imagine (Institute of molecular genetics and genetic engineering)
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Semantic unification and search of bioinformatics databases
Get PDFAnalyzing biological data from various sources offers a comprehensive perspective of a
domain, facilitating the identification of patterns that would otherwise be challenging or
impossible to observe when focusing solely on individual biological entities. The process
of linking data from different databases can present challenges due to inconsistencies in
properties and identifiers assigned to the same entity across databases. Although certain
databases include a range of identifiers from multiple sources, the search capabilities
are restricted to exact property matching, preventing the execution of complex queries
involving multiple metadata attributes.
We designed a novel data framework that aims to address these challenges by facilitating
the linkage and retrieval of information from diverse interconnected biological data
sources. To evaluate the effectiveness of the model, we conducted tests and created a
knowledge graph using metadata extracted from five separate public datasets: DisProt,
HGNC, Tantigen 2.0, IEDB, and DisGeNET. The resulting graph establishes connections
between more than 17 million nodes, comprising 2.5 million distinct biological entity
objects, and encompasses over 4 million relationships.
Additionally, we designed and implemented a general-purpose procedure for extracting
new relationships based on semantic similarity from data transformed into the BioGraph
data model.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Profiling Pre-Replication Complex Mutations in Cancer
Get PDFThe pre-replication complex (preRC) consists of 15 proteins that mark DNA replication
initiation sites and regulate replication timing. Deficiency in preRC proteins results in
genomic instability (re-replication) and developmental defects (Meier-Gorlin syndrome).
Our aim was to assess the scope of preRC gene aberrations in cancer. Variations in
preRC genes were studied using CBio Portal software and TCGA PanCancer dataset. The
functional impact of detected variants was evaluated in silico by three different prediction
tools: SIFT (sequence and evolutionary conservation - based), PolyPhen2 (protein
sequence and structure – based) and MutPred2 (supervised learning method based on
neural networks).
No mutational hotspots were observed in any of the 15 preRC genes and no mutual
exclusivity between mutations in preRC genes were detected. The highest alteration
incidence in preRC genes was found in endometrial carcinoma and melanoma. The majority
of the variations seen in preRC genes were non-synonymous. The functional assessment
has shown that 253/1215 (21%) preRC gene mutations were predicted to be pathogenic
with high confidence by 2/3 computational algorithms. None of the variants reached the
high confidence pathogenicity score by all 3 prediction tool. In contrast, 49% of variants
were predicted to be either benign by all three tools or benign by 2/3 or 1/3 tools, with the
remaining 1/3 or 2/3, respectively, classifying them as low confidence pathogenic.
These finding suggest that mutations in preRC proteins might be passenger mutations
and that cancer cells can tolerate them. The future step is to see whether incidence of
coding vs. noncoding preRC mutations correlates with Tumor Mutation Burden (TMB) and
Genome Instability Index (GII) of cancer.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Mining for the data about glycosylation in the bovines-the analysis of the recently published studies
Get PDFpotential for improvement regarding reproduction, herd health management, and the
quality and safety of milk and meat products. The PubMed database was searched for
“glycosylation” and “B. taurus” using the following filters: full text available, the publication
date of five years, and the preprints excluded. The search retrieved 244 results, and after
the content analysis by the authors, 88 remained relevant. All publications were Research
Articles except one Review. The assessment of the glycan profile composition was among
the aims in 34, the functional aspects in 33, and the protein glycoforms in 12 studies. Ten
studies brought data about the total glycome profile of the milk, tissue, or meat sample,
while the other contained glycosylation-related features of the individual protein(s).
Most often, the studies used milk (25), individual proteins (23), or tissue (20 studies)
as the samples. Usually, the milk was material to analyze the glycosylation of casein,
immunoglobulin G, or the total glycans. The studies involving the individual proteins
most frequently analyzed fetuin, and the glycosylation of submaxillary gland mucin was
the target in the studies using tissue samples. These pioneer data mining results allow
for the conclusion on the availability of reliable data about glycosylation in the bovines,
eligible as the starting point for further scientific efforts on their continuous appending,
systematization, and multidisciplinary analyses.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Impact of different mapping tools on detection of small RNAs in bacterial outer membrane vesicles
Get PDFBacterial small RNAs (sRNAs) represent a highly diverse RNA class ranging from 8 to 200
nucleotides in length, originating from the bacterial chromosome, plasmids or phages.
After syntheses sRNAs can remain inside the bacterial cell, be secreted or packed into
outer membrane vesicles (OMV), enabling various intra- and inter-kingdom interactions.
Different sRNAs biotypes display differences in structure, mechanism of action and level
of regulation (i.e. transcription, translation, mRNA stability, etc.), but could be broadly
grouped in: trans-acting sRNAs (bind to target mRNAs) and cis-encoded sRNAs (or
antisense RNA that may interact not only with mRNAs, but also with proteins and DNA).
Even though the advancement of high-throughput sequencing technology led to a burst
of knowledge on small RNAs complexity and diversity, there are still specific challenges
related to sRNA-seq data analysis that need to be resolved. Two main challenges,
associated to short length of many bacterial sRNA biotypes, are: (i) to discriminate
between functional sRNAs synthesized by bacterial cell and degradation fragments
produced by sample preparation and (ii) to detect functional sRNAs displaying sequence
variation. While loss of very small sized sRNAs could easily be overcome by cutting-off
only the specific adapter sequences that were used in sRNA library preparation, providing
a proper mapping still remains a strenuous task.
The aim of this study was to test five different mapping tools that are widely used in NGS
data analysis (bbmap, bowtie2, bwa, minimap2 and segemehl) for their performances in
mapping of bacterial OMV sRNA-seq data to bacterial reference genome. For this test
publicly available NCBI sRNA-seq dataset from OMVs of Aliivibrio fischeri (PRJNA629425)
was used, as it contained sRNAs of different length and biotype and because A.fischeri
reference genome and annotation were available (PRJNA12986). We evaluated five
mappers using alignment and assignment rates as well as computational time. Alignment
rate was calculated as the ratio of aligned and input reads, while the assignment rate
was calculated as the ratio of assigned and aligned reads. Finally, totals of detected
sRNAs biotypes were compared between different mappers. The statistical analysis was
performed in R (version 4.3.0) and performance metrics are discussed.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Highly stable and versatile α-amylase from Anoxybacillus vranjensis ST4 suitable for various applications
No full textα-Amylase from the thermophilic bacterial strain Anoxybacillus vranjensis ST4 (AVA) was cloned into the pMALc5HisEk expression vector and successfully expressed and purified from the Escherichia coli ER2523 host strain. AVA belongs to the GH13_5 subfamily of glycoside hydrolases and has 7 conserved sequence regions (CSRs) distributed in three distinct domains (A, B, C). In addition, there is a starch binding domain (SBD) from the CBM20 family of carbohydrate binding modules (CBMs). AVA is a monomer of 66 kDa that achieves maximum activity at 60–80 °C and is active and stable over a wide pH range (4.0–9.0). AVA retained 50 % of its activity after 31 h of incubation at 60 °C and was resistant to a large number of denaturing agents. It hydrolyzed starch granules very efficiently, releasing maltose, maltotriose and maltopentaose as the main products. The hydrolysis rates of raw corn, wheat, horseradish, and potato starch, at a concentration of 10 %, were 87.8, 85.9, 93.0, and 58 %, respectively, at pH 8.5 over a 3 h period. This study showed that the high level of expression as well as the properties of this highly stable and versatile enzyme show all the prerequisites for successful application in industry
NANOMATERIALS-BASED STRATEGY FOR MYELOID CELLS ACTIVATION RESULTS IN EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS AMELIORATION AND GUT MICROBIOTA MODULATION
Get PDFntroduction: Recent studies implicated overactivated myeloid cells and gut microbiome, along with our work,
in multiple sclerosis (MS) pathogenesis. As we have shown before, prostaglandin (PG)E2 promotes
suppressive properties of myeloid cells leading to amelioration of symptoms in myelin oligodendrocyte
glycoprotein
(MOG)-induced experimental autoimmune encephalomyelitis
(EAE). Additionally, we
investigated how the changes of gut microbiota associate with EAE and the effects of therapy.
Materials & Methods: MOG35-55 in Complete Freund Adjuvans was used for EAE induction in C57BL/6
mice. Gold nanoparticles (GNP) conjugated with PGE2 and MOG were applied on the day 1, 3, 5, 7, and 9
post-immunization. We performed extensive immunophenotyping and metagenomic analysis in order to
decipher association between gut microbiome and efficacy of GNP-MOG-PGE2 treatment.
Results: GNP-MOG-PGE2 treatment alleviates EAE symptoms, decreased levels of pro-inflammatory
cytokines in sera, and increased proportion of suppressive MDSCs in CNS-infiltrates. Furthermore, EAE
induction significantly affected species richness, while GNP-MOG-PGE2 treatment increased the gut
microbiota diversity and preserved the richness of species with immunomodulatory properties.
Conclusion: Taken together, our data indicate that targeted activation of myeloid cells by GNP-MOG-PGE2
together with gut microbiota modification is very promising therapeutic strategy for MS.International Society of Microbiota 10th ISM World Congress on Targeting Microbiota October 17-19, 2023 – Venice, Ital
Identification of potentally causal variants for myasthenia gravis: a bioinformatics-driven fine-mapping approach combined with genetic association study
Get PDFIntroduction: Genome-wide association studies (GWAS) identify genomic loci that contain genetic determinants
of complex diseases. Subsequent functional genomic approaches, such as bioinformatic finemapping
and transcriptome-wide association studies (TWAS), can reveal potentially causal single
nucleotide variants (SNVs) that can be tested on patient samples. We applied this approach to study
causal SNVs for acetylcholine receptor (AChR) seropositive myasthenia gravis (MG). We focused on
CHRNA1 and CHRNB1 loci, coding AChR subunits, and CTLA-4 locus, coding protein transmitting an inhibitory
signal to T cells.
Methods: CHRNA1 was fine-mapped by PAINTOR using data from GWAS summary statistics, 1000
genome and RegulomeDB. Alongside, rs4151121 identified by TWAS in CHRNB1, and rs231735 and
rs231770 identified by fine-mapping in CTLA-4 were studied. SNVs were genotyped using allele discrimination
assays in 447 Serbian AChR-MG patients (183 early-onset and 264 late-onset) and 447 sex- and
age-matched controls.
Results: CHRNA1 rs35274388 was fine-mapped as a potentially causal variant (PIP2=92%) exhibiting
transcription factor binding and chromatin accessibility peaks. CHRNA1 rs35274388 minor allele A and
CHRNAB1 rs4151121 minor allele G increased the risk for late-onset MG (OR=1.669, 95% CI=1.05-2.638,
p=0.027, p10e6 permutation=0.031 and OR=1.322, 95% CI=1.063-1.644, p10e6 permutation=0.014, respectively).
On the other hand, CTLA-4 rs231735 recessive genotype TT decreased, while rs231735-
rs231770 haplotype GC increased the susceptibility to early-onset MG (OR=0.548, 95% CI=0.339-0.888,
p=0.014, p10e6 permutation=0.014 and OR=1.360, p=0.027, p10e6 permutation=0.027, respectively).
Conclusion: CHRNA1 rs35274388 and CHRNAB1 rs4151121 loci could be causal genetic factors for lateonset
MG while CTLA-4 rs231735 and rs231770 could be causal genetic factors for early-onset MG in Serbian
population
Identification of the new candidate NLRP3 inhibitor using combined computational approach
Get PDFThe NOD-like receptor pyrin domain-containing protein 3 (NLRP3), an important
intracellular sensor in the innate immune system, detects a plethora of exogenous and
endogenous stimuli, leading to inflammasome formation and caspase-1 activation. More
recently, it emerged as an attractive drug target due to abnormal NLRP3 inflammasome
activation implicated in many acute and chronic diseases (including diabetes,
atherosclerosis, metabolic syndrome, cardiovascular, and neurodegenerative diseases)
[1]. Several direct NLRP3 inhibitors that block its ATPase activity by keeping it in
closed conformation have been reported [1,2]. Some of them have entered clinical trials,
but still, none of them is FDA approved.
A powerful strategy in identifying potential NLRP3 inhibitors can be in silico drug
repurposing of compounds with already known safety profiles. In this study, we
performed a virtual screening protocol that considers both long- and short-range
interactions between molecules. First, the Informational spectrum method developed for
small molecules was applied for searching the Drugbank database. Selected candidates
were filtered by successive cross-correlation spectra analysis. Finally, after molecular
docking, we identified the most promising candidate and proposed it for further
experimental testing.Book of Abstracts: 9th Conference of Young Chemists of Serbia Novi Sad, 4th November 202
Study of PLA pre-treatment, enzymatic and model-compost degradation, and valorization of degradation products to bacterial nanocellulose
Get PDFIt is well acknowledged that microplastics are a major environmental problem and that the use of plastics, both petro- and bio- based, should be reduced. Nevertheless, it is also a necessity to reduce the amount of the already spread plastics. These cannot be easily degraded in the nature and accumulate in the food supply chain with major danger for animals and human life. It has been shown in the literature that advanced oxidation processes (AOPs) modify the surface of polylactic acid (PLA) materials in a way that bacteria more efficiently dock on their surface and eventually degrade them. In the present work we investigated the influence of different AOPs (ultrasounds, ultraviolet irradiation, and their combination) on the biodegradability of PLA films treated for different times between 1 and 6 h. The pre-treated samples have been degraded using a home model compost as well as a cocktail of commercial enzymes at mesophilic temperatures (37 °C and 42 °C, respectively). Degradation degree has been measured and degradation products have been identified. Excellent degradation of PLA films has been achieved with enzyme cocktail containing commercial alkaline proteases and lipases of up to 90% weight loss. For the first time, we also report valorization of PLA into bacterial nanocellulose after enzymatic hydrolysis of the samples
The pharmacogenomics of vincristine-induced peripheral neuropathy in pediatric acute lymphoblastic leukemia patients in Serbia
Get PDFVincristine (VCR) is one of the key drugs in current treatment protocols for pediatric acute
lymphoblastic leukemia (ALL). By destabilization of microtubules, VCR arrests cells in metaphase,
inducing apoptosis of malignant cells. VCR also causes axonal degradation and impairment of axonal
transport, which leads to vincristine-induced peripheral neuropathy (VIPN). The aim of this study was
to determine if the selected genetic variants are associated with the development of VIPN in ALL
children treated with VCR in Serbia. This study also aimed to discover candidate pharmacogenomic
markers of VIPN in Serbian population. PCR and sequencing-based methodology was used to detect
variants in following genes: CYP3А5 (rs776746), CEP72 (rs924607), ACTG1 (rs1135989), MIR3117
(rs12402181) and MIR4481 (rs7896283). Statistical analyses were performed for investigation of their
association with VIPN in 56 pediatric ALL patients. Population VCR pharmacogenomics analysis of 17
pharmacogenes from in-house next-generation sequencing data was also done. Data on allele frequency
distribution for European population were extracted from public databases. During the treatment,
17.86% of patients developed VIPN. Association analyses have shown that none of the investigated
genetic variants contributed to the occurrence of VIPN in our study group. Population
pharmacogenomics study didn’t reveal valid candidate pharmacovariants for the occurrence of VIPN.
Our results suggested that pre-emptive pharmacogenetic testing for VCR is not applicable. More
comprehensive approaches are needed to identify panel of genes that could explain the VIPN
development after VCR administration in ALL patients. Utilizing better designed GWAS studies and
more robust artificial intelligence-based tools would provide a panel of pharmacogenes for pre-emptive
tests of VIPN to individualize therapy for ALL in children.Book of abstracts: International Conference of Biochemists and Molecular Biologists in Bosnia and Herzegovina - ABMBBIH May, 202