Maintenance of Plant Species Diversity by Pathogens Bever, James D; Mangan, Scott A; Alexander, Helen M
Annual review of ecology, evolution, and systematics,
12/2015, Letnik:
46, Številka:
1
Journal Article
Recenzirano
We present strong evidence that pathogens play a critical role in structuring plant communities and maintaining plant diversity. Pathogens mediate plant species coexistence through trade-offs between ...competitive ability and resistance to pathogens and through pathogen specialization. Experimental tests of individual plant-pathogen interactions, tests of feedback through host-specific changes in soil communities, and field patterns and field experimentation consistently identify pathogens as important to plant species coexistence. These direct tests are supported by observations of the role of pathogens in generating the productivity gains from manipulations of plant diversity and by evidence that escape from native pathogens contributes to success of introduced plant species. Further work is necessary to test the role of pathogen dynamics in large-scale patterns of plant diversity and range limits, the robustness of coexistence to coevolutionary dynamics, the contribution of different pathogens, and the role of pathogens in plant succession.
Black carbon (BC) and light-absorbing organic carbon (brown carbon, BrC) play key roles in warming the atmosphere, but the magnitude of their effects remains highly uncertain. Theoretical modelling ...and laboratory experiments demonstrate that coatings on BC can enhance BC's light absorption, therefore many climate models simply assume enhanced BC absorption by a factor of ∼1.5. However, recent field observations show negligible absorption enhancement, implying models may overestimate BC's warming. Here we report direct evidence of substantial field-measured BC absorption enhancement, with the magnitude strongly depending on BC coating amount. Increases in BC coating result from a combination of changing sources and photochemical aging processes. When the influence of BrC is accounted for, observationally constrained model calculations of the BC absorption enhancement can be reconciled with the observations. We conclude that the influence of coatings on BC absorption should be treated as a source and regionally specific parameter in climate models.
The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform ...genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.
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•Diffuse large B cell lymphoma (DLBCL) consists of seven genetic subtypes•The LymphGen algorithm classifies a DLBCL biopsy into one or more genetic subtypes•The genetic subtypes have distinct clinical outcomes and pathway dependencies•The genetic subtypes will aid the development of rationally targeted therapy of DLBCL
Wright et al. identify seven genetic subtypes of diffuse large B cell lymphoma (DLBCL) with distinct outcomes and therapeutic vulnerabilities. The LymphGen probabilistic classification tool that can classify a DLBCL biopsy into the genetic subtypes is developed, which could be used for precision medicine trials.
The major clinical challenge in the treatment of high-grade serous ovarian cancer (HGSOC) is the development of progressive resistance to platinum-based chemotherapy. The objective of this study was ...to determine whether intra-tumour genetic heterogeneity resulting from clonal evolution and the emergence of subclonal tumour populations in HGSOC was associated with the development of resistant disease.
Evolutionary inference and phylogenetic quantification of heterogeneity was performed using the MEDICC algorithm on high-resolution whole genome copy number profiles and selected genome-wide sequencing of 135 spatially and temporally separated samples from 14 patients with HGSOC who received platinum-based chemotherapy. Samples were obtained from the clinical CTCR-OV03/04 studies, and patients were enrolled between 20 July 2007 and 22 October 2009. Median follow-up of the cohort was 31 mo (interquartile range 22-46 mo), censored after 26 October 2013. Outcome measures were overall survival (OS) and progression-free survival (PFS). There were marked differences in the degree of clonal expansion (CE) between patients (median 0.74, interquartile range 0.66-1.15), and dichotimization by median CE showed worse survival in CE-high cases (PFS 12.7 versus 10.1 mo, p = 0.009; OS 42.6 versus 23.5 mo, p = 0.003). Bootstrap analysis with resampling showed that the 95% confidence intervals for the hazard ratios for PFS and OS in the CE-high group were greater than 1.0. These data support a relationship between heterogeneity and survival but do not precisely determine its effect size. Relapsed tissue was available for two patients in the CE-high group, and phylogenetic analysis showed that the prevalent clonal population at clinical recurrence arose from early divergence events. A subclonal population marked by a NF1 deletion showed a progressive increase in tumour allele fraction during chemotherapy.
This study demonstrates that quantitative measures of intra-tumour heterogeneity may have predictive value for survival after chemotherapy treatment in HGSOC. Subclonal tumour populations are present in pre-treatment biopsies in HGSOC and can undergo expansion during chemotherapy, causing clinical relapse.
The Pacific Decadal Oscillation, Revisited Newman, Matthew; Alexander, Michael A.; Ault, Toby R. ...
Journal of climate,
06/2016, Letnik:
29, Številka:
12
Journal Article
Recenzirano
The Pacific decadal oscillation (PDO), the dominant year-round pattern of monthly North Pacific sea surface temperature (SST) variability, is an important target of ongoing research within ...themeteorological and climate dynamics communities and is central to the work of many geologists, ecologists, natural resource managers, and social scientists. Research over the last 15 years has led to an emerging consensus: the PDO is not a single phenomenon, but is instead the result of a combination of different physical processes, including both remote tropical forcing and local North Pacific atmosphere–ocean interactions, which operate on different time scales to drive similar PDO-like SST anomaly patterns. How these processes combine to generate the observed PDO evolution, including apparent regime shifts, is shown using simple autoregressive models of increasing spatial complexity. Simulations of recent climate in coupled GCMs are able to capture many aspects of the PDO, but do so based on a balance of processes often more independent of the tropics than is observed. Finally, it is suggested that the assessment of PDO-related regional climate impacts, reconstruction of PDO-related variability into the past with proxy records, and diagnosis of Pacific variability within coupled GCMs should all account for the effects of these different processes, which only partly represent the direct forcing of the atmosphere by North Pacific Ocean SSTs.
The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence-absence or quantitative species abundance data. ...PERMANOVA, a permutation-based extension of multivariate analysis of variance to a matrix of pairwise distances, partitions within-group and between-group distances to permit assessment of the effect of an exposure or intervention (grouping factor) upon the sampled microbiome. Within-group distance and exposure/intervention effect size must be accurately modeled to estimate statistical power for a microbiome study that will be analyzed with pairwise distances and PERMANOVA.
We present a framework for PERMANOVA power estimation tailored to marker-gene microbiome studies that will be analyzed by pairwise distances, which includes: (i) a novel method for distance matrix simulation that permits modeling of within-group pairwise distances according to pre-specified population parameters; (ii) a method to incorporate effects of different sizes within the simulated distance matrix; (iii) a simulation-based method for estimating PERMANOVA power from simulated distance matrices; and (iv) an R statistical software package that implements the above. Matrices of pairwise distances can be efficiently simulated to satisfy the triangle inequality and incorporate group-level effects, which are quantified by the adjusted coefficient of determination, omega-squared (ω2). From simulated distance matrices, available PERMANOVA power or necessary sample size can be estimated for a planned microbiome study.
A key resistance mechanism to platinum-based chemotherapies and PARP inhibitors in
-mutant cancers is the acquisition of
reversion mutations that restore protein function. To estimate the prevalence ...of
reversion mutations in high-grade ovarian carcinoma (HGOC), we performed targeted next-generation sequencing of circulating cell-free DNA (cfDNA) extracted from pretreatment and postprogression plasma in patients with deleterious germline or somatic
mutations treated with the PARP inhibitor rucaparib.
reversion mutations were identified in pretreatment cfDNA from 18% (2/11) of platinum-refractory and 13% (5/38) of platinum-resistant cancers, compared with 2% (1/48) of platinum-sensitive cancers (
= 0.049). Patients without
reversion mutations detected in pretreatment cfDNA had significantly longer rucaparib progression-free survival than those with reversion mutations (median, 9.0 vs. 1.8 months; HR, 0.12;
< 0.0001). To study acquired resistance, we sequenced 78 postprogression cfDNA, identifying eight additional patients with
reversion mutations not found in pretreatment cfDNA. SIGNIFICANCE:
reversion mutations are detected in cfDNA from platinum-resistant or platinum-refractory HGOC and are associated with decreased clinical benefit from rucaparib treatment. Sequencing of cfDNA can detect multiple
reversion mutations, highlighting the ability to capture multiclonal heterogeneity.
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Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been ...developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform research and management activities related to understanding and adapting marine fisheries management and conservation to climate change and decadal variability.
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