Real-Time Detection Reveals Responsive Cotranscriptional Formation of Persistent Intramolecular DNA and Intermolecular DNA:RNA Hybrid G-Quadruplexes Stabilized by R-Loop.

G-quadruplex (GQ) structures are implicated in important physiological and pathological processes. Millions of GQ-forming motifs are enriched near transcription start sites (TSSs) of animal genes. Transcription can induce the formation of GQs, which in turn regulate transcription. The kinetics of the formation and persistence of GQs in transcription is crucial for the role they play but has not yet been explored. We established a method based on the fluorescence resonance energy transfer (FRET) technique to monitor in real-time the cotranscriptional formation and post-transcriptional persistence of GQs in DNA. Using a T7 transcription model, we demonstrate that a representative intramolecular DNA GQ and DNA:RNA hybrid GQ promptly form in proportion to transcription activity and, once formed, are maintained for hours or longer at physiological temperature even after transcription is stopped. Both their formation and persistence strongly depend on R-loop, a DNA:RNA hybrid duplex formed during transcription. Enzymatic removal of R-loop dramatically slows their formation and accelerates their unfolding. These results suggest that a transcription event is promptly read-out by GQ-forming motifs and the GQ formed can either perform regulation in fast response to transcription and/or memorized in DNA to mediate time-delayed regulation under the control of RNA metabolism and GQ-resolving activity. Alternatively, GQs need to be timely resolved to warrant success of translocating activities such as replication. The kinetic characteristics of GQs and its connection with the R-loop may have implications in transcription regulation, signal transduction, G-quadruplex processing, and genome stability.

Research on aeromagnetic data error analysis and processing of multi-rotor UAV based on variational mode decomposition algorithm.

Aeromagnetic survey of multi-rotor UAV is widely used in small and medium-sized mineral resources survey, engineering investigation, non-explosive detection and other fields due to its advantages of high safety, low cost and convenient operation. The original data of UAV aeromagnetic survey includes interference from external environment, interference from UAV platform and interference from airborne electromagnetic equipment. The interference is mainly shown as striping anomaly along the direction of the survey line in the aeromagnetic anomaly map, which affects the accuracy of aeromagnetic compensation and information detection of geological anomaly body, thus affecting the accuracy of interpretation of geological anomaly body. In this paper, the algorithm of Variational Modal Decomposition (VMD) is introduced to filter and preprocess the aeromagnetic data to obtain high quality aeromagnetic data. At the same time, the source and characteristics of the errors are predicted according to the interference size and spectrum characteristics of the Modal function errors, which provides a reference for the optimization of aeromagnetic system.

Two isomers of HDTIC isolated from Astragali Radix decrease the expression of p16 in 2BS cells.

BACKGROUND: Astragali Radix, the root of Astragalus membranceus (Fish) Bunge Var. mongholicus (Bge), is a crude drug considered as one of the effective traditional Chinese anti-ageing material. The two isomers of 4-hydroxy-5-hydroxymethyl-[1, 3] dioxolan-2, 6'-spirane-5', 6', 7', 8'-tetrahydro-indolizine-3'-carbaldehyde (HDTIC), HDTIC-1 and HDTIC-2, were first extracted from the herb in 2002. We demonstrated previously that 0.1 micromol/L HDTIC-1 or 1.0 micromol/L HDTIC-2 strongly delay replicative senescence of human fetal lung diploid fibroblasts (2BS). In this study, we chose them to investigate their effects on the expression of senescence-associated genes to explore the mechanism of how HDTIC delays replicative senescence. METHODS: The effects of HDTIC-1 and HDTIC-2 on the expression of p16 and p21 were observed in vitro by RT-PCR and Western blot. The anti-oxidative activities of the compounds were also observed by phenotype alteration after treatment with antioxidants. RESULTS: There was an obvious expression of p16 in the control senescent cells. However, in the 2BS cells, after 56 population doublings (PDs) grown from PD28 in 0.1 micromol/L HDTIC-1 or 1.0 micromol/L HDTIC-2, there was a weak mRNA expression of p16 and no protein expression of p16 was observed. The expression level of p21 increased with cell ageing. Moreover, there was no difference between the expression level of p21 in the control cells and that in the same PD cells cultured with HDTIC compounds. The results also showed that 2BS cells exposed to 100 micromol/L H2O2 for 5 minutes return to their non-senescent phenotype and continue to be confluent after incubating the damaged cells with HDTIC-1 (1.0 micromol/L ) or HDTIC-2 (10 micromol/L ) for 1 hour. CONCLUSIONS: Expression of p16 by 2BS cells was strongly inhibited by HDTIC compounds, which could contribute to their delayed replicative senescence by the way of p16(INK4a)/Rb/MAPK. The anti-oxidative activities of HDTIC-1 and HDTIC-2, described in this study for the first time, might be indirectly related to their inhibition of p16 expression.

Aminoguanidine delays the replicative senescence of human diploid fibroblasts.

BACKGROUND: The accumulation of free radicals and advanced glycation end products (AGEs) in cell plays a very important role in replicative senescence. Aminoguanidine (AG) has potential antioxidant effects and decreases AGE levels. This study aimed to investigate its effect on replicative senescence in vitro. METHODS: The effects of aminoguanidine on morphology, replicative lifespan, cell growth and proliferation, AGEs, DNA damage, DNA repair ability and telomere length were observed in human fetal lung diploid fibroblasts (2BS). RESULTS: Aminoguanidine maintained the non-senescent phenotype of 2BS cells even at late population doubling (PD) and increased cumulative population doublings by at least 17 - 21 PDs. Aminoguanidine also improved the potentials of growth and proliferation of 2BS cells as detected by the MTT assay. The AGE levels of late PD cells grown from early PD in DMEM containing aminiguanidine decreased significantly compared with those of late PD control cells and were similar to those of young control cells. In addition, the cells pretreated with aminoguanidine had a significant reduction in DNA strand breaks when they were exposed to 200 micromol/L H(2)O(2) for 5 minutes which indicated that the compound had a strong potential to protect genomic DNA against oxidative stress. And most of the cells exposed to 100 micromol/L H(2)O(2) had much shorter comet tails and smaller tail areas after incubation with aminoguanidine-supplemented DMEM, which indicated that the compound strongly improved the DNA repair abilities of 2BS cells. Moreover, PD55 cells grown from PD28 in 2 mmol/L or 4 mmol/L aminoguanidine retain telomere lengths of 7.94 kb or 8.12 kb, which was 0.83 kb or 1.11 kb longer than that of the control cells. CONCLUSION: Aminoguanidine delays replicative senescence of 2BS cells and the senescence-delaying effect of aminoguanidine appear to be due to its many biological properties including its potential for proliferation improvement, its inhibitory effect of AGE formation, antioxidant effect, improvement of DNA repair ability and the slowdown of telomere shortening.

Optimization of reporter gene assay: several factors influencing detection of promoter activity.

BACKGROUND: Promoter analysis is currently applied to detect the expression of the targeted gene in studies of signal transduction and transcriptional regulation. As a reporter gene, luciferase plays an important role and has been used widely in the promoter assay. METHODS: Human embryonic lung fibroblast cells (2BS), HeLa cells and MCF-7 cells were transfected with various genes embedded by lipofectamine. This study determined various factors that affect promoter activity determination, such as the selection of the reporter genes and internal references, the dose and the type of the vectors carrying the transcription factors, the host cells and the instruments. RESULTS: The sensitivity of the luciferase assay was much higher than that of enhanced green fluorescence protein (EGFP). Moreover, promoter activity is increased in a dose-related manner only in certain ranges outside of which the results may be reversed and the promoter activity is related to the expression vector which is carrying the cDNA. Otherwise, the length of the promoter, internal references and the host cell can also influence the promoter activity. CONCLUSIONS: To detect the promoter activity accurately, a few factors including dose, vector, length and host cell which influence reporter gene assay aforementioned should be considered.

Posttranscriptional induction of p21Waf1 mediated by ectopic p16INK4 in human diploid fibroblast.

BACKGROUND: Both p16(INK4) and p21(Waf1) are tumor suppressors with similar biological functions in the regulation of cellular senescence. Previous reports showed that p16(INK4) could be activated by p21(Waf1) through transcriptional factor Sp1 in HeLa cells. This study was undertaken to determine the effects of p16(INK4) on the expression and functions of p21(Waf1). METHODS: Human diploid fibroblast 2BS cells were stably transfected with sense (2BS/p16(INK4)), antisense p16(INK4) (2BS/asp16(INK4)) or empty vector (2BS/neo). Then they were assayed by reverse-transcription polymerase chain reaction (RT-PCR), fluorescence activated cell sorting (FACS) and Western blot. RESULTS: 2BS/p16(INK4) cells exhibited cell cycle arrest in both G1 and G2/M phases. Endogenous p21(Waf1) protein levels increased twofold in the 2BS/p16(INK4) cells, but not decreased in the 2BS/asp16(INK4) cells. p21(Waf1) mRNA levels were not affected in neither 2BS/p16(INK4) nor 2BS/asp16(INK4) cells. CONCLUSION: p16(INK4) may play an important role in the regulation of cellular senescence by modulating the p21(Waf1) protein level via the posttranscriptional mechanism.

[Mechanisms of aging and its theories].

The velocity of aging is rather different in various species, and even in various tissues and cells of the same individual. Both genetic and environmental factors affect aging process. It is evident that life expectancy mainly relates to environment, while maximum life-span of a species more depends on its genetic background. Poor environment possibly affects genes or their products and then influences the process of human senescence. As aspect of genetic causes, aging is not totally depends on one gene, but rather on the interaction of networks of activated or repressed genes and their products. DNA (especially, mitochondrial DNA) is not as stable as previously conceived. The stability of genetic substance, including genes, could be affected by stresses from external or internal environment, which are particularly induced by harmful substances, such as reactive oxygen species, leading to accelerate aging process.

Age-dependent accumulation of mitochondrial DNA deletions in the aortic root of atherosclerosis-prone apolipoprotein E-knockout mice.

PURPOSE: To investigate whether mitochondrial DNA (mtDNA) damage, specifically deletion, contributes to the development of atherosclerosis or is simply a secondary effect of the primary factors causing atherosclerosis. MATERIALS AND METHODS: mtDNA deletion was detected by PCR in the aortic root of atherosclerosis-prone C57BL/6J apolipoprotein (Apo) E gene deficient (-/-) mice and control C57BL/6J mice at different ages. Atherosclerotic plaques in the Apo E-/- mice were assessed using frozen sections of the aortic root. The protein levels of COX III and 8-oxoguanine glycosylase (OGG1) were determined. RESULTS: while mtDNA deletions accumulated significantly in mice as young as 2- month-old, atherosclerotic plaques were not detected until mice were 6 months old or older, suggesting that mtDNA deletion occurs prior to the formation of atherosclerotic plaques in the aortic root of these mice. Moreover, the expression levels of mtDNA-encoded COX III protein in both 2-month-old and 16-month-old C57BL/6J ApoE-/- mice were significantly lower than those in C57BL/6J mice (p<0.05). Additionally, the protein level of 8-oxoguanine glycosylase (OGG1), a mitochondrial enzyme that functions in DNA excision repair, decreased with age in these mice, indicating that age-related down-regulation of mtDNA excision repair also contributes to atherosclerosis in C57BL/6J ApoE-/- mice. CONCLUSION: These results reveal that mtDNA deletions occur during the early "initiation" stage of atherosclerosis in C57BL/6J ApoE-/- mice and have the potential to promote atherosclerosis.

Antisense c-erbB-2 Decreases DNA Repair and Apoptosis Inducibility in Human Diploid Fibroblasts.

pDOR-erbB-2 sense and antisense retroviral expression vectors were introduced into normal human diploid fibroblasts(2BS), respectively, to construct 2BS-A cells(transfected with antisense recombinant vector) and 2BS-S cells (transfected with sense recombinant vector). Southern blot analysis verified that the exgenous c-erbB-2 cDNA were integrated into genomic DNA. Compared with the cells transfected with pDOR-neo empty vector, 2BS-A cells exhibited decreased ability not only to repair DNA damage, but also to undergo apoptosis. This was consistent with our observations that senescent phenotype was earlier appeared in these cells.

Exogenous p21(WAF1) Transfection Affects Apoptosis in Human Fibroblasts.

pDOR-p21 sense and pDOR-p21 antisense retroviral expression vectors were constructed and successfully transfected by Lipofectin into normal human diploid fibroblasts(2BS line), resulting in 2BS-p21s and 2BS-p21a cell lines, respectively. Southern blot analysis verified that the exogenous p21(WAF1) cDNA were integrated into genomic DNA. Compared with the cells transfected with pDOR-neo empty vector, p21(WAF1) mRNA expression increased in 2BS-p21s cells, which were less sensitive to apoptosis induced by NaBu, and showed higher cell viability, delayed appearance of DNA ladder, and less area of apoptosis peak. On the other hand, p21(WAF1) mRNA expression decreased in 2BS-p21a cells, which were more sensitive to apoptosis induced by NaBu. These results indicated that the expression amount of p21(WAF1) in 2BS cells was negatively related with its susceptibility to apoptosis induced by NaBu.

Age-dependent down-regulation of mitochondrial 8-oxoguanine DNA glycosylase in SAM-P/8 mouse brain and its effect on brain aging.

Mitochondrial DNA (mtDNA) damage has been hypothesized to be responsible for aging and various neurological diseases. Abnormalities in 8-oxoguanine DNA glycosylase (OGG1) function can promote DNA oxidative damage, especially in the mitochondria. Here we report changes in the expression of OGG1 targeting to the nucleus, cytosol, and mitochondria in both accelerated senescence mice (SAM-P/8) and normal counterpart SAM-R/1 mice during brain aging. Our results showed that mRNA and protein levels of OGG1, especially OGG1 targeting to mitochondria, and the expression level of cytochrome c oxidase subunit III (COX III) in the brain of both SAM-P/8 mice and SAM-R/1 mice, decreased with age. However, such an age-dependent decrease in SAM-P/8 mice was larger than that in normal SAM-R/1 mice. These findings support the concept that down-regulation of OGG1, especially mitochondrial OGG1(mtOGG1) in SAM-P/8 mice, may promote brain aging by its effect on imbalance in the mtDNA damage repair systems, which leads to accumulation of mtDNA damage and oxidative phosphorylation-related protein dysfunction. Overall, our results provide novel insight into underlying the molecular mechanisms during brain aging.

p21Waf1/Cip1 plays a critical role in modulating senescence through changes of DNA methylation.

It has been reported that genomic DNA methylation decreases gradually during cell culture and an organism's aging. However, less is known about the methylation changes of age-related specific genes in aging. p21(Waf1/Cip1) and p16(INK4a) are cyclin-dependent kinase (Cdk) inhibitors that are critical for the replicative senescence of normal cells. In this study, we show that p21(Waf1/Cip1) and p16(INK4a) have different methylation patterns during the aging process of normal human 2BS and WI-38 fibroblasts. p21(Waf1/Cip1) promoter is gradually methylated up into middle-aged fibroblasts but not with senescent fibroblasts, whereas p16(INK4a) is always unmethylated in the aging process. Correspondently, the protein levels of DNA methyltransferase 1 (DNMT1) and DNMT3a increase from young to middle-aged fibroblasts but decrease in the senescent fibroblasts, while DNMT3b decreases stably from young to senescent fibroblasts. p21(Waf1/Cip1) promoter methylation directly represses its expression and blocks the radiation-induced DNA damage-signaling pathway by p53 in middle-aged fibroblasts. More importantly, demethylation by 5-aza-CdR or DNMT1 RNA interference (RNAi) resulted in an increased p21(Waf1/Cip1) level and premature senescence of middle-aged fibroblasts demonstrated by cell growth arrest and high beta-Galactosidase expression. Our results suggest that p21(Waf1/Cip1) but not p16(INK4a) is involved in the DNA methylation mediated aging process. p21(Waf1/Cip1) promoter methylation may be a critical biological barrier to postpone the aging process.

Down-regulation of p21WAF1 promotes apoptosis in senescent human fibroblasts: involvement of retinoblastoma protein phosphorylation and delay of cellular aging.

It has been suggested that genes which exercise checkpoint control during cell cycle traverse are equally important to the process of apoptotic cell death. In this study, we show that the key cell cycle regulatory gene p21(WAF1) is also involved in the execution of apoptosis. p21(WAF1) expression was down-regulated during NaBu-induced apoptosis of senescent normal diploid human 2BS fibroblasts. Conversely, when p21(WAF1) expression was actively suppressed in 2BS cells by a stably transfected antisense p21(WAF1) construct, apoptosis was accelerated and senescence was delayed, as shown by several markers of cell aging. Down-regulation of p21(WAF1) by antisense caused an increase in the phosphorylation and inactivation of pRb. Phosphorylation of pRb was further enhanced upon induction of apoptosis by NaBu. Our results suggest that p21(WAF1), acting through the phosphorylation of pRb, regulates whether 2BS cells cease to proliferate and become senescent but resistant to apoptosis, or whether they accelerate proliferation while becoming more susceptible to apoptotic stimuli.