imagine (Institute of molecular genetics and genetic engineering)
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Lineage marker as a key player in complex forensic cases from the perspective of Y chromosome
Get PDFKako se Y hromozom kroz generacije ne menja rekombinacijama, prenosi se uglavnom nepromenjen
sa oca na sina. Haplotipovi dobijeni kombinovanom analizom kratkih tandemskih ponovaka na Y hromozomu
imaju široku primenu u forenzičkim analizama za definisanje paternalne linije muškog donora biološkog
traga, posebno u slučajevima gde standardna analiza autozomnih markera nije dovoljno
informativna. Y vezani haplotipovi se koriste i u evolucionim i genealoškim studijama, ali se za rekonstrukciju
filogenije Y hromozoma koristi analiza polimorfizama pojedinačnih nukleotida. Promene na Y
hromozomu se ipak dešavaju usled mutacija što može da dovede do diferencijacije Y vezanih haplotipova
između oca i sinova. Tako mutacije u lokusima sa kratkim tandemskim ponovcima mogu da omoguće
identifikaciju muškarca u okviru jedne paternalne linije, ali mogu i da dovedu do progrešnog isključenja
biološkog srodstva. Usled toga je za tačnu interpretaciju genetičkih profila neophodna precizna procena
stope mutacije pojedinačnih lokusa, za šta se koriste studije parova otac-sin ili velikih porodični stabala.Y chromosome is transmitted mostly unchanged from father to son due to the absence of recombination
events. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms
are widely used to define paternal line of unknown male perpetrator in forensic analysis, especially
when standard analysis of autosomal markers is not informative enough. Y-chromosomal haplotypes
are also used in evolutionary and genealogical studies, but single nucleotide polymorphisms are more
suitable for the reconstruction of the Y chromosome phylogeny. However, Y chromosome changes
due to mutations, which could lead to differentiation of Y haplotypes between father and sons. Thus,
mutations in short tandem repeats loci can enable the identification of a man within a single paternal
line, but they could also lead to an erroneous exclusion of biological paternity. Reliable mutation
rates, for the proper use and accurate interpretation of genetic profiles, could be estimated from
multi-generation pedigrees or father-son pairs
Antimicrobial and cytotoxic activity of pigmented Streptomyces spp. culture extracts
Get PDFBACKGROUND
Pigments from microbial origin have promising applications in food, cosmetics, textiles and therapeutics.
Compared to other natural sources pigments from bacteria are more stable, safer, and could be cheaper to
produce and extract. Bacterial genus Streptomyces has been known as a source of biologicaly active pigments
that exhibit several effects such as antimicrobial and cytotoxic.
OBJECTIVES
The aim of this study was the isolation of pigment-producing Streptomyces strain from soil, optimization of
growth parametres for pigment production and evaluation of antimicrobial and cytotoxic activity of extracted
bacterial pigments.
METHODS
Isolation and characterization of pigment-producing Streptomyces strain from soil was done following the
standard microbiological protocol, using four different growth media. The pigments were extracted by solvent
extraction using ethyl acetate. Antimicrobial activity was analyzed using the disc diffusion test. Cytotoxic activity
was tested on the HaCaT cell line following the standard protocol.
RESULTS
Extraction of pigments by solvent extraction resulted in crude pigment extracts with antimicrobial activities.
In total pigments from 14 bacterial strains have been extracted. Antimicrobial activity was evident on Gram +
bacteria Staphylococcus aureus (6 mm of inhibition zone at concentration 8.4 μg/ml and 4 mm of inhibition
zone at concentration 1.1 μg/ml) as well as on the fungus Candida albicans (4 mm of inhibition zone at concentration
13 μg/ml). Pigments showed dose-dependent inhibiton of proliferation of HaCaT cells, with the
lowest concentration at 25 μg/ml.ELECTRONIC ABSTRACT BOOK: FEMS Conference on Microbiology in association with Serbian Society of Microbiology 30 June - 2 July 2022; Serbi
Late embryogenesis abundant proteins: Structural characterisation and interaction with α-synuclein
Get PDFRessurection plants are extraordinary because of their ability to withstand long periods
without water, enter a state of anhydrobiosis, and fully recover upon water arrival.
Ramonda serbica is a relic and endemic species that belong to a very small group of
desiccation-tolerant plants in Europe. Underlying physiological, molecular and
morphological mechanisms that enable these plants to survive harsh environmental
conditions have been an appealing subject to many researchers. Most of the genes
responsible for this amazing ability are present in other plants, and this path of research
where those genes could be activated in crops is growing much more attention because of
the imminent crisis regarding food supplies in the near future. Key components involved in
the response to dehydration in R. serbica plants were analysed through a comprehensive
transcriptomic, proteomic, metabolite and photosynthetic study. Late embryogenesis
abundant proteins play a significant role in the complex defence processes involved in
desiccation tolerance. Defining physicochemical characteristics and specific physiological
functions of late embryogenesis abundant proteins – LEAPs may lead to their applicability
in other areas of research
Eco conversion of lower grade PET and mixed recalcitrant PET plastic waste into high performing biopolymers (EcoPlastiC)
Get PDFProject ‘EcoPlastiC’ is putting PET plastics into a perpetual bio-cyclable loop. Polyethylene
terephthalate (PET), a polymer used extensively in single-use packaging and beverage bottles as
well as in the textiles industry, is not very circular. There is a growing need to convert
unrecyclable post-use PET into new, high-performance bioplastics. In this case, post-use
materials become ingredients for new products. The EU-funded EcoPlastiC project will optimise
PET circularity. It will convert lower-grade PET and mixed recalcitrant PET plastic waste into
high-performing biopolymers, through the development of a suite of breakthrough
technologies adaptable to the waste input. For instance, it will develop a series of mechano-
green, chemical and biocatalytic technologies to depolymerise PET. Moreover, microbiome
processing will be used to produce new biopolymers.Principal Investigator: Dr Margaret Fournet, Athlone Institute of Technology, IrelandCoordinator for IMGGE: Dr Jasmina Nikodinović-RunićDuration period: 2022-202
Analysis of Alternative LDLRAD4 Gene Promoters and Transcripts in Colorectal Cancer
Get PDFGene LDLRAD4 plays a role in cell proliferation, apoptosis, immunosuppression and cancer
progression. Transcription of LDLRAD4 is regulated by several alternative promoters, two of which
were indicated by in silico analyses to be differentially active in rectal cancer. Promoter A encodes for a
truncated protein-coding transcript and is down-regulated in rectal cancer. Promoter B encodes for a
non-coding transcript up-regulated in rectal cancer identified as lnc-RNMT-2:5. The aim of this study
was to characterize the two alternative promoters in silico in order to explain their differential activity
and to investigate the profile of LDLRAD4 transcripts in colon cell lines. Nucleotide sequences used in
the analyses were downloaded from the Ensemble genome database (reference GRCh37). Three
bioinformatics tools were used for core promoter element prediction: GPMiner, YAPP and
CNNPromoter. Four bioinformatics tools were used for transcription factor binding site prediction:
PROMO, TFBIND, CiiiDER and Tfsitescan. Only the predictions made by two or more tools were
considered. Primer extension followed by fragment analysis was used to characterize LDLRAD4
transcripts present in colon cell lines. The promoter element predictions showed that the promoter A is
typical, while promoter B has most typical elements and lacks GC boxes. The transcription binding site
predictions indicate that three different transcription factors bind only to the promoter A (NF-kB,
EGR1 and IRF-7), while four different transcription factors bind only to the promoter B (HNF1,
POU2F1, POU2F2 and PTF1). The predicted transcription factors are mostly involved in regulation of
cell differentiation and proliferation. The primer extension experiment performed with primer specific
for exon 2-exon 3 junction produced multiple signals of relatively low intensity, indicating the presence
of multiple LDLRAD4 transcripts in colon cell lines. The results obtained by in silico analysis may
explain promoter B activation in rectal cancer. However, based on the results of primer extension, neither
of the LDLRAD4 transcripts is dominant in colon cell lines. Considering that promoter B generates
long non-coding RNA that can exert its function even at low expression level, it can serve as potential
colorectal cancer biomarker and its potential role in carcinogenesis should be investigated
RclS Sensor Kinase Modulates Virulence of Pseudomonas capeferrum
Get PDFSignal transduction systems are the key players of bacterial adaptation and survival. The orthodox two-component signal transduction systems perceive diverse environmental stimuli and their regulatory response leads to cellular changes. Although rarely described, the unorthodox three-component systems are also implemented in the regulation of major bacterial behavior such as the virulence of clinically relevant pathogen P. aeruginosa. Previously, we described a novel three-component system in P. capeferrum WCS358 (RclSAR) where the sensor kinase RclS stimulates the intI1 transcription in stationary growth phase. In this study, using rclS knock-out mutant, we identified RclSAR regulon in P. capeferrum WCS358. The RNA sequencing revealed that activity of RclSAR signal transduction system is growth phase dependent with more pronounced regulatory potential in early stages of growth. Transcriptional analysis emphasized the role of RclSAR in global regulation and indicated the involvement of this system in regulation of diverse cellular activities such as RNA binding and metabolic and biocontrol processes. Importantly, phenotypic comparison of WCS358 wild type and Delta rclS mutant showed that RclS sensor kinase contributes to modulation of antibiotic resistance, production of AHLs and siderophore as well as host cell adherence and cytotoxicity. Finally, we proposed the improved model of interplay between RclSAR, RpoS and LasIR regulatory systems in P. capeferrum WCS358
Attaching azoles to Hantzsch 1,4-dihydropyridines: Synthesis, theoretical investigation of nonlinear optical properties, antimicrobial evaluation and molecular docking studies
No full textIn the present study, we designed three novel compounds via the combination of two precious nitrogencontaining scaffolds; 1,4-dihydropyridine (DHP) and azole, in the same molecule. To synthesize the title compounds, initially, azolyl benzaldehydes were obtained through the nucleophilic aromatic substitution reaction of 4-fluorobenzaldehyde with pyrazole, imidazole or 1,2,4-triazole. Subsequently, an unsymmetrical Hantzsch reaction was applied to achieve DHP scaffold, thus the target molecules. After structural characterization, the effects of various azole rings on optical and non-linear optical (NLO) properties were investigated by computational methods. Band gaps, chemical hardness/softness, dipole moments, average polarizability, first hyperpolarizability values were computed for the target compounds at the CAM-B3LYP/6-31++G(d,p) level of theory. The comparable results confirmed the potential of DHP-azole hybrids to be utilized in NLO devices. The title molecules were further tested for their antibacterial and antifungal activities following the evaluation of their drug likeness properties. The compounds containing imidazole or triazole rings represented better antifungal properties than antibacterial activities. Molecular docking studies were performed in the catalytic site of lanosterol 14 alpha-demethylase, CYP51, from Candida albicans to explain the obtained biological results and suggest molecular modifications to endow this class of molecules with improved antifungal effects
Association between active pulmonary tuberculosis and miRNA-146a: A preliminary study from Serbia
Get PDFIntroduction: Tuberculosis (TB) continues to be a significant public health problem. The role of small non-coding RNAs, such as microRNAs (miRNAs), was investigated extensively in Mycobacterium tuberculosis (MTB) infection as well as in a variety of other pathophysiological processes in recent years. It was found that miRNAs act as regulators of both early reaction to MTB infection and in process of adaptation of the host immune cells during latent course of the disease. Molecule miRNA-146a is expressed exclusively in immune cells and it has the most prominent role in modulation of innate immunity. Methodology: We investigated the level of expression of miRNA-146a using an RT-qPCR technique in peripheral blood mononuclear cells of 44 patients with active pulmonary TB and 17 healthy individuals. We also analyzed the significance of miRNA-146a rs2910164 SNV for expression profile of miRNA-146a, in order to investigate potential usage of miRNA-146a as a biomarker for TB. Results: There was statistically significant decrease of expression of miRNA-146a in TB group compared to control group. When gender cohorts were analyzed, the expression levels in TB male and TB female subgroup were significantly lower than the expression levels in the same gender control subgroups. Conclusions: Our results indicate that miRNA-146a plays a significant role in the pathogenesis of TB, suggesting that miRNA-146a could be used as a biomarker for active pulmonary TB
Occurrence of root-knot nematode Meloidogyne arenaria in the potato field in Serbia
Get PDFKorenove nematode ili nematode korenovih gala mogu prouzrokovati značajne gubitke u prinosu krompira u toplim i hladnim regionima. Šest vrsta Meloidogine mogu parazitirati krompir. Vrste Meloidogyne chitvoodi, M. fallax i M. hapla prisutne su u hladnim regionima, dok su M. arenaria, M. incognita i M. javanica uobičajene u toplim regionima i pripadaju tropskoj grupi Meloidogyne vrsta. Meloidogyne arenaria je prisutna u regionima sa kontinentalnom klimom u zaštićenom prostoru i napada veliki broj biljaka domaćina. U oktobru 2018. primećen je usev krompira var. Balatonska ruža sa tumoroznim izraslinama na 70% krtola tokom posebnog nadzora karantinskih vrsta nematoda Meloidogyne chitvoodi i M. fallax na lokalitetu Horgoš, opština Kanjiža, Pokrajina Vojvodina. Uočeni su i simptomi usporenog rasta i uvenuća biljaka. Ženke su korišćene za morfološku i molekularnu identifikaciju. Morfološka analiza vulvalno-analnih konusa je utvrdila vrstu M. arenaria. Identifikacija vrste je potvrđena molekularnom analizom korišćenjem grupnih specifičnih prajmera u rDNK regionu i SCAR prajmera specifičnih za identifikaciju vrste M. arenaria. Prema našim saznanjima, ovo je prvi nalaz velike štetnosti na krompiru prouzrokovanim prisustvom M. arenaria u polju u Srbiji. Na delu Balkanskog poluostrva sa kontinentalnom klimom nisu ranije zabeležene velike štete usled prisustva M. arenaria na krompiru na otvorenom. Ova tropska vrsta Meloidogyne mogla bi u budućnosti da postane novi fitosanitarni problem u Evropi usled globalnog zagrevanja i klimatskih promena.Root-knot nematodes can cause significant losses in potato yield in warm and cool regions. Six Meloidogyne species can attack potato. Species Meloidogyne chitwoodi, M. fallax, M. hapla, are present in cool regions, while M. arenaria, M. incognita and M. javanica are common in warm regions and considered to belong to the Meloidogyne tropical group. Meloidogyne arenaria is present in regions with continental climate in glasshouses attacking a large number of host-plants. In October 2018, potato crop var. Balathon Rose with galls on 70% of all tubers was noticed during quarantine nematode species Meloidogyne chitwoodi and M. fallax survey in the locality Horgoš, municipality of Kanjiža, Vojvodina Province. Symptoms of stunted and wilted plants were detected as well. Females were used for morphological and molecular identification. Morphological identification of species based on females' perineal patterns indicated the sample as M. arenaria. Species identification was confirmed by molecular analyses using group-specific primers in the rDNA region and species-specific SCAR primers for M. arenaria species identification. To our knowledge, this is the first record of highly damaged potato crop caused by M. arenaria in the field in Serbia. The severity of the damage M. arenaria can cause to potato in the open field has not been observed in the part of Balkan peninsula with continental climate before. This tropical Meloidogyne species may become an emerging phytosanitary problem within Europe in the future due global warming and climate change
Identification and profiling of conserved microRNAs in different developmental stages of crown imperial (Fritillaria imperialis L.) using high-throughput sequencing
No full textBackground Novel strategies for improvement of ornamental plants and their properties relay on miRNA control of differential plant gene expression modulation. Still, in response to the same abiotic stresses, some conserved miRNA families show different expression patterns in different plant species. In parallel, the use of deep sequencing technologies reveals new levels of complexity of regulatory networks in plants through identification of new miRNAs. Methods and results Fritillaria imperialis plants were collected from their natural habitats in Koohrang, Chaharmahal va Bakhtiari, Iran. Several tissues including stamen, pistil, petal, sepal, leaf, stem, bulb and fruit were collected during three developmental stages (stem elongation, flower development and seed head stages). Using RNAseq and qRT-PCR approach, this research revealed 21 conserved miRNAs, matching 15 miRNA families, in Fritilaria imperialis. Conclusions The expression of seven conserved miRNAs (Fim-miR156b, Fim-miR159, Fim-miR166a-5p, Fim-miR169d-5p, Fim-miR171c, Fim-miR393 and Fim-miR396e-3p) was further investigated in different tissues and three developmental stages, suggesting different roles for these miRNAs during growth and development of crown imperial. Gained knowledge from this research can open the door to find efficient ways to secure crown imperial survival, preservation and utilization and if proven useful may be applied in other plant species as well