Dynamical Analysis of bantam-Regulated Drosophila Circadian Rhythm Model

2014 ◽  
Vol 24 (12) ◽  
pp. 1450161 ◽  
Author(s):  
Ying Li ◽  
Zengrong Liu
Keyword(s):  
Circadian Rhythm ◽  
Crucial Role ◽  
Target Genes ◽  
Classical Model ◽  
Dynamical Analysis ◽  
Biological Processes ◽  
Biological Mechanisms ◽  
Environmental Perturbations ◽  
Dynamical Behaviors ◽  
Important Regulator

MicroRNAs (miRNAs) interact with 3′untranslated region (UTR) elements of target genes to regulate mRNA stability or translation, and play a crucial role in regulating many different biological processes. bantam, a conserved miRNA, is involved in several functions, such as regulating Drosophila growth and circadian rhythm. Recently, it has been discovered that bantam plays a crucial role in the core circadian pacemaker. In this paper, based on experimental observations, a detailed dynamical model of bantam-regulated circadian clock system is developed to show the post-transcriptional behaviors in the modulation of Drosophila circadian rhythm, in which the regulation of bantam is incorporated into a classical model. The dynamical behaviors of the model are consistent with the experimental observations, which shows that bantam is an important regulator of Drosophila circadian rhythm. The sensitivity analysis of parameters demonstrates that with the regulation of bantam the system is more sensitive to perturbations, indicating that bantam regulation makes it easier for the organism to modulate its period against the environmental perturbations. The effectiveness in rescuing locomotor activity rhythms of mutated flies shows that bantam is necessary for strong and sustained rhythms. In addition, the biological mechanisms of bantam regulation are analyzed, which may help us more clearly understand Drosophila circadian rhythm regulated by other miRNAs.

scholarly journals Genetic and environmental perturbations lead to regulatory decoherence

2018 ◽  
Author(s):  
Amanda Lea ◽  
Meena Subramaniam ◽  
Arthur Ko ◽  
Terho Lehtimäki ◽  
Emma Raitoharju ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Target Genes ◽  
Morphological Characters ◽  
Biological Processes ◽  
Disease Emergence ◽  
Factors Associated ◽  
Environmental Perturbation ◽  
Environmental Perturbations ◽  
Mrna Transcripts

AbstractCorrelation among traits is a fundamental feature of biological systems. From morphological characters, to transcriptional or metabolic networks, the correlations we routinely observe between traits reflect a shared regulation that remains poorly understood and difficult to study. To address this problem, we developed a new and flexible approach that allows us to identify factors associated with variation in correlation between individuals. Here, we use data from three large human cohorts to study the effects of genetic variation and environmental perturbation on correlations among mRNA transcripts and among NMR metabolites. We first show that environmental exposures (namely, infection and disease) lead to a systematic loss of correlation, which we define as ‘decoherence’. Using longitudinal data, we show that decoherent metabolites are better predictors of whether someone will develop metabolic syndrome than metabolites commonly used as biomarkers of this disease. Finally, we show that correlation itself is a trait under genetic control: specifically, we mapped and replicated hundreds of ‘correlation QTLs’, which often involve transcription factors or their known target genes. Together, this work furthers our understanding of how and why coordinated biological processes break down, and highlights the role of decoherence in disease emergence.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2020 ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Biological Processes ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Backgroundlong non-coding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, there is little report about lncRNA in pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified.ResultsOverall, 135 DE lncRNAs and 1,360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, like XLOC_466330 , XLOC_532771 , XLOC_028449 targeting RRM2B and GSTK1 , XLOC_391199 targeting STMN1 , XLOC_503926 targeting RAG2 , XLOC_187711 targeting DLG4 were included.ConclusionAll of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Effect of Circadian Rhythm on Metabolic Processes and the Regulation of Energy Balance

2019 ◽  
Vol 74 (4) ◽  
pp. 322-330 ◽  
Author(s):  
Yeliz Serin ◽  
Nilüfer Acar Tek
Keyword(s):  
Circadian Rhythm ◽  
Energy Balance ◽  
Circadian Clock ◽  
Crucial Role ◽  
Hormone Secretion ◽  
Biological Processes ◽  
Metabolic Processes ◽  
Circadian Timing ◽  
Timing System ◽  
Circadian Timing System

Background: The circadian timing system or circadian clock plays a crucial role in many biological processes, such as the sleep-wake cycle, hormone secretion, cardiovascular health, glucose homeostasis, and body temperature regulation. Energy balance is also one of the most important cornerstones of metabolic processes, whereas energy imbalance is associated with many diseases (i.e., obesity, diabetes, cardiovascular disease). Circadian clock is the main regulator of metabolism, and this analysis provides an overview of the bidirectional effect of circadian rhythm on metabolic processes and energy balance. Summary: The circadian timing system or circadian clock plays a crucial role in many biological processes, but the increase in activities that operate 24/7 and the common usage of television, internet, and mobile phones almost 24 h a day leads to a gradual decrease in the adequate sleeping time. According to recent research, long-term circadian disruptions are associated with many pathological conditions such as premature mortality, obesity, impaired glucose tolerance, diabetes, psychiatric disorders, anxiety, depression, and cancer progression, whereas short-term disruptions are associated with impaired wellness, fatigue, and loss of concentration. In this review, the circadian rhythm in metabolic processes and their effect on energy balance were examined. Key Messages: Circadian rhythm has a bidirectional interaction with almost all metabolic processes. Therefore, understanding the main reason affecting the circadian clock and creating treatment guidelines using circadian rhythm may increase the success of disease treatment. Chronopharmacology, chrononutrition, and chronoexercise are the novel treatment approaches in metabolic balance.

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

scholarly journals Enantioselective Catalytic C-H Amidations: An Highlight

Catalysts ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 471
Author(s):  
Eleonora Tosi ◽  
Renata Marcia de Figueiredo ◽  
Jean-Marc Campagne
Keyword(s):  
Biological Activity ◽  
Chemical Synthesis ◽  
Crucial Role ◽  
Medicinal Chemistry ◽  
Life Sciences ◽  
Biological Processes ◽  
Chiral Molecules ◽  
Material Sciences ◽  
Innovative Approaches

The crucial role played by compounds bearing amide functions, not only in biological processes but also in several fields of chemistry, life polymers and material sciences, has brought about many significant discoveries and innovative approaches for their chemical synthesis. Indeed, a plethora of strategies has been developed to reach such moieties. Amides within chiral molecules are often associated with biological activity especially in life sciences and medicinal chemistry. In most of these cases, their synthesis requires extensive rethinking methodologies. In the very last years (2019–2020), enantioselective C-H functionalization has appeared as a straightforward alternative to reach chiral amides. Therein, an overview on these transformations within this timeframe is going to be given.

scholarly journals Emerging multifaceted roles of BAP1 complexes in biological processes

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Aileen Patricia Szczepanski ◽  
Lu Wang
Keyword(s):  
Transcriptional Repression ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Biological Processes ◽  
Multiprotein Complex ◽  
Downstream Target ◽  
Evolutionarily Conserved ◽  
Complex Forms ◽  
Polycomb Repressive Complex 1

AbstractHistone H2AK119 mono-ubiquitination (H2AK119Ub) is a relatively abundant histone modification, mainly catalyzed by the Polycomb Repressive Complex 1 (PRC1) to regulate Polycomb-mediated transcriptional repression of downstream target genes. Consequently, H2AK119Ub can also be dynamically reversed by the BAP1 complex, an evolutionarily conserved multiprotein complex that functions as a general transcriptional activator. In previous studies, it has been reported that the BAP1 complex consists of important biological roles in development, metabolism, and cancer. However, identifying the BAP1 complex’s regulatory mechanisms remains to be elucidated due to its various complex forms and its ability to target non-histone substrates. In this review, we will summarize recent findings that have contributed to the diverse functional role of the BAP1 complex and further discuss the potential in targeting BAP1 for therapeutic use.

scholarly journals Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu
Keyword(s):  
Pineal Gland ◽  
Expression Pattern ◽  
Noncoding Rna ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Important Regulator ◽  
Gsh Metabolism ◽  
Transcriptome Expression

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.

scholarly journals Circulating or tissue microRNAs and extracellular vesicles as potential lung cancer biomarkers: a systematic review

2017 ◽  
Vol 33 (1) ◽  
pp. 3-9 ◽  
Author(s):  
Yan Song ◽  
Xiuli Yu ◽  
Zongmei Zang ◽  
Guijuan Zhao
Keyword(s):  
Lung Cancer ◽  
Systematic Review ◽  
Cancer Patients ◽  
Extracellular Vesicles ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Cancer Biomarkers ◽  
Biological Processes ◽  
Lung Cancer Patients ◽  
Prediction Of Prognosis

For both lung cancer patients and clinical physicians, tumor biomarkers for more efficient early diagnosis and prediction of prognosis are always wanted. Biomarkers in circulating serum, including microRNAs (miRNAs) and extracellular vesicles, hold the greatest possibilities to partially substitute for tissue biopsy. In this systematic review, studies on circulating or tissue miRNAs and extracellular vesicles as potential biomarkers for lung cancer patients were reviewed and are discussed. Furthermore, the target genes of the miRNAs indicated were identified through the miRTarBase, while the relevant biological processes and pathways of miRNAs in lung cancer were analyzed through MiRNA Enrichment Analysis and Annotation (MiEAA). In conclusion, circulating or tissue miRNAs and extracellular vesicles provide us with a window to explore strategies for diagnosing and assessing prognosis and treatment in lung cancer patients.

Mobility and Solvation Structure of Hydroxyl Radical in a Water Nanodroplet: A Born-Oppenheimer Molecular Dynamics Study

2021 ◽  
Author(s):  
Mohammad Hadizadeh ◽  
Lewen Yang ◽  
Guoyong Fang ◽  
Zongyang Qiu ◽  
Zhenyu Li
Keyword(s):  
Molecular Dynamics ◽  
Hydroxyl Radical ◽  
Atmospheric Chemistry ◽  
Crucial Role ◽  
Biological Processes ◽  
Density Func Tional Theory ◽  
Condi Tions ◽  
Solvation Structure

Hydroxyl radical (OH*) plays a crucial role in atmospheric chemistry and biological processes. In this study, density func-tional theory (DFT)-based Born-Oppenheimer molecular dynamics (BOMD) simulations are performed under ambient condi-tions...

Morin Exerts Anti-Diabetic Effects in Human HepG2 Cells Via Down-Regulation of miR-29a

2018 ◽  
Vol 127 (09) ◽  
pp. 615-622 ◽  
Author(s):  
Toktam Razavi ◽  
Shideh Montasser Kouhsari ◽  
Khalil Abnous
Keyword(s):  
Insulin Signaling ◽  
High Glucose ◽  
Hepg2 Cells ◽  
Target Genes ◽  
Expression Level ◽  
Inhibitory Effects ◽  
Down Regulation ◽  
Insulin Mimetic ◽  
Important Regulator ◽  
First Time

Abstract Diabetes mellitus is a complex metabolic disease around the world that is characterized by hyperglycemia resulting from impaired insulin secretion, insulin action, or both. MicroRNA-29a is an important regulator of insulin signaling and gluconeogenesis pathways through IRS2, PI3K and PEPCK expressions which up regulates in Diabetes. Morin is a substantial bioflavonoid which has insulin mimetic effect, and interacting with nucleic acids and proteins. In this study HepG2 cells, were exposed to high glucose to induce diabetic condition. We have determined whether high glucose stimulation might promotes miR-29a expression level in HepG2 cells and subsequently evaluated the Morin treatment effects on this state. In HepG2 cells, high glucose increases miR-29a expression level and decreases its target genes, IRS2 and PI3K expression, and increases associated downstream gene in gluconeogenic pathway, PEPCK. Morin treatment down regulates miR-29a expression level and improves insulin signaling and glucose metabolism. To confirm the inhibitory effects of Morin on miR-29a, we have transfected cells with mimic and inhibitor-miR-29a. This study for the first time identifies that Morin improves diabetic condition through down regulation of the miR-29a level, and suggest that this new inhibitor of miR-29a may be a useful biomedicine to treat diabetes.

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