Hepatocyte growth factor in exhaled breath and BAL fluid in sarcoidosis

Wstęp: Wątrobowy czynnik wzrostu (HGF) jest silnym mitogenem stymulującym wzrost komórek nabłonka pęcherzyków płucnych. Wyższe stężenia HGF w różnych materiałach biologicznych stwierdzono między innymi w zespole ostrej niewydolności oddechowej (ARDS), u chorych po przebytym zapaleniu płuc i po pneumonektomii. Niekorzystnym zejściem sarkoidozy jest włóknienie płuc. Wątrobowy czynnik wzrostu mógłby być przydatny jako marker pozwalający na rozpoznanie chorych obarczonych ryzykiem włóknienia płuc. Celem pracy była ocena: 1) czy HGF jest wykrywalny w popłuczynach oskrzelowo-pęcherzykowych (BAL) i kondensacie powietrza wydechowego (EBC); 2) czy stężenia HGF w BAL-u i kondensacie chorych na sarkoidozę różnią się od stężeń osób zdrowych; 3) czy istnieją korelacje z parametrami aktywności i wybranymi czynnikami rokowniczymi. Materiał i metody: Zebrano kondensat od 64 i popłuczyny oskrzelowo-pęcherzykowe od 30 chorych na sarkoidozę. Grupę kontrolną stanowiły osoby zdrowe (n = 15 dla EBC, n = 9 dla BAL). Wątrobowy czynnik wzrostu oznaczono immunoenzymatycznie. Wyniki: Stężenia HGF w kondensacie przekroczyły próg detekcji u 62% badanych (56% chorych i 87% zdrowych) i we wszystkich próbkach BAL. Nie stwierdzono różnic w stężeniach w EBC i BAL pomiędzy osobami chorymi i zdrowymi. Nie stwierdzono korelacji pomiędzy HGF w EBC/BALF a stopniem radiologicznym, parametrami czynności płuc, czasem trwania choroby, liczbą nawrotów, odsetkiem limfocytów w BAL, stężeniem enzymu konwertującego angiotensynę i wapnia w surowicy, utratą dobową wapnia z moczem. Wnioski: Wątrobowy czynnik wzrostu jest wykrywalny w BAL i EBC. Jednak brak różnic pomiędzy chorymi na sarkoidozę i osobami zdrowymi oraz brak korelacji z markerami aktywności i czynnikami rokowniczymi uniemożliwiają jego zastosowanie w diagnostyce i monitorowaniu sarkoidozy.Introduction: Hepatocyte growth factor (HGF) is a strong mitogen stimulating lung epithelial cell growth. Elevated levels of HGF have been reported in various biological materials of patients with acute respiratory distress syndrome and in patients recovering from pneumonia or pneumonectomy. Sarcoidosis may be complicated by lung fibrosis. Consequently, HGF could be considered a new biomarker identifying patients with a higher risk of lung fibrosis. The aim of the study was to verify whether: 1. HGF is measurable in bronchoalveolar lavage fluid (BALF) and exhaled breath condensate (EBC); 2. HGF in BALF or EBC is impaired in sarcoidosis; and 3. HGF correlates with chosen activity and prognostic markers. Material and methods: Sixty-four EBC and 30 BALF of sarcoid patients, and 15 and 9 of healthy controls, respectively, were collected for the measurement of HGF using an ELISA test. Results: HGF was detectable in 62% of EBC samples (56% sarcoidosis and 87% of controls) and in all the BALF samples. EBC and BALF concentrations were not different in comparison to the controls. Moreover, no correlation was found between EBC/BALF concentrations and radiological stage, lung function tests, duration of disease, number of relapses, BALF lymphocytes, serum ACE, or serum and urine calcium concentrations. Conclusions: HGF is detectable in BAL and EBC. However, it does not distinguish sarcoidosis patients from healthy subjects. The above, as well as the lack of correlations with various parameters of disease activity and severity rule out EBC/ /BALF HGF as a biomarker for sarcoidosis monitoring

Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics

BACKGROUND: The histone H3/H4 chaperone Asf1 (anti-silencing function 1) is required for the establishment and maintenance of proper chromatin structure, as well as for genome stability in eukaryotes. Asf1 participates in both DNA replication-coupled (RC) and replication-independent (RI) histone deposition reactions in vitro and interacts with complexes responsible for both pathways in vivo. Asf1 is known to directly bind histone H3, however, high-resolution structural information about the geometry of this interaction was previously unknown. RESULTS: Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 Å crystal structure of the conserved N-terminal immunoglobulin fold domain of yeast Asf1 (residues 2–155) bound to the C-terminal helix of yeast histone H3 (residues 121–134). The structure defines a histone-binding patch on Asf1 consisting of both conserved and yeast-specific residues; mutation of these residues abrogates H3/H4 binding affinity. The geometry of the interaction indicates that Asf1 binds to histones H3/H4 in a manner that likely blocks sterically the H3/H3 interface of the nucleosomal four-helix bundle. CONCLUSION: These data clarify how Asf1 regulates histone stoichiometry to modulate epigenetic inheritance. The structure further suggests a physical model in which Asf1 contributes to interpretation of a "histone H3 barcode" for sorting H3 isoforms into different deposition pathways

Diversity of vertebrate remains from the Lower Gogolin Beds (Anisian) of southern Poland

Middle Triassic (Muschelkalk) limestones and dolostones of southern Poland contain vertebrate remains, which can be used for palaeoecological and palaeogeographical analyses. The results presented concern vertebrate remains uncovered at four localities in Upper Silesia and one on Opole Silesia, a region representing the south-eastern margin of the Germanic Basin in Middle Triassic times. The most abundant remains in this assemblage are fish remains, comprising mostly actinopterygian teeth and scales. Chondrichthyan and sauropsid remains are less common. Reptilian finds include vertebrae, teeth and fragments of long bones, belonging to aquatic or semi-aquatic reptiles, such as nothosaurids, pachypleusorosaurids, and ichthyosaurids. Also, coprolites of possibly durophagous and predacious reptiles occur. In the stratigraphic column of Mikołów, actinopterygian remains are the most numerous and no distinct changes of the taxonomic composition occur. Although this assemblage differs from those described at other localities (Ząbkowice with numerous chondrichthyans, Żyglin, and Płaza with common sauropsid fossils), sampling bias has to be considered

3DLigandSite: Structure-based prediction of protein-ligand binding sites

3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improves the accuracy of predictions and provides a confidence score for each residue predicted to be part of a binding site. Validation of 3DLigandSite on a set of 6416 binding sites obtained 92% recall at 75% precision for non-metal binding sites and 52% recall at 75% precision for metal binding sites. 3DLigandSite is available at https://www.wass-michaelislab.org/3dligandsite. Users submit either a protein sequence or structure. Results are displayed in multiple formats including an interactive Mol* molecular visualization of the protein and the predicted binding sites

Inflammatory Markers: Exhaled Nitric Oxide and Carbon Monoxide During the Ovarian Cycle

Nitric oxide (NO) production and carbon monoxide (CO) production are increased in inflammatory lung diseases. Although there are some pieces of evidence for hormonal modulation by estrogen, little is known about exhaled NO and CO during the ovarian cycle. In 23 subjects, we measured exhaled NO and CO by an online analyzer. Significantly higher levels of exhaled NO were found at the midcycle compared with those in the premenstrual period or during menstruation. Higher levels of CO were after ovulation and reached a peak in the premenstrual phase. The lowest levels of CO were observed in the first days of the estrogen phase. In males, there was no significant variation in exhaled NO and CO. Exhaled NO and CO levels vary during the ovarian cycle in women, and this fact should be taken into account during serial measurements of these markers in the female population