| 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. |
- Fu, Hong, et al.
(författare)
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Energetic Asymmetry Connected with Energy Flow Changes in Response to Eutrophication : A Study of Multiple Fish Species in Subtropical Shallow Lakes
- 2019
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Ingår i: Polish Journal of Ecology. - 1505-2249. ; 67:4, s. 305-315
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Tidskriftsartikel (refereegranskat)abstract
- Energy flow is a central characteristic in all ecosystems, and it has attracted considerable scientific attention due to its significant effects on the stability of food webs. Lake ecosystems that undergo regime shifts (clear water phase, phytoplankton dominated changed into turbid water, macrophytes dominated or vice versa) are characterized by a series of transformation in trophic structure. Although previous studies have mainly focused on the causes and consequences of regime shifts in shallow lakes, studies about responses of energy flow changes to regime shifts is far from complete. In this paper, we estimated trophic position and benthivory (i.e. degree of benthivory) of seventeen fish species from seven shallow lakes. Our data show that the trophic position and benthivory of fish species in clear water phase are significantly higher than in turbid water. This finding might help spark some ideas for subtropical lake eutrophication treatment.
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| 4. |
- 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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| 5. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 6. |
- Zhang, Huan, et al.
(författare)
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Plasticity in rotifer morphology induced by conflicting threats from multiple predators
- 2022
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 67:3, s. 498-507
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Tidskriftsartikel (refereegranskat)abstract
- One of the major research goals in ecology is to understand predator–prey interactions. However, our understanding of how prey express phenotypic plasticity in response to co-occurring multiple predators is limited in many systems. Here, we use the rotifer Brachionus calyciflorus as model organism to test how prey responds to co-occurring predators through a series of related experiments. Firstly, we examined the effects of the density of a fish predator Carassius auratus on morphological traits in B. calyciflorus. Secondly, we examined the effects of larval C. auratus and Asplanchna brightwellii (a rotifer predator) on morphological defensive traits (body length, body width, anterior spine length, and posterolateral spine length) of B. calyciflorus. We show that B. calyciflorus develops smaller body size and shorter spine length when exposed to media conditioned using larval fish, and that high larval fish densities induce more pronounced responses than low densities. We also show that B. calyciflorus is able to discriminate between the two predators by producing opposing morphological adaptations (i.e., larger body size and longer posterolateral spines against A. brightwellii, but smaller body size and shorter spine length when exposed to the visual predator [larval fish]). However, B. calyciflorus develops intermediate, trade-off responses in all morphological traits when exposed to conflicting threats from a combination of predators with different size and feeding strategies. These results show how prey are not necessarily passive victims, but rather, use countermeasures against predation – they actively develop responses to counteract their vulnerability to different predators by rapidly adjusting their morphology and life-history traits to the existing predator regimes.
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| 7. |
- Zhang, Huan, et al.
(författare)
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Synergistic effects of warming and eutrophication alert zooplankton predator–prey interactions along the benthic–pelagic interface
- 2021
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 27:22, s. 5907-5919
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Tidskriftsartikel (refereegranskat)abstract
- Contemporary evidence suggests that climate change and other co-occurring large-scale environmental changes, such as eutrophication, will have a considerable impact on aquatic communities. However, the interactions of these environmental changes on trophic interactions among zooplankton remain largely unknown. Here we present results of a mesocosm experiment examining how a couple of zooplankton predator and prey taxa with different life-history strategies respond to the combined effect of an increase in temperature (4.5°C) and in eutrophication (phosphorus addition), during the crucial recruiting and growing season. We show that the addition of phosphorus alone significantly weakened the top-down effects by the cyclopoid copepod predators on their rotifer prey. In contrast, warming strengthened the top-down effects from the predator, leading to a reduction in the abundance of the rotifer prey. These effects of warming were enhanced by phosphorus addition. Together, our results demonstrate that warming made plankton prey organisms more susceptible to top-down effects from predators, but reduced their sensitivity to nutrient enrichment. In terms of the phenological effects, warming advanced the termination of diapause for both rotifers and cyclopoid copepods by about 2 weeks, but these temporal shifts, akin for both groups, resulted in no apparent trophic mismatch. Hence, from a future perspective, cyclopoid copepods are likely to benefit more from the combination of nutrient enrichment and climate warming to the detriment of their rotifer prey.
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| 8. |
- Hansson, Lars Anders, et al.
(författare)
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Different climate scenarios alter dominance patterns among aquatic primary producers in temperate systems
- 2020
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Ingår i: Limnology and Oceanography. - : WILEY. - 0024-3590 .- 1939-5590. ; 65:10, s. 2328-2336
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Tidskriftsartikel (refereegranskat)abstract
- In a future climate change perspective, the interactions among different life-forms of primary producers will likely be altered, leading to changes in the relative dominance among macrophytes, filamentous, and planktonic algae. In order to improve the possibilities to forecast future ecosystem services and function, we therefore conducted a long-term mesocosm study where primary producers were exposed to different climate scenarios, including both a mean increase in temperature (4 degrees C) and a similar energy input, but delivered as "heat waves" (fluctuations 0-8 degrees C above ambient). We show that in shallow systems, future climate change scenarios will likely lead to higher total macrophyte biomasses, but also to considerable alterations in the macrophyte community composition. The biomass of filamentous algae (Cladophora) showed no significant difference among treatments, although effect size analyses identified a slight increase at heated conditions. We also show that future climate change will not necessarily lead to more phytoplankton blooms, although a considerable alteration in phytoplankton community composition is to be expected, with a dominance of cyanobacteria and Cryptophytes, whereas Chlorophyceae and diatoms will likely play a less pronounced role than at present. In a broader context, we conclude that the total biomass of macrophytes will likely increase in shallow areas, whereas phytoplankton may not show any strong changes in biomass in a future climate change scenario. Instead, the major changes among primary producers will likely be mirrored in a considerably different species composition than at present.
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| 9. |
- He, Huan
(författare)
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A multi-omics approach to uncover estrogen receptor (ER) and activator protein 1 (AP-1) signaling networks in breast cancer
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Estrogen receptor (ER) binds to DNA indirectly through other transcription factors (e.g. AP-1) to modulate gene expression, which is a tethering mechanism. The ER/AP-1 crosstalk plays an important role in tamoxifen therapy resistance. However, the overlap in DNA binding profiles of ER and AP-1 transcription factors at genome-wide level has not been described. Moreover, AP-1 plays a pivotal role in various cellular processes in breast cancer. The transcriptional activity of AP-1 is controlled by coregulators, thereby regulating the expression of specific genes. Understanding protein-protein interactions is fundamental to the mechanism of AP-1 signaling. In addition, ERα is one of the key biomarkers for diagnosis and endocrine therapy of breast cancer. However, ERα status is not considered to be a perfect marker for responsiveness to anti-estrogens. It has been shown that ERβ may act as a tumor suppressor and could be a therapeutic target for breast cancer, however the functions of ERβ in this setting remain to be further explored. The use of multi-functional genomic technologies to identify cistrome, transcriptome and proteome of ER or AP-1 has resulted in comprehensive deciphering of the role of the ER and AP-1 in breast cancer, which also provides information for developing novel therapeutic strategies for breast cancer. In Paper I, we investigated the genome-wide assessment of c-Jun, a potent member of AP-1 family, and ERα cistrome and transcriptome in ERα-positive breast cancer cells. Our findings demonstrate the genome-wide co-localization of ERα and c-Jun binding regions and suggest that ERα tethering to AP-1 is a global mechanism for gene transcription regulated by ERα. In addition, the results confirm that the sensitivity of ERα-positive breast cancer cells to tamoxifen therapy is reduced by c-Jun overexpression. Moreover, it is shown that expression of transforming growth factor β induced (TGFBI) protein is associated with poor outcomes of ERα-positive breast cancer patients receiving endocrine therapy and thus as a candidate gene that may cause tamoxifen resistance through ERα and AP-1 crosstalk. In Paper II, we elucidated the first Fra-1 associated interactome in triple-negative breast cancer (TNBC) cells using Rapid Immunoprecipitation Mass Spectrometry of Endogenous proteins (RIME) approach, showing that the most enriched Fra-1 interacting protein was DDX5. The cistrome and transcriptome of DDX5 extensively overlapped with that of Fra-1, which is highly associated with the TNBC cell growth. Furthermore, we found that DDX5 acts as a transcriptional coactivator for Fra-1, enhancing Fra-1-dependent TNBC cell proliferation through increasing the transcriptional activity of Fra-1. We also showed that higher expression level of DDX5 protein was detected in triple-negative basal-like tumors compared with that in non-basal-like ones. In addition, the direct target gene set of DDX5 can predict poor clinical outcome of breast cancer patients. In Paper III, we generated a novel breast cancer cell model with overexpression of ERβ in the absence of ERα. We used CRISPR/Cas9 system to knock out ERα in MCF7 breast cancer cells with stable Tet-Off-inducible ERβ expression. We found that only ERβ-expressing MCF7 cells displayed a significant reduction in cell proliferation in response to E2 compared with vehicle, conversely, only ERα-expressing MCF7 cells displayed an increased cell proliferation upon E2 treatment. The RNA-seq results indicated that ERβ could modulate specific gene expression profile different from that of ERα. Furthermore, functional enrichment analysis showed that the two ER isoforms regulate cell proliferation in opposite direction; ERβ is significantly involved in the biological process “negative regulation of cell proliferation”. In conclusion, the studies presented in the thesis contribute to comprehensive understanding of the mechanism of ER and AP-1 signaling in breast cancer. We characterized two molecules, TGFBI and DDX5, in breast cancer, suggesting that they could be the candidates of therapeutic targets. We also provided evidences that ERα and ERβ have opposite effects on E2-dependent breast cancer cell proliferation by regulating distinct gene sets.
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| 10. |
- He, Yafang, et al.
(författare)
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Metabolomic Changes Upon Conjugated Linoleic Acid Supplementation and Predictions of Body Composition Responsiveness
- 2022
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Ingår i: Journal of Clinical Endocrinology and Metabolism. - : The Endocrine Society. - 1945-7197 .- 0021-972X. ; 107:9, s. 2606-2615
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Tidskriftsartikel (refereegranskat)abstract
- Context Conjugated linoleic acid (CLA) may optimize body composition, yet mechanisms underlining its benefits are not clear in humans. Objective We aimed to reveal the CLA-induced changes in the plasma metabolome associated with body composition improvement and the predictive performance of baseline metabolome on intervention responsiveness. Methods Plasma metabolome from overnight fasted samples at pre- and post-intervention of 65 participants in a 12-week randomized, placebo-controlled trial (3.2 g/day CLA vs 3.2 g/day sunflower oil) were analyzed using untargeted LC-MS metabolomics. Mixed linear model and machine learning were applied to assess differential metabolites between treatments, and to identify optimal panel (based on baseline conventional variables vs metabolites) predicting responders of CLA-derived body composition improvement (increased muscle variables or decreased adiposity variables) based on dual-energy x-ray absorptiometry. Results Compared with placebo, CLA altered 57 metabolites (P
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