Evaluating the incidence of ampC-ß-lactamase genes, biofilm formation, and antibiotic resistance among hypervirulent and classical Klebsiella pneumoniae strains.

AIM: Both immunocompetent and healthy individuals can become life-threateningly ill when exposed to the hypervirulent (hvKp) strains of Klebsiella pneumoniae (Kp). The main objectives of this study were to evaluate the presence of ampC-lactamase genes, biofilm formation, and antibiotic resistance in clinical strains of hvKp and cKp (classical K. pneumoniae). MATERIALS AND METHODS: Kp strains were collected from patients referred to Shahidzadeh Hospital in Behbahan City, Khuzestan Province, Iran. Several techniques were used to identify hvKp. The hypermucoviscosity phenotype was determined using the string test. Isolates that developed dark colonies on tellurite agar were assumed to be hvKp strains. If any of the iucA, iutA, or peg-344 genes were detected, the isolates were classified as hvKp. Phenotypic and genotypic detection of AmpC ß-lactamases of hvKp strains was performed by the combined disk method and polymerase chain reaction, respectively. In addition, crystal violet staining was used to determine the biofilm formation of these isolates. RESULTS: For this study, 76 non-duplicative isolates of Kp were collected. Overall, 22 (28.94%) strains had positive string test results, and 31 (40.78%) isolates were grown in tellurite-containing medium. The genes iucA and iutA or peg-344 were found in 23.68% of all Kp strains and in 50% of tellurite-resistant isolates, respectively. The most effective antibiotics against hvKp isolates were tetracycline (85.52%) and chloramphenicol (63.15%). Using the cefoxitin disc diffusion method, we observed that 56.57% (43/76) of the strains were AmpC producer. A total of 30.26% (n = 23/76) of the isolates tested positive for at least one ampC gene, including blaDHA (52.63%, n = 40), blaCIT (40.78%, n = 31), blaACC (19.76%, n = 15), blaMOX (25%, n = 19), and blaFOX (43.42%, n = 33). Biofilm formation analysis revealed that most hvKp isolates were weak (n = 6, 40%) and moderate (n = 5, 33.33%) biofilm producers. CONCLUSION: Healthcare practitioners should consider the possibility of the existence and acquisition of hvKp everywhere. The exact mechanisms of bacterial acquisition are also unknown, and it is unclear whether the occurrence of infections is related to healthcare or not. Thus, there are still many questions about hvKp that need to be investigated.

Long non-coding RNAs (lncRNAs); roles in tumorigenesis and potentials as biomarkers in cancer diagnosis.

New research has indicated that long non-coding RNAs (lncRNAs) play critical roles in a broad range of biological processes, including the pathogenesis of many complex human diseases, including cancer. The detailed regulation mechanisms of many lncRNAs in cancer initiation and progression have yet to be discovered, even though a few of lncRNAs' functions in cancer have been characterized. In the present study, we summarize recent advances in the mechanisms and functions of lncRNAs in cancer. We focused on the roles of newly-identified lncRNAs as oncogenes and tumor suppressors, as well as the potential pathways these molecules could play. The paper also discusses their potential uses as biomarkers for the diagnosis and prognosis of cancer.

A review of highly sensitive electrochemical genosensors for microRNA detection: A novel diagnostic platform for neurodegenerative diseases diagnostics.

The significant role of microRNAs in regulating gene expression and in disease tracking has handed the possibility of robust and accurate diagnosis of various diseases. Measurement of these biomarkers has also had a significant impact on the preparation of natural samples. Discovery of miRNAs is a major challenge due to their small size in the real sample and their short length, which is generally measured by complex and expensive methods. Electrochemical nanobiosensors have made significant progress in this field. Due to the delicate nature of nerve tissue repair and the significance of rapid-fire feature of neurodegenerative conditions, these biosensors can be reliably promising. This review presents advances in the field of neurodegenerative diseases diagnostics. At the same time, there are still numerous openings in this field that are a bright prospect for researchers in the rapid-fire opinion of neurological diseases and indeed nerve tissue repair.

Review of electrochemical and optical biosensors for testosterone measurement.

Testosterone is an anabolic steroid and a major sex hormone in males. It plays vital roles, including developing the testis, penis, and prostate, increasing muscle and bone, and sperm production. In both men and women, testosterone levels should be in normal ranges. Besides, testosterone and its analogs are major global contributors to doping in sport. Due to the importance of testosterone testing, novel, accurate biosensors have been developed. This review summarizes the various methods for testosterone measurement. Also, recent optical and electrochemical approaches for the detection of testosterone and its analogs have been discussed.

Exosomal microRNAs and long noncoding RNAs: Novel mediators of drug resistance in lung cancer.

Lung cancer therapeutic resistance, especially chemoresistance, is a key issue in the management of this malignancy. Despite the development of novel molecularly targeted drugs to promote therapeutic efficacy, 5-year survival of lung cancer patients is still dismal. Molecular studies through the recent years have fortunately presented multiple genes and signaling pathways, which contribute to lung cancer chemoresistance, providing a better perception of the biology of tumor cells, as well as the molecular mechanisms involved in their resistance to chemotherapeutic agents. Among those mechanisms, transfer of extracellular vesicles, such as exosomes, between cancer cells and the surrounding noncancerous ones is considered as an emerging route. Exosomes can desirably function as signaling vesicles to transmit multiple molecules from normal cells to cancer cells and their microenvironment, or vice versa. Using this ability, exosomes may affect the cancer cells' chemoresistance/chemosensitivity. Recently, noncoding RNAs (esp. microRNAs and long noncoding RNAs), as key molecules transferred by exosomes, have been reported to play a substantial role in the process of drug resistance, through modulation of various proteins and their corresponding genes. Accordingly, the current review principally aims to highlight exosomal micro- and long noncoding RNAs involved in lung cancer chemoresistance. Moreover, major molecular mechanisms, which connect corresponding RNA molecules to drug resistance, will briefly be addressed, for better clarifying of possible roles of exosomal noncoding RNAs in promoting the effectiveness of lung cancer therapy.

Aptamer-based biosensors for Pseudomonas aeruginosa detection.

Pseudomonas aeruginosa possesses innate antibiotic resistance mechanisms, and carbapenem-resistant Pseudomonas aeruginosa has been considered the number one priority in the 2017 WHO list of antimicrobial-resistant crucial hazards. Early detection of Pseudomonas aeruginosa can circumvent treatment challenges. Various techniques have been developed for the detection of P. aeruginosa detection. Biosensors have recently attracted unprecedented attention in the field of point-of-care diagnostics due to their easy operation, rapid, low cost, high sensitivity, and selectivity. Biosensors can convert the specific interaction between bioreceptors (antibodies, aptamers) and pathogens into optical, electrical, and other signal outputs. Aptamers are novel and promising alternatives to antibodies as biorecognition elements mainly synthesized by systematic evolution of ligands by exponential enrichment and have predictable secondary structures. They have comparable affinity and specificity for binding to their target to antibody recognition. Since 2015, there have been about 2000 journal articles published in the field of aptamer biosensors, of which 30 articles were on the detection of P. aeruginosa. Here, we have focused on outlining the recent progress in the field of aptamer-based biosensors for P. aeruginosa detection based on optical, electrochemical, and piezoelectric signal transduction methods.

Gastrointestinal cancer drug resistance: the role of exosomal miRNAs.

Resistance of gastrointestinal (GI) cancer cells to therapeutic agents are one of the major problems in treating this type of cancer. Although the exact mechanism of drug resistance has not yet been fully elucidated, various factors have been identified as contributing factors involved in this process. Several studies have revealed the role of exosomes, especially exosomal microRNAs (miRNAs), in GI tumorigenesis, invasion, angiogenesis, and drug resistance. Exosomes, a type of small extracellular vesicles (EVs), are originated from endosomes and are released into the extracellular environment and body fluids by different cell types. Exosomes mediate cell-cell communication by transferring different cargos, including miRNAs, between parent and recipient cells. Therefore, identifying these exosomal miRNAs and their functions in GI cancers might provide new clues to further explore the secret of this process and thus help in drug-resistance management. This review article will discuss the roles of exosomal miRNAs and their mechanisms of action in drug resistance of different types of GI cancer cells (e.g., stomach, esophagus, liver, pancreas, and colon) to therapeutic agents.

Laccase: Various types and applications.

Laccase belongs to the polyphenol oxidase family and is very important in removing environmental pollutants due to its structural and functional properties. Recently, the ability of laccase to oxidize phenolic and nonphenolic substances has been considered by many researchers. This enzyme's application scope includes a broad range of chemical processes and industrial usages, such as bioremediation, nanobiotechnology, woodworking industries, bleaching of paper pulp, dyeing in the textile industry, biotechnological uses in food industries, biorefining, detoxification from wastewater, production of organic matter from phenolic and amine substrates, and biofuels. Although filamentous fungi produce large amounts of laccase, high-yield industrial-scale production of laccase is still faced with many problems. At present, researchers are trying to increase the efficiency and productivity and reduce the final price of laccase by finding suitable microorganisms and improving the process of production and purification of laccase. This article reviews the introduction of laccase, its properties, production processes, and the effect of various factors on the enzyme's stability and activity, and some of its applications in various industries.

A brief overview on the application and sources of α-amylase and expression hosts properties in order to production of recombinant α-amylase.

By reducing the activation energy, enzymes accelerate the chemical reaction; therefore, they are good alternative for industrial catalysts. Amylase is a suitable enzyme as a catalyst for the chemical decomposition of starch. This enzyme is of great importance, and its production is highly profitable. α-Amylase is among the most important amylases produced naturally by animals, plants, and microorganisms. Still, the α-amylases produced by bacteria have a special place in industry and commerce. Moreover, a large volume of this enzyme can be produced by selecting an appropriate and optimized host to clone and express the α-amylase gene. The present study briefly reviews the structure, application, sources, and hosts used to produce recombinant α-amylase.

ß-Galactosidase: From its source and applications to its recombinant form.

Carbohydrate-active enzymes are a group of important enzymes playing a critical role in the degradation and synthesis of carbohydrates. Glycosidases can hydrolyze glycosides into oligosaccharides, polysaccharides, and glycoconjugates via a cost-effective approach. Lactase is an important member of ß-glycosidases found in higher plants, animals, and microorganisms. ß-Galactosidases can be used to degrade the milk lactose for making lactose-free milk, which is sweeter than regular milk and is suitable for lactose-intolerant people. ß-Galactosidase is employed by many food industries to degrade lactose and improve the digestibility, sweetness, solubility, and flavor of dairy products. ß-Galactosidase enzymes have various families and are applied in the food-processing industries such as hydrolyzed-milk products, whey, and galactooligosaccharides. Thus, this enzyme is a valuable protein which is now produced by recombinant technology. In this review, origins, structure, recombinant production, and critical modifications of ß-galactosidase for improving the production process are discussed. Since ß-galactosidase is a valuable enzyme in industry and health care, a study of its various aspects is important in industrial biotechnology and applied biochemistry.

Glucose oxidase: Applications, sources, and recombinant production.

Glucose oxidase is a subset of oxidoreductase enzymes that catalyzes the transfer of electrons from an oxidant to a reductant. Glucose oxidases use oxygen as an external electron acceptor that releases hydrogen peroxide (H2 O2 ). Glucose oxidase has many applications in commercial processes, including improving the color and taste, increasing the persistence of food materials, removing the glucose from the dried egg, and eliminating the oxygen from different juices and beverages. Moreover, glucose oxidase, along with catalase, is used in glucose testing kits (especially in biosensors) to detect and measure the presence of glucose in industrial and biological solutions (e.g., blood and urine specimens). Hence, glucose oxidase is a valuable enzyme in the industry and medical diagnostics. Therefore, evaluating the structure and function of glucose oxidase is crucial for modifying as well as improving its catalytic properties. Finding different sources of glucose oxidase is an effective way to find the type of enzyme with the desired catalysis. Besides, the recombinant production of glucose oxidase is the best approach to produce sufficient amounts of glucose oxidase for various uses. Accordingly, the study of various aspects of glucose oxidase in biotechnology and bioprocessing is crucial.

Mammalian target of rapamycin (mTOR) signaling pathway and traumatic brain injury: A novel insight into targeted therapy.

Traumatic brain injury (TBI) is one of the most concerning health issues in which the normal brain function may be disrupted as a result of a blow, bump, or jolt to the head. Loss of consciousness, amnesia, focal neurological defects, alteration in mental state, and destructive diseases of the nervous system such as cognitive impairment, Parkinson's, and Alzheimer's disease. Parkinson's disease is a chronic progressive neurodegenerative disorder, characterized by the early loss of striatal dopaminergic neurons. TBI is a major risk factor for Parkinson's disease. Existing therapeutic approaches have not been often effective, indicating the necessity of discovering more efficient therapeutic targets. The mammalian target of rapamycin (mTOR) signaling pathway responds to different environmental cues to modulate a large number of cellular processes such as cell proliferation, survival, protein synthesis, autophagy, and cell metabolism. Moreover, mTOR has been reported to affect the regeneration of the injured nerves throughout the central nervous system (CNS). In this context, recent evaluations have revealed that mTOR inhibitors could be potential targets to defeat a group of neurological disorders, and thus, a number of clinical trials are investigating their efficacy in treating dementia, autism, epilepsy, stroke, and brain injury, as irritating neurological defects. The current review describes the interplay between mTOR signaling and major CNS-related disorders (esp. neurodegenerative diseases), as well as the mTOR signaling-TBI relationship. It also aims to discuss the promising therapeutic capacities of mTOR inhibitors during the TBI.

Exosomal noncoding RNAs: key players in glioblastoma drug resistance.

Glioma, as one of the most severe human malignancies, is defined as the Central Nervous System's (CNS) tumors. Glioblastoma (GBM) in this regard, is the most malignant type of gliomas. There are multiple therapeutic strategies to cure GBM, for which chemotherapy is often the first-line treatment. Still, various cellular processes, such as uncontrolled proliferation, invasion and metastasis, may disturb the treatment efficacy. Drug resistance is another process in this way, which can also cause undesirable effects. Thereupon, identifying the mechanisms, involved in developing drug resistance and the relevant mechanisms can be very helpful in GBM management. The discovery of exosomal non-coding RNAs (ncRNAs), RNA molecules that can be transferred between the cells and different tissues using the exosomes, was a milestone in this regard. It has been revealed that the key exosomal ncRNAs, including circular RNAs, microRNAs, and long ncRNAs, are able to modulate GBM drug resistance through different signaling pathways or by affecting regulatory proteins and their corresponding genes. Nowadays, researchers are trying to overcome the limitations of chemotherapy by targeting these RNA molecules. Accordingly, this review aims to clarify the substantial roles of exosomal ncRNAs in GBM drug resistance and involved mechanisms.

microRNAs in female infertility: An overview.

Infertility impacts a considerable number of women worldwide, and it affects different aspects of family life and society. Although female infertility is known as a multifactorial disorder, there are strong genetic and epigenetic bases. Studies revealed that miRNAs play critical roles in initiation and development of female infertility related disorders. Early diagnosis and control of these diseases is an essential key for improving disease prognosis and reducing the possibility of infertility and other side effects. Investigating the possible use of miRNAs as biomarkers and therapeutic options is valuable, and it merits attention. Thus, in this article, we reviewed research associated with female diseases and highlighted microRNAs that are related to the polycystic ovary syndrome (up to 30 miRNAs), premature ovarian failure (10 miRNAs), endometriosis (up to 15 miRNAs), uterine fibroids (up to 15 miRNAs), endometrial polyp (3 miRNAs), and pelvic inflammatory (6 miRNAs), which are involved in one or more ovarian or uterine disease-causing processes.

Design and evaluation of scFv-RTX-A as a novel immunotoxin for breast cancer treatment: an in silico approach.

Human epidermal growth factor receptor 2 (HER2) is overexpressed in breast cancer (BC) patients. Hence, immunotherapy is a proper treatment option for HER2-positive BC patients. Accumulating evidence has indicated that immunotoxin therapy is a novel approach to improve the potency of targeted therapy. Immunotoxins are antibodies or antibody fragments coupled with a toxin. We designed an immunotoxin. The physicochemical properties were evaluated using ProtParam servers and secondary structure was examined by PROSO II and GORV. Using I-TASSER, a 3D model was built and refined by GalaxyRefine. The model was validated using PROCHECK and RAMPAGE. To predict immunotoxin allergenicity and mRNA stability, AlgPred server and RNAfold were used. Furthermore, the immunotoxin and HER2 were docked by ZDOCK. The scFv+RTX-A could be a non-allergenic and stable chimeric protein, and the secondary structure of its components did not alter, and this protein had a proper 3D structure that might have stable mRNA structure which could bind to HER2. Given the fact that the designed immunotoxin was a non-allergenic and stable chimeric protein and that it could bind with high affinity to HER2 receptors, we proposed that this chimeric protein could be a useful candidate for HER-2 positive BC patients.

In Silico Design and Evaluation of PRAME+FliCΔD2D3 as a New Breast Cancer Vaccine Candidate.

Background: The most prevalent cancer in women over the world is breast cancer. Immunotherapy is a promising method to effectively treat cancer patients. Among various immunotherapy methods, tumor antigens stimulate the immune system to eradicate cancer cells. Preferentially expressed antigen in melanoma (PRAME) is mainly overexpressed in breast cancer cells, and has no expression in normal tissues. FliCΔD2D3, as truncated flagellin (FliC), is an effective toll-like receptor 5 (TLR5) agonist with lower inflammatory responses. The objective of the present study was to utilize bioinformatics methods to design a chimeric protein against breast cancer. Methods: The physicochemical properties, solubility, and secondary structures of PRAME+FliCΔD2D3 were predicted using the tools ProtParam, Protein-sol, and GOR IV, respectively. The 3D structure of the chimeric protein was built using I-TASSER and refined with GalaxyRefine, RAMPAGE, and PROCHECK. ANTIGENpro and VaxiJen were used to evaluate protein antigenicity, and allergenicity was checked using AlgPred and Allergen FP. Major histocompatibility complex )MHC( and cytotoxic T-lymphocytes )CTL( binding peptides were predicted using HLApred and CTLpred. Finally, B-cell continuous and discontinuous epitopes were predicted using ABCpred and ElliPro, respectively. Results: The stability and solubility of PRAME+FliCΔD2D3 were analyzed, and its secondary and tertiary structures were predicted. The results showed that the derived peptides could bind to MHCs and CTLs. The designed chimeric protein possessed both linear and conformational epitopes with a high binding affinity to B-cell epitopes. Conclusion: PRAME+FliCΔD2D3 is a stable and soluble chimeric protein that can stimulate humoral and cellular immunity. The obtained results can be utilized for the development of an experimental vaccine against breast cancer.

Autophagy regulation by microRNAs: Novel insights into osteosarcoma therapy.

Osteosarcoma (OS) is a kind of primary bone cancer that is considered as the leading cause of children death. Surgery and chemotherapy are considered as common treatment approaches for OS; the rate of survival for patients is almost 60-70%. Besides the used therapeutic approaches, it seems that there is a crucial need to launch new treatments for OS. In this regard, more understanding about cellular and molecular pathways involved in OS can contribute to recovery and develop new therapeutic platforms. Autophagy is a cellular machinery that digests and degrades dysfunctional proteins and organelles, so it can regulate the cell proliferation and survival. Most of the time, OS cells use autophagy to increase their survival and proliferation and to gain the ability to resist chemotherapy. Although, there are several controversial evidences on how OS cells use autophagy. A variety of cellular and molecular pathways, that is, microRNAs (miRNAs) can modulate autophagy. MiRNAs are some endogenous, approximately 22 nucleotide RNAs that have an important role in posttranscriptional regulation of mRNAs by targeting them. There are many evidences that the various miRNA expressions in OS cells are dysregulated, so it can propel a normal cell to cancerous one by influencing the cell survival, apoptosis, and autophagy, and eventually increased chemoresitance. Hence, miRNAs can be considered as new biomarkers for OS diagnosis, and according to the role of autophagy in OS progression, miRNAs can use inhibiting or promoting autophagy agents. The present review summarizes the effects of aberrant expression of miRNAs in OS diagnosis and treatment with focus on their roles in autophagy.

Exosomes and cancer: From oncogenic roles to therapeutic applications.

Exosomes belong to extracellular vehicles that were produced and secreted from most eukaryotic cells and are involved in cell-to-cell communications. They are an effective delivery system for biological compounds such as mRNAs, microRNAs (miRNAs), proteins, lipids, saccharides, and other physiological compounds to target cells. In this way, they could influence on cellular pathways and mediate their physiological behaviors including cell proliferation, tumorigenesis, differentiation, and so on. Many research studies focused on their role in cancers and also on potentially therapeutic and biomarker applications. In the current study, we reviewed the exosomes' effects on cancer progression based on their cargoes including miRNAs, long noncoding RNAs, circular RNAs, DNAs, mRNAs, proteins, and lipids. Moreover, their therapeutic roles in cancer were considered. In this regard, we have given a brief overview of challenges and obstacles in using exosomes as therapeutic agents.

Role of exosomes in malignant glioma: microRNAs and proteins in pathogenesis and diagnosis.

Malignant gliomas are the most common and deadly type of central nervous system tumors. Despite some advances in treatment, the mean survival time remains only about 1.25 years. Even after surgery, radiotherapy and chemotherapy, gliomas still have a poor prognosis. Exosomes are the most common type of extracellular vesicles with a size range of 30 to 100 nm, and can act as carriers of proteins, RNAs, and other bioactive molecules. Exosomes play a key role in tumorigenesis and resistance to chemotherapy or radiation. Recent evidence has shown that exosomal microRNAs (miRNAs) can be detected in the extracellular microenvironment, and can also be transferred from cell to cell via exosome secretion and uptake. Therefore, many recent studies have focused on exosomal miRNAs as important cellular regulators in various physiological and pathological conditions. A variety of exosomal miRNAs have been implicated in the initiation and progression of gliomas, by activating and/or inhibiting different signaling pathways. Exosomal miRNAs could be used as therapeutic agents to modulate different biological processes in gliomas. Exosomal miRNAs derived from mesenchymal stem cells could also be used for glioma treatment. The present review summarizes the exosomal miRNAs that have been implicated in the pathogenesis, diagnosis and treatment of gliomas. Moreover, exosomal proteins could also be involved in glioma pathogenesis. Exosomal miRNAs and proteins could also serve as non-invasive biomarkers for prognosis and disease monitoring. Video Abstract.

TGF-ß and WNT signaling pathways in cardiac fibrosis: non-coding RNAs come into focus.

Cardiac fibrosis describes the inappropriate proliferation of cardiac fibroblasts (CFs), leading to accumulation of extracellular matrix (ECM) proteins in the cardiac muscle, which is found in many pathophysiological heart conditions. A range of molecular components and cellular pathways, have been implicated in its pathogenesis. In this review, we focus on the TGF-ß and WNT signaling pathways, and their mutual interaction, which have emerged as important factors involved in cardiac pathophysiology. The molecular and cellular processes involved in the initiation and progression of cardiac fibrosis are summarized. We focus on TGF-ß and WNT signaling in cardiac fibrosis, ECM production, and myofibroblast transformation. Non-coding RNAs (ncRNAs) are one of the main players in the regulation of multiple pathways and cellular processes. MicroRNAs, long non-coding RNAs, and circular long non-coding RNAs can all interact with the TGF-ß/WNT signaling axis to affect cardiac fibrosis. A better understanding of these processes may lead to new approaches for diagnosis and treatment of many cardiac conditions. Video Abstract.