56 research outputs found
miRNA-regulated dynamics in circadian oscillator models
<p>Abstract</p> <p>Background</p> <p>We have studied the dynamics of miRNA regulation in two models of circadian oscillators. miRNAs are a class of small RNA molecules (18â24 nucleotides) that are known to regulate gene expression at the post-transcriptional level by reducing the amount of proteins produced by translation. This is done either by blocking translation or by degradation of mRNAs, the latter being mainly due to the initiation of a set of processes induced by formation of the miRNA:mRNA complex. Although miRNAs are known to regulate a large number of fundamental biological processes such as growth and development, their role in the dynamics of regulation is not completely understood. In exceptional cases, in particular, they can also up-regulate gene expression.</p> <p>Results</p> <p>We have studied simple biological systems wherein oscillations originate from negative auto regulation of gene expression. The regulation of gene expression by miRNAs is introduced into these models and the dynamics is studied via standard stochastic simulation techniques. We find that in addition to a reduction in the amplitude of the oscillation, inclusion of miRNAs in the models has the effect of altering the <it>frequency </it>of oscillation and thereby regulating the dynamics of protein production.</p> <p>Conclusion</p> <p>miRNAs can have a profound effect on the dynamics of regulatory modules, both by control of amplitude, namely by affecting the level of gene expression, as well as by control or alteration of frequency, namely by interference with the temporal sequence of gene production or delivery. We believe that our results are valid for a variety of regulatory systems, beyond the exemplars discussed here.</p
MicroRNAs Modulate the Dynamics of the NF-ÎșB Signaling Pathway
BACKGROUND: NF-ÎșB, a major transcription factor involved in mammalian inflammatory signaling, is primarily involved in regulation of response to inflammatory cytokines and pathogens. Its levels are tightly regulated since uncontrolled inflammatory response can cause serious diseases. Mathematical models have been useful in revealing the underlying mechanisms, the dynamics, and other aspects of regulation in NF-ÎșB signaling. The recognition that miRNAs are important regulators of gene expression, and that a number of miRNAs target different components of the NF-ÎșB network, motivate the incorporation of miRNA regulated steps in existing mathematical models to help understand the quantitative aspects of miRNA mediated regulation. METHODOLOGY/PRINCIPAL FINDINGS: In this study, two separate scenarios of miRNA regulation within an existing model are considered. In the first, miRNAs target adaptor proteins involved in the synthesis of IKK that serves as the NF-ÎșB activator. In the second, miRNAs target different isoforms of IÎșB that act as NF-ÎșB inhibitors. Simulations are carried out under two different conditions: when all three isoforms of IÎșB are present (wild type), and when only one isoform (IÎșBα) is present (knockout type). In both scenarios, oscillations in the NF-ÎșB levels are observed and are found to be dependent on the levels of miRNAs. CONCLUSIONS/SIGNIFICANCE: Computational modeling can provide fresh insights into intricate regulatory processes. The introduction of miRNAs affects the dynamics of the NF-ÎșB signaling pathway in a manner that depends on the role of the target. This "fine-tuning" property of miRNAs helps to keep the system in check and prevents it from becoming uncontrolled. The results are consistent with earlier experimental findings
Da prescrição do estupro de vulneråvel
O presente estudo tem como objetivo verificar a possĂvel chance de tornar o crime de estupro de vulnerĂĄvel imprescritĂvel, bem como aqueles elencados na Constituição Federal. A metodologia utilizada foi a qualitativa, pois busca examinar a parte subjetiva do problema, atravĂ©s de outras fontes, quanto Ă possibilidade ou nĂŁo de tornar o crime de estupro de vulnerĂĄvel em imprescritĂvel diante do ordenamento jurĂdico brasileiro. A pesquisa foi desenvolvida atravĂ©s da pesquisa bibliogrĂĄfica, sendo utilizados livros, jurisprudĂȘncias e legislaçÔes. De inĂcio o trabalho busca desenvolver o conceito de estupro bem como suas elementares, em seguida o instituto da prescrição penal do ordenamento jurĂdico brasileiro. Ao fim, o estudo irĂĄ trazer o Projeto de Lei 5102/20, realizando uma abordagem quanto aos seus aspectos, fundamentos e sua finalidade diante a sociedade, a conclusĂŁo busca estabelecer um posicionamento quanto ao referido projeto de lei citado
Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood
<p>Abstract</p> <p>Background</p> <p>MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post - transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack the ability to identify novel miRNAs and accurately determine expression at a range of concentrations. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts.</p> <p>Results</p> <p>The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 and HL60 are presented. In general K562 cells displayed overall low level of miRNA population and also low levels of DICER. Some of the highly expressed miRNAs in the leukocytes include several members of the let-7 family, miR-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 or HL60 cells revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Relative expression levels of individual miRNAs belonging to a cluster were found to be highly variable. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by Real-time RT-PCR and or RNase protection assay. Organization of some of the novel miRNAs in human genome suggests that these may also be part of existing clusters or form new clusters.</p> <p>Conclusions</p> <p>We conclude that about 904 miRNAs are expressed in human leukocytes. Out of these 370 are novel miRNAs. We have identified miRNAs that are differentially regulated in normal PBMC with respect to cancer cells, K562 and HL60. Our results suggest that post - transcriptional processes may play a significant role in regulating levels of miRNAs in tumor cells. The study also provides a customized automated computation pipeline for miRNA profiling and identification of novel miRNAs; even those that are missed out by other existing pipelines. The Computational Pipeline is available at the website: <url>http://mirna.jnu.ac.in/deep_sequencing/deep_sequencing.html</url></p
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Large-Scale microRNA Expression Profiling Identifies Putative Retinal miRNA-mRNA Signaling Pathways Underlying Form-Deprivation Myopia in Mice
Development of myopia is associated with large-scale changes in ocular tissue gene expression. Although differential expression of coding genes underlying development of myopia has been a subject of intense investigation, the role of non-coding genes such as microRNAs in the development of myopia is largely unknown. In this study, we explored myopia-associated miRNA expression profiles in the retina and sclera of C57Bl/6J mice with experimentally induced myopia using microarray technology. We found a total of 53 differentially expressed miRNAs in the retina and no differences in miRNA expression in the sclera of C57BL/6J mice after 10 days of visual form deprivation, which induced -6.93 ± 2.44 D (p < 0.000001, n = 12) of myopia. We also identified their putative mRNA targets among mRNAs found to be differentially expressed in myopic retina and potential signaling pathways involved in the development of form-deprivation myopia using miRNA-mRNA interaction network analysis. Analysis of myopia-associated signaling pathways revealed that myopic response to visual form deprivation in the retina is regulated by a small number of highly integrated signaling pathways. Our findings highlighted that changes in microRNA expression are involved in the regulation of refractive eye development and predicted how they may be involved in the development of myopia by regulating retinal gene expression
Licensed human natural killer cells aid dendritic cell maturation via TNFSF14/LIGHT
Interactions between natural killer (NK) cells and dendritic cells (DC) aid DC
maturation and promote T cell responses. Here, we have analysed the response of
human NK cells to tumor cells and we identify a pathway by which NK-DC
interactions occur. Gene expression profiling of tumor-responsive NK cells identified
the very rapid induction of TNFSF14 (also known as LIGHT), a cytokine implicated
in the enhancement of anti-tumor responses. TNFSF14 protein expression was
induced by three primary mechanisms of NK cell activation, namely via the
engagement of CD16, by the synergistic activity of multiple target cell-sensing NK
cell activation receptors and by the cytokines IL-2 and IL-15. For anti-tumor
responses, TNFSF14 was preferentially produced by the licensed NK cell population,
defined by the expression of inhibitory receptors specific for self-MHC class I
molecules. In contrast, IL-2 and IL-15 treatment induced TNFSF14 production by
both licensed and unlicensed NK cells, reflecting the ability of pro-inflammatory
conditions to override the licensing mechanism. Importantly, both tumor and cytokine
activated NK cells induced DC maturation in a TNFSF14-dependent manner. The
coupling of TNFSF14 production to tumor-sensing NK cell activation receptors links
the tumor immune surveillance function of NK cells to DC maturation and adaptive
immunity. Furthermore, regulation by NK cell licensing helps to safeguard against
TNFSF14 production in response to healthy tissues
Distinct regulatory networks control toxin gene expression in elapid and viperid snakes
Background
Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris).
Results
Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis.
Conclusions
Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype
Omecamtiv mecarbil in chronic heart failure with reduced ejection fraction, GALACTICâHF: baseline characteristics and comparison with contemporary clinical trials
Aims:
The safety and efficacy of the novel selective cardiac myosin activator, omecamtiv mecarbil, in patients with heart failure with reduced ejection fraction (HFrEF) is tested in the Global Approach to Lowering Adverse Cardiac outcomes Through Improving Contractility in Heart Failure (GALACTICâHF) trial. Here we describe the baseline characteristics of participants in GALACTICâHF and how these compare with other contemporary trials.
Methods and Results:
Adults with established HFrEF, New York Heart Association functional class (NYHA)ââ„âII, EF â€35%, elevated natriuretic peptides and either current hospitalization for HF or history of hospitalization/ emergency department visit for HF within a year were randomized to either placebo or omecamtiv mecarbil (pharmacokineticâguided dosing: 25, 37.5 or 50âmg bid). 8256 patients [male (79%), nonâwhite (22%), mean age 65âyears] were enrolled with a mean EF 27%, ischemic etiology in 54%, NYHA II 53% and III/IV 47%, and median NTâproBNP 1971âpg/mL. HF therapies at baseline were among the most effectively employed in contemporary HF trials. GALACTICâHF randomized patients representative of recent HF registries and trials with substantial numbers of patients also having characteristics understudied in previous trials including more from North America (n = 1386), enrolled as inpatients (n = 2084), systolic blood pressureâ<â100âmmHg (n = 1127), estimated glomerular filtration rate <â30âmL/min/1.73 m2 (n = 528), and treated with sacubitrilâvalsartan at baseline (n = 1594).
Conclusions:
GALACTICâHF enrolled a wellâtreated, highârisk population from both inpatient and outpatient settings, which will provide a definitive evaluation of the efficacy and safety of this novel therapy, as well as informing its potential future implementation
Analysis of the microRNA transcriptome and expression of different isomiRs in human peripheral blood mononuclear cells
Background: MicroRNAs (miRNAs) have been recognized as one of the key regulatory non-coding RNAs that are involved in a number of basic cellular processes. miRNA expression profiling helps to identify miRNAs that could serve as biomarkers. Next generation sequencing (NGS) platforms provide the most effective way of miRNA profiling, particularly as expression of different isoforms of miRNA (IsomiRs) can be estimated by NGS. Therefore, it is now possible to discern the overall complexity of miRNA populations that participate in gene regulatory networks. It is thus important to consider different isoforms of miRNA as part of total profiling in order to understand all aspects of the biology of miRNAs. Results: Here next generation sequencing data of small RNAs derived from normal peripheral blood mononuclear cells (PBMC) and Chronic myeloid leukemia (CML) patients has been used to generate miRNA profiles using a computation pipeline which can identify isomiRs that are natural variants of mature miRNAs. IsomiR profiles have been generated for all the 5p and 3p miRNAs (previously known as major mature miRNA and minor or miRNA*) and the data has been presented as a composite total miRNA transcriptome. The results indicated that the most abundant isomiR sequence of about 68% miRNAs, did not match the reference miRNA sequence as entered in the miRBase and that there is a definite pattern in relative concentration of different isomiRs derived from same precursors. Finally, a total of 17 potential novel miRNA sequences were identified suggesting that there are still some new miRNAs yet to be discovered. Conclusions: Inclusion of different isoforms provides a detailed miRnome of a cell type or tissues. Availability of miRnome will be useful for finding biomarkers of different cell types and disease states. Our results also indicate that the relative expression levels of different isoforms of a miRNA are likely to be dynamic and may change with respect to changes in the cell or differentiation status
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