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GENE EXPRESSION PROFILING OF IPSC-DERIVED NEURAL PROGENITORS FROM PATIENTS WITH 22Q11.2 DUPLICATION SYNDROME
No full textThe molecular mechanisms underlying neurodevelopmental disorders (NDDs) are understudied.
22q11.2 Duplication Syndrome (22q11.2DupS) is associated with an increased risk of NDDs,
including autism spectrum disorders, developmental delay, and intellectual disability, while
potentially having protective effect against schizophrenia. Here we performed transcriptomic
profiling of 22q11.2DupS neural progenitors (NPCs). Total RNA was isolated from
iPSCs-derived NPCs of a family trio consisting of a child with 22q11.2DupS, a carrier unaffected
mother, and a healthy control father. Paired-end RNA-sequencing was carried out by
commercial services. FASTQ files were processed on an NVIDIA platform and differential gene
expression analysis was carried out in RStudio using the DESeq2 R package. The resulting lists
of differentially expressed genes (DEGs) was utilized for pathway and gene ontology enrichment
analysis using clusterProfiler in RStudio. 60 DEGs with lower expression and 58 DEGs with
higher expression were obtained in 22q11.2DupS NPCs compared to both carrier and control
NPCs. For genes with lower expression in 22q11.2DupS NPCs, “miRNA targets in ECM and
membrane receptors” was the top enriched pathway. On the other hand, for genes with higher
expression in 22q11.2DupS NPCs, no biological pathways were identified as being significantly
enriched in the DEG list beyond what would be expected by chance. However, for genes with
higher expression in 22q11.2DupS NPCs, we obtained statistically significant enrichment of
molecular functions such as Histone demethylase activity. 22q11.2DupS NPCs exhibit altered
signaling pathways and molecular functions, providing preliminary insights into the impact of this
microduplication on neural differentiation.Abstract book: FENS Regional Meeting 2025 , Oslo, Norway, 16-19 June 202
Transgeneracijski efekti prajminga Plantago lanceolata L. na povećanje otpornosti potomaka na stres izazvan poplavom
No full textTransgeneracijska memorija biljaka pruža značajnu adaptivnu prednost, omogućavajući im da
se efikasnije suočavaju sa ponavljanim stresorima iz spoljašnje sredine. Iako je ovaj fenomen
sve češće proučavan u uslovima suše i saliniteta, njegovi mehanizmi u kontekstu poplavnog
stresa ostaju nedovoljno istraženi. U cilju popunjavanja ovog znanja, sproveli smo kontrolisani
dvogeneracijski eksperiment u kome je vodni stres izazvan plavljenjem primenjen tokom faze
cvetanja, razvojno osetljive faze koja u značajnoj meri determiniše reproduktivni uspeh biljke
Plantago lanceolata L. Polazna hipoteza bila je da će potomci ostvariti bolju adaptivnu
sposobnost ukoliko su i matične biljke prethodno bile izložene plavljenju. Antioksidativni
(katalaza (CAT), askorbat-peroksidaza (APX), superoksid dismutaza, peroxidaze i ukupni
fenoli) i oksidativni (malondialdehid (MDA) i vodonik peroksida (H2O2)) parametri su
analizirani spektrofotometrijski. Dobijeni rezultati potvrdili su ovu pretpostavku: potomci
majki izloženih stresu akumulirali su veću biomasu i ostvarili viši reproduktivni prinos kada
su obe generacije bile izložene identičnom stresnom režimu. Detaljne fiziološke i biohemijske
analize pokazale su da su ove prednosti zasnovane na jačanju antioksidativnog sistema, što je
potvrđeno povećanom aktivnošću CAT i APX, kao i povišenim sadržajem ukupnih fenolnih
jedinjenja. Paralelno sa tim, uočen je i smanjen stepen oksidativnih oštećenja, što su potvrdili
niži nivoi MDA i H2O2 kod potomaka. Naše istraživanje ukazuje na ključnu ulogu redoks
regulacije u formiranju memorije na stres izazvan plavljenjem, kao i na nove uvide u
molekularne i fiziološke (biohemijske) mehanizme nasledne tolerancije. Ovi rezultati ne samo
da produbljuju razumevanje adaptivnih strategija biljaka, već otvaraju i nove perspektive u
oplemenjivanju useva sa poboljšanom otpornošću na poplavni stres.Zbornik sažetaka: V simpozijum biologa i ekologa Republike Srpske sa međunarodnim učešćem - SBERS 2025 Prirodnomatematički fakultet, Univerzitet u Banjoj Luci, 13-15. novembar 202
Seasonal dynamics of metal and biocide resistance genes in airborne metagenomes across Belgrade
No full textAir as a vector for resistance gene dissemination remains understudied, particularly regarding
genes conferring resistance to metals and biocides, which are often co-located with antibiotic
resistance genes on mobile genetic elements. This study analyzed the diversity and abundance
of such resistance genes in airborne metagenomes collected from sites across Belgrade, Serbia,
during autumn and winter of 2024/2025. Air samples were collected using hydrophobic
polypropylene membrane filters, DNA was extracted by the phenol-chloroform method,
sequenced on the Illumina NovaSeq X Plus platform, and analyzed using the AMR++ v3.0
pipeline with the MEGARes database. The diversity and abundance of both metal and biocide
resistance genes were more pronounced in autumn, while winter samples showed greater
uniformity across sites. Quaternary ammonium compounds (QACs) and multibiocide
resistance genes dominated in 5 of 7 sites in autumn, reaching 70.4% in Leštane, 68.4% in
Zeleno Brdo, and 63.3% in Veliki Crljeni for QACs. Barajevo and Borča lacked QACs in
autumn and, along with all sites in winter, were dominated by multibiocide (up to 39.9%) and
acid resistance genes (up to 39.4%). In winter, QACs were entirely absent. For resistance to
metals, autumn samples were dominated by multimetal (up to 61,4%) and copper (up to
28.9%), with iron resistance genes uniquely abundant in Despota Stefana (13.5%). In winter,
iron resistance extended to Leštane (1.9%) and Veliki Crljeni (5.1%), alongside broader
representation of zinc (up to 11.4%) and nickel resistance genes (up to 9.2%). These findings
emphasize seasonal and spatial variability in airborne resistomes and the role of environmental
pressures in shaping their composition in Belgrade.Zbornik sažetaka: V simpozijum biologa i ekologa Republike Srpske sa međunarodnim učešćem - SBERS 2025 Prirodnomatematički fakultet, Univerzitet u Banjoj Luci, 13-15. novembar 202
Nekodirajuće RNK kao biomarkeri gestacijskog dijabetesa
No full textNon-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular
RNAs (circRNAs), show potential to serve as biomarkers of metabolic disorders, oxidative stress and inflammatory
status, and thus may have diagnostic and prognostic significance in gestational diabetes
mellitus (GDM). Aberrant expression of specific ncRNAs has been identified in placental tissue, plasma,
serum, extracellular vesicles, peripheral blood mononuclear cells (PBMCs), as well as in other maternal and
fetal sources. These ncRNAs exhibit high stability in circulation and can reflect underlying molecular alterations,
making them promising non-invasive biomarkers for diagnosis, prognosis, and disease monitoring.
Therefore, this article will review the major findings of GDM-related ncRNAs and highlight their potential
role in improving clinical outcomes through biomarker-based approaches.Nekodirajuće RNK (nkRNK), uključujući mikroRNK, duge nekodirajuće RNK i kružne RNK, pokazuju potencijal
da služe kao biomarkeri metaboličkih poremećaja, oksidativnog stresa i inflamatornog statusa, i stoga
mogu imati dijagnostički i prognostički značaj kod gestacijskog dijabetesa melitusa (GDM). Aberantna
ekspresija specifičnih nkRNK je identifikovana u tkivu placente, plazmi, serumu, ekstracelularnim vezikulama,
mononuklearnim ćelijama periferne krvi, kao i u drugim izvorima poreklom od majke ili fetusa. Ove
nkRNK pokazuju visoku stabilnost u cirkulaciji i mogu odražavati osnovne molekularne promene, što ih čini
obećavajućim neinvazivnim biomarkerima za dijagnozu, prognozu i praćenje bolesti. Stoga će ovaj članak
pregledati glavna saznanja o nkRNK povezanih sa GDM i istaći njihovu potencijalnu ulogu u poboljšanju
kliničkih ishoda kroz pristupe zasnovane na biomarkerima
Bacterial diversity analysis of glyphosate-exposed and pristine soil samples
No full textGlyphosate is the active ingredient in widely used broad-spectrum herbicides, and its extensive
application raises increasing concerns about environmental accumulation and ecological impact. It is
known to be toxic to aquatic organisms, while numerous studies have also reported adverse effects on
plant growth, insect gut microbiota, and human health. Therefore, research on soil bacterial communities
can significantly contribute to the discovery of novel and effective strategies for the bioremediation of
glyphosate-contaminated sites.
In this study, metagenomic analysis based on 16S rRNA gene amplicons was performed on soil samples
from an agricultural site with prolonged glyphosate exposure and a reference forest soil with no history
of herbicide application. The bacterial composition of each sample was evaluated, revealing high overall
microbial diversity. Actinobacteria and proteobacteria were the dominant phyla across all samples, while
the relative abundance of other phyla varied depending on the sampling site. Marked differences were
observed at the genus level, distinguishing the forest microbiome from those exposed to glyphosate. The
presence of species and genera previously reported to degrade glyphosate was also examined. Functional
profiling based on 16S rRNA amplicons predicted ABC transporters, glutathione S-transferases, and ECF
RNA polymerase sigma-70 factors—proteins typically associated with stress response—as differentially
abundant between samples.
These findings provide insight into how chronic glyphosate exposure shapes soil microbial communities
and their potential functional adaptations, highlighting microbial diversity as a valuable resource for
developing sustainable bioremediation strategies for glyphosate-polluted environments.Book of abstract: 75th Panhellenic Conference of the Hellenic Society of Biochemistry and Molecular Biology (EEBMB Athens, December 5-7, 202
The plastic-degrading capabilities of Pseudomonas aeruginosa
No full textThe global accumulation of synthetic and bio-based plastics has intensified the demand for effective and sustainable degradation strategies. This study explores the plastic-degrading potential of Pseudomonas aeruginosa, focusing on its degrading enzymes, biofilm formation, and biosurfactant production. The study highlights the limited degradability of C–C backbone plastics such as polyethylene (PE), polypropylene (PP), and polystyrene (PS), in contrast to ester-containing polymers like PET, PU, and bio-based plastics (PLA, PCL, PHA), which exhibit greater microbial susceptibility. While P. aeruginosa demonstrates only partial surface modification of recalcitrant plastics, it achieves substantial degradation of bio-based plastics such as PCL. Genomic profiling using PlasticsDB and PAZy databases reveals homologs of plastic-active enzymes, including esterases and depolymerases, with potential roles in polyester degradation. Furthermore, the integration of chemical pretreatment methods, such as pyrolysis of PE into metabolizable alkanes, combined with microbial conversion into polyhydroxyalkanoates (PHA), underscores the importance of hybrid chemo-biotechnological approaches. Despite biosafety concerns, P. aeruginosa emerges as a metabolically versatile and genetically tractable candidate for precision-engineered bioremediation. This work positions P. aeruginosa not as a standalone solution, but as a modular component within broader strategies for next-generation plastic waste valorization and upcycling
Expression dynamics of hsa-miR-18a-5p and hsa-miR-135b-5p are associated with pathological tumor stage and lymph node status in locally advanced rectal cancer patients undergoing neoadjuvant chemoradiotherapy
No full textLocally advanced rectal cancer (LARC) is characterized by tumor invasion into surrounding tissues and frequent lymph node involvement, often requiring neoadjuvant chemoradiotherapy (nCRT) followed by surgical resection. LARC presents a significant therapeutic challenge because it is typically diagnosed at an advanced stage and shows variable responses to standard nCRT, highlighting the need for predictive biomarkers. microRNAs are considered valuable biomarker candidates due to their biological characteristics. We investigated the expression dynamics of hsa-miR-18a-5p and hsa-miR-135b-5p and their predictive potential for response to nCRT. We demonstrate a significant post-nCRT decrease in tumor expression of hsa-miR-18a-5p. High pre-treatment hsa-miR-18a-5p expression was significantly associated with lower post-treatment pathological stage and absence of lymph node metastasis, indicating potential predictive value. The expression of hsa-miR-135b-5p after therapy was associated with advanced disease stage and positive lymph node status, indicating it may be linked to more aggressive disease after the treatment. Despite these associations with tumor characteristics, neither miRNA showed a significant association with therapy response. Our findings suggest that while hsa-miR- 18a-5p and hsa-miR-135b-5p are not predictive of nCRT response, their expression patterns before and after therapy may reflect underlying tumor biology and hold potential for LARC patient stratification
Mapping gene expression in developing zebrafish embryo using spatial transcriptomics
No full textZebrafish (Danio rerio) is a well-used model organism for research of vertebrate development because of its rapid and external development and transparent embryos. Spatial transcriptomics is a powerful tool for analyzing gene expression patterns across developmental stages, as it provides deeper insight by preserving the spatial context of gene expression within the tissue. In this study we used Stereo-seq Transcriptomics to characterize the spatial gene expression landscape in zebrafish embryos at 3 days post-fertilization, as this is a crucial stage for zebrafish organogenesis. Zebrafish AB were maintained according to The Zebrafish Book. Five embryos were fresh frozen, embedded in O.C.T. compound and cryosectioned (12 μm). Samples were prepared according to manufacturer's instructions in Stereo-seq Sample Preparation, Sectioning and Mounting Guide for Fresh Frozen Samples on Stereo-seq Chip Slides user manual. In situ whole-transcriptome capture was performed using Stereo-seq Transcriptomics T Kit, followed by fresh frozen library preparation using Stereo-seq Library Preparation Kit. Sequencing was done on DNBSEQ-G400. Image processing was performed using StereoMap, while sequencing data were analyzed using Stereo-seq Analysis Workflow. Bioinformatic analysis identified a total of 8 356 cells with a Mean MID (Molecular Identifier) of 2 297. Sixteen distinct cell clusters were characterized based on their unique gene expression. Cell populations were defined by differentially expressed genes, reflecting their specific biological functions. These results show that spatial transcriptomics is a valuable method for improving developmental research, as it enables the precise mapping of differentially expressed genes to their anatomical locations within the embryo.BeCELS 2025: Belgrade Conference for Early-Career Life Scientists, taking place on Friday, September 5, 2025, at the Institute of Molecular Genetics and Genetic Engineering (IMGGE) in Belgrad
Diagnostic potential of hsa-miR-146a-5p and its target gene SOX2 expression in oral cancer
No full textPost-operative recurrence of oral cancer occurs in about 30% of cases and represents the greatest risk to long-term survival, which remains low (~40%). Due to their widespread role in carcinogenesis, microRNAs are potential biological biomarkers that could help detect histopathologically normal cells exhibiting malignant gene expression. hsa-miR-146a-5p has not been extensively studied, and available data suggest its expression varies in cancer. The SOX2 gene is a downstream target of hsa-miR-146a-5p. The aim of this study was to analyze the diagnostic potential of hsa-miR-146a-5p and its target gene, SOX2, in oral cancer. The study group consisted of 48 oral cancer patients. Relative expression of hsa-miR-146a-5p and SOX2 was analyzed in cancerous and paired non-cancerous tissue from each patient using qRT-PCR. There were no significant differences in hsa-miR-146a-5p (p=0.891) or SOX2 expression (p=0.282) between cancerous and non-cancerous tissue. SOX2 expression in cancerous tissue showed a significant positive correlation with SOX2 expression in non-cancerous tissue (rho=0.400, p=0.005). Similarly, hsa-miR-146a-5p expression in cancerous tissue was significantly positively correlated with its expression in non-cancerous tissue (rho=0.668, p=0.001). According to ROC curve analysis, neither hsa-miR-146a-5p nor SOX2 can be used as diagnostic biomarkers for distinguishing between oral cancer and non-cancerous tissue. hsa-miR-146a-5p and SOX2 were negatively correlated in both cancerous and non-cancerous tissue, although not significantly (rho=–0.009, p=0.950). Our results indicate that hsa-miR-146a-5p and SOX2 cannot be used as diagnostic biomarkers in oral cancer.BeCELS 2025: Belgrade Conference for Early-Career Life Scientists, taking place on Friday, September 5, 2025, at the Institute of Molecular Genetics and Genetic Engineering (IMGGE) in Belgrad
Autophagy induction by SARS-CoV-2 ORF3a depends on JNK signaling
No full textSARS-CoV-2 open reading frame 3a (ORF3a) is a non-structural and an accessory protein that is
involved in the pathogenesis of COVID-19. ORF3a manipulates with autophagosomes and
lysosomal degradation to support SARS-CoV-2 replication and egress. The signaling pathways by
which ORF3a regulates autophagy are not fully understood. Therefore, we investigated ORF3amediated
signaling pathways involved in autophagy regulation. Plasmid encoding SARS-CoV-2
ORF3a was electroporated into H460 human lung epithelial cancer cells using the 4DNucleofector.
The activation of AMP-activated protein kinase (AMPK), mechanistic target of
rapamycin complex 1 (mTORC1), extracellular signal-regulated kinase (ERK), c-Jun N-terminal
kinase (JNK) and p38 was assessed by immunoblotting. Pharmacological inhibition of JNK with
SP600125 was used to determine the role of JNK in ORF3a-induced autophagy. Autophagy was
monitored by LC3-II and p62 immunoblotting and RT-qPCR analysis of autophagy-related (ATG)
gene expression. Our results showed that ORF3a activated JNK in H460 lung cancer cells.
However, no change in phosphorylation level was observed in other kinases involved in autophagy
such as AMPK, mTORC1, ERK and p38. ORF3a promoted LC3-II and p62 accumulation and
increased mRNA levels of ATG genes such as ULK-1, FIP200, LC3, p62, FOXO1 and FOXO3.
Treatment with a JNK pharmacological inhibitor SP600125 reduced LC3-II and p62 protein levels
and LC3, p62, ULK-1, and FOXO1 mRNA levels in ORF3a-expressing cells. Therefore, our study
supports the role of JNK in ORF3a-induced autophagosome formation, indicating JNK-mediated
autophagy as a potential therapeutic target for the COVID-19 and its chronic manifestations.BeCELS 2025: Belgrade Conference for Early-Career Life Scientists, taking place on Friday, September 5, 2025, at the Institute of Molecular Genetics and Genetic Engineering (IMGGE) in Belgrad