bluuebunny/crossref_metadata_2025 huggingface dataset:
Fecal microbial transplant abates tolerance to methylone-induced hyperthermia
Authors: Goldsmith Robert , Aburahma Amal , Pachhain Sudhan , Choudhury Sayantan Roy , Phuntumart Vipa , Larsen Ray , Sprague Jon E.
Published: January 2021

The microbiome-gut-brain axis has been implicated in multiple bodily systems and pathologies, and intentional manipulation of the gut-microbiome has yielded clinically significant results. Here, we examined the effects of bi-directional fecal microbial transplants (FMT) between methylone-induced hyperthermic tolerant (MHT) and methylone-naïve (MN) rats. Rats treated with methylone once per week developed tolerance to methylone-induced hyperthermia by the fourth week. Once tolerant, daily bi-directional FMT between the two groups were performed for seven days prior to the next methylone treatment. The FMT abated the developed tolerance in the MHT group. When treated with methylone for the first time following FMT, recipient MN rats displayed significant tolerance to hyperthermia despite it being their initial drug treatment. Post-FMT, MHT rats displayed elevations in norepinephrine and expression ofUCP1,UCP3andTGR5in brown adipose tissue, with reductions in expression ofTGR5andUCP3in skeletal muscle. The pre- and post-FMT methylone tolerance phenotypes of transplant recipients are concurrent with changes in the relative abundance of several Classes ofProteobacteria, most evident forGammaproteobacterandAlphaproteobacter.MHT recipients demonstrated a marked increase in the relative proportion of theFirmicutesClassErysipelotrichia. These findings suggest that transplantation of gut-microbiomes can confer phenotypic responses to a drug.
Low-pathogenic virus induced immunity against TBEV protects mice from disease but not from virus entry into the CNS
Authors: Petry Monique , Palus Martin , Leitzen Eva , Mitterreiter Johanna Gracia , Huang Bei , Kröger Andrea , Verjans Georges M.G.M , Baumgärtner Wolfgang , Rimmelzwaan Guus F. , Růžek Daniel , Osterhaus Albert , Prajeeth Chittappen Kandiyil
Published: January 2021

Tick-borne encephalitis virus (TBEV) is a leading cause of vector-borne viral encephalitis with expanding endemic regions across Europe. Although currently used inactivated whole virus vaccines are effective, vaccination breakthroughs have been reported for which the reasons are unclear. In this study we tested in mice the efficacy of pre-infection with a closely related low-virulent flavivirus, Langat virus (LGTV strain TP21), or a naturally avirulent TBEV strain (TBEV-280) in providing protection against lethal infection with the highly virulent TBEV strain TBEV-Hypr (referred to as TBEV-Hypr). LGTV has been evaluated as an experimental live vaccine against TBE, but further development was abandoned due to too high residual pathogenicity of a LGTV-based vaccine. Here we show that prior infection with TP21 or TBEV-280 is efficient in protecting mice from lethal TBEV-Hypr challenge. Histopathological analysis of brains from non-immunized control mice revealed neuronal TBEV infection and necrosis. Neuroinflammation, gliosis and neuronal necrosis was however also observed in some of the TP21 and TBEV-280 pre-infected mice although at reduced frequency as compared to the non-immunized TBEV-Hypr infected control mice. Interestingly, qPCR detected the presence of viral RNA in the brains and spinal cord of both TP21 and TBEV-280 immunized mice after TBEV-Hypr challenge, but significantly reduced compared to mock-immunized mice. Our results indicate that although TBEV-Hypr infection is effectively controlled in the periphery upon immunization with low-virulent LGTV or naturally avirulent TBEV-280, it may still enter the CNS of these animals. These findings improve our understanding of potential causes for vaccine failure in individuals vaccinated with TBE vaccines.
Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle ofSalmonella enterica
Authors: Powers TuShun R. , Haeberle Amanda L. , Hammarlöf Disa L. , Cundiff Jennifer A. , Predeus Alexander V. , Hokamp Karsten , Hinton Jay C.D. , Knodler Leigh A.
Published: January 2021

Salmonella entericaserovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis,S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract.S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derivedSalmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered byS.Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies ofS. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined thatSalmonellais exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimalS. Typhimurium replication in the cytosol, as well asentC,fepB,soxSandsitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namelySalmonellapathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolarS. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.

Author Summary

Intracellular pathogens reside either within a membrane-bound vacuole or are free-living in the cytosol and their virulence programs are tailored towards survival within a particular intracellular compartment. Some bacterial pathogens (such asSalmonella enterica) can successfully colonize both intracellular niches, but how they do so is unclear. Here we have exploited the parallel intracellular lifestyles ofS. entericain epithelial cells to identify the niche-specific bacterial expression profiles and environmental cues encountered byS. enterica. We have also discovered bacterial genes that are required for colonization of the cytosol, but not the vacuole. Our results advance our understanding of pathogen-adaptation to alternative replication niches and highlight an emerging concept in the field of bacteria-host cell interactions.
Characterization of 475 novel, putative small RNAs (sRNAs) in Carbon-starvedSalmonella entericaserovar typhimurium
Authors: Houserova Dominika , Dahmer Donavon J. , Amin Shivam V. , Crucello Aline , King Valeria M. , Barnhill Emmaline C. , Huang Yulong , Zambrano Mike E. , Dean Meghan A. , Aria Kevin M. , Spector Michael P. , Borchert Glen M.
Published: January 2021

An increasingly apparent role of noncoding RNA (ncRNAs) is to coordinate gene expression when bacteria faces various environmental stressors.Salmonella enterica, a well-studied foodborne pathogen, is known for its ability to survive in and adapt to various environmental challenges, making it a difficult pathogen to eliminate, as well as an important model for examining ncRNA contributions to cellular stress survival. A mounting body of evidence implicates small RNAs (sRNAs) as key drivers ofSalmonellastress response. Generally thought to be 50-500 nucleotides in length and to occur mainly in intergenic regions, sRNAs regulate protein expression through base pairing with mRNA targets. Through employing a refined definition of sRNAs that allows for shorter sequences and for sRNA loci to overlap with annotated protein-coding gene loci, we have identified 475 previously unannotated sRNAs that are significantly differentially expressed during Carbon starvation (C-starvation). Northern blotting and quantitative RT-PCRs confirm the expressions and identities of several of these novel sRNAs. Additionally, our computational analyses find the majority to be highly conserved and structurally-related to known sRNAs. Importantly, we show that deletion of one of the dynamic sRNAs, sRNA4130247, significantly impairs theSalmonellaC-starvation response (CSR), confirming its involvement (and suggesting the involvements of many other sRNAs identified in this work) in theSalmonellaCSR. Strikingly, the 475 novel sRNAs identified in this study more than double the number ofSalmonella entericaserovar Typhimurium SL1344 sRNAs described to date, increasing the total number of annotatedSalmonellasRNAs from 396 to 871. In conclusion, the work presented here provides the first-ever characterization of intragenic sRNAs inSalmonella, experimentally confirms that sRNAs dynamically expressed during the CSR are directly involved in stress survival, and strongly suggests that sRNA loci likely outnumber those of protein-coding genes inSalmonella.
Voxel-wise and spatial modelling of binary lesion masks: Comparison of methods with a realistic simulation framework
Authors: Kindalova Petya , Kosmidis Ioannis , Nichols Thomas E.
Published: January 2021

Objectives

White matter lesions are a very common finding on MRI in older adults and their presence increases the risk of stroke and dementia. Accurate and computationally efficient modelling methods are necessary to map the association of lesion incidence with risk factors, such as hypertension. However, there is no consensus in the brain mapping literature whether a voxel-wise modelling approach is better for binary lesion data than a more computationally intensive spatial modelling approach that accounts for voxel dependence.

Methods

We review three regression approaches for modelling binary lesion masks including massunivariate probit regression modelling with either maximum likelihood estimates, or mean bias-reduced estimates, and spatial Bayesian modelling, where the regression coefficients have a conditional autoregressive model prior to account for local spatial dependence. We design a novel simulation framework of artificial lesion maps to compare the three alternative lesion mapping methods. The age effect on lesion probability estimated from a reference data set (13,680 individuals from the UK Biobank) is used to simulate a realistic voxel-wise distribution of lesions across age. To mimic the real features of lesion masks, we propose matching brain lesion summaries (total lesion volume, average lesion size and lesion count) across the reference data set and the simulated data sets. Thus, we allow for a fair comparison between the modelling approaches, under a realistic simulation setting.

Results

Our findings suggest that bias-reduced estimates for voxel-wise binary-response generalized linear models (GLMs) overcome the drawbacks of infinite and biased maximum likelihood estimates and scale well for large data sets because voxel-wise estimation can be performed in parallel across voxels. Contrary to the assumption of spatial dependence being key in lesion mapping, our results show that voxel-wise bias-reduction and spatial modelling result in largely similar estimates.

Conclusion

Bias-reduced estimates for voxel-wise GLMs are not only accurate but also computationally efficient, which will become increasingly important as more biobank-scale neuroimaging data sets become available.
Cell cortex microtubules contribute to division plane positioning during telophase in maize
Authors: Bellinger Marschal A. , Uyehara Aimee N. , Martinez Pablo , McCarthy Michael C. , Rasmussen Carolyn G.
Published: January 2021

The phragmoplast is a plant-specific microtubule and microfilament structure that forms during telophase to direct new cell wall formation. The phragmoplast expands towards a specific location at the cell cortex called the division site. How the phragmoplast accurately reaches the division site is currently unknown. We show that a previously uncharacterized microtubule arrays accumulated at the cell cortex. These microtubules were organized by transient interactions with division-site localized proteins and were then incorporated into the phragmoplast to guide it towards the division site. A phragmoplast-guidance defective mutant,tangled1, had aberrant cortical-telophase microtubule accumulation that correlated with phragmoplast positioning defects. Division-site localized proteins may promote proper division plane positioning by organizing the cortical-telophase microtubule array to guide the phragmoplast to the division site during plant cell division.

One Sentence Summary

Microtubules accumulate at the cell cortex and interact with the plant division machinery to direct its movement towards the division site.
Deficiency of intellectual disability-related geneBrpf1reduced inhibitory neurotransmission andMap2k7expression in GABAergic interneurons
Authors: Cao Jingli , Xian Weiwei , Palihati Maierdan , Zhu Yu , Wang Guoxiang , Xie Yunli , Zhou Guomin , You Linya
Published: January 2021

Intellectual disability is closely related to impaired GABA neurotransmission.Brpf1was specifically expressed in medial ganglionic eminence (MGE), a developmental niche of GABAergic interneurons, and patients withBRPF1mutations were mentally retarded. To test its role in development and function of MGE-derived GABAergic interneurons, we performed immunofluorescence staining, whole-cell patch-clamp, MGE transplantation and mRNA-Seq to understand its effect on neuronal differentiation, dendritic morphology, electrophysiology, migration and gene regulation, using mouse MGE-derived GABAergic interneurons infected with AAV-shBrpf1. We found a decreasing trend on parvalbumin+interneuron differentiation. Moreover, increased firing threshold, decreased number of evoked APs, and a reduced amplitude of mIPSCs were observed before any significant change of MAP2+dendritic morphology andin vivomigration appeared. Finally, mRNA-Seq analysis revealed that genes related to neurodevelopment and synaptic transmission such asMap2k7were dysregulated. Our results demonstrated a key role ofBrpf1in inhibitory neurotransmission and related gene expression of GABAergic interneurons.
Cross-tissue, single-cell stromal atlas identifies shared pathological fibroblast phenotypes in four chronic inflammatory diseases
Authors: Korsunsky Ilya , Wei Kevin , Pohin Mathilde , Kim Edy Y. , Barone Francesca , Kang Joyce B. , Friedrich Matthias , Turner Jason , Nayar Saba , Fisher Benjamin A. , Raza Karim , Marshall Jennifer L. , Croft Adam P. , Sholl Lynette M. , Vivero Marina , Rosas Ivan O. , Bowman Simon J. , Coles Mark , Frei Andreas P. , Lassen Kara , Filer Andrew , Powrie Fiona , Buckley Christopher D. , Brenner Michael B. , Raychaudhuri Soumya
Published: January 2021

Pro-inflammatory fibroblasts are critical to pathogenesis in rheumatoid arthritis, inflammatory bowel disease, interstitial lung disease, and Sjögren’s syndrome, and represent a novel therapeutic target for chronic inflammatory disease. However, the heterogeneity of fibroblast phenotypes, exacerbated by the lack of a common cross-tissue taxonomy, has limited the understanding of which pathways are shared by multiple diseases. To investigate, we profiled patient-derived fibroblasts from inflamed and non-inflamed synovium, intestine, lung, and salivary glands with single-cell RNA-sequencing. We integrated all fibroblasts into a multi-tissue atlas to characterize shared and tissue-specific phenotypes. Two shared clusters, CXCL10+CCL19+immune-interacting and SPARC+COL3A1+vascular-interacting fibroblasts were expanded in all inflamed tissues and additionally mapped to dermal analogues in a public atopic dermatitis atlas. We further confirmed these human pro-inflammatory fibroblasts in animal models of lung, joint, and intestinal inflammation. This work represents the first cross-tissue, single-cell fibroblast atlas revealing shared pathogenic activation states across four chronic inflammatory diseases.
Synthesis, Characterization, and Nanodisc formation of Non-ionic Polymers
Authors: Ravula Thirupathi , Ramamoorthy Ayyalusamy
Published: January 2021

Despite lipid-nanodiscs are increasingly used in the structural studies of membrane proteins, drug delivery and other applications, the interaction between the nanodisc-belt and the protein to be reconstituted is a major limitation. To overcome this limitation and to further broaden the scope of nanodiscs, a family of non-ionic amphiphilic polymers synthesized by hydrophobic functionalization of fructo-oligosaccharides/inulin is reported. We show the stability of lipid-nanodiscs formed by these polymers against pH and divalent metal ions, and their magnetic-alignment properties. The reported results also demonstrate that the non-ionic polymers extract membrane proteins with unprecedented efficiency.
Cryo-EM Structures of the N501Y SARS-CoV-2 Spike Protein in Complex with ACE2 and Two Potent Neutralizing Antibodies
Authors: Zhu Xing , Mannar Dhiraj , Srivastava Shanti S. , Berezuk Alison M. , Demers Jean-Philippe , Saville James W , Leopold Karoline , Li Wei , Dimitrov Dimiter S. , Tuttle Katharine S. , Zhou Steven , Chittori Sagar , Subramaniam Sriram
Published: January 2021

The recently reported “UK variant” of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-EM structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. The additional interactions result in increased affinity of ACE2 for the N501Y mutant, accounting for its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to two representative potent neutralizing antibody fragments.

Short summary

The N501Y mutation found in the coronavirus UK variant increases infectivity but some neutralizing antibodies can still bind.
Alterations in gut microbiota linked to provenance, sex, and chronic wasting disease in white-tailed deer (Odocoileus virginianus)
Authors: Minich David , Madden Christopher , Evans Morgan V. , Ballash Gregory A. , Barr Daniel J. , Poulsen Keith P. , Dennis Patricia M. , Hale Vanessa L.
Published: January 2021

Chronic wasting disease (CWD) is a fatal, contagious, neurodegenerative prion disease affecting both free-ranging and captive cervid species. CWD is spread via direct or indirect contact or oral ingestion of prions. In the gastrointestinal tract, prions enter the body through microfold cells (M-cells), and the abundance of these cells can be influenced by the gut microbiota. To explore potential links between the gut microbiota and CWD, we collected fecal samples from farmed and free-ranging white-tailed deer (Odocoileus virginianus) around the Midwest. Farmed deer orignated from farms that were depopulated due to CWD. Free-ranging deer were sampled during annual deer harvests. All farmed deer were tested for CWD via ELISA and IHC, and we used 16S rRNA gene sequencing to characterize the gut microbiota. We report significant differences in gut microbiota by provenance (Farm 1, Farm 2, Free-ranging), sex, and CWD status. CWD-positive deer from Farm 1 and 2 had increased abundances ofAkkermansia,LachnospireaceaUCG-010, and RF39 taxa. Overall, differences by provenance and sex appear to be driven by diet, while differences by CWD status may be linked to CWD pathogenesis.
Screening by deep sequencing reveals mediators of microRNA tailing inC. elegans
Authors: Vieux Karl-Frédéric , Prothro Katherine , Kelley Leanne H. , Maine Eleanor M. , Veksler-Lublinsky Isana , McJunkin Katherine
Published: January 2021

microRNAs are frequently modified by addition of untemplated nucleotides to the 3’ end, but the role of this tailing is often unclear. Here we characterize the prevalence and functional consequences of microRNA tailingin vivo, usingC. elegans.MicroRNA tailing inC. elegansconsists mostly of mono-uridylation of mature microRNA species, with rarer mono-adenylation which is likely added to microRNA precursors. Through a targeted RNAi screen, we discover that the TUT4/TUT7 gene family member CID-1/CDE-1/PUP-1 is required for uridylation, whereas the GLD2 gene family member F31C3.2 – here namedGLD-2-related2(GLDR-2) – is required for adenylation. Thus, the TUT4/TUT7 and GLD2 gene families have broadly conserved roles in miRNA modification. We specifically examine the role of tailing in microRNA turnover. We determine half-lives of microRNAs after acute inactivation of microRNA biogenesis, revealing that half-lives are generally long (median=20.7h), as observed in other systems. Although we observe that the proportion of tailed species increases over time after biogenesis, disrupting tailing does not alter microRNA decay. Thus, tailing is not a global regulator of decay inC. elegans. Nonetheless, by identifying the responsible enzymes, this study lays the groundwork to explore whether tailing plays more specialized context- or miRNA-specific regulatory roles.
Quantitative analysis of signaling responses during mouse primordial germ cell specification
Authors: Morgani Sophie M. , Hadjantonakis Anna-Katerina
Published: January 2021

During early mammalian development, the pluripotent cells of the embryo are exposed to a combination of signals that drive exit from pluripotency and germ layer differentiation. At the same time, a small population of pluripotent cells give rise to the primordial germ cells (PGCs), the precursors of the sperm and egg, which pass on heritable genetic information to the next generation. Despite the importance of PGCs, it remains unclear how they are first segregated from the soma, and if this involves distinct responses to their signaling environment. To investigate this question, we mapped BMP, MAPK and WNT signaling responses over time in PGCs and their surrounding nichein vitroandin vivoat single-cell resolution. We showed that, in the mouse embryo, early PGCs exhibit lower BMP and MAPK responses compared to neighboring extraembryonic mesoderm cells, suggesting the emergence of distinct signaling regulatory mechanisms in the germline versus soma. In contrast, PGCs and somatic cells responded comparably to WNT, indicating that this signal alone is not sufficient to promote somatic differentiation. Finally, we investigated the requirement of a BMP response for these cell fate decisions. We found that cell lines with a mutation in the BMP receptor (Bmpr1a−/−), which exhibit an impaired BMP signaling response, can efficiently generate PGC-like cells revealing that canonical BMP signaling is not cell autonomously required to direct PGC-like differentiation.
High-content imaging to phenotype antimicrobial effects on individual bacteria at scale
Authors: Sridhar Sushmita , Forrest Sally , Warne Ben , Maes Mailis , Baker Stephen , Dougan Gordon , Scott Josefin Bartholdson
Published: January 2021

High-content imaging (HCI) is technique for screening multiple cells in high resolution to detect subtle morphological and phenotypic variation. The method has been commonly deployed on model eukaryotic cellular systems, often for screening new drugs and targets. HCI is not commonly utilised for studying bacterial populations but may be powerful tool in understanding and combatting antimicrobial resistance. Consequently, we developed a high-throughput method for phenotyping bacteria under antimicrobial exposure at the scale of individual bacterial cells. Imaging conditions were optimised on an Opera Phenix confocal microscope (Perkin-Elmer) and novel analysis pipelines were established for both Gram-negative bacilli and Gram-positive cocci. The potential of this approach was illustrated using isolates ofKlebsiella pneumoniae, Salmonella entericaserovar Typhimurium, andStaphylococcus aureus. HCI enabled the detection and assessment of subtle morphological characteristics, undetectable through conventional phenotypical methods, that could reproducibly distinguish between bacteria exposed to different classes of antimicrobials with distinct modes of action (MOA). In addition, distinctive responses were observed between susceptible and resistant isolates. By phenotyping single bacterial cells, we observed intra-population differences, which may be critical in identifying persistence or emerging resistance during antimicrobial treatment. The work presented here outlines a comprehensive method for investigating morphological changes at scale in bacterial populations under specific perturbation.

Importance

High-content imaging (HCI) is a microscopy technique that permits the screening of multiple cells simultaneously in high resolution to detect subtle morphological and phenotypic variation. The power of this methodology is that is can generate large datasets comprised of multiple parameters taken from individual cells subjected to range of different conditions. We aimed to develop novel methods for using HCI to study bacterial cells exposed to a range of different antibiotic classes. Using an Opera Phenix confocal microscope (Perkin-Elmer) and novel analysis pipelines we created a method to study the morphological characteristics ofKlebsiella pneumoniae, Salmonella entericaserovar Typhimurium, andStaphylococcus aureuswhen exposed to antibacterial drugs with differing modes of action. By imaging individual bacterial cells at high resolution and scale, we observed intra-population differences associated with different antibiotics. The outlined methods are highly relevant for how we begin to better understand and combat antimicrobial resistance.
Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities
Authors: Schandry Niklas , Jandrasits Katharina , Garrido-Oter Ruben , Becker Claude
Published: January 2021

Plants synthesize and release specialized metabolites into their environment that can serve as chemical cues for other organisms. Metabolites that are released from the roots are important factors in determining which microorganisms will colonize the root and become part of the plant rhizosphere. Root exudates can be converted by soil microorganisms, which can result in the formation of toxic compounds. How individual members of the plant rhizosphere respond to individual compounds and how the differential response of individual microorganisms contributes to the response of a microbial community remains an open question. Here, we investigated the impact of derivatives of benzoxazinoids, a class of plant root exudates released by important crops such as wheat and maize, on a collection of 180 root-associated bacteria. Phenoxazine, derived in soil from benzoxazinoids, inhibited the growth of root-associated bacteriain vitroin an isolate-specific manner, with sensitive and resistant isolates present in most of the studied clades. Using synthetic communities, we show that community stability is a consequence of the resilience of its individual members, with communities assembled from tolerant isolates being overall more tolerant to benzoxazinoids. However, the performance of an isolate in a community context was not correlated with its individual performance but appeared to be shaped by interactions between isolates. These interactions were independent of the overall community composition and were strain-specific, with interactions between different representatives of the same bacterial genera accounting for differential community composition.
Snake venom phospholipases A2 possess a strong virucidal activity against SARS-CoV-2 in vitro and block the cell fusion mediated by spike glycoprotein interaction with the ACE2 receptor
Authors: Siniavin Andrei E. , Nikiforova Maria A. , Grinkina Svetlana D. , Gushchin Vladimir A. , Starkov Vladislav G. , Osipov Alexey V. , Tsetlin Victor I. , Utkin Yuri N.
Published: January 2021

A new coronavirus was recently discovered and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the absence of specific therapeutic and prophylactic agents, the virus has infected almost hundred million people, of whom nearly two million have died from the viral disease COVID-19. The ongoing COVID-19 pandemic is a global threat requiring new therapeutic strategies. Among them, antiviral studies based on natural molecules are a promising approach. The superfamily of phospholipases A2 (PLA2s) consists of a large number of members that catalyze the hydrolysis of phospholipids at a specific position. Here we show that secreted PLA2s from the venom of various snakes protect to varying degrees the Vero E6 cells widely used for the replication of viruses with evident cytopathic action, from SARS-CoV-2 infection PLA2s showed low cytotoxicity to Vero E6 cells and the high antiviral activity against SARS-CoV-2 with IC50 values ranged from 0.06 to 7.71 μg/ml. Dimeric PLA2 HDP-2 from the viper Vipera nikolskii, as well as its catalytic and inhibitory subunits, had potent virucidal (neutralizing) activity against SARS-CoV-2. Inactivation of the enzymatic activity of the catalytic subunit of dimeric PLA2 led to a significant decrease in antiviral activity. In addition, dimeric PLA2 inhibited cell-cell fusion mediated by SARS-CoV-2 spike glycoprotein. These results suggest that snake PLA2s, in particular dimeric ones, are promising candidates for the development of antiviral drugs that target lipid bilayers of the viral envelope and may be good tools to study the interaction of viruses with host cell membranes.
Microbial retention and resistances in stormwater quality improvement devices treating road runoff
Authors: Liguori Renato , Rommel Steffen H. , Bengtsson-Palme Johan , Helmreich Brigitte , Wurzbacher Christian
Published: January 2021

Current knowledge about the microbial communities that occur in in urban road runoff is scarce. Road runoff of trafficked roads can be heavily polluted and is treated by stormwater quality improvement devices (SQIDs). However, microbes may influence the treatment process of these devices or could lead to stress resistant opportunistic microbial strains. In this study, the microbial community in the influent, effluent and the filter materials for the removal of dissolved heavy metals of two different SQIDs were analyzed to determine the microbial load, retention, composition, and mobile resistance genes. Although the microbes were replaced by new taxa in the effluent, there was no major retention of microbial genera. Further, the bacterial abundance of the SQIDs effluent was relatively stable over time. The heavy metal content correlated withintl1and with microbial genera. The filter media itself was enriched withIntl1gene cassettes, carrying several heavy metal and multidrug resistance genes (e.g.czrA,czcA, silP,mexWandmexI), indicating that this is a hot spot for horizontal gene transfer. Overall, the results shed light on road runoff microbial communities, and pointed to distinct bacterial communities within the SQIDs, which subsequently influence the microbial community and the genes released with the treated water.
Species substitution in the meat value chain by high-resolution melt analysis of mitochondrial PCR products
Authors: Njaramba Jane K. , Wambua Lillian , Mukiama Titus , Amugune Nelson Onzere , Villinger Jandouwe
Published: January 2021

Food fraud in several value chains including meat, fish, and vegetables has gained global interest in recent years. In the meat value chain, substitution of high commercial-value meats with similar cheaper or undesirable species is a common form of food fraud that raises ethical, religious, and dietary concerns. The presence of undeclared species could also pose public health risks caused by allergic reactions and the transmission of food-borne or zoonotic pathogens. Measures to monitor meat substitution are being put in place in many developed countries. However, information about similar efforts in sub-Saharan Africa is sparse. In this study, we used PCR coupled with high-resolution melting (PCR-HRM) analysis targeting the three mitochondrial genes, cytochrome oxidase 1 (CO1), cytochrome b (cyt b), and16S rRNA, to detect species substitution in meat sold to consumers in Nairobi, Kenya’s capital city. Out of 107 meat samples from seven common livestock animals (cattle, goat, sheep, pig, chicken, rabbit, and camel), 11 (10.3%) had been substituted. Of 61 samples sold as beef, two were goat and one was camel. Of 30 samples sold as goat meat, four were mutton (sheep) and three were beef. One of nine samples purchased as pork was beef. Our results indicate that PCR-HRM analysis is a cost and time effective technique that can be employed to detect species substitution. The combined use of the three markers produced PCR-HRM profiles that successfully allowed the distinction of species. We demonstrate its utility not only in analysis of raw meat samples, but also of cooked, dried, and rotten samples, meat mixtures, and with the use of different DNA extraction protocols. We propose that this approach has broad applications in authentication of meat products and protection of consumers from food fraud in the meat industry in low- and middle-income countries such as Kenya, as well as in the developed world.
Allosteric MAPKAPK2 Inhibitors Improve Plaque Stability in Advanced Atherosclerosis
Authors: Ozcan Lale , Kasikara Canan , Yurdagul Arif , Kuriakose George , Hubbard Brian , Serrano-Wu Michael H. , Tabas Ira
Published: January 2021

Atherosclerotic vascular disease resulting from unstable plaques is the leading cause of morbidity and mortality in subjects with type 2 diabetes (T2D), and thus a major therapeutic goal is to discover T2D drugs that can also promote atherosclerotic plaque stability. Genetic or pharmacologic inhibition of mitogen-activated protein kinase-activated protein kinase-2 (MK2) in obese mice improves glucose homeostasis and enhances insulin sensitivity. We developed two novel orally active small-molecule inhibitors of MK2, TBX-1 and TBX-2, and tested their effects on metabolism and atherosclerosis in high-fat Western diet (WD)-fedLdlr-/-mice.Ldlr-/-mice were first fed the WD to allow atherosclerotic lesions to become established, and the mice were then treated with TBX-1 or TBX-2. Both compounds improved glucose metabolism and lowered plasma cholesterol and triglyceride, without an effect on body weight. Most importantly, the compounds decreased lesion area, lessened plaque necrosis, and increased fibrous cap thickness in the aortic root lesions of the mice. Thus, in a preclinical model of high-fat feeding and established atherosclerosis, MK2 inhibitors improved metabolism and also enhanced atherosclerotic plaque stability, suggesting potential for further clinical development to address the epidemic of T2D associated with atherosclerotic vascular disease.
Restore mitophagy is essential to prevent cardiac oxidative stress during hypertrophy
Authors: Peugnet Victoriane , Chwastyniak Maggy , Lancel Steve , Bultot Laurent , Fourny Natacha , Beseme Olivia , Loyens Anne , Heyse Wilfried , Amouyel Philippe , Bertrand Luc , Pinet Florence , Dubois-Deruy Emilie
Published: January 2021

Heart failure, mostly associated with cardiac hypertrophy, is still a major cause of illness and death. Oxidative stress causes contractile failure and the accumulation of reactive oxygen species leads to mitochondrial dysfunction, associated with aging and heart failure, suggesting that mitochondria-targeted therapies could be effective in this context. The purpose of this work was to characterize how mitochondrial oxidative stress is involved in cardiac hypertrophy development and to determine if mitochondria-targeted therapies could improve cardiac phenotypes. We used neonatal and adult rat cardiomyocytes (NCMs and ACMs) hypertrophied by isoproterenol (Iso) to induce an increase of mitochondrial superoxide anion. Superoxide dismutase 2 activity and mitochondrial biogenesis were significantly decreased after 24h of Iso treatment. To counteract the mitochondrial oxidative stress induced by hypertrophy, we evaluated the impact of two different anti-oxidants, mitoquinone (MitoQ) and EUK 134. Both significantly decreased mitochondrial superoxide anion and hypertrophy in hypertrophied NCMs and ACMs. Conversely to EUK 134 which preserved cell functions, MitoQ impaired mitochondrial function by decreasing maximal mitochondrial respiration, mitochondrial membrane potential and mitophagy (particularly Parkin expression) and altering mitochondrial structure. The same decrease of Parkin was found in human cardiomyocytes but not in fibroblasts suggesting a cell specificity deleterious effect of MitoQ. Our data showed the importance of mitochondrial oxidative stress in the development of cardiomyocyte hypertrophy. Interestingly, we observed that targeting mitochondria by an anti-oxidant (MitoQ) impaired metabolism specifically in cardiomyocytes. Conversely, the SOD mimic (EUK 134) decreased both oxidative stress and cardiomyocyte hypertrophy and restored impaired cardiomyocyte metabolism and mitochondrial biogenesis.
α-actinin-4 drives invasiveness by regulating myosin IIB expression and myosin IIA localization
Authors: Barai Amlan , Mukherjee Abhishek , Das Alakesh , Saxena Neha , Sen Shamik
Published: January 2021

The mechanisms by which the mechanoresponsive actin crosslinking proteinα-actinin-4 (ACTN4) regulates cell motility and invasiveness remains incompletely understood. Here we show that in addition to regulating protrusion dynamics and focal adhesion formation, ACTN4 transcriptionally regulates expression of non-muscle myosin IIB (NMM IIB), which is essential for mediating nuclear translocation during 3D invasion. We further demonstrate association between NMM IIA and ACTN4 at the cell front ensures retention of NMM IIA at the cell periphery. A protrusion-dependent model of confined migration recapitulating experimental observations predicts a dependence of protrusion forces on the degree of confinement and on the ratio of nucleus to matrix stiffness. Together, our results suggest that ACTN4 is a master regulator of cancer invasion that regulates invasiveness by controlling NMM IIB expression and NMM IIA localization.
Coregulated assembly of actin-like FtsA polymers with FtsZ during Z-ring formation and division inEscherichia coli
Authors: Morrison Josiah J. , Conti Joseph , Camberg Jodi L.
Published: January 2021

InEscherichia coli, the actin homolog FtsA localizes the cell division machinery, beginning with the Z-ring, to the cytoplasmic membrane through direct interaction with FtsZ. FtsZ polymers are first to assemble at the Z-ring at midcell, where they direct constriction and septation. While FtsZ polymerization is critical for establishing a functional Z-ring that leads to constriction, the assembly state of FtsA and the role of FtsA ATP utilization during division inE. coliremain unclear. Here, we show that ATP hydrolysis, FtsZ interaction, and phospholipid vesicle remodeling by FtsA are impaired by a substitution mutation at the predicted active site for hydrolysis. This mutation, Glu 14 to Arg, also impairs Z-ring assembly and division in vivo. To further investigate the role of phospholipid engagement and ATP utilization in regulating FtsA function, we characterized a truncatedE. coliFtsA variant, FtsA(ΔMTS), which lacks the region at the C-terminus important for engaging the membrane and is defective for ATP hydrolysis. We show thatE. coliFtsA(ΔMTS) forms ATP-dependent actin-like filaments and assembly is antagonized by FtsZ. Polymerization of FtsZ with GTP, or a non-hydrolyzable analog, blocks inhibition of ATP-dependent FtsA assembly, and instead favors coassembly of stable FtsA/FtsZ polymers. In the cell, FtsA/FtsZ coassembly is favored at midcell, where FtsZ polymerizes, and inhibited at regions where FtsZ polymers are destabilized by regulators, such as MinC at the poles or SlmA at the nucleoid. We show that MinC prevents recruitment of FtsZ, via FtsA, to phospholipids, suggesting that local interactions of MinC with FtsZ block membrane tethering and uncouple the Z-ring from its major membrane contact. During Z-ring formation, the coassembly of FtsZ polymers with FtsA is coordinated and is a critical early step in division. This step also serves as a checkpoint by responding to the suite of FtsZ assembly regulators in the cell that modulate Z-ring position and dynamics prior to initiating cell wall synthesis.
NMDARs in Granule Cells contribute to parallel fiber - Purkinje cell synaptic plasticity and motor learning
Authors: Schonewille Martijn , Girasole Allison E. , Rostaing Philippe , Mailhes-Hamon Caroline , Ayon Annick , Nelson Alexandra B. , Triller Antoine , Casado Mariano , De Zeeuw Chris I. , Bouvier Guy
Published: January 2021

Long-term synaptic plasticity is believed to be the cellular substrate of learning and memory. Synaptic plasticity rules are defined by the specific complement of receptors at the synapse and the associated downstream signaling mechanisms. In young rodents, at the cerebellar synapse between granule cells (GC) and Purkinje cells (PC), bidirectional plasticity is shaped by the balance between transcellular nitric oxide (NO) driven by presynaptic NMDA receptor (NMDAR) activation and postsynaptic calcium dynamics. However, the role and the location of NMDAR activation in these pathways is still debated in mature animals. Here, we show in adult rodents that NMDARs are present and functional in presynaptic terminals where their activation triggers nitric oxide signaling. In addition, we find that selective genetic deletion of presynaptic, but not postsynaptic, NMDARs prevents synaptic plasticity at parallel fiber-Purkinje cell (PF-PC) synapses. Consistent with this finding, the selective deletion of GCs NMDARs affects adaptation of the vestibulo-ocular reflex. Thus, NMDARs presynaptic to PCs are required for bidirectional synaptic plasticity and cerebellar motor learning.

Significance Statement

Learning depends on synaptic plasticity. The signaling mechanisms that control induction of plasticity determine the learning rules at the specific synapse involved. Moreover, the relationship between the activity patterns of synaptic inputs and the type, direction, and level of plasticity induced may evolve during development. Here, we establish a key link between NMDA receptor activation presynaptic to cerebellar Purkinje cells, downstream signaling mechanisms, and the ability of adult animals to learn a cerebellar motor task.
A compact furnace for in situ X-ray absorption spectroscopy: design, fabrication and study of cationic oxidation states in Pr6O11 and NiO
Authors: Sattayaporn Suchinda , Rodporn Somboonsup , Kidkhunthod Pinit , Chanlek Narong , Yonchai Chutarat , Rujirawat Saroj
Published: January 2021

A well designed compact furnace has been designed for in situ X-ray absorption spectroscopy (XAS). It enables various heat ramps from 300 K to 1473 K. The furnace consists of heaters, a quartz tube, a circulated refrigerator and a power controller. It can generate ohmic heating via an induction process with tantalum filaments. The maximum heating rate exceeds 20 K min−1. A quartz tube with gas feedthroughs allows the mixing of gases and adjustment of the flow rate. The use of this compact furnace allows in situ XAS investigations to be carried out in transmission or fluorescence modes under controlled temperature and atmosphere. Moreover, the furnace is compact, light and well compatible to XAS. The furnace was used to study cationic oxidation states in Pr6O11 and NiO compounds under elevated temperature and reduced atmosphere using the in situ X-ray absorption near-edge structure (XANES) technique at beamline 5.2 SUT-NANOTEC-SLRI of the Synchrotron Light Research Institute, Thailand. At room temperature, Pr6O11 contains a mixture of Pr3+ and Pr4+ cations, resulting in an average oxidation state of +3.67. In situ XANES spectra of Pr (L
3-edge) show that the oxidation state of Pr4+ cations was totally reduced to +3.00 at 1273 K under H2 atmosphere. Considering NiO, Ni2+ species were present under ambient conditions. At 573 K, the reduction process of Ni2+ occurred. The Ni0/Ni2+ ratio increased linearly with respect to the heating temperature. Finally, the reduction process of Ni2+ was completely finished at 770 K.
Study on crystallographic and electronic structure of micrometre-scale ZnO and ZnO:B rods via X-ray absorption fine-structure spectroscopy
Authors: Erat Selma , Ozkendir Osman Murat , Yildirimcan Saadet , Gunaydin Selen , Harfouche Messaoud , Demir Bunyamin , Braun Artur
Published: January 2021

X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine-structure (EXAFS) spectra were recorded to investigate the electronic structure and local crystal structure of ZnO and ZnO:B powders produced via hydrothermal synthesis. ZnO and ZnO:B grow as micrometre-scale rods with hexagonal shape, as confirmed by scanning electron microscopy micrographs. The number of broken ZnO:B rods increases with increasing B concentration, as observed in the images, due to B atoms locating in between the Zn and O atoms which weakens and/or breaks the Zn–O bonds. However, no disorder within the crystallographic structure of ZnO upon B doping is observed from X-ray diffraction results, which were supported by EXAFS results. To determine the atomic locations of boron atoms in the crystal structure and their influence on the zinc atoms, EXAFS data were fitted with calculated spectra using the crystal structure parameters obtained from the crystallographic analysis of the samples. EXAFS data fitting and complementaryk-weight analysis revealed the positions of the B atoms – their positions were determined to be in between the Zn and O atoms.
The role of farmers and organizational networks in climate information communication: the case of Ghana
Authors: Ofoegbu Chidiebere , New Mark
Published: January 2021

Purpose

The nature of the collaborations that exists among the organizations in the climate change and agriculture sectors can influence the tailoring of climate forecasts into information useable for adapting agricultural practices to the risks posed by climate change. Also, the extent to which farmers are integrated into this organizational collaboration network can influence their access to climate information. This paper aims to examine how organizational collaborations in the process of climate information generation and dissemination acts as either barriers or enablers of farmers’ access to and use of climate information in Ghana.

Design/methodology/approach

This study used key informant interview and questionnaire survey to interview the organizations in the climate change and agriculture sectors. Using network analysis as an analytical framework, the authors estimated the networks’ core-periphery, density, reciprocity and degree centrality.

Findings

The authors observed that communication of climate information to farmers is mostly influenced by the collaborations between governmental organizations and nongovernmental organizations. Nevertheless, information flow and exchange through organizational collaboration network is having limited effect on improving farmers’ knowledge about climate risks, impacts and available risk response options. This is mostly because the feedback flow of information from farmers to national level organizations has not been effective in addressing localized climate/agro challenges.

Originality/value

This paper provides a critical overview of key issues in influencing the relevancy and usefulness of climate information in the Ghanaian agriculture sector. Insights gained and recommendations made are essential for deploying effective climate services in Ghana and can be relevant for many African countries because of similar socioeconomic contexts.