Projected climate and land use change alter western blacklegged tick phenology,seasonal host‐seeking suitability and human encounter risk in California

Global environmental change is having profound effects on the ecology of infectious disease systems, which are widely anticipated to become more pronounced under future climate and land use change. Arthropod vectors of disease are particularly sensitive to changes in abiotic conditions such as temperature and moisture availability. Recent research has focused on shifting environmental suitability for, and geographic distribution of, vector species under projected climate change scenarios. However, shifts in seasonal activity patterns, or phenology, may also have dramatic consequences for human exposure risk, local vector abundance and pathogen transmission dynamics. Moreover, changes in land use are likely to alter human–vector contact rates in ways that models of changing climate suitability are unlikely to capture. Here we used climate and land use projections for California coupled with seasonal species distribution models to explore the response of the western blacklegged tick (Ixodes pacificus), the primary Lyme disease vector in western North America, to projected climate and land use change. Specifically, we investigated how environmental suitability for tick host‐seeking changes seasonally, how the magnitude and direction of changing seasonal suitability differs regionally across California, and how land use change shifts human tick‐encounter risk across the state. We found vector responses to changing climate and land use vary regionally within California under different future scenarios. Under a hotter, drier scenario and more extreme land use change, the duration and extent of seasonal host‐seeking activity increases in northern California, but declines in the south. In contrast, under a hotter, wetter scenario seasonal host‐seeking declines in northern California, but increases in the south. Notably, regardless of future scenario, projected increases in developed land adjacent to current human population centers substantially increase potential human–vector encounter risk across the state. These results highlight regional variability and potential nonlinearity in the response of disease vectors to environmental change.     

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.     

Towards the integration of animal‐borne instruments into global ocean observing systems

Marine animals are increasingly instrumented with environmental sensors that provide large volumes of oceanographic data. Here, we conduct an innovative and comprehensive global analysis to determine the potential contribution of animal‐borne instruments (ABI) into ocean observing systems (OOSs) and provide a foundation to establish future integrated ocean monitoring programmes. We analyse the current gaps of the long‐term Argo observing system (>1.5 million profiles) and assess its spatial overlap with the distribution of marine animals across eight major species groups (tuna and billfishes, sharks and rays, marine turtles, pinnipeds, cetaceans, sirenians, flying seabirds and penguins). We combine distribution ranges of 183 species and satellite tracking observations from >3,000 animals. Our analyses identify potential areas where ABI could complement OOS. Specifically, ABI have the potential to fill gaps in marginal seas, upwelling areas, the upper 10 m of the water column, shelf regions and polewards of 60° latitude. Our approach provides the global baseline required to plan the integration of ABI into global and regional OOS while integrating conservation and ocean monitoring priorities.     

Phenology responses of temperate butterflies to latitude depend on ecological traits

Global change influences species’ seasonal occurrence, or phenology. In cold‐adapted insects, the activity is expected to start earlier with a warming climate, but contradictory evidence exists, and the reactions may be linked to species‐specific traits. Using data from the GBIF database, we selected 105 single‐brooded Holarctic butterflies inhabiting broad latitudinal ranges. We regressed patterns of an adult flight against latitudes of the records, controlling for altitude and year effects. Species with delayed flight periods towards the high latitudes, or stable flight periods across latitudes, prevailed over those that advanced their flight towards the high latitudes. The responses corresponded with the species’ seasonality (flight of early season species was delayed and flight of summer species was advanced at high latitudes) and oceanic vs. continental climatic niches (delays in oceanic, stability in continental species). Future restructuring of butterfly seasonal patterns in high latitudes will reflect climatic niches, and hence the evolutionary history of participating species.     

Shortlisting SARS‐CoV‐2 Peptides for Targeted Studies from Experimental Data‐Dependent Acquisition Tandem Mass Spectrometry Data

Detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a crucial tool for fighting the COVID‐19 pandemic. This dataset brief presents the exploration of a shotgun proteomics dataset acquired on SARS‐CoV‐2 infected Vero cells. Proteins from inactivated virus samples were extracted, digested with trypsin, and the resulting peptides were identified by data‐dependent acquisition tandem mass spectrometry. The 101 peptides reporting for six viral proteins were specifically analyzed in terms of their analytical characteristics, species specificity and conservation, and their proneness to structural modifications. Based on these results, a shortlist of 14 peptides from the N, S, and M main structural proteins that could be used for targeted mass‐spectrometry method development and diagnostic of the new SARS‐CoV‐2 is proposed and the best candidates are commented.     

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.     

Over‐Expression of RNA Processing,Heat Shock,and DNA Repair Proteins in Breast Tumor Compared to Normal Tissue

This study identifies the main changes in protein expression in human breast tumors compared to normal breast tissue. Malignant tumors (32) and normal breast tissue samples (23), from formaldehyde‐fixed, paraffin‐embedded specimens are subjected to discovery proteomics using liquid chromatography/tandem mass spectrometry, with spectral counts for quantitation. The dataset contains 1406 proteins. Differential expression is measured using a method that takes advantage of estimates of the percentage of tumor on a slide. This analysis shows that the major classes of proteins over‐expressed by tumors are RNA‐binding, heat shock and DNA repair proteins. RNA‐binding proteins, including heterogeneous nuclear ribonucleoproteins (HNRNPs), SR splice factors (SRSF) and elongation factors form the largest group. Comparison with results from another study demonstrates that the RNA‐binding proteins are associated specifically with malignant transformation, rather than with cell proliferation. HNRNP and SRSF proteins help define splice sites in normal cells. Their over‐expression may dysregulate splicing, which in turn has the potential to promote malignant transformation.     

Sequencing two Tyr::CreERT2 transgenic mouse lines

The Cre/loxP system is a powerful tool that has allowed the study of the effects of specific genes of interest in various biological settings. The Tyr::CreER^T2 system allows for the targeted expression and activity of the Cre enzyme in the melanocyte lineage following treatment with tamoxifen, thus providing spatial and temporal control of the expression of specific target genes. Two independent transgenic mouse models, each containing a Tyr::CreER^T2 transgene, have been generated and are widely used to study melanocyte transformation. In this study, we performed whole genome sequencing (WGS) on genomic DNA from the two Tyr::CreER^T2 mouse models and identified their sites of integration in the C57BL/6 genome. Based on these results, we designed PCR primers to accurately, and efficiently, genotype transgenic mice. Finally, we discussed some of the advantages of each transgenic mouse model.     

Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis

Recent advances in environmental DNA (eDNA) analysis using high‐throughput sequencing (HTS) enable evaluation of intraspecific genetic diversity in a population. As the intraspecific genetic diversity provides invaluable information for wildlife conservation and management, there is an increasing demand to apply eDNA analysis to population genetics and the phylogeography by quantitative evaluation of intraspecific diversity. However, quantitative evaluations of intraspecific genetic diversity using eDNA is not straightforward because the number of eDNA sequence reads obtained by HTS may not be an index of the quantity of eDNA. In this study, to quantitatively evaluate genetic diversity using eDNA analysis, we applied a quantitative eDNA metabarcoding method using the internal standard DNAs. We targeted Ayu (Plecoglossus altivelis altivelis) and added internal standard DNAs with known copy numbers to each eDNA sample obtained from three rivers during the library preparation process. The sequence reads of each Ayu haplotype were successfully converted to DNA copy numbers based on the relationship between the copy numbers and sequence reads of the internal standard DNAs. In all rivers, the calculated copy number of each haplotype showed a significant positive correlation with the haplotype frequency estimated by a capture‐based survey. Furthermore, estimates of genetic indicators such as nucleotide diversity based on the eDNA copy numbers were comparable with those estimated based on a capture‐based study. Our results demonstrate that eDNA analysis with internal standard DNAs enables reasonable quantification of intraspecific genetic diversity, and this method could thus be a promising tool in the field of population genetics and phylogeography.