imagine (Institute of molecular genetics and genetic engineering)
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Structural characterization and antitumor activity of platinum(II) complexes with phenothiazine and N-methylphenothiazine
Get PDFCisplatin is one of the most used anticancer agents, and along with carboplatin and
oxaliplatin, is a part of more than 50% of clinically applied anticancer regimens [1]. However,
the side effects of cisplatin are severe and include dose-limiting toxicity, such as neurotoxicity,
nephrotoxicity and ototoxicity. Platinum(II) complexes with different structure from cisplatin
provide many opportunities for design of novel antitumor drugs with improved
pharmacological properties. Considering this, in the present study, new platinum(II) complexes
with phenothiazine (phtz) and N-methylphenothiazine (N-Mephtz), [PtCl2(phtz)(CH3CN)] (1)
and [PtCl2(N-Mephtz)(CH3CN)] (2), were synthesized. These complexes were characterized by
elemental microanalysis, NMR (1H and 13C) and IR spectroscopic measurements, while the
structure of complex 1 was determined by single-crystal X-ray diffraction analysis. The
antitumor activity of the platinum(II) complexes was tested in vitro against a panel of human
cancer cell lines, including A549 (lung cancer), A375 (melanoma, skin cancer), MDA-MB-231
(breast cancer), and HCT116 (colon cancer). To check the selectivity of the synthesized
complexes 1 and 2, a healthy MRC-5 cell line (lung fibroblasts) was also included in this study.Book of abstract:16th International Symposium
on Applied Bioinorganic Chemistry
(16-ISABC)
11-14th June
University of Ioannina
Greec
DNA/BSA interactions and biological activity of prodigiosin and its copper(II) complex
Get PDFProdigiosin (PG) is a red biopigment produced as a secondary metabolite by
microorganisms such as Serratia marcescens and Streptomyces. In recent years, this tripyrrole
compound has attracted an increasing attention due to its antibacterial, antimalarial, and
immunosuppressive activities [1]. It is also known for its antitumor activity, inducing the cell
death by apoptosis in different human cancer cell lines [2]. Considering this, in the present
study, we investigated the interactions of prodigiosin and its copper(II) complex (CuPG; the
structural formula is presented below), whose crystal structure was determined previously [2],
with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) by fluorescence emission
spectroscopy to clarify their binding affinities toward these biomolecules. The antimicrobial
activity of the synthesized CuPG complex and PG ligand was evaluated in vitro against various
microorganisms that can lead to many infections. Moreover, CuPG and PG were evaluated in
a cell viability assay on a healthy MRC-5 cell line, as well as a panel of MDA-MB-231, A549,
A375, and HCT116 cancer cell lines.Book of abstract:16th International Symposium on Applied Bioinorganic Chemistry (16-ISABC) 11-14th June University of Ioannina Greec
Pathway analysis of CD8+ T cell transcriptome in glioblastoma patients reveales multiple sclerosis signaling pathway as the top rated upregulated disease pathway in tumor infiltrating cells
Get PDFThe significance of CD8+ T cell central nervous system migration and activation in the
progression of glioblastoma is well documented. However, molecular signaling pathways
regulation related to migration and activation in CD8+ cells in glioblastoma is scarce.
Therefore we have analyzed the molecular pathway regulation in differentially expressed
mRNAs of tumor infiltrating vs. peripheral blood CD8+ T cells from glioblastoma patients.
Tumor-infiltrating vs. peripheral blood differentially expressed mRNAs were obtained
by analyzing the FASTAQ files on the Galaxy platform using the LimmaVoom tool with
filtering low count mRNAs (CPM > 2). We used publically avaliable FASTAQ files with CD8+
T cells mRNA sequencing data deposited at NCBI’s GEO database (accession number
GSE171197). The differentially expressed mRNA were analyzed with Qiagen’s Ingenuity
pathway analysis (p adj. cutoff 0.05). Protein-protein interaction network was constructed
on the NetworkAnalyst platform using the IMeX database with minimal order parameters.
The top rated disease canonical pathway was the multiple sclerosis (MS) signaling
pathway, with 18 differentially expressed mRNA hits (out of possible 222), p adj. = 0.0009
and Z score = 2.828, implying significant upregulation of this pathway in tumor-infiltrating
CD8+ T cells.
The MS signaling pathway describes the molecular cascade which leads to the autoimmune
phenotype in lymphocytes, including activation and central nervous tissue infiltration. To
further specify the aspects of the canonical MS signaling pathway which might influence
tumor infiltrating phenotype we have constructed a minimal order protein-protein
interaction network. Results showed a number of lymphocyte migration and activation
KEGG terms within the network, such as: TNF signaling pathway (p adj. = 0.0000115),
IL-17 signaling pathway (p adj. = 0.00000427), sphingolipid signaling pathway (p adj. =
0.00171), NF-kappa B signaling pathway (p adj. = 0.0000694) and TCR signaling pathway
(p adj. = 0.0071).
We conclude that MS signaling pathway is an viable model for further understanding of
the transcriptional phenotype of glioblastoma infiltrating CD8+ T killer cells, illustrating
that same migration and activation mechanisms which mediate brain autoimmunity are
essential for brain antitumor adaptive immunity.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Protein structural differences in Cytochrome c oxidase subunit 1 of two Heterogynis species as a new approach for species delimitation
Get PDFInsects are the most diverse group in the animal kingdom, accounting for about two-thirds
of all animals. Cytochrome c oxidase subunit 1 (COI) is the most commonly used marker
gene for animal species delineation. However, the accuracy of this approach crucially
depends on the degree of overlap between the intra- and interspecific variations.
Recently, we have identified a new species, Heterogynis serbica sp. n. (Lepidoptera:
Zygaenoidea, Heterogynidae) found on the Mt. Kopaonik, Republic of Serbia, Balkan
Peninsula. This was done by integrating taxonomic approach using morpho-anatomical
characteristics by comparative scanning electron microscopy (SEM), linear wing
morphometry and COI-based DNA barcoding [1]. In this study, we have used a set of
bioinformatics tools available online, to determine the differences in secondary and
tertiary structure of the COI proteins from H. serbica sp. n. and H. zikici. We also compared
the amino acid distribution and COI motif profiles between the two species. Our results
provide strong evidence that protein structure of COI can help with COI-based DNA
barcoding for taxon-specific purposes of species identification and delimitation studies.
Millions of COI DNA sequences deposited in the public domain (which are still growing)
carry huge potential for a comprehensive assessment of genetic variation in COI among
insects by using here described analysis.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia
Get PDFThermal springs represent a habitat with extreme conditions that harbor a unique
microbial community adapted to thrive in this environment. In addition to the geothermal
springs in Iceland, the thermal springs of Vranjska Banja are considered the hottest in
Europe with a water temperature of 63-95°C. Due to global warming and climate change,
there is a growing need for knowledge about the biodiversity of extreme natural habitats.
Besides the exceptional importance of studying extremophilic microorganisms, the
difficulty in their cultivation limits the expanding necessity of research in this field. This
study provides information about the microbial community structure and physicochemical
characteristics of the thermal spring of Vranjska Banja. To determine and monitor the
microbiota diversity of the Vranjska Banja hot spring, for the first time, comprehensive
culture-independent metagenomic analysis in parallel with a culture-dependent
approach was applied. The culture-independent composition of bacterial communities of
the thermal water was investigated using MiSeq-Illumina technology and analyzed by
the computing environment QIIME2 v2021. The applied cultivation approach resulted
in the isolation of 17 strains belonging to genera Bacillus, Anoxybacillus, Hydrogenophilus,
and Geobacillus, based on 16S rRNA sequencing and whole genome sequencing of five
representative strains has been performed. The complete DNA was sequenced using
Illumina HiSeq from the MicrobesNG service. Genomic characterization and OrthoANI
analysis have shown that two of them are candidates for novel species. Products of
extremophilic microorganisms adapted to harsh conditions have great potential to be
used for biotechnological research and industrial application. Results of BAGEL4 and
AntiSMASH showed that the sequenced strains from Vranjska Banja hot spring have
the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase,
chitinase, and glucanase) and various antimicrobial molecules.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Pilot Study of the Ex Vivo Blood Leukocytes’ Proteomic Response to Prednisone Stimulation in Corticosteroid-responsive Asthma
No full textBackground: Leukocytes are key cellular effectors of inflammation in asthma and understandingtheir function in this disease is of crucial importance. Blood leukocytes reflect the actions oftheir counterparts in the lungs and they can be obtained through minimal invasive procedures as partof the peripheral blood.Objective: The aim of the study was to identify proteins in blood leukocyte proteomes that respond toex vivo treatment by prednisone in order to pinpoint candidates for predictive biomarkers in corticosteroid-responsive asthma.Methods: The study included five children diagnosed with asthma and five healthy children. After theex vivo treatment of blood samples with prednisone, lysis of erythrocytes was performed and proteinswere extracted from the remaining leukocytes by ultrasonic disintegration. Protein extracts were analyzedby reversed phase nano-liquidchromatography–tandem mass spectrometry (LC–MS/MS).Results: The stimulation of asthmatics' leukocytes with prednisone has led to an increase in the levelsof FYB (fold change 3.4) and LYZ (fold change 2.2) with a statistical significance of
Bioinformatics education course on gene networks reconstruction using online tools
Get PDFBioinformatics education requires the use of online computer tools for modeling protein-protein
interactions, visual presentation of the networks, access to open databases. The usage of online
bioinformatics tools makes it possible to reconstruct both protein and genes networks, and
develop modeling skills for students. We consider the issues of computer reconstruction of gene
networks - complexes of interacting macromolecules - using a list of genes associated with a
particular disease, or a complex disorder based on public online bioinformatics tools - STRINGDB,
GeneMANIA, Metascape, Cytoscape applications. Examples of computer reconstruction and
visualization of gene networks of oncological diseases including glioma, breast cancer, as well as
complex mental disorders such as Parkinson’s disease, schizophrenia, were recently published
in co-authorship with the students.
The use of only online bioinformatics tools is educational in nature, focused on students, both in
mathematics and in natural sciences and medical disciplines, who do not have enough skills in
computer science, programming, and writing their own code. Automatic construction of lists of
genes associated with a disease using open databases (OMIM, GeneCards, MalaCards), computer
reconstruction of gene networks, calculations of enrichment statistics for gene ontology categories
have been successfully mastered by students. The educational bioinformatics materials designed
for the students and with the students were tested at several universities in Russia, including
courses in English for foreign students studied in Russia.
The tasks of digitalization of medicine, the development of IT technologies are in the priority.
The epidemic situation that has existed in recent years and the forced transition to distance
learning had accelerated the adoption of measures to change the formats of education,
the emergence of new learning platforms. Note a number of qualitatively new tasks of
education in the field of digital healthcare, such as the use of blockchain technologies, the
use of Artificial Intelligence (AI) methods in support of medical decision-making. Overall,
the educational course developed includes a theoretical part (video lessons) and a practical
part - performing tasks on the use of computer programs and databases that have found a
number of applications for medical problems in the reconstruction and analysis of networks
of interactions of macromolecules.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
A New Framework for the Use of Variant Interpretation Tools in Clinical Practice
Get PDFCurrent ACMG/AMP guidelines for the use of sequence variants for genetic diagnosis
and treatment permit the use of in silico predictors as Supporting evidence (PP3 and
BP4 criteria). These criteria, however, lack quantitative support and leave clinicians and
scientists without standards for applying these criteria, leading to large interpretation
variability. To address this challenge, our team built upon previous work and introduced
a novel criterion that can be used to calibrate any computational model or any other
continuous-scale evidence on any variant type. We used it to estimate score intervals
corresponding to the four strengths of evidence for pathogenicity and benignity for
fourteen missense variant interpretation tools on a carefully assembled data sets of
known pathogenic and benign variants. We found that most tools achieved the Supporting
evidence level for both pathogenic and benign classification using newly established datadriven
thresholds. Importantly, at appropriate score thresholds, several in silico methods
can also provide Moderate and Strong evidence levels for a limited number of variants.
Based on these findings, we provided recommendations for quantitative revisions of the
PP3 and BP4 criteria within ACMG/AMP guidelines and the future assessment of in silico
methods for clinical interpretation.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
An integrated platform for genome assembly, comparative genomics and management of genomic variation databases
Get PDFThe use of long read DNA sequencing technologies is producing an explosion of high-quality
de-novo genome assemblies. The availability of these genomes represents a major step
forward for evolution, population genomics, epidemiology, among other applications. A major
bottleneck for many research groups continues to be the availability of tools to build and
analyze the large datasets of genomes that can be produced using these technologies. In this
talk, I summarize the functionalities developed by my research group in the version four of
the Next Generation Sequencing Experience Platform (NGSEP) to perform a comprehensive
analysis of long and short DNA sequencing reads. First, we designed new algorithms for
assembly of haploid and diploid samples from long DNA sequencing reads. A minimizers table
is constructed from the reads , using K-mer hash codes calculated from rankings relative to
the mode of the k-mer counts distribution. Statistics collected during this process are used as
features to build layout paths. For diploid samples, we integrated a reimplementation of the
ReFHap algorithm to perform molecular phasing. Benchmark experiments using PacBio HiFi
and Nanopore sequencing data for different species show that our solution has competitive
contiguity and efficiency, as well as superior accuracy in some cases, compared to other
currently used software. We also developed a functionality to perform ortholog identification
and gene-based alignment of assembled genomes. Proteomes for each genome are extracted
and homology relationships are efficiently predicted building indexes of aminoacid sequences
by k-mer ocurrance. Then, genes are clustered in orthogroups based on the topology of the
graph induced by the predicted relationships. Gene presence/absence matrices are derived
from these orthogroups. If genome assemblies are provided as input, synteny relationships
are identified for each pair of genomes. We also implemented algorithms to perform alignment
of short and long reads to a reference genome. Based on aligned long reads, we improved the
classical variants detector to detect long structural variants. Adding up these developments,
NGSEP is a comprehensive tool to perform de-novo and reference-based analysis of DNA
sequencing reads in a wide variety of experimental settings to solve different research goals.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Bioinformatics and evolution of non-model organisms
Get PDFThe textbooks are written based on Escherichia coli, Arabidopsis thaliana, Saccharomyces
cerevisiae, Drosophila melanogaster, and mouse biology, with some contribution
of less popular model species. However, interesting biology and evolution also happens
elsewhere, and I’ll tell three such stories that have an evolutionary aspect in common:
positive selection on mRNA editing in octopuses and their relatives, tetraplet codons
in some ciliate infusoria and their seemingly neutral evolution, and (time permitting)
recapitulation of the embryonic transcriptional program in insect pupae.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202