| 1. |
- 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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| 2. |
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| 3. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 4. |
- Bundschuh, Jochen, et al.
(författare)
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Arsenic removal from groundwater of the Chaco-Pampean Plain (Argentina) using natural geological materials as adsorbents
- 2011
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Ingår i: Journal of Environmental Science and Health. Part A. - : Informa UK Limited. - 1093-4529 .- 1532-4117. ; 46:11, s. 1297-1310
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Tidskriftsartikel (refereegranskat)abstract
- Use of natural geological materials for arsenic (As) removal is an emerging solution at a household level for poor people in remote rural settlements, especially when the materials are locally available and can be collected by the local population. Their low or zero cost makes these materials very attractive compared with synthetic or commercial materials. Sometimes, this may be the only option to provide safe water to very poor settlements. Their suitability for As removal from water is mainly due to adsorption, co-precipitation and ion exchange processes involving Fe- and Al-rich minerals and clay minerals present in the soils or sediments. In the present study, various clay-rich soils from the Santiago del Estero province (SDE, NW Argentina) and, for comparison, a laterite from the Misiones province have been tested as adsorbents for As in shallow naturally contaminated groundwaters of the Rio Dulce alluvial aquifer in SDE. Batch adsorption experiments showed higher As(V) removal for the Misiones laterite sample (99 %) as compared with the soils from SDE (40-53 %), which can be related to lower contents of water-soluble and oxalate extractable Al and Fe in the last samples. These results suggest the application of the Misiones laterite soil as an alternative for As removal. However, high transportation costs from Misiones to SDE can be an economical restriction for the low-income population of SDE.
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| 5. |
- Cortés, Marisol, et al.
(författare)
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CK2 oppositely modulates L-DOPA-induced dyskinesia via striatal projection neurons expressing D1 or D2 receptors
- 2017
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Ingår i: The Journal of Neuroscience. - 0270-6474. ; 37:49, s. 11930-11946
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Tidskriftsartikel (refereegranskat)abstract
- We have previously shown that casein kinase 2 (CK2) negatively regulates dopamine D1 and adenosine A2A receptor signaling in the striatum. Ablation of CK2 in D1 receptor-positive striatal neurons caused enhanced locomotion and exploration at baseline, whereas CK2 ablation in D2 receptor-positive neurons caused increased locomotion after treatment with A2A antagonist, caffeine. Because both, D1 and A2A receptors, play major roles in the cellular responses toL-DOPA in the striatum, these findings prompted us to examine the impact of CK2 ablation on the effects ofL-DOPA treatment in the unilateral 6-OHDA lesioned mouse model of Parkinson’s disease. We report here that knock-out of CK2 in striatonigral neurons reduces the severity ofL-DOPA-induced dyskinesia (LID), a finding that correlates with lowered pERK but unchanged pPKA substrate levels in D1 medium spiny neurons as well as in cholinergic interneurons. In contrast, lack of CK2 in striatopallidal neurons enhances LID and ERK phosphorylation. Coadministration of caffeine with a low dose ofL-DOPA reduces dyskinesia in animals with striatopallidal knock-out to wild-type levels, suggesting a dependence on adenosine receptor activity. We also detect reduced Golf levels in the striatonigral but not in the striatopallidal knock-out in response toL-DOPA treatment. Our work shows, in a rodent model of PD, that treatment-induced dyskinesia and striatal ERK activation are bidirectionally modulated by ablating CK2 in D1- or D2-positive projection neurons, in male and female mice. The results reveal that CK2 regulates signaling events critical to LID in each of the two main populations of striatal neurons.
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| 6. |
- Edwards, Robert A., et al.
(författare)
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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
- 2019
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Ingår i: Nature Microbiology. - : Springer Science and Business Media LLC. - 2058-5276. ; 4:10, s. 1727-1736
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Tidskriftsartikel (refereegranskat)abstract
- Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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| 7. |
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| 8. |
- Richards, Stephen, et al.
(författare)
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Genome Sequence of the Pea Aphid Acyrthosiphon pisum
- 2010
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 8:2, s. e1000313-
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Tidskriftsartikel (refereegranskat)abstract
- Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
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| 9. |
- Sedlacek, Janosch, et al.
(författare)
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Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats
- 2016
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 6:12, s. 3940-3952
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Tidskriftsartikel (refereegranskat)abstract
- Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early-and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.
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| 10. |
- Sedlacek, Janosch F., et al.
(författare)
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What role do plant-soil interactions play in the habitat suitability and potential range expansion of the alpine dwarf shrub Salix herbacea?
- 2014
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Ingår i: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791 .- 1618-0089. ; 15:4, s. 305-315
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Tidskriftsartikel (refereegranskat)abstract
- Mountain plants may respond to warming climates by migrating along altitudinal gradients or, because climatic conditions on mountain slopes can be locally very heterogeneous, by migrating to different microhabitats at the same altitude. However, in new environments, plants may also encounter novel soil microbial communities, which might affect their establishment success. Thus, biotic interactions could be a key factor in plant responses to climate change. Here, we investigated the role of plant soil feedback for the establishment success of the alpine dwarf shrub Salix herbacea L. across altitudes and late- and early snowmelt microhabitats. We collected S. herbacea seeds and soil from nine plots on three mountain-slope transects near Davos, Switzerland, and we transplanted seeds and seedlings to substrate inoculated with soil from the same plot or with soils from different microhabitats, altitudes and mountains under greenhouse conditions. We found that, on average, seeds from higher altitudes (2400-2700 m) and late-exposed snowbeds germinated better than seeds from lower altitudes (2200-2300 m) and early-exposed ridges. However, despite these differences in germination, growth was generally higher for plants from low altitudes, and there were no indications for a an home-soil advantage within the current range of S. herbacea. Interestingly, seedlings growing on soil from above the current altitudinal distribution of S. herbacea grew on average less well than on their own soil. Thus, although the lack of a home-soil advantage in the current habitat might be beneficial for S. herbacea in a changing environment, migration to habitats beyond the current altitudinal range might be limited, probably due to missing positive soil-feedback.
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