bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHigh-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.ImportanceHigh-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

AbstractPlants 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

AbstractA 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

AbstractCurrent 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

AbstractFood 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

ABSTRACTAtherosclerotic 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

AbstractHeart 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

AbstractThe 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

AbstractInEscherichia 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

AbstractLong-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 StatementLearning 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.