Marinobacter azerbaijanicus sp. nov., a moderately halophilic bacterium from Urmia Lake, Iran.

A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242T, was isolated from water of Urmia Lake in the Azerbaijan region of Iran. The cells were found to be rod-shaped and motile by a single polar flagellum, producing circular and yellowish colonies. The strain could grow in the presence of 0.5-10 % (w/v) NaCl (optimum, 2.5-5 %). The temperature and pH ranges for growth were 15-45 °C (optimum 30 °C) and pH 7.0-11.0 (optimum pH 8.0) on marine agar. The 16S rRNA gene sequence analysis revealed that strain TBZ242T belonged to the genus Marinobacter, showing the highest similarities to Marinobacter algicola DG893T (98.8 %), Marinobacter vulgaris F01T (98.8 %), Marinobacter salarius R9SW1T (98.5 %), Marinobacter panjinensis PJ-16T (98.4 %), Marinobacter orientalis W62T (98.0 %) and Marinobacter denitrificans JB2H27T (98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242T formed a distinct branch, closely related to a subclade accommodating M. vulgaris, M. orientalis, M. panjinensis, M. denitrificans, M. algicola, M. salarius and M. iranensis, within the genus Marinobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain TBZ242T and the type strains of the related species of Marinobacter were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242T represents a distinct species. The major cellular fatty acids of strain TBZ242T were C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242T is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242T represents a novel species within the genus Marinobacter, for which the name Marinobacter azerbaijanicus sp. nov. is proposed. The type strain is TBZ242T (= CECT 30649T = IBRC-M 11466T). Genomic fragment recruitment analysis showed that this species prefers aquatic saline environments with intermediate salinities, being detected on metagenomic databases of Lake Meyghan (Iran) with 5 and 18 % salinity, respectively.

Exosome Content-Mediated Signaling Pathways in Multiple Sclerosis.

Exosomes are small extracellular vesicles with a complex lipid-bilayer surface and 30-150 nm diameter. These vesicles play a critical role in intercellular signaling networks during physiopathological processes through data trafficking and cell reprogramming. It has been demonstrated that exosomes are involved in a variety of central nervous system (CNS) disorders such as multiple sclerosis (MS). Exosome mediators' cell-to-cell communication is possibly by delivering their contents such as proteins, RNAs (coding and non-coding), DNAs (mitochondrial and genomic), and transposable elements to the target cells. Exosomal microRNAs (miRNAs) differ in their expression patterns in MS disease, thereby providing novel diagnostic and prognostic biomarkers and therapeutic options for better treatment of MS disease. Furthermore, these microvesicles are non-immunogenic and non-toxic therapeutic tools for transferring miRNAs across the blood-brain barrier (BBB). Collectively, exosomes could be used as novel drug delivery devices for the treatment of MS patients. This review summarized research regarding the exosomes from serum, plasma, PBMC, and other cells in MS patients and experimental models. We also provide a critical view of exosome content-mediated signaling pathways in MS, including TNF-α, TGF-ß, NF-κB, and Wnt pathways. The use of exosomes as a therapeutic potential in MS has also been discussed.

A snapshot of miRNAs in oral squamous cell carcinoma: Difference between cancer cells and corresponding normal cells.

Oral squamous cell carcinoma (OSCC) constitutes the most aggressive tumors of the oral cavity and is one of the leading causes of cancer mortality worldwide. Although recent clinical treatment strategies have improved the survival rate, the outcome of OSCC patients still remains dismal because of the lack of efficient diagnostic and treatment tools. As one of the main actors of OSCC scenario, microRNAs (miRNAs) are involved in triggering, progression and metastasis through the regulation of various cancer-related signaling pathways. Identification followed by precise study of the biology and mechanism of action of miRNAs will greatly help to provide valuable insights regarding OSCC development and can be considered as an anti-OSCC target. In the current review, we have provided a focused summary of the latest published papers on the role of miRNAs in apoptosis, cell cycle, proliferation, EMT and metastasis of OSCC as well as the role of long noncoding RNAs in the modulation of miRNAs in OSCC.

Clinical Significance of Carnitine in the Treatment of Cancer: From Traffic to the Regulation.

Metabolic reprogramming is a common hallmark of cancer cells. Cancer cells exhibit metabolic flexibility to maintain high proliferation and survival rates. In other words, adaptation of cellular demand is essential for tumorigenesis, since a diverse supply of nutrients is required to accommodate tumor growth and progression. Diversity of carbon substrates fueling cancer cells indicate metabolic heterogeneity, even in tumors sharing the same clinical diagnosis. In addition to the alteration of glucose and amino acid metabolism in cancer cells, there is evidence that cancer cells can alter lipid metabolism. Some tumors rely on fatty acid oxidation (FAO) as the primary energy source; hence, cancer cells overexpress the enzymes involved in FAO. Carnitine is an essential cofactor in the lipid metabolic pathways. It is crucial in facilitating the transport of long-chain fatty acids into the mitochondria for ß-oxidation. This role and others played by carnitine, especially its antioxidant function in cellular processes, emphasize the fine regulation of carnitine traffic within tissues and subcellular compartments. The biological activity of carnitine is orchestrated by specific membrane transporters that mediate the transfer of carnitine and its derivatives across the cell membrane. The concerted function of carnitine transporters creates a collaborative network that is relevant to metabolic reprogramming in cancer cells. Here, the molecular mechanisms relevant to the role and expression of carnitine transporters are discussed, providing insights into cancer treatment.

Chrysin and chrysin-loaded nanocarriers induced immunogenic cell death on B16 melanoma cells.

Induction of immunogenic cell death (ICD) is a promising strategy for cancer immunotherapy. Chrysin, which has potential anticancer effects, faces limitations in clinical applications due to its poor water solubility. This study aimed to formulate chrysin with PEG-poly(α-benzylcarboxylate-ε-caprolactone) (PBCL) nanoparticles (NPs) and assess their anticancer and ICD-inducing potency in melanoma cells, comparing with free chrysin. The co-solvent evaporation method was employed to develop chrysin-loaded NPs. UV spectroscopy, dynamic light scattering, and the dialysis bag method were used to evaluate the encapsulation efficiency (EE), particle size, polydispersity index (PDI), and drug release profile, respectively. The anticancer effects of the drugs were assessed using the MTT and trypan blue exclusion assays. Flow cytometry was employed to evaluate apoptosis and calreticulin (CRT) expression. ELISA and western blotting were used to detect heat shock protein 90 (HSP90), Annexin A1, GRP78 (Glucose-related protein78), and activated protein kinase R-like endoplasmic reticulum kinase (p-PERK). Chrysin-loaded PEG-PBCL NPs (chrysin-PEG-PBCL) showed an EE of 97 ± 1%. Chrysin-PEG-PBCL was 38.18 ± 3.96 nm in size, with a PDI being 0.62 ± 0.23. Chrysin-PEG-PBCL showed an initial burst release, followed by sustained release over 24 h. Chrysin-PEG-PBCL exhibited a significantly stronger anticancer effect in B16 cells. Chrysin-PEG-PBCL was found to be more potent in inducing apoptosis. Both free chrysin and chrysin NPs induced ICD as indicated by an increase in the levels of ICD biomarkers. Interestingly, chrysin NPs were found to be more potent inducers of ICD than the free drug. These findings demonstrate that chrysin and chrysin-PEG-PBCL NPs can induce ICD in B16 cells. PEG-PBCL NPs significantly enhanced the potency of chrysin in inducing ICD compared to its free form.

Multiplex Analysis of Cerebrospinal Fluid and Serum Exosomes MicroRNAs of Untreated Relapsing Remitting Multiple Sclerosis (RRMS) and Proposing Noninvasive Diagnostic Biomarkers.

Exosomal microRNAs (miRNAs) are emerging diagnostic biomarkers for neurodegenerative diseases. In this study, we aimed to detect relapsing-remitting multiple sclerosis (RRMS)-specific miRNAs in cerebrospinal fluid (CSF) and serum exosomes with diagnostic potential. One ml of CSF and serum sample were collected from each of the 30 untreated RRMS patients and healthy controls (HCs). A panel of 18 miRNAs affecting inflammatory responses was applied, and qRT-PCR was conducted to detect differentially expressed exosomal miRNAs in CSF and serum of RRMS patients. We identified that 17 out of 18 miRNAs displayed different patterns in RRMS patients compared to HCs. Let-7 g-5p, miR-18a-5p, miR-145-5p, and miR-374a-5p with dual pro-inflammatory and anti-inflammatory actions and miR-150-5p and miR-342-3p with anti-inflammatory action were significantly upregulated in both CSF and serum-derived exosomes of RRMS patients compared to corresponding HCs. Additionally, anti-inflammatory miR-132-5p and pro-inflammatory miR-320a-5p were significantly downregulated in both CSF and serum-derived exosomes of RRMS patients compared to HCs. Ten of 18 miRNAs were differentially expressed in CSF and serum exosomes of the patients. Furthermore, miR-15a-5p, miR-19b-3p, and miR-432-5p were upregulated, and miR-17-5p was downregulated only in CSF exosomes. Interestingly, U6 housekeeping gene was differentially expressed in CSF and serum exosomes, in both RRMS and HCs. As the first report describing CSF exosomal miRNAs expression profile compared to that of serum exosomes in untreated RRMS patients, we showed that CSF and serum exosomes are not identical in terms of biological compounds and display different patterns in miRNAs and U6 expression.

The dynamicity of mutant KRAS ß2 strand modulates its downstream activation and predicts anticancer KRAS inhibition.

AIM: Oncogenic mutations involving KRAS are human cancer's most common driving force. We aimed to determine specific conformational features of the active KRAS regarding downstream signaling activation, especially in mutant forms of KRAS. MAIN METHODS: We applied Molecular Dynamics (MD) simulations in triplicate and post-MD analytical methods on the KRAS and its G12 mutant structures. In addition, clustering, umbrella sampling, and principal component analysis were conducted to improve the significant conformations related to the activity of the KRAS variants. The results were generally represented as the probability of the conformations regarding different structural aspects, including ß2-strand length, main residual distances, and critical residue interactions. KEY FINDINGS: Our results showed that the KRAS ß2-strand length was a convenient structural criterion to show the KRAS activity. Accordingly, the active conformations of KRAS were the most probable to have 9-10 residue numbers of ß2-strand. Based on this observation, it was also shown that the GDP forms of KRAS G12 mutants could be in the active mode because of increased ß2-strand length. Moreover, the distance between the E37 and A59 residues differed in relation to ß2-ß3 sheet length and can be considered another KRAS activity indicator. Interestingly, ß2-strand length could also predict the KRAS activity in the presence of a direct mutant KRAS inhibitor. SIGNIFICANCE: As a result, our observations provide a new mechanism regarding the high efficacy of direct inhibition of KRAS-GDP in cancer therapy. In addition, designing and screening the mutant KRAS inhibitors can be more achievable using the ß2-strand length probability.

Shewanella azerbaijanica sp. nov. a novel aquatic species with high bioremediation abilities.

A novel Gram-negative, facultative anaerobic, rod-shaped, and non-motile bacterium with bio-degradation potential of polycyclic aromatic hydrocarbons (PAHs) and uranium bio-reduction, designated as RCRI7T, was isolated from Qurugöl Lake water near Tabriz city. Strain RCRI7T can grow in the absence of NaCl and tolerates up to 3% NaCl (optimum, 0-0.5%), at the temperature range of 4-45 °C (optimum, 30 °C) and a pH range of 6-9 (optimum, pH 7 ± 0.5). Results of phylogenetic analysis based on 16S rRNA gene sequence indicated that strain RCRI7T is affiliated with the genus Shewanella, most closely related to Shewanella xiamenensis S4T (99.1%) and Shewanella putrefaciens JCM 20190T (98.9%). The genomic DNA G+C content of strain RCRI7T is 41 mol%. The major fatty acids are C16:1ω9c, C18:1ω9c and iso-C17:1ω5c. The OrthoANI and ANIb values between RCRI7T and Shewanella xiamenensis S4T were 87.4% and 87.7%, and between RCRI7T and Shewanella putrefaciens JCM 20190T were 79.5% and 79.7%, respectively. Strain RCRI7T displayed dDDH values of 30.2% and 39.8% to Shewanella xiamenensis S4T and Shewanella putrefaciens JCM 20190T, respectively. The major polar lipids include phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The respiratory quinone is Q8. Based on the polyphasic evidence presented in this paper, strain RCRI7T is considered to represent a novel species, with bioremediation potential, in the genus Shewanella, for which the name Shewanella azerbaijanica sp. nov. is proposed. The type strain is RCRI7T (= JCM 17276T) (= KCTC 62476T).

COVID-19 infection: an overview on cytokine storm and related interventions.

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a significant threat to global health. This virus affects the respiratory tract and usually leads to pneumonia in most patients and acute respiratory distress syndrome (ARDS) in 15% of cases. ARDS is one of the leading causes of death in patients with COVID-19 and is mainly triggered by elevated levels of pro-inflammatory cytokines, referred to as cytokine storm. Interleukins, such as interleukin-6 (1L-6), interleukin-1 (IL-1), interleukin-17 (IL-17), and tumor necrosis factor-alpha (TNF-α) play a very significant role in lung damage in ARDS patients through the impairments of the respiratory epithelium. Cytokine storm is defined as acute overproduction and uncontrolled release of pro-inflammatory markers, both locally and systemically. The eradication of COVID-19 is currently practically impossible, and there is no specific treatment for critically ill patients with COVID-19; however, suppressing the inflammatory response may be a possible strategy. In light of this, we review the efficacy of specific inhibitors of IL6, IL1, IL-17, and TNF-α for treating COVID-19-related infections to manage COVID-19 and improve the survival rate for patients suffering from severe conditions.

Halomonas azerica sp. nov., Isolated from Urmia Lake in Iran.

A novel moderately halophilic, Gram-staining negative and facultative aerobic bacterium, designated as TBZ9T, was isolated from water of Urmia Lake in Azerbaijan region of Iran. The cells were found to be rod-shaped and motile, growing in the form of creamy, convex and shiny colonies. The strain could grow in the presence of NaCl at concentrations 1-17% (w/v) (optimum, 3%), temperatures 10-40 °C (optimum, 30 °C) and pH 6.0-11.0 (optimum, pH 7.0) on marine agar. Strain TBZ9T 16S rRNA gene sequence was related to the genus Halomonas showing highest similarities to Halomonas arcis AJ282T (98.4%), Halomonas songnenensis NEAU-ST10-39T (98.0%) and Halomonas lutescens Q1UT (97.8%). In the phylogenetic trees, strain TBZ9T formed a distinct branch closely related to a subclade inside the Halomonas genus. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain TBZ9T and H. arcis AJ282T (20.0%, 74.0%) and H. songnenensis NEAU-ST10-39T (19.8%, 75.2%) indicated that TBZ9T represents a distinct species. Evaluation of fatty acid contents determined C10:0, C16:0, C12:0 3-OH, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) as major cellular fatty acids. The major quinone of strain TBZ9T was Q-9. Polar lipid patterns consisted of phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL) and four unidentified polar lipids (L). The average DNA G + C content of strain TBZ9T is 55.4 mol%. Results from phenotypic, chemotaxonomic and molecular analysis suggest that the strain TBZ9T represents a novel species within the genus Halomonas for which the name Halomonas azerica sp. nov. is proposed. The type strain is TBZ9T (= KACC 21783T = LMG 25775T).

Patient-Specific Induced Pluripotent Stem Cell-Derived Hepatocyte-Like Cells as a Model to Study Autosomal Recessive Hypercholesterolemia.

Autosomal recessive hypercholesterolemia (ARH) is a rare monogenic disorder caused by pathogenic variants in the low-density lipoprotein receptor (LDLR) adaptor protein 1 (LDLRAP1) gene, encoding for the LDLRAP1 protein, which impairs internalization of hepatic LDLR. There are variable responses of ARH patients to treatment and the pathophysiological mechanism(s) for this variability remains unclear. This is in part caused by absence of reliable cellular models to evaluate the effect of LDLRAP1 mutations on the LDLRAP1 protein function and its role in LDLR internalization. Here, we aimed to validate patient-specific induced pluripotent stem cell (iPSC)-derived hepatocyte-like cells (HLCs) as an appropriate tool to model ARH disease. Fibroblasts from an ARH patient carrying the recently reported nonsense mutation, c.649G>T, were reprogrammed into hiPSCs using Sendai viral vectors. In addition, we used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) to create an LDLRAP1 gene (also known as ARH) knockout in two different human iPSC lines. ARH patient-derived iPSCs, ARH-knockout iPSC lines, and control iPSCs were efficiently differentiated into HLCs. Western blot analysis demonstrated the absence of LDLRAP1 in HLCs derived from patient and knockout iPSCs, and this was associated with a decreased low-density lipoprotein cholesterol (LDL-C) uptake in ARH-mutant/knockout HLCs compared to control HLCs. In conclusion, we determined that the recently described c.649G>T point mutation in LDLRAP1 induces absence of the LDLRAP1 protein, similar to what is seen following LDLRAP1 knockout. This causes a decreased, although not fully absent, LDL-uptake in ARH-mutant/knockout HLCs. As knockout of LDLRAP1 or presence of the c.649G>T point mutation results in absence of LDLRAP1 protein, residual LDL uptake might be regulated by LDLRAP1-independent internalization mechanisms. Patient-specific iPSC-derived HLCs can therefore be a powerful tool to further decipher LDLRAP1 mutations and function of the protein.

T lymphocytes and preeclampsia: The potential role of T-cell subsets and related MicroRNAs in the pathogenesis of preeclampsia.

Innate and adaptive immune systems have a crucial role in initiating and progressing some pregnancy disorders such as preeclampsia (PE), which is one of the pregnancy-specific disorders that could result in neonatal and maternal morbidity and mortality. The dysregulation of the spiral artery and inadequate trophoblast invasion lead to PE symptoms through producing various inflammatory cytokines and anti-angiogenic factors from the placenta. T lymphocytes play a special role in the epithelium and stroma of the human endometrium. CD4+ T helper (Th) cells, Th1/Th2, and Th17/T regulatory (Treg) balance mainly contribute to the establishment of a pregnancy-favorable environment. This review examined the dysregulation of some cytokines produced from T cells, the dysregulation of the transcription factors of Th cells, the expression of chemokine receptors on T cells, as well as the effects of some factors including vitamin D on the activity of T cells, and finally, the dysregulation of various miRNAs related to T cells, which could cause PE.

Classification of seed members of five riboswitch families as short sequences based on the features extracted by Block Location-Based Feature Extraction (BLBFE) method.

Introduction: Riboswitches are short regulatory elements generally found in the untranslated regions of prokaryotes' mRNAs and classified into several families. Due to the binding possibility between riboswitches and antibiotics, their usage as engineered regulatory elements and also their evolutionary contribution, the need for bioinformatics tools of riboswitch detection is increasing. We have previously introduced an alignment independent algorithm for the identification of frequent sequential blocks in the families of riboswitches. Herein, we report the application of block location-based feature extraction strategy (BLBFE), which uses the locations of detected blocks on riboswitch sequences as features for classification of seed sequences. Besides, mono- and dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods as some feature extraction strategies were investigated. Methods: The classifiers of the Decision tree, KNN, LDA, and Naïve Bayes, as well as k-fold cross-validation, were employed for all methods of feature extraction to compare their performances based on the criteria of accuracy, sensitivity, specificity, and f-score performance measures. Results: The outcome of the study showed that the BLBFE strategy classified the riboswitches indicating 87.65% average correct classification rate (CCR). Moreover, the performance of the proposed feature extraction method was confirmed with average values of 94.31%, 85.01%, 95.45% and 85.38% for accuracy, sensitivity, specificity, and f-score, respectively. Conclusion: Our result approved the performance of the BLBFE strategy in the classification and discrimination of the riboswitch groups showing remarkable higher values of CCR, accuracy, sensitivity, specificity and f-score relative to previously studied feature extraction methods.

A new approach to the preeclampsia puzzle; MicroRNA-326 in CD4+ lymphocytes might be as a potential suspect.

BACKGROUND: Alongside many complications in understanding the etiology of Preeclampsia (PE), several determinants, such as the imbalanced proportion of anti-angiogenic/proangiogenic T-cell subsets, especially CD4+ (Th17/Treg), as well as alterations in the expression profile of related cytokines, miRNAs, and transcription factors might have been implicated in PE pathogenesis. MATERIAL AND METHOD: After sample collection and preparation, CD4+ cells were isolated from PE and non-PE pregnant woman and were cultured. Furthermore, analysis such as flow cytometry, real-time PCR, western blotting, and ELISA were performed to assess determinants related to PE manifestation, including sFlt-1, sEng, STAT-3, RORγt, SMAD-7, Foxp3, IL-17, IL-22, Ets-1, and miRNA-326. RESULTS: Our results showed that the miRNA-326 expression level increased in CD4+ Cells and Th17 in PE patients which downregulated Ets-1 expression that acts as a negative control for Th17 development. Furthermore, we showed that the number and expression level of Th17 s and transcription factor RORγt escalated, respectively. While Treg and its related transcription factor (Foxp3) demonstrated a decrease. Flow cytometry analysis illustrated that the Th17/Treg ratio increased in PE. Additionally, we demonstrated that expression and concentration levels of cytokines (IL-17 and IL22) and anti-angiogenic molecules (sEng and sFlt-1) soared in isolated CD4+ cells from PE patients, which could be correlated with PE pathogenicity. CONCLUSION: In conclusion, we comprehensively evaluated immunological factors and molecules involved in PE manifestation. Interestingly, the CD4+ T-cell subset could be an extra source of antiangiogenic factors for the maintenance of this hypertension disorder.

Halomonas azerbaijanica sp. nov., a halophilic bacterium isolated from Urmia Lake after the 2015 drought.

A novel, slightly halophilic bacterium, designated TBZ202T, was isolated from water of Urmia Lake, in the Azerbaijan region of north-west Iran. The strain was facultatively anaerobic, Gram-stain-negative, rod-shaped and motile. Colonies were creamy, circular, convex and shiny. It grew at NaCl concentrations of 0-12 % (w/v) (optimum 3-5 % w/v), at temperatures of 20-45 °C (optimum 30 °C) and at pH 5.0-10.0 (optimum pH 7.0). Based on the 16S rRNA gene sequence, strain TBZ202T belongs to the genus Halomonas in the Halomonadaceae and the most closely related species are Halomonas gudaonensis CGMCC 1.6133T (98.6 % similarity), Halomonas ventosae Al12T (96.8 %) and Halomonas rambilicola RS-16T (96.6%). The G+C content was 67.9 % and the digital DNA-DNA hybridization and average nucleotide identity values with H. gudaonensis were 35.8 and 83.8 %, respectively, indicating that the isolate differs from all species described. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c. The only respiratory quinone detected was Q-9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and three unknown phospholipids. On the basis of a polyphasic taxonomic analysis, the isolate is considered to represent a novel species of the genus Halomonas, for which the name Halomonas azerbaijanica sp. nov. is proposed. The type strain is TBZ202T (=KCTC 62817T=CECT 9693T).

Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates.

Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5'-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5'-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5'-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5'-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.

DNA damage repair response in mesenchymal stromal cells: From cellular senescence and aging to apoptosis and differentiation ability.

Mesenchymal stromal cells (MSCs) are heterogeneous and contain several populations, including stem cells. MSCs' secretome has the ability to induce proliferation, differentiation, chemo-attraction, anti-apoptosis, and immunomodulation activities in stem cells. Moreover, these cells recognize tissue damage caused by drugs, radiation (e.g., Ultraviolet, infra-red) and oxidative stress, and respond in two ways: either MSCs differentiate into particular cell lineages to preserve tissue homeostasis, or they release a regenerative secretome to activate tissue repairing mechanisms. The maintenance of MSCs in quiescence can increase the incidence and accumulation of various forms of genomic modifications, particularly upon environmental insults. Thus, dysregulated DNA repair pathways can predispose MSCs to senescence or apoptosis, reducing their stemness and self-renewal properties. For instance, DNA damage can impair telomere replication, activating DNA damage checkpoints to maintain MSC function. In this review, we aim to summarize the role of DNA damage and associated repair responses in MSC senescence, differentiation and programmed cell death.

Halomonas urmiana sp. nov., a moderately halophilic bacterium isolated from Urmia Lake in Iran.

In the course of screening halophilic bacteria in Urmia Lake in Iran, which is being threatened by dryness, a novel Gram-negative, moderately halophilic, heterotrophic and short rod-shaped bacteria was isolated and characterized. The bacterium was isolated from a water specimen and designated as TBZ3T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3T was observed to be at 10-45 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0.5-20 % (w/v) NaCl (optimum, 7.5 %). Strain TBZ3T contained C16 : 0, cyclo-C19 : 0 ω8c, summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (comprising C18 : 1 ω7c and/or C18 : 1 ω6c) as major fatty acids and ubiquinone-9 as the only respiratory isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid, unidentified phospholipid and unidentified polar lipids were detected as the major polar lipids. Strain TBZ3T was found to be most closely related to Halomonas saccharevitans AJ275T , Halomonas denitrificans M29T and Halomonas sediminicola CPS11T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3T grouped with Halomonas saccharevitans AJ275T contained within a large cluster within the genus Halomonas. Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3T represents a novel species of the Halomonas genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3T (=DSM 22871T=LMG 25416T).

Classification of Riboswitch Families Using Block Location-Based Feature Extraction (BLBFE) Method.

Purpose: Riboswitches are special non-coding sequences usually located in mRNAs' un-translated regions and regulate gene expression and consequently cellular function. Furthermore, their interaction with antibiotics has been recently implicated. This raises more interest in development of bioinformatics tools for riboswitch studies. Herein, we describe the development and employment of novel block location-based feature extraction (BLBFE) method for classification of riboswitches. Methods: We have already developed and reported a sequential block finding (SBF) algorithm which, without operating alignment methods, identifies family specific sequential blocks for riboswitch families. Herein, we employed this algorithm for 7 riboswitch families including lysine, cobalamin, glycine, SAM-alpha, SAM-IV, cyclic-di-GMP-I and SAH. Then the study was extended toward implementation of BLBFE method for feature extraction. The outcome features were applied in various classifiers including linear discriminant analysis (LDA), probabilistic neural network (PNN), decision tree and k-nearest neighbors (KNN) classifiers for classification of the riboswitch families. The performance of the classifiers was investigated according to performance measures such as correct classification rate (CCR), accuracy, sensitivity, specificity and f-score. Results: As a result, average CCR for classification of riboswitches was 87.87%. Furthermore, application of BLBFE method in 4 classifiers displayed average accuracies of 93.98% to 96.1%, average sensitivities of 76.76% to 83.61%, average specificities of 96.53% to 97.69% and average f-scores of 74.9% to 81.91%. Conclusion: Our results approved that the proposed method of feature extraction; i.e. BLBFE method; can be successfully used for classification and discrimination of the riboswitch families with high CCR, accuracy, sensitivity, specificity and f-score values.