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Choroba Parkinsona w podejściu metabolomicznym : od zaburzeń metabolizmu do wczesnej diagnostyki

Grzegorzek Alicja, Młynarz Piotr, Mielko-Niziałek Karolina Anna

Wiadomości Chemiczne

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2025

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[Z] 79, 9-10

597--612

EN

Parkinson’s disease is the second most common neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons and the emergence of both motor and non-motor symptoms. Despite the focus of current research, diagnosis remains a challenge, mainly due to the lack of specific biological markers. Metabolomics is a modern approach that enables the analysis of lowmolecular-weight chemical compounds (metabolites) in the body, offering new perspectives for understanding the pathophysiology of the disease and developing cutting-edge, effective diagnostic tools. This article discusses the application of the metabolomic approach in Parkinson’s disease. It also presents the potential of metabolomics and highlights its growing significance in early disease detection. This field may contribute to the development of faster, more accurate, and minimally invasive diagnostic methods, opening new possibilities in prevention and supporting clinical decision-making.

2

Środowisko sedymentacji oraz parametry geochemiczne dolnooligoceńskich margli dynowskich z jednostki śląskiej, polskie Karpaty zewnętrzne

Dziadzio Piotr S., Matyasik Irena, Leśniak Grzegorz, Bieleń Wojciech

Prace Naukowe Instytutu Nafty i Gazu

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2025

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nr 247

1--132

PL

Margle dynowskie (margle krzemionkowe) reprezentują zapis wydarzenia związanego ze spadkiem zasolenia, beztlenowymi warunkami osadu dennego oraz silnym endemizmem, które miało miejsce w całej Centralnej Paratetydzie w okresie dolnego oligocenu (NP 23) i jest określane wydarzeniem solenowskim (utrata połączenia Paratetydy z oceanem światowym). Szczegółowe badania margli dynowskich w skali regionalnej, w kontekście środowiska ich sedymentacji, potencjału macierzystości oraz znaczenia dla systemu naftowego, były prowadzone w Karpatach Zachodnich, głównie na obszarze Czech i Austrii. Uzyskane wyniki wskazują na płytkowodne warunki ich depozycji, co jest spójne z rekonstrukcjami paleogeograficznymi i paleoklimatycznymi. Utwory te występują w dolnej części warstw menilitowych w całym pasie łuku karpackiego. Sukcesja warstw menilitowych w polskiej części Karpat Zewnętrznych była uważana do niedawna za produkt sedymentacji głębokowodnej. W wyniku prac badawczych w obrębie południowej części jednostki śląskiej (fałd Gorlic) została ona zweryfikowana. W tym obszarze wykazano, że sedymentacja miała miejsce na płytkim okresowo istniejącym szelfie. Interpretacja ta tylko częściowo uwzględniała występowanie w profilu warstw menilitowych margli dynowskich (wyróżnianych w randze ogniwa), które mają kluczowe znaczenie dla potwierdzenia wcześniejszej interpretacji oraz określenia ich genezy w szerszym regionalnym kontekście. Dlatego na potrzeby komplementarnej interpretacji, pełnej sukcesji warstw menilitowych w obrębie jednostki śląskiej, przeprowadzono szczegółowe badania sedymentologiczne margli dynowskich, które zostały wsparte badaniami geochemicznymi w trzech wybranych profilach: w Gorlicach (profil A), Zborowicach (profil B) i Jabłonicy Polskiej (profil C). Wyróżniono w ich obrębie 6 facji osadowych: F.1 (łupki menilitowe), F.2 (rogowce), F.3 (margle warstwowane), F.4 (margle masywne i zapiaszczone), F.5 (heterolity marglisto-mułowcowe) i F.6 (piaskowce warstwowane-laminowane), o spójnej dla wszystkich interpretacji środowiska ich depozycji. Geneza facji, które w różnych profilach występują w różnym wzajemnym następstwie, daje logiczny obraz zmian, jakie następowały w czasie depozycji margli dynowskich, co również odzwierciedlają trzy zespoły facjalne: ZF.I, ZF.II i ZF.III. Facje, jak i zespoły (głównie w profilach B i C) wskazują na depozycję w płytkim basenie sedymentacyjnym (okresowo izolowanym i okresowo zalewanym), do którego oprócz materiału węglanowego dostarczany był materiał krzemionkowy (lub był produkowany na miejscu), w obrębie którego okresowo dochodziło do sedymentacji utworów o charakterze tsunamitów, śledzonych na dużym dystansie. Zapis w profilu margli dynowskich w Gorlicach (profil A) posiada wyraźne następstwo facji od strefy wyżej do międzypływowej, wskazujące dodatkowo na cykliczne zmiany głębokości basenu sedymentacyjnego. Potwierdzają to również obecne wśród margli dynowskich utwory zinterpretowane jako rytmity pływowe, z zapisem pływów syzygijnych i kwadraturowych. Następstwo facji oprócz fluktuacji głębokości basenu wskazuje na pogłębianie się płytkiego szelfu. W tym obszarze ponad marglami dynowskimi udokumentowany jest rozwój płytkiego systemu deltowego składającego się z zestawu parasekwencji powstałego w warunkach wymuszonej regresji (piaskowce magdaleńskie). Dodatkowo wyniki badań geochemicznych z obrębu facji F.1 z jednostki śląskiej porównano z wynikami badań geochemicznych uzyskanych z tej facji z jednostki skolskiej rejonu Dynowa (odsłonięcia Futoma i Straszydle). Wykazują one różnice w składzie biomarkerów, co może być spowodowane innymi warunkami ich depozycji niż w jednostce śląskiej. Zaproponowana płytkowodna interpretacja margli dynowskich z obrębu jednostki śląskiej nie wyklucza zatem istnienia obszarów z sedymentacją głębokowodną w innych częściach Paratetydy w okresie dolnego oligocenu. Wnioskowane dowody na pływy w badanych sekcjach, pomimo interpretowanych warunków jeziornych mogą odzwierciedlać połączenie basenu z otwartym oceanem w tym obszarze. To opisane i udokumentowane odkrycie występowania w obrębie margli dynowskich utworów pływowych (tidalitów) i utworów o charakterze tsunamitów jest ważnym krokiem w zrozumieniu paleoewolucji Karpat, ale również istotne jest z punktu widzenia zrozumienia warunków depozycji warstw menilitowych – głównej skały macierzystej dla węglowodorów. Uzyskane wyniki potwierdzają oraz uszczegóławiają dotychczasowe wyniki badań i zrekonstruowane wcześniej warunki paleogeograficzne.

EN

The Dynow Marls (siliceous marls) represent a sedimentary record of a salinity-decreasing event, anoxic bottom sediment conditions, and strong endemism that occurred throughout the Central Paratethys during the Lower Oligocene (NP 23), and is referred to the Solenovian Event (loss of connection of the Paratethys with the World Ocean). A comprehensive study of the Dynów Marls on a regional scale, in the context of their sedimentatary environment, source rock potential and importance for the petroleum system, were conducted in the Western Carpathians, mainly in the Czech Republic and Austria. The obtained results indicate shallow-water conditions of their deposition, which is consistent with paleogeographic and paleoclimatic reconstructions. The occurrence of these deposits has been identified in the lower part of the Menilite Beds throughout the Carpathian arc. The succession of Menilite Beds in the Polish Outer Carpathians was considered until recently to be a product of deep-water sedimentation. As a result of research work in the southern part of the Silesian Unit (Gorlice fold), this interpretation has been verified. In this area, it was shown that sedimentation took place on a shallow, periodically existing shelf. This interpretation only partially took into account the occurrence of Dynów Marls in the Menilite Beds profile (distinguished at the rank of a member), which are of key importance for confirming the previous interpretation and determining their origin in a broader regional context. Therefore, for a complementary interpretation of the entire succession of Menilite Beds within the Silesian Unit, detailed sedimentological studies of Dynów marls were conducted, which was supported by geochemical studies in three selected sections in Gorlice (section A), Zborowice (section B) and Jabłonica Polska (section C). providing support. Within these studies, six sedimentary facies F.1 (menilite shales), F.2 (cherts); F.3 (stratified marlstone); F.4 (massive and sandy-pebbles marlstone), F.5 (marly-mudstones heterolithes)’ F.6 (Stratified and laminated sandstone) were distinguished, with a consistent interpretation of their depositional environment being provided for all. The origin of facies, which in different sections occur in different relationships, gives a logical scheme of the changes that occurred during the deposition of the Dynów Marls, which is also reflected by three facies associations ZF.I, ZF.II and ZF.III. Both the facies and the associations (mainly in profiles B and C) indicate deposition in a shallow sedimentary basin, (in a periodically isolated and periodically flooded) basin, to which, in addition the carbonate deposit, siliceous material was supplied (or was produced in situ), where also tsunamites-like sedimentation occurred periodically, tracked over a large distance. The record in the Dynów Marls section in Gorlice (section A) has a clear succession of facies from the upper to the intertidal zone, additionally indicating cyclic changes in the depth of the sedimentary basin. This is also confirmed by present in the Dynów Marls deposits interpreted as tidal rhythmites, with a record of spring and neap tides. The facies succession, in addition to the fluctuations in the depth of the basin, indicates the deepening of the shallow shelf. In this area above the Dynów marls the development of a shallow deltaic system is documented consisting of series parasequences formed under forced regression condition (Magdalena Sandstones). Additionally, the results of geochemical studies from the F.1 facies from the area of the Silesian unit were compared with the results of geochemical studies obtained from this facies from the Skole unit, from the Dynów region (Futoma and Straszydle exposures), show differences in the composition of biomarkers, which may be caused by different conditions of their deposition than in the Silesian unit. The proposed shallow-water interpretation of the study area does not preclude the existence of deep-water regions elsewhere in the Paratethys sedimentary basin during Lower Oligocene time. The inferred evidence for tides in the studied sections, despite an interpreted lacustrine setting there, possibly reflects the basin’s connection to the open ocean in this area. This described and documented discovery of the occurrence of tidalites and tsunamites within the Dynów Marls is an important step in understanding the paleoevolution of the Carpathians, but is also important from the point of view of understanding the conditions of deposition of the Menilite Beds - the main source rock for hydrocarbons. The obtained results confirm and specify the previous research results and previously reconstructed paleogeographic conditions.

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Integrative biomarker approach to decode seasonal variation in biomarker responses of Scylla serrata and Penaeus monodon from Sundarbans estuarine system

Baag Sritama, Mandal Sumit

Oceanologia

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2025

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No. 67 (1)

Art. no. 67108

EN

Sundarbans Estuarine System is a highly productive estuary and is considered the most important spawning and nursery ground for various commercial fish and shellfish species. Estuarine organisms are frequently exposed to a wide variety of pollutants due to their vicinity to human habitation. Marine organisms residing in this area are also exposed to extensive fluctuations of environmental factors which vary with season. In the present study, effects of seasonal variation on oxidative stress biomarkers such as superoxide dismutase, catalase, glutathione-S-transferase, and lipid peroxidation in the hepatopancreas of mud crab Scylla serrata and shrimp Penaeus monodon, were studied during monsoon, winter, spring and summer seasons. The integrated biomarker response (IBR) was assessed with the biomarker scores for all four seasons in both species. Our results suggested seasonal discrepancies as the governing factor behind biomarkers’ variability. The breeding period of the animals also seems to play a significant role in their oxidative stress physiology. The IBR results indicated that moderately high temperatures and low salinity in the monsoon season are the most stressful for crabs. This stress might also be ascribed to the breeding period of these crabs which exacerbates the stress level during this season. However, in the case of shrimps, the highest IBR value was observed in the winter season due to impaired ROS elimination at low temperatures. This study also offers baseline values in various seasons that would be beneficial to be considered in environmental monitoring programs to avoid the misinterpretation of environmental factors, which change seasonally.

4

Detection of potential biomarkers of renal cancer using LDI MS

Frydrych Aleksandra

Chemical Technology & Biotechnology

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2025

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Vol. 5

121--128

EN

This article describes a study using laser desorption/ionization mass spectrometry to search for potential biomarkers of renal cell carcinoma. The studies were performed on a sample of healthy tissue and a sample of cancer tissue from the kidney of the same patient. Thirty-seven small-molecular-weight compounds were identified, and two of them had previous literature links to cancer.

5

Toxicology under the umbrella of proteomics and metabolomics

Kasprzyk-Pochopień Joanna, Piekoszewski Wojciech

Bio-Algorithms and Med-Systems

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2025

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Vol. 21, Special issue: OMICS innovations

1--7

EN

Objective: The integration of omics technologies has opened new opportunities in toxicological research. This article aims to explore how toxico-proteomics and toxico-metabolomics contribute to the understanding of xenobiotic mechanisms, biomarker discovery, and modern risk assessment frameworks. Methods: Relevant literature was analysed to highlight recent advances in proteomics and metabolomics applied to toxicology. Particular attention was given to mass spectrometry-based approaches, spatial omics, in silico modelling, and combined omics strategies. Case examples from drug- and environment-related toxicology were used to illustrate practical applications. Results: High-resolution mass-spectrometry-based proteomics enables the sensitive detection of changes in protein levels, post-translational modifications, and proteinprotein interactions. Toxico-proteomic studies have clarified mechanisms of cardio-, hepato-, and atd-neurotoxic effects. Metabolomics supports the profiling of low molecular weight compounds and early responses to toxicants. Toxico-metabolomic analyses identified changes related to energy metabolism and amino acid metabolism. In vitro models and zebrafish embryos provided organ-specific insights. Integrating omics data has led to the identification of candidate biomarkers of exposure and toxic effects. Conclusions: Toxico-proteomics and toxico-metabolomics represent powerful tools for toxicology. Their application enhances the sensitivity of toxicity detection, reduces reliance on animal models, and supports the development of predictive strategies. As analytical platforms and computational tools continue to evolve, these disciplines are expected to play an increasingly central role in environmental and biomedical toxicology, with implications for diagnostics, therapeutics, and regulatory demands.

6

Microscopic Studies of Activated Sludge Supported by Automatic Image Analysis Based on Deep Learning Neural Networks

Dziadosz Marcin, Majerek Dariusz, Łagód Grzegorz

Journal of Ecological Engineering

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2024

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Vol. 25, nr 4

360--369

EN

Paper presents microscopic studies of activated sludge supported by automatic image analysis based on deep learning neural networks. The organisms classified as Arcella vulgaris were chosen for the research. They frequently occur in the waters containing organic substances as well as WWTPs employing the activated sludge method. Usually, they can be clearly seen and counted using a standard optical microscope, as a result of their distinctive appearance, numerous population and passive behavior. Thus, these organisms constitute a viable object for detection task. Paper refers to the comparison of performance of deep learning networks namely YOLOv4 and YOLOv8, which conduct automatic image analysis of the afore-mentioned organisms. YOLO (You Only Look Once) constitutes a one-stage object detection model that look at the analyzed image once and allow real-time detection without a marked accuracy loss. The training of the applied YOLO models was carried out using sample microscopic images of activated sludge. The relevant training data set was created by manually labeling the digital images of organisms, followed by calculation and comparison of various metrics, including recall, precision, and accuracy. The architecture of the networks built for the detection task was general, which means that the structure of the layers and filters was not affected by the purpose of using the models. Accounting mentioned universal construction of the models, the results of the accuracy and quality of the classification can be considered as very good. This means that the general architecture of the YOLO networks can also be used for specific tasks such as identification of shell amoebas in activated sludge.

7

Zastosowanie technik chromatograficznych do oznaczania krótkołańcuchowych kwasów tłuszczowych jako potencjalnych biomarkerów w chorobie Parkinsona

Jeżyna Klaudia, Gątarek Paulina

Eliksir

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2024

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nr 13

13--19

8

Geochemical characterization and palaeoenvironmental implications of lipids in Neogene lignites and lignitic shales in NW Poland

Czechowski Franciszek, Polowczyk Marzena, Simoneit Bernt R. T., Grelowski Cezary, Hojniak Marek

Annales Societatis Geologorum Poloniae

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2023

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Vol. 93, No. 4

447--466

EN

The lipophilic biomarker distributions in lipids of Neogene lignites and lignitic shales in western Pomerania and the midlands of Poland are presented. Twenty-six lignite samples and seven lignitic shales were obtained from twenty-four boreholes. Their extracts were separated, using thin-layer chromatography, and the saturate and aromatic fractions were analyzed by gas chromatography-mass spectrometry. The molecular compositions of n-alkanes, isoprenoids, n-alkylcyclohexanes, n-alkylbenzenes, tri- and tetracyclic diterpenoids, pentacyclic triterpenoids, as well as polycyclic aromatic hydrocarbons (PAHs) with up to five rings, were determined. The samples displayed n-alkane distributions in the range of C14–C35 and high odd-over-even carbon number predominances (CPI(25–33) from 2.9 to 7.9). Diterpanes consisted primarily of phyllocladane, abietane, isopimarane, labdane, and kaurane structures, although their abundances varied among the samples. Hopanes exhibited the biological and geochemical characteristics of low-maturity organic matter. Minor oleanane triterpenoids from angiosperms were also found. A few samples displayed evidence of biodegradation on the basis of the advanced isomerization of αβ-hopanes and the presence of short-chained n-alkanes, n-alkylcyclohexanes, and n-alkylbenzenes. A more mature stage of the above biomarkers also may have resulted in part from the oxidation of organic matter. The lignite source materials were derived from conifer and angiosperm flora as well as microbial remnants. The contribution from marine phytoplankton was excluded on the basis of the lack of C27 steroids. PAHs were predominantly perylene or phenanthrene, with minor other analogues. Thus, the data support progressive lacustrine/lagoonal sedimentation in the palaeoenvironmental mires.

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Nieinwazyjne biomarkery do wykrywania raka pęcherza moczowego

Gruba Natalia

Wiadomości Chemiczne

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2022

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[Z] 76, 9-10

719--734

EN

Bladder cancer (BC) is one of the most common cancer in the world. About 3% of all new cancer diagnoses are due to urinary bladder cancer. BC is also a leading cause of cancer-related death, as 2.1% of all cancer deaths are caused by bladder cancer. However, lack of a reliable biomarker is the biggest issue for BC diagnosis, prognosis and treatment. Development of non-invasive, quick and economical methods in bladder cancer diagnosis still remains a great challenge. Highly specific, easy-to-perform tests are really needed. Ideally if they can identify the presence of a tumor before the first symptoms appear, as time plays an important role in cancer. In this article, an overview of the current established diagnostic tests and newly identified biomarkers will be provided.

10

Zastosowanie badań izotopowych do określania pochodzenia wybranych biomarkerów

Bieleń Wojciech, Janiga Marek

Nafta-Gaz

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2022

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R. 78, nr 5

336--342

PL

Badania izotopowe n-alkanów, pristanu (Pr) oraz fitanu (Ph) przeprowadzono przy pomocy aparatu GC-IRMS. Porównanie wartości δ13C – pristanu do n-C17 oraz fitanu do n-C18, a także zestawienie wartości δ13C pomiędzy pristanem a fitanem w obrębie jednej próbki pomaga zidentyfikować źródło pochodzenia tych izoprenoidów, co było celem pracy. Ta ostatnia informacja uwiarygadnia lub podaje w wątpliwość wskaźnik środowiska sedymentacji – Pr/Ph. Wartości δ13C n-alkanów dla rop naftowych z tego samego złoża: Bóbrka 113, Niepodległość 2, Bandrów wskazują na pochodzenie tych rop od roślin C3 (fotosynteza typu C3) oraz z osadów rzecznych lub/i jeziornych. N-alkany występujące w tych trzech ropach naftowych mogą mieć mieszane źródła i pochodzić zarówno od roślin lądowych, jak i wodnych. Ropa naftowa Łodyna 90K może pochodzić z różnorakich wyższych roślin. Wartości δ13C n-alkanów z próbek ekstraktów bitumicznych Dukla 2A i Dukla 2D są charakterystyczne dla roślin C3. Pristan i fitan w badanych próbkach rop naftowych i w przypadku dwóch próbek ekstraktów bitumicznych Dukla 2A i Dukla 2D mają wartości δ13C niższe niż wartości δ13C dla n-C17 i n-C18, co sugeruje pochodzenie od organizmów heterotroficznych. We wszystkich badanych próbkach rop naftowych (wyjątki: Łodyna 90K, Osobnica 35) wartości δ13C dla Pr i Ph w obrębie pojedynczej próbki świadczą o tym samym materiale źródłowym dla tych izoprenoidów. Ta informacja potwierdza, że wskaźnik Pr/Ph, mówiący o typie środowiska sedymentacji materii organicznej, jest wiarygodny. W dwóch ekstraktach bitumicznych (Dukla 2D i Krosno 8) wartości δ13C dla Pr i Ph są różne, dlatego istnieje duże prawdopodobieństwo odmiennego pochodzenia dla tych dwóch izoprenoidów (należy być ostrożnym co do wiarygodności wskaźnika środowiska sedymentacji Pr/Ph).

EN

Isotope analysis of n-alkanes, pristan (Pr) and phytane (Ph), were carried out on the GC-IRMS apparatus. Comparing the δ13C values of pristan to n-C17, phytane to n-C18 and pristan to phytane within one sample helps to identify the source of these isoprenoids. The latter information legitimises or questions the sedimentation environment index – Pr/Ph. The values of δ13C of n-alkanes for crude oil from one field: Bóbrka 113, Niepodległość 2, Bandrów indicate the origin of C3 plants (photosynthesis type C3) and river and / or lake sediments. The N-alkanes found in these three crude oils could have been sourced by organic matter from terrestrial and aquatic plants. Łodyna 90K crude oil was derived from a variety of higher plants. The δ13C values of n-alkanes for samples Dukla 2A and Dukla 2D bituminous extracts are characteristic for C3 plants. Pristan and phytan in the analyzed crude oil samples and in the case of two samples Dukla 2A and Dukla 2D bituminous extracts have δ13C values lower than the values of n-C17 and n-C18, which suggests their origin from heterotrophic organisms. In all analyzed crude oil samples (exceptions: Łodyna 90K, Osobnica 35) the δ13C values of Pr and Ph within a single sample indicate the same source material for these isoprenoids. This information confirms that the Pr/Ph ratio is reliable. In two bituminous extracts (Dukla 2D and Krosno 8) the δ13C values of Pr and Ph are different, therefore there is a high probability of different origins for these two isoprenoids (the Pr/Ph ratio may be unreliable).

11

Detection of ethane, methane, formaldehyde and water vapor in the 3.33 μm range

Winkowski Mateusz, Stacewicz Tadeusz

Metrology and Measurement Systems

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2022

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Vol. 29, nr 2

271--282

EN

We describe construction and investigation results of optical trace gas sensor working in the 3.334-3.337 μm spectral range. Laser spectroscopy was performed with a multipass cell. A setup was elaborated for detection of ethane at the 3.3368035 μm absorption line. Analysis of the gas spectra and the experiment have shown that, beside C2H6, the sensor is suitable for simultaneous detection of methane, formaldehyde and water vapor. Due to nonlinearity of the laser power characteristic we decided to detect the fourth harmonic of signal. Additional laser wavelength modulation was applied for optical interference suppression. In result, the precision of ethane detection of approximately 80 ppt has been achieved for the averaging time of 20 seconds. Long-term stability as well as the measurement linearity have also been positively tested. The system is suitable for detecting potential biomarkers directly in human breath.

12

Oddech codzienny

Ligor Tomasz, Rudnicka Joanna, Ratiu Ileana Andreea, Monedeiro Fernanda, Monedeiro-Milanowski Maciej, Buszewski Bogusław

Wiadomości Chemiczne

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2021

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[Z] 75, 7-8

911--922

EN

The odor of human body has facilitated diagnosis for a long time. Sniffing the body, breath, urine and even feces became one of the useful methods in ancient medicine. For centuries, the sweet smell of the breath was associated with diabetes, the fishy smell was associated with liver disease, measles was associated with the smell of feathers, typhoid with the smell of fresh bread, and tuberculosis with stale beer. Hippocrates also linked the smell of the human body and disease, claiming that the smell of a sick person is different from that of a healthy one. He classified the characteristic odors of the body into sweet, musty, fishy and rotten. The father of chemical analysis of breath was Antonie Lavoisier, who found that carbon dioxide is exhaled by guinea pigs. The pioneer of modem breath analysis was Linus Pauling, who in 1971 presented the results of breath studies using gas chromatography (GC), showing the presence of over 200 substances. Exhaled air containing approximately 78% N2, 17% OSub>2, 3% CO2 and up to 6% water vapor. The exact concentrations of individual inorganic gases depend on many factors, mainly physical exercise, cardiac output, and lung ventilation. A mixture of many volatile organic compounds is a much smaller group of substances at concentrations 100 ppm. The substances in the breath can come from human metabolism and enter into the body by inhaled air and food. Volatile organic compounds present in the breath that can be divided into different chemical classes e.g. saturated hydrocarbons (ethane, pentane, aldehydes), unsaturated hydrocarbons (isoprene), ketones (acetone), sulfur-containing compounds (methyl mercaptan, dimethyl sulfide, dimethyl disulphide, carbon disulphide, carbonyl sulphide) and containing nitrogen (amines). Endogenous substances in the breath can be used to track physiological and pathological processes in the body. Chemical analysis of the breath can provide information regarding biochemical processes in the organism and human health. Compared to many medical diagnostic methods, it is painless, non-invasive and safe. Nowadays, the main purpose of breath analysis is to identify volatile organic compounds that can be used as markers of various diseases. Research focused on detection of lung cancer based on specific volatile organic compounds in the exhaled air is carried out in many laboratories. Rapid and non-invasive methods for early detection of lung cancer and chronic obstructive pulmonary disease is crucial for early diagnosis. This mini review presents background of breath, briefly describes main volatiles, their biochemical origin as well as potential application of exhaled gases analysis.

13

Spektrometria masowa i analiza izotopowa biomarkerów frakcji nasyconej

Bieleń Wojciech, Janiga Marek

Nafta-Gaz

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2021

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R. 77, nr 8

512--520

PL

Analiza GC-IRMS poszerza i potwierdza (lub nie) interpretację opartą na wynikach z analiz GC-MS. Przykładowo jest bardzo przydatna w określaniu środowiska sedymentacji materii organicznej. Analiza GC-MS biomarkerów i oparte na niej wyniki są wiary- godne, ale dopiero badania GC-IRMS mogą je potwierdzić. W niniejszej pracy próbowano poprzez analizy izotopowe potwierdzić pochodzenie: BNH (28,30-bisnorhopanu) od bakterii chemoautotroficznych, a także wyższych karotenoidów i ich pochodnych od bakterii Chlorobiaceae czy Chromatiaceae. Przeprowadzono badania biomarkerów na aparacie GC-IRMS oraz EA-IRMS. Otrzymane chromatogramy z analiz IRMS porównywano z archiwalnymi analizami GC-MS dla tych samych próbek w celu identyfikacji poszczególnych związków chemicznych. Oprócz dotychczasowej metodyki przygotowania próbek do analiz zastosowano też niestandardową metodę polegającą na rozdziale n-alkanów od węglowodorów rozgałęzionych. Oznaczono na GC-IRMS powtarzalność metody oraz wartości δ13C wybranych biomarkerów z frakcji nasyconej. Stwierdzono, że próbki z małą zawartością biomarkerów nie nadają się do analiz. Z drugiej strony zbyt duże stężenie analitu podanego na chromatograf gazowy powoduje wzrost linii bazowej i gorszy rozdział pików, co również stanowi problem. Wstępnie oznaczono wartości δ13C dla biomarkerów frakcji nasyconej z grupy hopanów: bisnorhopanu (BNH), oleananu, C29 norhopanu, C30 hopanu, moretanu i serii C31–C35 homohopanów oraz dla surowych rop naftowych. Stwierdzono względnie niewielkie różnice w wartości δ13C pomiędzy BNH a hopanami i BNH a surowymi ropami, co sugeruje najprawdopodobniej to samo źródło pochodzenia wszystkich biomarkerów (w tym BNH). Próbowano również oznaczać biomarkery we frakcji aromatycznej metodą GC-IRMS, co jednak się nie udało. Chcąc w przyszłości przeprowadzać takie oznaczenia, należy najprawdopodobniej zastosować specjalną metodykę przygotowania próbek frakcji aromatycznej.

EN

GC-IRMS analysis extends and confirms (or not) the interpretation based on the results of GC-MS analyses. For example, it is very useful in determining the sedimentation environment of organic matter. GC-MS analysis of biomarkers and the results are reliable, but only GC-IRMS studies can confirm it. In this study, the origin of BNH (28,30-bisnorhopane from chemoautotrophic bacteria) and origin of higher carotenoids and their derivatives from Chlorobiaceae or Chromotiaceae bacteria were confirmed through isotopic analyzes. Biomarkers were analyzed using the GC-IRMS and EA-IRMS apparatus. The obtained chromatograms from the IRMS analyses were compared with the archival GC-MS analyses for the same samples in order to identify individual chemical compounds. In addition to the existing methodology of sample preparation for analyses, a non-standard method was also used, consisting in the separation of n-alkanes from branched hydrocarbons. The repeatability of the method was determined on the GC-IRMS and the values of δ13C for selected biomarkers from the saturated fraction were determined. It was found that samples with low biomarker content are not suitable for analysis. On the other hand, too high concentration of the analyte causes an increase of the chromatogram baseline and worse separation of the peaks, which is also a problem. For the crude oils the δ13C values were initially determined for the biomarkers of the saturated fraction from the hopanes group: bisnorhopane (BNH), oleanane, C29 norhopane, C30 hopane, moretane and the C31-C35 homohopane series. Relatively small differences in δ13C values were found between BNH/hopanes and BNH/crude oils, which suggests the same source of origin for all biomarkers (including BNH). Determining biomarkers in the aromatic fraction using the GC-IRMS method was not successful. In the future, a special methodology for preparing samples for carbon isotopic analyses of aromatic fraction will be required.

14

Fusion of feature selection methods in gene recognition

Gil Fabian, Osowski Stanislaw

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2021

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Vol. 69, nr 3

art. no. e136748

EN

The paper presents the fusion approach of different feature selection methods in pattern recognition problems. The following methods are examined: nearest component analysis, Fisher discriminant criterion, refiefF method, stepwise fit, Kolmogorov-Smirnov criteria, T2-test, Kruskall-Wallis test, feature correlation with class, and SVM recursive feature elimination. The sensitivity to the noisy data as well as the repeatability of the most important features are studied. Based on this study, the best selection methods are chosen and applied in the process of selection of the most important genes and gene sequences in a dataset of gene expression microarray in prostate and ovarian cancers. The results of their fusion are presented and discussed. The small selected set of such genes can be treated as biomarkers of cancer.

15

Positronium as a biomarker of hypoxia

Moskal Paweł, Stępień Ewa Ł.

Bio-Algorithms and Med-Systems

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2021

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Vol. 17, no. 4

311--319

EN

In this review article, we present arguments demonstrating that the advent of high sensitivity total-body PET systems and the invention of the method of positronium imaging, open realistic perspectives for the application of positronium as a biomarker for in-vivo assessment of the degree of hypoxia. Hypoxia is a state or condition, in which the availability of oxygen is not sufficient to support physiological processes in tissue and organs. Positronium is a metastable atom formed from electron and positron which is copiously produced in the intramolecular spaces in the living organisms undergoing positron emission tomography (PET). Properties of positronium, such as e.g., lifetime, depend on the size of intramolecular spaces and the concentration in them of oxygen molecules. Therefore, information on the partial pressure of oxygen (pO2) in the tissue may be derived from the positronium lifetime measurement. The partial pressure of oxygen differs between healthy and cancer tissues in the range from 10 to 50 mmHg. Such differences of pO2 result in the change of ortho-positronium lifetime e.g., in water by about 2–7 ps. Thus, the application of positronium as a biomarker of hypoxia requires the determination of the mean positronium lifetime with the resolution in the order of 2 ps. We argue that such resolution is in principle achievable for organ-wise positronium imaging with the total-body PET systems.

16

Novel biomarker and drug delivery systems for theranostics - extracellular vesicles

Stępień Ewa Ł., Rząca Carina, Moskal Paweł

Bio-Algorithms and Med-Systems

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2021

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Vol. 17, no. 4

301--309

EN

Extracellular vesicles (EVs) are nano- and micro-sized double-layered membrane entities derived from most cell types and released into biological fluids. Biological properties (cell-uptake, biocompatibility), and chemical (composition, structure) or physical (size, density) characteristics make EVs a good candidate for drug delivery systems (DDS). Recent advances in the field of EVs (e.g., scaling-up production, purification) and developments of new imaging methods (total-body positron emission tomography [PET]) revealed benefits of radiolabeled EVs in diagnostic and interventional medicine as a potential DDs in theranostics.

17

Comparative petrography and organic geochemistry of different types of organic matter occurring in the Outer Carpathians rocks

Zielińska Magdalena, Fabiańska Monika, Więcław Dariusz, Misz-Kennan Magdalena

Geological Quarterly

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2020

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Vol. 64, No. 1

165--184

EN

The characterization of organic matter (OM) in sedimentary rocks is important in many types of biological, geological and environmental research. The integrated use of microscopy and geochemistry, as here, is particularly useful in any attempt to define the origin and evolution of OM in sedimentary basins. The organic petrography and geochemistry different types of allogenic and authigenic OM from the Polish Outer Carpathian (POC) rocks were studied in present study to compare their genetic type, thermal maturity, depositional environment and post-sedimentation processes. Special attention was paid to redeposited coal clasts occurrences. The used techniques show differences in organic matter type originating from various sources. The organic petrography analysis shows that redeposited coal clasts (CC) and terrigenous organic matter (TOM) are composed predominantly of woody material (the gas-prone Type-III kerogen). Similar results were obtained during the Rock-Eval pyrolysis. Moreover, the GC-MS analysis of extracts indicated the additional source of OM, namely planktonic organic matter (POM) with oil-prone kerogen Type-I or II. This OM is in some cases high thermally mature and could potentially has allochthonous origin. The n-alkane, saturated and aromatic biomarker data revealed deposition of this POM in anoxic deltaic or close-shore sedimentary environments whereas the redeposited coal clasts were probably originally deposited in coal swamps as were the Upper Silesian bituminous coals.

18

Przydatność adipokin jako biomarkerów niedokrwiennej dysfunkcji mięśnia sercowego

Mocan Hognogi Larisa-Diana, Goidescu Cerasela-Mihaela, Farcaş Anca-Daniela, Tukaj Dorota

Laboratorium Medyczne

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2019

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nr 2

14--19

PL

Choroby układu sercowo-naczyniowego są główną przyczyną zgonów zarówno wśród kobiet, jak i mężczyzn, lecz wciąż jeszcze zdarza się duży odsetek niewłaściwych rozpoznań oraz brakuje jasno określonych kryteriów diagnostycznych. Postępy nauk biomolekularnych pozwoliły na udowodnienie kluczowej roli zapalenia i co ważniejsze – również modyfikującego wpływu adipokin we wszystkich stadiach choroby niedokrwiennej serca. Sugeruje się również, że zmagazynowana tkanka tłuszczowa, a dokładnie ta zlokalizowana w obrębie klatki piersiowej, ma duży wpływ na rozwój choroby niedokrwiennej serca, tworząc lokalne środowisko proaterogenne. Układ odpornościowy ściśle współdziała z metabolicznymi czynnikami ryzyka, inicjując, promując i nasilając powstawanie zmian miażdżycowych w ścianach tętnic, a wszystko to z „pomocą” adipokin. Toteż obecnie prowadzone badania intensywnie koncentrują się na odkrywaniu biomarkerów zapewniających zwiększenie szans wykrycia subklinicznej dysfunkcji mięśnia sercowego, a także mogących dodać stałą wartość do obecnych kryteriów ryzyka, ustalonych poprzez wytyczne.

EN

Cardiovascular disease is the leading cause of death among both women and men, but there is still a great percentage of misdiagnosis and lack of clearly defined criteria. Advances in biomolecular science have proven the crucial role of inflammation and, more importantly, the role of adipokines in mediating all stages of coronary artery disease. It has also been suggested that regional fat deposits, more precisely from thoracic region, have a major influence on the development of coronary artery disease by creating a local proatherogenic environment. The immune system closely interacts with metabolic risk factors to initiate, promote, and further aggravate the atherosclerotic lesions on the arterial wall all with the „help” of adipokines. So nowadays, research extensively focuses on uncovering biomarkers that would provide an increased chance of detecting subclinical cardiac distress and also add a consistent value to current guideline-imposed risk criteria.

19

Korelacja wybranych biomarkerów z etiologią i ciężkością posocznicy

Holub Michal, Džupová Olga, Růžková Michaela, Stráníková Alžběta, Bartáková Eva, Máca Jan, Beneš Jiří, Herwald Heiko, Beran Ondřej

Laboratorium Medyczne

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2019

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nr 4

14--23

PL

Zarówno rodzaj czynnika infekcyjnego wywołującego posocznicę, jak i punkt wyjścia zakażenia uogólnionego wpływają na przebieg odpowiedzi zapalnej. W prezentowanej pracy autorzy oceniali stężenia cytokin (IL-6, IL-8 i IL-10) w osoczu, chemokin (CCL2/MCP-1, MIP-1β), białka wiążącego heparynę (HBP), rozpuszczalnego CD14 (sCD14) i kortyzolu u pacjentów z posocznicą w ciągu pierwszych 96 godzin hospitalizacji na oddziale intensywnej terapii. Etiologię ustalono u 56 spośród 62 pacjentów objętych badaniem. Stężenia MCP-1, sCD14, IL-6 i IL-10 w osoczu były znamiennie wyższe u chorych z pozaszpitalnym zapaleniem płuc (community-acquired pneumonia, CAP) i infekcyjnym zapaleniem wsierdzia (infective endocarditis, IE) niż z bakteryjnym zapaleniem opon mózgowo-rdzeniowych (bacterial meningitis, BM). Stężenia kortyzolu były wyższe u chorych z IE niż z BM i CAP, a w jednym z punktów czasowych – wyższe u chorych z posocznicą wywołaną przez bakterie Gram-ujemne niż przez Gram-dodatnie. Co więcej, stężenia kortyzolu i MCP-1 wykazywały dodatnią korelację z obliczanym codziennie wynikiem w skali SOFA. Ponadto stężenia HBP były znamiennie wyższe u chorych z IE niż u chorych z BM. Powyższe odkrycia sugerują, że na wartości: MCP1, sCD14, IL-6, IL-10, kortyzolu i HBP, wpływa punkt wyjścia posocznicy oraz że podwyższone stężenia MCP-1 i kortyzolu w osoczu są związane z zaburzeniami czynności narządów wewnętrznych w przebiegu posocznicy.

20

Diagnostyka laboratoryjna sepsy

Zielińska-Borkowska Urszula, Skirecki Tomasz

Laboratorium Medyczne

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2019

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nr 1

34--39

PL

Sepsa to nieprawidłowa odpowiedź gospodarza na zakażenie wywołane przez patogeny. Dokładna i szybka diagnoza pozwala na wdrożenie szybkiej terapii. W pracy przedstawiono niektóre badania laboratoryjne wykonywane w podejrzeniu sepsy. Od 2016 roku zalecane jest oznaczanie mleczanów. Do badań włączono również poziom bilirubiny oraz kreatyniny, a raczej ich progresje w określaniu niewydolności wielonarządowej. Zaproponowano kilka nowych markerów do rozpoznawania sepsy, jak i wskaźników prognostycznych. Do chwili obecnej nie ma jednego laboratoryjnego testu pozwalającego na jego podstawie rozpoznać sepsę.

EN

Sepsis is the host response to microbial pathogens. An accurate and timely diagnosis of sepsis allows for prompt and appropriate treatment. This paper discusses selected laboratory tests that are carried out when sepsis is suspected. The 2016 sepsis consensus definitions include lactate concentrations. Also included in the 2016 definitions are the measurements of bilirubin and creatinine, or rather their progressions, in order to determine multisystem organ failure. Several new biomarkers have been proposed to diagnose sepsis or to predict mortality. So far there has been no single laboratory test that accurately diagnoses sepsis.