| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Behzadi, Payam, et al.
(author)
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The Interleukin-1 (IL-1) Superfamily Cytokines and Their Single Nucleotide Polymorphisms (SNPs)
- 2022
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In: Journal of Immunology Research. - : Hindawi Publishing Corporation. - 2314-8861 .- 2314-7156. ; 2022
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Research review (peer-reviewed)abstract
- Interleukins (ILs)-which are important members of cytokines-consist of a vast group of molecules, including a wide range of immune mediators that contribute to the immunological responses of many cells and tissues. ILs are immune-glycoproteins, which directly contribute to the growth, activation, adhesion, differentiation, migration, proliferation, and maturation of immune cells; and subsequently, they are involved in the pro and anti-inflammatory responses of the body, by their interaction with a wide range of receptors. Due to the importance of immune system in different organisms, the genes belonging to immune elements, such as ILs, have been studied vigorously. The results of recent investigations showed that the genes pertaining to the immune system undergo progressive evolution with a constant rate. The occurrence of any mutation or polymorphism in IL genes may result in substantial changes in their biology and function and may be associated with a wide range of diseases and disorders. Among these abnormalities, single nucleotide polymorphisms (SNPs) can represent as important disruptive factors. The present review aims at concisely summarizing the current knowledge available on the occurrence, properties, role, and biological consequences of SNPs within the IL-1 family members.
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| 3. |
- Costa, Nathalia, et al.
(author)
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A Definition of "Flare" in Low Back Pain: A Multiphase Process Involving Perspectives of Individuals With Low Back Pain and Expert Consensus
- 2019
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In: Journal of Pain. - : CHURCHILL LIVINGSTONE. - 1526-5900 .- 1528-8447. ; 20:11, s. 1267-1275
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Journal article (peer-reviewed)abstract
- Low back pain (LBP) varies over time. Consumers, clinicians, and researchers use various terms to describe LBP fluctuations, such as episodes, recurrences and flares. Although "flare" is use commonly, there is no consensus on how it is defined. This study aimed to obtain consensus for a LBP flare definition using a mixed-method approach. Step 1 involved the derivation of a preliminary candidate flare definition based on thematic analysis of views of 130 consumers in consultation with an expert consumer writer. In step 2, a workshop was conducted to incorporate perspectives of 19 LBP experts into the preliminary flare definition, which resulted in 2 alternative LBP flare definitions. Step 3 refined the definition using a 2-round Delphi consensus with 50 experts in musculoskeletal conditions. The definition favored by experts was further tested with 16 individuals with LBP in step 4, using the definition in three scenarios. This multiphase study produced a definition of LBP flare that distinguishes it from other LBP fluctuations, represents consumers views, involves expert consensus, and is understandable by consumers in clinical and research contexts: "A flare-up is a worsening of your condition that lasts from hours to weeks that is difficult to tolerate and generally impacts your usual activities and/or emotions." Perspective: A multiphase process, incorporating consumers views and expert consensus, produced a definition of LBP flare that distinguishes it from other LBP fluctuations. (C) 2019 by the American Pain Society
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| 4. |
- Oliveira, Helena Rodrigues, et al.
(author)
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Biogas potential of biowaste: A case study in the state of Rio de Janeiro, Brazil
- 2024
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In: Renewable energy. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0960-1481 .- 1879-0682. ; 221
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Journal article (peer-reviewed)abstract
- Anaerobic digestion has been widely applied for waste treatment, renewable energy generation , biofertilizer production. The biogas potential in Brazil is sizable, but the state of Rio de Janeiro is largely dependent on fossil fuels , there is a lack of biogas potential assessments in the state. Thus, this study evaluated biomethane, electricity and biofertilizer potentials in the region. Three different scenarios of biomass supply were considered for four major biowaste streams: sewage sludge; cattle manure; sugarcane processing waste; and food waste. Biomethane generation from the assessed sources could reach 0.6-1.3 billion Nm(3) year(-1), corresponding to 1,768-3,961 GWh year(-1) of electricity , 1.6-3.3 million Mg year- 1 of biofertilizer. Cattle manure was responsible for 73-84% of the projected biomethane production, presenting an opportunity to reduce the sig-nificant emissions from livestock farming. The estimated biofertilizer production could meet the demands of the state , the produced electricity could offset up to 10% of the demand. The gas grid could facilitate the dis-tribution of upgraded biomethane, and 10-22% of the natural gas demand could be met. The findings of this work highlight the high potential for biogas generation in Rio de Janeiro, which is up to seven times larger than the current production.
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| 5. |
- Rekena, Alina J., et al.
(author)
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Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
- 2023
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In: PLoS Computational Biology. - 1553-734X .- 1553-7358. ; 19:4
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Journal article (peer-reviewed)abstract
- Rhodotorula toruloides is a non-conventional, oleaginous yeast able to naturally accumulate high amounts of microbial lipids. Constraint-based modeling of R. toruloides has been mainly focused on the comparison of experimentally measured and model predicted growth rates, while the intracellular flux patterns have been analyzed on a rather general level. Hence, the intrinsic metabolic properties of R. toruloides that make lipid synthesis possible are not thoroughly understood. At the same time, the lack of diverse physiological data sets has often been the bottleneck to predict accurate fluxes. In this study, we collected detailed physiology data sets of R. toruloides while growing on glucose, xylose, and acetate as the sole carbon source in chemically defined medium. Regardless of the carbon source, the growth was divided into two phases from which proteomic and lipidomic data were collected. Complemental physiological parameters were collected in these two phases and altogether implemented into metabolic models. Simulated intracellular flux patterns demonstrated the role of phosphoketolase in the generation of acetyl-CoA, one of the main precursors during lipid biosynthesis, while the role of ATP citrate lyase was not confirmed. Metabolic modeling on xylose as a carbon substrate was greatly improved by the detection of chirality of D-arabinitol, which together with D-ribulose were involved in an alternative xylose assimilation pathway. Further, flux patterns pointed to metabolic trade-offs associated with NADPH allocation between nitrogen assimilation and lipid biosynthetic pathways, which was linked to large-scale differences in protein and lipid content. This work includes the first extensive multi-condition analysis of R. toruloides using enzyme-constrained models and quantitative proteomics. Further, more precise k(cat) values should extend the application of the newly developed enzyme-constrained models that are publicly available for future studies. Author summaryTransition towards a biobased, circular economy to reduce the industrial dependence on fossil-based resources requires new technologies. One of the options is to convert available biomass feedstocks into valuable chemicals using microbes as biocatalysts. Rhodotorula toruloides is a nonpathogenic, nonconventional yeast that has recently emerged as one of the most promising yeasts for sustainable production of chemicals and fuels due to its natural ability to synthesize large amounts of lipids. However, its unique metabolic properties are not yet fully understood. We have computationally predicted metabolic fluxes in R. toruloides while growing in economically viable growth conditions inducing lipid accumulation and analyzed them together with absolute proteome quantification. Our holistic approach has highlighted metabolic pathways important for lipid biosynthesis and revealed metabolic trade-offs associated with NADPH allocation during lipogenesis. In addition, our work highlighted the necessity for accurate computational approaches in characterizing enzymatic kinetic properties that would improve the metabolic studies of R. toruloides.
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| 6. |
- Tarnoki, Adam Domonkos, et al.
(author)
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Lumbar spine abnormalities in patients with obstructive sleep apnoea
- 2021
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Journal article (peer-reviewed)abstract
- Previous studies suggested cervical spondylosis as a risk factor for development of obstructive sleep apnoea (OSA). We aimed to assess lumbar disc degeneration in patients with OSA and correlate the findings with symptoms and disease severity. Twenty-seven patients with OSA and 29 non-OSA controls underwent sleep studies and lumbar magnetic resonance imaging (MRI), and completed the Epworth Sleepiness Scale and the 24-item Roland-Morris Disability Questionnaire (RMDQ) questionnaires. Plasma klotho was determined with enzyme-linked immunosorbent assay. Patients with OSA had higher number of disc bulges (4.6 ± 3.7 vs. 1.7 ± 2.5, p < 0.01) and anterior spondylophytes (2.7 ± 4.2 vs. 0.8 ± 2.1, p < 0.01), increased disc degeneration (total Pfirrmann score 16.7 ± 4.7 vs. 13.2 ± 4.1, p < 0.01) and vertebral fatty degeneration (7.8 ± 4.7 vs. 3.8 ± 3.7, p < 0.01). There was no difference in the RMDQ score (0/0-3.5/ vs. 0/0-1/, p > 0.05). Markers of OSA severity, including the oxygen desaturation index and percentage of total sleep time spent with saturation < 90% as well as plasma levels of klotho were correlated with the number of disc bulges and anterior spondylophytes (all p < 0.05). OSA is associated with lumbar spondylosis. Our study highlights the importance of lumbar imaging in patients with OSA reporting lower back pain.
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| 7. |
- Abbafati, Cristiana, et al.
(author)
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- 2020
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Journal article (peer-reviewed)
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