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ADP-ribosylation is a technically challenging PTM which has just emerged into the field of PTM-specific proteomics. But this fragile modifier requires special treatment on both a data acquisition and data processing level: it is highly labile under higher-energy collisional dissociation (HCD), and the degree of lability can depend on the site it modifies. Its behavior thus violates some assumptions on which proteomics algorithms are based. Here we present nonlocalized ADPr searching: a simple principle for maximizing sensitivity toward ADP-ribosylation when searching conventional HCD data. By scoring the strong fragment ions generally observed in ADPr spectra rather than the weak and often absent localization-dependent ions, nonlocalized searches are more sensitive. They also run significantly faster, due to reduced search space, and require no assumptions about which amino acids can be modified. We illustrate implementation in three search systems: Morpheus, MaxQuant, and MASCOT, and we also present a means of rapidly finding and extracting ADP-ribosylated peptide spectra from large datasets for more focused searching. This approach both improves identification of ADP-ribosylated peptides and avoids mis-localization of the modification sites.

ADP-ribosylation is a post-translational modification that can alter the physical and chemical properties of target proteins and that controls many important cellular processes. Macrodomains are evolutionarily conserved structural domains that bind ADP-ribose derivatives and are found in proteins with diverse cellular functions. Some proteins from the macrodomain family can hydrolyze ADP-ribosylated substrates and therefore reverse this post-translational modification. Bacteria and Streptomyces, in particular, are known to utilize protein ADP-ribosylation, yet very little is known about their enzymes that synthesize and remove this modification. We have determined the crystal structure and characterized, both biochemically and functionally, the macrodomain protein SCO6735 from Streptomyces coelicolor This protein is a member of an uncharacterized subfamily of macrodomain proteins. Its crystal structure revealed a highly conserved macrodomain fold. We showed that SCO6735 possesses the ability to hydrolyze PARP-dependent protein ADP-ribosylation. Furthermore, we showed that expression of this protein is induced upon DNA damage and that deletion of this protein in S. coelicolor increases antibiotic production. Our results provide the first insights into the molecular basis of its action and impact on Streptomyces metabolism.

Refrigeration cycle system modelling of the vapor compression experimental unit with the goal to predict the system performance of the cycle and geometry of the helical coil evaporator flooded in the water is presented in the paper. Design of the experimental unit is based on the commercially available scroll compressor and air cooled condenser. In order to determine the thermodynamic conditions of refrigeration cycle and heat transfer process in the evaporator the simulation model is developed. The model takes into account the specific data, dimensions and characteristics of the main components. Evaporation process, observed in three parts, and condensation process are described with appropriate heat transfer correlations. With two approximation functions, developed based on manufacturer data, the model of compression process is described. Results show relations between thermal resistance and geometrical quantities of evaporator with influence on the system performance. Analysis of thermal resistance shows that geometry of the evaporator may have important effect on the final design of these types of refrigeration applications.

Cilj: Svrha ovog rada je procijeniti rizik javljanja akutnih transfuzijskih reakcija (ATR) prema vrsti krvnih pripravaka i skupinama bolesnika nakon uvo|enjatransfuzijskog lije~enja samo s krvnim pripravcima sa smanjenim brojem leukocita (FKP). Metode: Analizirane su prijavljene ATR u dva razdoblja: Razdoblje FKP : od 2010. do 2012. kada su svi bolesnici lije~eni s FKP i Razdoblje NP : razdoblje od 2002. do 2004. kada je primjena FKP bila ograni~ena na primjenu prema nacionalnim preporukama (NP). Bolesnici su analizirani prema skupinama: internisti~ki, hematolo{;ki, pedijatrijski, kirur{;ki i ginekolo{;ki. Pedijatrijski bolesnici su ve}; i u ranijem razdoblju lije~eni s FKP. Transfuzijske reakcije klasificirane su prema ISBT definicijama. Za usporedbu razlika me|u skupinama obzirom na pojavu ATR prije i nakon implementacije lije~enja svih bolesnika s FKP izra~unat je omjer izgleda (OR) uz pripadaju};i interval pouzdanosti za testiranje hipoteze uz razinu 95% pouzdanosti (95% CI). Rezultati: Omjer izgleda za reakcije na FKE u odnosu na KE bio je 0, 40 (95% CI, 0, 30–0, 52) {;to upu};uje da FKE imaju zna~ajno manji rizik reakcija u odnosu na FKE (p

The students’ approaches to learning have been significantly researched in the last few decades, particularly since Marton and Säljö in 1979. elaborated about a deep/surface approach dichotomy. The above dichotomy appears to be very useful in the assessing of teaching, based on which one can obtain parameters according to which teaching can be improved. Precisely for these purposes the term approach to learning is more suitable than the term learning style. Learning style addresses ability-like dimensions while the term approach means that person can choose to learn in different ways depending on his/her motivation, the nature of the course taken and subject-matter, as well as the host of other variables. We use The Approaches and Study Skills Inventory for Students (ASSIST), developed by N.J. Entwistle, to investigate learning approaches of the first-year undergraduate engineering students in compulsory mathematics course. We emphasize that this inventory considers an additional type of approach, the strategic one. Inventory explored which of three approaches to learning (deep, strategic or surface) was chosen the most to cope with demands of the specific mathematics course, and how the chosen approach relates to the students’ grades obtained in the course. The results showed that majority choose strategic approach, what might indicate that it was the nature of the mathematics course that resulted in this approach. Also, in this paper we discuss the potential main factors that could result in such a selection.

ackground:Therapeutic phlebotomy (TP), the standard method of treating heredi-tary hemochromatosis (HH) is being partially replaced by erythrocytapheresis (EF)since the introduction of cell separator.Aim:The aim was to retrospectively compare the effectiveness of TP and EF inpatients with HH.Methods: In the period of 4 years (2007–2011.), 29 patients withHH were treated in the Clinical Hospital Centre Zagreb. Twelve patients (10 M, 2 F)were treated with EF and 17 patients (13 M and 4 F) with TP. Therapies wereconducted until ferritin was reduced to

The purpose of the research was to improve osteogenic differentiation of human bone marrow derived-mesenchymal stem cells (hMSCs) and to evaluate the level of remaining undifferentiated stem cells in culture. Standard cell culture protocol includes continuous exposure to the dexamethasone which is not easy to reproduce in human body. Therefore, our experiment was designed to investigate the possibility of using short-term dexamethasone exposure in order to induce osteogenic differentiation. Human bone marrow-derived MSCs were expanded with FGF-2 supplemented media. Afterwards cells were cultured in osteogenic media (DMEM low glucose, 10% FBS, 10mM β-glycerophosphate, 5μg/ml ascorbic acid, 1mM piruvat) and treated with different concentrations of dexamethasone, both short-term and continuous. The differentiation status of the cells was estimated using several osteogenic markers - alkaline phosphatase (AP) activity, the bone sialoprotein (BSP) and dentin matrix protein 1 (DMP-1) mRNAs. The stemness of the cells was estimated by the presence of pluripotency markers - SRY (sex determining region Y)-box 2 (SOX2) and octamer-binding transcription factor 4 (OCT4). The measurements were conducted on the days 7 and 14 after osteogenic conditions had been introduced. Our results show that continuous treatment induces the highest level of osteogenesis, but 2 hour exposure also induced differentiation in comparison with control. Overall, 10-5 M concentration of dexamethasone was the most powerful in the short-term induction of osteogenesis. SOX2 has not been detected in hMSCs. OCT4 was expressed in undifferentiated pluripotent hMSCs and its expression subsequently went down, indicating that the differentiation process is proceeding

The small ubiquitin-like modifiers (SUMOs) alter the function of cellular proteins by covalent attachment to lysine side-chains. SUMOs can target themselves for modification so generating SUMO polymers, the functions of which are beginning to be unraveled.The identification and quantitation of SUMO chains is essential for the functional investigation of SUMO polymerization. Classical techniques, such as site-directed mutagenesis and western blotting, are indirect and often inconclusive methods for the study of SUMO polymers. On the contrary, direct detection is possible with mass spectrometry (MS) by the identification of the SUMO-SUMO branched peptide remnant after proteolytic digestion. In this chapter, we describe a straightforward workflow that incorporates a modified database to efficiently detect SUMO polymers from simple and complex protein samples. In combination with stable isotope labeling by amino acids in cell culture (SILAC), this proteomic strategy allows accurate relative quantitation of SUMO polymers from different biological samples.

Severe trauma brain injury influence on surgical outcome in injured patients.

Cilj ovog rada je procena bioremedijacionog potencijala sedimenata Čukaričkog kanala zagađenog naftom i njenim derivatima. Poster: [https://cherry.chem.bg.ac.rs/handle/123456789/5422]

Udgivelsesdato: 2009-null The identification of target proteins for small ubiquitin-like modifiers (SUMOs) is a critical step towards a detailed understanding of the cellular functions of SUMOs. Substrate protein identification for SUMOs is hampered by the low abundance of SUMO targets, the finding that only a small fraction of these target proteins is sumoylated, and the high activity of deconjugating enzymes. Quantitative proteomics is a powerful tool to overcome these challenges, because it allows discrimination between contaminating proteins in SUMO-enriched preparations and true target proteins. In this chapter, the methodological details of the application of stable isotope labeling of amino acids in cell culture (SILAC) for the identification of target proteins for SUMOs are described. In addition to steady state sumoylation, the sumoylated proteome undergoes dynamic rearrangements in response to a diverse array of stimuli. SILAC also allows the study of sumoylation dynamics in response to these stimuli.

The aim of the study was to assess the possible correlation between catecholamine and cortisol levels and changes in cerebral hemodynamics in patients with chronic posttraumatic stress disorder (PTSD). The study included 50 patients with chronic PTSD first ever hospitalized for psychiatric treatment and 50 healthy control subjects. All study subjects were aged 30-50. In PTSD patients, 24-h urine levels of the epinephrine and norepinephrine metabolites vanillylmandelic acid (VMA) and cortisol were determined and transcranial Doppler ultrasonography was performed on day 1 of hospital stay and repeated after 21-day psychiatric medicamentous treatment. On initial testing, increased level of 24-h VMA, decreased cortisol level and elevated mean blood flow velocity (MBFV) in the circle of Willis vessels were recorded in 25 (50.00%) patients. Repeat findings obtained after 21-day psychopharmaceutical therapy showed increased 24-h VMA, decreased cortisol and elevated MBFV in the circle of Willis vessels in seven (14.00%) patients (initial vs. repeat testing, P=0.0002). Such parameters were not recorded in any of the control subjects (initial PTSD patient testing vs. control group, P=0.0000). Study results pointed to a significant correlation between increased catecholamine levels, decreased cortisol level and elevated MBFV in the circle of Willis vessels caused by cerebral vasospasm. Psychiatric medicamentous therapy administered for three weeks significantly reduced the proportion of patients with concurrently altered cerebral hemodynamics, increased levels of catecholamine metabolites and decreased level of cortisol.

Priručnik sadrži originalne studije slučajeva i vježba namijenjene izučavanju problematike menadžmenta od strane studenata preddiplomskog i diplomskog studija.

AIM: To compare T-tube and pressure support ventilation (PSV) as two methods of mechanical ventilation weaning of patients with chronic obstructive pulmonary disease (COPD) after failed extubation. - - - - - METHODS: A prospective randomized trial carried out at the multidisciplinary intensive care unit (ICU) over 2 years included 136 patients with COPD who required mechanical ventilation longer than 24 hours. The patients who could be weaned from mechanical ventilation were randomized to either a T-tube or PSV 2-hour spontaneous breathing trial. The patients in whom 2-hour trial was successful were extubated and excluded from further research. Patients in whom 2-hour trial failed had mechanical ventilation reinstated and underwent the same weaning procedure after 24 hours in case they fulfilled the weaning criteria. The weaning outcome was assessed according to the following parameters: extubation success, mechanical ventilation duration, time spent in ICU, reintubation rate, and mortality rate. - - - - - RESULTS: Two-hour trial failed in 31 patients in T-tube and 32 patients in PSV group, of whom 17 and 23, respectively, were successfully extubated (P

In order to gain insight into oil transformations which occur during migration, and to contribute to the elucidation of migration mechanisms in water-wet environments, the content and composition of heavy fuel oil from an accidental oil spill near the railway station of Ušće (Kraljevo) was determined in crushed rock samples from various depths and distances from the oil spill. The group composition (saturated hydrocarbons, aromates, NSO-compounds and residue) of heavy fuel oil extracts was determined. n-Alkanes and isoprenoid alkanes, pristane (Pr) and phytane (Phyt), in the saturated hydrocarbon fraction were identified by gas chromatography (GC). X-ray diffraction analysis (XRD) was applied on the inorganic residue in order to determine its mineralogical composition. The observed differences in the group composition (increase in NSO-compounds content with depth and distance), and in the distribution of n-alkanes and isoprenoid alkanes (the shift of the n-alkane-maximum and the shift of Pr/n-C17-and Phyt/n-C18-ratios towards higher values with depth and distance) lead to the conclusion that heavy fuel oil migration through the crushed rock environment occurred in the presence of water by the colloidal micelle mechanism.