bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on Biofilm Formation byPsuedomonas Aeruginosain Different Urinary Catheters
Authors: Asante Emmanuel 
Published: February 2021

ABSTRACTUrinary Catheters are the leading cause of healthcare –associated Urinary Tract Infections (UTIs) making their use a necessary evil. Various models and approaches had been developed to help reduce the complications associated with the use of these catheters. This study aimed at investigating how two different types of urinary catheters (Silicone Catheter and Latex Coated Catheter) support biofilm formation ofPseudomonas aeruginosaisolates. The growth rate of the bacteria and the rate of formation of biofilm on each urinary catheter was determined by preparing biofilm assays, ranking them using crystal violet satins and measuring their absorbance using UV-VIS spectrophotometer. A difference in the level of biofilm in the catheters were observed. The differences in the level of biofilm observed in the catheters imply that different catheters may have different susceptibility for the formation of biofilms. The study recommends the assessment of biofilm formation in the quality evaluation of catheters. Also further studies should be done to investigate how different catheter material support biofilm formation and the mechanisms involved.
cpn60 barcode sequences accurately identify newly defined genera within theLactobacillaceae
Authors: Shukla Ishika , Hill Janet E. 
Published: February 2021

AbstractThe cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of “universal” PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species inLactobacillus, Paralactobacillusand the 23 newer genera showed that cpn60-based sequence relationships were consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.Significance and Impact of the StudyThe genusLactobacillusrecently underwent a major reorganization resulting in the definition of 23 new genera. Lactobacilli are widespread in environmental and host-associated microbiomes and are exploited in food and biotechnology applications, making methods for their accurate identification desirable. Here we show that the combination of a reference sequence database, “universal” barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.
RNase R, a new virulence determinant ofStreptococcus pneumoniae
Authors: Bárria Cátia , Mil-Homens Dalila , Fialho Arsénio M. , Arraiano Cecília Maria , Domingues Susana 
Published: February 2021

ABSTRACTPneumococcal infections have increasingly high mortality rates despite the availability of vaccines and antibiotics. The increase of bacterial resistance to antibiotics urges the discovery of new alternative therapeutics. Therefore, the identification of new virulence determinants, and the understanding of the molecular mechanisms behind pathogenesis and pneumococcal-host interactions has become of paramount importance in the search of new targets for drug development. The exoribonuclease RNase R has been involved in virulence in a growing number of pathogens. In this work, we have usedGalleria mellonellaas an infection model to demonstrate that the presence of ribonuclease R increases the pneumococcus virulence. Although the absence of RNase R does not affect exponential growth, the ability of the RNase R deleted strain to replicate in the hemolymph is compromised. Larvae infected with the RNase R mutant strain show an increased expression level of antimicrobial peptides, and have a lower bacterial load in the haemolymph in the later stages of infection, leading to a higher survival rate. Interestingly RNase R carrying pneumococci suffer a sudden drop in bacterial numbers immediately after infection, resembling the eclipse phase observed after intravenous inoculation in mice. Together our results suggest that RNase R might be involved in the ability of pneumococci to evade the host immune response, probably by interfering with internalisation and/or replication inside the larval hemocytes.
Downregulation of Extraembryonic Tension Controls Body Axis Formation in Avian Embryos
Authors: Kunz Daniele , Wang Anfu , Chan Chon U , Pritchard Robyn H. , Wang Wenyu , Gallo Filomena , Bradshaw Charles R. , Terenzani Elisa , Müller Karin H. , Huang Yan Yan Shery , Xiong Fengzhu 
Published: February 2021

AbstractEmbryonic tissues undergoing shape change draw mechanical input from extraembryonic substrates. In avian eggs, the early blastoderm disk is under the tension of the vitelline membrane (VM). Here we report that the chicken VM characteristically downregulates tension and stiffness to facilitate stage-specific embryo morphogenesis. Experimental relaxation of the VM early in development impairs blastoderm expansion, while maintaining VM tension in later stages resists the convergence of the posterior body causing stalled elongation, failure of neural tube closure, and axis rupture. Biochemical and structural analysis shows that VM weakening is associated with the reduction of outer-layer glycoprotein fibers, which is caused by an increasing albumen pH due to CO2release from the egg. Our results identify a previously unrecognized potential cause of body axis defects through mis-regulation of extraembryonic tissue tension.
Metabolic characteristics of taste differences under the soil and hydroponic cultures of sweet potato leaves by using non-targeted metabolomics
Authors: Lin Zhaomiao , Li Guoliang , Zhang Hong , Ji Rongchang , Xu Yongqing , Xu Guochun , Li Huawei , Liu Zhonghua , Luo Wenbin , Qiu Yongxiang , Qiu Sixin , Tang Hao 
Published: February 2021

ABSTRACTSweet potato leaves are consumed as green leafy vegetables in most of the world due to their nutritional and functional values, and the taste characteristics determine their commodity value and consumer acceptance. However, the metabolic composition and formation mechanism of taste quality in its leaves are not clear. In this study, we found that sweet potato leaves under different growing patterns, soil culture and hydroponic culture, which result in different taste quality. In particular, the taste quality in leafy sweet potato was effectively improved under hydroponic culture. Meanwhile, we further profiled metabolites in leaves of sweet potatoes under different growing patterns by using GC–QToF–MS. A total of 200 metabolites were identified, covering most of the metabolic pathways in plants. A comparison of the good taste and poor taste of sweet potato leaves resulted in 71 metabolites related to taste quality formation. In addition, the leaves with poor taste had lower levels of metabolites regarding amino acids metabolism, whereas was accompanied by high levels of metabolites in carbohydrates and secondary metabolism. This study provides new insights into the improvement of taste quality in leafy sweet potato.
Free Energy Landscape of RNA Binding Dynamics in Start Codon Recognition by Eukaryotic Ribosomal Pre-Initiation Complex
Authors: Kameda Takeru , Asano Katsura , Togashi Yuichi 
Published: February 2021

AbstractSpecific interaction between the start codon, 5’-AUG-3’, and the anticodon, 5’-CAU-3’, ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. GUG and CUG) can play a role in initiating translation in eukaryotes. However, the mechanism allowing initiation through mismatched base-pairs at the ribosomal decoding site is still unclear at an atomic level. In this work, we propose an extended simulation-based method to evaluate free energy profiles, through computing the distance between each base-pair of the triplet interactions (d1,d2andd3) involved in recognition of start codons in eukaryotic translation pre-initiation complex. Our method provides not only the free energy penalty (ΔΔG) for mismatched start codons relative to the AUG start codon, but also the preferred pathways of transitions between bound and unbound states, which has not been described by previous studies. To verify the method, the binding dynamics of cognate (AUG) and near-cognate start codons (CUG and GUG) were simulated. Evaluated free energy profiles agree with experimentally observed changes in initiation frequencies from respective codons. This work proposes for the first time how a G:U mismatch at the first position of codon (GUG)-anticodon base-pairs destabilizes the accommodation in the initiating eukaryotic ribosome and how initiation at a CUG codon is nearly as strong as, or sometimes stronger than, that at a GUG codon. Our method is expected to be applied to study the affinity changes for various mismatched base-pairs.
Chitosan-olive oil microparticles for phenylethyl isothiocyanate delivery: optimal formulation
Authors: Coscueta Ezequiel R. , Sousa Ana Sofia , Reis Celso A. , Pintado Manuela 
Published: February 2021

AbstractPhenylethyl isothiocyanate (PEITC), a chemopreventive compound, is highly reactive due to its considerably electrophilic nature. Furthermore, it is hydrophobic and has low stability, bioavailability and bioaccessibility, restricting its use in biomedical and nutraceutical or food applications. Thus, the encapsulation of this agent has the function of overcoming these limitations, promoting its solubility in water, and stabilizing it, preserving its bioactivity. So, polymeric microparticles were developed using chitosan-olive oil-PEITC systems. For this, an optimisation process (factors: olive oil: chitosan ratio and PEITC: chitosan ratio) were implemented through a central composite design. The responses were: the particle size, zeta-potential, polydisperse index, and entrapment efficiency. The optimal formulation was further characterized by FTIR and biocompatibility in Caco-2 cells. Optimal conditions were olive oil: chitosan and PEITC: chitosan ratios of 1.46 and 0.25, respectively. These microparticles had a size of 629 nm, a zeta-potential of 32.3 mV, a polydispersity index of 0.329, and an entrapment efficiency of 98.49%. We found that the inclusion process affected the optical behaviour of the PEITC, as well as the microparticles themselves and their interaction with the medium. Furthermore, the microparticles did not show cytotoxicity within the therapeutic values of PEITC. Thus, PEITC was microencapsulated with characteristics suitable for potential biomedical, nutraceutical and food applications.
A missense variant effect prediction and annotation resource for SARS-CoV-2
Authors: Dunham Alistair , Jang Gwendolyn M , Muralidharan Monita , Swaney Danielle , Beltrao Pedro 
Published: February 2021

AbstractThe COVID19 pandemic is a global crisis severely impacting many people across the world. An important part of the response is monitoring viral variants and determining the impact they have on viral properties, such as infectivity, disease severity and interactions with drugs and vaccines. In this work we generate and make available computational variant effect predictions for all possible single amino-acid substitutions to SARS-CoV-2 in order to complement and facilitate experiments and expert analysis. The resulting dataset contains predictions from evolutionary conservation and protein and complex structural models, combined with viral phosphosites, experimental results and variant frequencies. We demonstrate predictions’ effectiveness by comparing them with expectations from variant frequency and prior experiments. We then identify higher frequency variants with significant predicted effects as well as finding variants measured to impact antibody binding that are least likely to impact other viral functions. A web portal is available atsars.mutfunc.com, where the dataset can be searched and downloaded.
Population monitoring of snow leopards using camera trapping in Naryn State Reserve, Kyrgyzstan, between 2016 and 2019
Authors: Rode Julie , Lambert Claire , Marescot Lucile , Chaix Bastien , Beesau Julie , Bastian Suzanne , Kyrbashev Joldoshbek , Cabanat Anne-Lise 
Published: February 2021

AbstractFour field seasons of snow leopard (Panthera uncia) camera trapping inside Naryn State Reserve, performed thanks to citizen science expeditions, allowed detecting a minimal population of five adults, caught every year with an equilibrated sex ratio (1.5:1), and reproduction: five cubs or subadults have been identified from three litters of two different females. Crossings were observed one to three times a year, in front of most camera traps, and several times a month in front of one of them. Overlap of adults’ territories was observed in front of several camera traps regardless of their sex. Significant snow leopard presence was detected in the buffer area and at Ulan, situated at the reserve border. To avoid poaching on this umbrella species and its preys, extending the more stringent protection measures of the core zone to both the Southern buffer area and land adjacent to Ulan is necessary.
Disruption of the mitochondrial geneorf352partially restores pollen development in cytoplasmic male sterile rice
Authors: Omukai Shiho , Arimura Shin-ich , Toriyama Kinya , Kazama Tomohiko 
Published: February 2021

AbstractPlant mitochondrial genomes sometimes carry cytoplasmic male sterility (CMS)-associated genes. These genes have been harnessed in agriculture to produce high-yielding F1hybrid seeds in various crops. The geneorf352was reported to be an RT102-type CMS gene in rice (Oryza sativa), although a causal demonstration of its role in CMS is lacking. Here, we employed mitochondrion-targeted transcription activator-like effector nucleases (mitoTALENs), to knock outorf352from the mitochondrial genome in the cytoplasmic male sterile rice RT102A. We isolated 18 independent transformation events in RT102A that resulted in genome editing oforf352, including its complete removal from the mitochondrial genome in several plants. Sequence analysis around the mitoTALEN target sites revealed the repair of their induced double-strand breaks via homologous recombination. Near the 5ʹ target site, repair involved sequences identical toorf284, while repair of the 3ʹ target site yielded various new sequences that generated new chimeric genes consistingorf352fragments. Plants with a new mitochondrial gene encoding amino acids 179 to 352 of ORF352 exhibited the same shrunken pollen grain phenotype as RT102A, whereas plants either lackingorf352or harboring a new gene encoding amino acids 211 to 352 of ORF352 showed partial rescue of pollen viability and germination, although they failed to set seed. These results demonstrated that disruption oforf352partially restored pollen development, indicating that amino acids 179 to 210 from ORF352 may contribute to the establishment of pollen abortion.
Intra-helical salt bridge contribution to membrane protein insertion
Authors: Duart Gerard , Lamb John , Ortiz-Mateu Juan , Elofsson Arne , Mingarro Ismael 
Published: February 2021

ABSTRACTSalt bridges between negatively (D, E) and positively charged (K, R, H) amino acids play an important role in protein stabilization. This has a more prevalent effect in membrane proteins where polar amino acids are exposed to a very hydrophobic environment. In transmembrane (TM) helices the presence of charged residues can hinder the insertion of the helices into the membrane. This can sometimes be avoided by TM region rearrangements after insertion, but it is also possible that the formation of salt bridges could decrease the cost of membrane integration. However, the presence of intra-helical salt bridges in TM domains and their effect on insertion has not been properly studied yet. In this work, we use an analytical pipeline to study the prevalence of charged pairs of amino acid residues in TM α-helices, which shows that potentially salt-bridge forming pairs are statistically over-represented. We then selected some candidates to experimentally determine the contribution of these electrostatic interactions to the translocon-assisted membrane insertion process. Using bothin vitroandin vivosystems, we confirm the presence of intra-helical salt bridges in TM segments during biogenesis and determined that they contribute between 0.5-0.7 kcal/mol to the apparent free energy of membrane insertion (ΔGapp). Our observations suggest that salt bridge interactions can be stabilized during translocon-mediated insertion and thus could be relevant to consider for the future development of membrane protein prediction software.
Transport Dynamics of MtrD: an RND Multidrug Efflux Pump fromNeisseria gonorrhoeae
Authors: Ammerman Lauren , Mertz Sarah B. , Park Chanyang , Wise John G. 
Published: February 2021

AbstractThe MtrCDE system confers multidrug resistance toNeisseria gonorrhoeae, the causative agent of gonorrhea. Using free and directed Molecular Dynamics (MD) simulations, we analyzed the interactions between MtrD and Azithromycin, a transport substrate of MtrD and a last-resort clinical treatment for multidrug resistant gonorrhea. We then simulated the interactions between MtrD and Streptomycin, an apparent non-substrate of MtrD. Using known conformations of MtrD homologues, we simulated a potential dynamic transport cycle of MtrD using Targeted MD techniques (TMD), and we note that forces were not applied to ligands of interest. In these TMD simulations, we observed the transport of Azithromycin and the rejection of Streptomycin. In an unbiased, long-timescale simulation of AZY-bound MtrD, we observed the spontaneous diffusion of Azithromycin through the periplasmic cleft. Our simulations show how the peristaltic motions of the periplasmic cleft facilitate the transport of substrates by MtrD. Our data also suggest that multiple transport pathways for macrolides may exist within the periplasmic cleft of MtrD.
Identical Sequences, Different Behaviors: Protein Diversity Captured at the Single-Molecule Level
Authors: Tapia-Rojo Rafael , Alonso-Caballero Alvaro , Badilla Carmen L. , Fernandez Julio M. 
Published: February 2021

AbstractThe classical “one sequence, one structure, one function” paradigm has shaped much of our intuition of how proteins work inside the cell. Partially due to the insight provided by bulk biochemical assays, individual biomolecules are assumed to behave as identical entities, and their characterization relies on ensemble averages that flatten any conformational diversity into a unique phenotype. While the emergence of single-molecule techniques opened the gates to interrogating individual molecules, technical shortcomings typically limit the duration of these measurements to a few minutes, which prevents to completely characterize a protein individual and, hence, to capture the heterogeneity among molecular populations. Here, we introduce a magnetic tweezers design, which showcases enhanced stability and resolution that allows us to measure the folding dynamics of a single protein during several uninterrupted days with a high temporal and spatial resolution. Thanks to this instrumental development, we do a complete characterization of two proteins with a very different force-response: the talin R3IVVIdomain and protein L. Days-long recordings on the same single molecule accumulate several thousands of folding transitions sampled with sub-ms resolution, which allows us to reconstruct their free energy landscapes and describe how they evolve with force. By mapping the nanomechanical identity of many different protein individuals, we directly capture their molecular diversity as a quantifiable dispersion on their force response and folding kinetics. Our instrumental development offers a new tool for profiling individual molecules, opening the gates to the characterization of biomolecular heterogeneity.
Implications of central carbon metabolism in SARS-CoV-2 replication and disease severity
Authors: Krishnan Shuba , Nordqvist Hampus , Ambikan Anoop T. , Gupta Soham , Sperk Maike , Svensson-Akusjärvi Sara , Mikaeloff Flora , Benfeitas Rui , Saccon Elisa , Ponnan Sivasankaran Munusamy , Rodriguez Jimmy Esneider , Nikouyan Negin , Odeh Amani , Ahlén Gustaf , Asghar Muhammad , Sällberg Matti , Vesterbacka Jan , Nowak Piotr , Végvári Ákos , Sönnerborg Anders , Treutiger Carl Johan , Neogi Ujjwal 
Published: February 2021

AbstractViruses hijack host metabolic pathways for their replicative advantage. Several observational trans-omics analyses associated carbon and amino acid metabolism in coronavirus disease 2019 (COVID-19) severity in patients but lacked mechanistic insights. In this study, using patient- derived multi-omics data andin vitroinfection assays, we aimed to understand i) role of key metabolic pathways in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) reproduction and ii) its association with disease severity. Our data suggests that monocytes are key to the altered immune response during COVID-19. COVID-19 infection was associated with increased plasma glutamate levels, while glucose and mannose levels were determinants of the disease severity. Monocytes showed altered expression pattern of carbohydrate and amino acid transporters, GLUT1 and xCT respectively in severe COVID-19. Furthermore, lung epithelial cells (Calu-3) showed a strong acute metabolic adaptation following infectionin vitroby modulating central carbon metabolism. We found that glycolysis and glutaminolysis are essential for virus replication and blocking these metabolic pathways caused significant reduction in virus production. Taken together, our study highlights that the virus utilizes and re-wires pathways governing central carbon metabolism leading to metabolic toxicity. Thus, the host metabolic perturbation could be an attractive strategy to limit the viral replication and disease severity.
Postembryonic development of the two-spotted field cricket (Gryllus bimaculatus): a staging system
Authors: Neiro Jakke 
Published: February 2021

AbstractThe two-spotted field cricketGryllus bimaculatushas emerged as a central model for studies on insect development, regeneration, and physiology.G. bimaculatushas the most sophisticated functional genetic toolkit of any hemimetabolous insect, making it a foremost model to understand the evolutionary developmental biology and comparative physiology of insects. However, the morphology and stages of postembryonic development have never been comprehensively reported. Here, 8 morphologically defined stages are described. Size, coloration, and the morphology of wing buds, hind tibial spines, and the ovipositor are the best landmarks for staging. The stages correspond to the 8-12 moult-based instars present in the literature. The staging system aims to standardise studies on the postembryonic development ofG. bimaculatusand serve as a point of reference for delineating interspecific postembryonic homologies within Orthoptera.