imagine (Institute of molecular genetics and genetic engineering)
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Machine learning-based data correlation between scanning electron microscopy images and energy-dispersive X-ray spectroscopy profiles
Get PDFCharacterisation of organic and inorganic microparticles has long been an important
topic in the field of environmental health sciences. Especially, combined analytical
method of scanning electron microscopy (SEM) associated with energy-dispersive X-ray
spectroscopy (EDX) is a commonly exploited approach to obtain extensive data on the size,
morphological, and elemental information from the particulate specimens. Particulate
matter (PM) is a representative atmospheric pollutant that may exert adverse effects
on the human respiratory system, and SEM-EDX is a widely used tool for extracting
PM analysis data, which can be subsequently utilised as physicochemical features for
toxicological predictions.
In this presentation, we show a machine learning-based automation of SEM-EDX
correlation of environmental PM data. First, we segment SEM images using WEKA
trainable segmentation which is based on a random forest algorithm to classify pixels as
foreground and background groups, followed by finding connected components (pixels
that are foreground and connected vertically or horizontally). These regions are used to
calculate PM shape parameters. Next, element maps are obtained from EDX using curve
fitting with HyperSpy Python package. PM regions from SEM images are utilised to sum
intensities in the same spatial location for the element maps to obtain elemental profiles.
We finally build two models to predict PM elements: (1) Element maps from SEMEDX
data using image-to-image translation, and (2) regression to predict PM element
percentages from shape features. Results from model 1 and 2 are then applied to extract
PM elemental profiles associated with PM morphology information. Our results show
how to efficiently predict EDX and element maps from SEM images with a high degree of
accuracy. This method has a potential to significantly reduce time and labour required for
environmental PM monitoring.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Potentially relevant variants of unknown significance in NGS-tested patients with suspected skeletal dysplasia
Get PDFACMG recognizes five different categories of sequence variants identified by next
generation sequencing (pathogenic, likely pathogenic, variants of unknown significance,
likely benign and benign). Sometimes, potentially relevant gene variants could be
categorized as variants of unknown significance according to the level of available
evidences. Because of that, detailed assessment of the phenotype-genotype correlation
by the clinical geneticist in each individual case is crucially important. The interpretation
and classification of a variant may change over time. Variant reinterpretation is defined as
the practice of reevaluating all the evidence available about the pathogenicity of a genetic
variant and taking into account any new evidence that is made available since the previous
interpretation.
For the last seven years, we had 168 patients with clinically suspected locus heterogeneous
skeletal dysplasia. Next generation sequencing (NGS) using clinical exome sequencing
or whole exome sequencing was performed for all. All patients underwent detailed
phenotype-genotype correlation investigation.
Molecular diagnosis by determining the pathogenic or likely pathogenic causative gene
variant(s) was established for 102 out of 168 patients (60.71%). Additionally, in 10 patients
(5.95%) variant of unknown significance (VUS) with good phenotype-genotype correlation
was identified. These VUS variants could be potentially, and possibly are, causal, although
there are no reliable evidences of their pathogenicity at the moment. In one of the positive
patients in our study, the variant was initially classified as VUS, but with new evidence it
was reclassified as likely pathogenic.
In the present study, a potentially relevant variant of unknown significance was detected
in 5.95% of patients, which is a non-negligible proportion. For all these patients, we have
organized clinical follow-up with periodic reinterpretation and reclassification of the
detected variants.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Advancing PHBV Biomedical Potential with the Incorporation of Bacterial Biopigment Prodigiosin
Get PDFThe quest for sustainable biomaterials with excellent biocompatibility and tailorable properties has put polyhydroxyalkanoates (PHAs) into the research spotlight. However, high production costs and the lack of bioactivity limit their market penetration. To address this, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) was combined with a bacterial pigment with strong anticancer activity, prodigiosin (PG), to obtain functionally enhanced PHBV-based biomaterials. The samples were produced in the form of films 115.6–118.8 µm in thickness using the solvent casting method. The effects of PG incorporation on the physical properties (morphology, biopolymer crystallinity and thermal stability) and functionality of the obtained biomaterials were investigated. PG has acted as a nucleating agent, in turn affecting the degree of crystallinity, thermal stability and morphology of the films. All samples with PG had a more organized internal structure and higher melting and degradation temperatures. The calculated degree of crystallinity of the PHBV copolymer was 53%, while the PG1, PG3 and PG3 films had values of 64.0%, 63.9% and 69.2%, respectively. Cytotoxicity studies have shown the excellent anticancer activity of films against HCT116 (colon cancer) cells, thus advancing PHBV biomedical application potential
QSAR and machine learning models of redox potentials of some organic pigments
Get PDFThe organic pigments offer promising opportunities for developing new sustainable electrode materials for lithium batteries. Some of them have been identified as cathode material with very encouraging reversible lithium ion storage characteristics. One of them is a naturally occurring purpurin extracted from the Madder plant (Rubia tinctorum) for which we confirmed this good electrochemical behavior by cyclic voltammetry. One of the strategies towards obtaining materials with even better characteristics is a structural modification of already existing pigments. Building a theoretical model that could predict the redox properties of these new compounds can be very useful towards achieving that goal. In order to build a 3D QSAR (quantitative structure–activity relationship) model for material redox potential prediction, 9 organic pigments with known redox potentials were extracted from the literature. Based on molecular interaction field (MIF) probes we calculated standard GRIND (grid-independent) descriptors and constructed following principal PLS (partial least squares) model. By validation with the literature data, but also with the obtained experimental data for purpurin, this model proved very reliable in predicting the redox potential. A comparison was also made with the machine learning model that was formed in parallel.Book of abstract: Twenty-FirstYoung Researchers Conference –Materials Science and EngineeringNovember 29 –December 1, 2023, Belgrade, Serbi
Medium chain length polyhyoxyalkanoates (mcl-PHA) model compounds for the discovery of novel PHA depolymerases
Get PDFPHAs are naturally made microbial polyesters that
have been commercialized as biodegradable
plastics. However, it has been shown that these
materials are not so easily biodegraded in natural
environments [1]. PHA depolymerases are key PHA
degrading enzymes and their identification and
characterization is of great interest and importance.
Currently, screening is done on polymeric
substrates using techniques such as clear zone
assays on agar or weight loss measurements.
Results obtained using these different methods
cannot be directly compared, since they depend
highly on the polymer used, PHA granules
preparation and assay conditions [2].
In order to design a more specific test for the
determination of PHA depolymerase activity, we
synthesized 3-hyoxyalkanoate monomers (3-HA
monomer) and 3-hyoxyalkanoic acid dimers (3-HA
dimer) and their respective p-nitrophenyl esters,
allowing for spectrophotometric determination of
their activity [3]. Compounds were characterized
using N and FTIR. Para-nitrophenyl labeled
substrates were then used in the enzymatic activity
assay with the benchmark polyhyoxyoctanoate
(PHO) depolymerase from Pseudomonas
fluorescens GK13 expressed in Escherichia coli
CodonPlus-RIPL hosts. This activity was compared
to recombinantly expressed leaf-branch compost
cutinase (LCC cutinase) and
polyethyleneterephtalate (PET) hyolyzing esterase
from Ideonella sakaiensis (IsPETase). Our initial
results revealed increased specificity of PHO
depolymerase towards newly synthetized
substrates, suggesting their suitability for specific
screens and isolation of new mcl-PHA
depolymerases, as well as in high throughput
screening assays designed for guiding their
directed evolution.10th International Conference of MIKROBIOKOSMOS, Larissa from 30 Novewmber to 2 December 2023
PHACTR1 u kardiovaskularnim bolestima: od studija asocijacije na celokupnom genomu do funkcionalnih studija
Get PDFGen za regulator protein fosfataze i aktina 1 (eng. protein phosphatase and actin regulator 1, PHACTR1) je
ušao u žižu interesovanja kada je u studijama asocijacije na celokupnom genomu pokazao značajnu
povezanost sa različitim fenotipovima kardiovaskularnih bolesti (KVB). Nekoliko validacionih studija je istaklo
uticaj varijanti gena PHACTR1 na koronarnu bolest, infarkt miokarda, kalcifikaciju arterija i disekciju
cervikalnih arterija. Vodeća varijanta rs9349379 je pokazala protektivan ili štetan efekat na KVB, jasno
definišući podelu na bolesti u čijoj osnovi je ateroskleroza i one do kojih dovode drugi procesi. U srpskoj
populaciji, analiziran je haplotipski efekat tri varijante gena PHACTR1, rs9349379 A/G, rs2026458 C/T i
rs2876300 A/G, na aterosklerozu karotidnih i koronarnih arterija, kao i njihov efekat na transkripciju gena
PHACTR1 u karotidnom plaku i mononuklearnim ćelijama periferne krvi. Na ovom polju se vodi
dugogodišnja polemika oko toga da li je varijanta rs9349379 povezana sa KVB preko funkcionalnog uticaja
na PHACTR1 ili na gen za endotelin 1, EDN1. U funkcionalnim studijama je predloženo nekoliko mehanizama
delovanja PHACTR1 na kardiovaskularni sistem imajući u vidu da interaguje sa dva esencijalna
ćelijska proteina, protein fosfatazom 1 i G-aktinom. U ovom radu dat je pregled dosadašnjih istraživanja
PHACTR1 u KVB.Protein phosphatase and actin regulator 1 (PHACTR1) gene entered the spotlight when it showed a significant
association with various phenotypes of cardiovascular diseases (CVD) in genome-wide association
studies. Several validation studies have highlighted the impact of PHACTR1 variants on coronary artery
disease, myocardial infarction, arterial calcification, and cervical artery dissection. The leading PHACTR1
variant rs9349379 showed a protective or pathogenic effect on CVD, clearly defining the division into atherosclerosis-
based diseases and those caused by other processes. In Serbian population, analysis has been
conducted on haplotype effect of three PHACTR1 gene variants, rs9349379 A/G, rs2026458 C/T and
rs2876300 A/G, on carotid and coronary atherosclerosis, as well as their effect on PHACTR1 mRNA level in
carotid plaque tissue and peripheral blood mononuclear cells. However, there is a long-standing controversy
about whether the rs9349379 variant is associated with CVD through a functional effect on PHACTR1
or on the endothelin 1 gene, EDN1. Several mechanisms of action of PHACTR1 on the cardiovascular system
have been proposed in functional studies, considering that it interacts with two essential cellular proteins,
protein phosphatase 1 and G-actin. This paper provides an overview of the up to date research
conducted on the PHACTR1 in CVD
Natural Substances vs. Approved Drugs in the Treatment of Main Cardiovascular Disorders—Is There a Breakthrough?
Get PDFCardiovascular diseases (CVDs) are a group of diseases with a very high rate of morbidity and mortality. The clinical presentation of CVDs can vary from asymptomatic to classic symptoms such as chest pain in patients with myocardial infarction. Current therapeutics for CVDs mainly target disease symptoms. The most common CVDs are coronary artery disease, acute myocardial infarction, atrial fibrillation, chronic heart failure, arterial hypertension, and valvular heart disease. In their treatment, conventional therapies and pharmacological therapies are used. However, the use of herbal medicines in the therapy of these diseases has also been reported in the literature, resulting in a need for critical evaluation of advances related to their use. Therefore, we carried out a narrative review of pharmacological and herbal therapeutic effects reported for these diseases. Data for this comprehensive review were obtained from electronic databases such as MedLine, PubMed, Web of Science, Scopus, and Google Scholar. Conventional therapy requires an individual approach to the patients, as when patients do not respond well, this often causes allergic effects or various other unwanted effects. Nowadays, medicinal plants as therapeutics are frequently used in different parts of the world. Preclinical/clinical pharmacology studies have confirmed that some bioactive compounds may have beneficial therapeutic effects in some common CVDs. The natural products analyzed in this review are promising phytochemicals for adjuvant and complementary drug candidates in CVDs pharmacotherapy, and some of them have already been approved by the FDA. There are insufficient clinical studies to compare the effectiveness of natural products compared to approved therapeutics for the treatment of CVDs. Further long-term studies are needed to accelerate the potential of using natural products for these diseases. Despite this undoubted beneficence on CVDs, there are no strong breakthroughs supporting the implementation of natural products in clinical practice. Nevertheless, they are promising agents in the supplementation and co-therapy of CVDs
Three lines of evidence of the hepatotoxicity young researchers of a mixture containing phthalates and bisphenol a: in silico and two in vivo models
Get PDFThe extensive usage of bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), and bisphenol A
(BPA) creates a lot of opportunities for combined human exposure to these hazardous compounds in
everyday life and a variety of negative outcomes, including hepatotoxicity. In silico research and two
in vivo models were used to investigate the links between a mixture including DEHP, DBP and BPA and
liver injury. Bioinformatic analysis was performed by Comparative Toxicogenomics Database, ShinyGO,
ToppCluster, and Cytoscape. In vivo subacute study included five groups of rats (n = 6): (1) Control: corn
oil, (2) DEHP: 50 mg/kg b.w./day, (3) DBP: 50 mg/kg b.w./day, (4) BPA: 25 mg/kg b.w./day, (5) MIX: DEHP
+ DBP + BPA. Zebrafish embryos were exposed to the investigated substances in multiple dosages, both
alone and in combination (binary and ternary mixtures). Liver damage was linked to 75 DEHP, DBP, and
BPA genes, the majority of which were associated with inflammation/oxidative stress, identified as the
most relevant molecular pathways. In rats, significant changes in redox status/bioelements’ level and
pathohistology were more pronounced or evident only in MIX group, suggesting probable additivity.
In a dose-dependent manner, BPA reduced the liver area (LA) index. LA values were decreased by DEHP
(2 μg/mL) and DBP (5 μg/mL), whereas LA index was raised by their higher concentrations. In binary
mixtures, DBP had a lethal effect at the two highest concentrations, whereas BPA directed hepatotoxicity
of the DEHP/DBP/BPA mixture
Insights into proteolysis, textural evolution, microstructural changes and sensory attributes of white brined cheese from frozen-stored caprine milk
No full textLong-term frozen storage of caprine milk is an important way of overcoming seasonal production. White brined cheese, matured for 56 days, was made from frozen-stored caprine milk. Several properties of experimental and control cheese variants were investigated throughout the maturation period: physico-chemical, sensory, proteolytic (by urea-PAGE electrophoresis), texture attributes, microstructure (by scanning electron microscopy). Most of investigated properties were influenced by frozen storage and maturation period, but differences were less pronounced on the 56th day of maturation. Moreover, sensory analysis showed that both cheese variants were well accepted by consumers
E-cigarette liquid and condensate leads to impaired embryonic development of zebrafish
Get PDFIntroduction: E-cigarettes are advertised as safer alternative to tradicional cigarettes. However, they
contain chemicals that can exhibit toxic effects on the organism. Notably, effects of e-cigarettes on in
utero development are not well studied. We wanted to compare potential toxic effects of e-cigarette liquid and vapor condensate on development of zebrafish embryos.
Methods: Six hour old zebrafish embryos were exposed to different concentrations of e-cigarette liquid
or vapour condensate – 0.1% and 1%. Untreated embryos were used as control. Each treatment and control were set up in triplicate, with at least 20 embryos per treatment. The effects on survival, hatching and
developmental malformations were monitored using light microscopy, at 3 timepoints - 24, 48 and 72
hours post fertilization (hpf).
Results: No noticeable differences between control and treated groups were observed 24 hpf. Hatched
larvae (35%) treated with 0.1% condensate had scoliosis and malformations- yolk sac and pericardial
edema at 48 hpf. In groups treated with 1% of condensate or liquid, hatching was delayed and did not
start 48 hpf. At 72 hpf timepoint, in wells with 1% condensate, less than 30% of larvae hatched in total,
which was comparable to wells with e-cigarette liquid (25%). Malformations that were observed in all
treatements are hemagglutionation, pericardial or yolk sac edema, and scoliosis. In groups with 0.1%
condensate these maformations were observed in lower number of embryos, but the percentage of
hatched larvae was higher (approximately 80%) at 72 hpf.
Conclusions: Chronic exposure to e-cigarette vapor condensate and liquid leads to severe disorders of
zebrafish embryonic development