Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition

Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry–based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor–fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here, we introduce a scan mode for the combination of trapped ion mobility spectrometry with parallel accumulation—serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor–fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock-and-key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.     

Quantitative changes of forest landscapes over the last century across Italy

A key topic in landscape ecology and vegetation science is the quantitative analysis of changes in forest cover over time, through the use of geomatics monitoring tools. Ecologists and landscape researchers are pointing out that a full understanding of ecosystems and landscapes should be based on the analysis of their functioning over long time series. Under this perspective, a long-term historical reconstruction of forest cover is essential. This study has aimed at examining the long-term dynamics of forest landscapes in Italy, over the last century, using recent remote-sensing based map (2012) and an accurate historical map (1936). A forest-non forest approach has been followed by the computation of a variety of landscape metrics using two analysis tools, with the final objective of quantifying changes in forest cover patterns and in the composition of specific landscape elements. Results show that forest landscape structure has significantly changed across Italy, resulting in a general trend of decreasing fragmentation and patchiness, mainly through enlargement of existing forest patches, which have also assumed a more geometrically regular shape. In relative terms, the greatest expansion of forest areas has occurred mainly in lowland districts characterised by the highest level of human pressure in the country.     

Excision of chromosomal DNA loops by treatment of permeabilised cells with Bal 31 nuclease

The specificity of long-range fragmentation of human nucleolar genes by Bal 31 nuclease was studied using fractionation of cleavage products by pulsed field gel electrophoresis, followed by Southern hybridization. It was found that limited treatment of permeabilised cells with this nuclease results in accumulation of DNA scissions in matrix attachment areas. Consequently, chromosomal DNA loops and their oligomers are released from the genome.