bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-Dimensional Impedance Tomographic Mapping of Metabolically Active Endolumen
Authors: Abiri Parinaz , Luo Yuan , Huang Zi-Yu , Roustaei Mehrdad , Duarte-Vogel Sandra , Cui Quinyu , Sevag Packard René R. , Ebrahimi Ramin , Benharash Peyman , Tai Yu-Chong , Hsiai Tzung K.
Published: September 2020

Real-time detection of vulnerable atherosclerotic lesions, characterized by a high content of oxidized low-density lipoprotein (oxLDL)-laden macrophages or foam cells, remains an unmet clinical need. While fractional flow reserve (FFR)-guided revascularization in angiographically intermediate stenoses is utilized to assess hemodynamic significance,in vivodetection of oxLDL-rich plaques may provide a new paradigm for treating metabolically unstable lesions. Herein, we have demonstrated endoluminal mapping of lipid-laden lesions using 3-D electrical impedance spectroscopy-derived impedance tomography (EIT) in a pre-clinical swine model. We performed surgical banding of the right carotid arteries of Yucatan mini-pigs, followed by 16 weeks of high-fat diet, to promote the development of lipid-rich lesions. We implemented an intravascular sensor combining an FFR pressure transducer with a 6-point micro-electrode array for electrical impedance spectroscopy (EIS) measurements. 3-D EIT mapping was achieved using an EIS-based reconstruction algorithm. We demonstrated that EIT mapping corresponds to endoluminal histology for oxLDL-laden lesions. We further used computational models to theoretically predict and validate EIS measurements. Thus, our 3-D EIS-derived EIT providesin vivodetection of metabolically active plaques with the goal of guiding optimal intravascular intervention.

One Sentence Summary

This work demonstratesin vivomapping of oxidized LDL-laden endolumen by deploying an intravascular dual-sensor to a swine model of atherosclerosis.
Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies
Authors: Doepker Laura E. , Danon Sonja , Harkins Elias , Ralph Duncan , Yaffe Zak , Dhar Amrit , Wagner Cassia , Stumpf Megan M. , Arenz Dana , Williams James A. , Jaoko Walter , Mandaliya Kishor , Lee Kelly K. , Matsen Frederick A. , Overbaugh Julie M.
Published: September 2020

A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naïve antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of human ADCC antibodies may require mutations that first enable high affinity antigen recognition, followed by mutations that optimize factors contributing to functional ADCC activity.
Intelligence-associated Polygenic Scores Predict g, Independent of Ancestry, Parental Educational Levels, and Color among Hispanics in comparison to European, European- African, and African Americans
Authors: Pesta Bryan J. , Fuerst John G. R. , Piffer Davide , Kirkegaard Emil O. W.
Published: September 2020

Polygenic scores for educational attainment and intelligence (eduPGS), genetic ancestry, and cognitive ability have been found to be inter-correlated in some admixed American populations. We argue that this could either be due to causally-relevant genetic differences between ancestral groups or be due to population stratification-related confounding. Moreover, we argue that it is important to determine which scenario is the case so to better assess the validity of eduPGS. We investigate the confounding vs. causal concern by examining, in detail, the relation between eduPGS, ancestry, and general cognitive ability in East Coast Hispanic and non-Hispanic samples. European ancestry was correlated withgin the admixed Hispanic (r= .30,N= 506), European-African (r= .26,N= 228), and African (r= .084,N= 2,179) American samples. Among Hispanics and the combined sample, these associations were robust to controls for racial / ethnic self-identification, genetically predicted color, and parental education. Additionally, eduPGS predictedgamong Hispanics (B= 0.175,N= 506) and all other groups (European:B= 0.230,N= 4914; European-African:B= 0.215,N= 228; African:B= 0.126,N= 2179) with controls for ancestry. Path analyses revealed that eduPGS, but not color, partially statistically explained the association betweengand European ancestry among both Hispanics and the combined sample. Of additional note, we were unable to account for eduPGS differences between ancestral populations using common tests for ascertainment bias and confounding related to population stratification. Overall, our results suggest that eduPGS derived from European samples can be used to predictgin American populations. However, owing to the uncertain cause of the differences in eduPGS, it is not yet clear how the effect of ancestry should be handled. We argue that more research is needed to determine the source of the relation between eduPGS, genetic ancestry, and cognitive ability.
Representational drift in primary olfactory cortex
Authors: Schoonover Carl E. , Ohashi Sarah N. , Axel Richard , Fink Andrew J.P.
Published: September 2020

Representations of the external world in sensory cortices may define the identity of a stimulus and should therefore vary little over the life of the organism. In the olfactory system the primary olfactory cortex, piriform, is thought to determine odor identity1–6. We have performed electrophysiological recordings of single units maintained over weeks to examine the stability of odor representations in the mouse piriform cortex. We observed that odor representations drift over time, such that the performance of a linear classifier trained on the first recording day approaches chance levels after 32 days. Daily exposure to the same odorant slows the rate of drift, but when exposure is halted that rate increases once again. Moreover, behavioral salience does not stabilize odor representations. Continuous drift poses the question of the role of piriform in odor identification. This instability may reflect the unstructured connectivity of piriform7–15and may be a property of other unstructured cortices.
JIB-04 has broad-spectrum antiviral activity and inhibits SARS-CoV-2 replication and coronavirus pathogenesis
Authors: Son Juhee , Huang Shimeng , Zeng Qiru , Bricker Traci L. , Case James Brett , Zhou Jinzhu , Zang Ruochen , Liu Zhuoming , Chang Xinjian , Harastani Houda H. , Chen Lu , Gomez Castro Maria Florencia , Zhao Yongxiang , Kohio Hinissan P. , Hou Gaopeng , Fan Baochao , Niu Beibei , Guo Rongli , Rothlauf Paul W. , Bailey Adam L. , Wang Xin , Shi Pei-Yong , Martinez Elisabeth D. , Whelan Sean P.J. , Diamond Michael S. , Boon Adrianus C.M. , Li Bin , Ding Siyuan
Published: September 2020

Pathogenic coronaviruses represent a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified several small-molecule inhibitors that potently block the replication of the newly emerged severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with an EC50of 695 nM, with a specificity index of greater than 1,000. JIB-04 showedin vitroantiviral activity in multiple cell types against several DNA and RNA viruses, including porcine coronavirus transmissible gastroenteritis virus. In anin vivoporcine model of coronavirus infection, administration of JIB-04 reduced virus infection and associated tissue pathology, which resulted in improved weight gain and survival. These results highlight the potential utility of JIB-04 as an antiviral agent against SARS-CoV-2 and other viral pathogens.
Genome-wide analyses point to differences in genetic architecture of BMI between tall and short people
Authors: Lin Bochao D. , Mullin Benjamin H. , Wilson Scott G. , Walsh John P. , Li Yue , Adan Roger , Luykx Jurjen J.
Published: September 2020

To examine differences in the genetic architecture of BMI between tall and short people, we conducted genome-wide and follow-up analyses using UK Biobank data. We identify 57 loci as height-specific, detect differences in SNP-based heritability between tall and short people and show how genetic correlations between the two rises during the lifespan. Using phenome-wide analyses (PHEWAS), a significant association between a short people-specific locus onMC4Rand energy portion size was detected. We identify one locus (GPC5-GPC6)with different effect directions on BMI in short and tall people. PHEWAS indicates this locus is associated with bone mineral density. Transcriptome-wide analyses hint that genes differentially associated with BMI in short vs tall people are enriched in brain tissue. Our findings highlight the role of height in the genetic underpinnings of BMI, provide biological insight into mechanisms underlying height-dependent differences in BMI and show that in short and tall people obesity is a risk factor that differentially increases susceptibility for disease.
Field testing of biohybrid robotic jellyfish to demonstrate enhanced swimming speeds
Authors: Xu Nicole W. , Townsend James P. , Costello John H. , Colin Sean P. , Gemmell Bradford J. , Dabiri John O.
Published: September 2020

Biohybrid robotic designs incorporating live animals and self-contained microelectronic systems can leverage the animals’ own metabolism to reduce power constraints and act as natural chassis and actuators with damage tolerance. Previous work established that biohybrid robotic jellyfish can exhibit enhanced speeds up to 2.8 times their baseline behavior in laboratory environments. However, it remains unknown if the results could be applied in natural, dynamic ocean environments and what factors can contribute to large animal variability. Deploying this system in the coastal waters of Massachusetts, we validate and extend prior laboratory work by demonstrating increases in jellyfish swimming speeds up to 2.3 times greater than their baseline, with absolute swimming speeds up to 6.6 ± 0.3 cm s-1. These experimental swimming speeds are predicted using a hydrodynamic model with morphological and time-dependent input parameters obtained from field experiment videos. The theoretical model can provide a basis to choose specific jellyfish with desirable traits to maximize enhancements from robotic manipulation. With future work to increase maneuverability and incorporate sensors, biohybrid robotic jellyfish can potentially be used track environmental changes in applications for ocean monitoring.
Sequence dependence of biomolecular phase separation
Authors: Weiner Benjamin G. , Meir Yigal , Wingreen Ned S.
Published: September 2020

Cells are home to a wide variety of biomolecular condensates - phase-separated droplets that lack a membrane. In addition to nonspecific interactions, phase separation depends on specific binding motifs between constituent molecules. Nevertheless, few rules have been established on how these specific, heterotypic interactions drive phase separation. Using lattice-polymer simulations and mean-field theory, we show that the sequence of binding motifs strongly affects a polymer’s ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity and polymer diffusion). We find that sequences with large blocks of a single motif typically form more inter-polymer bonds which promote phase separation. Notably, the sequence of binding motifs influences phase separation primarily by determining the conformational entropy of self-bonding by single polymers. This contrasts with systems where the molecular architecture primarily affects the energy of the dense phase, providing a new entropy-based mechanism for the biological control of phase separation.
Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic?
Authors: Chen Mingliang , Harrison Odile B. , Bratcher Holly B. , Bo Zhiyan , Jolley Keith A. , Rodrigues Charlene M.C. , Bray James E. , Guo Qinglan , Zhang Xi , Chen Min , Maiden Martin C.J.
Published: September 2020

The expansion of quinolone-resistantNeisseria meningitidisclone ChinaCC4821-R1-C/Bfrom ST-4821 clonal complex (cc4821) caused a serogroup shift from serogroup A to C in invasive meningococcal disease (IMD) in China. To establish the relationship among globally distributed cc4821 meningococci, we analysed whole genome sequence data from 173 cc4821 meningococci isolated in four continents from 1972-2019. These meningococci clustered into four sub-lineages (1-4), with sub-lineage 1 primarily comprising serogroup C IMD isolates (82%, 41/50). Most isolates from outside China formed a distinct sub-lineage (81.6%, 40/49, the Europe-USA cluster), with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(cc4821) and harbouring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/Bhas expanded to other countries. The increasing global distribution of B:cc4821 meningococci raises concern that cc4821 has the potential to cause a global pandemic and, this would be challenging to control though there is indirect evidence that Trumenba®vaccine might afford some protection.
Hits-Based Quantitative Characterization of SOBI-Recovered P3 Network Configuration: an EEG Source-Imaging Study
Authors: Privitera Adam John , Fung Renee , Hua Yunqing , Tang Akaysha C.
Published: September 2020

One frequently studied biomarker for health and disease conditions is the P3 component extracted from scalp recorded electroencephalography (EEG). The spatial origin of this significant neural signal is known to be distributed, typically involving large regions of the cerebral cortex as well as subcortical structures. Unlike the temporal characterization of the P3 by amplitude or latency measures from event-related potentials (ERPs), the spatial characterization of the P3 component is relatively rare, typically qualitative, and often reported as differences between populations (group differences between healthy controls and clinical groups). Here we introduce a novel approach to quantitatively characterize the spatial origin of the P3 component by (1) applying second-order blind identification (SOBI) to continuous, high-density EEG data to extract the P3 component, (2) modeling the underlying generators of the SOBI P3 component as a set of equivalent current dipoles (ECDs) in Talairach space using BESA; (3) using the application Talairach Client to determine the “hits” associated with the anatomical structures at three level of resolution (lobe, gyrus, and cell type). We show that the hits information provided by Talairach Client can enable a quantitative characterization of the spatial configuration of the network underlying the P3 component (P3N) via two quantities: cross-individual reliability (or consistency) of a given brain structure as a part of the P3N, and within-individual contribution of a given brain structure to the whole P3N network. We suggest that this method may be used to further differentiate individuals in the absence of differences in P3 amplitude or latency, or when scientific questions or practical application cannot be supported by a yes-no answer regarding the source of a P3 component. Finally, application of our method to a group of 13 participants revealed that frontal structures, particularly BA10, play a special role in the function of a global cortical network underlying novelty processing.
A high-affinity RBD-targeting nanobody improves fusion partner’s potency against SARS-CoV-2
Authors: Yao Hebang , Cai Hongmin , Li Tingting , Zhou Bingjie , Qin Wenming , Lavillette Dimitri , Li Dianfan
Published: September 2020

A key step to the SARS-CoV-2 infection is the attachment of its Spike receptor-binding domain (S RBD) to the host receptor ACE2. Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. Simple and effective strategies to increase potency are desirable for such studies when antibodies are only modestly effective. Here, we identify and characterize a high-affinity synthetic nanobody (sybody, SR31) as a fusion partner to improve the potency of RBM-antibodies. Crystallographic studies reveal that SR31 binds to RBD at a conserved and ‘greasy’ site distal to RBM. Although SR31 distorts RBD at the interface, it does not perturb the RBM conformation, hence displaying no neutralizing activities itself. However, fusing SR31 to two modestly neutralizing sybodies dramatically increases their affinity for RBD and neutralization activity against SARS-CoV-2 pseudovirus. Our work presents a tool protein and an efficient strategy to improve nanobody potency.
Disinhibitory circuitry gates associative synaptic plasticity in olfactory cortex
Authors: Canto-Bustos Martha , Friason F. Kathryn , Bassi Constanza , Oswald Anne-Marie M.
Published: September 2020

Inhibitory microcircuits play an essential role in regulating cortical responses to sensory stimuli. Interneurons that inhibit dendritic or somatic integration in pyramidal neurons act as gatekeepers for neural activity, synaptic plasticity and the formation of sensory representations. Conversely, interneurons that specifically inhibit other interneurons can open gates through disinhibition. In the rodent piriform cortex, relief of dendritic inhibition permits long-term potentiation (LTP) of the recurrent synapses between pyramidal neurons (PNs) thought to underlie ensemble odor representations. We used an optogenetic approach to identify the inhibitory interneurons and disinhibitory circuits that regulate LTP. We focused on three prominent inhibitory neuron classes-somatostatin (SST), parvalbumin (PV), and vasoactive intestinal polypeptide (VIP) interneurons. We find that LTP is gated by the inactivation SST or PV interneurons or by activation of VIP interneurons. Further, activation of VIP interneurons strongly inhibits putative SST-cells during LTP induction, but only weakly inhibit PV-interneurons. Taken together, these findings suggest that VIP-interneurons mediate a disinhibitory circuit that can regulate synaptic plasticity during olfactory processing.
Increased oxidative stress tolerance of a spontaneously-occurringperRgene mutation inStreptococcus mutansUA159
Authors: Kajfasz Jessica K. , Zuber Peter , Ganguly Tridib , Abranches Jacqueline , Lemos José A.
Published: September 2020

The ability of bacteria such as the dental pathogenStreptococcus mutansto coordinate a response against damage-inducing oxidants is a critical aspect of their pathogenicity. The oxidative stress regulator SpxA1 has been proven to be a major player in the ability ofS. mutansto withstand both disulfide and peroxide stresses. While studying spontaneously-occurring variants of anS. mutansΔspxA1strain, we serendipitously discovered that ourS. mutansUA159 host strain bore a single nucleotide deletion within the coding region ofperR, resulting in a premature truncation of the encoded protein. PerR is a metal-dependent transcriptional repressor that senses and responds to peroxide stress such that loss of PerR activity results in activation of oxidative stress responses. To determine the impact of loss of PerR regulation, we obtained a UA159 isolated bearing an intactperRcopy and created a cleanperRdeletion mutant. Our findings indicate that loss of PerR activity results in a strain that is primed to tolerate oxidative stresses in the laboratory setting. Interestingly, RNA-Seq and targeted transcriptional expression analyses reveal that PerR has a minor contribution to the ability ofS. mutansto orchestrate a transcriptional response to peroxide stress. Furthermore, we detected loss-of-functionperRmutations in two other commonly used laboratory strains ofS. mutanssuggesting that this may be not be an uncommon occurrence. This report serves as a cautionary warning regarding the so-called domestication of laboratory strains and advocates for the implementation of more stringent strain authentication practices.

Importance

A resident of the human oral biofilm,Streptococcus mutansis one of the major bacterial pathogens associated with dental caries. This report highlights a spontaneously-occurring mutation within the laboratory strainS. mutansUA159, found in the coding region ofperR, a gene encoding a transcriptional repressor associated with peroxide tolerance. ThoughperRmutant strains ofS. mutansshowed a distinct growth advantage and enhanced tolerance toward H2O2, a ΔperRdeletion strain showed a small number of differentially expressed genes as compared to the parent strain, suggesting few direct regulatory targets. In addition to characterizing the role of PerR inS. mutans, our findings serve as a warning to laboratory researchers regarding bacterial adaptation toin vitrogrowth conditions.
TgIF2K-B is an eIF2α kinase inToxoplasma gondiithat responds to oxidative stress and optimizes pathogenicity
Authors: Augusto Leonardo , Martynowicz Jennifer , Amin Parth H. , Carlson Kenneth R. , Wek Ronald C. , Sullivan William J.
Published: September 2020

Toxoplasma gondiiis an obligate intracellular parasite that persists in its vertebrate hosts in the form of dormant tissue cysts, which facilitate transmission through predation. The parasite must strike a balance that allows it to disseminate throughout its host without killing it, which requires the ability to properly counter host cell defenses. For example, oxidative stress encountered byToxoplasmais suggested to impair parasite replication and dissemination. However, the strategies by whichToxoplasmamitigates oxidative stress are not completely clear. Among eukaryotes, environmental stresses induce the integrated stress response via phosphorylation of a translation initiation factor, eIF2. Here, we show that theToxoplasmaeIF2 kinase, TgIF2K-B, is activated in response to oxidative stress and affords protection. Knockout of TgIF2K-B, Δtgif2k-b, disrupted parasite responses to oxidative stresses and enhanced replication, diminishing the ability of the parasite to differentiate into tissue cysts. In addition, parasites lacking TgIF2K-B exhibited resistance to activated macrophages and showed greater virulence in anin vivomodel of infection. Our results establish that TgIF2K-B is essential forToxoplasmaresponses to oxidative stress, which are important for the parasite’s ability to establish persistent infection in its host.

IMPORTANCE

Toxoplasma gondiiis a single-celled parasite that infects nucleated cells of warm-blooded vertebrates, including one-third of the human population. The parasites are not cleared by the immune response and persist in the host by converting into a latent tissue cyst form. Development of tissue cysts can be triggered by cellular stresses, which activate a family of TgIF2 kinases to phosphorylate the eukaryotic translation initiation factor, TgIF2α. Here, we establish that the TgIF2 kinase TgIF2K-B is activated by oxidative stress and is critical for maintaining oxidative balance in the parasite. Depletion of TgIF2K-B alters gene expression, leading to accelerated growth and a diminished ability to convert into tissue cysts. This study establishes that TgIF2K-B is essential for the parasite’s oxidative stress response and its ability to persist in the host as a latent infection.
Temporal stability and genetic diversity of 48-year old T-series phages
Authors: Subedi Dinesh , Barr Jeremy J.
Published: September 2020

T-series phages have been model organisms for molecular biology since the 1940s. Given that these phages have been stocked, distributed, and propagated for decades across the globe, there exists the potential for genetic drift to accumulate between stocks over time. Here we compared the temporal stability and genetic relatedness of laboratory-maintained phage stocks with a T-series collection from 1972. Only the T-even phages produced viable virions. We obtained complete genomes of these T-even phages, along with two contemporary T4 stocks. Performing comparative genomics, we found 12 and 16 nucleotide variations, respectively, in the genomes of T2 and T6; whereas there were ~172 nucleotide variations between T4-sublines when compared with NCBI RefSeq genome. To account for the possibility of artefacts in the NCBI RefSeq, we used the 1972 T4 stock as a reference and compared genetic and phenotypic variations between T4-sublines. Genomic analysis predicted nucleotide variations in genes associated with DNA metabolism and structural proteins. We did not however, observe any differences in growth characteristics or host range between the T4-sublines. Our study highlights the potential for genetic drift between individually maintained T-series phage stocks, yet after 48-years, this has not resulted in phenotypic alternations in these important model organisms.

Importance

T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology – from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories. However, we observed genetic variability when compared contemporary sublines of T4-phages to a 48-year old stock of T4. This may have effects in the comparability of results obtained using T4 phage. Here, we highlighted the genomic differences between T4 sublines and examined phenotypic differences in phage replication parameters. We observed limited genomic changes but no phenotypic variations between T4 sublines. Our research highlights the possibility of genetic drift in model bacteriophages.
The level of oncogenic Ras controls the malignant transformation of Lkb1 mutant tissue in vivo
Authors: Rackley Briana , Seong Chang-Soo , Kiely Evan , Parker Rebecca E. , Rupji Manali , Dwivedi Bhakti , Heddleston John M. , Giang William , Anthony Neil , Chew Teng-Leong , Gilbert-Ross Melissa
Published: September 2020

The genetic and metabolic heterogeneity of RAS-driven cancers has confounded therapeutic strategies in the clinic. To address this, rapid and genetically tractable animal models are needed that recapitulate the heterogeneity of RAS-driven cancers in vivo. Here, we generate aDrosophila melanogastermodel of Ras/Lkb1mutant carcinoma. We show that low-level expression of oncogenic Ras (RasLo) promotes the survival of Lkb1 mutant tissue, but results in autonomous cell cycle arrest and non-autonomous overgrowth of wild-type tissue. In contrast, high-level expression of oncogenic Ras (RasHi) transforms Lkb1 mutant tissue resulting in lethal malignant tumors. Using simultaneous multiview light-sheet microcopy, we have characterized invasion phenotypes ofRas/Lkb1tumors in living larvae. Our molecular analysis reveals sustained activation of the AMPK pathway in malignantRas/Lkb1tumors, and demonstrate the genetic and pharmacologic dependence of these tumors on CaMK-activated Ampk. We further show that LKB1 mutant human lung adenocarcinoma patients with high levels of oncogenic KRAS exhibit worse overall survival and increased AMPK activation. Our results suggest that high levels of oncogenic KRAS is a driving event in the malignant transformation of LKB1 mutant tissue, and uncover a novel vulnerability that may be used to target this aggressive genetic subset of RAS-driven tumors.

One Sentence Summary

A multivariable Ras-drivenDrosophilamodel reveals a novel LKB1 mutant lung adenocarcinoma patient subpopulation and targetable effector pathway.
Structure and substrate specificity determinants of the taurine biosynthetic enzyme cysteine sulphinic acid decarboxylase
Authors: Mahootchi Elaheh , Raasakka Arne , Luan Weisha , Muruganandam Gopinath , Loris Remy , Haavik Jan , Kursula Petri
Published: September 2020

Pyridoxal 5′-phosphate (PLP) is an important cofactor for amino acid decarboxylases with many biological functions, including the synthesis of signalling molecules, such as serotonin, dopamine, histamine,γ-aminobutyric acid, and taurine. Taurine is an abundant amino acid with multiple physiological functions, including osmoregulation, pH regulation, antioxidative protection, and neuromodulation. In mammalian tissues, taurine is mainly produced by decarboxylation of cysteine sulphinic acid to hypotaurine, catalysed by the PLP-dependent cysteine sulphinic acid decarboxylase (CSAD), followed by non-enzymatic oxidation of the product to taurine. We determined the crystal structure of mouse CSAD and compared it to other PLP-dependent decarboxylases in order to identify determinants of substrate specificity and catalytic activity. Recognition of the substrate involves distinct side chains forming the substrate-binding cavity. In addition, the backbone conformation of a buried active-site loop appears to be a critical determinant for substrate side chain binding in PLP-dependent decarboxylases. Phe94 was predicted to affect substrate specificity, and its mutation to serine altered both the catalytic properties of CSAD and its stability. Using small-angle X-ray scattering, we further showed that similarly to its closest homologue, GADL1, CSAD presents open/close motions in solution. The structure of apo-CSAD indicates that the active site gets more ordered upon internal aldimine formation. Taken together, the results highlight details of substrate recognition in PLP-dependent decarboxylases and provide starting points for structure-based inhibitor design with the aim of affecting the biosynthesis of taurine and other abundant amino acid metabolites.
Role of the SUT1 and SUT2 sugar transporters during stolbur phytoplasma infection in tomato
Authors: Marco Federica De , Batailler Brigitte , Thorpe Michael R. , Razan Frédérique , Hir Rozenn Le , Vilaine Françoise , Bouchereau Alain , Martin-Magniette Marie-Laure , Eveillard Sandrine , Dinant Sylvie
Published: September 2020

Phytoplasmas inhabit phloem sieve elements and cause abnormal growth and altered sugar partitioning. But how they interact with phloem functions is not clearly known. The phloem responses were investigated in tomato infected by ‘CandidatusPhytoplasma solani’, at the beginning of the symptomatic stage of infection, both in symptomatic and asymptomatic leaves, the first symptoms appearing in the sink top leaf at the stem apex. Antisense lines impaired in the phloem sucrose transporters SUT1 and SUT2 were included. The infection in source leaves was not associated with symptoms. In the symptomatic, sink leaf, yellowing and leaf curling was associated with higher starch accumulation and expression of defense genes. The transcriptional analysis of symptomatic leaf midribs indicated that transcript levels for genes acting in the glycolysis and peroxisome metabolism in infected plants differed from these in non-infected plants. Phytoplasma multiplied actively in at least three additional lower leaves although they were symptomless, with no sign of activation of defense markers, although the rate of exudation of sucrose from these symptomless, source leaves was lower for infected plants. A few metabolites in phloem-enriched exudate were affected by the infection, such as glycolate and aspartate, and some of them were also affected in the controlSUT1- andSUT2- antisense lines, in which sucrose retrieval or release in the sieve elements are impaired. A metabolic switch could explain the delivery of more glycolate into the sieve elements of infected plants. The findings suggest a link between sugar transport and redox homeostasis.

One sentence summary

An impairment of sucrose retrieval and release in the sieve elements occurs during phytoplasma infection, associated with changes in sugar and peroxisome metabolism
Prophylactic intranasal administration of a TLR2 agonist reduces upper respiratory tract viral shedding in a SARS-CoV-2 challenge ferret model
Authors: Proud Pamela C. , Tsitoura Daphne , Watson Robert J. , Chua Brendon Y , Aram Marilyn J. , Bewley Kevin R. , Cavell Breeze E. , Cobb Rebecca , Dowall Stuart , Fotheringham Susan A. , Ho Catherine M. K. , Lucas Vanessa , Ngabo Didier , Rayner Emma , Ryan Kathryn A. , Slack Gillian S. , Thomas Stephen , Wand Nadina I. , Yeates Paul , Demaison Christophe , Jackson David C. , Bartlett Nathan W. , Mercuri Francesca , Carroll Miles W.
Published: September 2020

Respiratory viruses such as coronaviruses represent major ongoing global threats, causing epidemics and pandemics with huge economic burden. Rapid spread of virus through populations poses an enormous challenge for outbreak control. Like all respiratory viruses, the most recent novel human coronavirus SARS-CoV-2, initiates infection in the upper respiratory tract (URT). Infected individuals are often asymptomatic, yet highly infectious and readily transmit virus. A therapy that restricts initial replication in the URT has the potential to prevent progression of severe lower respiratory tract disease as well as limiting person-to-person transmission.

We show that prophylactic intra-nasal administration of the TLR2/6 agonist INNA-051 in a SARS-CoV-2 ferret infection model effectively reduces levels of viral RNA in the nose and throat. The results of our study support clinical development of a therapy based on prophylactic TLR2/6 innate immune activation in the URT to reduce SARS-CoV-2 transmission and provide protection against COVID-19.
Molecular basis of F-actin regulation and sarcomere assemblyviamyotilin
Authors: Kostan Julius , Pavšič Miha , Puž Vid , Schwarz Thomas C. , Drepper Friedel , Molt Sibylle , Graewert Melissa Ann , Schreiner Claudia , Sajko Sara , van der Ven Peter F.M. , Svergun Dmitri I. , Warscheid Bettina , Konrat Robert , Fürst Dieter O. , Lenarčič Brigita , Djinović-Carugo Kristina
Published: September 2020

Sarcomeres, the basic contractile units of striated muscle cells, contain arrays of thin (actin) and thick (myosin) filaments that slide past each other during contraction. The Ig-like domain containing protein myotilin provides structural integrity to Z-discs - the boundaries between adjacent sarcomeres. Myotilin binds to Z-disc components, including F-actin and α-actinin-2, but the molecular mechanism of binding and implications of these interactions on Z-disc integrity are still elusive. We used a combination of small angle X-ray scattering, cross-linking mass spectrometry, biochemical and molecular biophysics approaches. We discovered that myotilin displays conformational ensembles in solution. We generated a structural model of the F-actin:myotilin complex that revealed how myotilin interacts with and stabilizes F-actinviaits Ig-like domains and flanking regions. Mutant myotilin designed with impaired F-actin binding showed increased dynamics in cells. Structural analyses and competition assays uncovered that myotilin displaces tropomyosin from F-actin. Our findings suggest a novel role of myotilin as a co-organizer of Z-disc assembly and advance our mechanistic understanding of myotilin’s structural role in Z-discs.

Significance Statement

Sarcomeres are the primary structural and functional unit of striated muscles, conferring movement in all animals. The Z-disk is the boundary between adjacent sarcomeres, where actin filaments (F-actin) are anchored. Z-disc protein myotilin, is a scaffold protein, which provides structural integrity to the Z-disc by multiple interactions to its central components, including F-actin and α-actinin-2. Here we provide the structure of myotilin, revealing its structural plasticity in solution and the first integrative structural model of its complex with F-actin. We further show that myotilin displaces tropomyosin from F-actin, implying a novel role of myotilin in sarcomere biogenesis beyond being an interaction hub for Z-disk partners.

Highlights

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Myotilin is structurally described as a dynamic ensemble

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Flanking regions enhance F-acting binding to tandem Ig domains

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Integrative structural model of myotilin bound to F-actin

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Myotilin displaces tropomyosin from F-actin, suggesting an organisational role in Z-disc
Type III-A CRISPR systems as a versatile gene knockdown technology
Authors: Woodside Walter T. , Vantsev Nikita , Terns Michael P.
Published: September 2020

CRISPR-Cas systems are functionally diverse prokaryotic anti-viral defense systems, which encompass six distinct types (I-VI) that each encode different effector Cas nucleases with distinct nucleic acid cleavage specificities. By harnessing the unique attributes of the various CRISPR-Cas systems, a range of innovative CRISPR-based DNA and RNA targeting tools and technologies have been developed. Here, we exploit the ability of type III-A CRISPR-Cas systems to carry out RNA-guided and sequence-specific target RNA cleavage for establishment of research tools for post-transcriptional control of gene expression. Type III-A systems from three bacterial species (L. lactis, S. epidermidisandS. thermophilus) were each expressed on a single plasmid inE. coliand the efficiency and specificity of gene knockdown was assessed by Northern blot analysis. We show that engineered type III-A modules can be programmed using tailored CRISPR RNAs to efficiently knock down gene expression of both coding and non-coding RNAsin vivo. Moreover, simultaneous degradation of multiple cellular mRNA transcripts can be directed by utilizing a CRISPR array expressing corresponding gene-targeting crRNAs. Our results demonstrate the utility of distinct type III-A modules to serve as effective gene knockdown platforms in heterologous cells. This transcriptome engineering technology has the potential to be further refined and exploited for key applications including gene discovery and gene pathway analyses in additional prokaryotic and perhaps eukaryotic cells and organisms.
Sequence Analysis for SNP Detection and Phylogenetic Reconstruction of SARS-CoV-2 Isolated from Nigerian COVID-19 Cases
Authors: Taiwo Idowu A. , Adeleye Nike , Anwoju Fatimah O. , Adeyinka Adeyemi , Uzoma Ijeoma C. , Bankole Taiwo T.
Published: September 2020

Background

Coronaviruses are a group of viruses that belong to the Family Coronaviridae, GenusBetacoronavirus. In December 2019, a new coronavirus disease (COVID-19) characterized by severe respiratory symptoms was discovered. The causative pathogen was a novel coronavirus known as 2019-nCoV and later as SARS-CoV-2. Within two months of its discovery, COVID-19 became a pandemic causing widespread morbidity and mortality.

Methodology

Whole genome sequence data of SARS-CoV-2 isolated from Nigerian COVID-19 cases were retrieved by downloading from GISAID database. A total of 18 sequences that satisfied quality assurance (length ≥ 29700 nts and number of unknown bases denoted as ‘N’ ≤ 5%) were used for the study. Multiple sequence alignment (MSA) was done in MAFFT (Version 7.471) while SNP calling was implemented in DnaSP (Version 6.12.03) respectively and then visualized in Jalview (Version 2.11.1.0). Phylogenetic analysis was with MEGA X software.

Results

Nigerian SARS-CoV-2 had 99.9% genomic similarity with four large conserved genomic regions. A total of 66 SNPs were identified out of which 31 were informative. Nucleotide diversity assessment gave Pi = 0.00048 and average SNP frequency of 2.22 SNPs per 1000 nts. Non-coding genomic regions particularly 5’UTR and 3’UTR had a SNP density of 3.77 and 35.4 respectively. The region with the highest SNP density was ORF10 with a frequency of 8.55 SNPs/1000 nts). Majority (72.2%) of viruses in Nigeria are of L lineage with preponderance of D614G mutation which accounted for 11 (61.1%) out of the 18 viral sequences. Nigeria SARS-CoV-2 revealed 3 major clades namely Oyo, Ekiti and Osun on a maximum likelihood phylogenetic tree.

Conclusion and Recommendation

Nigerian SARS-CoV-2 reveals high mutation rate together with preponderance of L lineage and D614G mutants. Implication of these mutations for SARS-CoV-2 virulence and the need for more aggressive testing and treatment of COVID-19 in Nigeria is discussed. Additionally, attempt to produce testing kits for COVID-19 in Nigeria should consider the conserved regions identified in this study. Strict adherence to COVID-19 preventive measure is recommended in view of Nigerian SARS-CoV-2 phylogenetic clustering pattern, which suggests intensive community transmission possibly rooted in communal culture characteristic of many ethnicities in Nigeria.
On the Origins of Conductive-Pulse Sensing Inside a Nanopore
Authors: Lastra Lauren S. , Bandara Y. M. Nuwan D. Y. , Nguyen Michelle , Farajpour Nasim , Freedman Kevin J.
Published: September 2020

Nanopore sensing is nearly synonymous with resistive pulse sensing due to the characteristic reduction of ionic flux during molecular occupancy of a pore, particularly at high salt concentrations. However, conductive pulses are widely reported at low salt conditions wherein electroosmotic flow can be quite significant. Aside from transporting molecules like DNA, we investigated whether electroosmotic flow has other potential impacts on sensing attributes such current enhancements due to the analyte molecule. The overwhelming majority of literature reports counterions as the dominant mechanism of conductive events (a moleculecentric theory for conductive events). Conductive events are not well understood due to the complex interplay between (charged) nanopore walls, DNA grooves, ion mobility, and counterion clouds. Yet, the prevailing consensus of counterions being introduced into the pore by the molecule does not fit well with a growing number of experiments including the fact that proteins can generate conductive events despite having a heterogeneous surface charge. Herein, we demonstrate theory and experiments underpinning the translocation mechanism (i.e., electroosmosis or electrophoresis), pulse direction (i.e., conductive or resistive) and shape (e.g., monophasic or biphasic) through fine control of chemical, physical, and electronic parameters. Results from these studies predict strong electroosmosis plays a role in driving DNA events and generating conductive events due to polarization effects (i.e. a pore-centric theory). We believe these findings will stimulate a useful discussion on the nature of conductive events and their impact on molecular sensing in nanoscale pores.
Differential modulation of thermal preference after sensitization by optogenetic or pharmacological activation of heat-sensitive nociceptors
Authors: Li Jerry , Zain Maham , Bonin Robert P.
Published: September 2020

Common approaches to studying chronic pain in pre-clinical animal models paradoxically involve measuring reflexive withdrawal responses that are more indicative of acute nociceptive pain. These methods typically do not capture the ongoing nature of chronic pain nor report on behavioral changes associated with pain. In addition, data collection and analysis protocols are often labour-intensive and require direct investigator interactions, potentially introducing bias. In this study, we develop and characterize a low-cost, easily assembled behavioral assay that yields self-reported temperature preference from mice which is sensitive to peripheral sensitization protocols. This system uses a partially automated and freely available analysis pipeline to streamline the data collection process and enable objective analysis. We found that after intraplantar administration of the TrpV1 agonist, capsaicin, mice preferred to stay in cooler temperatures than control injected mice. We further observed that gabapentin, a non-opioid analgesic commonly prescribed to treat chronic pain, reversed this aversion to higher temperatures. We further observed that optogenetic activation of the central terminals of TrpV1+ primary afferents viain vivospinal light delivery did not induce a similar change in thermal preference, indicating a role for peripheral nociceptor activity in the modulation of temperature preference. We conclude that this easily produced and robust sensory assay provides an alternative approach to investigate the contribution of central and peripheral mechanisms to pathological sensory processing that does not rely on reflexive responses evoked by noxious stimuli.
Regulation of gene transcription by thyroid hormone receptor β agonists in clinical development for the treatment of non-alcoholic steatohepatitis (NASH)
Authors: Luong Xuan G. , Stevens Sarah K. , Jekle Andreas , Lin Tse-I , Gupta Kusum , Misner Dinah , Chanda Sushmita , Mukherjee Sucheta , Williams Caroline , Stoycheva Antitsa , Blatt Lawrence M. , Beigelman Leonid N. , Symons Julian A. , Raboisson Pierre , McGowan David , Vandyck Koen , Deval Jerome
Published: September 2020

Thyroid hormones are important modulators of metabolic activity in mammals and alter cholesterol and fatty acid levels through activation of the nuclear thyroid hormone receptor (THR). Currently, there are several THRβ agonists in clinical trials for the treatment of non-alcoholic steatohepatitis (NASH) that have demonstrated the potential to reduce liver fat and restore liver function. In this study, we tested three THRβ-agonism-based NASH treatment candidates, GC-1 (sobetirome), MGL-3196 (resmetirom), and VK2809, and compared their selectivity for THRβ and their ability to modulate the expression of genes specific to cholesterol and fatty acid biosynthesis and metabolismin vitrousing human hepatic cells andin vivousing a rat model. Treatment with GC-1 upregulated the transcription ofCPT1Ain the human hepatocyte-derived Huh-7 cell line with a dose-response comparable to that of the native THR ligand, triiodothyronine (T3). VK2809A (active parent of VK2809), MGL-3196, and VK2809 were approximately 30-fold, 1,000-fold, and 2,000-fold less potent than T3, respectively. Additionally, these relative potencies were confirmed by quantification of other direct gene targets of THR, namely,ANGPTL4andDIO1. In primary human hepatocytes, potencies were conserved for every compound except for VK2809, which showed significantly increased potency that was comparable to that of its active counterpart, VK2809A. In high-fat diet fed rats, a single dose of T3 significantly reduced total cholesterol levels and concurrently increased liverDio1andMe1RNA expression. MGL-3196 treatment resulted in concentration-dependent decreases in total and low-density lipoprotein cholesterol with corresponding increases in liver gene expression, but the compound was significantly less potent than T3. In conclusion, we have implemented a strategy to rank the efficacy of THRβ agonists by quantifying changes in the transcription of genes that lead to metabolic alterations, an effect that is directly downstream of THR binding and activation.