bluuebunny/crossref_metadata_2025 huggingface dataset:
Heightened resistance to type 1 interferons characterizes HIV-1 at transmission and following analytical treatment interruption
Authors: Gondim Marcos V. P. , Sherrill-Mix Scott , Bibollet-Ruche Frederic , Russell Ronnie M. , Trimboli Stephanie , Smith Andrew G. , Li Yingying , Liu Weimin , Avitto Alexa N. , DeVoto Julia , Connell Jesse , Fenton-May Angharad E. , Pellegrino Pierre , Williams Ian , Papasavvas Emmanouil , Lorenzi Julio C. C. , Salantes D. Brenda , Mampe Felicity , Monroy M. Alexandra , Cohen Yehuda Z. , Heath Sonya , Saag Michael S. , Montaner Luis J. , Collman Ronald G. , Siliciano Janet M. , Siliciano Robert F. , Plenderleith Lindsey , Sharp Paul M. , Caskey Marina , Nussenzweig Michel C. , Shaw George M. , Borrow Persephone , Bar Katharine J. , Hahn Beatrice H.
Published: August 2020

Type 1 interferons (IFN-I) are potent innate antiviral effectors that constrain HIV-1 transmission. However, harnessing these cytokines for HIV-1 cure strategies has been hampered by an incomplete understanding of their anti-viral activities at later stages of infection. Here, we characterized the IFN-I sensitivity of 500 clonally-derived HIV-1 isolates from plasma and CD4+ T cells of 26 individuals sampled longitudinally following transmission and/or after antiretroviral therapy (ART) and analytical treatment interruption (ATI). Determining the concentration of IFNα2 and IFNβ that reduced HIV-1 replication by 50% (IC50), we found remarkably consistent changes in the sensitivity of viruses to IFN-I inhibition, both across individuals and over time. IFN-I resistance was uniformly high during acute infection, decreased in all subjects in the first year post-infection, was reacquired concomitant with CD4+ T cell loss, and remained elevated in subjects with accelerated disease. Isolates obtained by viral outgrowth during suppressive ART were relatively IFN-I sensitive, resembling viruses circulating just prior to ART initiation. However, viruses that rebounded following treatment interruption displayed the highest levels of IFNα2 and IFNβ resistance observed at any time during the infection course. These findings indicate a dynamic interplay between host innate immune responses and the evolving HIV-1 quasispecies, with the relative contribution of IFN-I to HIV-1 control impacted by both ART and ATI. Although elevated at transmission, IFN-mediated pressures are the highest during viral rebound, limiting the viruses that successfully reactivate from latency.

One Sentence Summary

HIV-1 resistance to IFN-I is highest during acute infection and following analytic treatment interruption, indicating a dynamic interplay between host innate immunity and virus biology.
Universal properties of the dynamics of the Covid-19 pandemic
Authors: Chruściel Piotr T. , Szybka Sebastian J.
Published: August 2020

We present evidence for existence of a universal lower bound for the initial growth rate of the epidemic curve of the SARS-CoV-2 coronavirus. This can be used to infer that, on average, an asymptomatic infected individual is infectious during 5.6 ± 0.3 days. We further present evidence of an average time scale of 12 days for halving the number of new cases, or new deaths, during the extinction period of the first phase of the epidemic.
Automatic late blight lesion recognition and severity quantification based on field imagery of diverse potato genotypes by deep learning
Authors: Gao Junfeng , Westergaard Jesper Cairo , Sundmark Ea Høegh Riis , Bagge Merethe , Liljeroth Erland , Alexandersson Erik
Published: August 2020

The plant pathogenPhytophthora infestanscauses the severe disease late blight in potato, which results in a huge loss for potato production. Automatic and accurate disease lesion segmentation enables fast evaluation of disease severity and assessment of disease progress for precision crop breeding. Deep learning has gained tremendous success in computer vision tasks for image classification, object detection and semantic segmentation. To test whether we could extract late blight lesions from unstructured field environments based on high-resolution visual field images and deep learning algorithms, we collected ~500 field RGB images in a set of diverse potato genotypes with different disease severity (0-70%), resulting in 2100 cropped images. 1600 of these cropped images were used as the dataset for training deep neural networks. Finally, the developed model was tested on the 250 cropped images. The results show that the intersection over union (IoU) values of background (leaf and soil) and disease lesion classes in the test dataset are 0.996 and 0.386, respectively. Furthermore, we established a linear relationship (R2= 0.655) between manual visual scores of late blight and the number of lesions at the canopy level. We also learned that imbalance weights of lesion and background classes improved segmentation performance, and that fused masks based on the majority voting of the multiple masks enhanced the correlation with the visual scores. This study demonstrates the feasibility of using deep learning algorithms for disease lesion segmentation and severity evaluation based on proximal imagery for crop resistance breeding in field environments.
New insights on species divergence in red panda
Authors: Joshi Bheem Dutt , Dalui Supriyo , Singh Sujeet Kumar , Mukherjee Tanoy , Chandra Kailash , Sharma Lalit Kumar , Thakur Mukesh
Published: August 2020

With the recent classification of red panda into two phylogenetic species, we propose ‘Siang river’ as a potential boundary for species divergence between the Himalayan red panda (Ailurus fulgens) and the Chinese red panda (Ailurus styani). Bayesian based phylogeny and MJ network splited all the sequences into two distinct clusters in accordance to the origin of the samples collected from the east and west side of the Siang river. The clade 1, that represented Himalayan red panda, was formed by inclusion of samples originated from the north West Bengal, Sikkim, and central Arunachal Pradesh and South Tibet. While, clade 2 represented Chinese red panda by inclusion of the samples originated from Dibang valley of eastern Arunachal Pradesh, India and Southwest China. We suggest being associated with diverse habitats, threats and transboundary distribution, both species of red panda require regional as well as multilateral cooperation for making species survival plan.
Structural characterization ofMyxococcus xanthusMglC, a component of polarity control system, and its interactions with MglB
Authors: Kapoor Srajan , Kodesia Akriti , Kalidas Nidhi , Ashish  , Thakur Krishan Gopal
Published: August 2020

Myxococcus xanthusdisplays two types of motilities i.e. Social (S) and Adventurous (A). The pole-to-pole reversals of these motility regulator proteins is the key to this process. Here, we determined ~1.85 Å resolution crystal structure of MglC, which revealed that despite sharing <9% sequence identity, both MglB and MglC adoptRegulatoryLightChain 7 (RLC7) family fold. Interestingly, MglC is structurally unique compared to the other known RLC7 family proteins having ~30°-40° shift in the orientation of functionally important α2 helix. Using isothermal titration calorimetry and gel filtration chromatography, we show that MglC binds MglB in 2:4 stoichiometry with submicromolar range dissociation constant. Using combination of small angle X-ray scattering and molecular docking studies, we show that MglBC complex is formed by MglC homodimer sandwiched between two homodimers of MglB.

In Brief

Kapooret al. report the crystal structure ofMyxococcus xanthusMglC, aRoadblockLightChain 7 (RLC7) family protein, involved in polarity reversal. The structure reveals a distinct orientation of α2 helix compared to other RLC7 proteins. They also demonstrate that MglC binds a GTPase activating protein, MglB, with submicromolar range dissociation constant.

Highlights

MglC adopts RLC7 fold and has distinct structural features.

MglC interacts MglB to form a stable complex having submicromolar range dissociation constant.

MglC homodimer is sandwiched between two MglB homodimers to form a 2:4 stoichiometric complex.
Color Polymorphism is a Driver of Diversification in the Lizard Family Lacertidae
Authors: Brock Kinsey M. , McTavish Emily Jane , Edwards Danielle L.
Published: August 2020

Color polymorphism – two or more heritable color phenotypes maintained within a single breeding population – is an extreme type of intra-specific diversity widespread across the tree of life but rarely studied in a comparative framework. Color polymorphism is thought to be an engine for speciation, where morph loss or divergence between distinct color morphs within a species results in the rapid evolution of new lineages, and thus, color polymorphic lineages are expected to display elevated diversification rates. Lizards of the family Lacertidae have evolved multiple lineages with color polymorphism, but lack of a complete and robust phylogeny for the group has made comparative analysis difficult. Here, we produce a comprehensive species-level phylogeny of the lizard family Lacertidae to reconstruct the evolutionary history of color polymorphism and test if color polymorphism has been a driver of diversification. Accounting for phylogenetic uncertainty, we estimate an ancient macroevolutionary origin of color polymorphism within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most likely evolved several times in the Lacertidae and has been lost at a much faster rate than gained. Evolutionary transitions to color polymorphism are associated with shifts in increased net diversification rate in this family of lizards. Taken together, our empirical results support long-standing theoretical expectations that color polymorphism is a driver of diversification.
The novel roles of choline transporter-like 1 and 2 in ethanolamine transport
Authors: Taylor Adrian , Grapentine Sophie , Ichhpuniani Jasmine , Bakovic Marica
Published: August 2020

We examined a novel function of mammalian Choline-Transporter-Like proteins CTL1/SLC44A1 and CTL2/SLC44A2 in ethanolamine transport. We established two distinct ethanolamine transport systems of a high affinity (K1= 55.6 - 66.5 μM), mediated by CTL1, and of a low affinity (K2= 275 - 299 μM), mediated by CTL2. Both types of transport are Na+-independent and mediated in a pH dependent manner, as expected for ethanolamine/H+antiporters. Primary human fibroblasts with separate frameshift mutations (M1=SLC44A1ΔAsp517and M2=SLC44A1ΔSer126) are devoid of CTL1 ethanolamine transport but maintain unaffected CTL2 transport. The lack of CTL1 or CTL2 reduced the ethanolamine transport, the flux by the CDP-ethanolamine Kennedy pathway and PE synthesis. Overexpression of CTL1 inSLC44A1ΔSer126(M2) cells improved the ethanolamine transport and PE synthesis. TheSLC44A1ΔSer126cells are reliant on CTL2 function and CTL2 siRNA almost completely abolished ethanolamine transport in the whole cells and mitochondria. Overexpression of CTL1 and CTL2 cDNAs increased ethanolamine transport in control andSLC44A1ΔSer126cells. CTL1 and CTL2 facilitated mitochondrial ethanolamine uptake, but the transport mediated by CTL1 is predominant in the whole cells and mitochondria. These data firmly established that CTL1 and CTL2 are the first identified ethanolamine transporters in the whole cells and mitochondria, with intrinsic roles inde novoPE synthesis by the CDP-Etn Kennedy pathway and compartmentation of intracellular ethanolamine.

Significance

The lack of Choline Transporter Like 1 (SLC44A1/CTL1) is the primary cause of a new neurodegenerative disorder with elements of childhood-onset parkinsonism and mitochondrial dysfunction.SLC44A2/CTL2 encodes the human neutrophil antigen 3, causes autoimmune hearing loss and Meniere’s disease, and has been recently identified as the main risk factor for thrombosis-the major cause of death in Covid-19 patients. Our investigation provides insights into the novel functions of CTL1 and CTL2 as intrinsic ethanolamine transporters. CTL1 and CTL2 are high and low affinity transporters, with direct roles in the membrane phospholipid synthesis. The work contributes to new knowledge for CTL1 and CTL2 independent transport functions and the optimization of prevention and treatment strategies in those various diseases.
Base Pairing and Functional Insights intoN3-methylcytidine (m3C) in RNA
Authors: Mao Song , Haruehanroengra Phensinee , Ranganathan Srivathsan V. , Shen Fusheng , Begley Thomas J. , Sheng Jia
Published: August 2020

N3-methylcytidine (m3C) is present in both eukaryotic tRNA and mRNA and plays critical roles in many biological processes. We report the synthesis of the m3C phosphoramidite building block and its containing RNA oligonucleotides. The base-pairing stability and specificity studies show that the m3C modification significantly disrupts the stability of the Watson-Crick C:G pair. Further m3C decreases the base pairing discrimination between C:G and the other mismatched C:A, C:U, and C:C pairs. Our molecular dynamic simulation study further reveals the detailed structural insights into the m3C:G base pairing pattern in an RNA duplex. More importantly, the biochemical investigation of m3C using reverse transcription shows thatN3-methylation specifies the C:A pair and induces a G to A mutation using HIV-1-RT, MMLV-RT and MutiScribe™-RT enzymes, all with relatively low replication fidelity. For other reverse transcriptases with higher fidelity like AMV-RT, the methylation could completely shut down DNA synthesis.
Genome-wide analysis ofcis-regulatory changes in the metabolic adaptation of cavefish
Authors: Krishnan Jaya , Seidel Chris W. , Zhang Ning , VanCampen Jake , Peuß Robert , Xiong Shaolei , Kenzior Alexander , Li Hua , Conaway Joan W. , Rohner Nicolas
Published: August 2020

Changes in cis-regulatory elements play important roles in adaptation and phenotypic evolution. However, their contribution to metabolic adaptation of organisms is less understood. Here we have utilized a unique vertebrate model,Astyanax mexicanus,different morphotypes of which survive in nutrient-rich surface and nutrient-deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide epigenetic profiling in the liver tissue of one surface and two independently derived cave populations. We find that many cis-regulatory elements differ in their epigenetic status/chromatin accessibility between surface fish and cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. These differentially accessible regions are associated with genes of key pathways related to lipid metabolism, circadian rhythm and immune system that are known to be altered in cavefish. Usingin vitroandin vivofunctional testing of the candidate cis-regulatory elements, we find that genetic changes within them cause quantitative expression differences. We characterized one cis-regulatory element in thehpdbgene and found a genomic deletion in cavefish that abolishes binding of the transcriptional repressor IRF2in vitroand derepresses enhancer activity in reporter assays. Genetic experiments further validated a cis-mediated role of the enhancer and suggest a role of this deletion in the upregulation ofhpdbin wild cavefish populations. Selection of this mutation in multiple independent cave populations supports its importance in the adaptation to the cave environment, providing novel molecular insights into the evolutionary trade-off between loss of pigmentation and adaptation to a food-deprived cave environment.
Glassiness in cellular Potts model of biological tissue is controlled by disordered energy landscape
Authors: Sadhukhan Souvik , Nandi Saroj Kumar
Published: August 2020

Glassy dynamics in a confluent monolayer is indispensable in morphogenesis, wound healing, bronchial asthma, and many others; a detailed theoretical understanding for such a system is, therefore, important. We combine numerical simulations of a cellular Potts model and an analytical study based on random first order transition (RFOT) theory of glass, develop a comprehensive theoretical framework for a confluent glassy system, and show that glassiness is controlled by the underlying disordered energy landscape. Our study elucidates the crucial role of geometric constraints in bringing about two distinct regimes in the dynamics, as the target perimeterP0is varied. The extended RFOT theory provides a number of testable predictions that we verify in our simulations. The unusual sub-Arrhenius relaxation results from the distinctive interaction potential arising from the perimeter constraint in a regime controlled by geometric restriction. Fragility of the system decreases with increasingP0in the low-P0regime, whereas the dynamics is independent ofP0in the other regime. The mechanism, controlling glassiness in a confluent system, is different in our study in comparison with vertex model simulations, and can be tested in experiments.
An 8 Dipole Transceive and 24 Loop Receive Array for Non-Human Primate Head Imaging at 10.5T
Authors: Lagore Russell L. , Moeller Steen , Zimmermann Jan , DelaBarre Lance , Radder Jerahmie , Grant Andrea , Ugurbil Kamil , Yacoub Essa , Harel Noam , Adriany Gregor
Published: August 2020

A 32-channel RF coil was developed for brain imaging of anesthetized non-human primates (Rhesus Macaque) at 10.5 tesla. The coil is composed of an 8-channel dipole transmit/receive array, close-fitting 16-channel loop receive array headcap, and 8-channel loop receive array lower insert.

The transceiver dipole array is composed of eight end-loaded dipole elements self-resonant at the 10.5 tesla proton Larmor frequency. These dipole elements were arranged on a plastic cylindrical former which was split in two to allow for convenient animal positioning. Nested into the bottom of the dipole array former is located an 8-channel loop receive array which contains 5×10 cm2square loops arranged in two rows of four loops. Arranged in a close-fitting plastic headcap is located a high-density 16-channel loop receive array. This array is composed of 14 round loops 37 mm in diameter and two partially detachable, irregularly shaped loops that encircle the ears. Imaging experiments were performed on anesthetized non-human primates on a 10.5 tesla MRI system equipped with body gradients with a 60 cm open bore.

The coil enabled submillimeter (0.58 mm isotropic) high resolution anatomical and functional imaging as well as tractography of fasciculated axonal bundles. The combination of a close-fitting loop receive array and dipole transceiver array allowed for a higher channel count receiver and consequent higher SNR and parallel imaging gains. Parallel imaging performance supports high resolution fMRI and dMRI with a factor of three reduction in sampling. The transceive array elements during reception contributed approximately one quarter of SNR in the lower half of the brain which was farthest from the close-fitting headcap receive array.
Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19
Authors: Ghandikota Sudhir , Sharma Mihika , Jegga Anil G.
Published: August 2020

Knowledge about the molecular mechanisms driving COVID-19 pathophysiology and outcomes is still limited. To learn more about COVID-19 pathophysiology we performed secondary analyses of transcriptomic data from twoin vitro(Calu-3 and Vero E6 cells) and onein vivo(Ad5-hACE2-sensitized mice) models of SARS-CoV-2 infection. We found 1467 conserved differentially expressed host genes (differentially expressed in at least two of the three model system transcriptomes compared) in SARS-CoV-2 infection. To find potential genetic factors associated with COVID-19, we analyzed these conserved differentially expressed genes using known human genotype-phenotype associations. Genome-wide association study enrichment analysis showed evidence of enrichment for GWA loci associated with platelet functions, blood pressure, body mass index, respiratory functions, and neurodegenerative and neuropsychiatric diseases, among others. Since human protein complexes are known to be directly related to viral infection, we combined and analyzed the conserved transcriptomic signature with SARS-CoV-2-host protein-protein interaction data and found more than 150 gene clusters. Of these, 29 clusters (with 5 or more genes in each cluster) had at least one gene encoding protein that interacts with SARS-CoV-2 proteome. These clusters were enriched for different cell types in lung including epithelial, endothelial, and immune cell types suggesting their pathophysiological relevancy to COVID-19. Finally, pathway analysis on the conserved differentially expressed genes and gene clusters showed alterations in several pathways and biological processes that could enable in understanding or hypothesizing molecular signatures inducing pathophysiological changes, risks, or sequelae of COVID-19.
Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1]
Authors: Stern Chaya D , Bayly Christopher I , Smith Daniel G A , Fass Josh , Wang Lee-Ping , Mobley David L , Chodera John D
Published: August 2020

Accurate molecular mechanics force fields for small molecules are essential for predicting protein-ligand binding affinities in drug discovery and understanding the biophysics of biomolecular systems. Torsion potentials derived from quantum chemical (QC) calculations are critical for determining the conformational distributions of small molecules, but are computationally expensive and scale poorly with molecular size. To reduce computational cost and avoid the complications of distal through-space intramolecular interactions, molecules are generally fragmented into smaller entities to carry out QC torsion scans. However, torsion potentials, particularly for conjugated bonds, can be strongly affected by through-bond chemistry distal to the torsion it-self. Poor fragmentation schemes have the potential to significantly disrupt electronic properties in the region around the torsion by removing important, distal chemistries, leading to poor representation of the parent molecule’s chemical environment and the resulting torsion energy profile. Here we show that a rapidly computable quantity, the fractional Wiberg bond order (WBO), is a sensitive reporter on whether the chemical environment around a torsion has been disrupted. We show that the WBO can be used as a surrogate to assess the robustness of fragmentation schemes and identify conjugated bond sets. We use this concept to construct a validation set by exhaustively fragmenting a set of druglike organic molecules and examine their corresponding WBO distributions derived from accessible conformations that can be used to evaluate fragmentation schemes. To illustrate the utility of the WBO in assessing fragmentation schemes that preserve the chemical environment, we propose a new fragmentation scheme that uses rapidly-computable AM1 WBOs, which are available essentially for free as part of standard AM1-BCC partial charge assignment. This approach can simultaneously maximize the chemical equivalency of the fragment and the substructure in the larger molecule while minimizing fragment size to accelerate QC torsion potential computation for small molecules and reducing undesired through-space steric interactions.
Regulation of Decay Accelerating Factor primes human germinal center B cells for phagocytosis
Authors: Dernstedt Andy , Leidig Jana , Holm Anna , Mjösberg Jenny , Ahlm Clas , Henriksson Johan , Hultdin Magnus , Forsell Mattias NE
Published: August 2020

Germinal centers (GC) are sites for extensive B cell proliferation and homeostasis is maintained by programmed cell death. The complement regulatory protein Decay Accelerating Factor (DAF) blocks complement deposition host cells and therefore also phagocytosis of cells. Here, we show that B cells downregulate DAF upon BCR engagement and that T cell-dependent stimuli preferentially led to activation of DAFloB cells. Consistent with this, a majority of light and dark zone GC B cells were DAFloand susceptible to complement-dependent phagocytosis, as compared with DAFhiGC B cells. We could also show that the DAFhiGC B cell subset had increased expression of the plasma cell marker Blimp-1. DAF expression was also modulated during B cell hematopoiesis in the human bone marrow. Collectively, our results reveal a novel role of DAF to pre-prime activated human B cells for phagocytosis prior to apoptosis.
Immune modulatory effects of probioticStreptococcus thermophiluson human monocytes
Authors: Dargahi Narges , Johnson Joshua , Apostolopoulos Vasso
Published: August 2020

Ingesting probiotics contributes to the development of a healthy microflora in the gastrointestinal tract with established benefits to human health. Some of these beneficial effects may be through modulating of the immune system and probiotics have become more common in the treatment of many inflammatory and immune disorders. We demonstrate a range of immune modulating effects ofStreptococcus thermophilusby human monocytes, including, decreased mRNA expression of IL-1R, IL-18, IFNγR1, IFNαR1, CCL2, CCR5, TLR-1, TLR-2, TLR-4, TLR-5, TLR-6, TLR-8, CD14, CD86, CD4, ITGAM, LYZ, TYK2, IFNR1, IRAK-1, NOD2, MYD88, ITGAM, SLC11A1, and, increased expression of IL-1α, IL-1β, IL-2, IL-6, IL-8, IL-23, IFNγ, TNFα, CSF-2. Routine administration ofStreptococcus thermophilusin fermented dairy products, and their consumption may be beneficial to the treatment/management of inflammatory and autoimmune diseases.
A dual mechanism of enhancer activation by FOXA pioneer factors induces endodermal organ fates
Authors: Geusz Ryan J. , Wang Allen , Lam Dieter K. , Vinckier Nicholas K. , Alysandratos Konstantinos-Dionysios , Roberts David A. , Wang Jinzhao , Kefalopoulou Samy , Qiu Yunjiang , Chiou Joshua , Gaulton Kyle J. , Ren Bing , Kotton Darrel N. , Sander Maike
Published: August 2020

FOXA pioneer transcription factors (TFs) displace nucleosomes and prime chromatin across enhancers of different endodermal organs in multipotent precursors before lineage induction. Here, we examined patterns and mechanisms of FOXA target site engagement using human pluripotent stem cell models of endodermal organ development. Unexpectedly, we find that only a subset of pancreatic, hepatic, and alveolar enhancers are FOXA-primed, whereas the majority are unprimed and engage FOXA only upon lineage induction. Analysis of sequence architecture revealed more abundant and stronger FOXA motifs at primed than unprimed enhancers and enrichment for lineage-specific TF motifs at unprimed enhancers. We show that FOXA recruitment to unprimed enhancers specifically depends on lineage-specific TFs, suggesting that regulatory DNA sequence logic governs temporal FOXA recruitment. Our findings suggest that FOXA-mediated enhancer priming broadly facilitates initiation of organ lineage programs, while secondary FOXA recruitment by lineage-specific TFs to the majority of enhancers confers organ specificity to gene expression.
Role of channels in the oxygen permeability of red blood cells
Authors: Zhao Pan , Geyer R. Ryan , Salameh Ahlam I. , Wass Amanda B. , Taki Sara , Huffman Dale E. , Meyerson Howard J , Gros Gerolf , Occhipinti Rossana , Moss Fraser J. , Boron Walter F.
Published: August 2020

Many have believed that oxygen (O2) crosses red blood cell (RBC) membranes by dissolving in lipids that offer no resistance to diffusion. However, using stopped-flow (SF) analyses of hemoglobin (Hb) absorbance spectra during O2off-loading from mouse RBCs, we now report that most O2traverses membrane-protein channels. Two agents excluded from the RBC interior markedly slow O2off-loading: p-chloromercuribenzenesulfonate (pCMBS) reduces inferred membrane O2permeability (PMembrane) by ∼82%, and 4,4’-diisothiocyanatostilbene-2,2’-disulfonate (DIDS), by ∼56%. Because neither likely produces these effects via membrane lipids, we examined RBCs from mice genetically deficient in aquaporin-1 (AQP1), the Rh complex (i.e., rhesus proteins RhAG + mRh), or both. The double knockout (dKO) reducesPMembraneby ∼55%, and pCMBS+dKO, by ∼91%. Proteomic analyses of RBC membranes, flow cytometry, hematology, and mathematical simulations rule out explanations involving other membrane proteins, RBC geometry, or extracellular unconvected fluid (EUF). By identifying the first two O2channels and pointing to the existence of other O2channel(s), all of which could be subject to physiological regulation and pharmacological intervention, our work represents a paradigm shift for O2handling.
Two bi-functional cytochrome P450 CYP72 enzymes from olive (Olea europaea) catalyze the oxidative C-C bond cleavage in the biosynthesis of secoxy-iridoids - flavor and quality determinants in olive oil
Authors: Rodríguez-López Carlos E. , Hong Benke , Paetz Christian , Nakamura Yoko , Koudounas Konstantinos , Passeri Valentina , Baldoni Luciana , Alagna Fiammetta , Calderini Ornella , O’Connor Sarah E.
Published: August 2020

Olive (Olea europaea) is an important crop in Europe, with high cultural, economic, and nutritional significance. Olive oil flavor and quality depend on phenolic secoiridoids, but the biosynthetic pathway of these iridoids remains largely uncharacterized.

We discovered two novel, bi-functional cytochrome P450 enzymes, catalysing the rare oxidative C-C bond cleavage of 7-epi-loganin to produce oleoside methyl ester (OeOMES) and secoxyloganin (OeSXS), both through a ketologanin intermediary. Although these enzymes are homologous to the previously reportedCatharanthus roseusSecologanin Synthase (CrSLS), the substrate and product profiles differ.

Biochemical assays provided mechanistic insights into the two-step OeOMES and CrSLS reactions. Model-guided mutations of OeOMES changed the product profile in a predictable manner, revealing insights into the molecular basis for this change in product specificity.

Our results suggest that, in contrast to published hypotheses,in plantaproduction of secoxy-iridoids is secologanin independent. Notably, sequence data of cultivated and wild olives, points to a relation between domestication and OeOMES expression. Thus, the discovery of this key biosynthetic gene suggests a link between domestication and secondary metabolism, and could potentially be used as a genetic marker to guide next-generation breeding programs.
An integrative approach points to membrane composition as a key factor inE. colipersistence
Authors: Cañas-Duarte SJ , Perez-Lopez MI , Herrfurth C , Sun Lei , Contreras LM , Feussner I , Leidy C , Riaño-Pachón DM , Restrepo S , Pedraza JM
Published: August 2020

In spite of its medical importance, the genetic mechanisms of bacterial persistence, particularly spontaneous (type II) persistence, remain largely unknown. We use an integrative approach, combining mutant genome analysis, transcriptomics and lipid membrane composition analysis, to elucidate said mechanisms. In particular, we analyzed the genome of the high persistence mutantE. coliDS1 (hipQ), to identify candidate mutations responsible for the high persistence phenotype. Contrary to a recent study, we find no mutation in ydcI. We compared the expression of spontaneous persistent and growing cells using RNAseq, and find that the activation of stress response mechanisms is likely less important in spontaneous persistence than recent reports suggest. It also indicated that modifications in the cell membrane could play an important role. This hypothesis was then validated by the analysis of the fatty acid composition of persister cells of both types, which have markedly different saturation from growing cells and between each other. Taken together, our results indicate that changing membrane composition might be a key process in persistence.

Highlights

RNAseq analysis of spontaneous persistence shows no evidence of stress response

Identification of candidate SNPs for hipQ phenotype, excludes ydcI

Membrane fatty acid composition is involved in both types of bacterial persistence
Two-step multi-omics modelling of drug sensitivity in cancer cell lines to identify driving mechanisms
Authors: Kusch Nina , Schuppert Andreas
Published: August 2020

Drug sensitivity prediction models for human cancer cell lines constitute important tools in identifying potential driving factors of responsiveness in a pre-clinical setting. Integrating information derived from a range of heterogeneous data is crucial, but remains non-trivial, as differences in data structures may hinder fitting algorithms from assigning adequate weights to complementary information that is contained in distinct omics data. In order to counteract this effect that tends to lead to just one data type dominating supposedly multi-omics models, we developed a novel tool that enables users to train single-omics models separately in a first step and to integrate them into a multi-omics model in a second step. Extensive ablation studies are performed in order to facilitate an in-depth evaluation of the respective contributions of singular data types and of combinations thereof, effectively identifying redundancies and interdependencies between them. Moreover, the integration of the single-omics models is realized by a range of distinct classification algorithms, thus allowing for a performance comparison. Sets of molecular events and tissue types found to be related to significant shifts in drug sensitivity are returned to facilitate a comprehensive and straightforward analysis of potential drivers of drug responsiveness. Our two-step approach yields sets of actual multi-omics pan-cancer classification models that are highly predictive for a majority of drugs in the GDSC data base. In the context of targeted drugs with particular modes of action, its predictive performances compare favourably to those of classification models that incorporate multi-omics data in a simple one-step approach. Additionally, case studies demonstrate that it succeeds both in correctly identifying known key drivers of specific drug compounds as well as in providing sets of potential candidates for additional driving factors of drug sensitivity.
A Transferable Deep Learning Approach to Fast Screen Potent Antiviral Drugs against SARS-CoV-2
Authors: Wang Shiwei , Sun Qi , Xu Youjun , Pei Jianfeng , Lai Luhua
Published: August 2020

The COVID-19 pandemic calls for rapid development of effective treatments. Although various drug repurpose approaches have been used to screen the FDA-approved drugs and drug candidates in clinical phases against SARS-CoV-2, the coronavirus that causes this disease, no magic bullets have been found until now. We used directed message passing neural network to first build a broad-spectrum anti-beta-coronavirus compound prediction model, which gave satisfactory predictions on newly reported active compounds against SARS-CoV-2. Then we applied transfer learning to fine-tune the model with the recently reported anti-SARS-CoV-2 compounds. The fine-tuned model was applied to screen a large compound library with 4.9 million drug-like molecules from ZINC15 database and recommended a list of potential anti-SARS-CoV-2 compounds for further experimental testing. As a proof-of-concept, we experimentally tested 7 high-scored compounds that also demonstrated good binding strength in docking study against the 3C-like protease of SARS-CoV-2 and found one novel compound that inhibited the enzyme with an IC50of 37.0 μM. Our model is highly efficient and can be used to screen large compound databases with billions or more compounds to accelerate the drug discovery process for the treatment of COVID-19.
Sequence analysis of Indian SARS-CoV-2 isolates shows a stronger interaction of mutated receptor binding domain with ACE2 receptor
Authors: Dash Pujarini , Turuk Jyotirmayee , Behera Santosh Ku. , Palo Subrata Ku. , Raghav Sunil K. , Ghosh Arup , Sabat Jyotsnamayee , Rath Sonalika , Subhadra Subhra , Bhattacharya Debadutta , Kanungo Srikant , Kshatri Jayasingh , Mishra Bijaya kumar , Dash Saroj , Mahapatra Namita , Parida Ajay , Pati Sanghamitra
Published: August 2020

SARS-CoV-2 is a RNA Coronavirus responsible for the pandemic of the Severe Acute Respiratory Syndrome (COVID-19). It has affected the whole world including Odisha, a state in eastern India. Many people migrated in the state from different countries as well as states during this SARS-CoV-2 pandemic. As per the protocol laid by ICMR and Health & Family welfare of India, all the suspected cases were tested for SARS-CoV-2 infection. The aim of this study was to analyze the RNA binding domain (RBD) sequence of spike protein from the isolates collected from the throat swab samples of COVID-19 positive cases and further to assess the RBD affinity with ACE2 of different species including human.

Whole genome sequencing for 35 clinical SARS-CoV-2 isolates from COVID-19 positive patients was performed using ARTIC amplicon based sequencing. Sequence analysis and phylogenetic analysis was carried out for the Spike and RBD region of all isolates. The interaction between the RBD and ACE2 receptor of five different species was also analysed.

Except three isolates, spike region of 32 isolates showed one/multiple alterations in nucleotide bases in comparison to the Wuhan reference strain. One of the identified mutation at 1204 (Ref A, RMRC 22 C) in the RBD of spike protein was identified which depicted a stronger binding affinity with human ACE2 receptor compared to the wild type RBD. Furthermore, RBDs of all the Indian isolates are capable of binding to ACE2 of human, bat, hamster and pangolin.

As mutated RBD showed stronger interaction with human ACE2, it could potentially result in higher infectivity. The study shows that RBDs of all the studied isolates have binding affinity for all the five species, which suggests that the virus can infect a wide variety of animals which could also act as natural reservoir for SARS-CoV-2.
Targeting Oncogenic Src Homology 2 Domain-Containing Phosphatase 2 (SHP2) by Inhibiting its Protein-Protein Interactions
Authors: Bobone Sara , Pannone Luca , Biondi Barbara , Solman Maja , Flex Elisabetta , Canale Viviana , Calligari Paolo , Faveri Chiara De , Gandini Tommaso , Quercioli Andrea , Torini Giuseppe , Venditti Martina , Lauri Antonella , Fasano Giulia , Hoeksma Jelmer , Santucci Valerio , Cattani Giada , Bocedi Alessio , Carpentieri Giovanna , Tirelli Valentina , Sanchez Massimo , Peggion Cristina , Formaggio Fernando , Hertog Jeroen den , Martinelli Simone , Bocchinfuso Gianfranco , Tartaglia Marco , Stella Lorenzo
Published: August 2020

We developed a new class of inhibitors of protein-protein interactions of the SHP2 phosphatase, which is pivotal in multiple signaling pathways and a central target in the therapy of cancer and rare diseases. Currently available SHP2 inhibitors target the catalytic site or an allosteric pocket but lack specificity or are ineffective on disease-associated SHP2 mutants. Based on the consideration that pathogenic lesions cause signaling hyperactivation due to increased SHP2 association with cognate proteins, we developed peptide-based molecules with low nM affinity for the N-terminal Src homology domain of SHP2, good selectivity, stability to degradation and an affinity for pathogenic variants of SHP2 up to 20 times higher than for the wild-type protein. The best peptide reverted the effects of a pathogenic variant (D61G) in zebrafish embryos. Our results provide a novel route for SHP2-targeted therapies and a tool to investigate the role of protein-protein interactions in the function of SHP2.
Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2
Authors: Ghahremanpour Mohammad M. , Tirado-Rives Julian , Deshmukh Maya , Ippolito Joseph A. , Zhang Chun-Hui , de Vaca Israel Cabeza , Liosi Maria-Elena , Anderson Karen S. , Jorgensen William L.
Published: August 2020

A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID-19. 42 drugs emerged as top candidates, and after visual analyses of the predicted structures of their complexes with Mpro, 17 were chosen for evaluation in a kinetic assay for Mproinhibition. Remarkably 14 of the compounds at 100-μM concentration were found to reduce the enzymatic activity and 5 provided IC50values below 40 μM: manidipine (4.8 μM), boceprevir (5.4 μM), lercanidipine (16.2 μM), bedaquiline (18.7 μM), and efonidipine (38.5 μM). Structural analyses reveal a common cloverleaf pattern for the binding of the active compounds to the P1, P1’, and P2 pockets of Mpro. Further study of the most active compounds in the context of COVID-19 therapy is warranted, while all of the active compounds may provide a foundation for lead optimization to deliver valuable chemotherapeutics to combat the pandemic.
TweetyNet: A neural network that enables high-throughput, automated annotation of birdsong
Authors: Cohen Yarden , Nicholson David , Sanchioni Alexa , Mallaber Emily K. , Skidanova Viktoriya , Gardner Timothy J.
Published: August 2020

Songbirds have long been studied as a model system of sensory-motor learning. Many analyses of birdsong require time-consuming manual annotation of the individual elements of song, known as syllables or notes. Here we describe the first automated algorithm for birdsong annotation that is applicable to complex song such as canary song. We developed a neural network architecture, “TweetyNet”, that is trained with a small amount of hand-labeled data using supervised learning methods. We first show TweetyNet achieves significantly lower error on Bengalese finch song than a similar method, using less training data, and maintains low error rates across days. Applied to canary song, TweetyNet achieves fully automated annotation of canary song, accurately capturing the complex statistical structure previously discovered in a manually annotated dataset. We conclude that TweetyNet will make it possible to ask a wide range of new questions focused on complex songs where manual annotation was impractical.
FRETboard: semi-supervised classification of fret traces
Authors: de Lannoy Carlos , Filius Mike , Kim Sung Hyun , Joo Chirlmin , de Ridder Dick
Published: August 2020

Abstract

Förster resonance energy transfer (FRET) is a useful phenomenon in biomolecular investigations, as it can be leveraged for nano-scale measurements. The optical signals produced by such experiments can be analyzed by fitting a statistical model. Several software tools exist to fit such models in an unsupervised manner, but their operating system-dependent installation requirements and lack of flexibility impede wide-spread adoption. Here we propose to fit such models more efficiently and intuitively by adopting a semi-supervised approach, in which the user interactively guides the model to fit a given dataset, and introduce FRETboard, a web tool that allows users to provide such guidance. We show that our approach is able to closely reproduce ground truth FRET statistics in a wide range of simulated single-molecule scenarios, and correctly estimate parameters for up to eleven states. Onin vitrodata we retrieve parameters identical to those obtained by laborious manual classification in a fraction of the required time. Moreover, we designed FRETboard to be easily extendable to other models, allowing it to adapt to future developments in FRET measurement and analysis.

Availability

source code is available athttps://github.com/cvdelannoy/FRETboard. The FRETboard classification tool is also available as a browser application athttps://www.bioinformatics.nl/FRETboard.
PrkC modulates MreB filament density and cellular growth rate by monitoring cell wall precursors
Authors: Sun Yingjie , Garner Ethan
Published: August 2020

How bacteria link their rate of growth to the external nutrient conditions is not known. To explore howBacillus subtilismodulates the rate cells expand their encapsulating cell wall, we compared the single-cell growth rate to the density of moving MreB filaments under different conditions. MreB filament density scales with the growth rate, and is modulated by themurgenes that create the cell wall precursor lipid II. Lipid II is sensed by the serine/threonine kinase PrkC, which, among other proteins, phosphorylates RodZ. Phosphorylated RodZ then increases MreB filament density, increasing growth. Strikingly, increasing the activity of this pathway results in cells elongating far faster than wild type in nutrient-poor media, indicating slow-growing bacteria contain spare growth capacity. Overall, this work reveals that PrkC functions as a cellular rheostat, tuning the activities of cellular processes in response to lipid II, allowing cells to grow robustly across a broad range of nutrient conditions.

One-sentence summary

The serine/threonine kinase PrkC modulates both MreB filament density and cellular growth rate by sensing lipid II inBacillus subtilis.
A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice
Authors: Powell Abigail E. , Zhang Kaiming , Sanyal Mrinmoy , Tang Shaogeng , Weidenbacher Payton A. , Li Shanshan , Pham Tho D. , Pak John E. , Chiu Wah , Kim Peter S.
Published: August 2020

Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.
ß2-Arrestin germline knockout does not attenuate opioid respiratory depression
Authors: Bachmutsky Iris , Durand Adelae , Yackle Kevin
Published: August 2020

Opioids are perhaps the most effective analgesics in medicine. However, from 1999 to 2018, they also killed more than 400,000 people in the United States by suppressing breathing, a common side-effect known as opioid induced respiratory depression. This doubled-edged sword has inspired the dream of developing novel therapeutics that provide opioid-like analgesia without respiratory depression. One such approach has been to develop so-called ‘biased agonists’ that activate some, but not all pathways downstream of the µ-opioid receptor (MOR), the target of morphine and other opioid analgesics. This hypothesis stems from a study suggesting that MOR-mediated activation of ß2-Arrestin is the downstream signaling pathway responsible for respiratory depression, whereas inhibition of adenylyl cyclase produces analgesia. To further verify this model, which represents the motivation for the biased agonist approach, we examined respiratory behavior in mice lacking the gene for ß2-Arrestin. Contrary to previous findings, we find no correlation between ß2-Arrestin function and opioid-induced respiratory depression, suggesting that any effect of biased agonists must be mediated through an as-yet to be identified signaling mechanism.