imagine (Institute of molecular genetics and genetic engineering)
Not a member yet
3088 research outputs found
Sort by
Uticaj različitih uslova čuvanja uzoraka i kontaminacije uzoraka bakterijama na koncentracije rutinskih biohemijskih parametara
No full textBackground: The pre-analytical (PA) phase is the most vulnerable phase of the laboratory testing procedure, with critical procedures-collection, handling, sample transport, and time and temperature of sample storage. This study aimed to examine the stability of basic biochemical parameters depending on the samples' storage conditions and the number of freeze-thaw cycles (FTCs). In parallel, the presence of sample bacterial contamination during routine laboratory work was examined. Methods: Two plasma pools (ethylenediaminetetraacetic acid (EDTA), and sodium-fluoride/potassium oxalate plasma (NaF)) were stored at +4 ˚C/-20 ˚C. Total chole - sterol (TC), glucose, triglycerides (TG), urea, and albumin concentrations were measured using BioSystems reagents (cholesterol oxidase/peroxidase, glucose oxidase/per - oxidase, glycerol phosphate oxidase/peroxidase, urease/ salicylate, and bromcresol green method, respectively) on Ilab 300+. Sample bacterial contamination was determined by 16S rRNA sequence analysis. The expe - riment encompassed a 5 day-period: Day 1-fresh sample, Day 2-1st FTC, Day 3-2nd FTC, Day 4-3rd FTC, Day 5-4th FTC. The appearance of bacteria in two consecutive samples was the experiment's endpoint. Results: During 4 FTCs, there were no changes in plasma urea concentrations. Glucose was stable in EDTA +4 ˚C and NaF -20 ˚C until the 3rd FTC (P=0.008, P=0.042, respectively). TG concentrations changed significantly in the EDTA -20 ˚C sample after 1st and 4th FTCs (P=0.022, P=0.010, respectively). In NaF samples, no bacterial contamination was observed during 4 FTCs. Conclusion: Urea and glucose concentrations were robust. Changes in lipid concentrations after FTCs follow complex patterns. Bacterial growth was not observed in NaF plasma samples. This can promote NaF use in analytical procedures in which bacterial contamination affects the quality of analysis.Uvod: Preanalitička (PA) faza je složen proces koji čine: prikupljanje, rukovanje, transport i skladištenje uzoraka, i predstavlja najznačajniji izvor laboratorijskih grešaka. Cilj ovog istraživanja je bio da se ispita stabilnost osnovnih biohemijskih parametara u zavisnosti od uslova skladištenja uzoraka i broja ciklusa zamrzavanja-odmrzavanja (FTC). Pored toga, ispitivano je prisustvo bakterijske kontaminacije uzoraka tokom rutinskog laboratorijskog rada. Metode: Dva "pool"-a plazme (etilendiaminotetrasirćetna kiselina (EDTA) i natrijum-fluorid/kalijum oksalat (NaF)) su skladištena na +4 ˚C/-20 ˚C. Koncentracije ukupnog hole sterola (TC), glukoze, triglicerida (TG), uree i albumina su određene korišćenjem BioSystems reagenasa (holesterol oksi daza/peroksidaza, glukoza oksidaza/peroksidaza, glice rol fosfat oksidaza/peroksidaza, ureaza/salicilat, od - nosno bromkrezol zeleno metodama, sukcesivno) na Ilab 300+ analizatoru. Bakterijska kontaminacija uzoraka je potvrđena 16S rRNA sekvencioniranjem. Eksperiment je sproveden tokom 5 uzastopnih dana: 1. dan - svež uzorak, 2. dan - 1. FTC, 3. dan -2. FTC, 4. dan - 3. FTC, 5. dan - 4. FTC. Završnu tačku eksperimenta predstavljala je pojava bakterija u dva uzastopna uzorka. Rezultati: Tokom 4 FTC koncentracije uree u plazmi se nisu značajno razlikovale. Koncentracija glukoze je bila stabilna u EDTA +4 ˚C i NaF -20 ˚C do 3.FTC (P=0,008, P=0,042, redom). Koncentracije TG su se značajno pro - menile u uzorku EDTA -20 ˚C nakon 1. i 4. FTC-a (P=0,022, P=0,010, redom). U uzorcima NaF plazme nije došlo do bakterijske kontaminacije tokom 4. FTC. Zaključak: Koncentracije uree i glukoze su bile stabilne tokom trajanja eksperimenta. Promene u koncentracijama lipida nakon FTC prate složene obrasce. Rast bakterija nije primećen u uzorcima NaF plazme, te upotreba ovog anti-koagulansa može biti opravdana u analitičkim procedurama podložnim uticaju mikrobiološke kontaminacije
Unveiling Anticancer Potential of COX-2 and 5-LOX Inhibitors: Cytotoxicity, Radiosensitization Potential and Antimigratory Activity against Colorectal and Pancreatic Carcinoma
No full textApart from cytotoxicity, inhibitors of the COX-2 enzyme have demonstrated additional effects important for cancer treatment (such as radiosensitization of tumor cells and cell antimigratory effects); however, the relationship between the inhibition of other inflammation-related enzyme 5-LOX inhibitors and anticancer activity is still not well understood. In our study, the cytotoxicity of thirteen COX-2 and 5-LOX inhibitors previously presented by our group (1–13) was tested on three cancer cell lines (HCT 116, HT-29 and BxPC-3) and one healthy cell line (MRC-5). Compounds 3, 5, 6 and 7 showed moderate cytotoxicity, but good selectivity towards cancer cell lines. IC50 values were in the range of 22.99–51.66 µM (HCT 116 cell line), 8.63–41.20 µM (BxPC-3 cell line) and 24.78–81.60 µM (HT-29 cell line; compound 7 > 100 µM). In comparison to tested, commercially available COX-2 and 5-LOX inhibitors, both cytotoxicity and selectivity were increased. The addition of compounds 6 and 7 to irradiation treatment showed the most significant decrease in cell proliferation of the HT-29 cell line (p < 0.001). The antimigratory potential of the best dual COX-2 and 5-LOX inhibitors (compounds 1, 2, 3 and 5) was tested by a wound-healing assay using the SW620 cell line. Compounds 1 and 3 were singled out as compounds with the most potent effect (relative wound closure was 3.20% (24 h), 5,08% (48 h) for compound 1 and 3.86% (24 h), 7.68% (48 h) for compound 3). Considering all these results, compound 3 stood out as the compound with the most optimal biological activity, with the best dual COX-2 and 5-LOX inhibitory activity, good selectivity towards tested cancer cell lines, significant cell antimigratory potential and a lack of toxic effects at therapeutic doses
Comparison of the ABC and ACMG systems for variant classification
No full textThe ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as “maybe report” after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known
Association of variants in AGTR1, ACE, MTHFR genes with microalbuminuria and risk factors for the onset of diabetic nephropathy in adolescents with type 1 diabetes in the population of Serbia
No full textIntroduction Genetic studies may provide valuable information about patients who are at high risk of developing diabetes nephropathy. Before the appearance of albuminuria, there are genetic mutations that can predispose the development of kidney disease. Material and methods The study included 130 adolescents with type 1 diabetes. Patients were divided into two groups according to the presence of microalbuminuria. This study was performed to examine clinical and laboratory differences between adolescents with type 1 diabetes with and without microalbuminuria and the distribution of the ACE, AGTR1, and MTHFR gene polymorphisms. Results The mean microalbuminuria in the first group 6.41±7.35 significantly differs from the second group 0.82±0.48 (p<0.001). HbA1c, 24-hour proteinuria, and day-time systolic blood pressure were significantly higher in the MA group (p<0.05). Smaller systolic blood pressure percentage nocturnal decline was observed in the microalbuminuric group (p 0.030). The frequencies of the ACE DD, ID, and II genotypes were 12.5%, 50.0%, and 37.5%, respectively, among T1D patients with MA, and 19.3%, 56.1%, 24.6%, in the control group without MA (P = .510). The frequencies of the AGTR1 AA, AC, and CC genotypes were 62.5%, 25.0%, and 12.5% among TID patients with MA, and 49.1%, 43.9%, 8.0%, in the group without MA (p 0.326). The frequencies of the MTHFR CC, CT and TT genotypes were 37.5%, 50.0%, 12.5% among TID patients with MA, and 37.7%, 45.6%, 16.7% in the group without MA (p 0.901). Conclusion Our data suggest that common variants in the AGTR1, ACE, and MTHFR genes are not strongly associated with diabetic nephropathy in our patients with type 1 diabetes
NEW TERT VARIANT IN A FAMILY WITH APLASTIC ANEMIA
No full textTERT gene, the most frequently mutated gene in patients with telomere biology disorders
(telomeropathies), encode telomerase reverse transcriptase enzyme. Heterozygous variants in the TERT
gene impair telomerase activity by haploinsufficiency and pathogenic variants are associated with bone
marrow failure syndrome and acute myeloid leukemia predisposition. TERT variants show incomplete
penetrance and can also be found in asymptomatic family members. Due to the rarity of the disease and
the small number of clinical trials, telomeropathies are often unrecognized and misdiagnosed. To report
a novel variant in TERT gene in familial hematopoetic disorder. Methodology: Next Generation
Sequencing of DNA isolated from peripheral blood of a patient (older sister) with clinical diagnosis of
aplastic anemia, using TruSight One MiSeq platform (Illumina®) and segregation sequencing analysis
of patient’s mother and younger sister. We identified a novel missense heterozygous variant
c.2605G>A p.(Asp869Asn) in TERT gene in a family of mother and two daughters. This variant
results in replacement of aspartic amino acid on 869 position in TERT enzyme polypeptide chain by
asparagine. It is located in highly conserved protein region and is very likely to disrupt the function of
the enzyme. According to ACMG classification, detected variant is characterized as likely pathogenic,
class 2. As patients with telomeropathies often have a history of macrocytosis and thrombocytopenia,
often wrongly diagnosed as immune-mediated thrombocytopenia, myelodysplastic syndrome or aplastic
anemia, our findings indicate that TERT rare variants pass under-recognized in these patients. For that
reason, our findings point out the importance for routine deep genetics screening for TERT rare variants
in patients with family history of different bone marrow failure syndromes. Which could identify
clinically inapparent telomere biology disorder and improve outcomes through forehand diagnosis
setting, genetic counseling and the precise therapy consideration.Book of abstracts: 2nd B&H Symposium of Laboratory Geneticists and Molecular Biologists (with International Participation) May, 202
What do amyloidosis, antimicrobial peptides, and the Spike RBD of SARS-CoV-2 have in common
No full textSome proteins and peptides are known to have antimicrobial and amyloidogenic
properties. Understanding the mechanism of aggregation can be used to combat bacterial
and viral diseases.
Using modern data on the process of formation of amyloid structures, we have developed
and successfully tested amyloidogenic antimicrobial peptides (AAMPs) with a new
mechanism of antimicrobial action - “protein knockout”. This mechanism is based on
the principle of directed coaggregation of AAMP and bacterial ribosomal protein S1. The
innovative peptide interacts with the target protein of model or pathogenic bacteria,
forming aggregates and removing this protein, which is essential for the life of the bacteria,
from its working state. During the work, the antimicrobial effects of the developed peptides
were examined on two model organisms (Thermus thermophilus and Escherichia coli) and
two pathogenic microorganisms (Staphylococcus aureus and Pseudomonas aeruginosa).
Since the emergence of the original variant in Wuhan in 2019, many different variants
of SARS-CoV-2 have been described and characterized, varying in transmissibility and
pathogenicity in the human population, although the molecular basis of this difference
remains controversial. Thus, the Omicron variant is known for its contagiousness, transmissibility,
and lower pathogenicity (mortality). A significant role in this is played by amino
acid substitutions on the surface of the Spike protein, which interact with the ACE2
receptor, which can facilitate the penetration of the virus into the cell or help it to evade
the immune response. Mutations in this strain result in increased amyloidogenicity of
the Omicron strain in the ACE2 receptor binding regions, resulting in an increase in the
strength of this interaction for the Omicron BA.1 RBD compared to the Wuhan-Hu-1 or
Delta RBD, and this effect was more pronounced at pH 5. This result is associated with
Omicron variants’ increased ability to spread through the population.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Sleep Apnea Monitoring using Wearable Heart Rate Sensors
No full textSleep apnea is a serious sleep disorder characterized by intermittent stopping and
starting of breathing during sleep. It affects approximately 20% of adults globally.
Notably, approximately 85% of individuals with moderate to severe sleep apnea remain
undiagnosed. Possible complications of sleep apnea include fatigue, high blood pressure,
and increased risk of cardiovascular disease. Uncontrolled sleep apnea increases risk or
worsens the prognosis of type 2 diabetes, metabolic syndrome, and liver problems.
Sleep apnea diagnosis uses polysomnography (PSG), a monitoring system that records
multiple physiological parameters including heart rate, ECG, and oxygen levels during
sleep. Although simplified home tests are available, they require multiple concurrent
measurements and post-analysis by medical professionals, making them unsuitable
for routine home monitoring. The average cost of a sleep apnea test in the USA is
approximately $1,100 per test.
We introduce a novel system that utilizes heart rate data from wearable sensors for the
monitoring and assessment of sleep apnea suitable for home-based healthcare. Our
system utilizes advanced machine learning algorithms to analyze overnight heart rate
data collected by wearable sensors. Data analysis is performed using edge computing
device. The monitoring system segments the data, employs density maps for feature
extraction, deploys machine learning, and assesses the presence and severity of sleep
apnea. Finaly, a detailed, clinically relevant report is generated by the system.
The testing of our sleep apnea monitoring system indicates that the accuracy is
approximately 90%. Misclassification of existing sleep apnea occurred in patients that have
very low heart rate variation. Home-based monitoring systems for sleep apnea can help
improve correct diagnosis in affected population and reduce the number of unnecessary
tests. Furthermore, the progression of diagnosed sleep apnea can be monitored using a
single heart rate sensor.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Bioinformatics tools for reconstruction of gene networks of complex diseases
No full textdemanding data integration. Despite the existing wide range of computer programs, their
adaptation is necessary for clinical data analysis. The adaptation assumes preparation of
tutorials, textbooks and training materials for students, interns, and workers of medical
institutions without mathematical or computer science background. Such tutorials should
be based on available online bioinformatics tools. Here we discuss a scientific project for
the study of complex diseases in which it is difficult to identify genetic components, such
as cancers, mental disorders, schizophrenia, and Parkinson’s disease.
The available software tools have been collected, a data processing pipeline for creating a
list of genes associated with given complex disease has been prepared. The list of genes
could be compiled based on queries to GEO NCBI (RefSeq), the OMIM (Online Mendelian
Inheritance in Man), GeneCards, and MalaCards databases. Then such a list of genes could
be refined using other data, such as data on the differential expression of genes (GEO
Dataset Browser resource), including non-coding RNAs (from the TCGA database), and
information from published papers. The gene ontologies analysis could be performed
using open resources for bioinformatic analysis: PANTHER (http://pantherdb.org) and
DAVID (https://davidbioinformatics.nih.gov), the g:GOSt resource for visualization of gene
ontologies (http://biit.cs.ut.ee/gprofiler/gost).
Next set of tools for gene targets search is related to gene expression. The computer study
of sequencing data is based on the integration of available sequencing data (RNA-seq and
ChIP-seq) and computer resources: ArrayExpress, TCGA, CCGA, ENCODE (ENCyclopedia
Of DNA Elements), as well as local computer resources ANDSystem, TRRD, GeneNet
(wwwmgs.bionet.nsc.ru) and ICGenomics (https://www-bionet.sscc.ru/icgenomics/).
As the main examples of applications, the tasks of analyzing brain tumors are considered –
for glioma, meningioma, with the study of complications associated with virus infections,
including available data published after the coronavirus pandemic. As applications we
consider computer reconstruction of gene networks for a number of oncological diseases
- glioma, breast cancer, colorectal cancer, and a number of mental disorders such as
Parkinson’s disease.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
De novo genome sequencing for endangered bird of prey species
No full textThe Eastern Imperial Eagle (Aquila heliaca) is a large migratory bird of prey, with breeding
sites spanning from eastern Czechia and Austria to Northwestern China and Mongolia.
Due to the decline of its populations throughout its area of distribution, the IUCN Red
List categorized species as vulnerable. Thus, it has become a subject of numerous
conservation efforts. To develop effective conservation strategies, it is crucial to have a
comprehensive understanding of the genetic variability of these populations. Establishing
a reference genome serves as a cornerstone for conservationists, offering a starting tool
to assess population dynamics, adaptive potential and evolutionary history with further
analyses. Therefore, we performed the whole genome sequencing of A. heliaca.
The genome sequencing of a male A. heliaca was conducted using Illumina paired-end
150bp short reads, and de novo assembly was conducted as there is no reference genome
available. After the use of paired-end information for scaffolding the assembly remained
very fragmented, with the genome being represented with hundreds of thousands of
contigs, primarily due to the inherent limitations of short-read sequencing in resolving
repetitive regions and regions with strong nucleotide composition bias. To enhance
scaffolding, we used a chromosome-level assembly of a closely related species, Aquila
chrysaetos, available in the GenBank. BLAST analysis revealed high sequence similarity
(~94%) between sequences from our assembly compared to the A. chrysaetos reference
genome. The absence of major rearrangements or inversions in the selected contigs
supported the usage of the A. chrysaetos reference genome for scaffolding. Thus, we
generated a chromosome-level assembly for A. heliaca, encompassing 26 autosomes and
the Z sex chromosome. Even though our assembly contained a few thousand unplaced
scaffolds ranging in size from over 700Kb to very small fragments, the vast majority
(>98%) of the assembly was assigned to 27 chromosomal-level scaffolds. The assembly
demonstrated a completeness score of 97.2% according to the BUSCO assessment.Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024
Personality and COMT gene: molecular-genetic and epigenetic associations with NEO-PI-R personality domains and facets in monozygotic twins
No full textBackgroundThis study investigates the relationship between MB-COMT DNA methylation (DNAm) and the personality traits outlined in the NEO-PI-R model through an epigenetic study of monozygotic twins. DNAm, a critical epigenetic mechanism, regulates gene expression and has been linked to various biological processes and disorders. By leveraging the genetic similarities of monozygotic twins, this research explores how epigenetic variations influenced by environmental factors correlate with personality differences.MethodsThe study utilized the Five-Factor Model (FFM) to categorize personality traits into five domains: Neuroticism, Extraversion, Conscientiousness, Agreeableness, and Openness to Experience. Each domain comprises six facets, providing a granular view of personality. The research centered on the catechol-O-methyltransferase (COMT) gene, focusing on its role in dopamine metabolism, which is hypothesized to influence personality traits through the dopaminergic system. DNAm status in the MB-COMT promoter region was examined to determine its association with personality facets.ResultsPreliminary findings suggest a complex interaction between MB-COMT DNAm patterns and personality traits. Specific methylation patterns at different CpG sites were linked to varying expressions of traits such as impulsivity and aggression, highlighting the nuanced impact of epigenetics on personality.ConclusionThis study underscores the potential of integrating genetic, epigenetic, and environmental data to enhance our understanding of personality formation. The results contribute to a broader understanding of how genetic predispositions shaped by environmental factors manifest in complex trait differences, paving the way for future research in genetic psychiatry and personalized medicine