity and the post-mating transcript abundance profile of axenic or control females after mating with either axenic or control males. We observed interactions between the female’s microbiome and her mating status: transcripts of genes involved in reproduction and genes with neuronal functions were differentially abundant depending on the females’ microbiome status, but only in mated females. In addition, immunity genes showed varied responses to either the microbiome, mating, or a combination of those two factors. We further observed that the male’s microbiome status influences the fecundity of both control and axenic females, while only influencing the transcriptional profile of axenic females. Our results indicate that the microbiome plays a vital role in the post-mating switch of the female’s transcriptome.
Lmo7a Coordinates Neural Crest Migration and Lineage Specification by Regulating Cell Adhesion Dynamics
Authors: Tatarakis David , Tuttle Adam , Schilling Thomas F.
Published: May 2020

Cell migration requires dynamic regulation of cell-cell signaling and cell adhesion. Neural crest (NC) cells are highly migratory cells, which undergo an epithelial-mesenchymal transition (EMT) to leave the neural epithelium and migrate throughout the body to give rise to many different derivatives. We have identified a Lim-domain only (Lmo) protein, Lmo7a, expressed in early NC cells that controls both actin cytoskeletal dynamics and Wnt signaling during NC migration. In embryos deficient in Lmo7a, many NC cells fail to migrate away from the dorsal midline, and form aggregates. Unlike the majority of NC cells that appear to migrate normally, cells that aggregate in Lmo7a-deficient embryos mislocalize paxillin (Pxn) and have reduced levels of phosphorylated focal adhesion kinase (pFAK). Lmo7a loss-of-function also disrupts canonical Wnt signaling such that after the onset of NC cell migration, Wnt responses and nuclear β-catenin levels increase in the cells that aggregate. However, this increase in Wnt signaling appears secondary to the defect in migration. Similar to mutants for other Wnt regulators in NC cells, the NC cells in Lmo7a-deficient aggregates exhibit gene expression signatures of pigment cell progenitors, but also express markers of Schwann cell progenitors, suggesting a role for Lmo7a in pigment-glial specification. We propose that Lmo7a modulates cell adhesion to facilitate both robust NC cell migration and a subset of lineage decisions.
How the brain negotiates divergent executive processing demands: Evidence of network reorganization during fleeting brain states
Authors: Liu Mengting , Backer Robert A. , Amey Rachel C. , Forbes Chad E.
Published: May 2020

During performance in everyday contexts, multiple networks draw from shared executive resources to maintain attention, regulate arousal, and problem solve. At times, requirements for attention and self-regulation appear to be in competition for a “limited pool” of resources. How does the brain attempt to resolve conflicts arising from multiple processing demands? In the present study, participants were exposed to either a stress or control prime, after which electroencephalographic (EEG) activity was recorded as they solved math problems. Phase-locking was examined within four networks implicated in math-solving and evaluative stress: frontopareital (FP), default mode (DM), emotion generation (EG), and emotion regulation (ER) networks. Findings revealed differing strategies, depending on the presence of stress: states dominated by frontopareital and emotion regulation network dynamics supported optimum performance generally, while during stress, states dominated by emotion regulation and default mode networks are more important for performance. Implications for networks’ cooperative dynamics and DMN’s role in coping are considered.
Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes
Authors: Hsieh Ching-Lin , Goldsmith Jory A. , Schaub Jeffrey M. , DiVenere Andrea M. , Kuo Hung-Che , Javanmardi Kamyab , Le Kevin C. , Wrapp Daniel , Lee Alison Gene-Wei , Liu Yutong , Chou Chia-Wei , Byrne Patrick O. , Hjorth Christy K. , Johnson Nicole V. , Ludes-Meyers John , Nguyen Annalee W. , Park Juyeon , Wang Nianshuang , Amengor Dzifa , Maynard Jennifer A. , Finkelstein Ilya J. , McLellan Jason S.
Published: May 2020

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has led to accelerated efforts to develop therapeutics, diagnostics, and vaccines to mitigate this public health emergency. A key target of these efforts is the spike (S) protein, a large trimeric class I fusion protein that is metastable and difficult to produce recombinantly in large quantities. Here, we designed and expressed over 100 structure-guided spike variants based upon a previously determined cryo-EM structure of the prefusion SARS-CoV-2 spike. Biochemical, biophysical and structural characterization of these variants identified numerous individual substitutions that increased protein yields and stability. The best variant, HexaPro, has six beneficial proline substitutions leading to ∼10-fold higher expression than its parental construct and is able to withstand heat stress, storage at room temperature, and multiple freeze-thaws. A 3.2 Å-resolution cryo-EM structure of HexaPro confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for SARS-CoV-2.
Natural-abundance17O NMR spectroscopy of magnetically aligned lipid nanodiscs
Authors: Ravula Thirupathi , Sahoo Bikash , Dai Xiaofeng , Ramamoorthy Ayyalusamy
Published: May 2020

Natural-abundance17O NMR experiments are used to investigate the hydrated water in magnetically alligned synthetic polymer based lipid-nanodiscs. Residual quadrupole couplings (RQCs) measured from the observed five17O (central and satellite) transitions, and molecular dynamics simulations, are used to probe the ordering of water moecules across the lipid bilayer.
Threshold assessment, categorical perception, and the evolution of reliable signaling
Authors: Peniston James H. , Green Patrick A. , Zipple Matthew N. , Nowicki Stephen
Published: May 2020

Animals often use assessment signals to communicate information about their quality to a variety of receivers, including potential mates, competitors, and predators. But what maintains reliable signaling and prevents signalers from signaling a better quality than they actually have? Previous work has shown that reliable signaling can be maintained if signalers pay fitness costs for signaling at different intensities and these costs are greater for lower quality individuals than higher quality ones. Models supporting this idea typically assume that continuous variation in signal intensity is perceived as such by receivers. In many organisms, however, receivers have threshold responses to signals, in which they respond to a signal if it is above a threshold value and do not respond if the signal is below the threshold value. Here, we use both analytical and individual-based models to investigate how such threshold responses affect the reliability of assessment signals. We show that reliable signaling systems can break down when receivers have an invariant threshold response, but reliable signaling can be rescued if there is variation among receivers in the location of their threshold boundary. Our models provide an important step towards understanding signal evolution when receivers have threshold responses to continuous signal variation.
Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier
Authors: Kim Eiru , Hart Traver
Published: May 2020

Identifying essential genes in genome-wide loss of function screens is a critical step in functional genomics and cancer target finding. We previously described the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm for accurate classification of gene essentiality from short hairpin RNA and CRISPR/Cas9 genome wide genetic screens. Here, we introduce an updated version, BAGEL2, which employs an improved model that offers greater dynamic range of Bayes Factors, enabling detection of tumor suppressor genes, and a multi-target correction that reduces false positives from off-target CRISPR guide RNA. We also suggest a metric for screen quality at the replicate level and demonstrate how different algorithms handle lower-quality data in substantially different ways. BAGEL2 is written in Python 3 and source code, along with all supporting files, are available on github (https://github.com/hart-lab/bagel).
Structure-aided development of small molecule inhibitors of ENPP1, the extracellular phosphodiesterase of the immunotransmitter cGAMP
Authors: Carozza Jacqueline A , Brown Jenifer A. , Böhnert Volker , Fernandez Daniel , AlSaif Yasmeen , Mardjuki Rachel E. , Smith Mark , Li Lingyin
Published: May 2020

Cancer cells initiate an innate immune response by synthesizing and exporting the small molecule immunotransmitter cGAMP, which activates the anti-cancer Stimulator of Interferon Genes (STING) pathway in the host. An extracellular enzyme, ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1), hydrolyzes cGAMP and negatively regulates this anti-cancer immune response. Small molecule ENPP1 inhibitors are much needed as tools to study basic biology of extracellular cGAMP and as investigational cancer immunotherapy drugs. Here, we surveyed structure-activity relationships around a series of cell-impermeable and thus extracellular-targeting phosphonate inhibitors of ENPP1. Additionally, we solved the crystal structure of an exemplary phosphonate inhibitor to elucidate the interactions that drive potency. This study yielded several best-in-class compounds withKi< 2 nM and excellent physicochemical and pharmacokinetic properties. Finally, we demonstrate that an ENPP1 inhibitor delays tumor growth in a breast cancer mouse model. Together, we have developed ENPP1 inhibitors that are excellent tool compounds and potential therapeutics.
Patterns of speciation are similar across mountainous and lowland regions for a Neotropical plant radiation (Costaceae:Costus)
Authors: Vargas Oscar M. , Goldston Brittany , Grossenbacher Dena L. , Kay Kathleen M.
Published: May 2020

High species richness and endemism in tropical mountains are recognized as major contributors to the latitudinal diversity gradient. The processes underlying mountain speciation, however, are largely untested. The prevalence of steep ecogeographic gradients and the geographic isolation of populations by topographic features are predicted to promote speciation in mountains. We evaluate these processes in a species-rich Neotropical genus of understory herbs that range from the lowlands to montane forests and have higher species richness in topographically complex regions. We ask whether climatic niche divergence, geographic isolation, and pollination shifts differ between mountain-influenced and lowland Amazonian sister pairs inferred from a 756-gene phylogeny. NeotropicalCostusancestors diverged in Central America during a period of mountain formation in the last 3 My with later colonization of Amazonia. Although climatic divergence, geographic isolation, and pollination shifts are prevalent in general, these factors don’t differ between mountain-influenced and Amazonian sister pairs. Despite higher climatic niche and species diversity in the mountains, speciation modes inCostusappear similar across regions. Thus, greater species richness in tropical mountains may reflect differences in colonization history, diversification rates, or the prevalence of rapidly evolving plant life forms, rather than differences in speciation mode.
Deforestation and bird habitat loss in Colombia
Authors: Negret Pablo Jose , Maron Martine , Fuller Richard A. , Possingham Hugh P. , Watson James E.M. , Simmonds Jeremy S.
Published: May 2020

Tropical forests harbor most of the planet’s terrestrial biodiversity, and their loss means destruction of habitat for many species. Tropical deforestation continues at high rates in many regions, but it is often reported only in terms of area lost or its impacts on high-profile threatened species. We estimated the impact of both past and projected future deforestation on habitat extent for the entire assemblage of forest-dependent birds across Colombia, the country with more bird species than any other. Of the 550 forest-dependent species analysed, Almost all (n=536; 96.5%) had lost habitat, and 18% had lost at least half of their habitat by 2015. We used the recently developed Loss Index (LI) to capture the severity of habitat loss for the forest bird assemblage, discovering that the current LI for Colombia is 35, which means 35% of bird species have lost at least 35% of their habitat. The national LI for Colombia is projected to rise to 43 by 2040 if recent forest loss trends continue. There were large regional differences; Caribe had an LI of 82 while for the Pacific it was 14. A threat assessment for the regionally endemic species in the country showed that 12 (30%) of the species that are projected to lose 50% or more of their historical habitat by 2040 are not currently classified as threatened by the IUCN, suggesting that there are many species that are not listed but that face an imminent extinction threat from habitat loss. This extensive habitat depletion affecting entire species assemblages has significant implications for tropical forest ecosystems, and risks eroding ecosystem function and ecosystem service provision.
EasyCOV : LAMP based rapid detection of SARS-CoV-2 in saliva
Authors: L’Helgouach Nicolas , Champigneux Pierre , Schneider Francisco Santos , Molina Laurence , Espeut Julien , Alali Mellis , Baptiste Julie , Cardeur Lise , Dubuc Benjamin , Foulongne Vincent , Galtier Florence , Makinson Alain , Marin Grégory , Picot Marie-Christine , Prieux-Lejeune Alexandra , Quenot Marine , Robles Francisco Checa , Salvetat Nicolas , Vetter Diana , Reynes Jacques , Molina Franck
Published: May 2020

Covid-19 crisis showed us that rapid massive virus detection campaign is a key element in SARS-CoV-2 pandemic response. The classical RT-PCR laboratory platforms must be complemented with rapid and simplified technologies to enhance efficiency of large testing strategies.

To this aim, we developed EasyCOV, a direct saliva RT-LAMP based SARS-CoV-2 virus detection assay that do not requires any RNA extraction step. It allows robust and rapid response under safe and easy conditions for healthcare workers and patients.

EasyCOV test was assessed under double blind clinical conditions (93 asymptomatic healthcare worker volonteers, 10 actively infected patients, 20 former infected patients tested during late control visit). EasyCOV results were compared with classical laboratory RT-PCR performed on nasopharyngeal samples.

Our results show that compared with nasopharyngeal laboratory RT-PCR, EasyCOV SARS-CoV-2 detection test has a sensitivity of 72.7%. Measured on healthcare worker population the specificity was 95.7%. LAMP technology on saliva is clearly able to identify subjects with infectivity profile. Among healthcare worker population EasyCOV test detected one presymptomatic subject.

Because it is simple, rapid and painless for patients, EasyCOV saliva SARS-Cov-2 detection test may be useful for large screening of general population.
SIGLEC5: An immune checkpoint ligand in sepsis
Authors: Lozano-Rodríguez Roberto , Avendaño-Ortíz José , Montalbán-Hernández Karla , Ruiz-Rodríguez Juan Carlos , Ferrer Ricardo , Martín-Quirós Alejandro , Maroun-Eid Charbel , González-López Juan José , Fàbrega Anna , Terrón Verónica , Fresno Carlos del , Toledano Víctor , Marín Elvira , Guitiérrez-Fernández María , Alonso-López Elisa , Cubillos-Zapata Carolina , Stringa Pablo , Pérez de Diego Rebeca , Pelegrin Pablo , García-Palenciano Carlos , Valentín Jaime , Gómez-Campelo Paloma , Aguirre Luis A. , López-Collazo Eduardo
Published: May 2020

Sepsis is a global health priority. Despite thorough studies in mice models, its molecular and cellular basis remain unclear and there is no pharmacological effective treatment other than antimicrobial and supportive therapy. During sepsis, T cells exhaustion compromises patients’ outcome, and immune checkpoints (ICs) become crucial players in disease management. Here, a total of 425 patients with systemic inflammatory response criteria and 127 controls were studied. Soluble SIGLEC5 (sSIGLEC5) levels in plasma were higher in patients with sepsis compared to the other groups and even higher in those patients with septic-shock. sSIGLEC5 plasma levels were higher in non-survivors than in survivors and ROC curves analysis revealed sSIGLEC5 as a survival marker (cut-off ≤ 523.6 ng/mL). In vitro experiments illustrated how SIGLEC5 impaired CD8+ proliferation through binding to PSGL1. Blocking the SIGLEC5/PSGL1 axis reverted the latter effect. Mechanistically, SIGLEC5 overexpression was driven by HIF1α. Exogenous sSIGLEC5 accelerated death and magnified acute lung injury in mice models. Our data demonstrates how plasma sSIGLEC5 level on admission predicts death and stratifies patients with sepsis. This molecule exhibits the hallmarks of an IC ligand.