imagine (Institute of molecular genetics and genetic engineering)
Not a member yet
3088 research outputs found
Sort by
Rare metabolic diseases in the genomics era
Get PDFIntroduction: All inborn metabolic diseases are rare, having a prevalence less than 1:2000. Vast majority of them are monogenic and finding pathogenic genetic variantsis needed to setthe correct diagnosis, enable adequate treatment and provide genetic counseling to members of affected family. Thisstudy is an overview of genomic studies of rare metabolic diseases in Serbia. Methods: Since 2005, more than 300 patients suspected to have a rare metabolic or neurometabolic disease have been analyzed using sanger sequencing, clinical-exome sequencing, whole-exome sequencing or whole-genome sequencing in order to find disease-causing or disease-modifying variants. Novel variants were characterized using in silico modelling or in in vitro eukaryotic assays (standard or CRISPR/Cas9 developed). Results: Disease-causing variants were found in more than 60 different genes associated with a metabolic or neurometabolic disease. The most frequent disease was phenylketonuria (109 patients), followed by glycogen storage disease Ib (30 patients), while majority of diseases is seen only in a single patient. More than 40 new genetic variants were comprehensively characterized in silico or in vitro. For the first time, candidate modifiers (SHANK gene family) were identified in a group of phenylketonuria patients with an unusual phenotype. Conclusion: In the genomics era, next-generation sequencing significantly shortens time to diagnosis and allowsstudying genetic modifiers of monogenic diseases and genotype-phenotype correlation. Furthermore, characterization of novel genetic targets boosts development of precision medicin
E-cigarette vapor condensate affects mitochondrial function in A549 cells
Get PDFIntroduction: E-cigarettes are becoming increasingly popular, but their potentially harmful effects are
not well studied. Although they are used to aid smoking cessation, there is evidence that the chemicals
they contain can affect lung cells, and the effects may also be important for lung cancer cells. Our objective wasto investigate the effects of e-cigarette vapor condensate on mitochondrial function of A549
cells.
Methods: We used the Agilent Seahorse Mito Stress Test, according to the manufacturer’s protocol to
evaluate the mitochondrial function of A549 cells under the treatment with different concentrations of
e-cigarette vapor condensates. Vapor condensates were prepared from e-cigarette liquid base (PG/VG),
base with nicotine (PG/VG+N), with flavoring (PG/VG+F), or with nicotine and flavoring (PG /VG+F+N).
The cells were exposed to 2% or 3% PG /VG, PG /VG+F, PG/VG+N, and PG/VG+F+N for 24 hours before
testing.
Results: All treatments with 2% vapor condensates affected mitochondrial function of A549 cells. Basal
and maximal respiration were decreased, indicating mitochondrial dysfunction. Higher concentrations
of vapor condensate (3%) significantly increased proton leak and decreased mitochondrial coupling efficiency, indicating mitochondrial damage. However, the increased spare respiratory capacity, in 3%
vapor condensate treated cells, may indicate activation of a compensatory response in mitochondria.
Conclusion: Our resultssuggest that e-cigarette vapor condensate may have deleterious effects on mitochondria. Further analysis of mitochondrial function and morphology would further elucidate the effects of e-cigarette vapor condensate
Herbicide-resilient bacterial consortia in plant growth promotion
Get PDFModern agriculture relies heavily on agrochemicals that can adversely affect
non-target organisms, including microorganisms. In terms of agricultural sustainability,
herbicideresilient plant growth-promoting (PGP) bacteria that can
improve crop yield are critical. Previously, we isolated 122 high herbicide concentration
tolerant (HHCT) bacteria from soils contaminated with S-metolachlor,
a widely used herbicide. Initially, in vitro experiments were conducted to screen
potential candidates for further evaluation. Our goal was to identify HHCT bacteria
with high PGP potential, and the ability to improve soil quality and biocontrol
activity. Subsequently, the most promising candidates were grouped
into three consortia and evaluated in pot for their effects on corn seed germination,
early-stage plant development, and root colonization. Experiments were
conducted with seeds of commercial maize hybrids under controlled conditions,
with and without the presence of the herbicide S-metolachlor. The results
showed that the consortia positively affected seed germination and promoted
higher germination rates. The bacterial isolates showed the ability to colonize
the root system of maize, with significant effects of the consortia on shoot and
root biomass and shoot and root length. However, it was observed in some
consortia that the presence of herbicides resulted in plant damage. Markedly,
the presence of the herbicide S-metolachlor reduced or reversed the beneficial
effects of bacterial consortia. This could be due to incomplete biotransformation
of the herbicide leading to the formation of toxic intermediates. The selection
of bacterial consortia that not only promote plant growth but also have the ability
to fully biotransform herbicides is critical. In conclusion, the isolated HHCT
bacteria showed promising PGP potential and formed an effective consortium
to promote maize seed germination and early-stage development. However,
careful consideration of the selection of bacterial consortia is required to ensure
their compatibility with herbicides and to minimize negative impacts on plant
health and environmental sustainability.Book of abstract: ICGEB WORKSHOP; Trends in microbial solutions for sustainable agriculture, 13 – 15 September 2023. Belgrade, Serbi
Outer membrane vesicles of plant beneficial bacterial strain Paraburkholderia phytofirmans PsJN make a contact with Arabidopsis thaliana roots
Get PDFExtracellular vesicles (EVs) are recognized as important mediators of intercellular
communication in both eukaryotes and prokaryotes. These lipid membrane –
coated spherical nanoparticles carry proteins, nucleic acids and other cellular
products, and facilitate exchange of these biomolecules among cells within an
organism, but also between cells of different organisms, belonging to different
species and even kingdoms. Outer membrane vesicles (OMVs), EVs produced
by Gram-negative bacteria, are a significant mediator of microbial communication,
involved in biofilm formation, virulence, and modulation of host immunity.
OMVs of both pathogenic and plant beneficial bacteria have been shown
to elicit plant immune responses. Investigations on the modes of OMV-plant
cells interactions are still in their infancy, but gain rising attention. Aiming to
monitor the interaction between OMVs of Paraburkholderia phytofirmans PsJN,
a plant growth promoting bacteria, and Arabidopsis thaliana roots, we isolated
OMVs from bacterial culture in mineral medium, using an ion-exchange chromatography
system. Isolated OMVs were labeled with lipid binding fluorescent
dye Vybrant™ DiD and unbound dye was removed by washing vesicles on ultrafiltration
columns. The same dye concentration in phosphate buffer saline,
equivalently washed, was used as a control. A. thaliana roots, grown on Murashige
and Skoog medium, were incubated with DiD-OMVs or control dye/buffer
mixture, washed and observed under confocal laser scanning microscope. Red
signals were observed in root hairs and epidermis in DiD-OMV treated plants,
while in control-treated roots the same signals were missing. The results indicate
direct contact of bacterial vesicles with epidermis and root hairs, which are
indispensable for nutrient acquisition and plant-microbe interactions in rhizosphere.
Further investigation will address the questions of the nature of OMVplant
cell interaction, including potential delivery of OMVs cargo into host plant
cells. Considering that OMVs are increasingly recognized as promising tools in
biomedicine, exploring their potential for agronomical applications would be
highly appreciated.Book of abstract: ICGEB WORKSHOP; Trends in microbial solutions for sustainable agriculture, 13 – 15 September 2023. Belgrade, Serbi
High herbicide concentration tolerant bacteria in plant growth promotion
Get PDForganisms, including microorganisms. In the global effort to increase agriculture sustainability, there
is an emerging need for herbicide-resilient plant growth-promoting (PGP) bacteria that improve
essential crops yield. From S-metolachlor-contaminated soils, we isolated 122 strains of high herbicide
concentration tolerant (HHCT) bacteria capable of growing on or using herbicide as their sole carbon
source. The aim of our study was to identify HHCT bacteria with the highest PGP potential, soil quality
improvement ability, biocontrol activity, and plant colonization capability; then combine them into
consortia that include all these traits, and test them in planta. PGP property evaluation included assays
for nitrogen fixation, phosphate solubilization, IAA, siderophore, and exopolysaccharide production,
detection of extracellular enzymatic activities, and motility. Strains were identified through 16S rDNA
sequencing. Biocontrol potential was evaluated against plant pathogens such as Fusarium sp. , and P.
fuscovaginae. The most promising candidates were combined in three consortia for growth-chamber
experiments to investigate the promotion of maize seed germination, early-stage plant development,
and root colonization evaluated by metagenomic analysis. The HHCT bacteria showed promising
PGP potential. 32% of the collection exhibited 3-4 of four tested direct PGP mechanisms. 22 isolates
had antifungal, and 13 had antibacterial activity. The strains with the highest in vitro PGP activity
predominantly belonged to Serratia, Pseudomonas, and Sphingobacterium genera. These strains
formed the most effective consortium that promoted seed germination and increased shoot and root
dry weight at the early-stage development.Book of abstracty: CEESMECentral and Eastern Europe Symposium
on Microbial Ecology
12-15 September 2023
Budapest, Hungar
Differential Antioxidant Response to Supplemental UV-B Irradiation and Sunlight in Three Basil Varieties
Get PDFThree basil plant varieties (Ocimum basilicum var. Genovese, Ocimum × citriodorum, and Ocimum basilicum var. purpurascens) were grown under moderate light (about 300 µmol photons m−2 s−1) in a glasshouse or growth chamber and then either transferred to an open field (average daily dose: 29.2 kJ m−2 d−1) or additionally exposed to UV-B irradiation in a growth chamber (29.16 kJ m−2 d−1), to reveal the variety-specific and light-specific acclimation responses. Total antioxidant capacity (TAC), phenolic profile, ascorbate content, and class III peroxidase (POD) activity were used to determine the antioxidant status of leaves under all four light regimes. Exposure to high solar irradiation at the open field resulted in an increase in TAC, total hydroxycinnamic acids (HCAs, especially caffeic acid), flavonoids, and epidermal UV-absorbing substances in all three varieties, as well as a two-fold increase in the leaf dry/fresh weight ratio. The supplemental UV-B irradiation induced preferential accumulation of HCAs (rosmarinic acid) over flavonoids, increased TAC and POD activity, but decreased the ascorbate content in the leaves, and inhibited the accumulation of epidermal flavonoids in all basil varieties. Furthermore, characteristic leaf curling and UV-B-induced inhibition of plant growth were observed in all basil varieties, while a pro-oxidant effect of UV-B was indicated with H2O2 accumulation in the leaves and spotty leaf browning. The extent of these morphological changes, and oxidative damage depended on the basil cultivar, implies a genotype-specific tolerance mechanism to high doses of UV-B irradiation
A Machine-Learning-Based Approach to Prediction of Biogeographic Ancestry within Europe
Get PDFData obtained with the use of massive parallel sequencing (MPS) can be valuable in population genetics studies. In particular, such data harbor the potential for distinguishing samples from different populations, especially from those coming from adjacent populations of common origin. Machine learning (ML) techniques seem to be especially well suited for analyzing large datasets obtained using MPS. The Slavic populations constitute about a third of the population of Europe and inhabit a large area of the continent, while being relatively closely related in population genetics terms. In this proof-of-concept study, various ML techniques were used to classify DNA samples from Slavic and non-Slavic individuals. The primary objective of this study was to empirically evaluate the feasibility of discerning the genetic provenance of individuals of Slavic descent who exhibit genetic similarity, with the overarching goal of categorizing DNA specimens derived from diverse Slavic population representatives. Raw sequencing data were pre-processed, to obtain a 1200 character-long binary vector. A total of three classifiers were used—Random Forest, Support Vector Machine (SVM), and XGBoost. The most-promising results were obtained using SVM with a linear kernel, with 99.9% accuracy and F1-scores of 0.9846–1.000 for all classes
Detection rate of 22q11.2 microdeletion using strict diagnostic criteria
Get PDFBackground/Objectives: 22q11.2 microdeletion, detected in
patients with 22q11.2 Deletion Syndrome (22q11.2DS), is the most
common microdeletion syndrome in humans. 22q11.2DS has high
risk for neurodevelopmental disorders and is associated with more than 180 malformations. Many investigations of the 22q11.2
microdeletion applying different recruitment criteria, revealed
detection rate ranging from zero to 34.7%. Here we analyzed the
frequency of 22q11.2 microdeletion among children having at
least two out of five major characteristics of 22q11.2DS: congenital
heart malformations (CHM), facial dysmorphism, immunological
problems, palatal clefts and hypocalcemia.
Methods: Children with clinical characteristics of 22q11.2DS
were analyzed. Fluorescence in situ hybridization and multiplex
ligation-dependent probe amplification analysis were applied for
detection of 22q11.2 microdeletion.
Results: 22q11.2 microdeletion was detected in approximately
40% of children. CHM was found in all patients with 22q11.2
microdeletion. Dysmorphic facial features were present in about
45%, immunological problems in 30%, overt cleft palate in about
4% and hypocalcemia in approximately 60% of patients with
22q11.2 microdeletion.
Conclusion: When at least two major features of 22q11.2DS are
taking into consideration higher detection rate is obtained compared
to one-feature criterion. These criteria could be considered
by centers in low-income countries.Abstracts from the 55th European Society of Human Genetics
(ESHG) Conference: e-Poster
4th Belgrade Bioinformatics Conference
No full textDear colleagues and friends, The 4th Belgrade Bioinformatics Conference - BelBi2023, where many high- quality scientific contributions were presented, has just ended. With great thanks to all participants, we now proudly present a book of abstracts that both reflects the scientific abundance and diversity of the conference and serves as a reminder of a memorable event. Several research institutions, faculties, and scientific societies from Serbia joined forces in organizing this international conference, which covered numerous topics in computational biology, bioinformatics, and biomedical and health informatics. The main goal of BelBi2023 was to foster contact between scientists, both early stage career and senior researchers, allowing them to share experiences and latest advances in their fields. We sincerely hope that BelBi2023 has served as a platform for researchers from around the world to meet, initiate new collaborations, and expand professional contacts, and that all of you would become a part of the growing BelBi community. We are grateful and proud to have welcomed more than 250 researchers from 21 countries. We have had 28 scientific sessions, consisting of more than 60 lectures (including eight Keynote talks), 47 presented posters, as well as three workshops and one satellite event – COST action. We have also organized seven industry lectures, including the NGS Challenge, two Meet the Expert Sessions, and one Business Coffee Break where ten start-up companies took part. And finally, the future BIO4 campus was presented and first panel on Serbia’s resources for storage and analyses of genetic data was organized. We would like to thank all the members of the International Advisory Board and the International Program Committee for their efforts and help in making this event a success. We are very grateful to the Ministry of Science, Technological Development and Innovation of the Republic of Serbia, SAIGE project, and UNDP-Serbia for their support. Finally, the Local Organizing Committee is very grateful to all the sponsors of the conference - BGI, Illumina & Elta’90MS, PacBio & East Diagnostics, ThermoFisher Scientific & Vivogen, Huawei, Labena, DSP Chromatography, RNIDS, Telekom Srbija, Alfa Genetics, Kefo and Superlab, hoping that they will stay with us for many years to come. Looking forward to seeing you again at the 5th Belgrade Bioinformatics Conference. Belgrade, July 2023Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Анализа алтернативних транскрипата гена CD81 у колоректалном карциному
Get PDFTranskripcija gena CD81, čiji proteinski produkt ostvaruje brojne biološke
uloge i uključen je u razvoj maligniteta, regulisana je alternativnim
promotorima. U prethodnoj in silico studiji pokazali smo da se regulatorni
proteini diferencijalno vezuju za alternativne promotore gena CD81 označene
kao A i B, za koje je prethodno pokazano da su diferencijalno aktivni u
kolorektalnom karcinomu.1,2 Cilj ovog rada bio je da se u kolorektalnom
karcinomu in vitro analiziraju transkripti koji nastaju usled aktivnosti ovih
promotora. Ekspresija alternativnih transkripata, kao i ukupna ekspresija gena
CD81 analizirane su u humanim ćelijskim linijama kolona metodom PCR u
realnom vremenu. Pokazano je da alternativni promotori doprinose ukupnoj
ekspresiji gena CD81 sa relativno malim udelom: promotor A 0,43-12,86%, a
promotor B 0,40-4,13%. U nemalignoj ćelijskoj liniji HCEC-1CT, pokazan je
približno jednak nivo ekspresije transkripata oba promotora, dok je u malignim
ćelijskim linijama HT29, Caco-2, HCT116, SW480 i SW620, ekspresija
transkipata promotora A bila veća u odnosu na promotor B, što je očekivano na
osnovu prethodnih in silico studija. Dobijeni rezultati ukazuju na potencijal
alternativnih transkripata gena CD81 kao biomarkera za kolorektalni karcinom.
Kako uloga transkripata nije poznata, njihova struktura i ekspresija sugerišu da
treba ispitati mogućnost da neki od njih mogu biti duge nekodirajuće RNK.Транскрипција гена CD81, чији протеински продукт остварује бројне биолошке
улоге и укључен је у развој малигнитета, регулисана је алтернативним
промоторима. У претходној in silico студији показали смо да се регулаторни
протеини диференцијално везују за алтернативне промоторе гена CD81 означене
као А и Б, за које је претходно показано да су диференцијално активни у
колоректалном карциному.1,2 Циљ овог рада био је да се у колоректалном
карциному in vitro анализирају транскрипти који настају услед активности ових
промотора. Експресија алтернативних транскрипата, као и укупна експресија гена
CD81 анализиране су у хуманим ћелијским линијама колона методом ПЦР у
реaлном времену. Показано је да алтернативни промотори доприносе укупној
експресији гена CD81 са релативно малим уделом: промотор А 0,43-12,86%, а
промотор Б 0,40-4,13%. У немалигној ћелијској линији HCEC-1CT, показан је
приближно једнак ниво експресије транскрипата оба промотора, док је у малигним
ћелијским линијама HT29, Caco-2, HCT116, SW480 и SW620, експресија
транскипата промотора А била већа у односу на промотор Б, што је очекивано на
основу претходних in silico студија. Добијени резултати указују на потенцијал
алтернативних транскрипата гена CD81 као биомаркера за колоректални карцином.
Како улога транскрипата није позната, њихова структура и експресија сугеришу да
треба испитати могућност да неки од њих могу бити дуге некодирајуће РНК.Knjiga sažetaka: Treći Kongres biologa Srbije, Zlatibor, Srbija 21 - 25. 9. 2022