Western pine beetle voltinism in a changing California climate

1. Recent hot droughts in California resulted in ponderosa pine (Pinus ponderosa) mortality attributed to drought and western pine beetle (WPB, Dendroctonus brevicomis). While drought alone can cause tree death, direct warming effects on WPB are a contributing factor. Research on WPB generation timing (voltinism), however, is lacking.
2. We monitored WPB tree attacks and adult emergence timing at two California sites and developed a degree-day model from field-observed data. Historical, contemporary, and future temperatures for several California sites were used with the model to examine trends in WPB voltinism.
3. Field data showed a single summer and an overwinter generation at a northern California site. As summer temperatures increased beyond 1900–1980 averages, the predicted number of full and partial WPB generations by 2021 had increased from ~2 annual (one summer and one overwinter) generations historically to ~2.3 at two northern California sites and from ~2.3 to ~3.2 at two warmer California sites.
4. Historical and contemporary data suggest winter warming was not sufficient for an additional generation overwinter. Instead, increases in generations were driven by summer and fall temperatures.
5. Unconstrained increases in the number of future annual generations will be limited by complex, but not well understood, WPB thermal adaptations. Increased knowledge of temperature-driven WPB population growth will improve forest vegetation models aimed at predicting ponderosa pine mortality in a changing climate.

     

Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence-based metabarcoding

Environmental DNA (eDNA)-based methods of species detection are enabling various applications in ecology and conservation including large-scale biomonitoring efforts. qPCR is widely used as the standard approach for species-specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species-specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14- to 29-fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales.     

A relational database for sequence-specific protein NMR data

Summary A protein NMR database has been designed and is being implemented. The database is intended to contain solution NMR results from proteins and peptides (larger than 12 residues). A relational database format has been chosen that indexes data by: primary journal citation, molecular species, sequence-related and atom-specific assignments, and experimental conditions. At present, all data are entered from the primary refereed literature. Examples are given of sample queries to the database. Possible distribution formats are discussed.     

Molecular cloning of PCR fragments with cohesive ends

Use of the polymerase chain reaction (PCR) provides a convenient means of generating DNA fragments for insertion into plasmids. Large quantities of the desired insert, bounded by convenient restriction sites, may be synthesized. The primers are chosen to span a known region of interest, and extended at their 5′-ends to include the desired restriction sites. Amplification of the target sequence is followed by precipitation of the product with ammonium acetate and ethanol to remove the primers. A small amount of product is analyzed by gel electrophoresis to ensure correct amplification, the remainder is digested with the appropriate restriction enzyme(s). Restricted insert DNA is added to similarly restricted plasmid DNA in several ratios and incubated with DNA ligase to recircularize. Ligation products are used to transform competent bacteria. Clones containing inserts are identified by restriction digestion of plasmid minipreps from bacterial colonies.