| 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. |
- Wu, Shi-Xun, et al.
(author)
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Expression profiles of genes involved in apoptosis and selenium metabolism in articular cartilage of patients with Kashin-Beck osteoarthritis.
- 2014
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In: Gene. - : Elsevier. - 0378-1119 .- 1879-0038. ; 535:2, s. 124-130
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Journal article (peer-reviewed)abstract
- Kashin-Beck disease (KBD) is a special type of endemic osteoarthritis. It has been suggested that alterations in selenium metabolism and apoptosis play a role in KBD. However, the underlying molecular mechanism remains largely unclear. We performed a microarray analysis using RNA isolated from cartilages of KBD patients and healthy controls, through Significance Analysis of Microarray (SAM) software. Functional gene networks and crucial molecules associated with differentially expressed genes were investigated via Ingenuity Pathway Analysis (IPA) and hub gene analysis. Quantitative real-time PCR was used to check the validation of chip test. We identified 52 up-regulated apoptosis-related genes and 26 down-regulated selenium-related genes between KBD and controls, and these genes associated with the "MYC-mediated apoptosis signaling pathway". We confirmed the results from array studies with quantitative real-time PCR analysis. Our results suggest that abnormal regulation of selenium metabolism and apoptosis through the MYC mediated signaling pathway contributes to the pathogenesis of KBD, but the relationship between apoptosis gene and selenium gene was not found.
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| 3. |
- Lamichhaney, Sangeet, 1984-, et al.
(author)
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Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
- 2016
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In: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 48:1, s. 84-88
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Journal article (peer-reviewed)abstract
- The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females1,2,3,4. This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles5,6. Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.
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| 4. |
- Pecunia, Vincenzo, et al.
(author)
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Roadmap on energy harvesting materials
- 2023
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In: Journal of Physics. - : IOP Publishing. - 2515-7639. ; 6:4
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Journal article (peer-reviewed)abstract
- Ambient energy harvesting has great potential to contribute to sustainable development and address growing environmental challenges. Converting waste energy from energy-intensive processes and systems (e.g. combustion engines and furnaces) is crucial to reducing their environmental impact and achieving net-zero emissions. Compact energy harvesters will also be key to powering the exponentially growing smart devices ecosystem that is part of the Internet of Things, thus enabling futuristic applications that can improve our quality of life (e.g. smart homes, smart cities, smart manufacturing, and smart healthcare). To achieve these goals, innovative materials are needed to efficiently convert ambient energy into electricity through various physical mechanisms, such as the photovoltaic effect, thermoelectricity, piezoelectricity, triboelectricity, and radiofrequency wireless power transfer. By bringing together the perspectives of experts in various types of energy harvesting materials, this Roadmap provides extensive insights into recent advances and present challenges in the field. Additionally, the Roadmap analyses the key performance metrics of these technologies in relation to their ultimate energy conversion limits. Building on these insights, the Roadmap outlines promising directions for future research to fully harness the potential of energy harvesting materials for green energy anytime, anywhere.
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| 5. |
- Shi, Xun, et al.
(author)
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Ultrafast electron calorimetry uncovers a new long-lived metastable state in 1T-TaSe2 mediated by mode-selective electron-phonon coupling
- 2019
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:3
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Journal article (peer-reviewed)abstract
- Quantum materials represent one of the most promising frontiers in the quest for faster, lightweight, energy-efficient technologies. However, their inherent complexity and rich phase landscape make them challenging to understand or manipulate. Here, we present a new ultrafast electron calorimetry technique that can systematically uncover new phases of quantum matter. Using time- and angle-resolved photoemission spectroscopy, we measure the dynamic electron temperature, band structure, and heat capacity. This approach allows us to uncover a new long-lived metastable state in the charge density wave material 1T-TaSe2, which is distinct from all the known equilibrium phases: It is characterized by a substantially reduced effective total heat capacity that is only 30% of the normal value, because of selective electron-phonon coupling to a subset of phonon modes. As a result, less energy is required to melt the charge order and transform the state of the material than under thermal equilibrium conditions.
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