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期刊名称:Nucleosides, Nucleotides & Nucleic Acids
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A general and efficient approach to synthesize the phosphoramidites of 5′-18O labeled purine nucleosides
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-05-26 , DOI: 10.1080/15257770.2023.2218421
Nan-ShengLi,QingDai,BenjaminWeissman,MichaelEHarris,JosephAPiccirilli
Abstract5′-18O labeled RNA oligos are important probes to investigate the mechanism of 2′-O-transphosphorylation reactions. Here we describe a general and efficient synthetic approach to the phosphoramidite derivatives of 5′-18O labeled nucleosides starting from the corresponding commercially available 5′-O-DMT protected nucleosides. Using this method, we prepared 5′-18O-guanosine phosphoramidite in 8 steps (13.2% overall yield), 5′-18O-adenosine phosphoramidite in 9 steps (10.1% overall yield) and 5′-18O-2′-deoxyguanosine phosphoramidite in 6 steps (12.8% overall yield). These 5′-18O labeled phosphoramidites can be incorporated into RNA oligos by solid phase synthesis for determination of heavy atom isotope effects in RNA 2′-O-transphosphorylation reactions.
Alterations in the expression levels of long intergenic non-coding RNA APOC1P1-3 in cervical cancer tissue samples
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2022-12-23 , DOI: 10.1080/15257770.2022.2160459
NargesDastmalchi,SamaAkbarzadeh,FarnazAmini,AliRajabi,RezaSafaralizadeh
AbstractlncRNAs play a crucial role in the carcinogenesis process. Thus, they have been recognized as the potential therapeutic and diagnostic biomarkers of cancers. This study assessed the alteration in the expression of APOC1P1-3 lncRNA in cancerous tissues compared to their adjacent non-tumorous tissues sampled from cervical cancer patients. one hundred fifteen pairs of cancerous and adjacent non-cancerous biopsy of cervical cancer specimens were collected. RNA isolation and cDNA synthesis were carried out. The qRT-PCR was used to assess the changes in the expression of APOC1P1-3 lncRNA. Moreover, the biomarker function of the lncRNA and the correlations between APOC1P1-3 and clinicopathological parameters were measured. The APOC1P1-3 expression was significantly increased in cervical cancer specimens as compared to adjacent non-tumorous specimens (p < 0.0001). A significant association was also observed between APOC1P1-3 expression and lymph node involvement (p = 0.031). Additionally, APOC1P1-3 expression demonstrated a significant association with the depth of tumor invasion (p = 0.035), and squamous type of cervical cancer (p = 0.019). The overexpression of APOC1P1-3 was significantly observed in patients younger than 50 years old as compared to another age group (p = 0.033). The results of ROC curve exhibited that APOC1P1-3 with area under the curve (AUC), specificity, and sensitivity of 0.96, 93.91%, and 78.26%, respectively can be considered as a potential biomarker. Regarding overexpression of APOC1P1-3 in human cervical cancer samples, this lncRNA may be considered as an oncogenic factor in cervical cancer patients. Besides, APOC1P1-3 may be a possible biomarker for the diagnosis and treatment of cervical cancer patients.
Alkylation of 6-thiopurine derivatives by the Mitsunobu reaction
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-01-02 , DOI: 10.1080/15257770.2022.2163501
RafaelDiasdoEspíritoSanto,BiancaNascimentoMonteirodaSilva,JaimeA.Rabi,VagnerD.Pinho
AbstractAlkylation of thiopurine derivatives with alcohols by the Mitsunobu reaction are reported in moderated to good yields. The method was applied in synthesis of number of thiopurine and thiopurine ribosides derivatives.
Association of rs1800795 and rs1800796 polymorphisms in interleukin-6 gene and osteoarthritis risk: evidence from a meta-analysis
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2022-11-17 , DOI: 10.1080/15257770.2022.2147541
XiaonanDeng,KeYe,JidongTang,YonghongHuang
AbstractMultiple studies have investigated the association of interleukin-6 (IL-6) gene polymorphisms and osteoarthritis (OA) risk, but failed to reach a consistent conclusion. Therefore, this study was designed to elucidate the association of IL-6 polymorphisms and OA by a meta-analysis approach. Literature retrieval was carried out on PubMed, EMBASE, Web of Science, CNKI, and Wanfang databases. The strength of association was appraised by odds ratios (ORs) and 95% confidence intervals (95%CIs) in five genetic models. The data were merged by using RevMan 5.3 software. Ten studies with 4944 cases and 4651 controls were analyzed. Overall, no significant association was identified between rs1800795 polymorphism and OA. Subgroup analysis by ethnicity and OA site also suggested rs1800795 polymorphism was not associated with OA. For rs1800796 polymorphism, G-allele and GG-genotype carriers appeared to have an increased risk to OA (G vs. C, OR = 1.66, 95%CI 1.30-1.96, P < 0.01; GG vs. CC, OR = 1.75, 95%CI 1.07-2.84, P = 0.03; GG vs. GC + CC, OR = 1.82, 95%CI 1.42-2.34, P < 0.01). Findings of this study indicate that the rs1800795 polymorphism is not correlated to OA susceptibility, regardless of ethnicity or OA site. However, rs1800796 polymorphism trends to be associated with susceptibility to OA.
Association of eNOS gene 4a/4b VNTR and T786C polymorphism with Crimean-Congo hemorrhagic fever
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2022-12-30 , DOI: 10.1080/15257770.2022.2162542
UmutSafiyeSayCoskun,SerbulentYigit,ZelihaCanselOzmen,KoksalDeveci,AkinTekcan,HuseyinSenerBarut,YeldaDagcioglu
AbstractThe most common viral hemorrhagic fever is Crimean-Congo hemorrhagic fever (CCHF). Endothelial nitric oxide synthase (eNOS) gene polymorphisms have been linked to both hemorrhagic fevers and viral diseases. The study’s goal is to evaluate if the eNOS gene 4a/4b and T786C polymorphisms are related to CCHF. The study included 54 CCHF RNA-positive patients and 60 control subjects. The Bosphore CCHF virus Quantification Kit v1 was used to obtain CCHF RNA, and the Magnesia 16 isolation device was used to isolate DNA (Anatolia Gene works, Turkey). Polymerase chain reaction and restriction fragment length polymorphism were used to genotype the samples. The frequency of the eNOS 4a/4a, 4a/4b, and 4 b/4b genotypes in patients and the control was 6.6% versus 1.7%, 37.0% versus 43.3%, and 57.4% versus 55%, respectively. 4a: 24.07% of patients and 23.33% of controls; and 4 b: 75.92% of patients and 76.66% of controls. The frequency of the eNOS-786 T/C, T/T, T/C, and C/C genotypes in patients and the control group was 35.2% versus 68.3%; 51.9% versus 26.73%; and 13.0% versus 5.0%, respectively. The allele and genotype frequencies of the eNOS T786C variant differ statistically between patients and the control (p < 0.05). The eNOS T786C variant could be a genetic determinant for susceptibility to CCHF. To our knowledge, this is the first study to figure out the association between eNOS gene T786C polymorphisms and CCHF disease.
Association of ACE ID, MTHFR C677T, and MIF-173GC variants with the clinical course of COVID-19 patients
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-03-27 , DOI: 10.1080/15257770.2023.2194341
AkınTekcan,MustafaCihangiroglu,MustafaCapraz,AylinCapraz,SerbülentYigit,AyseFeydaNursal,ElifMenekse,ZeynepHülyaDurmaz,HaticeDortokDemir,BurakOzcelik
AbstractThe course of coronavirus disease-2019 (COVID-19) differs from person to person. The relationship between the genetic variations of the host and the course of COVID-19 has been a matter of interest. In this study, we investigated whether Angiotensin-Converting Enzyme (ACE) ID, Methylenetetrahydrofolate Reductase (MTHFR) C677T, and Macrophage Migration Inhibitory Factor (MIF)-173GC variants are risk factors for the clinical course of COVID-19 disease in Turkish patients. One hundred COVID-19 patients were included in the study. The diagnosis of COVID-19 was made using Reverse Transcription Polymerase Chain Reaction (RT-PCR) and Chest Computed Tomography (CT). The patients were evaluated in 3 groups: intensive care, service, and outpatient treatment. ACE ID, MTHFR C677T, and MIF-173GC variants were genotyped by PCR-Restriction Fragment Length Polymorphism (RFLP) methods. When the genotype distribution between the groups was examined, it was found that the frequency of the ACE DD genotype and the D allele was higher in the intensive care group compared to the hospitalized and outpatient groups. MTHFR C677T CT genotype T allele and MIF-173GC, CC genotype C allele were more prevalent in the intensive care group compared to other groups. Patients with PCR-positive results had a higher MTHFR C677T C/C genotype and C allele. In CT-positive patients, the MTHFR C677T CT genotype and the MIF-173GC, G allele were more common. It is predicted that genetic predisposition may contribute to COVID-19 morbidity and mortality. Our results show that ACE ID, MTHFR C677T, and MIF-173GC variants affect the course of COVID-19 disease in the Turkish population.
Downregulation of fibrosis related hsa-miR-29c-3p in human CAKUT
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-06-08 , DOI: 10.1080/15257770.2023.2218430
NatasaMacak,IvanJovanovic,MajaZivkovic,KristinaMitrovic,MirjanaCvetkovic,MirjanaKostic,AleksandraStankovic
AbstractCongenital anomalies of the kidney and urinary tract (CAKUT) represent structural and functional urinary system malformations and take place as one of the most common congenital malformations with an incidence of 1:500. Ureteral obstruction-induced hydronephrosis is associated with renal fibrosis and chronic kidney diseases in the pediatric CAKUT. We aimed to construct interaction network of previously bioinformatically associated miRNAs with CAKUT differentially expressed genes in order to prioritize those associated with fibrotic process and to experimentally validate the expression of selected miRNAs in CAKUT patients compared to control group. We constructed interaction network of hsa-miR-101-3p, hsa-miR-101-5p and hsa-miR-29c-3p that showed significant association with fibrosis. The top enriched molecular pathway was extracellular matrix-receptor interaction (adjusted p = .0000263). We experimentally confirmed expression of three miRNAs (hsa-miR-29c-3p, hsa-miR-101-3p and hsa-miR-101-5p) in obstructed ureters (ureteropelvic junction obstruction and primary obstructive megaureter) and vesicoureteral reflux. The hsa-miR-29c-3p was shown to have lower expression in both patient groups compared to controls. Relative levels of hsa-miR-101-5p and hsa-miR-101-3p showed significant positive correlations in both groups of patients. Statistically significant correlation was observed between hsa-miR-101 (-3p and -5p) and hsa-miR-29c-3p only in the obstructed group. The significant downregulation of anti-fibrotic hsa-miR-29c-3p in obstructive CAKUT could explain activation of genes involved in fibrotic processes. As miRNAs are promising candidates in therapeutic approaches our results need further measurement of fibrotic markers or assessment of extent of fibrosis and functional evaluation of hsa-miR-29c.
Efficient chemical synthesis of N2-modified guanosine derivatives: a versatile probes for mRNA labeling
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-05-21 , DOI: 10.1080/15257770.2023.2215828
SenthilvelanAnnamalai,ShanmugasundaramMuthian,AnilkumarRKore
AbstractAn efficient method for the synthesis of N2-modified guanosine nucleotides such as N2-[benzyl-N-(propyl)carbamate]-guanosine-5′-O-monophosphate, N2-[benzyl-N-(propyl)carbamate]-guanosine-5′-O-diphosphate, N2-[benzyl-N-(propyl)carbamate]-guanosine-5′-O-triphosphate, and N2-[benzyl-N-(propyl)carbamate]-N7-methyl-guanosine-5′-O-diphosphate, starting from the corresponding nucleotide is described. The overall reaction involves the condensation between the exocyclic amine of guanosine nucleotide with 3-[(benzyloxycarbonyl)amino]propionaldehyde in aqueous methanol, followed by reduction using sodium cyanoborohydride to furnish the corresponding N2-modified guanosine nucleotide in moderate yield with high purity (>99.5%).
Genetic polymorphism of IL-17F rs763780 contributes to the susceptibility to bipolar disorder but not to schizophrenia in the Turkish population
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-05-12 , DOI: 10.1080/15257770.2023.2211124
YaseminOyaci,HasanMervanAytac,MustafaPehlivan,SacidePehlivan
AbstractThis study aims to investigate the genetic polymorphism in the interleukin-17F (IL-17F) (rs763780, 7488 A/G) gene in bipolar disorder (BD) and schizophrenia (SCZ) patients by comparing it with healthy controls considering clinical parameters. A sample of 107 patients with BD, 129 patients with SCZ, and 100 healthy volunteers were included. SCID-I was used to confirm the diagnosis according to DSM-IV-TR criteria. The Young Mania Rating Scale (YMRS) and the Hamilton Depression Rating Scale (HAM-D) were administered to BD patients. The Positive and Negative Symptoms Scale (PANSS) was applied to the patients with SCZ. PCR-RFLP was used to determine IL-17F gene polymorphism. Our results demonstrated that the distributions of the IL-17F genotype and the allele frequencies of BD patients were statistically significantly different from the control group. The AA genotype (OR: 0.283; 95% Cl: 0.140–0.573; p<.001) and A allele (OR: 0.333; 95% Cl: 0.171–0.646; p=.001) frequencies were significantly higher in the control group than in the BD group. The IL-17F genotype and the allele frequency distributions of SCZ patients were not statistically significantly different from the control group. When comparing scale scores due to the IL-17F genotype distributions in patients with BD or SCZ, there was no statistically significant difference between the groups of IL-17F genotypes. In summary, whereas the IL-17F polymorphism may be associated with BD, this polymorphism was not related to SCZ.
Has_circ_0048764 promotes breast cancer progression by sponging miR-578 and regulating HMGA2 expression
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-01-08 , DOI: 10.1080/15257770.2022.2155300
MingjianDing,DianluDai,WenhuaYang,CuizhiGeng,GuozhongCui
AbstractBackground Circular RNAs (circRNAs) function as important regulators in the progression of cancers. The role of circRNA_0048764 (circ_0048764) in the development of breast cancer (BC) remains inconclusive. This work investigates the biological function and molecular mechanism of circ_0048764 in BC.Methods Quantitative real-time PCR (qRT-PCR) was conducted to measure the expression levels of circ_0048764, microRNA-578 (miR-578) and high mobility group AT-hook 2 (HMGA2) mRNA. The viability of BC cells was examined by cell counting kit 8 (CCK-8) assay. Besides, cyclin D1, proliferating cell nuclear antigen (PCNA) and HMGA2 expression levels were detected by western blot. The migrative and invasive capability of BC cells were probed by transwell assay. The relationships between miR-578 and circ_0048764 or HMGA2 3′-UTR were validated by dual-luciferase reporter gene assay.Results Circ_0048764 was highly expressed in BC tissues and cells, which was significantly associated with tumor size (≥2 cm), lymph node status (positive), and higher TNM stage of BC patients. Circ_0048764 depletion suppressed the proliferative, migrative, and invasive abilities of BC cells, which was rescued by transfection of miR-578 inhibitors. The binding sites were verified between circ_0048764 and miR-578. HMGA2 was identified to be a target of miR-578 in BC cells, and circ_0048764 positively regulated HMGA2 expression in BC cells via repressing miR-578.Conclusion Circ_0048764 promotes BC cell growth, migration and invasion via absorbing miR-578 and up-regulating HMGA2.
Molecular docking and spectroscopic study of bovine serum albumin interaction with new anticancer Pt complex with isopentyl dithiocarbamate ligand
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-07-15 , DOI: 10.1080/15257770.2023.2233576
ZahraArabpourShiraz,NasrinSohrabi,MahboubeEslamiMoghadam,MohsenOftadeh
AbstractAlthough cisplatin is useful in the treatment of cancer, it has a series of side effects that limit its use. Dithiocarbamates reduce the toxicity of platinum due to their structure and the presence of S, and N donating groups. In this article, the interaction of [Pt(bpy)(isopentyl.dtc)]NO3, where bpy is bipyridine and isopentyl.dtc is isopentyl-dithiocarbamate, with BSA, bovine serum albumin has been studied. The molecular binding method, including UV-Vis and fluorescence titration, was carried out in conditions including pH = 7.4 and temperatures of 27 and 37 °C. The negative values of enthalpy (ΔH°b) and entropy (ΔS°b) show that the driving forces of this interaction are hydrogen and van der Waals, and the negative value of the Gibbs free energy, ΔG°b indicates that the interaction proceeds spontaneously. The fluorescence results showed that the quenching mechanism is the static type and the Stern Volmer constant, KSV, was also obtained. The fluorescence titration method data displayed that the quenching mechanism is static. Binding constant (Kb), binding point (n), Hill coefficients, nH, Hill constant, KH, number of binding sites, g, BSA melting temperature, Tm, were also obtained. Finally, the molecular docking method result shows the binding constant, Ki and binding free energy for the platinum complex are −6.53 and 16.39 kcal mol−1, respectively, and also the proper position of binding on BSA can be considered the site I in the subdomain IIA.
Synthesis and antiviral activity of 1,2,3-triazolyl nucleoside analogues with N-acetyl-d-glucosamine residue
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-03-24 , DOI: 10.1080/15257770.2023.2189914
BulatFGarifullin,LeysanRKhabibulina,MayaGBelenok,LiliyaFSaifina,VladimirVZarubaev,AlexanderVSlita,AlexandrinaSVolobueva,VyacheslavESemenov,VladimirEKataev
AbstractA series of 1,2,3-triazolyl nucleoside analogues bearing N-acetyl-D-glucosamine residue was synthesized by the copper-catalyzed alkyne-azide cycloaddition (CuAAC) reaction of N1-ω-alkynyl derivatives of uracil, 6-methyluracil, thymine and 3,4,6-tri-O-acetyl-2-deoxy-2-acetamido-β-D-glucopyranosyl azide. Antiviral assays revealed the lead compound 3f which showed both the same activity against the influenza virus A H1N1 (IC50=70.7 µM) as the antiviral drug Rimantadine in control (IC50=77 µM) and good activity against Coxsackievirus B3 (IC50=13.9 µM) which was one and a half times higher than the activity of the antiviral drug Pleconaril in control (IC50=21.6 µM). According to molecular docking simulations, the antiviral activity of the lead compound 3f against Coxsackie B3 virus can be explained by its binding to a key fragment of the capsid surface of this virus.
The investigation of host genetic variants of toll-like receptor 7 and 8 in COVID-19
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-02-14 , DOI: 10.1080/15257770.2023.2176515
GokhanBagci,OguzGundogdu,AyseNurPektas,BinnurBagci,OnurAvci,SinanGursoy,KenanKaygusuz,NazifElaldi
AbstractToll-like receptors (TLRs) recognize infectious agents and play an important role in the innate immune system. Studies have suggested that TLR single nucleotide polymorphisms (SNPs) are associated with poor antiviral responses against SARS-CoV-2. Therefore, we aimed to investigate the relationship of TLR7 and TLR8 (SNPs) with COVID-19 disease prognosis. A total of 120 COVID-19 patients, 40 outpatients, 40 clinical ward patients and 40 intensive care unit (ICU) patients were included in the study. TLR7 (rs179009), TLR8-129 C/G (rs3764879) and TLR8 Met1Val (rs3764880) SNPs were genotyped using the PCR-RFLP method. In female patients, individuals carrying AG genotype and G allele for TLR8 Met1Val SNP were found at a higher frequency in patients hospitalized in the ICU than in patients followed in the clinical ward (p < 0.05). In terms of the other two SNPs, no significant difference was found between the groups in females. Furthermore, in male patients, A allele of TLR7 rs179009 SNP was at a higher frequency in patients who have at least one comorbidity than in patients who have no comorbidity (p < 0.05). Our results suggest that TLR8 Met1Val SNP is important in the COVID-19 disease severity in females. Furthermore, TLR7 rs179009 SNP is important in male patients in the presence of comorbid diseases.
Unusual seven-membered ring sugars and nucleosides: synthesis and biological properties
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2022-11-30 , DOI: 10.1080/15257770.2022.2151623
StellaManta,NikolaosKollatos
AbstractMethods of the synthesis and the investigation of the properties of unnatural seven-memebered cyclic sugars and nucleosides, are of high interest. Septanoses provide conformationally more flexible sugars and due to their similarity to natural carbohydrates they have interesting and potentially useful physical, chemical, and biological properties. Additionally, nucleosides with seven-membered sugar moiety are commonly found in natural products and biologically active molecules. Modification of such nucleosides hold great promise as therapeutic agents. The present review describes the chemical synthesis and biological properties of septanoses as well as nucleosides containing septanosyl moieties.
The effect of DNA repair gene variants on COVID-19 disease: susceptibility, severity, and clinical course
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-01-28 , DOI: 10.1080/15257770.2023.2172183
NaciSenkal,IstemiSerin,SacidePehlivan,MustafaPehlivan,AlpayMedetalibeyoglu,TimurhanCebeci,HilalKonyaoglu,YaseminOyacı,GozdeYesilSayın,UmmuhanIsoglu-Alkac,TufanTukek,MuratKose
AbstractOxidative stress (OS), which leads to DNA damage, plays a role in the pathogenesis of Coronavirus disease 2019 (COVID-19). We aimed to evaluate the role of DNA repair gene variants [X-ray repair cross complementing 4 (XRCC4) rs28360071, rs6869366, and X-ray cross-complementary gene 1 (XRCC1) rs25487] in susceptibility to COVID-19 in a Turkish population. We also evaluated its effect on the clinical course of the disease. A total of 300 subjects, including 200 COVID-19 patients and 100 healthy controls, were included in this study. These variants were genotyped using polymerase chain reaction (PCR) and/or PCR-restriction fragment length polymorphism (RFLP) methods. The patients were divided into three groups: those with a mild or severe infection; those who died or lived at the 28-day follow-up; those who required inpatient treatment or intensive care. There were 87 women (43.5%) and 113 men (56.5%) in the patient group. Hypertension was the most common comorbidity (26%). In the patient group, XRCC4 rs6869366 G/G genotype and G allele frequency were increased compared to controls, while XRCC4 rs6869366 G/T and T/T genotype frequencies were found to be higher in controls compared to patients. For XRCC1 rs25487, the A/A and A/G genotypes were significantly associated with COVID-19 disease. All of the patients hospitalized in the intensive care unit had the XRCC4 rs6869366 G/G genotype. In this study, we evaluated for the first time the impact of DNA repair gene variants on COVID-19 susceptibility. Results suggested that XRCC4 rs6869366 and XRCC1 rs25487 were associated with COVID-19 suspectibility and clinical course.
Interactive effects of FTO rs9939609 and obesogenic behavioral factors on adiposity-related anthropometric and metabolic phenotypes
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-02-23 , DOI: 10.1080/15257770.2023.2182886
SobiaRana,HinaNawaz
AbstractNumerous genetic variants have been linked to obesity predisposition, however, the interplay of genetic and behavioral factors is very crucial in determining the final phenotype. Therefore, this study examined the interactive effects of the FTO rs9939609 and various obesogenic behavioral factors on adiposity-related anthropometric and metabolic phenotypes in a sample of Pakistani population. A total of 612 participants encompassing 306 overweight/obese (cases) and an equal number (306) of age- and sex-matched normal-weight (controls) individuals were included in the study. Adiposity-related anthropometric parameters were collected by taking corresponding body measurements by following standard procedures. The metabolic parameters were assessed by performing corresponding biochemical assays. A standard questionnaire was devised for the collection of adiposity-related behavioral information. The FTO rs9939609 was genotyped by employing TaqMan allelic discrimination assay. The data was analyzed by using SPSS software. Interactive effects of the FTO rs9939609 and behavioral factors on obesity-related anthropometric and metabolic phenotypes were examined via linear regression by adjusting potential confounders and making correction for multiple comparisons. The results implied that the interaction between the FTO rs9939609 and low physical activity may significantly increase various adiposity-related anthropometric variables (p < 0.05). However, no such interactive effects were found on any adiposity-related metabolic variable. In conclusion, the interaction between the FTO rs9939609 and low physical activity may have a significant impact on obesity-related anthropometric traits in the Pakistani population.
Genetic association of vitamin D receptor gene with female infertility
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-07-26 , DOI: 10.1080/15257770.2023.2236167
MussaratAshraf,HaqNawazKhan,RababIbrahim,MaheenShahid,SherKhan,AmbrinFatima,SaifUllah,RehanaRehman
AbstractBackground Infertility is defined as failure to achieve a clinical pregnancy after 12 months of unprotected intercourse. It affects 15% of couples globally and 22% of couples within Pakistan. Female infertility can be caused by numerous genetic or environmental factors including hormone imbalances and exposure to chemicals or radiation. The prevalence of vitamin D deficiency among the adult population was reported to be 14–59% with a higher prevalence in Asian countries. Furthermore, the expression of Vitamin D receptor (VDR) can play a vital role in the reproductive organs of females. Hence, the aim of our present study was to check the association of VDR polymorphisms with infertile females. For this purpose, blood samples were collected for genotyping of four known VDR mutations [FokI (rs2228570), TaqI (rs731236), ApaI (rs7975232), and BsmI (rs1544410)] via PCR-based RFLP assay.Results Genotyping indicated that FokI, TaqI, and ApaI are associated with infertility (p = 0.004*, p = 0.013*, and p = 0.033*, respectively). However, BsmI did not show any significance. Multinomial regression analysis indicated that FokI heterozygous genotypes increase the risk of infertility by 2.5 times (hetero: OR = 2.5, 95%, p = 0.001*) as compared to wild type. Heterozygous genotypes of TaqI and ApaI were found to play a protective role and reduce the risk of infertility by 58 and 52%, respectively [TaqI: OR = 0.42, 95%, p = 0.004*, ApaI: OR = 0.48, 95%, p = 0.01*, respectively] as compared to wild type. Multinomial logistic regression analysis was also performed for allelic data as well.Conclusion Thus, it could be summarized that among the studied polymorphisms of VDR, FokI SNP greatly increased the risk of infertility, while TaqI and ApaI genotypes protect from infertility. However, BsmI does not influence the risk of infertility in Pakistani females.
The lncRNA expression profile signature of leukemia stem cells is altered upon PI3K/mTOR inhibition: an in vitro and in silico study
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-07-20 , DOI: 10.1080/15257770.2023.2236143
CaglaKayabasi,CumhurGunduz
AbstractGenetic and/or epigenetic alterations in hematopoietic stem cells (HSCs) contribute to leukemia stem cell (LSC) formation. We aimed to identify alterations in the lncRNA expression profile signature of LSCs upon inhibition of PI3K/Akt/mTOR signaling, which provides selective advantages to LSCs. We also aimed to elucidate the potential interaction networks and functions of differentially expressed lncRNAs (DELs). We suppressed PI3K/Akt/mTOR signaling in LSC and HSC cell-lines by specific PI3K/mTOR dual-inhibitor (VS-5584) and confirmed the inhibition by antibody-array. We defined DELs by qRT-PCR. Increased SRA, ZEB2-AS1, antiPeg11, DLX6-AS, SNHG4, and decreased H19, PCGEM1, CAR-Intergenic-10, L1PA16, IGF2AS, and SNHG5 levels (|log2fold-change|>5) were strictly associated with PI3K/Akt/mTOR pathway inhibition in LSC. We performed in silico analyses for DELs. ZEB2-AS1 was found to be specifically expressed in normal bone marrow and predominantly lower in leukemic cell-lines. Three sub-clusters were identified for DELs and they were associated with “abnormality of multiple cell lineages in the bone marrow.” DELs were most highly enriched for “glucuronidation” Reactome pathway and “ascorbate and aldarate metabolism” and “inositol phosphate metabolism” KEGG pathways. Transcription factors, MBD4, NANOG, PAX6, RELA, CEBPB, and CEBPA were predicted to be associated with the DEL profile. SRA was predicted to interact with CREB1, RARA, and PPARA. The possible DELs’ targets were predicted to form six ontological groups, be highly enriched for phosphoprotein, and be involved in “PPAR signaling pathway” and “ChREBP regulation by carbohydrates and cAMP.” These results will help to elucidate the roles of lncRNAs in the mechanisms that provide selective advantages to leukemia stem cells.
Artificial intelligence model with deep learning in nonalcoholic fatty liver disease diagnosis: genetic based artificial neural networks
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2022-11-30 , DOI: 10.1080/15257770.2022.2152046
YakupÜlger,AnılDelik
AbstractNonalcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver disease in the world. The NAFLD spectrum includes simple steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Genetic, nutritional factors, obesity, insulin resistance, gut microbiota are among the risk factors for NAFLD. The genetic variant Patatin-like phospholipase domain-containing protein 3 (PNPLA3) plays an important role in the development of a number of liver diseases ranging from steatosis, chronic hepatitis, cirrhosis and HCC. Due to the increase in the prevalence of NAFLD, new models are being developed with machine learning, deep learning, artificial neural network (ANN) algorithms in the field of artificial intelligence (AI) to determine low-cost, noninvasive diagnostic methods. Models developed with ANN from AI modules are important in order to examine biochemical and genomic information in detail in the diagnosis of NAFLD. The aim of this study is to develop a simple ANN model using biochemical and genotypic parameters in the diagnosis of NAFLD. A total of 300 patients followed up with the diagnosis of NAFLD and 100 controls were included in the study. The data set was divided into two as training and test set. Genotyping of PNPLA3 (CC, CG, GG) as genomic analysis was performed with real time PCR device. The algorithm used for the diagnosis of NAFLD was designed using age, body mass index (BMI), mean platelet volume (MPV), insulin resistance (IR), alanine aminotransferase (ALT), genotype PNPLA3 (CC, CG, GG) parameters. MLP Classifier algorithm from ANN was used in the development of the model. ANN algorithms are used in python programming language. Statistical analyzes were made in SPSS program. Percent accuracy, area under the ROC curve, confusion matrix, Positive (PPV) and Negative Predicted Value (NPV) values, precision, recall, and f1-score results were determined. The accuracy percentage was determined as 0.979 in the train set and 0.970 in the test set. The Log Loss value was set to 0.09. The developed neural network achieved an accuracy percentage of 97.0% during testing, with an area under the ROC curve value of 0.95. We think that the ANN model developed with genomic and biochemical parameters can be used as a cost-effective, noninvasive new predictive diagnostic model in clinical practice in the diagnosis of NAFLD.
Association between CDKN1A gene rs1801270 polymorphisms and susceptibility to colorectal cancser in an Iranian population
Nucleosides, Nucleotides & Nucleic Acids ( IF 0 ) Pub Date : 2023-01-24 , DOI: 10.1080/15257770.2023.2169934
NedaZali,SanazSavabkar,RaziyeTajali,VahidChaleshi,EhsanNazemalhosseiniMojarad,MohsenVahedi,MehrdadHashemi,HamidAsadzadehAghdaei
AbstractCDKN1A gene is implicated in cell differentiation, development process, repair, apoptosis, senescence, migration, and tumorigenesis. Somatic alterations and polymorphisms may interfere in the function of CDKN1A, and this could affect the individual susceptibility to colorectal cancer (CRC). Here in, we evaluated the importance of single nucleotide polymorphic variants in codon 31 of CDKN1A (rs1801270: C > A) for the development of colorectal cancer in an Iranian population. A total of 150 CRC patients and 150 healthy controls were enrolled in this study. Genomic DNA was extracted from peripheral blood specimens. Genotypes were determined using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In CRC patients, the genotype frequencies detected were 90%, 8.0% and 2.0%2 for CC, AC and AA genotypes while the genotype frequencies in control group were 78%, 20.7% and 1.35% 1.35% for CC, AC and AA genotype, respectively. There were statistically significant differences in the distribution of CDKN1A rs1801270 genotypes and allele frequencies between colorectal cancer patients and healthy controls (p value = 0.021). Also, results indicated a significant negative association between AC genotype and risk of colorectal cancer occurrence. (Odds ratio (OR)=0.357; 95% confidence interval (CI)=0.168–0.760, p = 0.007). Our data suggest that the AC genotype may have a protective role in the development of CRC in an Iranian population.
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自引率 H-index SCI收录状况 PubMed Central (PML)
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