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-β, 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.

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.

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.

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 β-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.

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.

Phenotypic and phylogenetic characterization of Lactobacillus species isolated from traditional Lighvan cheese

Abstract

Lighvan cheese (Lighvan panir) is among the most famous traditional cheese in Iran for its desired aroma and flavor. Undoubtedly, the lactic acid bacteria especially the genus Lactobacillus are the critical factors in developing the aroma, flavor, and texture in Lighvan cheese. In this study, the Lactobacillus population of the main Lighvan cheese was investigated. The Lactobacillus of the main Lighvan cheese was isolated using specific culture methods according to previously published Guidelines. Then, the phylogenetic features were investigated and the phenotypic characteristics were examined using specific culture methods. Twenty-eight Gram-positive bacterial species were identified belonged to the genus Lactobacillus. According to the same sequences as each other, three groups (A, B, and C) of isolates were categorized with a high degree of similarity to L. fermentum (100%) and L. casei group (L. casei, L. paracasei, and L. rhamnosus) (99.0 to 100%). Random amplified polymorphic DNA (RAPD) fingerprint analysis manifested the presence of three clusters that were dominant in traditional Lighvan cheese. Cluster І was divided into 4 sub-clusters. By the result of carbohydrate fermentation pattern and 16S rRNA sequencing, isolates were identified as L. rhamnosus. The isolates in clusters II and III represented L. paracasei and L. fermentum, respectively as they were identified by 16S rRNA sequencing and fermented carbohydrate patterns. Our result indicated that the specific aroma and flavor of traditional Lighvan cheese can be related to its Lactobacillus population including L. fermentum, L. casei, L. paracasei, and L. rhamnosus.

Graphical abstract

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

A novel moderately halophilic, Gram-staining negative and facultative aerobic bacterium, designated as TBZ9^T, 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 TBZ9^T 16S rRNA gene sequence was related to the genus Halomonas showing highest similarities to Halomonas arcis AJ282^T (98.4%), Halomonas songnenensis NEAU-ST10-39^T (98.0%) and Halomonas lutescens Q1U^T (97.8%). In the phylogenetic trees, strain TBZ9^T 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 TBZ9^T and H. arcis AJ282^T (20.0%, 74.0%) and H. songnenensis NEAU-ST10-39^T (19.8%, 75.2%) indicated that TBZ9^T represents a distinct species. Evaluation of fatty acid contents determined C_10:0, C_16:0, C_12:0 3-OH, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) as major cellular fatty acids. The major quinone of strain TBZ9^T 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 TBZ9^T is 55.4 mol%. Results from phenotypic, chemotaxonomic and molecular analysis suggest that the strain TBZ9^T represents a novel species within the genus Halomonas for which the name Halomonas azerica sp. nov. is proposed. The type strain is TBZ9^T (= KACC 21783^T = LMG 25775^T).

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.

Mechanistic Insight on Ras Inhibition Strategies in Cancer Therapy

Ras proteins are considered as one of the most critical cancer initiators. Mutations of this protein family lead to the continuous activation of the proliferation pathways. Therefore, many efforts have been taken to design the anti-mutant Ras drug candidates. Regardless of the development of promising inhibitors of Ras G12C mutant in a specific cancer type, there is no approved inhibitor of Ras mutants in the clinic. One of the significant limitations is to inhibit particular mutants and not to affect the wild-type Ras variants. Here we present a review on the mechanism of action of the Ras proteins to get a better insight into the strategies utilized to inhibit Ras-mutated cancers. The direct Ras inhibition strategies are then highlighted to obtain a better perspective of possible promising approaches to target Ras proteins in cancer therapy.

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.

CpG Islands Methylation Analysis of CDH11, EphA5, and HS3ST2 Genes in Gastric Adenocarcinoma Patients

PURPOSE

Gastric cancer is an aggressive disease which is the fourth prevalent malignancy in the world. Beside the genetic factors, epigenetic alterations such as promoter CpG island hyper methylation are involved in the emergence of gastric cancer. Herein, we investigated the methylation status of CDH11, EphA5, and HS3ST2 genes in patients with and without gastric adenocarcinoma for the first time.

METHODS

In the study 40 paraffin-embedded tissue sections from gastric adenocarcinoma patients and 40 specimens from patients with functional dyspepsia were taken. DNA extraction was performed using a modified salting out method. Epizen DNA methylation kit was used to the bisulfite DNA conversion. The methylation status of CDH11, EphA5, and HS3ST2 genes were analyzed by methylation-specific PCR (MSP) technique.

RESULTS

Among the 80 specimens, 71 DNA samples were achieved (34 gastric adenocarcinoma patients and 37 control patients). The results showed that CDH11, EphA5, and HS3ST2 genes are methylated in 28 (82.45%), 19 (55.88%), and 26 (76.47%) of 34 DNA samples from gastric adenocarcinoma patients, respectively, whereas, these genes are methylated in 7 (18.91%), 9 (24.32%) and 7 (18.91%) of 37 samples from noncancerous patients, respectively. Statistical analyses using a chi-squared test showed that there is a statistically significant difference in methylation level of CDH11, EphA5, and HS3ST2 genes between gastric cancer and uncancerous patients (p < 0.05).

CONCLUSION

To the best of our knowledge, this is the first report on methylation of CDH11, EphA5, and HS3ST2 promoters' in gastric adenocarcinoma patients using MSP. Identification of novel cancer-related molecular mechanisms can be useful in detection of new treatment strategies.

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

A novel, slightly halophilic bacterium, designated TBZ202^T, 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 TBZ202^T belongs to the genus Halomonas in the Halomonadaceae and the most closely related species are Halomonas gudaonensis CGMCC 1.6133^T (98.6 % similarity), Halomonas ventosae Al12^T (96.8 %) and Halomonas rambilicola RS-16^T (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 C_{18 : 1} ω7c, C_{16 : 0} and C_{16 : 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 TBZ202^T (=KCTC 62817^T=CECT 9693^T).

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.

CDK9 as an Appealing Target for Therapeutic Interventions

Cyclin Dependent Kinase 9 (CDK9) as a serine/threonine kinase belongs to a great number of CDKs. CDK9 is the main core of PTEF-b complex and phosphorylates RNA polymerase (RNAP) II besides other transcription factors which regulate gene transcription elongation in numerous physiological processes. Multi-functional nature of CDK9 in diverse cellular pathways proposes that it is as an appealing target. In this review, we summarized the recent findings on the molecular interaction of CDK9 with critical participant molecules to modulate their activity in various diseases. Furthermore, the presented review provides a rationale supporting the use of CDK9 as a therapeutic target in clinical developments for crucial diseases; particularly cancers will be reviewed.

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.

Polycyclic Aromatic Hydrocarbons Degradation by Aquatic Bacteria Isolated from Khazar Sea, the World’s Largest Lake

Background: Aquatic microorganisms have an important role in the bioremediation of environmental pollutants. Polycyclic Aromatic Hydrocarbons (PAHs) are described as dangerous pollutants that can bind covalently to the nucleic acids, causing mutations. Therefore, they have carcinogenic and toxic properties. Also, are involved in diseases such as asthma, lung dysfunction, and chronic bronchitis. This study aimed to isolate and characterize aquatic bio-degrading bacteria from the world’s largest lake, Khazar, with the ability to use PAHs as only carbon source. Methods: Samples were taken from the estuary of Siah Rud River (Mazandaran province, Iran) and Fereydunkenar beach leading to isolation of twenty-three bacteria on marine agar and sea water media. The isolates were cultured on separate ONR7a medium, each supplemented with only one PAH; as the sole carbon source; including naphthalene, phenanthrene, and anthracene. Results: Eleven bacterial isolates were able to grow on supplemented media: TBZ-E1, TBZ-E2, TBZ-E3, TBZ-S12, TBZ-S16, TBZ-E20, TBZ-SF2, TBZ-F1, TBZ-F2, TBZ-F3 and TBZ2. These isolates belong to Alteromonas, Marivivens, Pseudoalteromonas, Vibrio, Shewanella, Photobacterium, Mycobacterium and Pseudomonas genera. The qualitative analysis showed that the consortium of isolates TBZ-F1, TBZ-F2, TBZ-F3, TBZ-SF2, and TBZ2 displayed the highest degradation rate for phenanthrene and naphthalene. Naphthalene, phenanthrene, and anthracene were potently degraded by TBZ2 and TBZ-SF2 and accordingly were subjected to measure degradation potential of mentioned PAHs. Conclusion: The bacterial isolates of Caspian lake have a critical duty in biodegradation of PAHs. These isolates are representative samples of the bacterial population of this lake, participating in the purification process of this habitat.

Elioraea thermophila sp. nov., a thermophilic bacterium from hot spring of the class Alphaproteobacteria, emended description of the genus Elioraea and proposal of Elioraeaceae fam. nov

A Gram-staining-negative, aerobic, curved rod-shaped and thermophilic bacterial strain, designated YIM 72297^T, was isolated from a sediment sample collected from a hot spring in Tengchong county, Yunnan province, south-west China. Growth was observed at pH 5.0-9.0 with an optimum of pH 7.0-7.5, and at 45-60 °C with an optimum of 55 °C. Positive for catalase and oxidase. The 16S rRNA gene sequence comparison indicated that strain YIM 72297^T was most closely related to Elioraea tepidiphila DSM 17972^T (96.9 %) and showed <91 % sequence similarities to members of the order Rhodospirillales. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 72297^T formed a distinct lineage within the genus Elioraea, and revealed that the genus Elioraea formed a novel family-level clade in the order Rhodospirillales. The ANI and the dDNA-DNA hybridization estimate values between strains YIM 72297^T and Elioraea tepidiphila DSM 17972^T were 70.8 and 20.1 %, respectively. Strain YIM 72297^T contained Q-10 as the predominant ubiquinone. The major fatty acids (>5 %) were summed C_18 : 0 (35.8 %), summed feature 8 (30.1 %), C_16 : 0 (12.6 %), C_18 : 1 2OH (5.6 %) and C_16 : 0 2OH (5.4 %). The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, diphosphosphatidylglycerol and phosphatidylglycerol in addition to two unidentified aminolipids. The DNA G+C content of YIM 72297^T was 70.8 mol% (draft genome). On the basis of the polyphasic taxonomic evidence presented in this study, strain YIM 72297^T should be classified as representing a novel species of the genus Elioraea, for which the name Elioraea thermophila sp. nov. is proposed, with the type strain YIM 72297^T (=CCTCC AB 2017169^T=KCTC 62323^T). In addition, a novel family, Elioraeaceae fam. nov., is proposed to accommodate the genus Elioraea.

Antibacterial and Antifungal Activity of Novel Freshwater Bacterium Tabrizicola aquatica as a Prominent Natural Antibiotic Available in Qurugol Lake

Background : Recently, resistant pathogenic microorganisms have become increasingly wide spread. The search for new natural antibiotics is a viable solution to this problem. For this aim we investigated the antimicrobial ability of Tabrizicola aquatica, the novel bacterium isolated from Qurugol Lake located nearby Tabriz city, Iran. Methods: The antimicrobial properties of Tabrizacola aquatica was investigated using well diffusion test. Tabtizicola aquatica was incubated at 40℃ in shaking incubator at 150 rpm for 14 days. The culture was centrifuged to obtain cell free supernatant, which was sterilized using 0.2 μm filter paper and lyophilized. Microorganisms were lawn and then wells were prepared over the agar plates. About 100 ml of the diluted lyophilized supernatant was added to the wells. The plates then were incubated at 37℃. After 48 hours, antimicrobial activity was defined by measuring the inhibition zone diameter. Results: The bacterial filtrates had considerable antagonistic effect against Escherichia coli, Rhizobium radiobacter, Pseudomonas syringae, Erwinia amylovora, Botrytis cinerea, Neurospora crassa and Fusarium oxysporum. However, the filtrates did not show any inhibitory action on the Aspergillus flavus and Klebsiella pneumonia. The supernatant decreased the growth zone on Streptococcus aureus, Pseudomonas aeruginosa, Shigella flexneri, Xanthomonas camoestris and Bassilus cereos. The result of MIC against pathogens was found for Neurospora crassa in the 50 µg/mL. Conclusion: The results, suggested that Tabrizicola aquatica and similar bacteria can be helpful to control freshwater natural water sources from pathogenic microorganism. Moreover, microbial natural products are still the most promising source of new antibiotics. Our results point out a scope for characterization of the metabolites and could be a candidate in the identification of novel antibiotics.

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 TBZ3^T. Colonies were found to be creamy yellow, with catalase- and oxidase-positive activities. The growth of strain TBZ3^T 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 TBZ3^T contained C_16 : 0, cyclo-C_19 : 0  ω8c, summed feature 3 (comprising C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 8 (comprising C_18 : 1  ω7c and/or C_18 : 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 TBZ3^T was found to be most closely related to Halomonas saccharevitans AJ275^T , Halomonas denitrificans M29^T and Halomonas sediminicola CPS11^T with the 16S rRNA gene sequence similarities of 98.93, 98.15 and 97.60 % respectively and in phylogenetic analysis strain TBZ3^T grouped with Halomonas saccharevitans AJ275^T contained within a large cluster within the genus Halomonas. Based on phenotypic, chemotaxonomic and molecular properties, strain TBZ3^T represents a novel species of the Halomonas genus, for which the name Halomonas urmiana sp. nov. is proposed. The type strain is TBZ3^T (=DSM 22871^T=LMG 25416^T).

Development of a new oligonucleotide block location-based feature extraction (BLBFE) method for the classification of riboswitches

As knowledge of genetics and genome elements increases, the demand for the development of bioinformatics tools for analyzing these data is raised. Riboswitches are genetic components, usually located in the untranslated regions of mRNAs, that regulate gene expression. Additionally, their interaction with antibiotics has been recently suggested, implying a role in antibiotic effects and resistance. Following a previously published sequential block finding algorithm, herein, we report the development of a new block location-based feature extraction strategy (BLBFE). This procedure utilizes the locations of family-specific sequential blocks on riboswitch sequences as features. Furthermore, the performance of other feature extraction strategies, including mono- and dinucleotide frequencies, k-mer, DAC, DCC, DACC, PC-PseDNC-General and SC-PseDNC-General methods, was investigated. KNN, LDA, naïve Bayes, PNN and decision tree classifiers accompanied by V-fold cross-validation were applied for all methods of feature extraction, and their performances based on the defined feature extraction strategies were compared. Performance measures of accuracy, sensitivity, specificity and F-score for each method of feature extraction were studied. The proposed feature extraction strategy resulted in classification of riboswitches with an average correct classification rate (CCR) of 90.8%. Furthermore, the obtained data confirmed the performance of the developed feature extraction method with an average accuracy of 96.1%, an average sensitivity of 90.8%, an average specificity of 97.52% and an average F-score of 90.69%. Our results implied that the proposed feature extraction (BLBFE) method can classify and discriminate riboswitch families with high CCR, accuracy, sensitivity, specificity and F-score values.

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.

Hsp70 in Cancer: Partner or Traitor to Immune System

Heat shock protein 70.1 (Hsp70.1), also known as Hsp70, is a highly conserved member of the heat shock protein family that exists in all living organisms and determines the protein fate as molecular chaperones. Hsp70 basal expression is undetectable or low in most unstressed normal cells, however, its abundant presence in several types of human cancer cells is reported. Several studies support upregulated Hsp70 involved in tumor progression and drug resistance through modulation of cell death pathways and suppresses anticancer immune responses. However, numerous studies have confirmed that Hsp70 can also induce anticancer immune responses through the activation of immune cells in particular antigen-presenting cells (APCs). Regarding the significant and the promising role of vaccines in cancer immunotherapy, identification and characterization of the overexpressed Hsp70 as a potential immune stimulatory factor can pave the path for development of highly effective anticancer vaccines. In this review, we will discuss the interactions of Hsp70 with components of the immune system in cancers as well as possible strategies to harness Hsp70 for eliciting anticancer immune responses.

Pseudomonas khazarica sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Khazar Sea sediments

A novel Gram-negative, aerobic, motile and rod-shaped bacterium with the potential to biodegrade polycyclic aromatic hydrocarbons, was isolated from Khazar (Caspian) Sea. Strain TBZ2^T grows in the absence of NaCl and tolerates up to 8.5% NaCl. Growth occurred at pH 3.0-10.0 (optimum, pH 6.0-7.0) and 10-45 °C (optimum, 30 °C). The major fatty acids are C_18:1ω7C, C_16:1ω7C/ C_15:0 iso 2-OH, C_16:0, C_12:0, C_10:0 3-OH, C_12:0 3-OH. The major polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and the predominant respiratory quinone is ubiquinone Q-9. The 16S rRNA gene sequence analysis showed that strain TBZ2^T is a member of the genus Pseudomonas with the highest similarity to P. oleovorans subsp. oleovorans DSM 1045^T (98.83%), P. mendocina NBRC 14162^T (98.63%), P. oleovorans subsp. lubricantis RS1^T (98.61%) and P. alcaliphila JCM 10630^T (98.49%) based on EzBioCloud server. Phylogenetic analyses using housekeeping genes (16S rRNA, rpoD, gyrB and rpoB) and genome sequences demonstrated that the strain TBZ2^T formed a distinct branch closely related to the type strains of P. mendocina and P. guguanensis. Digital DNA-DNA hybridisation and average nucleotide identity values between strain TBZ2^T and its closest relatives, P. mendocina NBRC 14162^T (25.3%, 81.5%) and P. guguanensis JCM 18146^T (26.8%, 79.0%), rate well below the designed threshold for assigning prokaryotic strains to the same species. On the basis of phenotypic, chemotaxonomic, genomic and phylogenetic results, it is recommended that strain TBZ2^T is a novel species of the genus Pseudomonas, for which the name Pseudomonas khazarica sp. nov., is proposed. The type strain is TBZ2^T (= LMG 29674^T = KCTC 52410^T).

The Role of Nrf2 signaling in cancer stem cells: From stemness and self-renewal to tumorigenesis and chemoresistance

Cancer stem cells (CSCs) are subpopulation of tumor mass with exclusive abilities in self-renewing, stemness maintaining, and differentiation into the various non-stem cancer cells to provoke tumorigenesis, metastasis dissemination, drug-resistant, and cancer recurrence. Reactive oxygen species (ROS) impair cellular function by oxidizing cell components containing proteins, lipids, and DNA. Tumor oxidant status is elevated due to high metabolic activity under influence of abnormal growth factors, cytokines and function ROS-producing enzymes, including nitric oxide synthases, cyclooxygenases, and lipoxygenases. Nuclear factor-erythroid 2-related factor 2 (NRF2) is a transcriptional master regulator element which is believed to recognize cellular oxidative stress followed by binding to promoter of cyto-protective and anti-oxidative genes to maintain cellular redox status through promoting antioxidant response participants (glutathione peroxidase, glutathione reductase, thioredoxin reductase, ferritin, NADPH: quinone oxidoreductase 1). However, Nrf2 signaling protects malignant cells from ROS damage against tumor growth and chemoresistance. In addition, Nrf2 is able to participate in differentiation of certain stem cells by modulating autophagy procedure, also NRF2 provokes DNA damage response and facilitates drug metabolism and drug resistance by controlling of downstream enzyme and transporter members. In this review, we discuss the role of NRF2 in stemness, self-renewal ability, tumorigenesis and chemoresistance of CSCs.

Transient induction of Cdk9 in the early stage of differentiation is critical for myogenesis

Cdk9 is a serine-threonine protein kinase that has been recognized as a regulator of cardiac differentiation. Recently, we have reported that transient induction of Cdk9 using noncoding RNA targeting Cdk9 sequences results in efficient cardiac differentiation. Concerning Cdk9 regulatory roles, here, we proposed whether constant overexpression of Cdk9 might influence the differentiation of myoblast C2C12 cells into myotubes. We overexpressed Cdk9 in mouse myoblast C2C12 cells to investigate its regulatory roles on myogenic differentiation. Upon Cdk9 overexpression, the expression level of myogenic regulatory factors was determined. Moreover, the expression profile of three important myomiRs consist of miR 1, 133 and 206 was examined during the differentiation process. Although Cdk9 expression is necessary for inducing differentiation in the early stage of myogenesis, continuous Cdk9 expression inhibits differentiation by modulating myomiRs and myogenic gene expression. Our results indicate that the transient induction of Cdk9 in the early stage of differentiation is critical for myogenesis.

Layered double hydroxide nanoparticles as an appealing nanoparticle in gene/plasmid and drug delivery system in C2C12 myoblast cells

Gene and drug delivery systems need crucial update in the issue of nanocarriers. Layered double hydroxides (LDHs) are known as biocompatible inorganic lamellar nanomaterials with versatile properties. In the present study, Zn/Al-LDH nanoparticle was synthesized and characterized by FTIR, XRD, SEM, TEM and Zeta potential tests and then intercalated with valproate and methyldopa by co-precipitation and ion exchange methods. These nanocarriers were applied as high activity nanolayers-based delivery systems. On the other hand, Zn/Al-LDH + plasmid/gene (pCEP4/Cdk9) evaluated on C2C12 myoblast cells. Co-operation loading indicated high efficiency of sorting and release of drugs. Additionally, the Real-Time PCR and Western blotting results for plasmid-gene (pCEP4/Cdk9) delivery showed that Zn/Al-LDH nanoparticles can be used as an effective carrier in cellular uptake and release of genes for gene therapy. Easy and cost-effective production of Zn/Al-LDH nanoparticles proposed them as potential alternatives for the traditional routs of drug/gene delivery.

Emended description of the genus Tabrizicola and the species Tabrizicola aquatica as aerobic anoxygenic phototrophic bacteria

The genus Tabrizicola with its type species and strain Tabrizicola aquatica RCRI19^T was previously described as a purely chemotrophic genus of Gram-negative, aerobic, non-motile and rod-shaped bacteria. With the present study, we expand the description of the metabolic capabilities of this genus and the T. aquatica type strain to include chlorophyll-dependent phototrophy. Our results confirmed that T. aquatica, does not grow under anaerobic photoautotrophic or photoheterotrophic conditions. However, the presence of the photosynthesis-related genes pufL and pufM could be demonstrated in the genomes of several Tabrizicola strains. Additionally, photosynthetic pigments (bacteriochlorophyll a) were formed under aerobic, heterotrophic and low light conditions in T. aquatica strain RCRI19^T. Furthermore, all the genes necessary for a fully operational photosynthetic apparatus and bacteriochlorophyll a are present in the T. aquatica type strain genome. Therefore, we suggest categorising T. aquatica RCRI19^T, isolated from freshwater environment of Qurugöl Lake, as an aerobic anoxygenic phototrophic (AAP) bacterium.

Exosomes: from carcinogenesis and metastasis to diagnosis and treatment of gastric cancer

Exosomes represent an important group of extracellular vesicles with a defined size between 40 and 150 nm and cup-shaped construction which have a pivotal role in elimination of intracellular debris and intercellular signaling networks. A line of evidence revealed the impact of different types of exosomes in initiation, progression, and metastasis of gastric cancer (GC). These bioactive vesicles mediate tumor and stromal communication network through modulation of cell signaling for carcinogenesis and pre-metastatic niche formation in distant organs. Exosomes contain various cargos including DNAs (mitochondrial and genomic), proteins, transposable elements, and RNAs (coding and noncoding) with different compositions related to functional status of origin cells. In this review, we summarize the main roles of key exosomal cargos in induction of exosome-mediated signaling in cancer cells. Body fluids are employed frequently as the source of exosomes released by tumor cells with a potential role in early diagnosis of GC and chemoresistance. These vesicles as non-toxic and non-immunogenic carriers are also found to be applied for novel drug delivery systems.

Potential of Peptide Nucleic Acids in Future Therapeutic Applications

Peptide nucleic acids (PNA) are synthetic analog of DNA with a repeating N-(2-aminoethyl)-glycine peptide backbone connected to purine and pyrimidine nucleobases via a linker. Considering the unique properties of PNA, including resistance to enzymatic digestion, higher biostability combined with great hybridization affinity toward DNA and RNA, it has attracted great attention toward PNA- based technology as a promising approach for gene alteration. However, an important challenge in utilizing PNA is poor intracellular uptake. Therefore, some strategies have been developed to enhance the delivery of PNA in order to reach cognate site. Although PNAs primarily demonstrated to act as an antisense and antigene agents for inhibition of transcription and translation of target genes, more therapeutic applications such as splicing modulation and gene editing are also used to produce specific genome modifications. Hence, several approaches based on PNAs technology have been designed for these purposes. This review briefly presents the properties and characteristics of PNA as well as different gene modulation mechanisms. Thereafter, current status of successful therapeutic applications of PNA as gene therapeutic intervention in different research areas with special interest in medical application in particular, anti-cancer therapy are discussed. Then it focuses on possible use of PNA as anti-mir agent and PNA-based strategies against clinically important bacteria.

Anoxybacillus sediminis sp. nov., a novel moderately thermophilic bacterium isolated from a hot spring

A Gram-stain positive, moderately thermophilic, aerobic, spore-forming and rod-shaped bacterium, designated YIM 73012^T, was isolated from a sediment sample collected from a hot spring located in Tibet, China, and was characterized by using a polyphasic taxonomy approach. The strain is oxidase positive and catalase negative. Growth occurred at 37-65 °C (optimum, 45-50 °C), at pH 6.0-8.5 (optimum, pH 7.0-7.5) and with 0.5-3.5% NaCl (optimum, 0.5-1.0%, w/v). The major fatty acids were iso-C_15:0, iso-C_16:0 and C_16:0. The major polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylglycerol. The cell wall peptidoglycan contained meso-diaminopimelic acid. The respiratory quinone was MK-7. The G+C content of genomic DNA was 43.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain YIM 73012^T forms a distinct lineage with respect to the genus Anoxybacillus in the family Bacillaceae. Based on 16S rRNA gene sequence identities the closely related phylogenetic neighbours are Anoxybacillus caldiproteolyticus DSM 15730^T (96.7%) and Saccharococcus thermophilus DSM 4749^T (96.6%). Strain YIM 73012^T was distinguishable from the closely related reference strains by the differences in phenotypic, chemotaxonomic and genotypic characteristics, and represents a novel species of the genus Anoxybacillus, for which the name Anoxybacillus sp. nov. is proposed. The type species is Anoxybacillus sediminis sp. nov., with the type strain YIM 73012^T (= KCTC 33884^T = DSM 103835^T).

siRNA-Mediated Silencing of CIP2A Enhances Docetaxel Activity Against PC-3 Prostate Cancer Cells

Purpose: Cancerous inhibitor of protein phosphatase 2A (CIP2A) is an identified human oncoprotein which modulates malignant cell growth. It is overexpressed in human prostate cancer and in most of the human malignancies. The aim of this study was to investigate the effects of CIP2A silencing on the sensitivity of PC-3 prostate cancer cells to docetaxel chemotherapy.

Methods: PC-3 cells were transfected using CIP2A siRNA. CIP2A mRNA and protein expression were assessed after CIP2A gene silencing using q-RT PCR and Western blotting. Proliferation and apoptosis were analyzed after treatment with docetaxol using MTT assay, DAPI staining, and flow cytometry, respectively.

Results: Silencing of CIP2A enhanced the sensitivity of PC-3 cells to docetaxel by strengthening docetaxel induced cell growth inhibition and apoptosis against PC-3 cells.

Conclusion: Silencing of CIP2A may potentiate the cytotoxic effects of docetaxel and this might be a promising therapeutic approach in prostate cancer treatment.

Development of a new sequential block finding strategy for detection of conserved sequences in riboswitches

Introduction: Some non-coding RNAs have an important role in the regulation of gene expression and consequently cellular function. Riboswitches are examples of these regulatory RNAs. Riboswitches are classified into various families according to sequential and structural similarities.

Methods: In this study, a block finder algorithm for identification of frequently appearing sequential blocks in five families of riboswitches from Rfam 12.0 database, without the use of alignment methods, was developed.

Results: The developed program identified 21 frequently appearing blocks in five families of riboswitches.

Conclusion: Comparison of the results of the proposed algorithm with those of sequential alignment methods revealed that our method can recognize most of the patterns present in conserved areas of individual riboswitch families and determine them as specific blocks, implying potential of the developed program as a platform for further studies and developments.

CDK9 Regulates Apoptosis of Myoblast Cells by Modulation of microRNA-1 Expression

Cdk9 is the catalytic core of the positive transcription elongation factor b (P-TEFb) and regulates transcriptional elongation factors by phosphorylation of RNA pol II. Apart from its role on myogenic gene expression, Cdk9 regulation of muscle-specific microRNAs in the early stage of cardiomyogenesis is poorly understood. Here we demonstrate that Cdk9 not only regulates myogenic transcription factors, but also controls muscle-specific microRNAs. During cardiac differentiation of mouse embryonic stem cells, high Cdk9 expression preceded up-regulation of miR-1. To investigate potential regulatory roles of Cdk9 on cardiac microRNAs and myogenesis genes, we overexpressed Cdk9 in myoblast C2C12 cells, which resulted in significant induction of miR-1 and miR-206, while miR-133 was downregulated. Moreover, expression levels of MyoD and Srf, key regulators of myogenesis, also increased in cells with overexpression of Cdk9. We further observed Cdk9-mediated apoptosis in C2C12 cells corresponding to induction of miR-1 expression levels. Thus, Cdk9 plays a complex role in myocyte progenitor differentiation and apoptosis by regulating myogenic protein and muscle-specific microRNA expression. J. Cell. Biochem. 119: 547-554, 2018. © 2017 Wiley Periodicals, Inc.

TPP riboswitch characterization in Alishewanella tabrizica and Alishewanella aestuarii and comparison with other TPP riboswitches

Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environmental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5' UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized. Moreover, affinity analysis of TPP binding to the TPP aptamer domains originated from A. tabrizica, A. aestuarii, E.coli, and B. subtilis were studied and compared using In-line probing and Surface Plasmon Resonance (SPR). TPP binding to the studied RNAs from A. tabrizica and A. aestuarii caused distinctive changes of the In-line cleavage pattern, demonstrating them as functional TPP riboswitches. With dissociation constant of 2-4nM (depending on the method utilized), the affinity of TPP binding was highest in A. tabrizica, followed by the motifs sourced from A. aestuarii, E. coli, and B. subtilis. The observed variation in their TPP-binding affinity might be associated with adaptation to the different environments of the studied bacteria.

Multifunctional Superparamagnetic Nanoparticles: From Synthesis to siRNA Delivery

BACKGROUND

Targeted delivery of small interfering RNA (siRNA) to the specific tumor tissues and cells is the key challenge in the development of RNA interference as a therapeutic application.

METHODS

To target breast cancer, we developed a cationic nanoparticle as a therapeutic delivery system. The successful synthesis of the magnetic nanoparticles modified by polyaspartate (PAA) and polyethyleneimine (PEI) was confirmed using fourier transform infrared (FT-IR) measurements. The designed nanoparticle has been characterized evaluating its size and charge before and after nanoplex formation with siRNA.

RESULTS

The designed nanoparticle could effectively form nanoplex with siRNA in 2:1 w/w ratio. Survivin siRNA was used to suppress the antiapoptotic gene, survivin, in MCF-7 cells. According to the importance of combinational therapy, Mitoxantrone (MTX) was used as a chemotherapeutic agent as well. The multifunctional nanoparticles have been successfully entered into about 63% of the MCF-7 cells shown via microscopic and flowcytometric methods. This effective cellular uptake led to the cell apoptosis. Down regulation of survivin was determined in mRNA and protein levels using Real Time PCR and western blotting, respectively.

CONCLUSION

Gathering all obtained data, it was concluded that Fe3O4-PAA-PEI nanoparticles can deliver siRNA effectively into the cytoplasm of the MCF-7 breast cancer cells and induce apoptosis.

Removal of U(VI) from aqueous solutions using Shewanella sp. RCRI7, isolated from Qurugöl Lake in Iran

Isolation, genotypic and phenotypic characterization of an aqueous bacterium, Shewanella sp RCRI7, from Qurugöl Lake in Iran and uranium removal from aqueous solutions using the isolate is described. Based on 16S rRNA gene sequence analysis and phylogenetic tree, strain RCRI7T falls into genus Shewanella. Closely related type strains include Shewanella xiamenensis S4T KJ542801, Shewanella profunda DSM15900T FR733713, Shewanella putrefaciens LMG 26268T X81623 and Shewanella oneidensis MR-1T AE014299. Anaerobic incubation of the bacteria in the presence of U(VI) led to uranium removal from the solution and formation of a black precipitate. Analysis of the precipitate using UV-vis confirmed the reduction of U(VI) to U(IV). The effects of pH, temperature, U(VI) concentration and cell density on uranium removal were elucidated. The maximum uranium removal was 97%. As a conclusion, the findings revealed the ability of the local strain RCRI7 for U(VI) bioreduction as an effective bacterium for uranium immobilization.

Riboswitches: From living biosensors to novel targets of antibiotics

Riboswitches are generally located in 5'-UTR region of mRNAs and specifically bind small ligands. Following ligand binding, gene expression is controlled mostly by transcription termination, translation inhibition or mRNA degradation processes. More than 30 classes of known riboswitches have been identified by now. Most riboswitches consist of an aptamer domain and an expression platform. The aptamer domain of each class of riboswitch is a conserved structure and stabilizes specific structures of the expression platforms through binding to specific compounds. In this review, we are highlighting most aspects of riboswitch research including the novel riboswitch discoveries, routine methods for discovering and investigating riboswitches along with newly discovered classes and mechanistic principles of riboswitch-mediated gene expression control. Moreover, we will give an overview about the potential of riboswitches as therapeutic targets for antibiotic design and also their utilization as biosensors for molecular detection.

The role of Six1 signaling in paclitaxel-dependent apoptosis in MCF-7 cell line

The resistance of cancer cells to chemotherapeutic agents represents the main problem in cancer treatment. Despite intensive research, mechanisms of resistance have not yet been fully elucidated. Six1 signaling has an important role in the expansion of progenitor cell populations during early embryogenesis. Six1 gene overexpression has been strongly associated with aggressiveness, invasiveness, and poor prognosis of different cancers. In this study, we investigated the role of Six1 signaling in resistance of MCF-7 breast cancer cells to taxanes. We first established in vitro paclitaxel-resistant MCF-7 breast cancer cells. Morphological modifications in paclitaxel-resistant cells were examined via light microscopic images and fluorescence-activated cell sorting analysis. Applying quantitative real-time polymerase chain reaction, we measured Six1, B-cell lymphoma/leukemia(BCL-2), BAX, and P53 mRNA expression levels in both non-resistant and resistant cells. Resistant cells were developed from the parent MCF-7 cells by applying increasing concentrations of paclitaxel up to 64 nM. The inhibitory concentration 50% value in resistant cells increased from 3.5 ± 0.03 to 511 ± 10.22 nM (p = 0.015). In paclitaxel-resistant cells, there was a significant increase in Six1 and BCL-2 mRNA levels (p = 0.0007) with a marked decrease in pro-apoptotic Bax mRNA expression level (p = 0.03); however, there was no significant change in P53 expression (p = 0.025). Our results suggest that identifying cancer patients with high Six1 expression and then inhibition of Six1 signaling can improve the efficiency of chemotherapeutic agents in the induction of apoptosis.

Doxorubicin Changes Bax /Bcl-xL Ratio, Caspase-8 and 9 in Breast Cancer Cells

PURPOSE

Doxorubicin is administrated as a single agent in first-line therapy of breast cancer to induce apoptosis in tumor cells. Bax, Bcl-xL, Caspase-8 and 9 proteins are involved in induction of apoptosis. The present study describes Bax, Bcl-xL gene expression and Caspase-8 and 9 protein levels in MCF-7 cells incubated with doxorubicin at different doses an incubation times.

METHODS

The cytotoxic effects of doxorubicin were studied using MTT assay. MCF-7 cells were treated with three concentrations of doxorubicin (0.1, 0.5, 1 μM) and incubated for 24, 48 and 72 hours then expression levels of Bax and Bcl-xL genes were elucidated by Real-time RT-PCR technique and protein levels of caspase-8 and caspase-9 proteins were measured using ELISA method. Morphological modifications of the cells were also monitored via light microscopic images.

RESULTS

Doxorubicin decreased the anti-apoptotic Bcl-xL and increased pro-apoptotic Bax mRNA levels. Doxorubicin induced a significant increase in Bax /Bcl-xL ratio in all doses and incubation times (p<0.05). Highest (more than 10 fold) increase in Bax /Bcl-xL ratio was revealed after 48 h incubation of the cells with in all doses of doxorubicin. Doxorubicin also increased caspase-9 level in a time and dose-dependent manner, while caspase-8 level didn't follow time and dose dependency pattern.

CONCLUSION

Our results confirm that doxorubicin induces mitochondrial-dependent apoptosis by down-regulation of Bcl-xL and up- regulation of Bax and caspase-9 expressions.