The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia
TL;DR: It is found that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees, suggesting that most taxonomic groups respond to the same overall diversity gradients at large spatial scales.
Abstract: Most knowledge on biodiversity derives from the study of charismatic macro-organisms, such as birds and trees. However, the diversity of micro-organisms constitutes the majority of all life forms on Earth. Here, we ask if the patterns of richness inferred for macro-organisms are similar for micro-organisms. For this, we barcoded samples of soil, litter and insects from four localities on a west-to-east transect across Amazonia. We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three molecular markers. We then compared OTU richness with species richness of two relatively well-studied organism groups in Amazonia: trees and birds. We find that OTU richness shows a declining west-to-east diversity gradient that is in agreement with the species richness patterns documented here and previously for birds and trees. These results suggest that most taxonomic groups respond to the same overall diversity gradients at large spatial scales. However, our results show a different pattern of richness in relation to habitat types, suggesting that the idiosyncrasies of each taxonomic group and peculiarities of the local environment frequently override large-scale diversity gradients. Our findings caution against using the diversity distribution of one taxonomic group as an indication of patterns of richness across all groups.
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TL;DR: A higher concentration of platelet EVs in serum than plasma is validated by contemporary EV methods, which implicates that EVs carry both intravesicular and extravesicular cargo, which will expand their applicability for biomarker discovery.
Abstract: Extracellular vesicles (EVs) in human blood are a potential source of biomarkers To which extent anticoagulation affects their concentration, cellular origin and protein composition is largely unexplored To study this, blood from 23 healthy subjects was collected in acid citrate dextrose (ACD), citrate or EDTA, or without anticoagulation to obtain serum EVs were isolated by ultracentrifugation or by size-exclusion chromatography (SEC) for fluorescence-SEC EVs were analyzed by micro flow cytometry, NTA, TEM, Western blot, and protein mass spectrometry The plasma EV concentration was unaffected by anticoagulants, but serum contained more platelet EVs The protein composition of plasma EVs differed between anticoagulants, and between plasma and serum Comparison to other studies further revealed that the shared EV protein composition resembles the "protein corona" of synthetic nanoparticles incubated in plasma or serum In conclusion, we have validated a higher concentration of platelet EVs in serum than plasma by contemporary EV methods Anticoagulation should be carefully described (i) to enable study comparison, (ii) to utilize available sample cohorts, and (iii) when preparing/selecting biobank samples Further, the similarity of the EV protein corona and that of nanoparticles implicates that EVs carry both intravesicular and extravesicular cargo, which will expand their applicability for biomarker discovery
125 citations
TL;DR: This review surveys the understanding of the structural biology of the cannabinoids and their target receptors including both a critical comparison of the extant crystal structures and the computationally derived homology models, as well as an in-depth discussion about the binding modes of the major cannabinoids.
95 citations
TL;DR: The findings suggest cannabidiol and Δ9 -tetrahydrocannabinol are possible drugs against human coronavirus that might be used in combination or with other drug molecules to treat COVID-19 patients.
66 citations
TL;DR: In this article, the authors quantified the occurrence and severity of marine heatwaves over 60 years in warm range edge kelp forests on both sides of the North Atlantic, and experimentally demonstrated a relationship between strong and severe 2018 heatwaves and high kelp mortality in both regions.
Abstract: Extreme climatic events including marine heatwaves (MHWs) are becoming more frequent and severe in the Anthropocene. However, our understanding of how these events affect population dynamics of ecologically important species is limited, in part because extreme events are rare and difficult to predict. Here, we quantified the occurrence and severity of MHWs over 60 years in warm range edge kelp forests on both sides of the North Atlantic. The cumulative annual intensity of MHWs increased two- to four-fold during this period, coinciding with the disappearance of kelps. We experimentally demonstrated a relationship between strong and severe 2018 heatwaves and high kelp mortality in both regions. Patterns of kelp mortality were strongly linked to maximum temperature anomalies, which crossed lethal thresholds in both regions. Translocation and tagging experiments revealed similar kelp mortality rates on reefs dominated by healthy kelp forests and degraded sediment-laden algal ‘turfs’, indicating equal vulnerability to extreme events. These results suggest a mechanistic link between MHWs and broad-scale kelp loss, and highlight how warming can make ecosystem boundaries unstable, forcing shifts to undesirable ecosystem states under episodically extreme climatic conditions.
64 citations
TL;DR: A review of the potential application of nanocellulose in food packaging and discuss new challenges and opportunities for starch biocomposites enriched with nano cellulose is presented in this article.
61 citations
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TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
272,030 citations
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
70,111 citations
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Abstract: In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
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47,038 citations
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
18,256 citations
TL;DR: The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% correct bases commonly reported by other methods.
Abstract: Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
11,329 citations