bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches
Authors: Kothe Caroline Isabel , Bolotin Alexander , Kraïem Bochra-Farah , Dridi Bedis , Team FoodMicrobiome , Renault Pierre 
Published: November 2020

ABSTRACTHalophilic and halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have only been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses in order to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA andrpoBgene sequences, whose whole genome was sequenced. The most frequently isolated species are the halotolerant Gram-positive bacteriaBrevibacterium aurantiacum(6) andStaphylococcus equorum(3), which are also frequently added as starters. Their genomic analyses confirm the high genetic diversity ofB. aurantiacumand reveal the presence of two subspecies inS. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic cheese bacteria, in particular for the generaHalomonasandPsychrobacter. The use of these genomes as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic and halotolerant bacteria in 74 cheese rind metagenomes. The Gram-negative species are particularly abundant in a wide variety of cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.IMPORTANCESalt is commonly added to food to avoid the growth of pathogens by lowering water activity, resulting in profound changes in the medium that lead to the development of particular ecosystems dominated by halophilic and halotolerant bacteria, communities that probably originate in the natural environment. In order to explore these communities that have been poorly studied in food up until now, we developed a combined approach that includes cultures, genomics and metagenomics to deconstruct these ecosystems in cheese rinds. This approach allowed us to isolate 26 different species, ten of which belong to still undescribed species that could be used as references to promote advances in functional studies of this particular world. The metagenomic scan of 74 cheese rind samples for the assembly of 66 halophilic and halotolerant species showed that these bacteria are widely distributed and form moderately complex ecosystems where related species coexist and probably jointly contribute to safe and efficient cheese development.
Endometrium-on-a-chip reveals the endometrial transcriptome, and protein content of secretome are altered by changes in circulating concentrations of insulin and glucosein vitro
Authors: De Bem Tiago H. C. , Tinning Haidee , Vasconcelos Elton J. R. , Wang Dapeng , Forde Niamh 
Published: November 2020

ABSTRACTThe molecular interactions between the maternal environment and developing embryo that are key for early pregnancy success are known to be influenced by factors such as the metabolic status. We are, however, limited in our understanding of the mechanism by which these individual nutritional stressors alter endometrial function and thein uteroenvironment for early pregnancy success. Here we report for the first time the use of endometrium-on-a-chip microfluidics approach to produce a multi-cellular endometriumin vitro, that is exposed to glucose and insulin concentrations associated with maternal metabolic stressors. Following isolation of endometrial cells (epithelial and stromal) from the uteri of non-pregnant cows in early-luteal phase (Day 4-7 approximately) epithelial cells were seeded into the upper chamber (4-6 104cells/mL) and stromal cells seeded in the lower chamber (1.5-2 104cells/mL). Three different concentration of glucose 1) 0.5 mM 2) 5.0 mM or 3) 50 mM or insulin 1) Vehicle, 2) 1 ng/mL or 3) 10 ng/mL were performed in the endometrial cells at a flow rate of 1µL/min for 72 hr to mimic the rate of secretionin vivo. Quantitative differences in the transcriptomic response of the cells and the secreted proteome ofin vitro-derived uterine luminal fluid (ULF) were determined by RNA-sequencing andTMTrespectively. Changes in maternal glucose altered 21 and 191 protein coding genes in epithelial and stromal cells respectively (p<0.05). While there was a dose-dependent quantitative change in protein secretome (1 and 23 proteins). Insulin resulted in limited transcriptional changes including insulin-like binding proteins that were cell specific (5, 12, and 20) but altered the quantitative secretion of 196 proteins including those involved in extracellular matrix-receptor interaction and proteoglycan signaling in cancer. Collectively, these highlight the potential mechanism by which changes to maternal glucose and insulin alter uterine function.
Baculovirus actin-rearrangement-inducing factor ARIF-1 induces the formation of dynamic clusters of invadosome-like structures
Authors: Lauko Domokos I. , Ohkawa Taro , Mares Sergio E. , Welch Matthew D. 
Published: November 2020

AbstractThe baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV), a pathogen of lepidopteran insects, has a striking dependence on the host cell actin cytoskeleton. During the delayed-early stage of infection, AcMNPV was shown to induce the accumulation of actin at the cortex of infected cells. However, the dynamics and molecular mechanism of cortical actin assembly remained unknown. Here, we show that AcMNPV induces dynamic cortical clusters of dot-like actin structures that resemble clusters of invadosomes in mammalian cells. Furthermore, we find that the AcMNPV protein actin-rearrangement-inducing factor-1 (ARIF-1), which was previously shown to be necessary and sufficient for cortical actin assembly and efficient viral infection in insect hosts, is both necessary and sufficient for invadosome-like structure formation. We mapped the sequences within the C-terminal cytoplasmic region of ARIF-1 that are required for invadosome-like structure formation and identified individual tyrosine and proline residues that are required for organizing these structures. Additionally, we found that ARIF-1 and the invadosome-associated proteins cortactin and the Arp2/3 complex localize to invadosome-like structures, and Arp2/3 complex is required for their formation. These ARIF-1-induced invadosome-like structures may be important for the function of ARIF-1 in systemic virus spread.
Overcoming Resistance to BRAFV600EInhibition in Melanoma by Deciphering and Targeting Personalized Protein Network Alterations
Authors: Vasudevan S. , Flashner-Abramson E. , Adejumobi I. Adesoji , Vilencki D. , Stefansky S. , Rubinstein A.M. , Kravchenko-Balasha N. 
Published: November 2020

AbstractBRAFV600Emelanoma patients, despite initially responding to the clinically prescribed anti-BRAFV600Etherapy, often relapse and their tumors develop drug resistance. While it is widely accepted that these tumors are originally driven by the BRAFV600Emutation, they often eventually diverge and become supported by various signaling networks. Therefore, patient-specific altered signaling signatures should be deciphered and treated individually.In this study, we design individualized melanoma combination treatments based on personalized network alterations. Using an information-theoretic approach, we compute high-resolution patient-specific altered signaling signatures. These altered signaling signatures each consist of several co-expressed subnetworks, which should all be targeted to optimally inhibit the entire altered signaling flux. Based on these data, we design smart, personalized drug combinations, often consisting of FDA-approved drugs. We validate our approach in vitro and in vivo showing that individualized drug combinations that are rationally based on patient-specific altered signaling signatures are more efficient than the clinically used anti-BRAFV600Eor BRAFV600E/MEK targeted therapy. Furthermore, these drug combinations are highly selective, as a drug combination efficient for one BRAFV600Etumor is significantly less efficient for another, and vice versa. The approach presented herein can be broadly applicable to aid clinicians to rationally design patient-specific anti-melanoma drug combinations.
Shock and Detonation Waves at an Interface and the Collision of Action Potentials
Authors: Shrivastava Shamit 
Published: November 2020

ABSTRACTAction potentials in neurons are known to annihilate each other upon collision, while there are cases where they might penetrate each other. Compression waves that travel within the plasma membrane of a neuron have previously been proposed as a thermodynamic basis for the propagation of action potentials. In this context, it was recently shown that two-dimensional compressive shock waves in the model system of lipid monolayers can nearly annihilate each other upon head-on collision when excited close to a phase transition. However, weaker shock waves showed penetration. In general, once the approximation of small perturbation is not valid, compression waves do not interact linearly anymore. While experiments in lipid monolayers demonstrated this principle, a mechanism remained unclear. In this article, we summarise the fundamentals of shock physics as applied to an interface and how it previously explained the observation of threshold and saturation of shockwaves in the lipid monolayer (all – or – none). While the theory has the same fundamental premise as the soliton model, i.e. the conservation laws and thermodynamics, we elaborate on how the two approaches make different predictions with regards to collisions and the detailed structure of the wave-front. As a case study and a new result, we show that previously unexplained annihilation of shock waves in the lipid monolayer is a direct consequence of the nature of state changes, i.e. jump conditions, within these shockwaves, and elaborate on the consequence of these results for the general understanding of the excitation waves in a thermo-fluids framework.
Antibiotic resistance amongEscherichia coliandSalmonellaisolated from dairy cattle feces in Texas
Authors: Manishimwe Rosine , Moncada Paola M. , Bugarel Marie , Scott H. Morgan , Loneragan Guy H. 
Published: November 2020

AbstractThis study was conducted to develop and field-test a low cost protocol to estimate the isolate- and sample-level prevalence of resistance to critically important antibiotic drugs amongEscherichia coliandSalmonellaisolated from dairy cattle feces.E. coliandSalmonellawere isolated from and screened on selective media, with and without antibiotics respectively. Bacterial isolates were further tested for susceptibility to a suite of antibiotics using disk diffusion. Molecular methods were performed on select bacterial isolates to identify and distinguish genetic determinants associated with the observed phenotypes. Among 85 non-type-specificE. colirandomly isolated from MacConkey agar without antibiotics, the isolate-level prevalence of resistance to tetracycline was the highest (8.2%), there was no isolate resistant to third-generation cephalosporin (0.0%) and one isolate was resistant to nalidixic acid (1.2%). Among 37E. colirecovered from MacConkey agar with cefotaxime at 1.0µg/ml, 100% were resistant to ampicillin and 56.8% were resistant to a third-generation cephalosporin (ceftriaxone). Among 22E. coliisolates recovered from MacConkey agar with ciprofloxacin at 0.5µg/ml, 90.9% were resistant to tetracycline whereas 77.3% and 54.5% were resistant to nalidixic acid and ciprofloxacin respectively. SixteenSalmonellawere isolated and only one demonstrated any resistance (i.e., single resistance to streptomycin). AmongE. coliisolates that were either resistant or intermediate to ceftriaxone, an AmpC phenotype was more common than an extended spectrum beta-lactamase (ESBL) phenotype (29 versus 10 isolates, respectively). Among 24E. coliisolates that were whole genome sequenced, phenotypic profiles of antibiotic resistance detected were generally substantiated by genotypic profiles. For instance, all isolates with an AmpC phenotype carried ablaCMY2gene. The protocol used in this study is suited to detecting and estimating prevalence of antimicrobial resistance in bacteria isolated from food animal feces in resource-limited laboratories in the developing world.
Cryopreservation ofHydractinia symbiolongicarpussperm to support community-based repository development for preservation of genetic resources
Authors: Huene Aidan L. , Nicotra Matthew L. , Weis Virginia M. , Tiersch Terrence R. 
Published: November 2020

AbstractHydractinia symbiolongicarpusis an emerging model organism in which cutting-edge genomic tools and resources are being developed for use in a growing number of research fields. However, one limitation of this model system is the lack of long-term storage for genetic resources. Our goal in this study was to establish a generalizable approach to sperm cryopreservation that would support future repository development and could be applied to many species according to available resources. Our approach was to: 1) Assess sperm characteristics and standardize collection and processing; 2) Assess acute toxicity to cryoprotectants, and 3) Evaluate and refine freezing conditions to permit post-thaw fertilization and produce viable offspring. By following this approach, we found thatHydractiniasperm incubated in 5% DMSO, equilibrated at 4°C for 20 min, and cooled at a rate of 20°C/min to - 80°C at a cell concentration of 108-109/mL in 0.25-mL aliquots were able to fertilize 150-300 eggs which yielded offspring that could metamorphose into juvenile polyps. In addition, improvements were made for processing sperm using a customized 3-D printed collection system. Other opportunities for improvement include optimizing the volumetric sperm-to-egg ratio for fertilization. Establishing repository capabilities for theHydractiniaresearch community will be essential for future development, maintenance, protection, and distribution of genetic resources. More broadly, this application-based approach highlights the long-term value of establishing repository-level resources that can be expanded to fit community needs.
Multiplex detection of “CandidatusLiberibacter asiaticus” andSpiroplasma citriby qPCR and droplet digital PCR
Authors: Maheshwari Yogita , Selvaraj Vijayanandraj , Godfrey Kristine , Hajeri Subhas , Yokomi Raymond 
Published: November 2020

Abstract“CandidatusLiberibacter asiaticus” (CLas) andSpiroplasma citriare phloem-limited bacteria that infect citrus and are transmitted by insect vectors.S. citricauses citrus stubborn disease (CSD) and is vectored by the beet leafhopper in California.CLas is associated with the devastating citrus disease, Huanglongbing (HLB), and is vectored by the Asian citrus psyllid.CLas is a regulatory pathogen spreading in citrus on residential properties in southern California and is an imminent threat to spread to commercial citrus plantings. CSD is endemic in California and has symptoms in citrus that can be easily confused with HLB. Consequently, a multiplex qPCR and duplex droplet digital PCR (ddPCR) were developed for simultaneous detection ofCLas andS. citri. The multiplex qPCR assay was designed to detect multicopy genes ofCLas - RNR (5 copies) andS. citri– SPV1 ORF1 (13 copies), respectively, and citrus cytochrome oxidase (COX) as internal positive control. Absolute quantitation of these pathogens was achieved by duplex ddPCR as a supplement for marginal qPCR results. Duplex ddPCR allowed higher sensitivity than qPCR for detection ofCLas andS. citri. ddPCR showed higher resilience to inhibitors and yielded highly reproducible results. The multiplex qPCR assay has the benefit of testing both pathogens at reduced cost and can serve to augment the official regulatory protocol forCLas detection in California. Moreover, the ddPCR provided unambiguous absolute detection ofCLas andS. citriat very low concentrations without any standards for pathogen titer.
Signalling Network of Breast Cancer Cells in Response to Progesterone
Authors: Wright Roni H. G. , Vastolo Viviana , Oliete Javier Quilez , Carbonell-Caballero José , Beato Miguel 
Published: November 2020

AbstractBreast cancer cells enter into the cell cycle following progestin exposure by the activation of signalling cascades involving a plethora of enzymes, transcription factors and co-factors that transmit the external signal from the cell membrane to chromatin, ultimately leading to a change of the gene expression program. Although many of the events within the signalling network have been described in isolation, how they globally team up to generate the final cell response is unclear. In this study we use antibody microarrays and phosphoproteomics to provide a dynamic global signalling map that reveals new key regulated proteins and links between previously known and novel pathways. Detailed analysis of the data revealed intriguing changes in protein complexes involved in nuclear structure, EMT, cell adhesion, as well as transcription factors previously not associated with breast cancer proliferation. As different post-translational modifications can mediate complex crosstalk mechanisms and massive PARylation is also rapidly induced by progestins, we provide details of important chromatin regulatory complexes containing both phosphorylated and PARylated proteins. This study contributes an important resource for the scientific community, as it identifies novel players and connections meaningful for breast cancer cell biology and potentially relevant for cancer management. (197 w)
ZIKA virus effects on neuroprogenitors are exacerbated by the main pyriproxyfen metabolite via thyroid hormone signaling disruption
Authors: Spirhanzlova Petra , Sébillot Anthony , Vancamp Pieter , Gothié Jean-David , Mével Sébastien Le , Leemans Michelle , Wejaphikul Karn , Meima Marcel , Mughal Bilal B. , Butruille Lucile , Roques Pierre , Remaud Sylvie , Fini Jean-Baptiste , Demeneix Barbara A. 
Published: November 2020

AbstractNorth-Eastern Brazil saw intensive application of the insecticide pyriproxyfen (PPF) during the microcephaly outbreak caused by Zika virus (ZIKV). ZIKV requires the neural RNA-binding protein Musashi-1 to replicate. TH repressesMSI1. Being a suspected TH disruptor, we hypothesized that co-exposure to the main metabolite of PPF, 4’-OH-PPF, would exacerbate ZIKV effects through increased MSI1 expression. This was tested usingin vitromouse neurospheres and anin vivoTH signaling reporter model,Xenopus laevis. TH signaling was decreased by 4’-OH-PPF in both models. In mouse-derived neurospheres the metabolite reduced neuroprogenitor proliferation as well as markers of neuronal differentiation. The results demonstrated that 4’-OH-PPF significantly induced MSI1 at both the mRNA and protein level, as well asFasnmRNA. Other TH target genes were also significantly modified. Importantly, several key genes implicated in neuroprogenitor fate and commitment were not dysregulated by 4’-OH-PPF alone, but were in combination with ZIKV infection. These included the neuroprogenitor markersNestin, Egfr, Gfap, Dlx2andDcx. Unexpectedly, 4’-OH-PPF decreased ZIKV replication, although only at the fourth and last day of incubation, and RNA copy numbers stayed within the same order of magnitude. However, intracellular RNA content of neuroprogenitors was significantly decreased in the combined presence of the PPF metabolite and ZIKV. We conclude that 4’-OH-PPF interferes with TH actionin vivoandin vitro, inhibiting neuroprogenitor proliferation. In the presence of ZIKV, TH signaling pathways crucial for cortical development are significantly impacted. This provides another example of viral effects that are exacerbated by drug or pesticide use.Significance statementIn 2015, an increase in children born with unusually small heads (microcephaly) in North-Eastern Brazil was linked to infection with the ZIKA virus. An insecticide with thyroid hormone disruptive properties was used in the same areas. We investigated whether simultaneous exposure to the insecticide could increase viral susceptibility. The main metabolite 4’-OH-PPF dysregulated thyroid hormone signaling pathways crucial for brain development in both models used. Neural stem cells proliferated less and contained more Musashi-1, a protein the virus needs to replicate. Infecting stem cells pre-exposed to the endocrine disruptor did not amplify viral replication, but aggravated expression of genes implicated in brain development. Our results suggest the insecticide is particularly deleterious to brain development in areas with ZIKA virus prevalence.
Early immune response in mice immunized with a semi-split inactivated vaccine against SARS-CoV-2 containing S protein-free particles and subunit S protein
Authors: Petráš Marek , Lesný Petr , Musil Jan , Limberková Radomíra , Pátíková Alžběta , Jirsa Milan , Krsek Daniel , Březovský Pavel , Koladiya Abhishek , Vaníková Šárka , Macková Barbora , Jírová Dagmar , Krijt Matyáš , Králová Lesná Ivana , Adámková Věra 
Published: November 2020

AbstractThe development of a vaccine against COVID-19 is a hot topic for many research laboratories all over the world. Our aim was to design a semi-split inactivated vaccine offering a wide range of multi-epitope determinants important for the immune system including not only the spike (S) protein but also the envelope, membrane and nucleocapsid proteins. We designed a semi-split vaccine prototype consisting of S protein-depleted viral particles and free S protein. Next, we investigated its immunogenic potential in BALB/c mice. The animals were immunized intradermally or intramuscularly with the dose adjusted with buffer or addition of aluminum hydroxide, respectively. The antibody response was evaluated by plasma analysis at 7 days after the first or second dose. The immune cell response was studied by flow cytometry analysis of splenocytes. The data showed a very early onset of both S protein-specific antibodies and virus-neutralizing antibodies at 90% inhibition regardless of the route of vaccine administration. However, significantly higher levels of neutralizing antibodies were detected in the intradermally (geometric mean titer - GMT of 7.8 ± 1.4) than in the intramuscularly immunized mice (GMT of 6.2 ± 1.5). In accordance with this, stimulation of cellular immunity by the semi-split vaccine was suggested by elevated levels of B and T lymphocyte subpopulations in the murine spleens. These responses were more predominant in the intradermally immunized mice compared with the intramuscular route of administration. The upward trend in the levels of plasmablasts, memory B cells, Th1 and Th2 lymphocytes, including follicular helper T cells, was confirmed even in mice receiving the vaccine intradermally at a dose of 0.5 μg.We demonstrated that the semi-split vaccine is capable of eliciting both humoral and cellular immunity early after vaccination. Our prototype thus represents a promising step toward the development of an efficient anti-COVID-19 vaccine for human use.