imagine (Institute of molecular genetics and genetic engineering)
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Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature
Get PDFFinding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.Book of Abstracts: Belgrade BioInformatics Conference 202
Value-added biologics through eco-sustainable routes (BioECOLogics)
Get PDFAvailable biologics have revolutionized cancer treatment, proven efficient in complex
infections, changed the lives of people with rare diseases, and offered hope for many patients
who previously had no effective treatment options for their condition. Downside is that these
biopharmaceuticals are extremely expensive and as such, not widely available. BioECOLogics
will provide economic and environmental value via novel bio-upcycling and innovative
formulations to obtain next generation eco-friendly therapeutics. The project will exploit the
great potential of bacterially derived natural products (pyocyanin, pyrrolnitrin, pyoverdines,
undecylprodigiosin and staurosporine) with proven bioactivities (i.e. anticancer, antifungal,
antibiofilm, antiviral) to generate value-added biologics. Functional 100% bio-based biologicals
exhibiting advanced properties (improved activity, sustained release, synergy with essential and
noble metal ions, reduced price and carbon footprint) will be produced, formulated and
processed using innovative techniques such as fermentative bioprocess intensification,
structural optimization via biocatalysis and formulations using essential and noble metals, as
well as biopolymeric drug carriers. Therefore, BioECOLogics will result in a set of unique
products that offer real solutions for a spectrum of biomedical problems. In doing so, the
project contributes towards the shortage of novel biomedicines, but at the same time,
recognizes EU’s 2050 long-term strategy for a climate-neutral Europe by replacing fossil-based
material with a bio-based, renewable material. Novel bio-upcycling routes will be developed
based on the biotechnological valorization of waste materials into new formulations of
biopharmaceuticals resulting from bacterial fermentations and innovative formulations of
obtained molecules. The project approach will be transdisciplinary by combining microbiology,
biotechnology, process and inorganic chemistry, and pharmaceuticals knowledge. In addition to
the multidisciplinary nature, the knowledge transfers between researchers, industrial and other
stakeholders will contribute positively to the overall relevance of the impact for dissemination
and exploitation of results.Principal Investigator: Dr Jasmina Nikodinovic-Runić, IMGGEDuration period: 2021-202
Genetic and environmental influences on psychological adaptation of children and adults (GENIUS)
Get PDFBuilding upon the research within the first twin study in Serbia, GENIUS is focused on examining
the mechanisms that shape human behavior and adaptation styles. The main novelty of the
GENIUS project is the introduction of epigenetic research and the inclusion of children and
adolescents, which will result in the first national full life-span behavioral genetics research.
Additionally, new methodology (e.g. experimental and family design) will be introduced and
evaluated. The study will include 2000 twins of all ages and their family members, who will
participate in the assessment of dispositional characteristics, physical attributes, cognitive
abilities, environmental factors, and adaptation styles. All research will be underpinned by the
creation of the Serbian Twin Advanced Registry (STAR) and the STAR Biobank containing twins
buccal-derived DNA samples. The second segment of the Project will be an epigenetic study, i.e.
genome-wide methylation study in MZ adult twin pairs having discordant adaptation styles.
Next-generation sequencing (NGS), as the state-of-the-art method in the field, will be used to
detect broad regions of DNA methylation. The results of the Project will unravel the nature of
interactions among specific and common genetic and environmental factors, and their
influences on epigenetic changes and health-related habits and characteristics. GENIUS is
expected to have significant scientific, social, healthcare, and educational impacts. Apart from
the general contribution to the scientific knowledge, the creation of the STAR and STAR Biobank
will provide a solid ground and valuable resource for future multidisciplinary research in
psychology, molecular biology, genetics, and health sciences. The citizen science approach
should advance scientific culture among the various stakeholders outside academia. The results
of the research will be used to promote desirable upbringing patterns and individually tailored
medical and psychological guidelines.Principal Investigator: Dr Snezana Smederevac, Faculty of Philosophy, University of Novi SadCoordinator for IMGGE: Dr Jelena Kusic Tisma Duration period: 2023-2024Duration period: 2021-202
Genetic and epigenetic characterization of variant DMPK expansions as a modifier of phenotype in myotonic dystrophy type 1
Get PDFPovećanje broja ponovljenih motiva u mikrosatelitskim lokusima ili dinamične mutacije uzrokuju skoro 50
neuroloških oboljenja, označenih kao bolesti ekspanzija ponovljenih motiva. Kvantitativan efekat broja
ponovljenih motiva na fenotip i inheretno nestabilna priroda dinamičnih mutacija objašnjavaju jedinstvene
karakteristike ove grupe bolesti, kao što su genetička anticipacija – ranije i teže ispoljavanje bolesti u narednim
generacijama, i izrazito varijabilni klinički fenotipovi. Miotonična distrofija tip 1 (DM1) je uzrokovana
ekspanzijama CTG tripleta u DMPK genu, čiji broj predstavlja glavnu determinantu ekstremno varijabilne
kliničke prezentacije koja otežava predviđanje toka bolesti. Deo fenotipske varijabilnosti, neobjašnjene veličinom
ekspanzije, ukazuje na postojanje dodatnih modifikatora bolesti. Kod ~5% DM1 bolesnika opisane su
ekspanzije sa varijantnim tripletima (CCG, CTC, CAG), koji su dovedeni u vezu sa neobičnim i/ili blažim simptomima
nego što bi se očekivalo na osnovu veličine ekspanzije datog bolesnika. Ovaj rad daje pregled
dosadašnjih znanja o tipovima varijantnih tripleta u DMPK ekspanzijama, kliničkim karakteristikama
bolesnika i mehanizmima kojim varijantni tripleti ostvaruju svoj modifikujući efekat na fenotip. Ključna uloga
pripisuje se stabilišućem efektu varijantnih tripleta na DMPK ekspanzije u somatskim ćelijama, što objaš -
njava kasniji uzrast početka simptoma bolesti, kao i stabilišućem efektu u polnim ćelijama što objašnjava
odsustvo najteže forme bolesti u porodicama sa varijantnim tripletima. Takođe, rad predstavlja naše originalno
otkriće metilacije varijantnih CCG tripleta, koje otvara pitanje uloge epigenetičkih mehanizama u stabilizaciji
DMPK lokusa. Dosadašnja znanja ističu kliničku relevantnost varijantnih tripleta u pogledu pružanja
adekvatnog genetičkog saveta i regrutovanja bolesnika za kliničke studije, i podržavaju somatsku nestabilnost
ekspanzija kao metu za nove terapeutike.Repeat expansions in microsatellites or dynamic mutations cause ~50 neurological diseases, known as repeat
expansion diseases. Quantitative effect of the repeat number and inherent instability of dynamic mutations
underlie unique features of these diseases, such as genetic anticipation – an earlier and more severe
disease presentation in successive generations, and a pronounced variability in clinical presentation. Myotonic
dystrophy type 1 (DM1) is caused by expansion of CTG repeats in DMPK gene, whose number is the
main determinant of an extremely variable phenotype, making prognosis of the disease course challenging.
A part of unexplained phenotype variability suggests the existence of disease modifiers. Variant repeats
(CCG, CTC, CAG) are present in ~5% of patients and have been associated with unusual and/or milder symptoms than expected for a given expansion size. In this review, we provide an overview of types of variant repeats,
clinical characteristics of patients, and mechanisms by which variant repeats modify DM1 phenotype.
The key role is attributed to their stabilizing effect on DMPK expansions in the somatic cells, explaining a later
age at symptoms onset, as well as in the germline cells, clarifying the absence of the most severe DM1 form
in families with variant repeats. Additionally, we present our discovery of the methylation of CCG variant repeats,
raising the question of the role of epigenetic mechanisms in the stabilization of DMPK locus. Current
knowledge highlights the clinical relevance of variant repeats for genetic counseling and patient recruitment
for clinical studies, and supports somatic instability of expansions as therapeutic targets
Synthesis and characterization of polyethylene terephthalate (PET) precursors and potential degradation products: Toxicity study and application in discovery of novel PETases
Get PDFPolyethylene terephthalate (PET) is widely used material and as such became highly enriched in nature. It is generally considered inert and safe plastic, but due to the recent increased efforts to break-down PET using biotechnological approaches, we realized the scarcity of information about structural analysis of possible degradation products and their ecotoxicological assessment. Therefore, in this study, 11 compounds belonging to the group of PET precursors and possible degradation products have been comprehensively characterized. Seven of these compounds including 1-(2-hydroxyethyl)-4-methylterephthalate, ethylene glycol bis(methyl terephthalate), methyl bis(2-hydroxyethyl terephtahalate), 1,4-benzenedicarboxylic acid, 1,4-bis[2-[[4-(methoxycarbonyl)benzoyl]oxy]ethyl] ester and methyl tris(2-hydroxyethyl terephthalate) corresponding to mono-, 1.5-, di-, 2,5- and trimer of PET were synthetized and structurally characterized for the first time. In-silico druglikeness and physico-chemical properties of these compounds were predicted using variety of platforms. No antimicrobial properties were detected even at 1000 μg/mL. Ecotoxicological impact of the compounds against marine bacteria Allivibrio fischeri proved that the 6 out of 11 tested PET-associated compounds may be classified as harmful to aquatic microorganisms, with PET trimer being one of the most toxic. In comparison, most of the compounds were not toxic on human lung fibroblasts (MRC-5) at 200 μg/mL with inhibiting concentration (IC50) values of 30 μg/mL and 50 μg/mL determined for PET dimer and trimer. Only three of these compounds including PET monomer were toxic to nematode Caenorhabditis elegans at high concentration of 500 μg/mL. In terms of the applicative potential, PET dimer can be used as suitable substrate for the screening, identification and characterization of novel PET-depolymerizing enzymes.This is the peer-reviewed version of the article: Djapovic, M.; Milivojevic, D.; Ilic-Tomic, T.; Lješević, M.; Nikolaivits, E.; Topakas, E.; Maslak, V.; Nikodinovic-Runic, J. Synthesis and Characterization of Polyethylene Terephthalate (PET) Precursors and Potential Degradation Products: Toxicity Study and Application in Discovery of Novel PETases. Chemosphere 2021, 275, 130005. [https://doi.org/10.1016/j.chemosphere.2021.130005]Supplementary material: [https://imagine.imgge.bg.ac.rs/handle/123456789/1733
Comparative Study of the Antimicrobial Activity of Selenium Nanoparticles With Different Surface Chemistry and Structure
Get PDFAlthough selenium nanoparticles (SeNPs) have gained attention in the scientific community mostly through investigation of their anticancer activity, a great potential of this nanomaterial was recognized recently regarding its antimicrobial activity. The particle form, size, and surface chemistry have been recognized as crucial parameters determining the interaction of nanomaterials with biological entities. Furthermore, considering a narrow boundary between beneficial and toxic effects for selenium per se, it is clear that investigations of biomedical applications of SeNPs are very demanding and must be done with great precautions. The goal of this work is to evaluate the effects of SeNPs surface chemistry and structure on antimicrobial activity against several common bacterial strains, including Staphylococcus aureus (ATCC 6538), Enterococcus faecalis (ATCC 29212), Bacillus subtilis (ATCC 6633), and Kocuria rhizophila (ATCC 9341), as well as Escherichia coli (ATCC 8739), Salmonella Abony (NCTC 6017), Klebsiella pneumoniae (NCIMB 9111) and Pseudomonas aeruginosa (ATCC 9027), and the standard yeast strain Candida albicans (ATCC 10231). Three types of SeNPs were synthesized by chemical reduction approach using different stabilizers and reducing agents: (i) bovine serum albumin (BSA) + ascorbic acid, (ii) chitosan + ascorbic acid, and (iii) with glucose. A thorough physicochemical characterization of the obtained SeNPs was performed to determine the effects of varying synthesis parameters on their morphology, size, structure, and surface chemistry. All SeNPs were amorphous, with spherical morphology and size in the range 70–300 nm. However, the SeNPs obtained under different synthesis conditions, i.e. by using different stabilizers as well as reducing agents, exhibited different antimicrobial activity as well as cytotoxicity which are crucial for their applications. In this paper, the antimicrobial screening of the selected systems is presented, which was determined by the broth microdilution method, and inhibitory influence on the production of monomicrobial and dual-species biofilm was evaluated. The potential mechanism of action of different systems is proposed. Additionally, the cytotoxicity of SeNPs was examined on the MRC-5 cell line, in the same concentration interval as for antimicrobial testing. It was shown that formulation SeNPs-BSA expressed a significantly lower cytotoxic effect than the other two formulations
Genetic evaluation of newborns with critical congenital heart defects admitted to the intensive care unit
No full textRapid and efficient diagnostics is crucial for newborns with congenital heart defects (CHD) in intensive care unit (ICU) but is often challenging. Given that genetic factors play a role in 20-30% cases of CHD, it is likely that genetic tests could improve both its speed and efficiency. We aimed to analyze the utility of rapid and cost-effective multiplex ligation dependent probe amplification analysis (MLPA) for chromosomal analysis in newborns with critical CHD. One hundred consecutive newborns admitted with critical CHD to the ICU were included in the study. Those with normal MLPA findings were further tested by chromosomal microarray and clinical exome sequencing. Overall, pathogenic/likely pathogenic variants were determined in ten (10%) newborns by MLPA, three (3%) by chromosomal microarray, and three (3%) by clinical exome sequencing. The most common variant detected was deletion of 22q11.2 region. Conclusion: MLPA is fast and cost-effective analysis that could be used as the first-tier test in newborns with critical CHD admitted to the ICU. What is Known: center dot MLPA is an established method for chromosome analysis in patients with CHD, but detection rate in newborns with critical CHD is unknown. What is New: center dot Study suggests that detection rate of casual variants using MLPA in newborns with critical CHD is 10%
Different Functions of Recombinantly Expressed Domains of Tenascin-C in Glial Scar Formation (vol 11, 3944, 2021)
Get PDFPolyhydroxyalkanoate/Antifungal Polyene Formulations with Monomeric Hydroxyalkanoic Acids for Improved Antifungal Efficiency
Get PDFNovel biodegradable and biocompatible formulations of "old" but "gold" drugs such as nystatin (Nys) and amphotericin B (AmB) were made using a biopolymer as a matrix. Medium chain length polyhydroxyalkanoates (mcl-PHA) were used to formulate both polyenes (Nys and AmB) in the form of films (similar to 50 mu m). Thermal properties and stability of the materials were not significantly altered by the incorporation of polyenes in mcl-PHA, but polyene containing materials were more hydrophobic. These formulations were tested in vitro against a panel of pathogenic fungi and for antibiofilm properties. The films containing 0.1 to 2 weight % polyenes showed good activity and sustained polyene release for up to 4 days. A PHA monomer, namely 3-hydroxydecanoic acid (C10-OH), was added to the films to achieve an enhanced synergistic effect with polyenes against fungal growth. Mcl-PHA based polyene formulations showed excellent growth inhibitory activity against both Candida yeasts (C. albicans ATCC 1023, C. albicans SC5314 (ATCC MYA-2876), C. parapsilosis ATCC 22019) and filamentous fungi (Aspergillus fumigatus ATCC 13073; Trichophyton mentagrophytes ATCC 9533, Microsporum gypseum ATCC 24102). All antifungal PHA film preparations prevented the formation of a C. albicans biofilm, while they were not efficient in eradication of mature biofilms, rendering them suitable for the transdermal application or as coatings of implants
Toxicity investigation of CeO2 nanoparticles coated with glucose and exopolysaccharides levan and pullulan on the bacterium Vibrio fischeri and aquatic organisms Daphnia magna and Danio rerio
No full textCerium oxide nanoparticles (nCeO(2)) have widespread applications, but they can be hazardous to the environment. Some reports indicate the toxic effect of nCeO(2) on tested animals, but literature data are mainly contradictory. Coating of nCeO(2) can improve their suspension stability and change their interaction with the environment, which can consequently decrease their toxic effects. Herein, the exopolysaccharides levan and pullulan, due to their high water solubility, biocompatibility, and ability to form film, were used to coat nCeO(2). Additionally, the monosaccharide glucose was used, since it is a common material for nanoparticle coating. This is the first study investigating the impact of carbohydrate-coated nCeO(2) in comparison to uncoated nCeO(2) using different model organisms. The aim of this study was to test the acute toxicity of carbohydrate-coated nCeO(2) on the bacterium Vibrio fischeri NRRL B-11177, the crustacean Daphnia magna, and zebrafish Danio rerio. The second aim was to investigate the effects of nCeO(2) on respiration in Daphnia magna which was performed for the first time. Finally, it was important to see the relation between Ce bioaccumulation in Daphnia magna and Danio rerio and other investigated parameters. Our results revealed that the coating decreased the toxicity of nCeO(2) on Vibrio fischeri. The coating of nCeO(2) did not affect the nanoparticles' accumulation/adsorption or mortality in Daphnia magna or Danio rerio. Monitoring of respiration in Daphnia magna revealed changes in CO2 production after exposure to coated nCeO(2), while the crustacean's O-2 consumption was not affected by any of the coated nCeO(2). In summary, this study revealed that, at 200 mg L-1 uncoated and carbohydrate-coated nCeO(2) are not toxic for the tested organisms, however, the CO2 production in Daphnia magna is different when they are treated with coated and uncoated nCeO(2). The highest production was in glucose and levan-coated nCeO(2) according to their highest suspension stability. Daphnia magna (D. magna), Danio rerio (D. rerio), Vibrio fischeri (V. fischeri)Accepted version: [https://imagine.imgge.bg.ac.rs/handle/123456789/2819