Long‐term research avoids spurious and misleading trends in sustainability attributes of no‐till

Agricultural management recommendations based on short‐term studies can produce findings inconsistent with long‐term reality. Here, we test the long‐term environmental sustainability and profitability of continuous no‐till agriculture on yield, soil water availability, and N₂O fluxes. Using a moving window approach, we investigate the development and stability of several attributes of continuous no‐till as compared to conventional till agriculture over a 29‐year period at a site in the upper Midwest, US. Over a decade is needed to detect the consistent effects of no‐till. Both crop yield and soil water availability required 15 years or longer to generate patterns consistent with 29‐year trends. Only marginal trends for N₂O fluxes appeared in this period. Relative profitability analysis suggests that after initial implementation, 86% of periods between 10 and 29 years recuperated the initial expense of no‐till implementation, with the probability of higher relative profit increasing with longevity. Importantly, statistically significant but misleading short‐term trends appeared in more than 20% of the periods examined. Results underscore the importance of decadal and longer studies for revealing consistent dynamics and emergent outcomes of no‐till agriculture, shown to be beneficial in the long term.     

A Comparison of Protein and mRNA Expression during Development of the Soil Dwelling Prokaryote (S. coelicolor)

In this paper, correlation analysis of protein and mRNA levels in the soil dwelling bacteria Streptomyces coelicolor (S. coelicolor M145) is presented during development of the population as it grew in liquid medium using three biological and two technical replicates, measured during exponential growth, and its entry into the stationary phase. The proteome synthesis time series are compared with the gene expression time series measured previously under identical experimental conditions. Results reveal that about one third of protein/mRNA synthesis profiles are well correlated while another third are correlated negatively. Functional analysis of the highly correlated groups is presented. Based on numerical simulation, the negative correlation between protein and mRNA is shown to be caused by the difference between the rate of translation and protein degradation.     

MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non‐Modified Peptides

A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license.     

Functional analysis of RPS27 mutations and expression in melanoma

Next‐generation sequencing has enabled genetic and genomic characterization of melanoma to an unprecedent depth. However, the high mutational background plus the limited depth of coverage of whole‐genome sequencing performed on cutaneous melanoma samples make the identification of novel driver mutations difficult. We sought to explore the somatic mutation portfolio in exonic and gene regulatory regions in human melanoma samples, for which we performed targeted sequencing of tumors and matched germline DNA samples from 89 melanoma patients, identifying known and novel recurrent mutations. Two recurrent mutations found in the RPS27 promoter associated with decreased RPS27 mRNA levels in vitro. Data mining and IHC analyses revealed a bimodal pattern of RPS27 expression in melanoma, with RPS27‐low patients displaying worse prognosis. In vitro characterization of RPS27‐high and RPS27‐low melanoma cell lines, as well as loss‐of‐function experiments, demonstrated that high RPS27 status provides increased proliferative and invasive capacities, while low RPS27 confers survival advantage in low attachment and resistance to therapy. Additionally, we demonstrate that 10 other cancer types harbor bimodal RPS27 expression, and in those, similarly to melanoma, RPS27‐low expression associates with worse clinical outcomes. RPS27 promoter mutation could thus represent a mechanism of gene expression modulation in melanoma patients, which may have prognostic and predictive implications.     

Assessing influence in biofuel production and ecosystem services when environmental changes affect plant–pest relationships

Climate change is currently affecting both biodiversity and human activities; land use change and greenhouse gas emissions are the main drivers. Many agricultural services are affected by the change, which in turn reflects on the basic provisioning services, which supply food, fibre and biofuels. Biofuels are getting increasing interest because of their sustainability potential. Jatropha curcas gained popularity as a biodiesel crop, due to its ease of cultivation even in harsh environmental conditions. Notwithstanding its high economic importance, few studies are available about its co‐occurrence with pests of the genus Aphthona in sub‐Saharan Africa, where these insects feed on J. curcas, leading to relevant economic losses. Using ecological niche modelling and GIS post‐modelling analyses, we infer the current and future suitable territories for both these taxa, delineating areas where J. curcas cultivations may occur without suffering the presence of Aphthona, in the context of future climate and land use changing. We introduce an area‐normalized index, the ‘Potential‐Actual Cultivation Index’, to better depict the ratio between the suitable areas shared both by the crop and its pest, and the number of actual cultivations, in a target country. Moreover, we find high economic losses (~?50%) both in terms of carbon sequestration and in biodiesel production when J. curcas co‐occur with the Aphthona cookei species group.     

The latest Ordovician Hirnantia brachiopod fauna of Myanmar: Significance of new data from the Mandalay Region

A new, latest Ordovician brachiopod fauna is systematically described from the Hwe Mawng Purple Shale Member (Hirnantian) of the Naungkangyi Group of the Pa-thin area, Mandalay Region, Myanmar, revealing one of the most diverse representatives of the typical Hirnantia Fauna. Rhynchonelliformean, craniiformean and linguliformean brachiopods studied belong to 23 genera and a few indeterminate taxa, among which the most abundant genus Kinnella, along with the four common genera (Paromalomena, Pseudopholidops, Fardenia, and Dalmanella), and other genera (such as Cliftonia, Draborthis, Hindella, Hirnantia, Leptaena, Mirorthis, Plectothyrella, Skenidioides, and Xenocrania) are recorded for the first time. This high diversity Hirnantia Fauna represents an ecological differentiation within the benthos of the Sibumasu Terrane during the end Ordovician global crisis. The palaeoeco-unit named herein as the Kinnella-Paromalomena Association is assigned to lower BA3. This paper includes a taxonomic revision with the following conclusions: 1) Sinomena Zeng et al. and Yichangomena Zeng et al. are treated as junior synonyms of Eostropheodonta Bancroft; 2) Hubeinomena Zeng et al. is regarded as a juvenile form of Coolinia Bancroft; 3) Paramirorthis Zeng et al. is considered an immature growth stage of Mirorthis Zeng; 4) Shanomena Cocks and Fortey is treated as a junior synonym of Paromalomena Rong; 5) Scenidium? medlicotti Reed is redesignated as the type species of Kinnella Bergström to replace Hirnantia? kielanae Temple. The distribution of the Hirnantia Fauna in Myanmar, Thailand and western Yunnan of the Sibumasu Terrane highlights the distinctive nature of the Mandalay fauna, and the analyses of the Hirnantia Fauna and others of Sibumasu shows that Sibumasu was not located far from the South China and Lhasa palaeoplates during late Middle and Late Ordovician.     

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

The process of adaptation can be highly dependent upon historical and contemporary factors, especially in environmentally and topographically complex regions affected by Pleistocene glaciations. Here, we investigate Hilaria jamesii (Poaceae), a dryland C₄ graminoid, to test how patterns of adaptive genetic variation are linked to its glacial and post-glacial history. We show that the species persisted in a single, southern refugium during the last glacial period and subsequently migrated throughout its current distribution concurrent with post-glacial warming. The species’ putative adaptive genetic variation correlates with climatic gradients (e.g. monsoon precipitation and mean diurnal temperature range) that covary with the species’ probable route of demographic expansion. The short timescale and multiple climatic dimensions of adaptation imply that natural selection acted primarily upon standing genetic variation. These findings suggest that restoration and conservation practices should prioritize the maintenance of standing genetic variation to ensure that species have the capacity to respond to future environmental changes.     

A comparison of diversity estimators applied to a database of host–parasite associations

Understanding the drivers of biodiversity is important for forecasting changes in the distribution of life on earth. However, most studies of biodiversity are limited by uneven sampling effort, with some regions or taxa better sampled than others. Numerous methods have been developed to account for differences in sampling effort, but most methods were developed for systematic surveys in which all study units are sampled using the same design and assemblages are sampled randomly. Databases compiled from multiple sources, such as from the literature, often violate these assumptions because they are composed of studies that vary widely in their goals and methods. Here, we compared the performance of several popular methods for estimating parasite diversity based on a large and widely used parasite database, the Global Mammal Parasite Database (GMPD). We created artificial datasets of host–parasite interactions based on the structure of the GMPD, then used these datasets to evaluate which methods best control for differential sampling effort. We evaluated the precision and bias of seven methods, including species accumulation and nonparametric diversity estimators, compared to analyzing the raw data without controlling for sampling variation. We find that nonparametric estimators, and particularly the Chao2 and second-order jackknife estimators, perform better than other methods. However, these estimators still perform poorly relative to systematic sampling, and effect sizes should be interpreted with caution because they tend to be lower than actual effect sizes. Overall, these estimators are more effective in comparative studies than for producing true estimates of diversity. We make recommendations for future sampling strategies and statistical methods that would improve estimates of global parasite diversity.     

Brenneria alni,causal agent bark canker of Alnus subcordata

In 2014, bark cankers were observed on Caucasian alder (Alnus subcordata) trees in Iran. The disease was characterized by a dark watery liquid often exuding from longitudinal cankers in the bark of the tree trunks which stained the surface. Symptomatic tissue from A. subcordata was sampled from a number of sites in the Mazandaran province. Isolations were performed on nutrient agar supplemented with sucrose (SNA) and yielded bacterial colonies that were uniform, round and whitish. The bacterial strains isolated from alder trees in Iran were similar to Brenneria alni based on phenotypic and genotypic (nucleotide sequences of the 16S rRNA, and housekeeping genes gyrB, and infB) characteristics. The pathogenicity of the representative strains was determined by inoculating stem pieces of A. subcordata. All tested strains caused longitudinal necrotic lesions 30 days after inoculation and were re-isolated from this tissue. To our knowledge, this is the first report of the occurrence of B. alni in Iran, and on A. subcordata globally.