imagine (Institute of molecular genetics and genetic engineering)
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Raw data for article: Péter, G., Lukić, J., Milla, S., Sándor, Z. J., Brlás-Molnár, Z., Ardó, L., Bekefi, E.,& Ljubobratović, U.. (2023). Reproduction of Hatchery-Reared Pike-Perch (Sander lucioperca) Fed Diet with Low-Marine-Ingredients: Role of Dietary Fatty Acids. in Fishes, 8(5), 219. https://doi.org/10.3390/fishes8050219
No full textRelated to published version: [https://imagine.imgge.bg.ac.rs/handle/123456789/1827]Raw data for article: [https://doi.org/10.3390/fishes8050219
Carbon and Nitrogen Allocation between the Sink and Source Leaf Tissue in Response to the Excess Excitation Energy Conditions
No full textPlants are inevitably exposed to extreme climatic conditions that lead to a disturbed balance between the amount of absorbed energy and their ability to process it. Variegated leaves with photosynthetically active green leaf tissue (GL) and photosynthetically inactive white leaf tissue (WL) are an excellent model system to study source–sink interactions within the same leaf under the same microenvironmental conditions. We demonstrated that under excess excitation energy (EEE) conditions (high irradiance and lower temperature), regulated metabolic reprogramming in both leaf tissues allowed an increased consumption of reducing equivalents, as evidenced by preserved maximum efficiency of photosystem II (ФPSII) at the end of the experiment. GL of the EEE-treated plants employed two strategies: (i) the accumulation of flavonoid glycosides, especially cyanidin glycosides, as an alternative electron sink, and (ii) cell wall stiffening by cellulose, pectin, and lignin accumulation. On the other hand, WL increased the amount of free amino acids, mainly arginine, asparagine, branched-chain and aromatic amino acids, as well as kaempferol and quercetin glycosides. Thus, WL acts as an important energy escape valve that is required in order to maintain the successful performance of the GL sectors under EEE conditions. Finally, this role could be an adaptive value of variegation, as no consistent conclusions about its ecological benefits have been proposed so far.The APC was funded by the Ministry of Education, Science and Technological Development, the Republic of Serbia (Contract No. 451-03-68/2022-14/200042, 2022)
Food waste utilization in the production of pyocyanin, a valuable bacterial biopigment
Get PDFIndustrialization, as well as improper waste management, has led to the accumulation
of a large amount of kitchen and food waste, making it omnipresent in every corner of the
world [1]. This waste stream is considered to be a significant portion of the total
biodegradable waste and a major contributor to greenhouse gases induced pollution [2].
According to the Food and Agriculture Organization official data, an astonishing 1.3 billion
tons of food is wasted annually, emphasizing the need to establish multiple biorefining
strategies in order to minimize waste pollution, whilst producing different valuable products
in a sustainable process [3].KNJIGA IZVODA: 9. simpozijum Hemija i zaštita životne sredine Kladovo, 4-7. jun 2023. BOOK OF ABSTRACTS : 9th Symposium Chemistry and Environmental Protection Kladovo, 4-7th June 202
Biodegradable and active zein-gelatin-based electrospun mats and solvent-cast films incorporating sage extract: Formulation and comparative characterization
No full textThis study aimed to develop active, biodegradable materials for food packaging by incorporating sage extract (SE) within a zein-gelatin blend by electrospinning and solvent casting. The fabrication techniques, SE incorporation, and its content (5, 10% w/w) determined the materials’ properties. Electrospinning produced 0.36–0.53 mm thick, non-transparent fibrous mats (mean fiber diameter 1.12–1.36 µm). Solvent casting generated 0.34–0.41 mm thick, transparent continuous films. The analysis indicated the constituents’ compatibility, homogenous dispersion, and efficient SE incorporation without strong chemical interactions and phase separation. The solvent-cast films presented more ordered structures, higher mechanical resistance, elongation, and water vapor barrier performance than the electrospun mats. The SE-incorporating formulations showed phenolics’ delivery ability to food simulants influenced by structure, SE content, and media polarity. The electrospun mats expressed higher DPPH• radicals’ inhibition, while the solvent-cast films showed stronger Staphylococcus aureus and Escherichia coli growth inhibition, increased by SE incorporation. All formulations showed rapid complete bio-disintegration in compost (18–25 days).This is the peer-reviewed version of the article: Salević-Jelić, A., Lević, S., Stojanović, D., Jeremić, S., Miletić, D., Pantić, M., Pavlović, V., Ignjatović, I. S., Uskoković, P.,& Nedović, V.. (2023). Biodegradable and active zein-gelatin-based electrospun mats and solvent-cast films incorporating sage extract: Formulation and comparative characterization. in Food Packaging and Shelf Life, 35, 101027.[https://doi.org/10.1016/j.fpsl.2023.101027
Machine intelligence and network science for complex systems big data analysis
Get PDFI will present our research at the Center for Complex Network Intelligence (CCNI) that I
recently established in the Tsinghua Laboratory of Brain and Intelligence at the Tsinghua
University in Beijing. We adopt a transdisciplinary approach integrating information
theory, machine learning and network science to investigate the physics of adaptive
complex networked systems at different scales, from molecules to ecological and social
systems, with a particular attention to biology and medicine, and a new emerging interest
for the analysis of complex big data in social and economic science.
Our theoretical effort is to translate advanced mathematical paradigms typically adopted
in theoretical physics (such as topology, network and manifold theory) to characterize
many-body interactions in complex systems. We apply the theoretical frameworks we
invent in the mission to develop computational tools for machine intelligent systems and
network analysis. We deal with: prediction of wiring in networks, sparse deep learning,
network geometry and multiscale-combinatorial marker design for quantification of
topological modifications in complex networks. This talk will focus on two main theoretical
innovation. Firstly, the development of machine learning and computational solutions for
network geometry, topological estimation of nonlinear relations in high-dimensional data
(or in complex networks) and its relevance for applications in big data, with a emphasis on
brain connectome analysis. Secondly, we will discuss the Local Community Paradigm (LCP)
and its recent extension to the Cannistraci-Hebb network automata, which are braininspired
theories proposed to model local-topology-dependent link-growth in complex
networks and therefore are useful to devise topological methods for link prediction in
sparse deep learning, or monopartite and bipartite networks, such as molecular drugtarget
interactions and product-consumer networks.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Complexity driven evolution of Alternative splicing
Get PDFBased on the animal model of agonistic interactions, we observed co-varied (linked)
alternative exons (LEs) in the genes with alternative splicing phenotype in brain. As a result,
we have found 263 positively co-varied pairs, and 26 pairs with negative co-variation. To
ascertain the data consistency, we employed three organisms cross-validation: human,
mouse and rat with available hippocampus brain region SRA repositories, which supported
the co-varied effect of the corresponding exons.
From 142 genes with LE events the maximum LE pairs were observed in insulin – related
Sorbs1 (Sorbin And SH3 Domain Containing 1; 18 LE AS events), and synaptic Nrcam (12
LE events). 104 genes maintain only 1 LE pair and 36 genes maintain 2-7 LE pairs. Notably
there is a mode at 3 LE pairs per gene (14 genes) in genes vs LE events distribution. GO
analysis reveals that the majority of genes maintaining LE events have belong to the
synaptic genes, RNA-splicing machinery, and chromatin remodeling.
The ‘complexity’ (entropic) measure of gene is calculated as Σ
=
−
i 1,n
ψ log 2(ψ ) ,
where (Ψ) psi is a percent inclusion rate of a particular AS exon, n – number of AS
exons in the gene. It is evident that linked AS exons decrease gene complexity rate [3],
allowing coordinated splicing in high splicing dynamics rate genes, such as synaptic,
RNA processing, chromatin remodeling genes. Herein we speculate if LE AS events are
of evolutionary advantage for the high splicing turnover genes working in homeostasis
equilibrium.
Next step of the work is to elucidate features providing the linking phenomenon, including
mRNA secondary structure, the splicing factor binding sites within and around the
corresponding exons.
We will present the results on the issue featuring some complex interactions between
exons.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Exploring the impact of rare Copy Number Variants on miRNA genes in CAKUT: Insights from integrated bioinformatic analysis and experimental validation
Get PDFRare copy number variants (CNVs) play a significant role in CAKUT development. However,
the specific genetic drivers in certain CNVs associated with CAKUT remain unknown. To
explore the genetic elements within CAKUT-associated CNVs, beyond the protein-coding
genes, we leveraged the recently described comprehensive CNV landscape of CAKUT.
MicroRNAs (miRNAs) are intriguing regulators of genomic networks and have the potential
to be involved in CAKUT. Hereby, a pipeline for comprehensive analysis of miRNA genes
affected by known, rare CNVs associated with CAKUT will be presented. The procedure
is consisted of collection and synchronization of CNV regions specified in different hg
assemblies with the hg19 assembly, mapping of the miRNA precursors, identification of
the most frequently affected miRNAs and miRNA families by rare CNVs, bioinformatic
interpretation of the top-rated miRNAs and prioritisation of key miRNAs for functional
validation. Additionally, a method for estimation of the overall burden of rare CNVs on
miRNA genes in CAKUT will be discussed. Remarkably, it was found that 80% of CAKUT
patients with underlying rare CNV had at least one miRNA gene overlapping the identified
CNV. Network analysis of the most frequently affected miRNAs has revealed the dominant
regulation of the two miRNAs, hsa-miR-484 and hsa-miR-185-5p. Additionally, miR-
548 family members have shown substantial enrichment in rare CNVs in CAKUT. The in
vitro model which depicts the heterozygous deletion of the MIR484 has confirmed the
study concept implying that rare CNVs affect the corresponding miRNA expression and
subsequently dysregulatres miRNA target genes. The translational capacity of miRNA to
be employed in therapeutic approaches is nowadays increasingly investigated. Therefore,
the untangling of the mechanisms affected by dysregulated miRNAs could serve for future
extension of genetic testing and the development of novel miRNA targeting strategies in
CAKUT.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Computational tools and repositories for precision therapeutics in the post-genomic era
Get PDFIn the post-genomic era, the rapid evolution of high-throughput genotyping technologies and the increased pace of production of genetic research data, are continually prompting the development of appropriate informatics tools, systems and databases as we attempt to cope with the flood of incoming genetic information. Alongside new technologies that serve to enhance data connectivity, emerging information systems should contribute to the creation of a powerful knowledge environment for genotype-to-phenotype information in the context of translational medicine. In the area of pharmacogenomics and personalized medicine, it has become evident that database applications providing important information on the occurrence and consequences of gene variants involved in pharmacokinetics, pharmacodynamics, drug efficacy and drug toxicity, will become an integral tool for researchers and medical practitioners alike. At the same time, two fundamental issues are inextricably linked to current developments, namely data sharing and data protection. In this lecture, the impact of high throughput and next generation sequencing technology and its impact on pharmacogenomics research and clinical implementation of genomic medicine will be addressed. In addition, advances and challenges in the field of pharmacogenomics information systems will be discussed, which in turn prompted the development of an integrated electronic ‘pharmacogenomics assistant’. The system is designed to provide personalized drug recommendations based on linked genotype-to-phenotype pharmacogenomics data, as well as to support biomedical researchers in the identification of pharmacogenomic related gene variants.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
The complete solution and interpretation algorithms for large field-of-view and high-resolution spatial transcriptomics
Get PDFThe large field-of-view and high-resolution spatial transcriptomics technology can
reveal and answer scientific questions that cannot be discovered or elucidated by lowresolution
spatial transcriptomics. Obtaining expression profiles at the single-cell level
from high-resolution spatial transcriptomics requires sophisticated data processing and
interpretation strategies, including extensive image data processing, transcriptome data
processing, integration analysis. At the same time, the introduction of spatial information
helps with the annotation of single cells at the tissue level and the study of tissue
structure and function, while cell clustering and cell annotation are important foundations
for subsequent in-depth analysis. Cell annotation can be divided into clustering and reannotation
based on marker genes and end-to-end cell annotation based on reference
datasets. The choice between the two depends on whether markers are easier to obtain
or whether reference datasets with consistent data backgrounds are easier to obtain. The
algorithm team at BGI Research Institute has conducted extensive algorithm research
and development on data interpretation strategies, cell clustering algorithms, and cell
annotation algorithms for large field-of-view and high-resolution spatial transcriptomics
technology, with the aim of providing comprehensive, efficient, and highly reliable data
analysis algorithms, tools and platform support.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Dehydrins in the service of protecting the DNA helix from the aspect of molecular dynamics (MD)
Get PDFDrought stress is one of the greatest threats to global food security, posing a major challenge
to agriculture. Understanding the molecular mechanisms underlying desiccation tolerance
in resurrection plants like Ramonda serbica Panc., can provide valuable insights for improving
crop resilience. Dehydrins are intrinsically disordered proteins known to accumulate in these
plants in response to desiccation. Among several proposed physiological roles, it has been
suggested that dehydrins can protect DNA from damage during water shortage. Here, we
have characterised dehydrins from R. serbica, selected a representative one and evaluated
its potential to interact with DNA.
Most of the R. serbica dehydrins were designated as hydrophilins (glycine content >6%;
GRAVY index <1). They exhibit a high disorder propensity, making them quite dynamic
in solution. Furthermore, they were predicted to localize in the nucleus. To examine the
potential interactions with DNA in silico, we have selected a representative, highly hydrophilic
dehydrin (Gravy index: –1.29) containing a high percentage of glycine (22.6%) and charged
amino acids (lysine, glutamate and aspartate). Its 3D structures were determined using the
Phyre 2 intensive modelling and AlphaFold.
The dehydrin-DNA complex was manually adjusted, following molecular dynamic simulation
(MDS) in both cases of hydration and desiccation. To simulate complete hydration, the DNAdehydrin
complex was solvated in a water box, with final dimensions of 100×69×82 Å,
neutralised with 0.15 M NaCl. The system underwent a 10,000-step energy minimization,
consecutive 1250 ps equilibration NVE (constant number of atoms, volume and energy)
heating from 10 K to 298 K and 100 ns NPT (constant number of atoms, pressure and
temperature) MD production at 1 bar, and 1 fs integration step. In all simulations, periodic
boundary conditions (PBC) were implemented and the CHARMM36 force field was used.
The obtained results revealed that selected dehydrin can interact with both minor and major
DNA grooves. The phosphate groups from the DNA molecule form salt bridges with the
positively charged lysines from polylysine, K-segment, contributing to the complex stability.
Overall, we have provided evidence for possible dehydrin-DNA interactions. However, the
exact nature and significance of these interactions is still an area of active research in vitro.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202