imagine (Institute of molecular genetics and genetic engineering)
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Shotgun metagenomics reveals gut microbiota features associated with the efficacy of myeloid derived suppressor cells in the prevention of neuroinflammation
Get PDFAlthough genetic predisposition to Multiple Sclerosis (MS) may play an essential role in disease
development, myeloid cell overactivation and gut microbiota dysbiosis are key contributors to MS
pathogenesis. Myeloid-Derived Suppressor Cells (MDSC)s are immature myeloid cells with strong
immunosuppressive functions which can be exploited in the treatment of autoimmune diseases.
Considering the limited data on MDSCs application in MS therapy and their poorly studied effects
on the gut microbiota, we have investigated the therapeutic potential of mice MDSC differentiated
according to the standard protocol (MDSC) and modified with the addition of prostaglandin (PG)
E2 (MDSC-PGE2) to ameliorate experimental autoimmune encephalomyelitis (EAE) induced with
MOG35-55/CFA/PtX in C57BL/6 mice. Additionally, we analyzed the changes in gut microbiota
features in control and MDSC-treated animals by using a shotgun metagenomics approach. In
mice, PGE2-activated MDSC significantly inhibited the onset and clinical course of EAE. This effect
correlated with increased IL-10, TGF-β, IL-4 production, and Arginase-1 level in MDSC-PGE2,
as well as with reduced leukocyte infiltrates in the spinal cord. MDSC-PGE2 protective effect is
also reflected in the maintenance of gut microbiota composition based on Kraken2/Bracken2
and LEfSe analysis. We observed an increase of MS-associated species Romboutsia ilealis in
the control EAE group, while in both MDSC treatments the increase in relative abundances of
Muribaculum gordoncarteri and Duncaniella dubiosis, associated with immunoregulatory properties,
was observed. Microbial metabolic pathways profiling using Humann3 pipeline also reveals the
increase in pathways involved in the production of potentially immunoregulatory metabolites
in the MDSC-PGE2 group. In conclusion, we pointed to the significant association between the
efficacy of MDSC-PGE2 treatment and gut microbiota features which can be further exploited in
order to improve MDSC-based EAE therapy.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
The 70th anniversary of the discovery of DNA secondary structure
Get PDFGodina 2023. je godina jubileja u kojoj se obeležava 70 godina od otkrića sekundarne strukture molekula
DNK. U ovom radu preglednog tipa dat je istorijski osvrt na otkrića i eksperimente koji su doveli do razvoja
molekularne biologije, a kasnije i genomike kao nove naučne discipline. Poseban osvrt dat je na događaje
i ljude koji su doprineli postavljanju trodimenzionalnog modela molekula DNK.This year marks the 70th anniversary of the discovery of the secondary structure of DNA molecule. This review-
type paper provides an overview of the most important discoveries and experiments that led first to
the development of molecular biology, and later to the development of genomics as a new scientific discipline.
A special review is given to the events and people who contributed to the establishment of the
three-dimensional model of the DNA molecule
Long read sequencing – the next level in genomic research
Get PDFSekvenciranje dugih fragmenata ili treća generacija sekvenciranja u realnom vremenu produkuje očitavanja
pojedinačnih molekula DNK dužine od 1 kb do nekoliko Mb sa očuvanim epigenetičkim oznakama.
Dostupne tehnologije su sekvenciranje pojedinačnih molekula u realnom vremenu (eng. single-molecule
real-time sequencing, PacBio) i sekvenciranje kroz proteinske nanopore (Oxford Nanopore Technologies).
PacBio tehnologija zasnovana je na detekciji ugradnje nukelotida od strane pojedinačnog molekula DNK
polimeraze u realnom vremenu, korišćenjem fluoresecencije kao surogat markera. PacBio HiFi očitavanja
su dužine ~15 kb sa tačnošću >99,9%. Oxford Nanopore tehnologija izvodi sekvencu nukleotida iz promena
u intenzitetu jonske struje dok DNK prolazi kroz stohastički senzor – proteinsku nanoporu.Može sekvencirati
fragmente DNK u rasponu od pet redova veličina (20 bp do nekoliko Mb) sa tačnošću dupleks
očitavanja >99,9% kada se koriste R10.4.1 nanopore. Sa elektronskim „čitanjem” nukleinskih kiselina, inovacije
kao što su minijaturni uređaj veličine dlana sa cenom <1000 dolara, sekvenciranje na terenu, digitalno
obogaćivanje ciljnih sekvenci (adaptivno uzorkovanje) i direktno sekvenciranje RNK, postali su
stvarnost. Sekvenciranje dugih fragmenata omogućilo je kompletiranje sekvence genoma čoveka, objavljivanje
drafta ljudskog pangenoma i ubrzalo je sekvenciranje genoma eukariota. Od uvođenja metode
2011. godine sekvencirano je ~1000 od 1065 genoma deponovanih u NCBI bazi. Puni potencijal metode
u izučavanju transkriptoma i epigenoma biće vidljiv u godinama koje slede. Sekvenciranje dugih fragmenata
postaje osnova precizne medicine efikasne za sve ljudske populacije i očuvanja biodiverziteta, i zavredelo
je da bude metoda 2022. godine prema časopisu Nature Methods.Long read or third-generation sequencing produces reads from 1 kb to several Mb in length with preserved
epigenetic marks, at the single-molecule level and in real-time. Single-molecule real-time sequencing
(PacBio) and protein nanopore sequencing (Oxford Nanopore Technologies) are available technologies.
PacBio technology is based on monitoring the nucleotide incorporation by a single DNA polymerase molecule
in real time using fluorescence as a surrogate marker. PacBio HiFi reads are ~15 kb in length with
>99.9% accuracy. Oxford Nanopore sequencing infers nucleotide sequence from the changes in ion current
intensity while DNA passes through a stochastic sensor – a protein nanopore. It can sequence DNA
fragments ranging in five orders of magnitude (20 bp to several Mb), with duplex read accuracy >99.9%
when using R10.4.1 nanopores. Innovations such as a miniature device of the palm-size with a price <1000
dollars, sequencing in the field, digital enrichment of target sequences (adaptive sampling) and direct
RNA sequencing have become a reality with the electronic „reading“ of nucleic acids. Long read sequencing
enabled completing the human genome sequence and releasing a draft of the human pangenome
reference. It has also accelerated genome sequencing of eukaryotic species. Out of 1065 genomes deposited
in the NCBI database, ~1000 were sequenced since its development. The full potential of the method
in studying transcriptome and epigenome will be visible in the years to come. Long read sequencing is becoming
the basis of precision medicine effective for all human populations and biodiversity conservation
and was announced as the method of the year 2022 according to Nature Methods
Microbial degradation of terephtalic acid as a PET-derived compound
Get PDFPolyethylene terephthalate (PET) is a plastic material that poses a significant global concerndue to its durability and resistance to degradation. One effective method for minimizing PETwaste is through microbial degradation, resulting in the production of ethylene glycol andterephthalic acid (TA). Terephthalic acid, as a PET monomer, holds promise as a modelcompound for further exploration into PET plastic degradation and valorisation.Book of abstract: Twenty-FirstYoung Researchers Conference –Materials Science and EngineeringNovember 29 –December 1, 2023, Belgrade, Serbi
Differences in MB-COMT DNA methylation in monozygotic twins on phenotypic indicators of impulsivity
Get PDFEpigenetic modifications of the membrane bound catechol-O-methyltransferase (MB-COMT) gene may affect the enzymatic degradation of dopamine, and consequently, human behavior. This study investigated the association between membrane bound catechol-O-methyltransferase DNA methylation (DNAm) differences in 92 monozygotic (MZ) twins with phenotypic manifestations of cognitive, behavioral, and personality indicators associated with reward-related behaviors and lack of control. We used pyrosequencing to determine DNAm of the regulatory region of membrane bound catechol-O-methyltransferase in saliva DNA. Results of intrapair differences in the percentage of membrane bound catechol-O-methyltransferase DNAm at each of five CpG sites show that there are associations between phenotypic indicators of lack of control and membrane bound catechol-O-methyltransferase DNAm differences on CpG1, CpG2 and CpG4, suggesting the common epigenetic patterns for personality traits, cognitive functions, and risk behaviors
Copper(II) and silver(I) complexes with dimethyl 6-(pyrazine-2-yl)pyridine-3,4-dicarboxylate (py-2pz): the influence of the metal ion on the antimicrobial potential of the complex
Get PDFDimethyl 6-(pyrazine-2-yl)pyridine-3,4-dicarboxylate (py-2pz) was used as a ligand for the synthesis of new copper(II) and silver(I) complexes, [CuCl2(py-2pz)]2 (1), [Cu(CF3SO3)(H2O)(py-2pz)2]CF3SO3·2H2O (2), [Ag(py-2pz)2]PF6 (3) and {[Ag(NO3)(py-2pz)]·0.5H2O}n (4). The complexes were characterized by spectroscopic and electrochemical methods, while their structures were determined by single crystal X-ray diffraction analysis. The X-ray analysis revealed the bidentate coordination mode of py-2pz to the corresponding metal ion via its pyridine and pyrazine nitrogen atoms in all complexes, while in polynuclear complex 4, the heterocyclic pyrazine ring of one py-2pz additionally behaves as a bridging ligand between two Ag(I) ions. DFT calculations were performed to elucidate the structures of the investigated complexes in solution. The antimicrobial potential of the complexes 1–4 was evaluated against two bacterial (Pseudomonas aeruginosa and Staphylococcus aureus) and two Candida (C. albicans and C. parapsilosis) species. Silver(I) complexes 3 and 4 have shown good antibacterial and antifungal properties with minimal inhibitory concentration (MIC) values ranging from 4.9 to 39.0 μM (3.9–31.2 μg mL−1). All complexes inhibited the filamentation of C. albicans and hyphae formation, while silver(I) complexes 3 and 4 had also the ability to inhibit the biofilm formation process of this fungus. The binding affinity of the complexes 1–4 with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) was studied by fluorescence emission spectroscopy to clarify the mode of their antimicrobial activity. Catechol oxidase biomimetic catalytic activity of copper(II) complexes 1 and 2 was additionally investigated by using 3,5-di-tert-butylcatechol (3,5-DTBC) and o-aminophenol (OAP) as substrates.Supplementary material: [https://imagine.imgge.bg.ac.rs/handle/123456789/1791
Antimicrobial and UV protective chitosan/lignin multilayer nanocoating with immobilized silver nanoparticles
No full textPoor antimicrobial activity and lack of protection against UV irradiation are weaknesses of cotton
textiles. In an attempt to impart superior antimicrobial and UV-protective properties to cotton, layer-by-
layer deposition of chitosan and magnesium lignosulfonate, and in situ synthesis of silver (Ag)
nanoparticles (NPs), was performed. Lignin, in a chitosan/lignin multilayer, simultaneously acts as a UV
protective macromolecule and natural reducing and stabilizing agent, allowing formation of Ag NPs. Four
bilayers of this coating is sufficient for fabrication of a chitosan/lignin/Ag-NP textile nanocomposite
treatment with 50+ UV protection. 100% reduction of Gram-negative bacteria Escherichia coli, gram-
positive bacteria Staphylococcus aureus, and yeast Candida albicans can be achieved with a 12-bilayer
coating, when 20 mM silver nitrate solution and sodium borohydride are applied. On the other hand,
four bilayers impregnated with Ag NPs, using 10 mM silver nitrate solution, provides sufficient
antimicrobial activity independent of an added reducing agent. This treatment exhibits no inhibition of
human keratinocyte cells growth on the skin, indicating low cytotoxicity.The authors would like to thank the NATO Science for
Peace and Security (SPS) program for their funding
through the G5905 (MULProTex) project. The authors
would also like to acknowledge the Texas A&M Materials
Characterization Facility (MCF) for infrastructural
support
Upcycling of food waste streams to valuable biopigments pyocyanin and 1-hydroxyphenazine
No full textPhenazines, including pyocyanin (PYO) and 1-hydroxyphenazine (1-HP) are extracellular secondary metabolites and multifunctional pigments of Pseudomonas aeruginosa responsible for its blue-green color. These versatile molecules are electrochemically active, involved in significant biological activities giving fitness to the host, but also recognized as antimicrobial and anticancer agents. Their wider application is still limited partly due to the cost of carbon substrate for production, which can be solved by the utilization of carbon from food waste within the biorefinery concept. In this study, a variety of food waste streams (banana peel, potato peel, potato washing, stale bread, yoghurt, processed meat, boiled eggs and mixed canteen waste) was used as sole nutrient source in submerged cultures of P. aeruginosa BK25H. Stale bread was identified as the most suitable substrate to support phenazine biopigments production and bacterial growth. This was further increased in 5-liter fermenter when on average 5.2mgL-1 of PYO and 4.4mgL-1 of 1-HP were purified after 24h batch cultivations from the fermentation medium consisting of homogenized stale bread in tap water. Purified biopigments showed moderate antimicrobial activity, and showed different toxicity profiles, with PYO not being toxic against Caenorhabditis elegans, a free-living soil nematode up to 300µgmL-1 and 1-HP showing lethal effects at 75µgmL-1. Therefore, stale bread waste stream with minimal pretreatment should be considered as suitable biorefinery feedstock, as it can support the production of valuable biopigments such as phenazines
The Role of Autophagy and Apoptosis in Affected Skin and Lungs in Patients with Systemic Sclerosis
Get PDFSystemic sclerosis (SSc) is a complex autoimmune inflammatory disorder with multiple organ involvement. Skin changes present the hallmark of SSc and coincide with poor prognosis. Interstitial lung diseases (ILD) are the most widely reported complications in SSc patients and the primary cause of death. It has been proposed that the processes of autophagy and apoptosis could play a significant role in the pathogenesis and clinical course of different autoimmune diseases, and accordingly in SSc. In this manuscript, we review the current knowledge of autophagy and apoptosis processes in the skin and lungs of patients with SSc. Profiling of markers involved in these processes in skin cells can be useful to recognize the stage of fibrosis and can be used in the clinical stratification of patients. Furthermore, the knowledge of the molecular mechanisms underlying these processes enables the repurposing of already known drugs and the development of new biological therapeutics that aim to reverse fibrosis by promoting apoptosis and regulate autophagy in personalized treatment approach. In SSc-ILD patients, the molecular signature of the lung tissues of each patient could be a distinctive criterion in order to establish the correct lung pattern, which directly impacts the course and prognosis of the disease. In this case, resolving the role of tissue-specific markers, which could be detected in the circulation using sensitive molecular methods, would be an important step toward development of non-invasive diagnostic procedures that enable early and precise diagnosis and preventing the high mortality of this rare disease
Small Cellular Particles from European Spruce Needle Homogenate
Get PDFSmall cellular particles (SCPs) are being considered for their role in cell-to-cell communication. We harvested and characterized SCPs from spruce needle homogenate. SCPs were isolated by differential ultracentrifugation. They were imaged by scanning electron microscope (SEM) and cryogenic transmission electron microscope (cryo TEM), assessed for their number density and hydrodynamic diameter by interferometric light microscopy (ILM) and flow cytometry (FCM), total phenolic content (TPC) by UV-vis spectroscopy, and terpene content by gas chromatography-mass spectrometry (GC-MS). The supernatant after ultracentrifugation at 50,000× g contained bilayer-enclosed vesicles whereas in the isolate we observed small particles of other types and only a few vesicles. The number density of cell-sized particles (CSPs) (larger than 2 μm) and meso-sized particles (MSPs) (cca 400 nm–2 µm) was about four orders of magnitude lower than the number density of SCPs (sized below 500 nm). The average hydrodynamic diameter of SCPs measured in 10,029 SCPs was 161 ± 133 nm. TCP decreased considerably due to 5-day aging. Volatile terpenoid content was found in the pellet after 300× g. The above results indicate that spruce needle homogenate is a source of vesicles to be explored for potential delivery use