A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry

Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions

Circulating adrenomedullin estimates survival and reversibility of organ failure in sepsis: the prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock-1 (AdrenOSS-1) study

Background: Adrenomedullin (ADM) regulates vascular tone and endothelial permeability during sepsis. Levels of circulating biologically active ADM (bio-ADM) show an inverse relationship with blood pressure and a direct relationship with vasopressor requirement. In the present prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock 1 (, AdrenOSS-1) study, we assessed relationships between circulating bio-ADM during the initial intensive care unit (ICU) stay and short-term outcome in order to eventually design a biomarker-guided randomized controlled trial. Methods: AdrenOSS-1 was a prospective observational multinational study. The primary outcome was 28-day mortality. Secondary outcomes included organ failure as defined by Sequential Organ Failure Assessment (SOFA) score, organ support with focus on vasopressor/inotropic use, and need for renal replacement therapy. AdrenOSS-1 included 583 patients admitted to the ICU with sepsis or septic shock. Results: Circulating bio-ADM levels were measured upon admission and at day 2. Median bio-ADM concentration upon admission was 80.5 pg/ml [IQR 41.5-148.1 pg/ml]. Initial SOFA score was 7 [IQR 5-10], and 28-day mortality was 22%. We found marked associations between bio-ADM upon admission and 28-day mortality (unadjusted standardized HR 2.3 [CI 1.9-2.9]; adjusted HR 1.6 [CI 1.1-2.5]) and between bio-ADM levels and SOFA score (p < 0.0001). Need of vasopressor/inotrope, renal replacement therapy, and positive fluid balance were more prevalent in patients with a bio-ADM > 70 pg/ml upon admission than in those with bio-ADM ≤ 70 pg/ml. In patients with bio-ADM > 70 pg/ml upon admission, decrease in bio-ADM below 70 pg/ml at day 2 was associated with recovery of organ function at day 7 and better 28-day outcome (9.5% mortality). By contrast, persistently elevated bio-ADM at day 2 was associated with prolonged organ dysfunction and high 28-day mortality (38.1% mortality, HR 4.9, 95% CI 2.5-9.8). Conclusions: AdrenOSS-1 shows that early levels and rapid changes in bio-ADM estimate short-term outcome in sepsis and septic shock. These data are the backbone of the design of the biomarker-guided AdrenOSS-2 trial. Trial registration: ClinicalTrials.gov, NCT02393781. Registered on March 19, 2015

Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More.

The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.journal article2020importe

Energia aktywacji pęcznienia drewna buka (Fagus sylvatica L.) w wodzie

The activation energy of swelling beech wood (Fagus sylvatica L.) in water. This paper shows the results of the activation energy of swelling beech wood in water. The results showed that activation energy depends on the density. Increasing that values increase activation energy of swelling.Energia aktywacji pęcznienia drewna buka (Fagus sylvatica L.) w wodzie. W pracy przedstawiono wyniki oznaczeń energii aktywacji procesu pęcznienia drewna w wodzie. Uzyskane rezultaty wykazały, że wartość tej wielkości zależy od gęstości. Wraz ze wzrostem gęstości drewna buka wzrasta energia aktywacji jego pęcznienia

Energia aktywacji pęcznienia bielastego drewna sosny (Pinus sylvestris L.) w wodzie

The activation energy of swelling sap of pine wood (Pinus sylvestris L.) in water. This paper shows the results of the activation energy of swelling sapwood of pine wood in water. The results showed that activation energy value range from 4.8 to 10.7 kJ/mol. It is also noted that its depend on the density.Energia aktywacji pęcznienia bielastego drewna sosny (Pinus sylvestris L.) w wodzie. W pracy przedstawiono wyniki oznaczeń energii aktywacji procesu pęcznienia bielu drewna sosny zwyczajnej w wodzie. Uzyskane rezultaty wykazały, że wartość tej energii mieści się w przedziale od 4,8 do 10,7 kJ/mol i jest słabo zależna od gęstości drewna

Physical properties of Scots pine wood from the Notecka Forest

The aim of the study was to determine the relationship between the quality of habitat and the quality of Scots pine wood. We focused on the wood from mature stands growing on poor habitats on inland dunes in the Notecka Forest and on former farmlands (central and western Poland). We selected 12 trees, from which we took wood samples for tree ring investigation. We determined the age of trees, width of increments, share of late− and hardwood, and the moisture and density of the wood. Samples were weighed with 0.001 g accuracy and their volume was determined with hydrostatic method. Next, samples were dried and their mass was determined again. The obtained results were used to calculate: initial and conventional wood density as well as moisture content of each sample. Properties of the examined wood derived both from Notecka Forest as well as from farmlands were advantageous from the point of view of its technical quality. Mean width of annual increments, both near−pith and near−circumferential, ranged from 1.70 to 1.99 mm and qualified analysed wood as the narrow−ringed. The examined wood characterised high proportion of latewood, close to the upper limit given in literature for standard conifer wood and by high density. Mean share of latewood in the near−pith increments ranged from 18.9 to 30.6%, while in near−circumferential increments – from 34.3 to 45.7%. The highest average conventional density amounted to 507 kg/m³, whereas the lowest – to 466 kg/m³. The obtained results revealed that the wood from the Notecka Forest had favorable properties in terms of technical quality. It had the characteristics of slow−grown wood and was characterized by a high proportion of latewood in annual increments and a conventional density higher than the one reported in the literature