Competing Endogenous RNA: The Key to Posttranscriptional Regulation

Competing endogenous RNA, ceRNA, vie with messenger RNAs (mRNAs) for microRNAs (miRNAs) with shared miRNAs responses elements (MREs) and act as modulator of miRNA by influencing the available level of miRNA. It has recently been discovered that, apart from protein-coding ceRNAs, pseudogenes, long noncoding RNAs (lncRNAs), and circular RNAs act as miRNA “sponges” by sharing common MRE, inhibiting normal miRNA targeting activity on mRNA. These MRE sharing elements form the posttranscriptional ceRNA network to regulate mRNA expression. ceRNAs are widely implicated in many biological processes. Recent studies have identified ceRNAs associated with a number of diseases including cancer. This brief review focuses on the molecular mechanism of ceRNA as part of the complex post-transcriptional regulatory circuit in cell and the impact of ceRNAs in development and disease

DIETARY ADMINISTRATION OF ETHANOL AND METHANOL EXTRACTS OF Withania somnifera ROOT STIMULATES INNATE IMMUNITY, PHYSIOLOGICAL PARAMETERS AND GROWTH IN NILE TILAPIA Oreochromis niloticus

U istraživanju je procijenjena učinkovitost etanola i metanolnih ekstrakata korijena ljekovite biljke Withania somnifera na imunostimulativna svojstva i rast Nilsketilapije Oreochromis niloticus. Korijeni Withanie ekstrahirani su vodom, etanolom, metanolom, metilenkloridom, heksanom i sukcesivnim metanolom. Izmjereni su sadržaji fenola i flavonoida te antiradikalna aktivnost svih ekstrakata. Nakon toga, izvršena je hranidba nilske tilapije (n=126) hranom koja je sadržavala različite koncentracije (0, 0,3, 0,5 i 0,7 g kg-1 hrane) etanola i metanolnih ekstrakata korijena W. somnifera tijekom 30 dana kroz 3 ponavljanja. Pri usporedbi s kontrolnom hranidbom, ribe hranjene hranom obogaćenom biljnim ekstraktom indicirale suznačajno bolje (P <0,05) imunološke, hematološke i biokemijske pokazatelje te parametre rasta. Riba hranjena hranom koja sadrži ekstrakt etanola u koncentraciji od 0,7g kg-1 imala je najveće imunološke (fagocitna aktivnost, aktivnost respiratornog praska, lizozim u serumu, ukupni protein, ukupni imunoglobulin), hematološke (ukupna crvena krvna zrnca, hemoglobin, hematokrit, ukupnobijelih krvnih zrnaca, limfocita) i biokemijske (smanjena aktivnost glutationa, glutation-reduktaza) pokazatelje te najviše parametre rasta (masa, prirast, specifičnu stopurasta). Prema rezultatima, istraživani biljni ekstrakt može djelovati kao sredstvo za uklanjanje slobodnih radikala u ribljim tkivima te posjeduje sposobnost zaštite tkiva,pritom povećavajući zdravlje riba.Efficacy of ethanol and methanol extracts of medicinal herb Withania somnifera roots was evaluated in Nile tilapia Oreochromis niloticus on immunostimulation and growth. Withania roots were extracted with water, ethanol, methanol, methylene chloride, hexane, successive methanol. Phenol, flavonoid content and antiradical activity of all the extracts weremeasured. Ethanol extract showed the highest phenol, flavonoid content and antiradical activity followed by methanol extract. Subsequently, Nile tilapia (n = 126) were fed diets containing different concentrations (0.0, 0.3, 0.5 and 0.7 g kg-1 feed) of ethanol and methanol extracts of W. somnifera roots for 30 days (3 replicates). Fish fed plant extract fortified diets showed significantly better (P<0.05) immunological, haematological, biochemical and growth parameters compared to the fish fed control diet. Fish fed dietcontaining ethanol extract at the concentration of 0.7 g kg-1 feed showed the highest immunological (phagocytotic activity, respiratory burst activity, serum lysozyme, total protein, total immunoglobulin), haematological (total red blood cells, haemoglobin, hematocrit, total white blood cells, lymphocyte), biochemical (reduced glutathione, glutathione reductase activity) and growth (final weight, weight gain, daily weight gain, specific growth rate) parameters. The plant extract might act as potent free radical scavenger in fish tissues and have tissue protecting ability, thus increasingfish health

Multiplex PCR technique could be an alternative approach for early detection of leprosy among close contacts - a pilot study from India

<p>Abstract</p> <p>Background</p> <p>Implementation of Multi drug Therapy (MDT) regimen has resulted in the decline of the total number of leprosy cases in the world. Though the prevalence rate has been declining, the incidence rate remains more or less constant and high in South East Asian countries particularly in India, Nepal, Bangladesh, Pakistan and Srilanka. Leprosy, particularly that of multibacillary type spreads silently before it is clinically detected. An early detection and treatment would help to prevent transmission in the community. Multiplex PCR (M-PCR) technique appears to be promising towards early detection among contacts of leprosy cases.</p> <p>Methods</p> <p>A total of 234 paucibacillary (PB) and 205 multibacillary (MB) leprosy cases were studied in a community of an endemic area of Bankura district of West Bengal (Eastern India). They were assessed by smear examination for acid-fast bacilli (AFB) and M-PCR technique. These patients were treated with Multidrug Therapy (MDT) as prescribed by WHO following detection. A total of 110 MB and 72 PB contacts were studied by performing M-PCR in their nasal swab samples.</p> <p>Results</p> <p>83.4% of MB patients were observed to be positive by smear examination for AFB and 89.2% by M-PCR. While 22.2% of PB patients were found to be positive by smear examination for AFB, 80.3% of these patients were positive by M-PCR. Among leprosy contacts (using M-PCR), 10.9% were found to be positive among MB contacts and 1.3% among PB contacts. Interestingly, two contacts of M-PCR positive MB cases developed leprosy during the period of two years follow up.</p> <p>Conclusion</p> <p>The M-PCR technique appears to be an efficient tool for early detection of leprosy cases in community based contact tracing amongst close associates of PB and MB cases. Early contact tracing using a molecular biology tool can be of great help in curbing the incidence of leprosy further.</p

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs. lnCeDB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.Downloadable freely from http://gyanxet-beta.com/lncedb/

SeedSeq: Off-Target Transcriptome Database

Detection of potential cross-reaction between a short oligonucleotide sequence and a longer (unintended) sequence is crucial for many biological applications, such as high content screening (HCS), microarray nucleotide probes, or short interfering RNAs (siRNAs). However, owing to a tolerance for mismatches and gaps in base-pairing with target transcripts, siRNAs could have up to hundreds of potential target sequences in a genome, and some small RNAs in mammalian systems have been shown to affect the levels of many messenger RNAs (off-targets) besides their intended target transcripts (on-targets). The reference sequence (RefSeq) collection aims to provide a comprehensive, integrated, nonredundant, well-annotated set of sequences, including mRNA transcripts. We performed a detailed off-target analysis of three most commonly used kinome siRNA libraries based on the latest RefSeq version. To simplify the access to off-target transcripts, we created a SeedSeq database, a new unique format to store off-target information

Melatonin ameliorates H2O2-induced oxidative stress through modulation of Erk/Akt/NFkB pathway

Abstract Background Improper control on reactive oxygen species (ROS) elimination process and formation of free radicals causes tissue dysfunction. Pineal hormone melatonin is considered a potent regulator of such oxidative damage in different vertebrates. Aim of the current communication is to evaluate the levels of oxidative stress and ROS induced damage, and amelioration of oxidative status through melatonin induced activation of signaling pathways. Hepatocytes were isolated from adult Labeo rohita and exposed to H2O2 at three different doses (12.5, 25 and 50 µM) to observe peroxide induced damage in fish hepatocytes. Melatonin (25, 50 and 100 μg/ml) was administered against the highest dose of H2O2. Enzymatic and non-enzymatic antioxidants such as malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT) and glutathione (GSH) was measured spectrophotometrically. Expression level of heat shock proteins (HSP70 and HSP90), HSPs-associated signaling molecules (Akt, ERK, cytosolic and nuclear NFkB), and melatonin receptor was also measured by western blotting analysis. Results H2O2 induced oxidative stress significantly altered (P < 0.05) MDA and GSH level, SOD and CAT activity, and up regulated HSP70 and HSP90 expression in carp hepatocytes. Signaling proteins exhibited differential modulation as revealed from their expression patterns in H2O2-exposed fish hepatocytes, in comparison with control hepatocytes. Melatonin treatment of H2O2-stressed fish hepatocytes restored basal cellular oxidative status in a dose dependent manner. Melatonin was observed to be inducer of signaling process by modulation of signaling molecules and melatonin receptor. Conclusions The results suggest that exogenous melatonin at the concentration of 100 µg/ml is required to improve oxidative status of the H2O2-stressed fish hepatocytes. In H2O2 exposed hepatocytes, melatonin modulates expression of HSP70 and HSP90 that enable the hepatocytes to become stress tolerant and survive by altering the actions of ERK, Akt, cytosolic and nuclear NFkB in the signal transduction pathways. Study also confirms that melatonin could act through melatonin receptor coupled to ERK/Akt signaling pathways. This understanding of the mechanism by which melatonin regulates oxidative status in the stressed hepatocytes may initiate the development of novel strategies for hepatic disease therapy in future