imagine (Institute of molecular genetics and genetic engineering)
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Structural characteristics of YtnP lactonase originating from Stenotrophomonas maltophilia 6960
No full textAntibiotic resistance represents a serious global health threat. Available antibiotics
progressively lose efficacy against many bacterial pathogens. This phenomenon
underscores the urgent need for alternative strategies to combat bacterial infections.
Progress in understanding the regulation of bacterial pathogenicity has prompted
researchers to explore potential antivirulence drugs as a promising alternative. Quorum
quenching enzymes capable of degrading N-acyl homoserine lactones can impede
bacterial virulence and biofilm formation by disrupting cell-to-cell communication. In
this study, we employed in silico structural characterization of YtnP lactonase originating
from Stenotrophomonas maltophilia 6960, utilizing various online software tools, including
AlphaFold2, I-TASSER, PSIPRED, Phyre2, and SWISS-MODEL algorithms. The results
obtained from these programs were compared to each other.
The analysis revealed a 278 amino acid residue protein with a molecular weight of 31.02
kDa, predicted to be a transmembrane protein with an N-terminal extracellular domain
and a C-terminal cytoplasmic domain, predominantly comprised of extracellular amino
acid residues. Experimental validation demonstrated the quorum quenching activity
of S. maltophilia 6960 towards exogenous AHLs, supporting the predicted role of YtnP
lactonase in modulating quorum sensing of the surrounding bacteria. Furthermore, the
observation of QQ activity in the crude extract and not in the cell-free supernatant of
bacterial strain 6960 indicates that the YtnP lactonase is active within the bacterial cells.
Secondary structure predictions revealed a balanced distribution of alpha-helices and
beta-sheets, while tertiary structure predictions suggested a homodimeric configuration
with four Zn2+ binding sites.
These findings, which combine in silico predictions with experimental validation, provide
a solid foundation for further exploration in the development of effective antivirulence
therapeutics. Leveraging in silico methodologies to predict and characterize the functional
properties of potential antivirulence agents holds promise for accelerating the translation
of research findings into clinical applications.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Metals on the Menu—Analyzing the Presence, Importance, and Consequences
No full textMetals are integral components of the natural environment, and their presence in the food supply is inevitable and complex. While essential metals such as sodium, potassium, magnesium, calcium, iron, zinc, and copper are crucial for various physiological functions and must be consumed through the diet, others, like lead, mercury, and cadmium, are toxic even at low concentrations and pose serious health risks. This study comprehensively analyzes the presence, importance, and consequences of metals in the food chain. We explore the pathways through which metals enter the food supply, their distribution across different food types, and the associated health implications. By examining current regulatory standards for maximum allowable levels of various metals, we highlight the importance of ensuring food safety and protecting public health. Furthermore, this research underscores the need for continuous monitoring and management of metal content in food, especially as global agricultural and food production practices evolve. Our findings aim to inform dietary recommendations, food fortification strategies, and regulatory policies, ultimately contributing to safer and more nutritionally balanced diets
GERMLINE VARIANTS IN CANCER PREDISPOSITION GENES IN PEDIATRIC PATIENTS WITH CENTRAL NERVOUS SYSTEM TUMORS
No full textBackground: Central nervous system (CNS) tumors comprise around 20% of childhood malignancies.
Germline variants in cancer predisposition genes (CPGs) are found in approximately 10% of pediatric
patients with CNS tumors. This study aimed to characterize variants in CPGs in pediatric patients with
CNS tumors and correlate these findings with clinically relevant data.
Methods: Genomic DNA was isolated from the peripheral blood of 51 pediatric patients and further
analyzed by the next-generation sequencing approach. Bioinformatic analysis was done using an "inhouse"
gene list panel, which included 144 genes related to pediatric brain tumors, and the gene list
panel Neoplasm (HP:0002664).
Results: High-grade gliomas were the most prevalent tumor type comprising almost one-third of all
cases, followed by medulloblastomas and low-grade gliomas, ependymomas, atypical teratoid
rhabdoid tumors and choroid plexus tumors. Our study found that 27% of pediatric patients with CNS
tumors have a germline variant in some of the known CPGs, like ALK, APC, CHEK2, ELP1, MLH1, MSH2,
NF1, NF2 and TP53. . Three novel variants were detected in the ELP1 gene, 3 in the ALK gene and 1 in
the MSH2 gene. Germline variants in the ELP1 gene have been associated with pilocytic astrocytoma
for the first time. This study represents the first comprehensive evaluation of germline variants in
pediatric patients with CNS tumors in the Western Balkans region.
Conclusion: Our results indicate the necessity of genomic research to reveal the genetic basis of
pediatric CNS tumors, as well as to define targets for the application and development of innovative
therapeutics that form the basis of the upcoming era of personalized medicine.32nd Meeting of the European Society of Paediatric Clinical Research (ESPCR) in Opatija, Croatia, May 24-25, 2024
CHARACTERIZATION OF 16 NOVEL GENETIC VARIANTS IN GENES ASSOCIATED WITH PAEDIATRIC EPILEPSY: IMPLICATIONS FOR TARGETED THERAPEUTIC STRATEGIES
No full textBackground: Childhood epilepsies are caused by heterogeneous underlying disorders where
approximately 40% of the origins of epilepsy can be attributed to genetic factors. The application of
next-generation sequencing has revolutionized molecular diagnostics and has enabled identification
of disease-causing genes and variants in childhood epilepsies.
Methods: In our study, 55 children with epilepsy of unknown etiology were analyzed combining
clinical-exome and whole-exome sequencing.
Results: Molecular genetic cause of epilepsy was identified in 31 patients and the overall diagnostic
success rate was 56%. We identified variants in 23 different genes associated with epilepsy that
correlate well with the observed phenotype. This includes genes such as ASH1L, CILK1, KCNMA1,
RHOBTB2 and SLC13A5, which have only recently been associated with epilepsy. Half (51.6%) of solved
patients carried novel variants. These sixteen novel variants were characterized using various in silico
algorithms including Phyre2, EzMol, Aminode and MutPred2 for structure prediction. Interestingly,
identification of a causative gene directed attention to 15 individuals, including six individuals who
carry entirely novel genetic variants, for whom therapeutic options may be available (ALDH7A1, GRIN1,
KCNQ2, PNPO, SCN1A and SCN2A).
Conclusion: Described novel variants will contribute to better understanding of the European genetic
landscape, while insights on genotype-phenotype correlation will contribute to better understanding
of childhood epilepsies around the globe. Given the expansion of molecular-based approaches, each
newly identified genetic variant could become a potential therapeutic target.32nd Meeting of the European Society of Paediatric Clinical Research (ESPCR) in Opatija, Croatia, May 24-25, 2024
Case report: Rapidly progressive neurocognitive disorder with a fatal outcome in a patient with PU.1 mutated agammaglobulinemia
No full textIntroductionPU.1-mutated agammaglobulinemia (PU.MA) represents a recently described autosomal-dominant form of agammaglobulinemia caused by mutation of the SPI1 gene. This gene codes for PU.1 pioneer transcription factor important for the maturation of monocytes, B lymphocytes, and conventional dendritic cells. Only six cases with PU.MA, presenting with chronic sinopulmonary and systemic enteroviral infections, have been previously described. Accumulating literature evidence suggests a possible relationship between SPI1 mutation, microglial phagocytic dysfunction, and the development of Alzheimer’s disease (AD).Case descriptionWe present a Caucasian female patient born from a non-consanguineous marriage, who was diagnosed with agammaglobulinemia at the age of 15 years when the immunoglobulin replacement therapy was started. During the following seventeen years, she was treated for recurrent respiratory and intestinal infections. At the age of 33 years, the diagnosis of celiac-like disease was established. Five years later progressive cognitive deterioration, unstable gait, speech disturbances, and behavioral changes developed. Comprehensive microbiological investigations were negative, excluding possible infective etiology. Brain MRI, 18FDG-PET-CT, and neuropsychological testing were suggestive for a diagnosis of a frontal variant of AD. Clinical exome sequencing revealed the presence of a novel frameshift heterozygous variant c.441dup in exon 4 of the SPI1 gene. Despite intensive therapy, the patient passed away a few months after the onset of the first neurological symptoms.ConclusionWe describe the first case of PU.MA patient presenting with a rapidly progressive neurocognitive deterioration. The possible role of microglial dysfunction in patients with SPI1 mutation could explain their susceptibility to neurodegenerative diseases thus highlighting the importance of genetic testing in patients with inborn errors of immunity. Since PU.MA represents a newly described form of agammaglobulinemia, our case expands the spectrum of manifestations associated with SPI1 mutation
Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria
No full textPlastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6–7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 – Na + K, Cl – Na + K and OH, Cl – Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer
Višeslojne ugljenične nanocevi kao nosač lipaze za organsku sintezu: pregled najnovijih trendova
Get PDFLipase-catalyzed organic reactions have been widely practiced in the past three decades. Especially interesting are insoluble/immobilized forms due to providing a possibility of facile use and recyclability, thus reducing process costs, and making the procedure more environmentally friendly. Carbon-based supports have been extensively exploited for this purpose, because of neutral and biodegradable nature and thermal and chemical stability. Their high specific surface area, characteristic surface morphology and lower mass transfer resistances play a vital role in the performance of the attached enzyme. This review paper presents an overview of the main aspects of lipase immobilized on multi-walled carbon nanotubes (MWCNTs). Moreover, different immobilization strategies to achieve a biocatalyst with improved performances are discussed. Furthermore, as lipases are considered to have high commercial worth for synthesis of valuable organic molecules, the second part of the paper is dedicated to the overview of the most important industrial sectors in which these nanobiocatalysts have been used. In specific, applications in biodiesel production, flavour ester synthesis and racemization are summarized.Lipaze su poslednjih decenija široko rasprostanjeni katalizatoriu raznovrsnim organskim reakcijama. Posebno su interesantne u imobilisanom/nerastvornom obliku jer je na ovaj način olakšana njihova upotreba uz mogućnost recikliranja i ponovne upotrebe čime se smanjuju troškovi samog procesa i postupak je ekološki prihvatljiviji. Kao nosači za vezivanje nanomaterijali na bazi ugljenika, posebno ugljenične nanocevi, su našli primenu zbog svojih izuzetnih fizičkih, mehaničkih i hemijskih svojstava. Njihova velika specifična površina, karakteristična površinska morfologija i smanjen otpor prenosu mase igraju vitalnu ulogu u performansama vezanog enzima. Ovaj pregledni rad predstavlja prikaz glavnih aspekata lipaze imobilisane na višeslojne ugljenične nanocevi i različitih strategija imobilizacije za dobijanje biokatalizatora sa poboljšanim svojstvima. Takođe, kako su lipaze enzimi od velikog komercijalnog značaja za organsku sintezu i primenu u biotehnologiji, drugi deo rada posvećen je pregledu najvažnijih industrijskih sektora u kojima su ovi nanobiokatalizatori našli primenu. Shodno tome, dat je pregled proizvodnje biodizela, mirisnih estara i racemizacij
Exogenous α-ketoglutarate Modulates Redox Metabolism and Functions of Human Dendritic Cells, Altering Their Capacity to Polarise T Cell Response
Get PDFAlpha-ketoglutarate (αKG) emerged as a key regulator of energetic and redox metabolism in cells, affecting the immune response in various conditions. However, it remained unclear how the exogenous αKG modulates the functions of dendritic cells (DCs), key cells regulating T-cell response. Here we found that non-toxic doses of αKG display anti-inflammatory properties in human APC-T cell interaction models. In a model of monocyte-derived (mo)DCs, αKG impaired the differentiation, and the maturation of moDCs induced with lipopolysaccharide (LPS)/interferon (IFN)-γ, and decreased their capacity to induce Th1 cells. However, αKG also promoted IL-1β secretion by mature moDCs, despite inflammasome downregulation, potentiating their Th17 polarizing capacity. αKG induced the expression of anti-oxidative enzymes and hypoxia-induced factor (HIF)-1α in moDCs, activated Akt/FoxO1 pathway and increased autophagy flux, oxidative phosphorylation (OXPHOS) and glycolysis. This correlated with a higher capacity of immature αKG-moDCs to induce Th2 cells, and conventional regulatory T cells in an indolamine-dioxygenase (IDO)-1-dependent manner. Additionally, αKG increased moDCs’ capacity to induce non-conventional T regulatory (Tr)-1 and IL-10-producing CD8+T cells via up-regulated immunoglobulin-like transcript (ILT3) expression in OXPHOS-dependent manner. These results suggested that exogenous αKG-altered redox metabolism in moDCs contributed to their tolerogenic properties, which could be relevant for designing more efficient therapeutic approaches in DCs-mediated immunotherapies
Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes
Get PDFThe application of enzymes is expanding across diverse industries due to their nontoxic and biodegradable characteristics. Another advantage is their cost-effectiveness, reflected in reduced processing time, water, and energy consumption. Although Gram-positive bacteria, Bacillus, and Streptomyces spp. are successfully used for production of industrially relevant enzymes, they still lag far behind Escherichia coli as hosts for recombinant protein production. Generally, proteins secreted by Bacillus and Streptomyces hosts are released into the culture medium; their native conformation is preserved and easier recovery process enabled. Given the resilience of both hosts in harsh environmental conditions and their spore-forming capability, a deeper understanding and broader use of Bacillus and Streptomyces as expression hosts could significantly enhance the robustness of industrial bioprocesses. This mini-review aims to compare two expression hosts, emphasizing their specific advantages in industrial surroundings such are chemical, detergent, textile, food, animal feed, leather, and paper industries. The homologous sources, heterologous hosts, and molecular tools used for the production of recombinant proteins in these hosts are discussed. The potential to use both hosts as biocatalysts is also evaluated. Undoubtedly, Bacillus and Streptomyces spp. as production hosts possess the potential to take on a more substantial role, providing superior (bio-based) process robustness and flexibility
Plant-Assisted Synthesis of Ag-Based Nanoparticles on Cotton: Antimicrobial and Cytotoxicity Studies
Get PDFThe syntheses of Ag-based nanoparticles (NPs) with the assistance of plant extracts have been shown to be environmentally benign and cost-effective alternatives to conventional chemical syntheses. This study discusses the application of Paliurus spina-christi, Juglans regia, Humulus lupulus, and Sambucus nigra leaf extracts for in situ synthesis of Ag-based NPs on cotton fabric modified with citric acid. The presence of NPs with an average size ranging from 57 to 99 nm on the fiber surface was confirmed by FESEM. XPS analysis indicated that metallic (Ag0) and/or ionic silver (Ag2O and AgO) appeared on the surface of the modified cotton. The chemical composition, size, shape, and amounts of synthesized NPs were strongly dependent on the applied plant extract. All fabricated nanocomposites exhibited excellent antifungal activity against yeast Candida albicans. Antibacterial activity was significantly stronger against Gram-positive bacteria Staphylococcus aureus than Gram-negative bacteria Escherichia coli. In addition, 99% of silver was retained on the samples after 24 h of contact with physiological saline solution, implying a high stability of nanoparticles. Cytotoxic activity towards HaCaT and MRC5 cells was only observed for the sample synthetized in the presence of H. lupulus extract. Excellent antimicrobial activity and non-cytotoxicity make the developed composites efficient candidates for medicinal applications