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1.
Bioorg Chem ; 146: 107294, 2024 May.
Article in English | MEDLINE | ID: mdl-38507997

ABSTRACT

Oxindoles are potent anti-cancer agents and are also used against microbial and fungal infections and for treating neurodegenerative diseases. These oxindoles are earlier established as estrogen receptor (ER)-targeted agents for killing ER (+) cancer cells. Our previously developed bis-arylidene oxindole, Oxifen (OXF) exhibits effective targeting towards ER (+) cancer cells which has a structural resemblance with tamoxifen. Herein, we have designed and synthesized few structural analogues of OXF such as BPYOX, ACPOX and ACPOXF to examine its cytotoxicity in different cancer as well as non-cancer cell lines and its potential to form self- aggregates in aqueous solution. Among these series of molecules, ACPOXF showed maximum toxicity in colorectal cancer cell line which are ER (-) but it also kills non-cancer cell line HEK-293, thereby reducing its cancer cell selectivity. Incidentally, ACPOXF exhibits self-aggregation, without the help of a co-lipid with nanometric size in aqueous solution. ACPOXF self-aggregate was co-formulated with glucocorticoid receptor (GR) synthetic ligand, dexamethasone (Dex) (called, ACPOXF-Dex aggregate) which could selectively kill ER (-) colorectal cancer cells and also could increase survivability of colon-tumour bearing mice. ACPOXF-Dex induced ROS up-regulation followed by apoptosis through expression of caspase-3. Further, we observed upregulation of antiproliferative factor, p53 and epithelial-to-mesenchymal (EMT) reversal marker E-cadherin in tumour mass. In conclusion, a typical structural modification in ER-targeting Oxifen moiety resulted in its self-aggregation that enabled it to carry a GR-ligand, thus broadening its selective antitumor property especially as colon cancer therapeutics.


Subject(s)
Antineoplastic Agents , Colorectal Neoplasms , Mice , Humans , Animals , Ligands , HEK293 Cells , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Apoptosis , Receptors, Estrogen/metabolism , Oxindoles/chemistry , Colorectal Neoplasms/drug therapy , Cell Line, Tumor , Cell Proliferation
2.
Br J Dermatol ; 191(1): 65-74, 2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38305572

ABSTRACT

BACKGROUND: Psoriasis is a genetically determined systemic skin disease, although environmental trigger factors are required for disease manifestation. Some of these triggers, such as stress, infections and drug exposure, have been identified. OBJECTIVES: To explore the role of early nutrition as a risk factor for the development of psoriasis. METHODS: Parents in the All Babies in Southeast Sweden (ABIS) prospective birth cohort (n = 16 415) answered questionnaires at birth and when their children were aged 1 and 3 years. A diagnosis of psoriasis was determined from the Swedish National Patient Register and National Drug Prescription Register. Statistical analyses were conducted using custom-written R scripts. RESULTS: Individuals breastfed for < 4 months and who received infant formula before 4 months of age had a higher risk of psoriasis [odds ratio (OR) 1.84 (P = 0.02) and OR 1.88 (P = 0.02), respectively]. At the 3-year follow-up, the increased consumption of fish, especially from the Baltic Sea, increased the risk of psoriasis (OR 9.61; P = 0.003). In addition, the risk of psoriasis increased following the consumption of a large volume of milk (OR 2.53; P = 0.04). CONCLUSIONS: Our study underscores, for the first time, the impact of very early nutrition on the manifestation of psoriasis through early adulthood. Exclusive breastfeeding for 4 months appears to be protective.


Subject(s)
Breast Feeding , Psoriasis , Humans , Psoriasis/epidemiology , Psoriasis/prevention & control , Breast Feeding/statistics & numerical data , Infant , Female , Male , Sweden/epidemiology , Child, Preschool , Prospective Studies , Risk Factors , Infant, Newborn , Infant Formula , Adult
4.
Eur J Cell Biol ; 102(1): 151286, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36645925

ABSTRACT

Circular RNAs (circRNAs) are covalently closed RNA molecules generated from precursor RNAs by the head-to-tail backsplicing of exons. Hundreds of studies demonstrated that circRNAs are ubiquitously expressed and regulate cellular events by modulating microRNA (miRNA) and RNA-binding protein (RBP) activities. A few circRNAs are also known to translate into functional polypeptides regulating cellular physiology. All these functions primarily depend on the full-length sequence of the circRNAs. CircRNA backsplice junction sequence is the key to identifying circRNAs and their full-length mature sequence. However, some multi-exonic circRNAs exist in different isoforms sharing identical backsplice junction sequences and are termed circRNA splice variants. Here, we analyzed the previously published HeLa cell RNA-seq datasets to identify circRNA splice variants using the de novo module of the CIRCexplorer2 circRNA annotation pipeline. A subset of circRNAs with splice variants was validated by the circRNA-rolling circle amplification (circRNA-RCA) method. Interestingly, several validated circRNAs were predicted to translate into proteins by the riboCIRC database. Furthermore, polyribosome fractionation followed by quantitative PCR confirmed the association of a subset of circRNAs with polyribosome supporting their protein-coding potential. Finally, bioinformatics analysis of proteins derived from splice variants of circCORO1C and circASPH suggested altered protein sequences and structures that could affect their physiological functions. Together, our study identified novel circRNA splice variants and their potential translation into protein isoforms which may regulate various physiological processes.


Subject(s)
MicroRNAs , Protein Biosynthesis , RNA, Circular , Humans , Alternative Splicing/genetics , HeLa Cells , MicroRNAs/genetics , Protein Isoforms/genetics , Protein Isoforms/metabolism , RNA, Circular/genetics , RNA, Circular/metabolism
5.
J Vis Exp ; (187)2022 09 16.
Article in English | MEDLINE | ID: mdl-36190278

ABSTRACT

Digital droplet polymerase chain reaction (dd-PCR) is one of the most sensitive quantification methods; it fractionates the reaction into nearly 20,000 water-in-oil droplets, and the PCR occurs in the individual droplets. The dd-PCR has several advantages over conventional real-time qPCR, including increased accuracy in detecting low-abundance targets, omitting reference genes for quantification, eliminating technical replicates for samples, and showing high resilience to inhibitors in the samples. Recently, dd-PCR has become one of the most popular methods for accurately quantifying target DNA or RNA for gene expression analysis and diagnostics. Circular RNAs (circRNAs) are a large family of recently discovered covalently closed RNA molecules lacking 5' and 3' ends. They have been shown to regulate gene expression by acting as sponges for RNA-binding proteins and microRNAs. Furthermore, circRNAs are secreted into body fluids, and their resistance to exonucleases makes them serve as biomarkers for disease diagnosis. This article aims to show how to perform divergent primer design, RNA extraction, cDNA synthesis, and dd-PCR analysis to accurately quantify specific circular RNA (circRNA) levels in cells. In conclusion, we demonstrate the precise quantification of circRNAs using dd-PCR.


Subject(s)
MicroRNAs , RNA, Circular , Biomarkers , DNA, Complementary , Exonucleases , MicroRNAs/genetics , RNA/genetics , RNA/metabolism , RNA, Circular/genetics , Real-Time Polymerase Chain Reaction/methods , Water
6.
mBio ; 13(3): e0089222, 2022 06 28.
Article in English | MEDLINE | ID: mdl-35532162

ABSTRACT

The coronavirus disease 2019, COVID-19, is a complex disease with a wide range of symptoms from asymptomatic infections to severe acute respiratory syndrome with lethal outcome. Individual factors such as age, sex, and comorbidities increase the risk for severe infections, but other aspects, such as genetic variations, are also likely to affect the susceptibility to SARS-CoV-2 infection and disease severity. Here, we used a human 3D lung cell model based on primary cells derived from multiple donors to identity host factors that regulate SARS-CoV-2 infection. With a transcriptomics-based approach, we found that less susceptible donors show a higher expression level of serine protease inhibitors SERPINA1, SERPINE1, and SERPINE2, identifying variation in cellular serpin levels as restricting host factors for SARS-CoV-2 infection. We pinpoint their antiviral mechanism of action to inhibition of the cellular serine protease, TMPRSS2, thereby preventing cleavage of the viral spike protein and TMPRSS2-mediated entry into the target cells. By means of single-cell RNA sequencing, we further locate the expression of the individual serpins to basal, ciliated, club, and goblet cells. Our results add to the importance of genetic variations as determinants for SARS-CoV-2 susceptibility and suggest that genetic deficiencies of cellular serpins might represent risk factors for severe COVID-19. Our study further highlights TMPRSS2 as a promising target for antiviral intervention and opens the door for the usage of locally administered serpins as a treatment against COVID-19. IMPORTANCE Identification of host factors affecting individual SARS-CoV-2 susceptibility will provide a better understanding of the large variations in disease severity and will identify potential factors that can be used, or targeted, in antiviral drug development. With the use of an advanced lung cell model established from several human donors, we identified cellular protease inhibitors, serpins, as host factors that restrict SARS-CoV-2 infection. The antiviral mechanism was found to be mediated by the inhibition of a serine protease, TMPRSS2, which results in a blockage of viral entry into target cells. Potential treatments with these serpins would not only reduce the overall viral burden in the patients, but also block the infection at an early time point, reducing the risk for the hyperactive immune response common in patients with severe COVID-19.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Serine Proteinase Inhibitors , Serpins , Antiviral Agents/pharmacology , Humans , Plasminogen Activator Inhibitor 1 , SARS-CoV-2 , Serine Endopeptidases , Serine Proteinase Inhibitors/pharmacology , Serpin E2 , Serpins/genetics , Virus Internalization , alpha 1-Antitrypsin
7.
Wiley Interdiscip Rev RNA ; 13(1): e1685, 2022 01.
Article in English | MEDLINE | ID: mdl-34342387

ABSTRACT

Functional proteins in the cell are translated from the messenger RNA (mRNA) molecules, constituting less than 5% of the cellular transcriptome. The majority of the RNA molecules in the cell are noncoding RNAs, including rRNA, tRNA, snRNA, piRNA, lncRNA, microRNA, and poorly characterized circular RNAs (circRNAs). Recent studies established that circRNAs regulate gene expression by associating with RNA-binding proteins and microRNAs. With the growing understanding of circRNA functions, a subset of circRNAs has been reported to translate into proteins. Interestingly, the presence of Open Reading Frames (ORFs), N6-methyladenosine (m6A) modifications, and internal ribosomal entry sites (IRES) in the circRNA sequences indicate their coding potential through the cap-independent translation initiation mechanism. The purpose of this review is to highlight the mechanism of circRNA translation and the importance of circRNA-encoded proteins (circ-proteins) in cellular physiology and pathology. Here, we discuss the computational and molecular methods currently utilized to systematically identify translatable circRNAs and the functional characterization of the circ-proteins. We foresee that the ongoing and future studies on circRNA translation will uncover the hidden proteome and their therapeutic implications in human health. This article is categorized under: RNA Methods > RNA Analyses in Cells Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Translation > Mechanisms.


Subject(s)
MicroRNAs , RNA, Circular , Humans , Internal Ribosome Entry Sites , Open Reading Frames , Proteome , RNA/genetics
8.
Methods Mol Biol ; 2392: 103-114, 2022.
Article in English | MEDLINE | ID: mdl-34773618

ABSTRACT

High-throughput RNA-sequencing (RNA-seq) technologies combined with novel bioinformatic algorithms discovered a large class of covalently closed single-stranded RNA molecules called circular RNAs (circRNAs ). Although RNA-seq has identified more than a million circRNAs, only a handful of them is validated with other techniques, including northern blotting, gel-trap electrophoresis, exonuclease treatment assays, and polymerase chain reaction (PCR). Reverse transcription (RT) of total RNA followed by PCR amplification is the most widely used technique for validating circRNAs identified in RNA-seq. RT-PCR is a highly reproducible, sensitive, and quantitative method for the detection and quantitation of circRNAs. This chapter details the basic guidelines for designing suitable primers for PCR amplification and validation of circRNAs .


Subject(s)
Polymerase Chain Reaction , RNA, Circular , Reverse Transcription , Sequence Analysis, RNA
9.
J Conserv Dent ; 25(6): 636-641, 2022.
Article in English | MEDLINE | ID: mdl-36591594

ABSTRACT

Objective: The purpose of the study is the evaluation and comparison of surface roughness and bond strength of glass fiber post (GFP) after different types of surface treatment and the application of a universal bonding agent. Materials and Methods: Forty GFPs were divided into four groups based on surface treatment: Group I, silane coupling agent application for 60 s; Group II, air abrasion with 30 µm silicon dioxide powder particles in 2.5 bar pressure from 2 cm distance for 10 s, followed by silane coupling agent application; Group III, 9% hydrofluoric acid application for 10 s, rinsed and air-dried, followed by silane coupling agent application; and Group IV, silane coupling agent application, followed by universal bonding agent application. Surface roughness evaluation is done by a profilometer. All posts were cemented in the root of the maxillary central incisor with resin cement. After that, root was placed in an acrylic mold, and the external end part of the post was mounted on another acrylic mold. Pull-out bond strength was measured by a universal testing machine. Results: Highest surface roughness and bond strength values were found in Group II. Conclusion: Pretreatment of GFP increases the surface roughness of post as well as bond strength of post to root dentin. There is a correlation between surface roughness and bond strength. However, the use of only universal bonding agent also showed comparable pull-out bond strength of GFP, which means only use of universal bonding agent also a new alternative as pretreatment of GFP and helps in increase in bond strength.

10.
Phys Chem Chem Phys ; 23(46): 26263-26272, 2021 Dec 01.
Article in English | MEDLINE | ID: mdl-34787133

ABSTRACT

Luminogens exhibiting aggregation-induced-emission characteristics (AIEgens) have been designed as sensitive biosensors thanks to their "turn-on" fluorescence upon target binding. However, their AIE mechanism in biomolecules remains elusive except for the qualitative picture of restricted intramolecular motions. In this work, we employed ab initio simulations to investigate the AIE mechanism of two tetraphenylethylene derivatives recently developed for sensitive detection of human serum albumin (HSA) in biological fluids. For the first time, we quantified the ab initio free energy surfaces and kinetics of AIEgens to access the conical intersections on the excited state in the protein and aqueous solution, using a novel first-principles electronic structure method that incorporates both static and dynamic electron correlations. Our simulations accurately reproduce the experimental spectra and high-level correlated electronic structure calculations. We found that in HSA the internal conversion through the cyclization reaction is preferred over the isomerization around the central ethylenic double bond, whereas in the aqueous solution the reverse is true. Accordingly, the protein environment is able to moderately speed up certain non-radiative decay pathways, a new finding that is beyond the prediction of the existing model of restricted access to a conical intersection (RACI). As such, our findings highlight the complicated effects of the protein confinement on the competing non-radiative decay channels, which has been largely ignored so far, and extend the existing theories of AIE to biological systems. The new insights and the multiscale computational methods used in this work will aid the design of sensitive AIEgens for bioimaging and disease diagnosis.


Subject(s)
Fluorescent Dyes/chemistry , Serum Albumin, Human/chemistry , Stilbenes/chemistry , Density Functional Theory , Fluorescence , Humans , Models, Molecular , Molecular Structure , Optical Imaging , Protein Aggregates
11.
Epigenetics Chromatin ; 14(1): 42, 2021 09 06.
Article in English | MEDLINE | ID: mdl-34488850

ABSTRACT

BACKGROUND: Environmental fluctuation during embryonic and fetal development can permanently alter an organism's morphology, physiology, and behaviour. This phenomenon, known as developmental plasticity, is particularly relevant to reptiles that develop in subterranean nests with variable oxygen tensions. Previous work has shown hypoxia permanently alters the cardiovascular system of snapping turtles and may improve cardiac anoxia tolerance later in life. The mechanisms driving this process are unknown but may involve epigenetic regulation of gene expression via DNA methylation. To test this hypothesis, we assessed in situ cardiac performance during 2 h of acute anoxia in juvenile turtles previously exposed to normoxia (21% oxygen) or hypoxia (10% oxygen) during embryogenesis. Next, we analysed DNA methylation and gene expression patterns in turtles from the same cohorts using whole genome bisulfite sequencing, which represents the first high-resolution investigation of DNA methylation patterns in any reptilian species. RESULTS: Genome-wide correlations between CpG and CpG island methylation and gene expression patterns in the snapping turtle were consistent with patterns observed in mammals. As hypothesized, developmental hypoxia increased juvenile turtle cardiac anoxia tolerance and programmed DNA methylation and gene expression patterns. Programmed differences in expression of genes such as SCN5A may account for differences in heart rate, while genes such as TNNT2 and TPM3 may underlie differences in calcium sensitivity and contractility of cardiomyocytes and cardiac inotropy. Finally, we identified putative transcription factor-binding sites in promoters and in differentially methylated CpG islands that suggest a model linking programming of DNA methylation during embryogenesis to differential gene expression and cardiovascular physiology later in life. Binding sites for hypoxia inducible factors (HIF1A, ARNT, and EPAS1) and key transcription factors activated by MAPK and BMP signaling (RREB1 and SMAD4) are implicated. CONCLUSIONS: Our data strongly suggests that DNA methylation plays a conserved role in the regulation of gene expression in reptiles. We also show that embryonic hypoxia programs DNA methylation and gene expression patterns and that these changes are associated with enhanced cardiac anoxia tolerance later in life. Programming of cardiac anoxia tolerance has major ecological implications for snapping turtles, because these animals regularly exploit anoxic environments throughout their lifespan.


Subject(s)
Cardiovascular System , Turtles , Animals , DNA Methylation , Epigenesis, Genetic , Gene Expression , Hypoxia/genetics , Reptiles , Turtles/genetics
12.
Bio Protoc ; 11(14): e4088, 2021 Jul 20.
Article in English | MEDLINE | ID: mdl-34395727

ABSTRACT

Circular RNAs (circRNAs) are a large family of noncoding RNA molecules that have emerged as novel regulators of gene expression by sequestering microRNAs (miRNAs) and RNA-binding proteins (RBPs). Several computational tools have been developed to predict circRNA interaction with target miRNAs and RBPs with a view to studying their potential effect on downstream target genes and cellular physiology. Biochemical assays, including reporter assays, AGO2 pulldown, ribonucleoprotein pulldown, and biotin-labeled RNA pulldown, are used to capture the association of miRNAs and RBPs with circRNAs. Only a few studies have used circRNA pulldown assays to capture the associated miRNAs and RBPs under physiological conditions. In this detailed protocol, the circRNA of interest (e.g., circHipk2) was captured using a biotin-labeled antisense oligo (ASO) targeting the circHipk2 backsplice junction sequence followed by pulldown with streptavidin-conjugated magnetic beads. The specific enrichment of circRNA was analyzed using reverse transcription quantitative PCR (RT-qPCR). Furthermore, the ASO pulldown assay can be coupled to miRNA RT-qPCR and western blotting analysis to confirm the association of miRNAs and RBPs predicted to interact with the target circRNA. In summary, the specific pulldown of circRNA using this quick and easy method makes it a useful tool for identifying and validating circRNA interaction with specific miRNAs and RBPs.

13.
Sex Dev ; 15(1-3): 47-68, 2021.
Article in English | MEDLINE | ID: mdl-34280932

ABSTRACT

Temperature-dependent sex determination (TSD) is a well-known characteristic of many reptilian species. However, the molecular processes linking ambient temperature to determination of gonad fate remain hazy. Here, we test the hypothesis that Wnt expression and signaling differ between female- and male-producing temperatures in the snapping turtle Chelydra serpentina. Canonical Wnt signaling involves secretion of glycoproteins called WNTs, which bind to and activate membrane bound receptors that trigger ß-catenin stabilization and translocation to the nucleus where ß-catenin interacts with TCF/LEF transcription factors to regulate expression of Wnt targets. Non-canonical Wnt signaling occurs via 2 pathways that are independent of ß-catenin: one involves intracellular calcium release (the Wnt/Ca2+ pathway), while the other involves activation of RAC1, JNK, and RHOA (the Wnt/planar cell polarity pathway). We screened 20 Wnt genes for differential expression between female- and male-producing temperatures during sex determination in the snapping turtle. Exposure of embryos to the female-producing temperature decreased expression of 7 Wnt genes but increased expression of 2 Wnt genes and Rspo1 relative to embryos at the male-producing temperature. Temperature also regulated expression of putative Wnt target genes in vivo and a canonical Wnt reporter (6x TCF/LEF sites drive H2B-GFP expression) in embryonic gonadal cells in vitro. Results indicate that Wnt signaling was higher at the female- than at the male-producing temperature. Evolutionary analyses of all 20 Wnt genes revealed that thermosensitive Wnts, as opposed to insensitive Wnts, were less likely to show evidence of positive selection and experienced stronger purifying selection within TSD species.


Subject(s)
Ovary , Turtles , Animals , Female , Gene Expression , Male , Ovary/metabolism , Reptiles/genetics , Temperature , Turtles/genetics , Wnt Signaling Pathway/genetics , beta Catenin/genetics , beta Catenin/metabolism
14.
Ann Oper Res ; 306(1-2): 295-320, 2021.
Article in English | MEDLINE | ID: mdl-33758456

ABSTRACT

This research proposes a differential evolution-based regression framework for forecasting one day ahead price of Bitcoin. The maximal overlap discrete wavelet transformation first decomposes the original series into granular linear and nonlinear components. We then fit polynomial regression with interaction (PRI) and support vector regression (SVR) on linear and nonlinear components and obtain component-wise projections. The sum of these projections constitutes the final forecast. For accurate predictions, the PRI coefficients and tuning of the hyperparameters of SVR must be precisely estimated. Differential evolution, a metaheuristic optimization technique, helps to achieve these goals. We compare the forecast accuracy of the proposed regression framework with six advanced predictive modeling algorithms- multilayer perceptron neural network, random forest, adaptive neural fuzzy inference system, standalone SVR, multiple adaptive regression spline, and least absolute shrinkage and selection operator. Finally, we perform the numerical experimentation based on-(1) the daily closing prices of Bitcoin for January 10, 2013, to February 23, 2019, and (2) randomly generated surrogate time series through Monte Carlo analysis. The forecast accuracy of the proposed framework is higher than the other predictive modeling algorithms.

15.
Genes (Basel) ; 12(2)2021 02 23.
Article in English | MEDLINE | ID: mdl-33672419

ABSTRACT

The reasons for selecting a gene for further study might vary from historical momentum to funding availability, thus leading to unequal attention distribution among all genes. However, certain biological features tend to be overlooked in evaluating a gene's popularity. Here we present a meta-analysis of the reasons why different genes have been studied and to what extent, with a focus on the gene-specific biological features. From unbiased datasets we can define biological properties of genes that reasonably may affect their perceived importance. We make use of both linear and nonlinear computational approaches for estimating gene popularity to then compare their relative importance. We find that roughly 25% of the studies are the result of a historical positive feedback, which we may think of as social reinforcement. Of the remaining features, gene family membership is the most indicative followed by disease relevance and finally regulatory pathway association. Disease relevance has been an important driver until the 1990s, after which the focus shifted to exploring every single gene. We also present a resource that allows one to study the impact of reinforcement, which may guide our research toward genes that have not yet received proportional attention.


Subject(s)
Computational Biology , Gene Regulatory Networks/genetics , Algorithms , Humans , Multigene Family/genetics
16.
G3 (Bethesda) ; 10(12): 4299-4314, 2020 12 03.
Article in English | MEDLINE | ID: mdl-32998935

ABSTRACT

Turtles are iconic reptiles that inhabit a range of ecosystems from oceans to deserts and climates from the tropics to northern temperate regions. Yet, we have little understanding of the genetic adaptations that allow turtles to survive and reproduce in such diverse environments. Common snapping turtles, Chelydra serpentina, are an ideal model species for studying adaptation to climate because they are widely distributed from tropical to northern temperate zones in North America. They are also easy to maintain and breed in captivity and produce large clutch sizes, which makes them amenable to quantitative genetic and molecular genetic studies of traits like temperature-dependent sex determination. We therefore established a captive breeding colony and sequenced DNA from one female using both short and long reads. After trimming and filtering, we had 209.51Gb of Illumina reads, 25.72Gb of PacBio reads, and 21.72 Gb of Nanopore reads. The assembled genome was 2.258 Gb in size and had 13,224 scaffolds with an N50 of 5.59Mb. The longest scaffold was 27.24Mb. BUSCO analysis revealed 97.4% of core vertebrate genes in the genome. We identified 3.27 million SNPs in the reference turtle, which indicates a relatively high level of individual heterozygosity. We assembled the transcriptome using RNA-Seq data and used gene prediction software to produce 22,812 models of protein coding genes. The quality and contiguity of the snapping turtle genome is similar to or better than most published reptile genomes. The genome and genetic variants identified here provide a foundation for future studies of adaptation to climate.


Subject(s)
Ecosystem , Turtles , Adaptation, Physiological/genetics , Animals , Female , North America , Phenotype , Reptiles/genetics , Turtles/genetics
17.
Int J Mol Sci ; 21(12)2020 Jun 17.
Article in English | MEDLINE | ID: mdl-32560282

ABSTRACT

Circular RNAs (circRNAs) are a large family of noncoding RNAs that have emerged as novel regulators of gene expression. However, little is known about the function of circRNAs in pancreatic ß-cells. Here, transcriptomic analysis of mice pancreatic islet RNA-sequencing data identified 77 differentially expressed circRNAs between mice fed with a normal diet and a high-fat diet. Surprisingly, multiple circRNAs were derived from the intron 2 of the preproinsulin 2 (Ins2) gene and are termed as circular intronic (ci)-Ins2. The expression of ci-Ins2 transcripts in mouse pancreatic islets, and ßTC6 cells were confirmed by reverse transcription PCR, DNA sequencing, and RNase R treatment experiments. The level of ci-Ins2 was altered in ßTC6 cells upon exposure to elevated levels of palmitate and glucose. Computational analysis predicted the interaction of several RNA-binding proteins with ci-Ins2 and their flanking region, suggesting their role in the ci-Ins2 function or biogenesis. Additionally, bioinformatics analysis predicted the association of several microRNAs with ci-Ins2. Gene ontology and pathway analysis of genes targeted by miRNAs associated with ci-Ins2 suggested the regulation of several key biological processes. Together, our findings indicate that differential expression of circRNAs, especially ci-Ins2 transcripts, may regulate ß-cell function and may play a critical role in the development of diabetes.


Subject(s)
Insulins/genetics , RNA, Circular , Alternative Splicing , Base Sequence , Computational Biology/methods , Exons , Gene Expression Profiling , Gene Expression Regulation , Insulin-Secreting Cells/metabolism , Introns , RNA Interference , RNA Splicing , RNA Splicing Factors/metabolism , Transcriptome
18.
Front Physiol ; 11: 35, 2020.
Article in English | MEDLINE | ID: mdl-32082193

ABSTRACT

Reptiles are critically affected by temperature throughout their lifespan, but especially so during early development. Temperature-induced changes in phenotype are a specific example of a broader phenomenon called phenotypic plasticity in which a single individual is able to develop different phenotypes when exposed to different environments. With climate change occurring at an unprecedented rate, it is important to study temperature effects on reptiles. For example, the potential impact of global warming is especially pronounced in species with temperature-dependent sex determination (TSD) because temperature has a direct effect on a key phenotypic (sex) and demographic (population sex ratios) trait. Reptiles with TSD also serve as models for studying temperature effects on the development of other traits that display continuous variation. Temperature directly influences metabolic and developmental rate of embryos and can have permanent effects on phenotype that last beyond the embryonic period. For instance, incubation temperature programs post-hatching hormone production and growth physiology, which can profoundly influence fitness. Here, we review current knowledge of temperature effects on phenotypic and developmental plasticity in reptiles. First, we examine the direct effect of temperature on biophysical processes, the concept of thermal performance curves, and the process of thermal acclimation. After discussing these reversible temperature effects, we focus the bulk of the review on developmental programming of phenotype by temperature during embryogenesis (i.e., permanent developmental effects). We focus on oviparous species because eggs are especially susceptible to changes in ambient temperature. We then discuss recent work probing the role of epigenetic mechanisms in mediating temperature effects on phenotype. Based on phenotypic effects of temperature, we return to the potential impact of global warming on reptiles. Finally, we highlight key areas for future research, including the identification of temperature sensors and assessment of genetic variation for thermosensitivity.

19.
Resour Policy ; 69: 101816, 2020 Dec.
Article in English | MEDLINE | ID: mdl-36569824

ABSTRACT

The global crude oil market has experienced a significant downturn following the novel coronavirus outbreak (COVID-19) in December 2019. Thereafter, all the major oil markets have become extremely volatile, and investments in these markets could lead to substantial losses. This paper empirically investigates the time-varying correlations between gold and oil markets to examine whether gold is a safe haven asset for the international crude oil markets during the COVID-19 period. For the purpose of comparison, the safe haven property of Bitcoin is tested as well. The results of the time-varying correlations obtained through the DCC-GARCH model suggest that gold is a safe haven asset for global crude oil markets. Bitcoin, on the other hand, acts only as a diversifier for crude oil. The results further show that the portfolio risk is minimized when investors include oil and gold in their portfolio rather than holding assets in oil and Bitcoin markets. Given that financial downturn, terrorist attacks, pandemics and similar global events often play a crucial role in portfolio risk analysis, our results could be of interest to those who invest in oil, gold and Bitcoin markets.

20.
Biochim Biophys Acta Gene Regul Mech ; 1863(4): 194372, 2020 04.
Article in English | MEDLINE | ID: mdl-30946990

ABSTRACT

Skeletal muscles have an immense ability to regenerate from the muscle stem cells called satellite cells. The process of skeletal muscle regeneration is called myogenesis, which starts with activation of quiescent satellite cells immediately after muscle injury followed by proliferation and fusion of myoblasts into myotubes. Myogenesis is orchestrated through the expression of a specific set of genes which, at each step regulated by complex gene regulatory networks. Besides the well-established roles of transcription factors, increasing evidence demonstrated that circular (circ)RNAs modulate gene expression during myogenesis and are involved in muscle-related diseases. Here we review the recent findings of circRNAs involved in myogenesis.


Subject(s)
Gene Expression Regulation , Muscle Development/genetics , Muscle, Skeletal/metabolism , RNA, Circular/physiology , Animals , Humans , MicroRNAs/metabolism
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