Search

This paper is concerned with the variance-constrained filtering problem for a class of discrete-time genetic regulatory networks (GRNs) with state delay and random one-step measurement delay. The phenomenon of the random one-step measurement delay is characterised by a random variable, which is assumed to obey the Bernoulli distribution with known occurrence probability. The purpose of the addressed problem is to design a filter such that, in the presence of state delay and random one-step measurement delay, an upper bound of the filtering error covariance matrix can be obtained and the explicit expression of the filter gain matrix is given. Then, the proposed variance-constrained filtering method can be used to approximate the concentrations of mRNAs and proteins. Finally, a numerical example is provided to illustrate the effectiveness of the designed filtering scheme. [ABSTRACT FROM AUTHOR]

The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions and roles of nuclear basket nucleoporins (Nups) upon nuclear docking and export for mRNAs. In this paper, we provide a review of our recent findings as well as an assessment of new techniques, updated models, and future perspectives in the studies of mRNA's nuclear export. [ABSTRACT FROM AUTHOR]

With the advent of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, several vaccines have been developed to mitigate its spread and prevent adverse consequences of the Coronavirus Disease 2019 (COVID-19). The mRNA technology is an unprecedented vaccine, usually given in two doses to prevent SARS-CoV-2 infections. Despite effectiveness and safety, inter-individual immune response heterogeneity has been observed in recipients of mRNA-based vaccines. As a novel disease, the specific immune response mechanism responsible for warding off COVID-19 remains unclear at this point. However, significant evidence suggests that humoral response plays a crucial role in affording immunoprotection and preventing debilitating sequelae from COVID-19. As such, this paper focused on the possible effects of age, sex, serostatus, and comorbidities on humoral response (i.e. total antibodies, IgG, and/or IgA) of different populations post-mRNA-based Pfizer-BioNTech vaccination. A systematic search of literature was performed through PubMed, Cochrane CENTRAL, Google Scholar, Science Direct, medRxiv, and Research Square. Studies were included if they reported humoral response to COVID-19 mRNA vaccines. A total of 32 studies were identified and reviewed, and the percent differences of means of reported antibody levels were calculated for comparison. Findings revealed that older individuals, male sex, seronegativity, and those with more comorbidities mounted less humoral immune response. Given these findings, several recommendations were proposed regarding the current vaccination practices. These include giving additional doses of vaccination for immunocompromised and elderly populations. Another recommendation is conducting clinical trials in giving a combined scheme of mRNA vaccines, protein vaccines, and vector-based vaccines. [ABSTRACT FROM AUTHOR]

Interleukin-2 (IL-2) is a cytokine involved in the development and maturation of the subsets of T cells, critically associated with the progression of several immune-related diseases (e.g. liver disease, bowel disease). Interestingly, a recent study suggests that coffee may contain several compounds to inhibit IL-2 expression in activated T-lymphocytic cells. However, there is little information about the potential effects of several coffee compounds (e.g. kahweol, cafestol, trigonelline, niacin and chlorogenic acids) on IL-2 expression in activated T-lymphocytic cells. Therefore, in this paper, their effects on IL-2 expression were evaluated in PHA/PMA-activated lymphocytic Jurkat cells. Among the tested compounds, only kahweol and cafestol were able to reduce IL-2 production significantly in the cells (p < 0.05). However, the inhibition of kahweol was a bit stronger than cafestol. Therefore, the molecular mechanism underlying the IL-2 inhibition was investigated using kahweol. Kahweol (≤ 20 µM) was able to inhibit the phosphorylations of ERK and c-Fos (p < 0.05) with little effects on p38 and JNK phosphorylations in the Jurkat cells. Subsequently, the inhibition of ERK/c-Fos led to the reduction of IL-2 mRNA expression in the Jurkat cells. In summary, the data suggest that kahweol may be a potential coffee compound to reduce IL-2 production via inhibiting the phosphorylations of ERK/c-Fos in PHA/PMA-activated lymphocytic Jurkat cells. [ABSTRACT FROM AUTHOR]

The article presents the findings of two studies related to virology. One study offers insights into the mechanism and evolution of the vaccinia virus mRNA cap N7 methyl-transferase. Another focuses on the link between a newly identified Rhinovirus genotype and severe respiratory tract infection in children in Germany.

This paper aims to study the effect of the dietary treatments on mRNA expression of urea transporter B (UT-B) and some aquaporins (AQP) in rumen epithelium of Italian Simmental young bulls. Eighty animals allocated to 16 pens were fed from about 500 to 650 kg body weight with four experimental diets, which resulted from the combination of two crude protein levels (125 and 110 g/kg dry matter, diets M and L, respectively) and two nitrogen sources (soybean meal (SBM) or SBM partly replaced by an isonitrogenous mixture of corn and urea; diets −U and +U, respectively). At slaughtering samples of blood and rumen epithelium were collected from six bulls for each diet. Blood samples were analysed for haematological parameters and quantitative PCR was carried out on the mRNA extracted from the rumen epithelium samples. The bulls fed diets M had lower plasma concentrations of aspartate aminotransferase than those receiving diets L (78.9 vs. 88.3 U/l, p = 0.04). Plasma urea was higher (p = 0.03) for diets M and lower for diets +U (2.0 vs. 2.5 and 1.73 vs. 2.00 mmol/l, respectively, in M and L diets, p = 0.04). The effect of dietary treatments on rumen UT expression were limited to AQP3, which was down regulated (p = 0.01) in diets +U. Finally, a high positive correlation (R2 = 0.871) between the expressions of AQP7 and AQP10 was found. In conclusion, the AQP3 appears very responsive to dietary treatments and therefore it is a candidate to be further studied in rumen metabolism experiments. The close relationship between mRNA expression of AQP7 and AQP10 indicates a similar function of these two proteins. [ABSTRACT FROM AUTHOR]

More and more studies have shown that genetic determinants may mediate variability among persons in the response to a drug. In other words, some therapeutics benefit only a subset of treated patients. Genomic technologies - such as DNA sequencing, mRNA transcript profiling, and comparative genomic hybridization - are providing biomarkers that can be used to predict which patients are most likely to respond to a given drug. In this paper, the sample size determination of a targeted clinical trial, an untargeted clinical trial and a random effect model is conducted. Treatment effect for the responder and non-responder patients, the assay specificity and sensitivity, and the proportion of the population for non-responder can affect sample size determination of the experimental design. [ABSTRACT FROM AUTHOR]

Rare cases of myocarditis and pericarditis after COVID-19 mRNA vaccination have been recently reported in male adolescents and young adults. Acute myocarditis and pericarditis following COVID-19 mRNA vaccination in male adolescents and young adults may be connected with age-related lower levels of T-bet and PD-1 in predisposed individulas with T-bet polymorphisms by the release od autoreactive CD8+CTL. Upregulatiomn of T-Bet and PD-1 by estrogen might explai the higher incidence of men developing myocarditis or pericarditis in comparison to women. [ABSTRACT FROM AUTHOR]

The article provides information on the European ALS Consortium's second annual research workshop, held in Nice, France, on May 14-16, 2005. The programme comprised 66 papers and posters. Twenty concerned the pathogenesis of human ALS and 16 dealt with the SOD1 transgenic mouse. Twenty papers were clinical and 10 dealt with animal models, cultured cells or slices, or drug discovery. Jaine Kirby and Christine Teitsma described the use of microarrays for mRNA in fibroblasts to study gene expression in SOD1 mice as an introduction to their use in humans. As described by Christopher Miller, protein transport is slowed in the motor nerves of SOD1 mutant mice and also in neurofilament mutants. Abnormalities of mitochondrial structure and function are found in animal models of ALS, including SOD1 mutants as well as VEGF deficiency and the wobbler mouse.

Myasthenia gravis (MG) is characterized clinically by skeletal muscle fatigue following the excessive exercise. Interestingly most of MG patients manifest parallely also some abnormalities of the thymus.AMP-deaminase (AMPD) from human thymus was not a subject of studies up to now. In this paper, mRNA expression and some physico-chemical and immunological properties of AMPD purified from the thymus of MG patients were described. Experiments performed identified the liver isozyme (AMPD2) as the main isoform of AMPD expressed in this organ. The activity of AMPD found in this organ was higher than in other human non-(skeletal) muscle tissues indicating on role the enzyme may play in supplying of guanylates required for the intensive multiplication of thymocytes. [ABSTRACT FROM PUBLISHER]

Inhalable messenger RNA (mRNA) has demonstrated great potential in therapy and vaccine development to confront various lung diseases. However, few gene vectors could overcome the airway mucus and intracellular barriers for successful pulmonary mRNA delivery. Apart from the low pulmonary gene delivery efficiency, nonnegligible toxicity is another common problem that impedes the clinical application of many non-viral vectors. PEGylated cationic peptide-based mRNA delivery vector is a prospective approach to enhance the pulmonary delivery efficacy and safety of aerosolized mRNA by oral inhalation administration. In this study, different lengths of hydrophilic PEG chains were covalently linked to an amphiphilic, water-soluble pH-responsive peptide, and the peptide/mRNA nano self-assemblies were characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The in vitro mRNA binding and release, cellular uptake, transfection, and cytotoxicity were studied, and finally, a proper PEGylated peptide with enhanced pulmonary mRNA delivery efficiency and improved safety in mice was identified. These results showed that a proper N-terminus PEGylation strategy using 12-monomer linear monodisperse PEG could significantly improve the mRNA transfection efficiency and biocompatibility of the non-PEGylated cationic peptide carrier, while a longer PEG chain modification adversely decreased the cellular uptake and transfection on A549 and HepG2 cells, emphasizing the importance of a proper PEG chain length selection. Moreover, the optimized PEGylated peptide showed a significantly enhanced mRNA pulmonary delivery efficiency and ameliorated safety profiles over the non-PEGylated peptide and LipofectamineTM 2000 in mice. Our results reveal that the PEGylated peptide could be a promising mRNA delivery vector candidate for inhaled mRNA vaccines and therapeutic applications for the prevention and treatment of different respiratory diseases in the future. Schematic illustration of proper PEGylation strategy of pH-responsive LAH4-L1 peptide-mRNA nano self-assemblies enhances the pulmonary delivery efficiency of aerosolized mRNA. [ABSTRACT FROM AUTHOR]

Messenger RNA (mRNA) therapeutics have recently demonstrated high clinical potential with the accelerated approval of SARS-CoV-2 vaccines. To fulfill the promise of unprecedented mRNA-based treatments, the development of safe and efficient carriers is still necessary to achieve effective delivery of mRNA. Herein, we prepared mRNA-loaded nanocarriers for enhanced in vivo delivery using biocompatible block copolymers having functional amino acid moieties for tunable interaction with mRNA. The block copolymers were based on flexible poly(ethylene glycol)-poly(glycerol) (PEG-PG) modified with glycine (Gly), leucine (Leu) or tyrosine (Tyr) via ester bonds to generate block catiomers. Moreover, the amino acids can be gradually detached from the block copolymers after ester bond hydrolyzation, avoiding cytotoxic effects. When mixed with mRNA, the block catiomers formed narrowly distributed polymeric micelles with high stability and enhanced delivery efficiency. Particularly, the micelles based on tyrosine-modified PEG-PG (PEG-PGTyr), which formed a polyion complex (PIC) and π–π stacking with mRNA, displayed excellent stability against polyanions and promoted mRNA integrity in serum. PEG-PGTyr-based micelles also increased the cellular uptake and the endosomal escape, promoting high protein expression both in vitro and in vivo. Furthermore, the PEG-PGTyr-based micelles significantly extended the half-life of the loaded mRNA after intravenous injection. Our results highlight the potential of PEG-PGTyr-based micelles as safe and effective carriers for mRNA, expediting the rational design of polymeric materials for enhanced mRNA delivery. [ABSTRACT FROM AUTHOR]

Several forms of autosomal dominant retinitis pigmentosa (adRP) are caused by mutations in genes encoding proteins that are ubiquitously expressed and involved in the pre-mRNA spliceosome such as PRPF31. This paper provides an overview of the molecular genetics, pathophysiology, and mechanism for incomplete penetrance and retina-specific disease in pedigrees of families who harbor mutations in PRPF31 (RP11). The molecular and clinical features of a family with a novel 3-base insertion, c.914_915insTGT (p.Val305_Asp306insVal) in exon 9 of PRPF31 are described to illustrate the salient clinical features of mutations in this gene. [ABSTRACT FROM AUTHOR]

Green computing, an emerging field of research that seeks to reduce excess power consumption in high-performance computing, is gaining popularity among researchers. Research in this field often relies on simulation or only uses a small cluster, typically 8 or 16 nodes, because of the lack of hardware support. In contrast, System G at Virginia Tech is a 2592 processor supercomputer equipped with power-aware components suitable for large-scale green computing research. DIRECT is a deterministic global optimisation algorithm, implemented in the mathematical software package VTDIRECT95. This paper explores the potential energy savings for the parallel implementation of DIRECT, called pVTdirect, when used with a large-scale computational biology application, parameter estimation for a budding yeast cell cycle model, on System G. Two power-aware approaches for pVTdirect are developed and compared against the CPUSPEED power saving system tool. The results show that knowledge of the parallel workload of the underlying application is beneficial for power management. [ABSTRACT FROM AUTHOR]

Cinnamaldehyde (1) is a pharmacologically active ingredient isolated from cassia twig (Ramulus Cinnamomi), which is commonly used in herbal remedies to treat fever-related diseases. Both TRPV1 and TRPM8 ion channel proteins are abundantly expressed in sensory neurons, and are assumed to act as a thermosensor, with the former mediating the feeling of warmth and the latter the feeling of cold in the body. Both of them have recently been reported to be involved in thermoregulation. The purpose of this paper is to further uncover the antipyretic mechanisms of 1 by investigating its effects on the mRNA expression levels and functions of both TRPV1 and TRPM8. The results showed that 1 could up-regulate the mRNA expression levels of TRPV1 at both 37 and 39°C, and its calcium-mediating function was significantly increased at 39°C, all of which could not be blocked by pretreatment of the neuronal cells with ruthenium red, a general transient receptor potential (TRP) blocker, indicating that the action of 1 was achieved through a non-TRPA1 channel pathway. In conclusion, the findings in our in vitro studies might account for part of the peripheral molecular mechanisms for the antipyretic action of 1. [ABSTRACT FROM AUTHOR]

Purpose: To determine the relationship between heterogeneous nuclear ribonucleoproteins (hnRNP) and DNA repair, particularly in response to ionising radiation (IR). Materials and methods: The literature was examined for papers related to the topics of hnRNP, IR and DNA repair. Results: HnRNP orchestrate the processing of mRNA to which they are bound in response to IR. HnRNP A18, B1, C1/C2 and K interact with important proteins from DNA Damage Response (DDR) pathways, binding DNA-dependent protein kinase (DNA-PK), the Ku antigen (Ku) and tumour suppressor protein 53 (p53) respectively. Notably, irregularities in the expression of hnRNP A18, B1, K, P2 and L have been linked to cancer and radiosensitivity. Sixteen different hnRNP proteins have been reported to show either mRNA transcript or protein quantity changes following IR. Various protein modifications of hnRNP in response to IR have also been noted: hnRNP A18, C1/C2 and K are phosphorylated; hnRNP C1/C2 is a target of apoptotic proteases; and hnRNP K degradation is controlled by murine double minute ubiquitin ligase (MDM2). Evidence points to a role for hnRNP A1, A18, A2/B1, C1/C2, K and P2 in regulating double-stranded break (DSB) repair pathways by promoting either homologous recombination (HR) or non-homologous end rejoining (NHEJ) repair pathways following IR. Conclusions: HnRNP proteins play a pivotal role in coordinating repair pathways following exposure to IR, through protein-protein interactions and transcript regulation of key repair and stress response mRNA. In particular, several hnRNP proteins are critical in coordinating the choice of HR or NHEJ to repair DSB caused by IR. [ABSTRACT FROM AUTHOR]

Induction of cytochrome P450 (CYP) 1A2, CYP2B6, and CYP3A4 by 22 prototypical inducers was evaluated in the Fa2N-4 immortalized human hepatic cell line. To facilitate this a duplex one-step quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay for CYP1A2 and CYP3A4 and a substrate cassette allowing simultaneous monitoring of CYP1A2, CYP2B6, CYP2C9, and CYP3A4 activity were developed. CYP1A2 messenger RNA (mRNA) and activity were induced by the prototypical aryl hydrocarbon receptor (AhR) ligand β-naphthoflavone (Emax = 217- and 11-fold, respectively, and EC50 = 8 µM). CYP3A4 mRNA and activity were induced by the prototypical pregnane X receptor (PXR) ligands, rifampicin (Emax = 36- and 6-fold, respectively, and EC50 = 4 µM) and phenobarbital (Emax = 12- and 4-fold, respectively, and EC50 = 205 µM). No induction of CYP2B6 was detected with several prototypical constitutive androstane receptor (CAR) ligands. A large mRNA-activity Emax ratio was observed for some time-dependent inhibitors of CYP3A4, whereas EC50 determinations appeared to be independent of the endpoint. In conclusion, Fa2N-4 cells are a good surrogate for primary human hepatocytes for assessing AhR and PXR-mediated CYP1A2 and CYP3A4 induction, respectively, but not for CAR-mediated CYP2B6 induction. The sensitive and selective methodologies presented in this paper afford maximal data generation and enhanced throughput capability and are readily transferable to primary human hepatocytes or alternate cellular systems. [ABSTRACT FROM AUTHOR]

We analyzed the mRNA expression of the insulin-like growth factor (IGF) family genes and of selected downstream pathway genes using the Affymetrix microarray system and confirmatory RT-PCR in the freshly prepared organ of Corti (OC), modiolus (MOD) and stria vascularis (SV) from neonatal rats (3-5 days old) and after 24 h in culture. Among the seven members of the IGF family analyzed in this paper, IGF1, IGF2 and IGF-binding protein (IGFBP2) had the highest basal expression in all regions. Preparatory stress and culture increased the expression of IGF2, IGFBP2, IGFBP3, IGFBP5, glucose transporter1 (GLUT1), signal transducer, and activator of transcription3 (STAT3), phosphoinositide-3-kinase regulatory subunit (Pik3r1), Jun oncogene (c-jun) and decreased that of mitogen-activated protein kinases MAPK3 and MAPK14 in all regions. Region-specific changes were observed in OC (GLUT1), MOD (IGFBP3 and c-jun) and SV (IGF2 and IGFBP2). [ABSTRACT FROM AUTHOR]

Purpose: This paper deals with the capability of the ciliary epithelium to express neurolysin, involved in the inactivation of numerous neuropeptides. Methods: Total RNAs from ciliary body (CB) were processed for RT-PCR, and the amplification products were sequenced. The whole-protein extracts of CBs were analyzed using the Western blot. The CBs were processed for neurolysin immunolocalization. Results: The RT-PCR detected the presence of neurolysin mRNA in the ciliary body. The Western blot assays demonstrated immunochemical cross-reactivity with neurolysin. The immunoreactivity to neurolysin was observed in ciliary epithelium. Conclusions: These results indicate that the ciliary epithelium expresses neurolysin. [ABSTRACT FROM AUTHOR]

In mussel Mytilus galloprovincialis tissues, metallothionein belongs to two different gene classes, mt10 and mt20, showing differential expression at both basal conditions and under heavy metal challenge. In this study, a new more highly sensitive technique, expression analysis of mt10 and mt20 mRNA levels by quantitative reverse transcription polymerase chain reaction, was used to assess the effects of heavy metal contamination in the digestive glands of mussels caged along the Tunisian coast. To validate the new assay, total metallothionein protein, amount of heavy metals (zinc, copper, cadmium), and a biomarker of oxidative stress such as malondialdehyde content, were assessed in the same tissues. At the investigated sites, the molecular assay showed variations of mt20 relative gene expression levels within one or two orders of magnitude, with maximum values at two sites severely polluted with cadmium, Mahres (100-fold) and Menzel Jemile (165-fold). Changes in mt10 expression were recorded at all sites where copper had significantly accumulated, although fold induction levels were less pronounced than those of mt20. In this paper, gene expression data are discussed in relation to the studied biomarkers, demonstrating that the molecular technique based on the differential expression of mt10 and mt20 genes represents (i) a useful and robust tool for studying and monitoring heavy metal pollution under field conditions, and (ii) an improvement in the application of metallothionein as a biomarker of response to exposure to heavy metals in marine mussels. [ABSTRACT FROM AUTHOR]

Codon usage bias reveals the silent molecular evolution pattern. Previous research showed the codon usage bias was associated with many biological processes, such as protein expression level, genetic coding error minimization, mRNA stability, codon context, tRNA richness, CpG suppression, DNA methylation, and tissue or organ specificity. In this paper we reviewed major methods of codon usage bias measurement. Since most of existing methods are only suitable for the comparison of codon usage bias within a single genome, we introduced a new informatics index, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias within and across genomes. In this method, Shannon informational theory was applied to describe the SCUO of each gene using a value ranging from 0 to 1, with larger values associated with greater codon usage bias. We compared our method with the codon adaptation index (CAI) method for measuring codon bias in Escherichia coli and Sacharomyces cerevisiae . We also studied the correlation between SCUO and CAI, and the relation of SCUO with gene length, gene function, and GC composition. In addition, we explored the correlation between SCUO and mRNA abundance in S. cerevisiae using SAGE expression data. The software package codonO is freely available at http://digbio.missouri.edu/~wanx/cu/codonO/. [ABSTRACT FROM AUTHOR]

Tryptase has been suggested to take part in the pathophysiology of psoriasis mainly through the production of C3a by cleaving C3. However, studies using tryptase preparations of high purity do not support this notion. Therefore, although tryptase is unanimously believed to be involved in the immunopathogenesis of psoriasis, no convincing mechanism has been proposed for its role. This paper proposes several mechanisms by which this enyme may exert its role in the pathobiology of psoriasis. Tryptase is a mitogen for epithelial cells and stimulates IL-8 production and ICAM-1 expression by these cells. It also induces the expression of mRNA for IL-1β and IL-8 and stimulates the selective release of IL-8 from endothelial cells and TNF-α, IL-1β, and IL-6 from lymphocytes and monocytes. Besides itself being a chemoattractant for neutrophils, tryptase activates mast cells and generates kinins from kininogen, thereby playing a crucial role in leukocyte infiltration into psoriatic lesions. This enzyme also induces leukocyte infiltration partly through activating endothelial PAR-2, which contributes to leukocyte rolling, adherence and recruitment by inducing the release of endothelial platelet-activating factor. Through activating PAR-2, tryptase could also trigger the development of Langerhans cells which play a crucial role in the pathophysiology of psoriasis. This enzyme is a mitogen for fibroblasts, which are probably involved in the pathophysiology of psoriasis through production of insulin-like growth factor-I (IGF-I). Tryptase is a gelatinase and also activates stromelysin-1 (MMP-3), thereby contributing to the disruption of psoriatic basement membrane and to the joint damage seen in psoriatic arthritis. Increase of tryptase levels following trauma could also provide a mechanism for Koebner phenomenon seen in psoriasis. [ABSTRACT FROM AUTHOR]

Eukaryotic and viral messenger RNAs contain a CAP structure that plays an important role in the initiation of translation and several other cellular processes that involve mRNAs. In this paper, we report a convenient chemical approach to the preparation of milligram quantities of short, capped RNA oligonucleotides, which overcomes some of the limitations of previous approaches. The method is based on the use of a reactive precursor, m7 GppQ [P1-7-methylguanosine-5'-O-yl, P2 -O-8-(5-chloroquinolyl) pyrophosphate]. The precursor reacts smoothly with 5'-phosphorylated unprotected short RNA in the presence of CuCl2 in organic media. The feasibility of this approach was demonstrated by the synthesis of the capped pentaribonucleotide m7 GpppGpApCpU. The synthesized capped oligonucleotide was isolated and purified by reverse phase and ion exchange HPLC with a final yield of 37%. The structure of the m7 GpppGpApCpU was confirmed by 31 P NMR, mass-spectrometry and enzymatic hydrolysis. [ABSTRACT FROM AUTHOR]

Previously, polymerase chain reaction (PCR) technology has been hampered by its inability to generate quantitative results, a drawback inherent to the high degree of amplification taking place in the reaction. Recently, PCR techniques have been described with the potential of quantifying the amount of mRNA or DNA in biological samples. In this study quantitative PCR was used to investigate the role of the EGF (epidermal growth factor) system in cancer both for measurements of mRNA concentrations and for measurements of the number of copies of specific genes. It is shown that the mRNA expression of a subset of ligands from the EGF system is increased in bladder cancer. Furthermore, measurement of the mRNA concentration gives important information such as the expression of these ligands correlated to the survival of the patients. In addition to the alterations at the mRNA level, changes also can occur at the DNA level in the EGF system. Thus, it has been demonstrated that the number of genes coding for the human epidermal growth factor receptor 2 (HER2) is increased in a number of breast tumors. It is now possible to treat breast cancer patients with a humanized antibody reacting with HER2, and the treatment is considered to be justified if the tumor displays an increased amount of HER2. For this reason there is a need for techniques suitable for HER2 measurements. A LightCycler real-time PCR method used for HER2/ neu DNA quantification was evaluated and the results compared with those obtained by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). Tumor biopsies were collected from 112 patients diagnosed with early breast cancer from January 1990 to March 1994. The samples were analyzed for HER2 DNA amplification by real-time PCR on LightCycler and by FISH and for HER2 protein expression by IHC. Inter-assay variation for HER2 measured by LightCycler was 10% (×=3.1; n=17). Amplification ≥2 was observed in 19% of the patients. Concordance rates between real-time PCR and the other methods were 91% (IHC) and 92% (FISH). The correlation between real-time PCR and FISH was highly significant (p<0.001). The "LightCycler-HER2/ neu DNA quantification kit" produces results with a high level of reproducibility and its ease of use allows rapid screening for amplification of HER2. In this paper useful information is given on how real-time PCR compares with FISH and IHC. The data show that results obtained for amplification of HER2 by real-time PCR on the LightCycler instrument are comparable to results obtained by IHC and FISH. [ABSTRACT FROM AUTHOR]

The liver is a multifunctional organ capable of steroid hormone catabolism. The steroid metabolizing enzyme activities have been identified in the liver and it has been demonstrated that neonatal testicular androgens irreversibly program several hepatic enzyme activities in the rat including 5α-reductase (5α-R). In this paper we have applied a quantitative RT-PCR method coupled to laser-induced fluorescence capillary electrophoresis (LIF-CE) to measure the mRNA levels of 5α-R type 1 isozyme (5α-R1) in the liver of female intact and ovariectomized rats. Both groups were treated with testosterone (T) to study the possible regulation of 5α-R1 by androgens in females and to allow comparison with our previous findings in the liver of male rats. Our results demonstrate that the 5α-R1 mRNA isozyme is higher in the liver of female rats than in males and that the regulation of 5α-R1 mRNA by T is different in the liver of female than in male rats. Finally, our results could point to hepatic 5α-Reductase participation in the female not only in the catabolism of steroids with Δ4,5 double bond, but also in other physiological functions such as the production of 3α,5α-reduced metabolites of progesterone and deoxycorticosterone (DOC), potent allosteric modulators of GABAA receptors. [ABSTRACT FROM AUTHOR]

Osteoblast-derived IL-6 functions in coupled bone turnover by supporting osteoclastogenesis favoring bone resorption instead of bone deposition. Gene regulation of IL-6 is complex occurring both at transcription and post-transcription levels. The focus of this paper is at the level of mRNA stability, which is important in IL-6 gene regulation. Using the MC3T3-E1 as an osteoblastic model, IL-6 secretion was dose dependently decreased by SB203580, a p38 MAPK inhibitor. Steady state IL-6 mRNA was decreased with SB203580 (2 μM) ca. 85% when stimulated by IL-1β (1-5 ng/ml). These effects require de novo protein synthesis as they were inhibited by cycloheximide. p38 MAPK had minor effects on proximal IL-6 promoter activity in reporter gene assays. A more significant effect on IL-6 mRNA stability was observed in the presence of SB203580. Western blot analysis confirmed that SB203580 inhibited p38 MAP kinase, in response to IL-1β in a dose dependent manner in MC3T3-E1 cells. Stably transfected MC3T3-E1 reporter cell lines (MC6) containing green fluorescent protein (GFP) with the 3'untranslated region of IL-6 were constructed. Results indicated that IL-1β, TNFα, LPS but not parathyroid hormone (PTH) could increase GFP expression of these reporter cell lines. Endogenous IL-6 and reporter gene eGFP-IL-6 3'UTR mRNA was regulated by p38 in MC6 cells. In addition, transient transfection of IL-6 3'UTR reporter cells with immediate upstream MAP kinase kinase-3 and -6 increased GFP expression compared to mock transfected controls. These results indicate that p38 MAPK regulates IL-1β-stimulated IL-6 at a post transcriptional mechanism and one of the primary targets of IL-6 gene regulation is the 3'UTR of IL-6. [ABSTRACT FROM AUTHOR]

Spinal muscular atrophy (SMA) is a lethal autosomal recessive disease. SMA is characterized by degeneration of motor neurons in the spinal cord, causing progressive weakness of the limbs and trunk, followed by muscle atrophy. The gene most highly associated with SMA is the survival motor neuron (SMN) gene. This paper describes the results concerning the development of a quantitative method for the molecular diagnosis of SMA by measuring the amount of cytosolic mRNA from human muscle cells. The procedures using radioactive material and the Enzyme-Linked Immunosorbent Assay (ELISA) non-radioactive method were developed using [sup 32]P-dCTP labeled and biotinylated nucleotide probes, respectively; the results obtained demonstrate that the measurement of specific mRNA could be used as a quantitative method for the molecular diagnosis of SMA. There was a perfect concordance of the results obtained between the procedure using radioactive material, the ELISA method and the single-strand conformation polymorphism (SSCP) analysis regarding negative and positive SMA samples. All values obtained for the control group were significantly greater than the ones obtained for the SMA positive samples (33-76% in radioactive method and 38-54% in ELISA method). The methods developed in this study may be applicable to the diagnosis (detection of homozygous and heterozygous deletions in exons 7 and 8 of the SMN gene) and the control of mRNA concentrations in future gene therapy of patients with SMA. [ABSTRACT FROM AUTHOR]

The first completed, circular mitochondrial genome and the first draft, linear chloroplastic genome of the blue diatom Haslea ostrearia (Simonsen 1974, Naviculaceae, Bacillariophyceae) were assembled from Illumina and PacBio sequencing. The mitochondrial genome was composed of 38,696 bases and contained 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome was composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfer messenger RNA gene). Phylogenetic trees, using the maximum-likehood method and partial genes currently available for Haslea ostrearia and other diatom species, suggested the proximity of all the Haslea ostrearia strains/isolates and the possibility of using these genomes as future references. [ABSTRACT FROM AUTHOR]

To report a case of a boy with acute keratoplasty rejection manifesting 12 days after receiving BNT162b2 messenger RNA (mRNA) vaccine for COVID-19. A case report. A 15-year-old boy with a history of penetrating keratoplasty due to acanthamoeba keratitis developed corneal decompensation 12 days after BNT162b2 messenger RNA vaccine for COVID-19 disease. One-week treatment with topical Dexamethasone 2% eye drops resulted in a complete resolution of corneal edema. This case suggests that BNT162b2 messenger RNA (mRNA) vaccine can be associated with acute keratoplasty rejection in children, which responds completely to topical steroids. Ophthalmologists should be aware of this risk of cornea decompensation after COVID-19 vaccine in children who received a cornea transplant. [ABSTRACT FROM AUTHOR]

Skin diseases are global health issues caused by multiple pathogenic factors, in which epigenetics plays an invaluable role. Post-transcriptional RNA modifications are important epigenetic mechanism that regulate gene expression at the genome-wide level. N6-methyladenosine (m6A) is the most prevalent modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, which is installed by methyltransferases called "writers", removed by demethylases called "erasers", and recognised by RNA-binding proteins called "readers". To date, m6A is emerging to play essential part in both physiological processes and pathological progression, including skin diseases. However, a systematic summary of m6A in skin disease has not yet been reported. This review starts by illustrating each m6A-related modifier specifically and their roles in RNA processing, and then focus on the existing research advances of m6A in immune homeostasis and skin diseases. [ABSTRACT FROM AUTHOR]

Eukaryotic mRNAs are modified by several chemical marks which have significant impacts on mRNA biology, gene expression, and cellular metabolism as well as on the survival and development of the whole organism. The most abundant and well-studied mRNA base modifications are m6A and ADAR RNA editing. Recent studies have also identified additional mRNA marks such as m6Am, m5C, m1A and Ψ and studied their roles. Each type of modification is deposited by a specific writer, many types of modification are recognized and interpreted by several different readers and some types of modifications can be removed by eraser enzymes. Several works have addressed the functional relationships between some of the modifications. In this review we provide an overview on the current status of research on the different types of mRNA modifications and about the crosstalk between different marks and its functional consequences. [ABSTRACT FROM AUTHOR]

The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions. [ABSTRACT FROM AUTHOR]

After receiving emergency approval during the COVID-19 pandemic, mRNA vaccines have taken center stage in the quest to enhance future vaccination strategies for both infectious diseases and cancer. Indeed, they have significantly overshadowed another facet of genetic vaccination, specifically DNA vaccines. Nevertheless, it is important to acknowledge that both types of genetic vaccines have distinct advantages and disadvantages that set them apart from each other. In this work, we delve extensively into the history of genetic vaccines, their mechanisms of action, their strengths, and limitations, and ultimately highlight ongoing research in key areas for potential enhancement of both DNA and mRNA vaccines. Here, we assess the significance of the primary benefits and drawbacks associated with DNA and mRNA vaccination. We challenge the current lines of thought by highlighting that the existing drawbacks of DNA vaccination could potentially be more straightforward to address compared to those linked with mRNA vaccination. In our view, this suggests that DNA vaccines should remain viable contenders in the pursuit of the future of vaccination. [ABSTRACT FROM AUTHOR]

Laryngeal squamous cell carcinoma (LSCC), is a prevalent malignant tumor, belongs to the category of head and neck tumors. N-acetyltransferase 10 (NAT10) can alter mRNA stability through N4- acetylcytidine (ac4C) modification. This study aimed to make an investigation into the role of NAT10-mediated ac4C modification in the malignant processes of LSCC cells. The NAT10 expression in LSCC tissues and cells was detected RT-qPCR and western blot. The ac4C dot blot was performed to detect ac4C level. Besides, the cell viability, migration, and invasion abilities were detected by CCK-8 and transwell assays. AcRIP-qPCR was performed to measure the abundance of ac4C on FOXM1 mRNA. RIP and Luciferase reporter assays were performed to demonstrate the interaction between NAT10 and FOXM1. Finally, the xenograft model was established to explore the role of NAT10 in vivo. NAT1 levels were significantly increased in the LSCC tissues and cells. Knockdown of NAT10 could significantly suppress the proliferation, migration, and invasion of LSCC cells. Additionally, NAT10 recognized the ac4C-modified sites in the 3'-untranslated regions (3' UTR) of forkhead box M1 (FOXM1) to enhance the ability of FOXM1 mRNA. Furthermore, FOXM1 overexpression reversed the suppressing effects of NAT10 knockdown on the proliferation, migration, and invasion of LSCC cells, according to the results of rescue assays. Finally, results of animal experiments showed that NAT10 promoted in vivo tumorigenesis of LSCC cells through upregulating FOXM1. Our current study demonstrated that NAT10-mediated ac4C modification of FOXM1 mRNA promoted the malignant processes of LSCC cells. [ABSTRACT FROM AUTHOR]

Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein–protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation. [ABSTRACT FROM AUTHOR]

Nucleic acid strand displacement reactions involve the competition of two or more DNA or RNA strands of similar sequence for binding to a complementary strand, and facilitate the isothermal replacement of an incumbent strand by an invader. The process can be biased by augmenting the duplex comprising the incumbent with a single-stranded extension, which can act as a toehold for a complementary invader. The toehold gives the invader a thermodynamic advantage over the incumbent, and can be programmed as a unique label to activate a specific strand displacement process. Toehold-mediated strand displacement processes have been extensively utilized for the operation of DNA-based molecular machines and devices as well as for the design of DNA-based chemical reaction networks. More recently, principles developed initially in the context of DNA nanotechnology have been applied for the de novo design of gene regulatory switches that can operate inside living cells. The article specifically focuses on the design of RNA-based translational regulators termed toehold switches. Toehold switches utilize toehold-mediated strand invasion to either activate or repress translation of an mRNA in response to the binding of a trigger RNA molecule. The basic operation principles of toehold switches will be discussed as well as their applications in sensing and biocomputing. Finally, strategies for their optimization will be described as well as challenges for their operation in vivo. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) have shown important regulatory roles in tumorigenesis. However, the role and working mechanism of circ_0000745 in acute lymphoblastic leukemia (ALL) development remain largely unclear. The expression of circ_0000745, sperm antigen with calponin homology and coiled-coil domains 1 (SPECC1), microRNA-494-3p (miR-494-3p), and neuroepithelial cell transforming 1 (NET1) messenger RNA (mRNA) and protein was analyzed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blot assay. Flow cytometry was performed to assess cell apoptosis and cell cycle progression. Extracellular acidification rate (ECAR) was assessed to analyze cell glycolysis. Cell viability was analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay. Ferroptosis was assessed through measuring the intracellular levels of iron and lipid reactive oxygen species (ROS). Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were conducted to validate the interaction between miR-494-3p and circ_0000745 or NET1. Circ_0000745 expression was elevated in ALL patients and cell lines. Circ_0000745 knockdown restrained cell cycle progression and glycolysis and triggered cell apoptosis and ferroptosis. Circ_0000745 acted as a molecular sponge for miR-494-3p in ALL cells. miR-494-3p silencing partly diminished circ_0000745 knockdown-induced anti-tumor effects in ALL cells. NET1 was a target of miR-494-3p, and miR-494-3p overexpression-induced anti-tumor influences were partly counteracted by the accumulation of NET1 in ALL cells. Circ_0000745 can positively regulate NET1 expression by sponging miR-494-3p in ALL cells. Circ_0000745 contributed to ALL development partly by binding to miR-494-3p to induce NET1 expression.0020. [ABSTRACT FROM AUTHOR]

Eggplant has recently suffered a serious threat from a virus infection that causes mosaic and fruit deformation in eggplant fields in Iraq. The infection ratio has registered between 1-80% in examined eggplant fields. The Illumina platform has been applied to sequencing genomic DNA and total RNAseq of symptomatic samples in addition to healthy genomic DNA. The analysis of an entire RNA data revealed Eggplant mild leaf mottle virus (EMLMV) as a causal agent of the symptoms. The sequence of EMLMV was composed of 9280 nt encodes ten protein domains and the transcripts per million (TPM) was 9. Two endogenous pararetroviruses registered, Caulimovirus - SMe and SmelV belong to Caulimovirus and Florendovirus genera with lengths of 8233 and 6198 nt respectively, and both were found interestingly in the RNA transcripts. Phylogeny has revealed EMLMV and endogenous elements' relations to related viruses. [ABSTRACT FROM AUTHOR]

To ensure the safety and quality of vaccines, especially the newest RNA-vaccines against COVID-19, is one of the World Health Organization's current highest priorities. Case description. We report three cases of sudden unilateral tinnitus following BNT162b2 mRNA-vaccine injection, which rapidly resolved in 2 out of 3 cases. The mechanism responsible for its development remains unclear. A hypersensitivity reaction with an abnormal autoimmune response or a vasculitic event may be implicated. Large-scale and well-designed studies are needed to improve surveillance of the COVID-19 vaccine and better define possible adverse reactions involving the cochleo-vestibular system and/or immunisation anxiety-related reactions. [ABSTRACT FROM AUTHOR]

Quantitative real-time RT-PCR (qRT-PCR) is currently the most popular method for measuring differential gene expression. However, selecting an inappropriate reference gene can lead to erroneous results by this approach. It is therefore important to identify the best reference gene(s) to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper, we evaluated the stability of expression of 13 different candidate reference genes in cucumber using the geNorm, NormFinder, and 'Stability Index' statistical algorithms. Twenty-six vegetative and 22 reproductive tissues or organs were sampled at different developmental stages. Based on our results, TUA, followed by ACT and UBI-ep, were found to be the most stably expressed genes, and were therefore suitable for normalisation purposes in vegetative tissue samples. ACT, ACT3, and TUA-1 exhibited high-stability expression and could be used as suitable reference genes to normalise gene expression in reproductive tissue samples. In addition, GAS1, which encodes galactinol synthase, displayed different levels of mRNA expression when normalised using stable or unstable reference genes. This identification and validation of suitable reference genes will facilitate future transcriptomic studies during cucumber development processes. [ABSTRACT FROM AUTHOR]

It is difficult for students to conceptualize biochemical processes that are portrayed as two-dimensional figures in a textbook. Instead of relying on overheads, PowerPoint, or textbook figures, the authors have students imagine themselves actually being inside a cell. Students have a specific role in the cell: helping with the transcription and translation process. [ABSTRACT FROM AUTHOR]

Buffaloes in Indian subcontinent play an important role as the producer of milk and milk products. The αs1-casein constitutes 38% of the total milk proteins. The present study was carried out to characterize the gene in Murrah breed of Riverine buffalo. Buffalo αs1-casein cDNA was synthesized by RT-PCR, then cloned using pDRIVE-cloning vector and sequenced. The sequencing revealed that the size of αs1-casein cDNA was of 645 bp with GC content of 45.58%. The αs1-casein gene coded 214 amino acids precursor with a signal peptide of 15 amino acid residues. The similarity of buffalo αs1-casein mRNA sequence with that of cattle, goat, sheep, pig, camel, equine and human were estimated as 97.2, 93, 92.3, 57.2, 59.5, 55.9 and 46.6%, respectively. A similar trend was observed when compared amino acid sequences of these species. In the phylogenetic trees, constructed from the data of the αs1-casein mRNA as well as protein sequences, it has been observed that buffalo, cattle, goat and sheep formed a cluster with a closer relationship between cattle and buffalo followed by goat and sheep. [ABSTRACT FROM AUTHOR]

Inflammatory conditions affecting the heart and surrounding tissues have been recently reported following mRNA vaccination. Evaluating trends in the epidemiology of these events and possible mechanisms related to vaccination will enhance vaccine safety surveillance and inform best practices for future vaccine campaigns. Epidemiology of the burden of vaccine-associated myocarditis are reviewed. Key summaries of available data from public health advisory bodies and vaccine safety surveillance databases are critically reviewed. The possible biological pathways for vaccine-associated heart inflammations are introduced. A critical synthesis of available information to inform vaccine recommendations and best practices is provided. The citations were selected by the authors based on PubMed searches of the literature, national vaccine safety surveillance databases and summaries from national public health bodies. Myocarditis may be associated with vaccination, through several biological mechanisms. Studies have shown that live viral vaccinations can act as a trigger for hypersensitivity inflammatory reactions, but further work is required to examine how the mRNA formulation may induce these autoimmune responses. Given that the risk of these adverse events is low, and the benefit of protection against disease is so great, the receipt of mRNA vaccines is recommended. [ABSTRACT FROM AUTHOR]

Mutations that affect phenotypes have been identified primarily as those that directly alter amino acid sequences or disrupt splice sites. However, some mutations not located in functionally important sites can also affect phenotypes, such as splice-site-creating mutations (SCMs). To investigate how frequent exon extension/shrinkage events induced by SCMs occur in normal individuals, we used personal genome sequencing data and transcriptome data of the corresponding individuals and identified 371 exon extension/shrinkage events in normal individuals. This number was about three times higher than the number of pseudo-exon activation events identified in the previous study. The average numbers of exon extension and exon shrinkage events in each sample were 3.3 and 11.2, respectively. We also evaluated the impact of exon extension/shrinkage events on the resulting transcripts and their protein products and found that 40.2% of the identified events may have possible functional impacts by either generating premature termination codons in transcripts or affecting protein domains. Our results indicated that a certain fraction of SCMs identified in this study can be pathogenic mutations by creating novel splice sites. [ABSTRACT FROM AUTHOR]

Cervical cancer (CC) is one of the most prevalent malignancies among females. Cytoprotective autophagy could confer cancer cell tolerance to hypoxic stress, promoting cell survival and adaptation. Aspartyl-tRNA synthetase 1 antisense 1 (DARS-AS1) is an oncogenic long non-coding RNA (lncRNA) in various cancers, but how DARS-AS1 regulates cytoprotective autophagy in hypoxic environment in CC remains unclear. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were conducted to explore the interaction between hypoxia-inducible factor 1 subunit alpha (HIF1a) and DARS-AS1 promoter. Methylated RNA immunoprecipitation (MeRIP) followed by quantitative real-time polymerasechain reaction (RT-qPCR) detected methylated RNA level. The process of autophagic maturation was monitored by immunofluorescence staining. Higher DARS-AS1 expression was found in CC tissues and cytoprotective. We also uncovered that hypoxic exposure induced cytoprotective autophagy via HIF1a/DARS-AS1/DARS axis. Moreover, DARS-AS1 was validated to facilitate DARS translation via recruiting N6- adenosine-methyltransferase methyltransferase like 3 (METTL3) and methyltransferase like 14 (METTL14), which bound with DARS mRNA DARS mRNA 5' untranslated region (5'UTR) and promoting its translation. The present study demonstrated that the 'HIF1a/DARS-AS1/DARS/ATG5/ATG3' pathway regulated the hypoxia-induced cytoprotective autophagy of CC and might be a promising target of therapeutic strategies for patients afflicted with CC. [ABSTRACT FROM AUTHOR]

Circadian clocks are an endogenous internal timekeeping mechanism that drives the rhythmic expression of genes, controlling the 24 h oscillatory pattern in behaviour and physiology. It has been recently shown that post-transcriptional mechanisms are essential for controlling rhythmic gene expression. Controlling the stability of mRNA through poly(A) tail length modulation is one such mechanism. In this study, we show that Cnot1, encoding the scaffold protein of the CCR4-NOT deadenylase complex, is highly expressed in the suprachiasmatic nucleus, the master timekeeper. CNOT1 deficiency in mice results in circadian period lengthening and alterations in the mRNA and protein expression patterns of various clock genes, mainly Per2. Per2 mRNA exhibited a longer poly(A) tail and increased mRNA stability in Cnot1+/- mice. CNOT1 is recruited to Per2 mRNA through BRF1 (ZFP36L1), which itself oscillates in antiphase with Per2 mRNA. Upon Brf1 knockdown, Per2 mRNA is stabilized leading to increased PER2 expression levels. This suggests that CNOT1 plays a role in tuning and regulating the mammalian circadian clock. [ABSTRACT FROM AUTHOR]

The effect of fisetin on autophagy in hepatocellular carcinoma remains uncovered. HepG2 cells were exposed to different concentrations of fisetin (25, 50, and 100 µM) for 24 h. The cells were also treated with rapamycin and chloroquine alone or in combination with fisetin. Autophagic flux formation and ATP levels were determined. The changes in autophagic markers and AMPK signaling proteins were analyzed using qRT-PCR and Western blotting. Cyto-ID staining followed by flow cytometry showed that fisetin decreased autophagic flux formation in a dose-dependent manner. In gene expression analysis, the mRNA levels of mTOR, Atg5, Atg16L, and LC3A were elevated, whereas the mRNA levels of Atg7 and Beclin1 were downregulated in a dose-dependent manner compared to control. In the Western blotting analysis, fisetin treatment inhibited the expression of Atg7, Atg16L, mTOR, and pACC and elevated the expression of Atg5, AMPKα, AMPKβ1/2, ACC and Akt. Taken together, the results revealed that fisetin inhibited autophagy by the activation of PI3K/Akt/mTOR and modulation of AMPK signaling pathways. Our findings indicate that suppression of autophagy by fisetin may serve as an effective therapeutic strategy against HCC. [ABSTRACT FROM AUTHOR]

To assess the effect of sequential treatment with Vitamin C (VC) and Quercetin (Q) on Nrf2-related oxidative stress in PC3 and DU145 cells, viability was measured by MTT assay. Intracellular ROS levels were determined, using 2'-7'-dichlorodihydrofluorescein diacetate fluorescent as a probe. Nrf2 gene expression was investigated by quantitative reverse transcription polymerase chain reaction, and Nrf2 protein levels were defined by western blot analysis. The activity of glutathione peroxidase (GPx), glutathione reductase (GR), nicotinamide adenine dinucleotide phosphate dehydrogenase quinone 1 (NQO1) and hemeoxygenase 1 (HO-1) enzymes were measured. The IC50 values for VC + Q were 263.03–372.1 µM and 144.2–194.1 µM respectively and 200 µM VC + 50 µM Q (dose no.1) and 100 µM VC + 75 µM Q (dose no.2) were selected. Sequential treatment of PC3 cells led to a significant reduction of Nrf2 mRNA expression and protein levels in addition to a significant reduction of GPx, GR and NQO1 enzymatic activity. Although the data was slightly different for DU145 cells after the treatments, in terms of Nrf2 gene expression, we obtained the same results. Our study revealed the significant effects of sequential treatment with VC + Q on Nrf2 suppression in prostate cancer cells. [ABSTRACT FROM AUTHOR]

In this study, we investigated whether olive leaf and oleuropein have the potential to stop cell motility, which a metastatic cell behavior by blocking voltage-gated sodium channels (VGSCs). For this purpose, it was first prepared the aqueous extract of olive leaves (AOLE). Then it was assayed the effect on the motility of MAT-LyLu, a highly metastatic Dunning rat prostate adenocarcinoma cells of this extract. The phenolic content of AOLE was analyzed using LC-MS/MS instrument. It was observed that oleuropein was the most finding compound in AOLE. Therefore, whether oleuropein was responsible for the inhibitory effect of AOLE on the MAT-LyLu cell movement was tested. Nontoxic oleuropein concentrations and those that did not affect proliferation on MAT-LyLu cells were determined. Subsequently, it was examined the effects of oleuropein on the lateral and vertical movement of MAT-LyLu cells. To elucidate the mechanism of oleuropein affecting cell motility, whether it suppressed mRNA expression of SCN9A, which encodes the VGSC was analyzed. Accordingly, oleuropein suppressed the movement of MAT-LyLu cells by reducing SCN9A mRNA expression. In conclusion, we report the first time that oleuropein might be considered as a potential antimetastatic agent for prostate cancer due to its blocking effect on VGSC-mediated cell motility. [ABSTRACT FROM AUTHOR]

Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD. [ABSTRACT FROM AUTHOR]