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Response of Benthic Biodiversity to Climate-Sensitive Regional and Local Conditions in a Complex Estuarine System
Published in Vyacheslav Lyubchich, Yulia R. Gel, K. Halimeda Kilbourne, Thomas J. Miller, Nathaniel K. Newlands, Adam B. Smith, Evaluating Climate Change Impacts, 2020
Ryan J. Woodland, Jeremy M. Testa
Multivariate analysis of assemblage composition was used to determine how, or if, community composition was changing along with species biodiversity under changing 5℃C DD annual thermal regimes identified during GAM analysis. Constrained canonical correspondence analysis (CCA; ter Braak, 1986; Leguendre and Leguendre, 2012) was used to test for assemblage composition differences at the whole-of-ecosystem scale between years associated with rapid (<130 d) or slow (>130 d) vernal warming (5℃C DDTime) and between years associated with high (>1400 DD), medium (1300–1400 DD), or low (<1300 DD) total accumulated warming (5℃C DDCum). Permutation-based analysis of variance under the constrained CCA model was used to test for the significance of group effects in the presence of conditional variables (salinity, depth, region). Indicator species associated with group-differences of interest were identified by calculating the Indicator Value index (IndVal) for species, a measure of the relationship between each species and each group. High IndVal indicates a strong association with sites within a grouping, and significance is determined using a permutation test (Dufrene and Legendre 1997). Multivariate species assemblage analysis was conducted in R (v 3.6.1), using the packages vegan (Oksanen et al, 2019) and indicspecies (De Cáceres and Jansen, 2019).
What are politicians for?
Published in John Spiers, Philip Booth, Who Decides Who Decides?, 2018
Here are 14 recent examples of this living detail – by contrast with politicised generalisations – with references. Each of these underlines that consumers are not customers. They have no power. If they had economic power, how many of the following problems would be tolerated? These examples might be viewed as what ecologists call ‘an indicator species’. Or messages about the underlying soil, the culture, context and disempowering realities. The list could be much longer, if space allowed. Better management by politicians seems unlikely to be sufficient for necessary change. And, as Sir Gerry Robinson showed in his enquiry into the NHS, to announce a policy is not necessarily to fix a problem.14
Pesticides and Chronic Diseases
Published in William J. Rea, Kalpana D. Patel, Reversibility of Chronic Disease and Hypersensitivity, Volume 4, 2017
William J. Rea, Kalpana D. Patel
Wild birds and mammals are damaged and destroyed by pesticides and these animals make excellent “indicator species.” Deleterious effects on wildlife include death from the direct exposure to pesticides or secondary poisonings from consuming contaminated food; reduced survival, growth, and reproductive rates from exposure to sublethal dosages; and habitat reduction through the elimination of food resources and refuges. In the United States, approximately 3 kg of pesticide is applied per hectare on about 160 million ha of cropland each.544
Non-small cell lung cancer patients treated with Anti-PD1 immunotherapy show distinct microbial signatures and metabolic pathways according to progression-free survival and PD-L1 status
Published in OncoImmunology, 2023
David Dora, Balazs Ligeti, Tamas Kovacs, Peter Revisnyei, Gabriella Galffy, Edit Dulka, Dániel Krizsán, Regina Kalcsevszki, Zsolt Megyesfalvi, Balazs Dome, Glen J. Weiss, Zoltan Lohinai
Others showed that a higher gut microbiota alpha diversity was associated with increased response rates to ICI therapy and improved PFS16,17. In contrast, we found no significant difference in alpha-diversity in any comparison, including PFS, CHT-treatment, and PD-L1 phenotype. However, beta-diversity significantly differed between patients with short and long PFS, as in the case of other NSCLC16,17 and melanoma studies9–11. Moreover, we detected a significant gut microbial compositional difference between CHT-treated and CHT-naive patients that underlines the effect of CHT on the gut microbiome. It is noteworthy that bacterial richness and alpha-diversity are parameters that are difficult to assess in the routine clinical practice, whereas detecting or quantifying individual species is cost-effective. Thus, we identified specific indicator species that could predict outcomes with high reliability and we established a hierarchical model stratifying taxa based on the extent of their predictive role regarding long or short PFS. Notably, apart from univariate statistical tests, we have also implemented various multivariate statistical models, such as Lasso- and Cox proportional hazard regression, to define the predictive relevance of a particular taxon based on solid evidence.
Functional signatures of ex-vivo dental caries onset
Published in Journal of Oral Microbiology, 2022
Dina G. Moussa, Ashok K. Sharma, Tamer A Mansour, Bruce Witthuhn, Jorge Perdigão, Joel D. Rudney, Conrado Aparicio, Andres Gomez
We corroborated these signatures using indicator species analyses and its indicator value ‘IndVal’ index to detect taxa that specifically characterized treatment (e.g. sucrose supplementation) and each time point (4-way comparisons, Supplemental Table 8). Representative taxa for each studied group showing IndVal index, >0.4, and corroborated using an FDR-adjusted p-value (multiple comparisons) are presented in (Figure 5b). The rest of the identified indicator taxa (25 in total) and their IndVal and probabilities are listed in (Supplemental Table 8). The ASVs with the strongest IndVals were associated with WS_T2, which represented overt lesions; these taxa belonged to Lactobacillus, Atopobium, and Enterococcus. Strong indicator ASVs for NS_T1 include Abiotrophia and Porphyromonas, while incipient early lesions (WS_T1) corroborated high abundance of Streptococcus (Supplemental Table 8).
Manganese dioxide nanosheets induce mitochondrial toxicity in fish gill epithelial cells
Published in Nanotoxicology, 2021
Cynthia L. Browning, Allen Green, Evan P. Gray, Robert Hurt, Agnes B. Kane
Fish serve as a valuable indicator species for both the detection of contaminated freshwater ecosystems and identifying potential toxicity of environmental pollutants (López-López and Sedeño-Díaz 2015). Fish gills are an initial target site of exposure to aquatic environmental pollutants and accumulate nanomaterials through their association with mucous proteins on the surface of the gill (Smith, Shaw, and Handy 2007; Evans, Piermarini, and Choe 2005). The well-characterized rainbow trout cell line, RTgill-W1, was derived from rainbow trout gill epithelial tissue, providing an alternative to animal toxicity testing and to further mechanistic toxicity studies (Bols et al. 1994). The RTgill-W1 cell line expresses xenobiotic metabolizing enzymes and membrane transporters and has been validated for aquatic toxicity testing (Nimmo 1985; Eyckmans et al. 2011; Lee et al. 2009). This model revealed that MnO2 nanosheets were taken up by fish gill cells prior to dissolution, resulting in decreased levels of glutathione, an important intracellular reducing agent (Gray et al. 2020).