imagine (Institute of molecular genetics and genetic engineering)
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Deciphering the effects of nanosized polystyrene particles
No full textTranscriptome profiling at the single cell level is crucial for understanding complex
biological systems and molecular mechanisms. We wanted to unravel the influence
of polystyrene nanoparticles on peripheral blood mononuclear cells (PBMCs), using
microfluidic technology. A total of 4 single-cell sequencing libraries were analyzed (one
control and three different treatments). Thousands of individual cells per sample are
Barcoded separately to index the transcriptome of each cell individually. Raw sequencing
data were analyzed with the Cell Ranger software and visualized using Loupe Browser
software. Set of analysis pipelines processes Chromium Single Gene Expression data
to align reads, generate Feature Barcode matrices, and perform clustering and gene
expression analysis. Each element of the matrix is the number of UMIs (Unique Molecular
Identifier) associated with a feature (row) and a barcode (column). Principal component
analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) algorithms on
single-cell sequencing samples were carried out. The expressed cells were clustered
during which typical cell marker genes were used for annotation. Genes showing adjusted
p-value 0.5 were considered to be marker genes. Loupe
Browser was used for visualization of clusters and analysis of the single-cell data. In this
way, gene markers for individual cell types obtained by single-cell sequencing represent a
good model for the analysis of biological events.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
ŠTA NAM RASTE PO DEPOIMA? ISTRAŽIVANJE ZAGAĐENOSTI UZORAKA ZEMLJIŠTA SA ARHEOLOŠKIH LOKALITETA I VAZDUHA IZ MUZEJSKIH I LABORATORIJSKIH DEPOA
No full textPlesni su ubikvitarni mikroorganizmi i nalaze se i u unutrašnjem i u spoljašnjem
životnom prostoru. Tamni i vlažni uslovi, koji su prisutni u zemlji,
ali i u muzejskim depoima, pogoduju razvoju i rastu gljiva. Gljive mogu napraviti
oštećenja na pokretnom kulturnom nasleđu, ali su mnogo veći problem
za ljudsko zdravlje, jer mogu uzrokovati različita alergijska stanja i
invazivne gljivične infekcije. Dodatno, kontinuirano izlaganje velikoj koncentraciji
gljivičnih spora u vazduhu predstavlja ozbiljnu zdravstvenu pretnju
po arheologe i muzejske radnike. Tokom ove godine autori su uradili pilot
istraživanje i uzorkovali vazduh iz osam muzejskih i laboratorijskih depoa,
kao i zemljište sa četiri arheološka lokaliteta. Cilj je bio da se identifikuje
prisustvo gljivica i bakterija u zemljištu sa arheoloških iskopavanja i vazduhu
u radnim i skladišnim prostorima, i time indirektno odredi rizik boravka u
ovakvim sredinama na zdravlje arheologa, kao i da se proceni biotehnološki
potencijal izolovanih zemljišnih mikroorganizama. Svi uzorci su poslati u
mikrobiološku laboratoriju na inkubaciju i na identifikaciju (direktna mikroskopija).
Bakterijska raznovrsnost je pokazana u svim uzorcima zemljišta,
a analiza plesni je pokazala prisustvo različitih vrsta u vazduhu, od kojih su
najprisutnije Aspergillus fumigatus i Aspergillus flavus. Iz svih uzoraka zemljišta
izolovan je Aspergillus terreus. U depoima dva muzeja identifikovana je gljiva Stachybotrys chartarum koja predstavlja ozbiljnu pretnju za razvoj
respiratornih alergijskih gljivičnih bolesti kod ljudi, kao što je bronhopulmonalna
mikoza. U radu će biti prikazani detaljni rezultati identifikacije izolovanih
gljiva iz uzorka zemljišta i vazduha i biće objašnjen njihov epidemiološki
značaj i potencijalni uticaj na razvoj različitih respiratornih bolesti povezanih
sa kontinuiranom ekspozicijom gljivičnim sporama iz vazduha, kao i predlog
epidemioloških mera i mere zaštite na radu.XLVII Скупштина и годишњи скуп САД, Ниш, 30. мај – 1. јун 2024. годин
The Relevance of β-Thalassemia Heterozygosity in Pediatric Clinical Practice: Croatian Experience
No full textBackground: Thalassemia syndromes are common monogenic disorders that represent a significant global health issue. No systematic epidemiological or molecular investigations on thalassemias in the Croatian population have been reported to date. (2) Methods: This prospective study included 70 children with a presumptive diagnosis of thalassemia and their 42 first-degree relatives. Molecular characterization was performed using direct sequencing and gap-PCR methods. (3) Results: We identified 46 (30 children and 16 first-degree relatives) β-thalassemia heterozygous carriers from 24 unrelated families, carrying eight different mutations and one hemoglobin variant. Five variants account for approximately 85% of all affected β-globin alleles: Hb Lepore-Boston-Washington (32.6%), HBB:c.93-21G>A (19.6%), HBB:c.315+1G>A (13.1%), HBB:c.92+1G>A (10.9%), and HBB:c.92+6T>C (8.7%) variants. (4) Conclusions: β-thalassemia carriers need more detailed genetic profiling since genetic modifiers can significantly impact their phenotype. Our study provides important new insights into the relevance of β-thalassemia heterozygosity in pediatric clinical practice
Chemical profiling of Anthriscus cerefolium (L.) Hoffm., biological potential of the herbal extract, molecular modeling and KEGG pathway analysis
No full textThis study was designed to investigate chemical composition and biological activities of the Anthriscus cerefolium methanolic extract. Chemical characterization of the extracts was performed by LC–HRMS/MS analysis. Antimicrobial activities of the extract were investigated on six bacteria and eight fungi while antioxidant activity was assessed by six different assays. Anti-enzymatic activity of the methanolic extract was tested on five enzymes associated with therapy of neurodegenerative diseases and diabetes mellitus type 2. Cytotoxic properties of the extract were tested on human immortalized keratinocytes (HaCaT) and tumor cell lines (SiHa, MCF7, HepG2). Anti-inflammatory activity of the extract was assessed on bacteria mediated inflammation model using HaCaT cell line. Molecular docking studies of enzymes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis were performed. The results showed that the obtained extract was rich in phenolic compounds (a total of seventy-two were identified), with malonyl-1,4-O-dicaffeoylquinic acid and 3,5-O-dicaffeoylquinic acid dominating in the sample. The extract expressed antimicrobial, antioxidant, anti-enzymatic, cytotoxic and anti-inflammatory properties. The identified compounds demonstrated strong binding to the acetylcholinesterase (AChE) and to a lesser extent, to the butyrylcholinesterase (BChE), glucosidase, amylase, and modestly, to tyrosinase. KEGG pathway analysis has shown that the certain phenolic compounds may be related to anti-tumor, anti-inflammatory and anti-microbial activities of the extract. The data obtained suggest that phenolic compounds of the extract and their mixtures should be considered for future research as ingredients in pharmaceutical and nutraceutical formulations
Markers of Epithelial–Mesenchymal Transition and Mucinous Histology Are Significant Predictors of Disease Severity and Tumor Characteristics in Early-Onset Colorectal Cancer
No full textApproximately 20% of patients with colorectal cancer (CRC) are diagnosed with a mucinous subtype of this tumor, have a worse prognosis, and often show resistance to available therapies. Molecules from the mucin family are involved in the regulation of epithelial–mesenchymal transition (EMT), which significantly determines the cancer aggressiveness. This study aimed to examine the diagnostic and prognostic significance of mucinous histology and EMT markers in patients with early-onset CRC and their association with disease severity and tumor characteristics. This study included tumor tissue samples from 106 patients diagnosed with CRC before the age of 45, 53 with mucinous and 53 with non-mucinous tumors. The EMT status was determined by immunohistochemical analysis of E-cadherin and Vimentin in tissue sections. Mucinous tumors had significantly higher Mucin-1 (p < 0.001) and cytoplasmic E-cadherin (p = 0.043) scores; they were significantly less differentiated (p = 0.007), more advanced (p = 0.027), and predominately affected right the colon (p = 0.039) compared to non-mucinous tumors. Epithelial tumors were significantly better differentiated (p = 0.034) and with less prominent tumor budding (p < 0.001) than mesenchymal tumors. Mucin-1 and Vimentin were independent predictors of tumor differentiation (p = 0.006) and budding (p = 0.001), respectively. Mucinous histology and EMT markers are significant predictors of disease severity and tumor characteristics in early-onset colorectal cancer
Copper(II) and Zinc(II) Complexes with Bacterial Prodigiosin Are Targeting Site III of Bovine Serum Albumin and Acting as DNA Minor Groove Binders
No full textThe negative environmental and social impacts of food waste accumulation can be mitigated by utilizing bio-refineries’ approach where food waste is revalorized into high-value products, such as prodigiosin (PG), using microbial bioprocesses. The diverse biological activities of PG position it as a promising compound, but its high production cost and promiscuous bioactivity hinder its wide application. Metal ions can modulate the electronic properties of organic molecules, leading to novel mechanisms of action and increased target potency, while metal complex formation can improve the stability, solubility and bioavailability of the parent compound. The objectives of this study were optimizing PG production through bacterial fermentation using food waste, allowing good quantities of the pure natural product for further synthesizing and evaluating copper(II) and zinc(II) complexes with it. Their antimicrobial and anticancer activities were assessed, and their binding affinity toward biologically important molecules, bovine serum albumin (BSA) and DNA was investigated by fluorescence emission spectroscopy and molecular docking. The yield of 83.1 mg/L of pure PG was obtained when processed meat waste at 18 g/L was utilized as the sole fermentation substrate. The obtained complexes CuPG and ZnPG showed high binding affinity towards target site III of BSA, and molecular docking simulations highlighted the affinity of the compounds for DNA minor grooves
Transforming discarded walnut green husk into a resource of valuable compounds for colored bioactive textiles with a focus on circular economy concept
No full textThis study takes a new look at a circular economy concept for discarded walnut green husks. Their ethanol extract was prepared and characterized using RP-HPLC, then diluted with water and employed for dyeing and/or functionalizing different fabrics. A diluted extract can dye wool (WO), cotton (CO), cellulose acetate (CA), and polyamide (PA) at pH 4.5. Extract:water ratio of 10:40, 65 °C and 75 min and extract:water ratio of 15:35, 45 °C, and 60 min were found suitable for dyeing WO and CA, respectively. Dyed WO and CA exhibited color strength values of 29.0 and 9.2, and excellent antioxidant activity (>97 %) before and after washing, and a significant level of efficacy against S. aureus. CA possessed excellent (5) and very good (4) color fastness to rubbing in a dry and wet state, respectively. WO showed very good (4) and good to very good (3–4) color fastness to rubbing in a dry and wet state, respectively. CO and PA displayed excellent antioxidant activity, with CO also exhibiting significant antibacterial activity against S. aureus even after washing. Moreover, the same dyebath can be reused for up to four dyeing cycles, enabling obtaining bioactive WO and CA fabrics in various brown shades suitable for different applications. Cytotoxicity assay confirmed the non-cytotoxic nature of dyed and washed CA, PA, and CO fabrics. Bioactive WO, CO, CA, and PA fabrics can be considered for the production of wound dressing, performance clothes, and tights for people with sensitive skin. Finally, this paper sheds new light on a novel circular economy concept since collected husks’ solid parts that remained after extraction were converted into activated carbon, which was then used for the preparation of supercapacitor having a specific capacitance of 144–275 F/g at current densities 0.1–2.0 A/g
ANTIOXIDANT AND ANTIPROLIFERATIVE ACTIVITY OF PLANT BIOACTIVE COMPOUNDS DURING IN VITRO SIMULATED DIGESTION IN THE PRESENCE OF FOOD MATRIX
No full textOne of the key factors that can hinder the beneficial effects of bioactive compounds found in food is
their bioavailability, which is contingent upon their digestive stability, release from the food matrix,
and efficiency in passing through the epithelial barrier. Our study investigated the impact of in vitro
digestion and the food matrix on polyphenols from chokeberry fruits and organosulfur compounds from
ramsons. Our results indicate that despite the significant transformation of chokeberry phenolics during
digestion in the presence of the food matrix, they retain their potency as antioxidants and
antiproliferative agents. Research on ramsons (Allium ursinum) suggests that its consumption may
provide health benefits, particularly regarding potential anticancer properties. The safety characteristics
of Lactobacillus fermentum strains associated with A. ursinum, including the absence of gelatinase and
hemolytic activity, susceptibility to clinically relevant antibiotics, and beneficial properties such as
survival in the simulated gastrointestinal environment, colonization of the intestinal mucosa, and
immunomodulatory effects, indicate their potential use as probiotics for human consumption. This
study represents the first comprehensive analysis of ramsons' antioxidant and antiproliferative
properties, followed by an investigation into its microbiota and the health-promoting effects of lactic
acid bacteria (LAB).Book of abstracts: 2nd European Symposium on Phytochemicals in Medicine and Food
2-EuSPMF
June, 202
Psychological Distress Is Associated With Inflammatory Bowel Disease Manifestation and Mucosal Inflammation
No full textStress is a potentially significant risk factor for the occurrence and progression of inflammatory bowel disease (IBD).The study analyzed the level of stress, anxiety, and depression in patients with Crohn’s disease (CD; n = 50) and ulcerative colitis (UC; n = 54) in comparison with non-IBD controls (n = 100), using Perceived Stress Scale (PSS), Patient Health Questionnaire (PHQ-9), and Hospital Anxiety and Depression Scale (HADS) questionnaires. Additionally, a correlation between psychological scores and expression of IL17A, IL17F, and IL23A genes in the intestinal mucosa of IBD patients was assessed.Compared to controls, CD and UC patients had higher PSS (P = 4 × 10−14, P = 2.5 × 10−16), PHQ-9 (P = 2 × 10−16, P = 2 × 10−16), HADS depression (P = 2.6 × 10−10, P = 2.5 × 10−11), and HADS anxiety (P = 3.5 × 10−9, P = 1.2 × 10−11). We found a positive correlation between PSS and IL17F mRNA (rs = 0.43, P = .036) while HADS depression and HADS anxiety positively correlated with the IL23A mRNA in inflamed ileal mucosa of CD subjects (rs = 0.55, P = .0048; rs = 0.53, P = .0062).A significantly higher psychological distress was identified in IBD patients. CD patients with increased ileal expression of IL17F and IL23A genes had higher PSS and HADS, suggesting a potential interplay between psychological distress and inflammation.The study found elevated levels of perceived stress, depression, and anxiety in IBD. IL17F mRNA correlated with perceived stress while IL23A mRNA correlated with anxiety and depression (HADS) in the ileal mucosa of CD patients
Genomics as a basis for precision medicine
No full textAlthough medicine always aimed to be personalized, true implementation of personalized medicine in
health care practice has started recently. Fascinating progress of molecular genetics has strongly
contributed to this great achievement of modern medicine. Personalized medicine, also known as
genome-based medicine and precision medicine, uses the knowledge of molecular basis of the disease in
order to individualize treatment for each patient. Development of novel powerful high-throughput
technologies has enabled better insight into “oms” landscape of many diseases, resulting in application
of precision medicine approaches in their treatment. There are four cornerstones of modern precision
medicine: “omics”-based diagnostics, pharmacogenomics, specific molecular targeted, gene and cellular
therapy and predictive genomics. One of the most important successes of precision medicine is a
discovery of novel diagnostic molecular markers. Furthermore, numerous newly discovered molecular
markers have contributed to more precise classification of patients in distinct prognostic groups, leading
to specific, more successful treatment protocols. Development of pharmacogenomics platforms and
application of molecular–targeted therapy have led to the individualization of therapy, tailored to genetic
profile of a disease in each patient. The development of gene therapies which can cure or prevent a disease
by targeting disease-causing molecular defect has confirmed that the precision medicine has responded
successfully to a great challenge. Additionally, cellular and tissue therapies have opened new possibilities
for personalized treatment of many patients. Growing knowledge in predictive genomics leads to the
preventive medicine, the most important goal of modern medicine. There is no doubt that we are getting
closer to full implementation of precision medicine in every day clinical practice.2ND B&H SYMPOSIUM OF LABORATORY GENETICISTS AND MOLECULAR BIOLOGISTS (WITH INTERNATIONAL PARTICIPATION) 10TH - 11TH MAY 2024, BANJA LUKA, BOSNIA AND HERZEGOVIN