| 1. |
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Ablikim, M., et al.
(författare)
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Measurements of cross section of e(+)e(-) -> p(p)over-bar pi(0) at center-of-mass energies between 4.008 and 4.600 GeV
- 2017
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Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 771, s. 45-51
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Tidskriftsartikel (refereegranskat)abstract
- Based on e(+)e(-) annihilation data samples collected with the BESIII detector at the BEPCII collider at 13 center-of-mass energies from 4.008 to 4.600 GeV, measurements of the Born cross section of e(+)e(-) -> p (p) over bar pi(0) are performed. No significant resonant structure is observed in the measured energy dependence of the cross section. The upper limit on the Born cross section of e(+)e(-) -> Y (4260) -> p (p) over bar pi(0) at the 90% C. L. is determined to be 0.01 pb. The upper limit on the ratio of the branching fractions B(Y(4260) -> p (p) over bar pi(0))/B(Y(4260) -> pi(+)pi(-) j/Psi) at the 90% C. L. is determined to be 0.02%.
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| 5. |
- Davies, Thomas G., et al.
(författare)
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Open data and digital morphology.
- 2017
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 284:1852, s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.
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| 6. |
- Dong, Xi-ping, et al.
(författare)
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Developmental biology of the early Cambrian cnidarian Olivooides.
- 2016
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Ingår i: Palaeontology. - : Wiley. - 0031-0239 .- 1475-4983. ; 59:3, s. 387-407
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Tidskriftsartikel (refereegranskat)abstract
- Fossilized embryos afford direct insight into the pattern of development in extinct organisms, providing unique tests of hypotheses of developmental evolution based in comparative embryology. However, these fossils can only be effective in this role if their embryology and phylogenetic affinities are well constrained. We elucidate and interpret the development of Olivooides from embryonic and adult stages and use these data to discriminate among competing interpretations of their anatomy and affinity. The embryology of Olivooides is principally characterized by the development of an ornamented periderm that initially forms externally and is subsequently formed internally, released at the aperture, facilitating the direct development of the embryo into an adult theca. Internal anatomy is known only from embryonic stages, revealing two internal tissue layers, the innermost of which is developed into three transversally arranged walls that partly divide the lumen into an abapertural region, interpreted as the gut of a polyp, and an adapertural region that includes structures that resemble the peridermal teeth of coronate scyphozoans. The anatomy and pattern of development exhibited by Olivooides appears common to the other known genus of olivooid, Quadrapyrgites, which differs in its tetraradial, as opposed to pentaradial symmetry. We reject previous interpretations of the olivooids as cycloneuralians, principally on the grounds that they lack a through gut and introvert, in embryo and adult. Instead we consider the affinities of the olivooids among medusozoan cnidarians; our phylogenetic analysis supports their classification as totalgroup Coronata, within crown-Scyphozoa. Olivooides and Quadrapyrgites evidence a broader range of life history strategies and bodyplan symmetry than is otherwise commonly represented in extant Scyphozoa specifically, and Cnidaria more generally.
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| 7. |
- Dong, Xi-ping, et al.
(författare)
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Embryos, polyps and medusae of the early Cambrian scyphozoan Olivooides.
- 2013
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Ingår i: Proceedings of the Royal Society Biological Sciences Series B. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 280:2130071, s. 1-8
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Tidskriftsartikel (refereegranskat)abstract
- The Early Cambrian organism Olivooides is known from both embryonic and post-embryonic stages and, consequently, it has the potential to yield vital insights into developmental evolution at the time that animal body plans were established. However, this potential can only be realized if the phylogenetic relationships of Olivooides can be constrained. The affinities of Olivooides have proved controversial because of the lack of knowledge of the internal anatomy and the limited range of developmental stages known. Here, we describe rare embryonic specimens in which internal anatomical features are preserved. We also present a fuller sequence of fossilized developmental stages of Olivooides, including associated specimens that we interpret as budding ephyrae ( juvenile medusae), all of which display a clear pentaradial symmetry. Within the framework of a cnidarian interpretation, the new data serve to pinpoint the phylogenetic position of Olivooides to the scyphozoan stem group. Hypotheses about scalidophoran or echinoderm affinities of Olivooides can be rejected.
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| 8. |
- Donoghue, Philip C.J., et al.
(författare)
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Embryology in deep time.
- 2015
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Ingår i: Evolutionary Developmental Biology of Invertebrates 1. - Wien : Springer Science+Business Media B.V.. - 9783709118610 ; , s. 45-63
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Bokkapitel (refereegranskat)abstract
- For anyone who has cared for animal embryos, it beggars belief that these squishy cellular aggregates could be fossilised. Hence, with hindsight, it is possible to empathise with palaeontologists who found such fossils and, in their naming of Olivooides, Pseudooides, etc., drew attention to their likeness to animal eggs and embryos but without going so far as to propose such an interpretation. However, in 1994, Zhang Xi-guang and Brian Pratt described microscopic balls of calcium phosphate from Cambrian rocks of China, one or two of which preserved polygonal borders that resembled blastomeres on the surface of an early cleaving animal embryo. In retrospect, these fossils are far from remarkable, some of them may not be fossils at all, and it is not as if anyone ever conceived Cambrian animals as having lacked an embryology. But Zhang Xi-guang and Brian Pratt dared the scientific world, not least their fellow palaeontologists, to believe that the fragile embryonic stages of invertebrate animals could be fossilised, that there was a fossil record of animal embryology, that this record hailed from the interval of time in which animal body plans were first established, and that it had been awaiting discovery in the rocks, for want of looking. The proof of this concept came a few years later, when phosphatised Cambrian fossils from China and Siberia were shown to display indisputable features of animal embryonic morphologies. In the case of Olivooides, a series of developmental stages from cleavage to morphogenesis through hatching and juvenile growth could be tentatively identified; in Markuelia, the coiled-up body of an annulated worm-like animal could be clearly seen within its fertilisation envelope.
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| 9. |
- Donoghue, Philip C. J., et al.
(författare)
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Synchrotron X-ray tomographic microscopy of fossil embryos
- 2006
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Ingår i: Nature. - 0028-0836. ; 442:7103, s. 601-718
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Tidskriftsartikel (refereegranskat)abstract
- Fossilized embryos from the late Neoproterozoic and earliest Phanerozoic have caused much excitement because they preserve the earliest stages of embryology of animals that represent the initial diversification of metazoans1, 2, 3, 4. However, the potential of this material has not been fully realized because of reliance on traditional, non-destructive methods that allow analysis of exposed surfaces only1, 2,3, 4, and destructive methods that preserve only a single two-dimensional view of the interior of the specimen5, 6. Here, we have applied synchrotron-radiation X-ray tomographic microscopy (SRXTM)7, obtaining complete three-dimensional recordings at submicrometre resolution. The embryos are preserved by early diagenetic impregnation and encrustation with calcium phosphate, and differences in X-ray attenuation provide information about the distribution of these two diagenetic phases. Three-dimensional visualization of blastomere arrangement and diagenetic cement in cleavage embryos resolves outstanding questions about their nature, including the identity of the columnar blastomeres. The anterior and posterior anatomy of embryos of the bilaterian worm-like Markuelia confirms its position as a scalidophoran, providing new insights into body-plan assembly among constituent phyla. The structure of the developing germ band in another bilaterian, Pseudooides, indicates a unique mode of germ-band development. SRXTM provides a method of non-invasive analysis that rivals the resolution achieved even by destructive methods, probing the very limits of fossilization and providing insight into embryology during the emergence of metazoan phyla.
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| 10. |
- Li, Wu Lue, et al.
(författare)
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Multiple Origins and Genomic Basis of Complex Traits in Sighthounds
- 2023
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Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 40:8
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Tidskriftsartikel (refereegranskat)abstract
- Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol"(gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149-T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007-T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.
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