imagine (Institute of molecular genetics and genetic engineering)
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Deciphering the reward-related impulsivity domains in rats: The big data study of historical control
Get PDFImpulsivity is a lack of ability to control own impulses, and encompasses many subdomains.
The variable-delay-to-signal (VDS) paradigm is behavioral procedure for assessing motor
impulsivity and delay intolerance in rats, but it was unclear whether all parameters
contributed to these domains. Therefore, the aim of this study was to uncover the
relationship between impulsivity parameters in a large cohort.
VDS adapted to a touchscreen environment was used to assess impulsivity in adult
Sprague-Dawley rats. After 1 week of training, animals were tested in a 3-stage testing
protocol. The first stage included 20 trials with 6s inter-trial interval (ITI6si) that suggested
motor impulsivity. The second stage, with 60 randomly distributed trials of ITI9s or 15s,
was interpreted as delay intolerance, whereas for the last stage (ITI6sf), which is similar
to the first stage, it was unclear to which type of impulsivity it was associated. Principal
component analysis (PCA) was used to determine the different behavioral domains. The
results of 132 controls from 11 independent VDS experiments were analyzed. Based on
the cumulative variance explained, scree plot, and eigenvalues, the main components were
extracted whereby varimax rotation was used on factor loadings to extract the components.
PCA with varimax rotation was performed in R studio.
PCA revealed that 96.45% of the variance could be explained by 3 principal components (PCs).
After varimax rotation, loadings for ITI9s and ITI15s were 0.8189 and 0.9419, respectively,
for rotated PC1 (RC1), loading for ITI6sf was 0.9482 for RC2, and loading for 6si was 0.9183
for RC3.
In the VDS paradigm, 3 different impulsivity domains could be determined. In addition to
motor impulsivity and delay intolerance, it is suggested that reflection impulsivity can also
be assessed as learning-based impulsivity.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Different approaches in microRNA analysis
Get PDFMicroRNA might serve as a predictive biomarker for treatment response in stem cell
treatment in knee osteoarthritis. Different sample types are going to be collected to
enlighten the true biological role. MicroRNA analysis necessitates diverse approaches
based on the sample type. In this study, we examined microRNA profiles in plasma
samples, synovial fluid, and adipose-derived fat tissue. We conducted a comparative
analysis of different microRNA analysis methods to assess the data.
The first approach involved a series of steps, including adapter trimming, quality filtering,
size filtering, and mapping of all reads to the human reference genome (GRCh38.p12).
Subsequently, genome-mapped reads were aligned to known miRNA sequences from
miRBase. Reads that did not match miRNAs were subjected to further classification using
additional databases, such as RNAcentral. The second pipeline also encompassed adapter
trimming, quality filtering, and size filtering. Additionally, it involved collapsing individual
reads into repeat sequences, followed by alignment to the mature index of miRBase.
Unaligned reads were classified as isomiRs based on their alignment to the hairpin index
of miRBase.
We processed sequences from three plasma samples, three adipose fat tissue samples,
and three synovial fluid samples. Although there were slight variations in microRNA
read counts, the average ratio between counts was 0.92 (SD=0.29). Notably, the second
pipeline yielded higher read counts compared to the first pipeline.
The results obtained from both microRNA bioinformatic pipelines demonstrated similar
outcomes, suggesting that the choice of pipeline is unlikely to have a significant impact on
the derived biological insights.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Groundwater and soil as a reservoir for polyurethane-degrading bacteria
Get PDFPlastic waste is a global environmental burden. Polyurethanes (PU), toxic and ubiquitous
synthetic polymers, do not biodegrade quickly, leading to their rapid accumulation in the
soil and water environments. Highly efficient PU-degrading microorganisms are rare in
nature and are of fundamental importance for achieving circular plastic economy. Bacterial
isolates from groundwater, originating from magmatogenic massif and Tertiary basin
within metamorphic area, as well as soil isolates collected from various pristine (PS) and
contaminated sites (CS), were screened using PU model compound Impranil® DLN-SD
(IMP) as sole C source to identify PU-degrading isolates. Phylogenetic analysis of 16S rRNA
gene sequences from IMP-degrading isolates was performed using the neighbor-joining
method to observe their clustering. Thirty one of 96 isolates (32.3 %) from groundwater and
18 of 220 isolates (8.2%) from soil produced prominent IMP-clearing zones. Thirteen IMPdegrading
isolates from each type of environment, belonging to 8 genera (Pseudomonas,
Proteus, Enterobacter, Flavobacterium, Serratia, Pantoea, Acinetobacter and Stenotrophomonas)
for groundwater and to 6 genera (Streptomyces, Pseudomonas, Rhodococcus, Achromobacter,
Bacillus and Paenibacillus) for soil environment, were included in phylogenetic analysis. No
clear grouping of groundwater and soil isolates was observed, indicating that isolates are
too distinct. Stronger clustering was observed for groundwater compared to soil isolates. For
groundwater, strongest clustering was observed for 2 isolates belonging to Proteus genus,
2 belonging to Flavobacterium and 2 to Pseudomonas. For soil samples, strongest clustering
was observed for 3 isolates belonging to genus Streptomyces. There was no clear grouping
within isolates from CS and PS. In the future, wider range of environmental niches should be
included in screening efforts for development of biocatalytic processes for management of
plastic waste. Subterranean ecosystems, which are not readily accessible for sampling and
represent largely unexplored reservoir of biotechnologically relevant enzymatic activities,
should also be more represented in such screenings.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia
Get PDFSerbia has one of the world’s highest incidences and mortality rates of ovarian cancer.
Germline or somatic mutations in BRCA1 and BRCA2 genes, such as single nucleotide
variants (SNVs), indels, insertions, deletions, commonly lead to development of breast
and ovary cancer. Targeted therapy with PARP inhibitors is the current standard of care for
serous epithelial BRCA-mutated ovarian cancer and depends on the accurate detection of
mutations in these genes.
In this study, a subset of patient specimens from Institute of Oncology and Radiology
were sequenced on MiSeq Illumina sequencer, raw data were analysed bioinformatically,
which included checking quality control of raw FASTQ sequences, trimming, mapping
them on reference genome(hg19), target coverage quality control and variant calling. We
tested various variant calling tools including Mutect2, GATK HaplotypeCaller, FreeBayes,
VarDict and MuSe callers. We evaluated the relative performance- concordance rate, false
positive and false negative rates between the callers for SNV/indel detection in BRCA1
and BRCA2 genes.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
The past, the present, and the future of RNA secondary structure prediction
Get PDFRNA is a biopolymer whose primary structure is a sequence of nucleobases. While
messenger RNA is probably the most known, an increasing number of non-coding RNAs
is being discovered. In order to become biologically active, ncRNA folds intramolecularly,
thus forming segments of paired bases. This secondary structure largely determines
the function of an ncRNA, so its prediction is important for newly discovered sequences.
Owing to the strong link between the two structural levels, most predictors are datadriven
and sequence-based.
The oldest and simplest algorithm was base pair maximization (BPM), which did not
presume important structural features. Another approach exploited the fact that
biophysics dictates RNA folding, so it searched for the thermodynamically optimal
structure. Statistical learning was the base of the third group, with probabilistic contextfree
grammars (PCFGs) being the most influential. These were the state-of-the-art
methods at the beginning of the century.
However, much has changed in the last years, since technological advancement allowed
the widespread use of machine learning. Its use in the RNA structure prediction ranges from
being the supplementary method (e.g., for estimating thermodynamical and statistical
parameters of traditional methods) to encapsulating the whole prediction process. The
highest success has been reported with transformers, recurrent, and convolutional neural
networks (CNN).
This paper was designed as a review and aimed to compare several methods theoretically
and assess them practically. As expected, model complexity was highly correlated with
accuracy. On the subset of simply structured transfer RNA, for example, BPM predicted
~22% of pairings correctly, PCFG ~86%, and CNN ~99%. Other subsets, such as 16S
ribosomal RNA, were more challenging, but deep learning always performed best. With
the continued growth of computational power and the amount of annotated data,
prediction accuracy is expected to get even closer to the experimental determination,
while still maintaining a much lower cost.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Bioisosteric ferrocenyl 1,3-thiazolidine-4-carboxylic acid derivatives: In vitro antiproliferative and antimicrobial evaluations
No full textTo improve the antiproliferative effect of ALC67 (diastereomeric mixture of ethyl 2-phenyl-3-propioloyl-1,3-thiazolidine-4-carboxylate), its structure was modified via (i) bioisosteric substitution of the phenyl ring by the ferrocene unit and (ii) replacing the propiolamide side-chain in ACL67 with other acyl groups having differing electrophilicities. In this way, a small library of methyl N-acyl-2-ferrocenyl-1,3-thiazolidine-4-carboxylates (13 compounds in total) was created and characterized by spectral and crystallographic means. The last N-acylation step was highly diastereoselective toward the cis-diastereomer. In solution, most of the obtained compounds existed as a mixture of two rotamers and displayed a preference for the syn-orientation around the CN bond. A twisted 5T4 envelope conformation was adopted by the derivative containing the N-phenoxyacetyl group in the crystalline state. Two derivatives with chloroacetyl and bromoacetyl groups in the N-3 side chain were cytotoxic to fibroblasts and hepatocellular cancer cells in the low micromolar range (IC50(MRC5) = 9.0 and 11.8 μM, respectively, and IC50(HepG2) = 10.6 and 18.4 μM, respectively) causing an effect similar to the lead compound (IC50(HepG2) = 10.0 μM) and cisplatin (IC50(MRC5) = 4.0 μM and IC50(HepG2) = 7.7 μM). Several derivatives also manifested modest antimicrobial effects against the studied microbial strains (MICs in the range from 0.44 to 4.0 μmol/mL). Our findings demonstrated that the introduction of a ferrocene core facilitated the preparation of optically pure analogs of ALC67 and that the cytotoxicity of compounds may be enhanced by adding proper electrophilic centers to the N-acyl side-chain
PB2260: Five-year single-center experience in the treatment of advanced stage classical Hodgkin lymphoma with ABVD
No full textBackground:
Advanced stage (AS) classical Hodgkin lymphoma (cHL) carries significant risk of refractoriness to the traditional
therapeutic options.
Aims:
To describe 5-year experience (2016-2020) of Clinic for Hematology, University Clinical Center of Serbia in the
treatment of AS cHL with ABVD.
Methods:
We retrospectively analyzed medical records of 49 patients (pts) who fulfilled criteria for diagnosis of AS cHL
according to GHSG. Clinical parameters at diagnosis were collected and correlated with outcome.
Results:
Median (m) follow up was 47 months (range [r]: 1-79). Median age at diagnosis was 34 years (r: 18-74) with male
to female ratio 1.6:1. The most frequent subtype was nodular sclerosis- 73.8%. According to EORTC/LYSA 7
(14.3%) pts were intermediate stage, the rest of 42 (85.7%) pts were AS. Seven (14.3%) pts were Ann Arbor stage
II, 26 (53%) pts III, and 16 (32.7%) pts IV. B symptoms were present in 38 (77.6%) pts, and bulky disease ≥7cm in
58% of pts (mostly mediastinal). 34.8% of pts presented with extranodal disease (EN). Low IPS was calculated in
19/35 pts (54.3%), and high IPS in 16/35 pts (45.7%).
All pts were treated with ABVD in the first line. Among 12 pts who underwent interim PET/CT, 3 pts were
escalated to BEACOPPesc, while 3 pts deescalated to AVD. Median number of cycles administered was 6 (range 3-
8). 10/45 pts (22%) received adjuvant radiotherapy (RT). Overall response rate was 72.3% (CR 61.7% + PR
10.6%), while the rest 27.7% of pts were refractory. There was no significant difference in treatment response
regarding age (<50y vs ≥50y), Stage, presence of B symptoms, EN, risk by IPS, and adjuvant RT. Median
progression-free (PFS) and overall survival (OS) were not reached (NR), while 4-year PFS and OS were 61%, and
89%, respectively. Pts with erythrocyte sedimentation rate (ESR) >50mm/h experienced significantly shorter PFS
after first therapeutic line (mPFS 19 months vs. NR; p=0.039, Log-Rank test). Sex, age, stage, B symptoms, END,
IPS and adjuvant RT did not make significant difference in PFS in our cohort. Primary refractory patients lived
significantly shorter than those who achieved CR/PR after first treatment line (mOS 54 months vs. NR; p=0.004,
Log-Rank test). Also, pts had significantly shorter OS if presented with bulky disease (≥7 cm) (p=0.044, Log-Rank
test). There was no significant difference in OS regarding sex, age, stage, B symptoms, END, IPS, and adjuvant RT
after first treatment line.
Among 18 relapsed (13)/refractory (5) (R/R) pts, 17 were treated with high dose chemotherapy (HDC) ±
autologous stem cell transplantation (ASCT). Patients who received ASCT after HDC experienced significantly
better response (p=0.05, Fisher exact test), and longer PFS (mPFS 14 months vs. 2 months, p=0.02, Long-Rank test) than those without ASCT, however, without significant difference in OS. Fourteen R/R pts were treated with
Brentuximab vedotin (BV), 3 pts in consolidation after ASCT (all in CR after BV), and the other 11 pts after
median of 3 previous treatment lines (range 2-4) (only 1 patient in CR, one still on BV, and the other 9 pts
refractory).
Summary/Conclusion:
Patients in our cohort experienced shorter PFS if presented with higher ESR, while bulky mass and primary R/R
disease were predictors of shorter OS. Patients with R/R cHL had significantly better prognosis if underwent
consolidation with ASCT. BV monotherapy was not benefitial in pretreated pts. A significant proportion of AS cHL
pts can not be cured with ABVD and require more intensive and/or novel first line treatment options.Book of abstract: 28th Congress of the European Hematology Association EHA2023 Annual Congress Edition June 2023PB226
Insight into the Postbiotic Potential of the Autochthonous Bacteriocin-Producing Enterococcus faecium BGZLM1-5 in the Reduction in the Abundance of Listeria monocytogenes ATCC19111 in a Milk Model
Get PDFThis study aimed to explore the probiogenomic characteristics of artisanal bacteriocin-producing Enterococcus faecium BGZLM1-5 and its potential application in reducing Listeria monocytogenes in a milk model. The BGZLM1-5 strain was isolated from raw cow’s milk from households in the Zlatar Mountain region. The whole genome sequencing approach and bioinformatics analyses reveal that the strain BGZLM1-5 is non-pathogenic to humans. Bacteriocin-containing supernatant was thermally stable and antimicrobial activity retained 75% of the initial activity compared with that of the control after treatment at 90 °C for 30 min. Antimicrobial activity maintained relative stability at pH 3–11 and retained 62.5% of the initial activity compared with that of the control after treatment at pH 1, 2, and 12. The highest activity of the partially purified bacteriocin was obtained after precipitation at 40% saturation with ammonium sulfate and further purification by mixing with chloroform. Applying 3% and 5% (v/v) of the bacteriocin-containing supernatant and 0.5% (v/v) of the partially purified bacteriocin decreased the viable number of L. monocytogenes ATCC19111 after three days of milk storage by 23.5%, 63.5%, and 58.9%, respectively
Triggering and identifying the polyurethane and polyethylene-degrading machinery of filamentous fungi secretomes
No full textThe uncontrollable disposal of plastic waste has raised the concern of the scientific community, which tries to face this environmental burden by discovering and applying new techniques. Regarding the biotechnology field, several important microorganisms possessing the necessary enzymatic arsenal to utilize recalcitrant synthetic polymers as an energy source have been discovered. In the present study, we screened various fungi for their ability to degrade intact polymers, such as ether-based polyurethane (PU) and low-density polyethylene (LDPE). For this, ImpranIil® DLN-SD and a mixture of long-chain alkanes were used as sole carbon sources, indicating not only the most promising strains in agar plate screening but also inducing the secretion of depolymerizing enzymatic activities, useful for polymer degradation. The agar plate screening revealed three fungal strains belonging to Fusarium and Aspergillus genera, whose secretome was further studied for its ability to degrade the aforementioned non-treated polymers. Specifically for ether-based PU, the secretome of a Fusarium species reduced the sample mass and the average molecular weight of the polymer by 24.5 and 20.4%, respectively, while the secretome of an Aspergillus species caused changes in the molecular structure of LDPE, as evidenced by FTIR. The proteomics analysis revealed that the enzymatic activities induced in presence of Impranil® DLN-SD can be associated with urethane bond cleavage, a fact which was also supported by the observed degradation of the ether-based PU. Although, the mechanism of LDPE degradation was not completely elucidated, the presence of oxidative enzymes could be the main factor contributing to polymer modification.The authors would like to thank the VIB Proteomics Core for the contribution regarding the mass spectrometry-based proteomics experiments (EPIC-XS, project number 823839, funded by the Horizon 2020 programme of the European Union).This is the peer reviewed version of the paper: Taxeidis, G., Nikolaivits, E., Siaperas, R., Gkountela, C., Vouyiouka, S., Pantelić, B., Nikodinović-Runić, J., & Topakas, E. (2023). Triggering and identifying the polyurethane and polyethylene-degrading machinery of filamentous fungi secretomes. Environmental Pollution, 325, 121460.[ https://doi.org/10.1016/j.envpol.2023.121460]Related to published version: [https://imagine.imgge.bg.ac.rs/handle/123456789/1797]Related to other materials: [https://zenodo.org/record/7767083#.ZCP8WXZBxPa
Expression levels of BCL2, BAX and MDR1 as pharmacotranscriptomic and prognostic markers of prognosis in acute myeloid leukemia
Get PDFAcute myeloid leukemia (AML) is a malignancy of hematopoetic tissue which occurs due to a halt in
differentiation, loss of proliferation control and dysregulated apoptosis of myeloid progenitor cells. In
many cancers, as well as AML, dysregulation of apoptosis constitutes the basis of pathogenesis and this
phenomenon is important for chemotherapy success. Pharmacotranscriptomic markers of AML
prognosis could be targets of specific therapy. The anti-apoptotic gene BCL2 (B-cell lymphoma protein
2), the pro-apoptotic BAX (BCL2-associated X) and genes involved in drug resistance, like MDR1
could have a significant impact on AML prognosis and therapy response. Bone-marrow samples at
diagnosis were collected from 51 adult patients with AML-NK. Expressions of BCL2, BAX and MDR1
were analysed using the real-time polymerase chain reaction method. Statistical evaluation was
performed. The presence of chemoresistance was found to be associated with overexpression of BCL2
(BCL2+) (p=0.018), while underexpression of BAX in patients has shown a greater affinity towards
relapse (p=0.034). Evaluating the expressions of BCL2 and BAX in a combined effect has shown that
87% of patients with BAX/BCL2low status were resistant to therapy (p=0.024). BCL2+ status was
associated with high expression of MDR1 (p<0.001). Likewise, high expression of MDR1 was
associated with the absence of NPM1 and FLT3-ITD mutations (p=0.048 and p=0.010, respectively).
This is the first study that focused only on AML-NK patients, when it comes to analysis of BCL2, BAX
and MDR1 gene expression profiles. The results of this preliminary study have shown that high BCL2
expression would likely lead to resistance from chemotherapy, making anti-BCL2 treatment a viable
option in patients with this expression profile. A study on a larger group of patients could clarify the
prognostic importance of the studied genes in adult AML-NK patients and improve the precision
medicine approach in the field of hematology.Book of abstracts: International Conference of Biochemists and Molecular Biologists in Bosnia and Herzegovina - ABMBBIH May, 202