Biology subjects

Warner, E.

Publications and source records attributed to Warner, E..

4 recordsLinked to original sources

bioRxiv2022

Higher aboveground carbon stocks in mixed-species planted forests than monocultures - a meta-analysis

Natural forest is declining globally as the area of planted forest increases. Planted forests are often monocultures, despite results suggesting that higher species richness improves ecosystem functioning and stability. To test if this is generally the case, we performed a meta-analysis of available results. We assessed aboveground carbon stocks in mixed-species planted forests vs (a) the average of constituent species monocultures, (b) the best constituent species monoculture, and (c) commercial species monocultures. We investigated whether any advantage of mixtures over monocultures was positively related to species richness, as well as potential mechanisms driving differences in carbon stocks between mixtures and monocultures. The meta-analysis dataset included 79 comparisons from 21 sites. Carbon stocks in mixed planted forests were higher than the average of stocks in monocultures of their constituent species, containing on average 70% more carbon. Mixed planted forests also out-performed commercial monocultures, containing on average 77% more carbon. There was c.25% more carbon in mixed planted forests relative to the best performing monocultures, although this difference was not statistically significant. Overyielding was highest in four-species mixtures (richness range 2-6 species). More data providing better coverage of richness and age gradients (study sites aged 3.5-28 years) is needed to increase confidence in these results. None of the potential mechanisms we examined (nitrogen-fixer present vs absent; native vs non-native/mixed origin; tree diversity experiment vs forestry plantation) consistently explained variation in the diversity effects. This suggests that our findings are driven by a combination of small (statistically insignificant) effects from these sources or further unidentified mechanisms or some combination of the two. We conclude that increasing tree species richness in planted forests can increase carbon stocks while bringing other potential benefits associated with diversification. However, implementation will depend on the balance of these benefits relative to the operational challenges and costs of diversification.

ecology↗

bioRxiv2020

Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli

Genome-wide protein-protein interaction (PPI) determination remains a significant unsolved problem in structural biology. The difficulty is twofold since high-throughput experiments (HTEs) have often a high false-positive rate in assigning PPIs, and PPI quaternary structures are more difficult to solve than tertiary structures using traditional structural biology techniques. We proposed a uniform pipeline to address both problems, which first recognizes PPIs by combining multi-chain threading alignments with HTE results using naive Bayesian classifiers, where the quaternary complex structures are then constructed by mapping the monomer models with the dimeric threading frameworks through interface-specific structural alignments. The pipeline was applied to the Escherichia coli genome and created 35,125 confident PPIs which is 4.5-fold higher than HTE alone. Graphic analyses of the PPI networks revealed a scale-free cluster size distribution, which was found critical to the robustness of genome evolution and the centrality of functionally important proteins that are essential to E. coli survival. Furthermore, complex structure models were constructed for all predicted E. coli PPIs based on the quaternary threading alignments, where 6,771 of them were found to have a high confidence score that corresponds to the correct fold of the complexes with a TM-score >0.5 and 93 showed a close consistency with the later released experimental structures with an average TM-score=0.73. These results demonstrated the significant usefulness of threading-based homologous modeling in both genome-wide PPI network detection and complex structural construction.

bioinformatics↗

bioRxiv2020

The RNA pseudoknots in foot-and-mouth disease virus are dispensable for genome replication but essential for the production of infectious virus.

The positive stranded RNA genomes of picornaviruses comprise a single large open reading frame flanked by 5' and 3' untranslated regions (UTRs). Foot-and-mouth disease virus (FMDV) has an unusually large 5' UTR (1.3 kb) containing five structural domains. These include the internal ribosome entry site (IRES), which facilitates initiation of translation, and the cis-acting replication element (cre). Less well characterised structures are a 5' terminal 360 nucleotide stem-loop, a variable length poly-C-tract of approximately 100-200 nucleotides and a series of two to four tandemly repeated pseudoknots (PKs). We investigated the structures of the PKs by selective 2' hydroxyl acetylation analysed by primer extension (SHAPE) analysis and determined their contribution to genome replication by mutation and deletion experiments. SHAPE and mutation experiments confirmed the importance of the previously predicted PK structures for their function. Deletion experiments showed that although PKs are not essential for replication, they provide genomes with a competitive advantage. However, although replicons and full-length genomes lacking all PKs were replication competent, no infectious virus was rescued from genomes containing less than one PK copy. This is consistent with our earlier report describing the presence of putative packaging signals in the PK region.

molecular biology↗

bioRxiv2019

Age and life expectancy clocks based on machine learning analysis of mouse frailty

The identification of genes and interventions that slow or reverse aging is hampered by the lack of non-invasive metrics that can predict life expectancy of pre-clinical models. Frailty Indices (FIs) in mice are composite measures of health that are cost-effective and non-invasive, but whether they can accurately predict health and lifespan is not known. Here, mouse FIs were scored longitudinally until death and machine learning was employed to develop two clocks. A random forest regression was trained on FI components for chronological age to generate the FRIGHT (Frailty Inferred Geriatric Health Timeline) clock, a strong predictor of chronological age. A second model was trained on remaining lifespan to generate the AFRAID (Analysis of Frailty and Death) clock, which accurately predicts life expectancy and the efficacy of a lifespan-extending intervention up to a year in advance. Adoption of these clocks should accelerate the identification of novel longevity genes and aging interventions.

physiology↗