imagine (Institute of molecular genetics and genetic engineering)
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To be folded, to be unfolded or to be aggregated with important functions: application of the directed coaggregation mechanism to combat bacterial communities
Get PDFOne of the reasons for the mortal danger to humans is the ability of pathogenic bacteria
to form biofilms. The formation of biofilms is an evolutionarily conservative defense
mechanism against adverse conditions. The use of this protection by pathogenic bacteria
reduces the effectiveness of the main means of combating them - antibiotics, which
complicates the production of new types of drugs. There are two types of antimicrobial
agents that are not known antibiotics: nanoparticles and antimicrobial peptides. We
demonstrated that peptides synthesized based on the amino acid sequence of proteins
and capable of amyloid formation and coaggregation with the whole protein exhibit
antimicrobial activity. The ability of peptides to coaggregate with target proteins can help
combat biofilm-forming bacterial communities.
We evaluated the antimicrobial effects of ten synthesized hybrid peptides, which were
obtained based on the sequences of the S1 ribosomal protein of P. aeruginosa and S.
aureus. It is important that some peptides demonstrated high antimicrobial activity
comparable to the antibiotic gentamicin sulfate against pathogenic strains of MRSA, S.
aureus, and P. aeruginosa. These peptides showed no toxicity to eukaryotic cells. Our study
demonstrates the promise of hybrid peptides based on the amyloidogenic regions of the
S1 ribosomal protein for the development of new antimicrobials against Gram-positive
and Gram-negative bacteria resistant to traditional antibiotic.Belgrade : Institute of molecular genetics and genetic engineerin
Modulating Horizontal Gene Transfer through Bistability in the Dynamics of Bacterial Restriction-Modification Systems
Get PDFRestriction-modification (R-M) systems consist of genes encoding restriction enzyme
and methyltransferase, often co-expressed with a specialized regulator (C protein).
These systems tightly regulate their function through complex cooperative positive and
negative feedback loops. R-M systems defend bacterial cells against invasion by foreign
DNA, such as plasmids and bacteriophages, consequently modulating horizontal gene
transfer, including transmitting pathogenic genes like antibiotic resistance determinants
or virulence factors. Recent experiments have directly confirmed that the R-to-M ratio
significantly impacts bacteriophage infection efficiency, rendering a subset of cells more
susceptible to horizontal gene transfer.
To understand the regulatory mechanisms of R-M systems, we develop a mathematical
model tightly constrained by biophysical measurements of system interaction
parameters. Despite the technical complexity arising from C protein forming dimer and
tetramer complexes, we analytically derive a system stability diagram that can be easily
modified for various R-M system architectures. A single free parameter determines the
bistability of the system, which we infer from experimental measurements across three
different architectures. Surprisingly, while one class exhibits monostability, the other two
demonstrate bistability.
Our model successfully explains the experimental data and reveals that modulation of
the barrier to horizontal gene transfer can occur through distinct mechanisms. Bistability
leads to long-lasting states susceptible to acquiring pathogenic genes, whereas stochastic
fluctuations only transiently lower the transfer barrier. The precise implications of these
differences for bacterial pathogenicity and evolution require further investigation.
However, we propose that R-M systems capable of bistable gene expression may give
rise to genetically distinct bacterial populations with potentially diverse phenotypes
concerning pathogenicity and antibiotic resistance.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Genetic Complexity and Synteny Analysis of Castanea Genomes: Unveiling the Significance of Chestnut Species in Ecological and Genomic Perspectives
Get PDFCastanea, a prominent genus within the Fagaceae family, thrives across the expansive
woodlands of eastern North America, Europe, and Asia, holding considerable ecological
and economic significance. Among the invaluable forest resources, chestnuts play a pivotal
role by providing both nourishment and wood products. Furthermore, they assume the
status of keystone species due to their indispensable ecological functions in afforestation
and the provision of crucial ecosystem services. The genomes of C. mollissima and C. sativa,
estimated to be around 800 Mb in size, add to the remarkable genetic complexity of these
species. We utilized the powerful Python module jcvi to conduct a thorough synteny
analysis, focusing on the Chinese and European chestnut genomes. To detect structural
variants between these genomes, we employed SyRI (Synteny and Rearrangement
Identifier). Additionally, TBtools was utilized to visually illustrate the syntenic genes
across different genomes. Our investigation involved a comprehensive synteny analysis
of the Chinese chestnut genome and the Sariaslama cultivar of the European chestnut.
Encouragingly, we observed a strong overall synteny between these genomes, indicating
significant conservation. To enhance the accuracy and completeness of the genome
assemblies, we employed Pacbio sequencing technology, which contributed to the highquality
results obtained for both the European and Chinese chestnut genomes.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Genomic Surveillance and Phylogenetic Analysis of SARS-CoV-2 Variants in Serbia: Insights into Evolutionary Dynamics and Genetic Diversity
Get PDFThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global
pandemic, resulting in significant morbidity and mortality worldwide. Understanding the evolutionary
dynamics and genetic diversity of the virus were crucial for virus control and management
strategies. With that aim we conducted genomic surveillance and phylogenetic analysis of
SARS-CoV-2 variants in Serbia, spanning from March 2020 to the end of January 2023.
Sequencing was conducted using three different platforms: Oxford Nanopore, Ion Torrent AmpliSeq
and BGISEQ-500. Consensus sequences obtained using platforms respective software were deposited
in the GISAID database. In this study 2109 good-quality sequences were included (doi.10.55876/
gis8.230411qh). Pangolin and Nextclade software were utilized for clade, lineage and variant
determination, while sequence alignment and construction of the phylogenetic tree was performed
using Nextstrain web-based application.
Variant analysis revealed over 125,000 mutations across the 2109 sequences, of which 38% occurred in
the S protein encoding gene. The most common mutations involved intragenic single nucleotide variants
(88%), followed by intragenic deletions (5%). All sequences were assigned to following 16 clades: 20A,
20B, 20C, 20D, 20E, 20G, 20I, 21J, 21K, 21L, 22A, 22B, 22C, 22D, 22E, and 22F.
Temporal analysis of the variants in Serbia revealed that the Alpha variant was predominant during 2020
and the first three months of 2021. The Delta variant emerged in June 2021, dominating until the end
of December 2021, when Omicron variant was detected for the first time, overtaking the dominance for
the remaining surveillance period. Notably, the Gamma and Epsilon variants were not detected in the
analyzed samples.
Phylogenetic analysis demonstrated that the SARS-CoV-2 variants circulating in Serbia were largely
comparable to the variants found in Europe. However, a slight delay in their emergence was observed,
potentially attributed to a lower travel rate during that period and a decreased frequency of sequencing
in certain months.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Expression profile of ankrd1a during repair of injured zebrafish skeletal muscle
Get PDFIn our previous work, using transgenic zebrafish line TgBAC(ankrd1a:EGFP), we showed activation
of the zebrafish ankrd1a gene in border zone cardiomyocytes of cryoinjured heart and in close
proximity of needle-stab wounds in skeletal muscle, indicating its involvement in muscle
regeneration. Our results implicated ankrd1a in zebrafish skeletal muscle tissue repair and
remodeling, as a sensor of stressed muscle. Here we take a closer look at the spatio-temporal
expression profile of the ankrd1a gene in injured zebrafish skeletal muscle by analyzing cryosections
prepared from wounded tissue of TgBAC(ankrd1a:EGFP) adults at 1, 3, 5, 7 and 10 days post-injury
(dpi). The expression of the fluorescent reporter was observed from 3 dpi and remained until 10 dpi.
At 3dpi, new GFP-positive muscle cells emerged inside the injury zone, at the site of needle entry,
while in the later days (5, 7 and 10 dpi), newly formed GFP-positive myofibers were visible in the
deeper tissue layers within the injury, indicating active repair of the injured tissue. To identify cells
in which ankrd1a is activated after injury, we stained the sections for markers of satellite-like cells,
undifferentiated and differentiated muscle cells, and mature myofibers. Since the reporter was
detected both in the newly formed myofibers that invade the wound and in the apparently uninjured
tissue surrounding the injury, we hypothesize that ankrd1a is not only involved in satellite celldependent tissue repair, but its expression might be a hallmark of adaptive process in undamaged
myofibers surrounding the physical injury.EZM2023 Abstract Book: 12th European Zebrafish Meeting July 9-13, 2023 Krakow, Polan
Comparative study of antimicrobial potential and DNA/BSA binding affinity of silver(I) and gold(III) coordination compounds with 1,6-naphthyridine
No full textIn the present study, synthesis of silver(I) and gold(III) coordination compounds with 1,6-naphthyridine (1,6-naph), {[Ag(1,6-naph)(H2O)](BF4)}n (1) and [AuCl3(1,6-naph)] (2), was reported. The methods used for the structural characterization of a new compound 1 included IR, NMR (1H and 13C) and UV-Vis spectroscopy, cyclic voltammetry and single-crystal X-ray diffraction analysis. The crystallographic results showed that compound 1 represents silver(I) coordination polymer, in which 1,6-naph ligand acts as a bidentate bridging ligand connecting two Ag(I) ions via its N1 and N6 nitrogen atoms, while the third coordination site of the metal ion is occupied by the water oxygen atom, resulted in a T-shape geometry. Compounds 1 and 2 were evaluated in vitro for antimicrobial activity against five bacterial and two Candida species, while their cytotoxicity was tested on the normal human lung fibroblast cell line (MRC-5). Compound 1 has manifested a remarkable antifungal activity on both tested Candida strains (C. albicans and C. parapsilosis) with minimal inhibitory concentrations (MICs) of 1.43 and 11.38 µM (0.49 and 3.9 µg/mL), respectively, while no significant antimicrobial activity was observed for 2. Moreover, silver(I) coordination polymer 1 inhibits the hyphae formation of C. albicans at subinhibitory concentration. The binding affinity of both compounds 1 and 2 with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) was studied by fluorescence spectroscopy, indicating their ability to interact with these biomolecules, with compound 2 being more reactive.Accepted version: [https://imagine.imgge.bg.ac.rs/handle/123456789/2076
Group 4 late embryogenesis abundant (LEA) proteins as a model to stydy propensity for oligomerisation
Get PDFAbstract book: 1st ML4NGP meeting on machine learning and non-globular proteins, July 5-7, 2023, Bratislava, Slovaki
Stereo-seq: Large Field of View-Spatially Resolved Transcriptomics at Nanoscale Resolution
Get PDFSTOmics’ Stereo-seq technology is a world-leading unbiased whole transcriptome spatial
omics platform that combines nanoscale resolution with the centimeter-level field of
view. The Stereo-seq chip comprises billions of probes, each with spatial barcodes, in a
patterned array. Biological tissue is sectioned and loaded to the Stereo-seq chip, followed
by fixation and permeabilization. Then mRNA molecules from the tissue section hybridize
with the barcoded probes, and reverse transcription produces spatially barcoded cDNA.
Following library preparation and sequencing to generate spatially resolved Stereo-seq
data from the tissue section. Proprietary cloud-based analysis reconstitutes the data
and enables visualization of the transcriptomics of the original tissue section in space,
empowering further research and assembly of spatial omics atlases.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Uncovering resistance to microtubule targeting drugs
Get PDFDrugs that alter microtubule dynamics have been used for decades for treating different
types of cancers. Such drugs arrest cell cycle progression in mitosis, and induce apoptosis.
However, a fraction of cells manages to survive, escapes from the arrest and resumes
proliferation. Understanding the strategies of these cells is important to uncover the
early stages of emergence of resistance. To this aim, we performed laboratory evolution
experiments in yeast and in mammalian cells when microtubule dynamics is impaired.
Our results show that cells follow reproducible strategies to escape the effect of the
drug. Via mutations, aneuplouidy and non genetics mechanisms they recover microtubule
functionality and decrease the propensity to die.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Advancing Genomics with OrthoDB, BUSCO, and the LEM Framework
Get PDFThe rapid growth of genomics data necessitates continuous advancements in bioinformatics
tools. This presentation highlights the latest updates to our toolbox, including OrthoDB v11,
BUSCO v5, and the LEM benchmarking framework.
OrthoDB (https://www.orthodb.org) is a leading resource for gene orthology and
functional annotations across diverse eukaryotes, prokaryotes, and viruses. Orthology
facilitates precise bridging of gene function knowledge within the genomics sphere.
OrthoDB v11 encompasses over 100 million genes from 18,000 prokaryotes and nearly
2,000 eukaryotes, providing extensive species coverage. The open-source OrthoLoger
software (https://orthologer.ezlab.org) allows mapping of novel gene sets to precomputed
orthologs, linking them to relevant annotations.
BUSCO (https://busco.ezlab.org) serves as a standard tool for assessing the completeness
of genome assemblies, transcriptomes, and predicted gene sets, complementing
assembly contiguity measures like N50 values. A spin-off of OrthoDB, BUSCO evaluates
the presence and coverage of marker genes, offering an evolutionarily-grounded
expectation of gene content completeness. BUSCO v5 now automatically selects the most
suitable dataset for evaluation, outperforming the popular CheckM tool. Its efficiency is
particularly evident in large eukaryotic genomes, and it is uniquely capable of assessing
both eukaryotic and prokaryotic species, making it applicable to metagenome-assembled
genomes of unknown origin.
The LEMMI (https://lemmi.ezlab.org) benchmarking framework, now in version 2, facilitates
informed software tool selection. This Live Evaluation of Methods (LEM) for Metagenome
Investigation uses a container-based approach for continuous benchmarking and effective
end-user distribution. The versatile framework can be extended to other procedures,
such as gene orthology inference with LEMOrtho (https://lemortho.ezlab.org). The LEM
benchmarking approach aims to become a community-driven effort, allowing developers
to showcase novel methods and users to access standardized, easy-to-use software. We
encourage researchers to apply this framework in their domain and welcome feedback.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202