PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease

The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value < 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers.Database URL: www.peptickddb.com

Identification of novel molecular signatures of IgA nephropathy through an integrative -omics analysis

IgA nephropathy (IgAN) is the most prevalent among primary glomerular diseases worldwide. Although our understanding of IgAN has advanced significantly, its underlying biology and potential drug targets are still unexplored. We investigated a combinatorial approach for the analysis of IgAN-relevant -omics data, aiming at identification of novel molecular signatures of the disease. Nine published urinary proteomics datasets were collected and the reported differentially expressed proteins in IgAN vs. healthy controls were integrated into known biological pathways. Proteins participating in these pathways were subjected to multi-step assessment, including investigation of IgAN transcriptomics datasets (Nephroseq database), their reported protein-protein interactions (STRING database), kidney tissue expression (Human Protein Atlas) and literature mining. Through this process, from an initial dataset of 232 proteins significantly associated with IgAN, 20 pathways were predicted, yielding 657 proteins for further analysis. Step-wise evaluation highlighted 20 proteins of possibly high relevance to IgAN and/or kidney disease. Experimental validation of 3 predicted relevant proteins, adenylyl cyclase-associated protein 1 (CAP1), SHC-transforming protein 1 (SHC1) and prolylcarboxypeptidase (PRCP) was performed by immunostaining of human kidney sections. Collectively, this study presents an integrative procedure for -omics data exploitation, giving rise to biologically relevant results

Preferencje kulinarnego wykorzystania roślin strączkowych w aspekcie ich właściwości prozdrowotnych

The purpose of the study was to conduct a pilot survey of respondents’ preferences for the culinary use of legumes (broad bean crops) in terms of their healthpromoting properties. The survey was conducted among 120 people, 2021 nationwide, electronically using a Google form. Based on the survey, it was found that respondents rarely consume legumes, but are aware of their high nutritional and health-promoting value. The main motive for eating them is sensory acceptance (taste) and the possibility of preparing a variety of dishes. The most common dish prepared from legume seeds was baked beans, bean soup or the use of cooked seeds as an addition to vegetable salads. Among the health-promoting properties of legumes, respondents most often cited intestinal regulation, low glycemic index, prevention of heart disease and atherosclerosis.Celem pracy było przeprowadzenie pilotażowego badania preferencji ankietowanych w zakresie kulinarnego wykorzystania roślin strączkowych (bobowatych grubonasiennych) w aspekcie ich właściwości prozdrowotnych. Badania ankietowe zostały przeprowadzone wśród 120 osób, w 2021 roku na obszarze całego kraju, w formie elektronicznej z wykorzystaniem formularza Google. Na podstawie przeprowadzonych badań stwierdzono, że badani rzadko spożywają rośliny strączkowe, ale mają świadomość ich wysokiej wartości odżywczej i prozdrowotnej. Główną motywacją do ich spożywania jest akceptacja sensoryczna (smak) oraz możliwość przygotowywania różnorodnych dań. Najczęściej przygotowywanymi potrawami z nasion roślinstrączkowych były fasola po bretońsku, zupa fasolowa lub stosowanie ugotowanych nasion jako dodatek do sałatek warzywnych. Spośród właściwości prozdrowotnych roślin strączkowych, respondenci najczęściej wskazywali na regulację pracy jelit, niski indeks glikemiczny, profilaktykę chorób serca i miażdżycy

Zawartość wybranych pierwiastków śladowych w bulwach słodkiego ziemniaka (Ipomoea batatas L. (Lam))

The aim of this study was to determine the accumulation of selected micro-elements in sweet potato tubers depending on their genotype and cultivation method. Thee field experiment was conducted in 2019 in Żyznów, Podkarpackie Province (49°49ʹ01 ̋N 21°50ʹ21 ̋E), in brown earth, on defective wheat complex. It was based on a randomized block design in three replicates.The experimental factors were cultivars (Carmen Rubin, Goldstar and White Triumph) of various morphological and physiological types, as well as cultivation methods (traditional – as control, PE – polyester film, PP – nonwoven). The fertilisation was maintained on a fixed level (organic – manure in the amount of 25 t.ha-1 in autumn, and mineral in spring, prior to planting, in theamount of: 80 kg N; 34.9 kg P; 99.6 kg K.ha-1). During vegetation, cultivation was carried out in accordance with normal agricultural practice. During harvest, medi- um-sized tuber samples were collected for chemical analyses, all sourced from 10 plants from each crop plot. The content of micro-elements (manganese, iron, copper, zinc) was determined with the use of atomic absorption spectroscopy. The research results were analysed statistically using one-way analysis of variance at a signicance level p=0.05. The accumulation of micro-elements in sweet potato tubers was connected both to cultivar properties and to their reaction to under-cover cultivation methods. Of the micronutrients tested, sweet potato tubers contained the most iron, and the least copper. The highest content of copper was White Triumph, while the most abundant in manganese, iron and zinc was the Goldstar variety.Celem pracy było określenie akumulacji wybranych mikropierwiastków w bulwach słodkiego ziemniaka w zależności od ich genotypu i technologii uprawy. Eksperyment polowy przeprowadzono w 2019 roku w Żyznowie, woj. podkarpackie (49°49ʹ01 ̋N 21°50ʹ21 ̋E), na glebie brunatnej, kompleksu pszennego wadliwego. Założono go metodą bloków zrandomizowanych, w 3 powtórzeniach. Czynnikiem eksperymentu były odmiany (Carmen Rubin, Goldstar i White Triumph) o zróżnicowanym typie morfologiczno-zjologicznym, a także technologie uprawy (Tradycyjna – jako kontrola, PE-folia, PP-włóknina). Nawożenie było na stałym poziomie (organiczne w formie obornika w ilości 25 t.ha-1 jesienią, a mineralne wiosną, przed sadzeniem w ilości: 80 kg N; 34,9 kg P; 99,6 kg K.ha-1). W okresie wegetacji prowadzono zabiegi uprawowe zgodnie z zasadami Dobrej Praktyki Rolniczej. W czasie zbiorów pobrano próby bulw średniej wielkości do analiz chemicznych, które pochodziły z 10 roślin każdego poletka. Zawartość mikropierwiastków (mangan, żelazo, miedź, cynk) oznaczono metodą spektrometrii absorpcji atomowej. Wyniki badań opracowano statystycznie, stosując jednoczynnikową analizę wariancji przy poziomie istotności p = 0,05. Akumulacja mikropierwiastków w bulwach słodkiego ziemniaka była związana zarówno z właściwościami odmianowymi, jak i ich reakcją na technologie uprawy pod osłonami. Z badanych mikropierwiastków bulwy słodkiego ziemniaka zawierały najwięcej żelaza, najmniej zaś miedzi. Największą zawartością miedzi odznaczała się odmiana WhiteTriumph, zaś w mangan, żelazo i cynk najbardziej zasobna była odmiana Goldstar

Właściwości przeciwutleniające wybranych herbat zielonych

The aim of this study was to determine the antioxidant activity of green teas as a factor shaping pro-health properties of these teas. e study involved the infusions of Chinese green teas from six dierent producers. e antiradical properties of the analyzed samples were determined by means of the DPPH radical test (2,2-diphenyl-1-picrylhydrazyl radical). In addition, the total polyphenol compounds were determined using the Folin-Ciocalteu method. Signicant dierentiation of antioxidant activity and content of polyphenol compounds was found. e content of polyphenolic compounds ranged from 35.29 to 91.32 mg / 100 ml of infusion. e deactivation capacity of DPPH was 25.3 to 59.8% of the initial amount of the radical by the tested raw materials.Celem pracy była próba określenia aktywności przeciwutleniającej herbat zielonych jako czynnika kształtującego prozdrowotne właściwości tychże herbat. Badaniu poddano napary chińskich herbat zielonych pochodzące od sześciu różnych producentów. Określono właściwości przeciwrodnikowe analizowanych prób za pomocą testu z rodnikiem DPPH (rodnik 2,2-difenyl-1-pikrylhydrazylowy). Ponadto oznaczono zawartość związków polifenolowych ogółem metodą Folina-Ciocalteu’a.Stwierdzono znaczne zróżnicowanie aktywności przeciwutleniającej oraz zawartości związków polifenolowych. Zawartość związków polifenolowych wynosiła od 35,29 do 91,32 mg/100 ml naparu. Zdolność dezaktywacji DPPH przez badane surowce kształtowała się na poziomie od 25,3 do 59,8% początkowej ilości rodnika

Urinary peptidomics analysis reveals proteases involved in diabetic nephropathy

Mechanisms underlying the onset and progression of nephropathy in diabetic patients are not fully elucidated. Deregulation of proteolytic systems is a known path leading to disease manifestation, therefore we hypothesized that proteases aberrantly expressed in diabetic nephropathy (DN) may be involved in the generation of DN-associated peptides in urine. We compared urinary peptide profiles of DN patients (macroalbuminuric, n = 121) to diabetic patients with no evidence of DN (normoalbuminuric, n = 118). 302 sequenced, differentially expressed peptides (adjusted p-value < 0.05) were analysed with the Proteasix tool predicting proteases potentially involved in their generation. Activity change was estimated based on the change in abundance of the investigated peptides. Predictions were correlated with transcriptomics (Nephroseq) and relevant protein expression data from the literature. This analysis yielded seventeen proteases, including multiple forms of MMPs, cathepsin D and K, kallikrein 4 and proprotein convertases. The activity of MMP-2 and MMP-9, predicted to be decreased in DN, was investigated using zymography in a DN mouse model confirming the predictions. Collectively, this proof-of-concept study links urine peptidomics to molecular changes at the tissue level, building hypotheses for further investigation in DN and providing a workflow with potential applications to other diseases

Comparison of urine and plasma peptidome indicates selectivity in renal peptide handling

Purpose: Urine is considered to be produced predominantly as a result of plasma filtration in the kidney. However, the origin of the native peptides present in urine has never been investigated in detail. Therefore, we aimed to obtain a first insight into the origin of urinary peptides based on a side‐by‐side comprehensive analysis of the plasma and urine peptidome. Methods: Twenty‐two matched urine and plasma samples were analyzed for their peptidome using capillary electrophoresis coupled to mass spectrometry (CE‐MS; for relative quantification) and CE‐ or LC coupled to tandem mass spectrometry (CE‐ or LC‐ MS/MS; for peptide identification). The overlap and association of abundance of the different peptides present in these two body fluids were evaluated. Results: We were able to identify 561 plasma and 1461 urinary endogenous peptides. Only 90 peptides were detectable in both urine and plasma. No significant correlation was found when comparing the abundance of these common peptides, with the exception of collagen fragments. This observation was also supported when comparing published peptidome data from both plasma and urine. Conclusions and clinical relevance: Most of the plasma peptides are not detectable in urine, possibly due to tubular reabsorption. The majority of urinary peptides may in fact originate in the kidney. The notable exception is collagen fragments, which indicates potential selective exclusion of these peptides from tubular reabsorption. Experimental verification of this hypothesis is warranted

Lonliness of older people as a challenge for social work

Celem pracy było przedstawianie problemu samotności dotykającego zwłaszcza osoby starsze w kontekście pracy socjalnej. Pierwszy rozdział pracy, wyjaśnia samo pojęcie starości oraz całą jej specyfikę. Między innymi zwróciłam dużą uwagę na zjawisko feminizacji starości wynikające ze statystyk demograficznych. Zostały wyodrębnione potrzeby, problemy oraz najważniejsze prawa seniorów. Drugi i trzecie zaś rozdział przedstawia już kluczowe rozważania na temat samotności i pracy socjalnej. Podałam różnicę między samotnością a osamotnieniem. Ukazano pracownika socjalnego, jako najważniejszą osobę po rodzinie w zakresie niesienia pomocy. Scharakteryzowałam najczęstsze metody pracy z seniorem. Zawarłam wybrane instytucjonalno – środowiskowe formy w obszarze wspierania osób starszych, aby podkreślić ważność działań podmiotów z zakresu pomocy społecznej. W ostatnim rozdziale przeprowadziłam badania w wybranym Miejskim Dziennym Domu Pomocy Społecznej. Na potrzeby badań został stworzony scenariusz wywiadu pogłębionego, którego głównym celem było poznanie opinii uczestników oraz pracowników na temat funkcjonowania Domu. Uzyskane informacje pozwoliły na wysunięcie wniosku, iż placówka przyczynia się do przezwyciężania poczucia samotności beneficjentów.The aim of the master thesis was to present the problem of loneliness, especially affecting the elderly in the context of social work. The first chapter of the work explains the very concept of old age and all its specificity. Among other things, great attention was paid to the phenomenon of old age feminization resulting from demographic statistics. The needs, problems and the most important rights of seniors were identified. The second and third chapter already presents key considerations on loneliness and social work. The difference between loneliness and solitude is given. A social worker was presented as the most important person after the family in providing help. The most common methods of working with seniors were characterized. Selected institutional and environmental forms were included in the area of supporting the elderly to emphasize the importance of social assistance entities' activities.In the last chapter, research was carried out at the selected Municipal Daily Care Center. For the purposes of the study, an in-depth scriptwriter of the interview was created, whose main purpose was to learn the opinions of participants and employees about the functioning of the House. The information obtained led to the conclusion that the institution contributes to overcoming the feeling of loneliness of the beneficiaries

Club of Social Integration as a form overcome unemployment of the underprivileged groups on the job market

Celem pracy była ocena Klubu Integracji Społecznej pod względem jego udziału w przezwyciężaniu bezrobocia grup defaworyzowanych na rynku pracy. Na początku zostało przedstawione samo zjawisko bezrobocia, jego przyczyny oraz skutki. Zostały wyodrębnione skutki ekonomiczne oraz społeczne. Wykluczeniu społecznemu oraz zawodowemu przede wszystkim mogą ulec osoby należące do grup defaworyzowanych. W pracy zostały przedstawione bariery uniemożliwiające prawidłowe ich funkcjonowanie na rynku pracy. Poświęcono również uwagę działaniom aktywizującym podejmowanym przez Ośrodek Pomocy Społecznej, w tym prowadzenie Klubu Integracji Społecznej, który zwiększa szansę na zatrudnienie beneficjentów. Duży nacisk kładziony jest na reintegrację społeczną, która jest niezbędna do dalszego rozwoju zawodowego. Aby podkreślić ważność działań podmiotu w obszarze minimalizowania przyczyn bezrobocia, omówiono Kluby pod względem dobrych praktyk. W ostatnim rozdziale poddano analizie wyniki przeprowadzonych badań na przykładzie jednego Klubu. Na potrzeby badań zostały stworzone ankieta ora z wywiad, których celem było poznanie opinii uczestników oraz pracowników omawianego podmiotu. Uzyskane informacje pozwoliły na wysunięcie wniosku, iż Klub przyczynia się do zwiększenia szans swoich uczestników na rynku pracy.The aim of this Bachelor Thesis was the evaluation of The Club of Social Integration with regard to its contribution to dealing with unemployment of the underprivileged groups on the job market. At the begining there was presented the phenomenon of unemployment itself, its causes and consequences. The economic and social consequences were pointed out. The people subject to the social and profession exclusion are, above all, those who belong to the underprivileged group. In the thesis there were presented the barriers which hinder the proper functioning of the of these people on the job market. A part of thesis was also devoted to the description of the activating actions undertaken by the Social Assistence Centre, including The Club of Social Integration, which increase the chanes of employment for the benefociares. In the thesis the social re-integration is greatly stressed the importance of the actions of the subject in the area of minimalising the causes of unemployment the Club were also described with regard to their positive practises. The last chapter presents the analysis of the results of the resarch carried out on the basis of one Club. In order to conduct the research there were prepared a survey and an interview whose aims were to get to know the options of the participants and the employees involved. The gathered information made it possible to draw the conclusion that the Club contributes to increasing the chanes of its participants on the job market

Integrative databases and systems analysis in the investigation of chronic kidney disease progression

The prevalence of chronic kidney disease (CKD) is estimated to be 8-16% worldwide. CKD is a multifactorial disease characterized by a gradual loss of kidney function and significant variability with regards to cause of pathology, severity and rate of progression. There is a need for novel biomarkers and therapeutic targets, since at present diagnosis and treatment options are generic and often fail to prevent disease progression. Current research largely benefits from employment of high-throughput technologies, which provide information about a large number of molecular features. Analysis of such data might help in the elucidation of biological processes, biomarker research and drug discovery. Additionally, data integration strategies and technologies gain on popularity, providing in-depth insights into human diseases by revealing novel relations and predicting links between molecular processes. A plethora of omics datasets have been published, nevertheless these remain to a large extent disparate and thus, underexplored. Appropriate data handling, structure and storage, ideally in a centralized platform, are greatly needed for scientists to effectively analyze, reuse and extract underlying knowledge and further incorporate it into their research. To address this need and improve the exploitation of existing information in the context of renal diseases, the consolidation of published proteomics and peptidomics datasets was performed. The presented thesis specifically focused on extracting and integrating peptidomics and proteomics datasets from clinical experiments aiming to identify the core elements of each study and render them comparable and compatible with multi-way analyses. This thesis resulted in development and establishment of the publicly accessible peptide- and protein-centric CKD database (peptiCKDdb; www.peptickddb.com), a resource currently integrating data from 119 relevant publications. The database was designed utilizing a relational data-model, organizing the information in the form of tables of defined structure. A dedicated web interface provides user friendly access to data and is equipped with a multiparametric search engine able to address user-defined specific data queries. The search output is generated in the form of at-a-glance summary of results in the form of graph, as well as of a more detailed presentation of the extracted data and study-specific analysis workflow. In addition, export tools give the possibility for data extraction for further custom analyses. The usefulness of the developed database as well as benefits from data integration were demonstrated by the identification of novel molecular targets for IgA nephropathy. In the performed study, a combinatorial approach was applied integrating data from peptiCKDdb, but also utilizing knowledge from other complementary data resources (Nephroseq, Human Protein Atlas, STRING databases). Extracted IgAN-relevant proteomics datasets were integrated into known biological pathways. Proteins predicted to be involved in the latter were subjected to a multi-step assessment shortlisting the most biologically relevant features. The differential expression of some of these proteins in IgAN in comparison to normal phenotypes and other CKD etiologies was further validated by immunohistochemistry in the human kidney tissue. Consequently, the way is open for further functional studies addressing the potential use of these proteins as therapeutic targets or biomarkers. Taken together, the newly established peptiCKDdb is a curated knowledgebase integrating proteomics and peptidomics studies related to CKD, serving as a high quality resource for data extraction, cross-correlation and ultimately knowledge generation. As such, biomarker discovery and verification, as well as modelling of molecular mechanisms underlying CKD are greatly facilitated, as evidenced by the IgAN study. CKD complexity underscores the need for integrative analyses towards understanding its pathophysiology, therefore, peptiCKDdb is expected to become a fruitful resource, bringing protein data closer to the investigator and allowing efficient information utilization