Comparative analysis of Escherichia coli Nissle 1917 ghosts quality: a study of two chemical methods.

The gram-negative bacterium Escherichia coli Nissle 1917 (EcN) has long been recognized for its therapeutic potential in treating various intestinal diseases. Bacterial ghosts (BGs) are empty shells of non-living bacterial cells that demonstrate enormous potential for medicinal applications. Genetic and chemical techniques can create these BGs. In the current study, we produced Escherichia coli Nissle 1917 ghosts (EcNGs) for the first time using benzoic acid (BA) and sodium hydroxide (SH). BA is a feeble acidic chemical that enhances gram-negative bacteria's external membrane permeability, reduces energy production, and decreases internal pH. SH has shown success in producing BGs from some gram-negative and gram-positive organisms. This research aims to produce EcNGs using the minimum inhibitory concentration (MIC) of SH and BA, specifically 3.125 mg/mL. We assessed the bacterial quality of the BGs produced using quantitative PCR (qPCR) and Bradford protein assays. Field emission scanning electron microscopy (FE-SEM) showed the three-dimensional structure of EcNGs. The study confirmed the presence of tunnel-like pores on the outer surface, indicating the preservation of cell membrane integrity. Importantly, this investigation introduces BA as a novel chemical inducer of EcNGs, suggesting its potential alongside SH for efficient EcNG formation.

Chromosome conformation capture-based DNA hybridization method for chromosomal translocation screening.

Background: DNA probes have been widely used as diagnostic tools for translocations. This study sought to design a screening tool using ssDNA probes and chromosome conformation capture (3C) library fragment hybridization. Method: The authors focused on developing a probe for the juxtaposed region of MYC and TRD. Fragments of the MYC gene with a thiol modification (MYC-Au NP probe) were functionalized by gold nanoparticles (Au NPs). Then TRD probes were immobilized on a nitrocellulose surface. Hybridization between DNA probes and 3C library fragments of SKW3 cells was determined by color intensity. Results: Optimal hybridization of the 3C library sample of the cell line to probes showed higher color intensity than human umbilical vein endothelial cells. Conclusion: Combining 3C-based techniques and DNA-DNA hybridization can identify rearrangements in cancer cells.

Carbon-based biosensors from graphene family to carbon dots: A viewpoint in cancer detection.

According to the latest report by International Agency for Research on Cancer, 19.3 million new cancer cases and 10 million cancer deaths were globally reported in 2020. Early diagnosis can reduce these numbers significantly, and biosensors have appeared to be a solution to this problem as, unlike the traditional methods, they have low cost, rapid process, and do not need experts present on site for use. These devices have been incorporated to detect many cancer biomarkers and measure cancer drug delivery. To design these biosensors, a researcher must know about their different types, properties of nanomaterials, and cancer biomarkers. Among all types of biosensors, electrochemical and optical biosensors are the most sensitive and promising sensors for detecting complicated diseases like cancer. The carbon-based nanomaterial family has attracted lots of attention due to their low cost, easy preparation, biocompatibility, and significant electrochemical and optical properties. In this review, we have discussed the application of graphene and its derivatives, carbon nanotubes (CNTs), carbon dots (CDs), and fullerene (C60), for designing different electrochemical and optical cancer-detecting biosensors. Furthermore, the application of these carbon-based biosensors for detecting seven widely studied cancer biomarkers (HER2, CEA, CA125, VEGF, PSA, Alpha-fetoprotein, and miRNA21) is reviewed. Finally, various fabricated carbon-based biosensors for detecting cancer biomarkers and anticancer drugs are comprehensively summarized as well.

Designing a fluorescence padlock probe-based biosensor and colorimetric assay for the detection of G12D KRAS mutation.

Aim: Cell-free DNA in the plasma is known to be a potential biomarker for noninvasive diagnosis of oncogenic mutations. The authors aimed to design an optimized padlock probe-based hyperbranched rolling circle amplification biosensor to detect the KRAS G12D mutation using fluorescence and colorimetric methods. Methods: Single-factor experiments, Plackett-Burman design and response surface methodology were applied to optimize the padlock probe-based hyperbranched rolling circle amplification reaction. Results: The maximum fluorescence intensity was achieved at a padlock probe concentration of 1.5 pM and target concentration of 9 pM at 38°C ligation temperature. The proposed biosensor has a low detection limit of 60 fM of target DNA and a linear response in the concentration range of 60 fM to 0.2 pM. Conclusion: The results indicated the power of these assays to detect KRAS point mutations in liquid state reactions.

Comparison of insulin secretion by transduced adipose-derived and endometrial-derived stem cells in 2D and 3D cultures on fibrin scaffold.

Type 1 diabetes is a metabolic disorder caused by the loss or dysfunction of ß-cells in the pancreas. Organ shortage is a critical concern of diabetic patients in need of beta islet transplantation. Tissue engineered islets are promising alternatives to traditional organ transplantation. Recent progress in stem cell biology and gene cloning techniques has raised hopes for the generation of insulin producing cells (IPCs) without the need of immunosuppression. The purpose of this study was to produce IPCs using human adipose-derived stem cells (hADSCs) and human endometrial-derived stem cells (hEnSCs) and also to compare the level of insulin secretion by these cells in 2D and 3D culture systems on fibrin scaffolding. Stem cells differentiation was carried out through transduction with an insulin over expression lentiviral vector. Real-time PCR and immunocytochemistry confirmed the successful transduction of both cell types. Both cell types showed comparable insulin secretion by ELISA.3D culture resulted in higher amounts of insulin secretion of the two cell types versus 2D as control. This study showed that insulin gene delivery to the stem cells could be an efficient method for producing IPCs and fibrin encapsulation enhances the functionality of these cells.

Application of Chromosome Conformation Capture Method for Detection MYC/TRD Chromosomal Translocation in Leukemia Cell Line.

Background: Chromosomal breakpoints are the most common cause of hereditary diseases and cancers. Today, many standard clinical methods such as cytogenetic and PCR based techniques are used which have limitation regarding detection resolution. Chromosome conformation capture is a method for detecting gene proximity and chromosomal rearrangements. Materials and Methods: In this study, SKW3 cell line was used for detecting t(8;14)(q24;q11) using a 3C-based technique. SKW3 cell line was used for 3C library preparation. For Inverse PCR, two regions were selected in upstream and downstream of the viewpoint locus on chromosome 8-MYC gene based on EcoRI restriction sites. The captured sequence with intra-chromosomal interaction between chr8-c-MYC and chr14-TRD was selected for the translocation PCR primer design. Results: The DNA fragment captured in 3C PCR showed a specific TRD sequence translocated downstream of the MYC gene. Translocation PCR demonstrated the existence of (8; 14) (q24; q11) MYC /TRD in both library and genomic DNA. Conclusion: This result demonstrated 3C- based method could be used as a useful low-cost easy operating technique in chromosomal rearrangements detection. In this study, the integration of whole genome library monitoring and PCR method was used as a high- through put method in chromosomal breakpoints detection.

Exosome loaded alginate hydrogel promotes tissue regeneration in full-thickness skin wounds: An in vivo study.

Wound healing is known as one of the most complicated biological processes for injured skin caused by surgical, trauma, burns, or diabetic diseases, which causes a nonfunctioning mass of fibrotic tissue. Recent reports have suggested that exosomes (EXOs) secreted by this type of stem cells may contribute to their paracrine effect. In this study, the EXOs were isolated from the supernatant of cultured adipose-derived stem cells (ADSCs) via ultracentrifugation and filtration. The EXO loaded in the alginate-based hydrogel was used as a bioactive scaffold to preserve the EXO in the wound site in the animal model. The physical and biochemical properties of EXO loaded Alg hydrogel were characterized and results proved that fabricated structure was biodegradable and biocompatible. This bioactive wound dressing technique has significantly improved wound closure, collagen synthesis, and vessel formation in the wound area. Results offer a new viewpoint and a cell-free therapeutic strategy, for wound healing through the application of the composite structure of EXO encapsulated in alginate hydrogel.

Developing a DNA aptamer-based approach for biosensing cystatin-c in serum: An alternative to antibody-based methods.

Oligonucleotide aptamers are short, synthetic and single-stranded DNA or RNA molecules capable of binding to a wide range of molecules, from small molecules to large cells. Nowadays, aptamers are valuable tools in research, clinical diagnosis and treatment. Their small size and high specificity in addition to their lack of immunogenicity make them great alternatives to other diagnosing candidates such as antibodies. In this study, we have introduced a new method based on competitive Enzyme-Linked Aptamer Sorbent Assay (ELASA) using single-stranded DNA (ssDNA) aptamers to measure cystatin-c levels in serum samples. To this aim, through a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process a number of aptamers were selected from which an aptamer with a Kd (dissociation constant) value of 65.5 ±â€¯0.007 nM was chosen for further analyses. The limit of detection (LoD) was found to be 216.077 pg/ml. The results of the analytical application of this method in serum samples were comparable to those of commonly used commercial kits.

Lentiviral-mediated BCL2 gene knockdown using comparative microRNA adaptive shRNAs.

B-cell lymphoma 2 (BCL2) family proteins play a critical role in tuning cell death processes. Almost in half of all human cancers, a dysregulation in BCL2 family gene expression has been shown which made it an impressive target for human gene therapy as a novel approach in cancers. In this study we will optimize lentiviral-mediated RNA interference (RNAi), recombinant lentiviruses accommodating anti-BCL2 micro adaptive short hairpin RNAs (shRNAs), to downregulate BCL2 in human embryonic kidney 293T (HEK293T) cells to produce stable cell lines. We tested 4 different Dharmacon™ GIPZ™ shRNAmir lentiviral vectors targeting BCL2 in different positions and a pGIPZ non-silencing shRNAmir lentiviral vector (as a negative control). Lentivirus packaging was performed by the calcium phosphate precipitation method. HEK293T cells were transduced by each type of recombinant lentiviruses individually and selected by puromycin within 10 days. The relative mRNA level and protein expression were assayed by using real-time polymerase chain reaction (PCR) technic and western blotting, respectively. Lentivirus (LV) packaging was performed in high efficiency (transfection rate was > 90%). Recombinant viruses of 4 expression vector addition to a control vector were produced then transduced to HEK293T cells successfully. All the 4 cell groups showed a significant down regulation of BCL2 gene (~90-95%) at mRNA level compared to the control group (p<0.01) but differences between silenced groups were not significant (P > 0.05). We showed that the lentivirus-mediated RNAi technique is an efficient method to establish HEK293 cell lines with stable down-regulation of BCL2 gene.

Differentiation of neural crest stem cells from nasal mucosa into motor neuron-like cells.

Cell transplantation is a potential therapeutic approach for repairing neuropathological and neurodegenerative disorders of central nervous system by replacing the degenerated cells with new ones. Among a variety of stem cell candidates to provide these new cells, olfactory ectomesenchymal stem cells (OE-MSCs) have attracted a great attention due to their neural crest origin, easy harvest, high proliferation, and autologous transplantation. Since there is no report on differentiation potential of these cells into motor neuron-like cells, we evaluated this potential using Real-time PCR, flowcytometry and immunocytochemistry after the treatment with differentiation cocktail containing retinoic acid and Sonic Hedgehog. Immunocytochemistry staining of the isolated OE-MSCs demonstrated their capability to express nestin and vimentin, as the two markers of primitive neuroectoderm. The motor neuron differentiation of OE-MSCs resulted in changing their morphology into bipolar cells with high expression of motor neuron markers of ChAT, Hb-9 and Islet-1 at the level of mRNA and protein. Consequently, we believe that the OE-MSCs have great potential to differentiate into motor neuron-like cells and can be an ideal stem cell source for the treatment of motor neuron-related disorders of central nervous system.

Performance and Predictive Value of First Trimester Screening Markers for Down Syndrome in Iranian Pregnancies.

Objective: To investigate the performance of first trimester Down syndrome (DS) screening markers in Iranian pregnancies.Although sonographic and serum markers are currently recommended for the first trimester screening of Down syndrome, the screening performance of the markers depends on the race and ethnicity. Materials and methods: A retrospective case-control study using first trimester screening results recorded with the prenatal diagnostic multi-centers in Iran. A total of 6,384 pregnant women were examined from March 2012 to February 2017. Totally 100 Down syndrome cases and 266 matched controls were selected and the maternal characteristics, sonographic and biochemical screening data were collected. Statistical analysis was performed using logistic regression and descriptive statistics. A decision tree model was designed using the chi-squared automatic interaction detection method based on serum markers. Results: For screening of DS pregnancies, PAPP-A (cut-off 0.795 MoM) yielded the highest sensitivity (86%) and NB marker presented highest specificity (96.24%). combination of the biochemical markers PAPP-A and ß-hCG (cut-off: 1.55 MoM) showed the highest sensitivity over other combined markers. The decision-tree model based on serum markers improved (91% DR For a 5% FPR) first trimester screening performance. Conclusion: The novel decision-tree model base on serum markers revealed a better predictive value to achieve high sensitivity and specificity of first trimester Down syndrome screening in Iranian population.