| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
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.
|
|
| 2. |
- Benoit, Julien, et al.
(författare)
-
Palaeoneurology and palaeobiology of the dinocephalian Anteosaurus magnificus
- 2021
-
Ingår i: Acta Palaeontologica Polonica. - Warsaw : Polish Academy of Science. - 0567-7920 .- 1732-2421. ; 66, s. 29-39
-
Tidskriftsartikel (refereegranskat)abstract
- Dinocephalians (Therapsida), some of the earliest amniotes to have evolved large body size, include the carnivorous Anteosauria and mostly herbivorous Tapinocephalia. Whilst the palaeoneurology of the Tapinocephalia has been investigated in Moschognathus whaitsi, that of the Anteosauria remains completely unknown. Here we used X-ray micro-Computed Tomography to study, for the first time, the palaeoneurology of Anteosaurus magnificus. Compared to Moschognathus, we reconstruct Anteosaurus as an agile terrestrial predator based on the enlarged fossa for the floccular lobe of the cerebellum and semicircular canals of the inner ear. A major difference between the two genera resides in the orientation of the braincase, as indicated by the angle between the long axis of the skull and the plane of the lateral semicircular canal. This angle is 25° in Anteosaurus, whereas it is 65° in Moschognathus, which suggests that the braincase of the latter was remodelled as an adaptation to head-butting. This is consistent with less cranial pachyostosis and the retention of a large canine in Anteosauria, which suggests that dentition may have been used for intraspecific fighting and display in addition to trophic interactions. The evolution of a thick skull, horns, and bosses in tapinocephalids parallels the evolutionary reduction of the canine, which lead to a shift of the agonistic function from the mouth to the skull roof, as observed in extant social ungulates. Similarly, tapinocephalians may have developed complex social behaviour.
|
|
| 3. |
- ELLIOTT, MARINA, et al.
(författare)
-
Expanded Explorations of the Dinaledi Subsystem,Rising Star Cave System, South Africa
- 2021
-
Ingår i: PaleoAnthropology. - 1545-0031. ; 2021:1, s. 15-22
-
Tidskriftsartikel (refereegranskat)abstract
- The Dinaledi Chamber of the Rising Star cave system has yielded a large assemblage of fossil hominin material, attributed to Homo naledi. The unusual taphonomic and geological situation of the assemblage suggested that the remains may have been deliberately deposited in the chamber. However, the route and mechanism of deposition of the remains within the Dinaledi Chamber are still uncertain. During the 2017—2018 field seasons, we expanded explorations of the passages surrounding the Dinaledi Chamber. These explorations improved our understandingof the cave’s spatial complexity, necessitating a revision of the way the spaces are named and described. The work supported the hypothesis that there is no alternate entrance into the system other than the Chute. The work also identified new fossil deposits in several remote passages, three of which contain material attributable to H. naledi. Here, we clarify the definition of the Dinaledi Subsystem and provide terminology for new fossil localities found in this portion of the Rising Star cave system. These results emphasize the complex depositional environment of the Dinaledi Subsystem and raise new questions about the process and timing of the fossil accumulations.
|
|
| 4. |
- Groenewald, David P., et al.
(författare)
-
Unique trackway on Permian Karoo shoreline provides evidence of temnospondyl locomotory behaviour
- 2023
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:3
-
Tidskriftsartikel (refereegranskat)abstract
- Large-bodied temnospondyl amphibians were the dominant predators in non-marine aquatic ecosystems from the Carboniferous to the Middle Triassic. In the Permian-aged lower Beaufort Group ofthe main Karoo Basin, South Africa, temnospondyls are represented exclusively by the family Rhinesuchidae and are well represented by body fossils, whereas trace fossils are scarce. Accordingly, most interpretations of the behaviour of this family are based on skeletal morphology and histological data. Here we document the sedimentology and palaeontology of a late Permian palaeosurface situated immediately below the palaeoshoreline ofthe Ecca Sea (transition from the Ecca Group to the Beaufort Group) near the town of Estcourt in KwaZulu-Natal Province. The surface preserves numerous ichnofossils, including tetrapod footprints and fish swim-trails, but most striking are seven body impressions and associated swim trails that we attribute to amedium-sized (~1.9 mlong) rhinesuchid temnospondyl. These provide valuable insight into the behaviour of these animals. The sinuous shape ofsome of the traces suggest that the tracemaker swam with continuous sub-undulatory propulsion of the tail.
|
|
| 5. |
- Hutchinson, Ashley, 1984-, et al.
(författare)
-
The Effect of Probiotics on Health Outcomes in the Elderly : A Systematic Review of Randomized, Placebo-Controlled Studies
- 2021
-
Ingår i: Microorganisms. - : MDPI. - 2076-2607. ; 9:6
-
Forskningsöversikt (refereegranskat)abstract
- Increasing evidence suggests that probiotic supplementation may be efficacious in counteracting age-related shifts in gut microbiota composition and diversity, thereby impacting health outcomes and promoting healthy aging. However, randomized controlled trials (RCTs) with probiotics in healthy older adults have utilized a wide variety of strains and focused on several different outcomes with conflicting results. Therefore, a systematic review was conducted to determine which outcomes have been investigated in randomized controlled trials with probiotic supplementation in healthy older adults and what has been the effect of these interventions. For inclusion, studies reporting on randomized controlled trials with probiotic and synbiotic supplements in healthy older adults (defined as minimum age of 60 years) were considered. Studies reporting clinical trials in specific patient groups or unhealthy participants were excluded. In addition to assessment of eligibility and data extraction, each study was examined for risk of bias and quality assessment was performed by two independent reviewers. Due to the heterogeneity of outcomes, strains, study design, duration, and methodology, we did not perform any meta-analyses and instead provided a narrative overview of the outcomes examined. Of 1997 potentially eligible publications, 17 studies were included in this review. The risk of bias was low, although several studies failed to adequately describe random sequence generation, allocation concealment, and blinding. The overall study quality was high; however, many studies did not include sample calculations, and the majority of studies had a small sample size. The main outcomes examined in the trials included microbiota composition, immune-related measurements, digestive health, general well-being, cognitive function, and lipid and other biomarkers. The most commonly assessed outcome with the most consistent effect was microbiota composition; all but one study with this outcome showed significant effects on gut microbiota composition in healthy older adults. Overall, probiotic supplementation had modest effects on markers of humoral immunity, immune cell population levels and activity, as well as the incidence and duration of the common cold and other infections with some conflicting results. Digestive health, general-well-being, cognitive function, and lipid and other biomarkers were investigated in a very small number of studies; therefore, the impact on these outcomes remains inconclusive. Probiotics appear to be efficacious in modifying gut microbiota composition in healthy older adults and have moderate effects on immune function. However, the effect of probiotic supplementation on other health outcomes remains inconclusive, highlighting the need for more well-designed, sufficiently-powered studies to investigate if and the mechanisms by which probiotics impact healthy aging.
|
|
| 6. |
|
|
| 7. |
- Krüger, Ashley, et al.
(författare)
-
3D imaging of shark egg cases (Palaeoxyris) from Sweden with new insights into Early Jurassic shark ecology
- 2021
-
Ingår i: GFF. - London : Taylor & Francis. - 1103-5897 .- 2000-0863. ; 143:2-3, s. 229-247
-
Tidskriftsartikel (refereegranskat)abstract
- Several shark species produce egg cases as protective casings in which their embryos develop. These casings are composed of multiple layers of collagen and are extremely durable, making them prone to fossilisation. Here we document Palaeoxyris (Spirangium) ‒ fossil shark egg cases from Lower Jurassic successions of southern Sweden. We present high-resolution 3D images of Palaeoxyris based on microfocus X-ray computed tomography (μCT) of seven specimens, including fossils that were embedded within a sandstone matrix. Our examination of the internal structure of the egg cases revealed the possible remnants of a yolk and foetus in one specimen. The cases were most likely produced by hybodont sharks, as outlined in previous studies, and the occurrence of hybodont teeth from Lower Jurassic successions of Sweden support this. Palynological analysis of the matrix from one of the specimens hosting Palaeoxyris, indicates an early Hettangian age. The high percentage of spores (c. 60%) reveals that the egg cases were laid during the Transitional Spore Spike Interval following the end-Triassic mass extinction. The egg cases are found in conjunction with fossil horsetails; with the broader palynological and sedimentological evidence, this suggests an estuarine depositional setting, and potentially indicates that newborn sharks were living in habitats comparable to modern mangroves, as is often the case today.
|
|
| 8. |
- Tingö, Lina, 1984-, et al.
(författare)
-
Potential Modulation of Inflammation by Probiotic and Omega-3 Supplementation in Elderly with Chronic Low-Grade Inflammation-A Randomized, Placebo-Controlled Trial
- 2022
-
Ingår i: Nutrients. - : MDPI. - 2072-6643. ; 14:19
-
Tidskriftsartikel (refereegranskat)abstract
- Probiotic and omega-3 supplements have been shown to reduce inflammation, and dual supplementation may have synergistic health effects. We investigated if the novel combination of a multi-strain probiotic (containing B. lactis Bi-07, L. paracasei Lpc-37, L. acidophilus NCFM, and B. lactis Bl-04) alongside omega-3 supplements reduces low-grade inflammation as measured by high-sensitivity C-reactive protein (hs-CRP) in elderly participants in a proof-of-concept, randomized, placebo-controlled, parallel study (NCT04126330). In this case, 76 community-dwelling elderly participants (median: 71.0 years; IQR: 68.0-73.8) underwent an intervention with the dual supplement (n = 37) or placebo (n = 39) for eight weeks. In addition to hs-CRP, cytokine levels and intestinal permeability were also assessed at baseline and after the eight-week intervention. No significant difference was seen for hs-CRP between the dual supplement group and placebo. However, interestingly, supplementation did result in significant increases in the level of the anti-inflammatory marker IL-10. In addition, dual supplementation increased levels of valeric acid, further suggesting the potential of the supplements in reducing inflammation and conferring health benefits. Together, the results suggest that probiotic and omega-3 dual supplementation exerts modest effects on inflammation and may have potential use as a non-pharmacological treatment for low-grade inflammation in the elderly.
|
|
| 9. |
- Vajda, Vivi, et al.
(författare)
-
Changes in Fe-redox and Fe-species across the end-Permian ‘Dead Zone’ in the Sydney Basin, Australia (252.10 ± 0.06 Ma): Evidence from X-ray absorption spectroscopy
- 2023
-
Ingår i: Evolving Earth. - : Elsevier. - 2950-1172. ; 1
-
Tidskriftsartikel (refereegranskat)abstract
- The end-Permian mass extinction event is traceable across several non-marine basins in Australia. In the Sydney Basin, the lithological succession is characterized by a change from coal seams to mudstones and sandstones, recording a major environmental change following the disappearance of the Permian vegetation. A few millimeter-thick iron-rich ‘rusty’ layer occurs between the uppermost Permian coal seam and the mudstone, a layer that extends laterally across the basin and which has also been documented from coeval successions in Antarctica. This layer is overlain by the <1.5-m-thick Frazer Beach Member, whose basal 10-cm-thick microbreccia bed comprises 99% kaolinite and quartz, and is dated as 252.10 ± 0.06 Ma. The Frazer Beach Member corresponds to the so-called end-Permian ‘Dead Zone’ lacking fossil pollen and leaves. This distinctive member was deposited directly following the extinction of the Permian peat-forming forests.Here we identify, through X-ray absorption spectroscopy, a drastic redox shift across the extinction interval with increasing amount of reduced Fe-species followed by highly oxidized Fe-species, most resembling Fe(III) complexed with organic matter. Values subsequently normalise in younger samples through the ‘Dead Zone’, attaining only slightly higher redox-levels than before the event. The organically complexed Fe-species in the event bed is consistent with the standard Suwannee River fulvic acid, an acid Fe-complex with iron bound to organic matter, whereas the samples above and below the extinction layer yield spectra predominantly resembling magnetite (Fe3O4) mineral phase. We consider that the iron redox fluctuation marking the extinction interval is related to significant environmental changes with accumulation of organic matter following the mass extinction. The highly reduced iron in the extinction layer may relate to methane release from bacterial degradation, or emissions from clathrates. The presence of fulvic acid in the distinct iron-rich extinction layer indicates that an abrupt onset of the process of degradation of plant matter, lipids and calcium hydroxide (CaOH) took place, resulting in this ‘Death layer’. This was followed by millions of years of erosive conditions before new, complex vegetation could establish.
|
|
| 10. |
- Vajda, Vivi, et al.
(författare)
-
End-Permian marine ecosystem collapse was a direct consequence of deforestation: Evidence from the Kockatea Shale of the Perth Basin, Western Australia
- 2023
-
Ingår i: Evolving Earth. - : Elsevier. - 2950-1172. ; 1
-
Tidskriftsartikel (refereegranskat)abstract
- The end-Permian mass extinction event resulted in devastated continental biomes, desolated land, and toxic waters. Anoxia led to widespread extinctions in marine ecosystems, affecting most oceanic clades. In this paper, the palynofacies of the marine Kockatea Shale, Western Australia, was studied in drill cores Hovea-3 and Redback-2, with the aim of linking changes in the marine and continental realms across the Permian–Triassic boundary interval in Australia. We show that the post-extinction ‘Dead Zone’ of the Frazer Beach Member of the Sydney Basin, eastern Australia, whose base is dated to 252.10 ± 0.06 Ma, directly correlates to the lower part of the Kockatea Shale in the Perth Basin, the so-called Inertinitic Interval. We demonstrate that the extinction of Permian Glossopteris forests observed in the Perth Basin had an immediateimpact on the marine faunas due to the massive buildup of organic matter, leading to euxinia in the photic zone and ultimately pushing the marine faunas to an ecological extinction. The last lingering occurrence of marine invertebrates of Permian aspect occur in layers that may tentatively mark the Permian –Triassic boundary, positioned just below the appearance of Triassic floras of the Kraeuselisporites saeptatus Zone (equivalent to the Lunatisporites pellucidus Zone). A striking feature at the base of the Early Triassic Sapropelic Interval of the Hovea Member is the sudden and synchronous appearances of anomalously abundant acritarchs and lycophyte spores, alongside the mass occurrence of the bivalve Claraia, allowing correlation with the rise of the eastern Australian post-extinction pioneer floras in the Early Triassic. This demonstrates a significant lag time between the recovery of the terrestrial versus the marine pioneer biota in high-latitude Gondwana, with a significant delay for the faunal recovery.
|
|
