LINE1 Research Articles

Peripheral mitochondrial DNA, telomere length and DNA methylation as predictors of live birth inin vitrofertilization cycles.

To evaluate whether telomere length (TL), mitochondrial-DNA (mt-DNA) or epigenetic age estimators based on DNA methylation (DNAm) pattern could be considered reliable predictors of in-vitro-fertilization (IVF) success in terms of live birth rate. Prospective cohort study. Infertility Unit of the Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico. 181 women aged 37-39 years who underwent IVF at a single-centre between January 2017 and December 2018. On the day of recruitment, blood samples were collected, and genomic DNA was isolated from white blood cells. TL, mt-DNA and DNAm assessment was performed using quantitative real-time polymerase chain reaction (qPCR). Biological age (DNAm age) was computed as the algorithm based on methylation pattern of five genes. Epigenetic age acceleration was estimated from the residuals of the linear model of epigenetic age regressed on chronological age. Long Interspersed Nuclear Elements (LINE)-1 methylation pattern was used as a surrogate for global DNA methylation. This study investigated whether peripheral TL, mt-DNA and DNAm could predict live birth in IVF cycles. TL, mt-DNA and LINE-1 methylation were not associated with IVF success. Conversely, DNAm age resulted significantly lower in women who had a live birth compared to women who did not (36.1 ± 4.2 and 37.3 ± 3.3 years, respectively, p = 0.04). For DNAm age, odds ratio (OR) for live birth per year of age was 0.90 (95%CI: 0.82-0.99, p = 0.036) after adjusting for FSH and antral follicle count (AFC) and 0.90 (95%CI: 0.82-0.99, p = 0.028) after adjusting also for number of oocytes retrieved. A significant association also emerged for epigenetic age acceleration after adjustments (OR = 0.91, 95%CI: 0.83-1.00, p = 0.048). DNAm age is associated with IVF success but the magnitude of this association is insufficient to claim a clinical use. However, our findings are promising and warrant further investigation. Assessment of biological age using different epigenetic clocks or focusing on different tissues may reveal new predictors of IVF success.

Individual and mixtures of metal exposures in associations with biomarkers of oxidative stress and global DNA methylation among pregnant women

BackgroundPrenatal exposure to metals has been linked with adverse pregnancy outcomes. Oxidative stress and epigenetic changes are potential mechanisms of action. ObjectivesWe aimed to examine the associations of individual and mixtures of metal exposures with oxidative stress and DNA methylation among pregnant women. MethodsWe measured a panel of 16 metals and 3 oxidative stress biomarkers including 8-hydroxydeoxyguanosine (8-OHdG), 4-hydroxy-2-nonenal-mercapturic acid (HNE-MA) and 8-isoprostaglandin F2α (8-isoPGF2α) in urine from 113 pregnant women in a Chinese cohort. Biomarkers of global DNA methylation including Alu and long interspersed nucleotide element-1 (LINE-1) in cord blood were measured. Multivariable linear regression and Bayesian kernel machine regression (BKMR) models were separately applied to estimate the associations between individual and mixtures of metal exposures and biomarkers of oxidative stress and global DNA methylation. ResultsIn single-metal analyses, we observed positive associations between 11 metals [arsenic (As), cadmium (Cd), thallium (Tl), barium (Ba), nickel (Ni), vanadium (V), cobalt (Co), zinc (Zn), copper (Cu), selenium (Se) and molybdenum (Mo)] and at least one of oxidative stress biomarkers (all FDR-adjusted P-values < 0.05). In mixture analyses, we found positive overall associations of metal mixtures with 8-OHdG and 8-isoPGF2α, and Se was the most important predictor. There was no evidence on associations of urinary metals as individual chemicals and mixtures with Alu and LINE-1 methylation. ConclusionUrinary metals as individual chemicals and mixtures were associated with increased oxidative stress, especially Se.

LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion.

How gene expression is controlled to preserve human T cell quiescence is poorly understood. Here we show that non-canonical splicing variants containing long interspersed nuclear element 1 (LINE1) enforce naive CD4+ T cell quiescence. LINE1-containing transcripts are derived from CD4+ T cell-specific genes upregulated during T cell activation. In naive CD4+ T cells, LINE1-containing transcripts are regulated by the transcription factor IRF4 and kept at chromatin by nucleolin; these transcripts act in cis, hampering levels of histone 3 (H3) lysine 36 trimethyl (H3K36me3) and stalling gene expression. T cell activation induces LINE1-containing transcript downregulation by the splicing suppressor PTBP1 and promotes expression of the corresponding protein-coding genes by the elongating factor GTF2F1 through mTORC1. Dysfunctional T cells, exhausted in vitro or tumor-infiltrating lymphocytes (TILs), accumulate LINE1-containing transcripts at chromatin. Remarkably, depletion of LINE1-containing transcripts restores TIL effector function. Our study identifies a role for LINE1 elements in maintaining T cell quiescence and suggests that an abundance of LINE1-containing transcripts is critical for T cell effector function and exhaustion.

The non-LTR retrotransposons of Entamoeba histolytica: genomic organization and biology.

Genome sequence analysis of Entamoeba species revealed various classes of transposable elements. While E. histolytica and E. dispar are rich in non-long terminal repeat (LTR) retrotransposons, E. invadens contains predominantly DNA transposons. Non-LTR retrotransposons of E. histolytica constitute three families of long interspersed nuclear elements (LINEs), and their short, nonautonomous partners, SINEs. They occupy ~ 11% of the genome. The EhLINE1/EhSINE1 family is the most abundant and best studied. EhLINE1 is 4.8kb, with two ORFs that encode functions needed for retrotransposition. ORF1 codes for the nucleic acid-binding protein, and ORF2 has domains for reverse transcriptase (RT) and endonuclease (EN). Most copies of EhLINEs lack complete ORFs. ORF1p is expressed constitutively, but ORF2p is not detected. Retrotransposition could be demonstrated upon ectopic over expression of ORF2p, showing that retrotransposition machinery is functional. The newly retrotransposed sequences showed a high degree of recombination. In transcriptomic analysis, RNA-Seq reads were mapped to individual EhLINE1 copies. Although full-length copies were transcribed, no full-length 4.8kb transcripts were seen. Rather, sense transcripts mapped to ORF1, RT and EN domains. Intriguingly, there was strong antisense transcription almost exclusively from the RT domain. These unique features of EhLINE1 could serve to attenuate retrotransposition in E. histolytica.

Phyllanthus debilis Methanolic Extract Reduces the Viability of Human Colorectal Adenocarcinoma (HT-29) Cells and Increases LINE-1 and Alu DNA Methylation

Phyllanthus debilis was shown to have a strong anti-proliferative effect on cancer cells with less effect in normal cells. However, its mechanism on the epigenetic mechanism at repeat sequences is unknown. This study was carried out to determine the effect of P. debilis extract on long interspersed nuclear element-1 (LINE-1) and Alu DNA methylation. The anti-proliferative effect of P. debilis methanolic extract on human colorectal adenocarcinoma (HT-29) at 24 hours was done using trypan blue assay. LINE-1 and Alu methylation measurement on the HT-29 cell line was done after 72 hours of treatment using Pyrosequencing. The effect of P. debilis methanolic extract at 24 hours on the viability of HT-29 cells was dose-dependent with the half-maximal inhibitory concentration (IC50) concentration of 0.1 mg/mL. Treatment with P. debilis methanolic extract showed significantly higher Alu DNA methylation when compared with the untreated HT-29 cells (37.0 ± 2.5% vs 32.3 ± 4.3%, p&lt;0.05). Similarly, treatment with 5-aza-2-deoxycytidine also significantly increased the Alu DNA methylation compared with the untreated HT-29 cells (46.0 ± 2.3% vs 37.0 ± 2.5%, p&lt;0.05). For LINE-1, there was a significant increase of LINE-1 methylation when treated with P. debilis extract (80.3 ± 1.3% vs 76.3 ± 2.1%, p&lt;0.05) and with 5-aza-2-deoxycytidine (81.8 ± 4.3% vs 76.3 ± 2.1%, p&lt;0.05) when compared with untreated cells. In conclusion, treatment of P. debilis methanolic extract on HT-29 cell line reduces the viability of HT-29 cells and increases the methylation of Alu and LINE 1. Similar changes in methylation were also seen in the 5-aza treatment. These epigenetic changes by P. debilis methanolic extract may contribute to its anti-cancer properties.

Transcriptome Analysis Reveals Higher Levels of Mobile Element-Associated Abnormal Gene Transcripts in Temporal Lobe Epilepsy Patients.

Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy, and temporal lobe epilepsy patients with hippocampal sclerosis (TLE-HS) show worse drug treatment effects and prognosis. TLE has been shown to have a genetic component, but its genetic research has been mostly limited to coding sequences of genes with known association to epilepsy. Representing a major component of the genome, mobile elements (MEs) are believed to contribute to the genetic etiology of epilepsy despite limited research. We analyzed publicly available human RNA-seq-based transcriptome data to determine the role of mobile elements in epilepsy by performing de novo transcriptome assembly, followed by identification of spliced gene transcripts containing mobile element (ME) sequences (ME-transcripts), to compare their frequency across different sample groups. Significantly higher levels of ME-transcripts in hippocampal tissues of epileptic patients, particularly in TLE-HS, were observed. Among ME classes, short interspersed nuclear elements (SINEs) were shown to be the most frequent contributor to ME-transcripts, followed by long interspersed nuclear elements (LINEs) and DNA transposons. These ME sequences almost in all cases represent older MEs normally located in the intron sequences. For protein coding genes, ME sequences were mostly found in the 3′-UTR regions, with a significant portion also in the coding sequences (CDSs), leading to reading frame disruption. Genes associated with ME-transcripts showed enrichment for the mRNA splicing process and an apparent bias in epileptic transcriptomes toward neural- and epilepsy-associated genes. The findings of this study suggest that abnormal splicing involving MEs, leading to loss of functions in critical genes, plays a role in epilepsy, particularly in TLE-HS, thus providing a novel insight into the molecular mechanisms underlying epileptogenesis.

Abstract 11232: Role of Line-1 Retrotransposition in Atherosclerosis

Introduction: LINE-1 (L1) retrotransposons are a class of transposable elements comprising ~21% of the human genome. L1-retrostransposed elements move within the genome, where they profoundly alter gene function. Somatic L1 insertions, or retrotranspositions (RTNs), were implicated in multiple diseases including cancer. However, this literature has been mainly confined to epithelial tissue, and the role of L1 in cardiovascular diseases is unknown. Specifically, whether L1 presence and activity in vascular cells has a functional role in atherosclerosis, a disease characterized by extensive vascular remodeling, inflammation and plaque formation, remains unexplored. Hypothesis: L1 expression and RTN in vascular endothelial cells (ECs) leads to endothelial activation in atherosclerosis. Methods: L1 mRNA expression was analyzed by qRT-PCR in postmortem coronary artery specimens from patients with atherosclerosis and non-diseased controls. Immunofluorescence (IF) in coronary tissue was performed for ORF1p, a L1 encoded polypeptide required for active RTN. In vitro, qRT-PCR was used to assess L1 expression in primary human aortic ECs (HAEC) treated with proatherogenic inflammatory stimuli TNFα, IL6, oxidized LDL (oxLDL) and IL1β. Active RTN was assessed by FACS and IF in a purpose-built human umbilical vein EC line (CRL2922) L1 RTN detection system. Results: L1 mRNA was increased in atherosclerotic human coronary arteries and positively correlated with age and histologically-assessed disease severity. ORF1p expression increased in EC of atherosclerotic plaques indicative of increased L1 activity. L1 expression and retrotransposition was induced in ECs in vitro by TNFα, IL-6 and oxLDL. Finally, de novo L1 insertion alone resulted in upregulation of genes involved in EC activation and atherosclerosis (ICAM1, MCP-1, IL6, NOR), and this effect was further enhanced by co-treatment with TNFα, IL-6 and oxLDL. Conclusions: Our results identify a disease-related increase in L1 in the vascular endothelium under atherosclerotic conditions that contributes to EC activation. These data support a permissive environment during atherosclerosis for L1 activity and unveil a previously unrecognized role for L1 in this disease’s pathophysiology.

Human Recombinant DNase I (Pulmozyme®) Inhibits Lung Metastases in Murine Metastatic B16 Melanoma Model That Correlates with Restoration of the DNase Activity and the Decrease SINE/LINE and c-Myc Fragments in Blood Cell-Free DNA.

Tumor-associated cell-free DNAs (cfDNA) play an important role in the promotion of metastases. Previous studies proved the high antimetastatic potential of bovine pancreatic DNase I and identified short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs)and fragments of oncogenes in cfDNA as the main molecular targets of enzyme in the bloodstream. Here, recombinant human DNase I (commercial name Pulmozyme®), which is used for the treatment of cystic fibrosis in humans, was repurposed for the inhibition of lung metastases in the B16 melanoma model in mice. We found that Pulmozyme® strongly reduced migration and induced apoptosis of B16 cells in vitro and effectively inhibited metastases in lungs and liver in vivo. Pulmozyme® was shown to be two times more effective when administered intranasally (i.n.) than bovine DNase I, but intramuscular (i.m.) administration forced it to exhibit as high an antimetastatic activity as bovine DNase I. Both DNases administered to mice either i.m. or i.n. enhanced the DNase activity of blood serum to the level of healthy animals, significantly decreased cfDNA concentrations, efficiently degraded SINE and LINE repeats and c-Myc fragments in the bloodstream and induced apoptosis and disintegration of neutrophil extracellular traps in metastatic foci; as a result, this manifested as the inhibition of metastases spread. Thus, Pulmozyme®, which is already an approved drug, can be recommended for use in the treatment of lung metastases.

Zidovudine inhibits telomere elongation, increases the transposable element LINE-1 copy number and compromises mouse embryo development.

Millions of pregnant, HIV-infected women take reverse transcriptase inhibitors, such as zidovudine (azidothymidine or AZT), during pregnancy. Reverse transcription plays important roles in early development, including regulation of telomere length (TL) and activity of transposable elements (TE). So we evaluated the effects of AZT on embryo development, TL, and copy number of an active TE, Long Interspersed Nuclear Element 1 (LINE-1), during early development in a murine model. Experimental study. In vivo fertilized mouse zygotes from B6C3F1/B6D2F1 mice were cultured for 48h in KSOM with no AZT (n = 45), AZT 1μM (n = 46) or AZT 10μM (n = 48). TL was measured by single-cell quantitative PCR (SC-pqPCR) and LINE-1 copy number by qPCR. The percentage of morulas at 48h, TL and LINE-1 copy number were compared among groups. Exposure to AZT 1μM or 10μM significantly impairs early embryo development. TL elongates from oocyte to control embryos. TL in AZT 1μM embryos is shorter than in control embryos. LINE-1 copy number is significantly lower in oocytes than control embryos. AZT 1μM increases LINE-1 copy number compared to oocytes controls, and AZT 10μM embryos. AZT at concentrations approaching those used to prevent perinatal HIV transmission compromises mouse embryo development, prevents telomere elongation and increases LINE-1 copy number after 48h treatment. The impact of these effects on the trajectory of aging of children exposed to AZT early during development deserves further investigation.

Factors Regulating the Activity of LINE1 Retrotransposons.

LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.

Characterization of full-length LINE-1 insertions in 154 genomes

Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations.

Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead.

The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.

Whole Ovary Immunofluorescence, Clearing, and Multiphoton Microscopy for Quantitative 3D Analysis of the Developing Ovarian Reserve in Mouse.

Female fertility and reproductive lifespan depend on the quality and quantity of the ovarian oocyte reserve. An estimated 80% of female germ cells entering meiotic prophase I are eliminated during Fetal Oocyte Attrition (FOA) and the first week of postnatal life. Three major mechanisms regulate the number of oocytes that survive during development and establish the ovarian reserve in females entering puberty. In the first wave of oocyte loss, 30-50% of the oocytes are eliminated during early FOA, a phenomenon that is attributed to high Long interspersed nuclear element-1 (LINE-1) expression. The second wave of oocyte loss is the elimination of oocytes with meiotic defects by a meiotic quality checkpoint. The third wave of oocyte loss occurs perinatally during primordial follicle formation when some oocytes fail to form follicles. It remains unclear what regulates each of these three waves of oocyte loss and how they shape the ovarian reserve in either mice or humans. Immunofluorescence and 3D visualization have opened a new avenue to image and analyze oocyte development in the context of the whole ovary rather than in less informative 2D sections. This article provides a comprehensive protocol for whole ovary immunostaining and optical clearing, yielding preparations for imaging using multiphoton microscopy and 3D modeling using commercially available software. It shows how this method can be used to show the dynamics of oocyte attrition during ovarian development in C57BL/6J mice and quantify oocyte loss during the three waves of oocyte elimination. This protocol can be applied to prenatal and early postnatal ovaries for oocyte visualization and quantification, as well as other quantitative approaches. Importantly, the protocol was strategically developed to accommodate high-throughput, reliable, and repeatable processing that can meet the needs in toxicology, clinical diagnostics, and genomic assays of ovarian function.

1221Baseline Global DNA Hypermethylation Increase the Risk of Cerebrovascular Disease Mortality in Japanese Population

Abstract Background DNA methylation plays an important role in progression of cardiovascular disease (CVD). The methylation status of long interspersed nuclear element-1 (LINE-1) reflects the global DNA methylation level and is associated with lipid profiles and glycemia. We conducted a longitudinal study to examine the association between LINE-1 DNA methylation and CVD mortality in a Japanese elderly population. Methods We targeted for 357 subjects (143 men and 214 women) who were more than 60 years, participated in the health checkup in 1990, and had no clinical history of cancer, stroke, or ischemic heart disease. During 29 years of follow-up period, total 69 subjects were died from CVD, and died of cerebrovascular disease (CBD) and ischemic heart disease (IHD) were 25 and 13, respectively. LINE-1 DNA methylation was measured using PBMCs. We defined the hypermethylation group as greater than median of the LINE-1 DNA methylation levels and hypomethylation group as others. Multivariable Hazard ratios (HRs) for each disease mortality were calculated by the Cox proportional hazard model. We adjusted for age, sex, smoking habits, and alcohol consumption. Results Significantly higher HRs for CVD and CBD mortality were observed in the hypermethylation group compared to the hypomethylation group (CVD: HR 1.67 [95%CI 1.02-2.73], CBD: HR 3.29 [95%CI 1.29-8.40]). However, IHD mortality did not associated with LINE-1 DNA methylation. Conclusions We found that LINE-1 DNA hypermethylation in PBMCs was associated with high CVD mortality, especially CBD mortality. Key messages Higher levels of LINE-1 methylation in PBMCs can be a predictive marker for CBD risk

IMPACT OF SUPEROVULATION AND IN VITRO FERTILIZATION ON LINE 1 COPY NUMBER AND TELOMERE LENGTH IN C57BL/6J MICE BLASTOCYSTS

Over 15 million babies have been conceived by IVF, yet debate about its safety to offspring continues. We hypothesized that superovulation and in vitro fertilization (IVF) promote genomic changes, including altered telomere length (TL) and activation of the retrotransposon LINE-1 (L1), and tested this hypothesis in a mouse model.

Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin.

Trematode parthenitae have long been believed to form clonal populations, but clonal diversity has been discovered in this asexual stage of the lifecycle. Clonal polymorphism in the model species Himasthla elongata has been previously described, but the source of this phenomenon remains unknown. In this work, we traced cercarial clonal diversity using a simplified amplified fragment length polymorphism (SAFLP) method and characterised the nature of fragments in diverse electrophoretic bands. The repetitive elements were identified in both the primary sequence of the H. elongata genome and in the transcriptome data. Long-interspersed nuclear elements (LINEs) and long terminal repeat retrotransposons (LTRs) were found to represent an overwhelming majority of the genome and the transposon transcripts. Most sequenced fragments from SAFLP pattern contained the reverse transcriptase (RT, ORF2) domains of LINEs, and only a few sequences belonged to ORFs of LTRs and ORF1 of LINEs. A fragment corresponding to a CR1-like (LINE) spacer region was discovered and named CR1-renegade (CR1-rng). In addition to RT-containing CR1 transcripts, we found short CR1-rng transcripts in the redia transcriptome and short contigs in the mobilome. Probes against CR1-RT and CR1-rng presented strikingly different pictures in FISH mapping, despite both being fragments of CR1. In silico data and Southern blotting indicated that CR1-rng is not tandemly organised. CR1 involvement in clonal diversity is discussed.

Bazı Domates Hatlarının Demir Noksanlığına Dayanıklılıklarının Belirlenmesi

Bu çalışmanın amacı, bazı domates hatlarının demir noksanlığına dayanıklılıklarının belirlenmesidir. Bu amaçla 445 g kuvars kumu ortamında, 12×3 (hat × demir dozu) şeklinde faktöriyel deneme yürütülmüştür. 12 farklı Tarbio (TB) domates hattına Fe-EDDHA formunda uygulanan demir dozları: Noksan (0,2 µM Fe), yeterli (45 µM Fe), yeterli (100 µM Fe)’dir. Denemede her muamele 3 tekerrürlü yapılmıştır. pH’sı 6,0’a ayarlı bitki besin çözeltisine yukarıda bildirilen demir konsantrasyonlarında Fe-EDDHA ilave edilmiştir. Bu şekilde farklı konsantrasyonlarda demir içeren besin çözeltisi deneme süresince günlük 50 mL olacak şekilde uygulanmıştır. Sera şartlarında deneme 50 gün sürdürülmüştür. Demir noksanlığı şartlarında birinci ana grupta TB-01, TB-10, TB-22 ve TB-65 nolu hatlar; ikinci ana grupta ise TB-14, TB-18, TB-28, TB-31, TB-35, TB-40, TB-90 ve TB-122 nolu hatlar yer almıştır. Birbirinden en uzak hatlar TB-01 ve TB-14 numaralı hatlar olup, bu hatlar karşılaştırıldığında TB-14 numaralı hattın demir noksalığı şartlarında kuru madde miktarı, klorofil-a, klorofil-b, toplam klorofil, karotenoid kapsamları ve yaprakta ferrik redüktaz aktivitesine ilişkin değerlerin TB-01 numaralı hatta göre daha yüksek olduğu tespit edilmiştir. Buna rağmen, demir noksanlığı şartlarında birbirine en uzak hatlar olmakla birlikte, TB-01 nolu hattın aktif demir kapsamının, kökte ferrik redüktaz aktivitesinin ve kök katyon değişim kapasitesinin TB-14 numaralı hatta göre daha yüksek olduğu görülmüştür. Demir noksanlığı şartlarında yetiştirilen domates hatlarından TB-18 ve TB-28 numaralı hatların birbirine en yakın hatlar oldukları da tespit edilmiştir.

Neighborliness: Finding God’s Beauty Across Dividing Lines, by David Docusen

Neighborliness: Finding God’s Beauty Across Dividing Lines, by David Docusen

Polyphenol-Rich Aronia melanocarpa Juice Consumption Affects LINE-1 DNA Methylation in Peripheral Blood Leukocytes in Dyslipidemic Women.

Cardiovascular disease (CVD) is associated with alterations in DNA methylation and polyunsaturated fatty acid (PUFA) profile, both modulated by dietary polyphenols. The present parallel, placebo-controlled study (part of the original clinical study registered as NCT02800967 at www.clinicaltrials.gov) aimed to determine the impact of 4-week daily consumption of polyphenol-rich Aronia melanocarpa juice (AMJ) treatment on Long Interspersed Nucleotide Element-1 (LINE-1) methylation in peripheral blood leukocytes and on plasma PUFAs, in subjects (n = 54, age range of 40.2 ± 6.7 years) at moderate CVD risk, including an increased body mass index, central obesity, high normal blood pressure, and/or dyslipidemia. The goal was also to examine whether factors known to affect DNA methylation (folate intake levels, MTHFR C677T gene variant, anthropometric and metabolic parameters) modulated the LINE-1 methylation levels upon the consumption of polyphenol-rich aronia juice. Experimental analysis of LINE-1 methylation was done by MethyLight method. MTHFR C677T genotypes were determined by the polymerase chain reaction–restriction fragment length polymorphism method, and folate intake was assessed by processing the data from the food frequency questionnaire. PUFAs were measured by gas–liquid chromatography, and serum lipid profile was determined by using Roche Diagnostics kits. The statistical analyses were performed using Statistica software package. In the comparison after vs. before the treatment period, in dyslipidemic women (n = 22), we observed significant decreases in LINE-1 methylation levels (97.54 ± 1.50 vs. 98.39 ± 0.86%, respectively; P = 0.01) and arachidonic acid/eicosapentaenoic acid ratio [29.17 ± 15.21 vs. 38.42 (25.96–89.58), respectively; P = 0.02]. The change (after vs. before treatment) in LINE-1 methylation directly correlated with the presence of MTHFR 677T allele, average daily folate intake, and the change in serum low-density lipoprotein cholesterol but inversely correlated with the change in serum triacylglycerols (R = 0.72, R2 = 0.52, adjusted R2 = 0.36, P = 0.03). The current results imply potential cardioprotective effects of habitual polyphenol-rich aronia juice consumption achieved through the modifications of DNA methylation pattern and PUFAs in subjects at CVD risk, which should be further confirmed. Hence, the precision nutrition-driven modulations of both DNA methylation and PUFA profile may become targets for new approaches in the prevention of CVD.

Correlation of LINE-1 Hypomethylation With Size and Pathologic Extent of Dysplasia in Colorectal Tubular Adenomas.

INTRODUCTION:Conventional adenomas (tubular adenoma [TA] or tubulovillous adenoma) and sessile serrated lesions (SSLs) are neoplastic precancerous lesions frequently detected in patients undergoing average risk screening colonoscopy and polyp surveillance. Metachronous risk stratification of adenomas is currently limited to histologic features and size of polyps. We report long interspersed nucleotide element-1 (LINE-1) methylation levels in SSL in comparison to TA and the impact of TA size and presence of high-grade dysplasia (HGD) on LINE-1 methylation.METHODS:LINE-1 methylation was assessed by pyrosequencing of bisulfite-converted DNA. We compared LINE-1 methylation between TA and SSL, among varying sizes of TA, and between TA with HGD and low-grade dysplasia (LGD).RESULTS:LINE-1 methylation declined with increasing polyp size in TA when comparing those <5 mm (72.31 ± 6.11), 5 to <10 mm (67.50 ± 7.00), and ≥10 mm (66.75 ± 11.89). There were lower LINE-1 methylation levels in TA with LGD (n = 119) compared with SSLs (n = 29) (69.11 ± 8.62 vs 81.41 ± 2.43, P < 0.001). TA containing HGD (n = 26) had lower LINE-1 methylation levels than those with LGD (n = 119) (59.86 ± 7.93 vs 69.11 ± 8.62, P < 0.001).DISCUSSION:HGD and increasing size of TA/tubulovillous adenoma were associated with lower LINE-1 methylation. This supports a hypothesis that LINE-1 hypomethylation in TAs indicates advancement along the CRC tumorigenesis pathway. Lower LINE-1 methylation and greater variance of global DNA methylation was seen in TA compared with SSL. LINE-1 methylation in adenomas correlates with polyp size and degree of dysplasia and deserves further study as a predictor of metachronous colorectal cancer risk.