Site-specific Phenomena Research Articles

Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing.

GoDig, a platform for targeted pathway proteomics without the need for manual assay scheduling or synthetic standards, is a powerful, flexible, and easy-to-use method that uses tandem mass tags to increase sample throughput up to 18-fold relative to label-free methods. Though the protein-level success rates of GoDig are high, the peptide-level success rates are more limited, hampering assays of harder-to-quantify proteins and site-specific phenomena. To guide the optimization of GoDig assays as well as improvements to the GoDig platform, we created GoDigViewer, a new stand-alone software that provides detailed visualizations of GoDig runs. GoDigViewer guided the implementation of "priming runs," an acquisition mode with significantly higher success rates. In this mode, two or more chromatographic priming runs are automatically performed to improve the accuracy and precision of target elution orders, followed by analytical runs which quantify targets. Using priming runs, success rates exceeded 97% for a list of 400 peptide targets and 95% for a list of 200 targets that are usually not quantified using untargeted mass spectrometry. We used priming runs to establish a quantitative assay of 125 macroautophagy proteins that had a >95% success rate and revealed differences in macroautophagy expression profiles across four human cell lines.

Public support for collaborative workspaces: Dispersed help to a place-based phenomenon?

The paper maps a range of policy initiatives for the support of collaborative workspaces (hereafter CWS) by examining the different ways such spaces have been funded, through what instruments, as well as what are the dominant reasons for receiving public support of any kind in urban and rural areas. Our analysis explores policy intentions as well as the funding tools of specific policy programmes that have supported CWS. This contribution aims to provide a categorization of existing policy initiatives about CWS and wishes to connect such policies with wider creative and urban and regional policy debates regarding the turn towards entrepreneurial forms of work and development in an era of economic uncertainty. The paper traces the evolution of CWS by examining the three overlapping waves of CWS and the specific reasons for their emergence. Then, it turns its focus on existing funding schemes and instruments for CWS, identifying five distinct categories of public support. It concludes by testifying in favour of understanding – and thus, supporting – CWS as place-based and site-specific phenomena. Thus, it calls for a new positioning of CWS into place-based development agendas, whilst taking into consideration the singularity of the place, the multiplicity of the actors and the particular institutional conditions and socio-economic characteristics involved.

Early arboreal colonization, postglacial resilience of deciduous Nothofagus forests, and the Southern Westerly Wind influence in central-east Andean Patagonia

The history and dynamics of deciduous Nothofagus forests along the eastern slopes of the central Patagonian Andes (44°-49°S) remain insufficiently studied and understood, particularly at timescales ranging from centuries to millennia. Available fossil pollen records point to time-transgressive responses of the arboreal vegetation to climatic changes during the Last Glacial Termination (T1) and early Holocene, and spatial heterogeneity since then along north-south, east-west, and elevation transects. The degree to which these results represent biogeographic and climatic trends, varying environmental gradients, or site-specific phenomena has not been assessed in detail. Here we present a fossil pollen and macroscopic charcoal record from Lago Churrasco (45°41′S, 71°49′W), a small closed-basin lake located in the deciduous Nothofagus forest zone of the central-east Andes of Chilean Patagonia. Our results suggest that Nothofagus trees colonized newly deglaciated terrains at ∼16,000 cal yr BP and formed scrublands/woodlands several millennia earlier than reported by previous studies east of the Andes. This suggests expansion and local densification of tree populations sourced from the eastern margin of the Patagonian Ice Sheet during the Last Glacial Maximum, with the additional implication that temperature and precipitation conditions favorable for tree survival and reproduction developed early during T1. We posit that the amount of moisture delivered by the Southern Westerly Winds was not a limiting factor for arboreal expansion during T1 in this sector of the central Patagonian Andes. Closed-canopy Nothofagus forests established at ∼10,000 cal yr BP and have remained essentially invariant despite climate change and natural disturbance regimes. This resilience was challenged and exceeded by human disturbance during the 20th century through the use of fire, leading to deforestation and spread of invasive exotic species in an extraordinarily rapid event. Our record suggests a permanent influence of the Southern Westerly Winds over the last 10,000 years, with relatively modest variations at centennial and millennial timescales.

Relationship between river water chemistry and shell chemistry of two tropical African freshwater bivalve species

Both climate change and land-use changes represent serious environmental issues throughout Africa, and are expected to lead to significant changes in river hydrology and geochemistry. Freshwater bivalve shell geochemistry may provide useful information about past river characteristics (discharge, geochemistry) providing a baseline to help understand modern environmental changes. Shells of two species of freshwater mussels (Chambardia wissmanni and Aspatharia dahomeyensis) were collected from two large African rivers (Oubangui and Niger Rivers) and were analyzed for Sr/Ca, Ba/Ca, Mg/Ca and Mn/Ca ratios along their maximal growth axis. Shell data were compared with geochemical data collected in these rivers every two weeks over a two-year period. To verify whether element ratios in shells were related to the host water, the elemental concentrations measured in the shells were set in a temporal context based on δ18Oshell cycles. Shells from the Oubangui River to some extent recorded water element ratios, with variations in water Sr/Ca ratios being reflected in all three bivalve specimens analyzed, while only the youngest specimen exhibited complete coverage. The two older specimens recorded only segments of the water data, which suggests an influence of growth rate. This relationship was not observed in A. dahomeyensis shells from the Niger, suggesting a species-specific relationship between freshwater shells and water. The Ba/Ca and Mg/Ca record showed no similarity between the water elements and analyzed shells, but an ontogenetic decrease was observed in older specimens. Shell Mn/Ca ratios tracked pH in shells from the Oubangui, with a time-lag, which might be due to bivalves taking up the increased Mn via phytoplankton which are expected to show a similar time-lag. This relationship was not observed in shells from the Niger, where due to the high turbidity throughout the year we expect very low primary production rates. In conclusion, no consistent relationships between water chemistry and shell chemistry were observed. While Sr/Ca and Mn/Ca ratios in shells of C. wissmanni from the Oubangui were most promising as proxies of water chemistry, the utility of element ratios as tracers is compromised by species-specific effects or by site-specific phenomena.

Extracting smallholder cropped area in Tigray, Ethiopia with wall-to-wall sub-meter WorldView and moderate resolution Landsat 8 imagery

Very high resolution (VHR) satellite data is experiencing rapid annual growth, producing petabytes of remotely sensed data per year. The WorldView constellation, operated by DigitalGlobe, images over 1.2billionkm2 annually at <2m spatial resolution. Due to computation, data cost, and methodological concerns, VHR satellite data has mainly been used to produce needed geospatial information for site-specific phenomena. This project produced a VHR spatiotemporally explicit wall-to-wall cropland area map for the rainfed residential cropland mosaic of the Tigray Region, Ethiopia, which is comprised mostly of smallholder farms. Moderate resolution satellite data do not have adequate spatial resolution to capture the total area occupied by smallholder farms, i.e., farms with agricultural fields of ≤45×45m in dimension. In order to accurately map smallholder cropped area over a large region, hundreds of VHR images spanning two or more years are needed. Sub-meter WorldView-1 and WorldView-2 segmentation results were combined with median phenology amplitude from Landsat 8 data to map cropped area. Over 2700 VHR WorldView-1, -2 data were obtained from the U.S. National Geospatial-Intelligence Agency (NGA) via the NextView license agreement and were processed from raw imagery to produce a smallholder crop map in ~1week using a semi-automated method with the large computing capacity of the Advanced Data Analytics Platform. We estimated cropped area in Tigray to be 46% with a commission error of 5%±10% and omission error of 15%±12%. This methodology is extensible to other regions with similar vegetation texture and can easily be expanded to run on much larger regions.

Regio-Selective Intramolecular Hydrogen/Deuterium Exchange in Gas-Phase Electron Transfer Dissociation.

Protein backbone amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) typically utilizes enzymatic digestion after the exchange reaction and before MS analysis to improve data resolution. Gas-phase fragmentation of a peptic fragment prior to MS analysis is a promising technique to further increase the resolution. The biggest technical challenge for this method is elimination of intramolecular hydrogen/deuterium exchange (scrambling) in the gas phase. The scrambling obscures the location of deuterium. Jørgensen's group pioneered a method to minimize the scrambling in gas-phase electron capture/transfer dissociation. Despite active investigation, the mechanism of hydrogen scrambling is not well-understood. The difficulty stems from the fact that the degree of hydrogen scrambling depends on instruments, various parameters of mass analysis, and peptide analyzed. In most hydrogen scrambling investigations, the hydrogen scrambling is measured by the percentage of scrambling in a whole molecule. This paper demonstrates that the degree of intramolecular hydrogen/deuterium exchange depends on the nature of exchangeable hydrogen sites. The deuterium on Tyr amide of neurotensin (9-13), Arg-Pro-Tyr-Ile-Leu, migrated significantly faster than that on Ile or Leu amides, indicating the loss of deuterium from the original sites is not mere randomization of hydrogen and deuterium but more site-specific phenomena. This more precise approach may help understand the mechanism of intramolecular hydrogen exchange and provide higher confidence for the parameter optimization to eliminate intramolecular hydrogen/deuterium exchange during gas-phase fragmentation. Graphical Abstract ᅟ.

Le motivazioni degli incendi boschivi in Italia: risultati preliminari di un’indagine pilota nelle Province a maggiore incidenza di incendi

Abstract: The percentage of forest fires of unknown origin, accounting in Italy for about 40% of the total number, hampers any attempt of efficacious prevention based on modification of causes. This work deals with the implementation of a simple though promising technique of motivation survey aimed at reducing such percentage, the Delphi method, a grouping technique using estimates from a panel of experts and feedback summaries from preceding responses for additional estimates. Sitting between knowledge and speculation, the informed deliberations of the panel of experts may be considered an informed judgment. Delphi surveys were carried out by CFS (National Forestry Service) in 23 of the most affected provinces, involving several panel of experts for a total of 1000 people, all of them on duty in the Forestry Stations of the Service. Results highlighted a remarkable prevalence of involuntary versus voluntary fires (54% and 42%, respectively). The panels of experts provided fairly homogeneous and convergent answers based on few motives, the majority of fire ignitions were attributed to: (i) creation or renewal of pastures; (2) residues elimination, including stubble burning; (iii) increasing the yield of wild plant foods; (iv) poaching probably related to limitation of hunting use and access control. The most recurrent motivations represent traditional uses of fire by rural societies. Other motivations presented less significant and negligible values. Cluster analysis clearly put in evidence that similar motivations characterize small and homogeneous groups of provinces, supporting the evidence that fire motivations are site and culture specific phenomena.

Si:2p site-specific excitation and fragmentation of bridged trihalosilyl–trimethylsilyl molecules: role of the bridge and final-state effect

To elucidate site-specific phenomena, we experimentally and computationally studied the spectroscopy and dynamics caused by Si:2p core-level photoexcitation of bridged trihalosilyl–trimethylsilyl molecules. We used the photoionization efficiency curve and the photoelectron photoion coincidence method to study the site-specific phenomena in the Si:2p photoexcitation of F 3SiCH 2CH 2CH 2Si(CH 3) 3, F 3SiCHCHSi(CH 3) 3 and Cl 3SiCCSi(CH 3) 3 in the vapor phase. The site-specific excitation was revealed in the photoionization efficiency curves of all the molecules. The site-specific fragmentation is likely to be more evident when the distance between the two Si sites is large. For the site-specific fragmentation to be caused by the Si:2p photoexcitation, there should not be a CC bond between the atomic site of interest and any other near atomic site around which bond dissociation is undesirable. Not only initial-state effect but also final-state effect is likely to contribute to the occurrence of the different chemical shifts between the two Si sites of the bridged trihalosilyl–trimethylsilyl molecules.

Site-specific phenomena in Si:2p core-level photoionization of X 3Si(CH 2) nSi(CH 3) 3 (X=F or Cl, n=0–2) condensed on a Si(111) surface

We used photoelectron spectroscopy and the energy-selected-photoelectron photoion coincidence (ESPEPICO) method to study site-specific phenomena in the Si:2p photoionization of X 3Si(CH 2) n Si(CH 3) 3 (X=F or Cl, n=0–2) condensed on a Si(111) surface. The site-specific excitation and the occurrence of different chemical shifts at two Si sites were revealed in the total electron-yield spectra and the photoelectron spectra of F 3Si(CH 2) n Si(CH 3) 3 ( n=1, 2), although they were not clearly revealed in those of Cl 3SiSi(CH 3) 3. We conclude that these site-specific phenomena are easily observed in molecules in which the two Si sites are located far apart and in which electron migration between the two Si-containing groups does not occur. This was supported by our ab initio calculation. Site-specific fragmentation was revealed in the ESPEPICO spectrum of F 3SiCH 2CH 2Si(CH 3) 3, although it was negligible for Cl 3SiSi(CH 3) 3 and was less remarkable in F 3SiCH 2Si(CH 3) 3 than in F 3SiCH 2CH 2Si(CH 3) 3. Site-specific fragmentation also occurred when the two Si sites were located far apart.