DNA Stability Research Articles

Phytoremediation and genetic adaptation potential of Jatropha curcas on heavy metals enriched mine tailings

BackgroundPhytoremediation is aninexpensive green method that uses metal-tolerant plants to extract these contaminants and restore the soil. MethodsThe phytoremediation potential and genomic DNA/genetic adaptability nature of Jatropha curcas was investigated by 90 days of greenhouse experiment.The genomic DNA stability was determined through RAPD analysis. Soil characterization results the magnesite mine tailing physicochemical parameters (pH, Total carbon, Total hardness, NPK, Cr, Pb, Mn, and Cd) were beyond the acceptable limits. Thus, the mine soil diluted with fertile soil (group a-f) to create different treatment groups. Significant FindingsThe results stated that soil diluted with maximum quantity of fertile soil showed maximum growth and considerably extracted the metals from the soil compared to undiluted (group e) soil and other groups. The BAF and TF values strongly suggests that the J.curcas is suitable candidature with phytoextraction potential. The RAPD analysis on whole genomic DNA revealed that the plan possesses considerable metal adaptation potential under metal stress condition confirmed by GTS and DNA polymorphism analyses through RAPD and also TSP analyses. Hence, this J. curcas can be employed as considerable plant with phytoextraction (as hyperaccumulator) potential to remove the heavy metals from the soil.

Effects of the size and concentration of depleting agents on the stabilization of the double-helix structure and DNA condensation: A single molecule force spectroscopy study

We perform a single molecule force spectroscopy study to characterize the role of the size (molecular weight) and concentration of depleting agents on DNA condensation and on the stabilization of the double-helix structure, showing that important features such as the threshold concentration for DNA condensation, the force in which the melting plateau occurs and its average length strongly depend on the depletant size chosen. Such results are potentially important to understand how the presence of surrounding macromolecules influences DNA stabilization inside living cells and therefore advance in the understanding of the crowded cell environment on DNA-related functions.

How to store a beetle larva? Comparing temporal effects of common fluid preservation methods on color, shape, and DNA quality.

Proper fixing and long-term preservation of entomological evidence are essential in collections and research and crucial in applied fields such as forensic entomology. Incorrectly stored samples may lose important morphological features over time, rendering molecular analyses exceedingly difficult. The most effective method for preserving soft samples such as larvae is fluid preservation. It uses a combination of a wide range of fixatives and storage fluids. However, very little comparative work has been done to determine the effects of long-term storage on sample quality in terms of color, shape, and DNA stability. Moreover, the current golden standard in forensic entomology has been tailored for age estimation of larvae of Diptera, which differ from larvae of Coleoptera in morphology and subsequently in applied methods. We compared the effects of combinations of 6 commonly used fixatives and 6 commonly used storage fluids on midsized larvae of the forensically important beetle, Necrodes littoralis (Linnaeus, 1758), in terms of color, shape, and suitability for DNA analyses over a 2-yr period. We were looking for combinations that can preserve specimens in a satisfactory state, can be used on a regular basis, do not require advanced protection or skills of the personnel, and are not toxic or too harmful to the environment. We found not only several methods that scored significantly better in the tested parameters compared with the golden standard but also several common methods that should be avoided. The effects of agents on each tested category are discussed in detail.

Metal-organic framework integrated hydrogel bioreactor for smart detection of metal ions

Bioreactors with environment responsiveness for smart detection has attracted widespread interest. Bioreactors that operate in liquid have excellent reaction speed and sensitivity, and those that operate at a solid interface have unique portability and stability. However, bioreactors that can simultaneously take advantage of both properties are still limited. Here, we developed a metal-organic framework (MOF) integrated hydrogel bioreactor that can accommodate both solid and liquid properties by using a hydrogel as a quasi-liquid medium. To enhance the stability and intelligence of the hydrogel bioreactor, we have opted for the utilization of europium metal-organic framework (Eu-MOF) as the optical output to withstand long-term storage challenges, and DNA as the highly programmable substance for intelligent target response. On this basis, smart detection of metal ions and biological micro-molecules have been achieved. Notably, this quasi-liquid hydrogel bioreactor has effectively tackled the intrinsic issues of inadequate dispersion stability of Eu-MOF in liquid systems and poor stability of DNA against environmental interference. Moreover, this MOF integrated hydrogel bioreactor has been applied to the construction of a portable hydrogel bioreactor, which enables platform-free and arrayed target detection via a smartphone, providing a new perspective for further promoting the application of quasi-liquid hydrogel bioreactors and intelligent nanobiological sensors.

From roads to biobanks: Roadkill animals as a valuable source of genetic data

To protect biodiversity we must understand its structure and composition including the bacteria and microparasites associated with wildlife, which may pose risks to human health. However, acquiring this knowledge often presents challenges, particularly in areas of high biodiversity where there are many undescribed and poorly studied species and funding resources can be limited. A solution to fill this knowledge gap is sampling roadkill (animals that die on roads as a result of collisions with circulating vehicles). These specimens can help characterize local wildlife and their associated parasites with fewer ethical and logistical challenges compared to traditional specimen collection. Here we test this approach by analyzing 817 tissue samples obtained from 590 roadkill vertebrate specimens (Amphibia, Reptilia, Aves and Mammalia) collected in roads within the Tropical Andes of Ecuador. First, we tested if the quantity and quality of recovered DNA varied across roadkill specimens collected at different times since death, exploring if decomposition affected the potential to identify vertebrate species and associated microorganisms. Second, we compared DNA stability across taxa and tissues to identify potential limitations and offer recommendations for future work. Finally, we illustrate how these samples can aid in taxonomic identification and parasite detection. Our study shows that sampling roadkill can help study biodiversity. DNA was recovered and amplified (allowing species identification and parasite detection) from roadkill even 120 hours after death, although risk of degradation increased overtime. DNA was extracted from all vertebrate classes but in smaller quantities and with lower quality from amphibians. We recommend sampling liver if possible as it produced the highest amounts of DNA (muscle produced the lowest). Additional testing of this approach in areas with different environmental and traffic conditions is needed, but our results show that sampling roadkill specimens can help detect and potentially monitor biodiversity and could be a valuable approach to create biobanks and preserve genetic data.

Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem

BackgroundActive hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms.ResultsWe found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 − 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K+ accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions.ConclusionsOur study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions.4ap83QbxwyKb6GHBwDJLyuVideo

Hematopoietic Stem/Progenitor Cell Intrinsic SAM Synthesis Is Required to Prevent p53 Pathway Activation By Maintaining DNA Stability

S-adenosylmethionine (SAM) is a principle methyl group donor to maintain epigenetic status. SAM is synthesized from methionine and ATP via the enzymatic activity of Mat2a (Methionine adenosyltransferase 2a). It has been reported that SAM reduction by methionine restriction or Mat2a inhibition suppresses the proliferation of leukemia cells to attract attentions as a potential therapeutic target for leukemia. To develop the therapy targeting methionine metabolism in leukemia, it is essential to elucidate the significance of methionine metabolism in non-leukemic hematopoiesis. However, still little is known about the importance of SAM synthesis in hematopoiesis, including hematopoietic stem/progenitor cells (HSPCs), in vivo. By using Mx1-Cre mediated Mat2a gene deletion in mice ( Mat2a fl/fl;Mx1-Cre mice), we investigated the roles of Mat2a in hematopoiesis in vivo. Reduction of Mat2a activity in Mat2a knockout (KO) mice in bone marrow (BM) was confirmed by ultra-high performance liquid chromatography tandem mass spectrometry analysis. Mat2a KO mice displayed severe pancytopenia in peripheral blood (PB). Mature cell fractions (Myeloid cells, B cells and T cells) and HSPCs (HSCs, MPP2s, MPP3s and MPP4s) in BM were also significantly decreased in Mat2a KO mice, suggesting that Mat2a is essential for the maintenance of hematopoiesis from HSPCs in vivo. To exclude the possible contributions of the effects induced by Mat2a KO in non-hematopoietic cells, we performed BM transplantation analyses in which hematopoietic cell specific KO or non-hematopoietic cell specific KO were achieved. These analyses clearly confirmed that HSPC intrinsic SAM synthesis is inevitable for the maintenance of hematopoiesis. To reveal the mechanistic insights of the regulatory roles for Mat2a in HSPCs, we performed RNA sequencing analysis ( Mat2a WT vs KO in HSPCs). GSEA (Gene Set Enrichment Analysis) using the Hallmark gene sets showed that p53 pathway was most highly enriched in Mat2a KO. In depth, genes downstream of p53 ( Bax, Apaf1, Bbc3, Casp3, Casp8, Fas, Cdkn1a etc.) were up-regulated by Mat2a KO, causing cell cycle arrest and apoptosis in HSPCs. On the other hand, gene expressions of the upstream of p53 ( Atr, Atm, Chek1, Chek2 etc.) were unchanged, suggesting that p53 activity was not increased at mRNA expression levels. In line with this, mRNA expression levels of Trp53 was unchanged, but total protein amount of p53 was increased in Mat2a KO HSPCs. Since DNA stability is known as a critical regulator of p53 pathway, we analyzed gH2AX levels as DNA damage marker and found that gH2AX levels were increased in Mat2a KO HSPCs. To be noted, expressions of genes involved in Fanc pathway ( Fanca, Fancc, Fancd2, Fance, Fancg, Fancl, Fanci etc), which is responsible for the DNA maintenance, were broadly down-regulated in Mat2a KO HSPCs at transcriptomic levels. Therefore, the Fanc pathway repression by SAM synthesis inhibition could cause DNA damage and p53 pathway dependent loss of maintenance in Mat2a KO HSPCs. To further understand the importance of SAM synthesis under stress hematopoiesis. We analyzed Mat2a expression changes in HSPCs by irradiation (5.5 Gy/mouse). Intriguingly, Mat2a expression was up-regulated by irradiation. We also found that dietary methionine restriction (MR) in mice prevents its hematopoietic recovery from irradiation stress. To be noted, long term MR (24 weeks) did not show any particular compared to control diet. Therefore, methionine metabolism possesses significant roles at least in the situation where acute hematopoietic recovery is required. Collectively, in this study, we found that cell intrinsic SAM synthesis is required for the maintenance (proliferation and survival) of HSPCs in vivo. SAM might be required for the prevention of DNA damage and p53 pathway activation by supporting Fanc pathway gene expressions. Methionine and/or SAM availability might possess critical roles for the regeneration of non-leukemic hematopoiesis. Further investigation about the significance of SAM synthesis in non-leukemic hematopoiesis is required for the proper establishment of SAM synthesis targeting therapy in cancers.

Interactions between Iron Overload, Oxidative Stress, and Somatic Mutations in Myelodysplastic Syndromes; Evidence from the Literature

Introduction: Somatic mutations (SM) are central to the pathophysiology of myelodyspastic syndromes (MDS). Iron overload (IOL) from transfusion of red blood cells (RBC) and the oxidative stress that results from the ability of iron to transfer electrons and undergo Fenton chemistry are common and are associated with adverse clinical endpoints (infections, cardiac events, exacerbation of bone marrow failure, event-free survival, progression-free survival, overall survival) in MDS. We reviewed the literature to elucidate what evidence is available indicating an interaction between iron, oxidative stress and specific SM in MDS. Methods: A series of PubMed searches were done including the key words of each specific mutation combined with iron, oxidative stress, and reactive oxygen species (ROS, a measure of oxidative stress), focusing on SM prevalent in MDS and/or included in the molecular International Prognostic Scoring System (IPSS-M; 31 mutations in all, including IPSS-M mutations and TET2). Citations relevant to hematopoietic stem and progenitor cells, cells of the hematopoietic microenvironment, and myeloid disorders were favoured for review. Mutations of familial predisposing conditions were also searched in combination with iron, oxidative stress and ROS. Results: Of 31 mutations found in the IPSS-M, an additional four mutations found in familial predisposing conditions (DDX41, GATA2, CHEK2, SAMD9) were searched as was TET2, for a total of 35 mutations. Fifty-four references were identified. Fifty-three references were preclinical/translational in nature, with one case report (WT1). The most frequent alterations in iron/ROS were with the SF3B1 mutation, with 11 citations. Thirteen of 31 (42%) of SM in combination with iron, oxidative stress/ROS had citations. Reports for combination with iron or oxidative stress/ROS, respectively, included early (TP53, IDH2, RUNX1, SF3B1, STAG2, TET2; and TP53, DNMT3A, IDH2, NPM1, U2AF1) and late (NRAS, CEBP3A; and CBL, NRAS) mutations. Both gain of function (TP53, IDH2, NRAS, SF3B1; and TP53, IDH2, NRAS, U2AF1) and loss of function (STAG2, TET2; and CBL) mutations had relevant citations identified. Cellular pathways affected included tumour suppressor (TP53 for both iron and oxidative stress/ROS), signal transduction (NRAS for both), splicing factors (SF3B1; U2AF1), DNA stability (STAG2) and (hypo) methylation (TET2; DNMT3A). There were reports of an impact at multiple levels on iron/ROS and cellular/systemic physiology in the context of SF3B1 mutation, for example: ERFE+12 (containing 12 additional nucleotides and translated to an ERFE protein containing 4 additional amino acids; 358 vs 354 in wild type) present in SF3B1 mutated MDS does like the usual ERFE suppress hepcidin, impacting iron at a systemic level; enzymes of iron, heme and iron sulfur cluster physiology are altered, impacting iron physiology at a cellular level; and mitochondrial ferritin sequesters iron, leading to cytoplasmic iron deficiency, lowering ROS and thus possibly protecting cells from oxidative damage. Table 1 shows examples of iron/ROS interactions with SF3B1, TET2, DNMT3A, U2AF1, STAG2, NRAS, TP53, IDH2, CBL, NPM, ETNK, PTPN11, WT1 and RUNX1. Figure 1 shows MDS pathophysiology and where interactions between SM and iron/oxidative stress/ROS may impact this pathophysiology. No investigations were identified relevant to the mutations of familial predisposing conditions, including DDX41, GATA2, CHEK2 and SAMD9 in combination with iron/oxidative stress/ROS. Discussion: Searching IOL, oxidative stress and ROS in combination with MDS somatic mutations uncovered information as to how iron/redox status may interact with SM to affect MDS pathophysiology. Of particular interest is the cytoplasmic iron deficiency induced in the presence of SF3B1 mutation, the only SM conferring favourable prognosis in MDS in the IPSS-M. Given the pleiotropic cellular, intracellular and subcellular mechanisms involved, investigation regarding when and how targeting iron overload by reducing RBC transfusion requirements, binding iron or attenuating ROS may alter cellular and clinical outcomes in the setting of specific somatic mutations is warranted.

Deciphering the Role of Anions of Ionic Liquids in Modulating the Structure and Stability of ct-DNA in Aqueous Solutions.

Stabilizing biomolecules under ambient conditions can be extremely beneficial for various biological applications. In this context, the utilization of ionic liquids (ILs) in enhancing the stability and preservation of nucleic acids in aqueous solutions is found to be promising. While the role of the cationic moiety of ILs in the said event has been thoroughly explored, the importance of the anionic moiety in ILs, if any, is rather poorly understood. Herein, we examine the function of anions of ILs in nucleic acid stabilization by examining the stability and structure of calf thymus-DNA (ct-DNA) in the presence of various ILs composed of a common 1-ethyl-3-methylimidazolium cations (Emim+) and different anions, which includes Cl-, Br-, , and by employing various spectroscopic techniques as well as Molecular Dynamics (MD) simulation studies. Analysis of our data suggests that the chemical nature of anions including polarity, basicity, and hydrophilicity become an important factor in the overall DNA-IL interaction event. At lower concentrations, the interplay of intermolecular interaction between the IL anions with their respective cations and the solvent molecules becomes a very crucial factor in inducing their stabilizing effect on ct-DNA. However, at higher concentrations of ILs, the ct-DNA stabilization is additionally governed by specific-ion effect. MD simulation studies have also provided valuable insights into molecular-level understanding of the DNA-IL interaction event. Overall, the present study clearly demonstrated that along with the cationic moiety of ILs, the anions of ILs can play a significant role in deciding the stability of duplex DNA in aqueous solution. The findings of this study are expected to enhance our knowledge on understanding of IL-DNA interactions in a better manner and will be helpful in designing optimized IL systems for nucleic acid based applications.

Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability

Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functions in promoter-proximal pausing and elongation processivity. Spt5 was also recognized for its roles in the transcription of expanded-repeat genes that are related to neurodegenerative diseases. Recently, a set of Spt5-Pol II small molecule inhibitors (SPIs) were reported, which selectively inhibit mutant huntingtin gene transcription. Inhibition mechanisms as well as interaction sites of these SPIs with Pol II and Spt5 are not entirely known. In this study, we predicted the binding sites of three selected SPIs at the Pol II-Spt5 interface by docking and molecular dynamics simulations. Two molecules out of three demonstrated strong binding with Spt5 and Pol II, while the other molecule was more loosely bound and sampled multiple binding sites. Strongly bound SPIs indirectly affected RNA and DNA dynamics at the exit site as DNA became more flexible while RNA was stabilized by increased interactions with Spt5. Our results suggest that the transcription inhibition mechanism induced by SPIs can be related to Spt5-nucleic acid interactions, which were altered to some extent with strong binding of SPIs.

Interaction of mitoxantrone with abasic sites - DNA strand cleavage and inhibition of apurinic/apyrimidinic endonuclease 1, APE1

Mitoxantrone (1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]-anthracene-9,10-dione) is a clinically-relevant synthetic anthracenedione that functions as a topoisomerase II poison by trapping DNA double-strand break intermediates. Mitoxantrone binds to DNA via both stacking interactions with DNA bases and hydrogen bonding with the sugar-phosphate backbone. It has been shown that mitoxantrone inhibits apurinic/apyrimidinic (AP) endonuclease 1 (APE1)-catalyzed incision of DNA containing a tetrahydrofuran (THF) moiety and more recently, that mitoxantrone forms Schiff base conjugates at AP sites in DNA. In this study, mitoxantrone-mediated inhibition of APE1 at THF sites was shown to be consistent with preferential binding to, and thermal stabilization of DNA containing a THF site as compared to non-damaged DNA. Investigations into the properties of mitoxantrone at AP and 3′ α,β-unsaturated aldehyde sites demonstrated that in addition to being a potent inhibitor of APE1 at these biologically-relevant substrates (∼ 0.5 μM IC50 on AP site-containing DNA), mitoxantrone also incised AP site-containing DNA by catalyzing β- and β/δ-elimination reactions. The efficiency of these reactions to generate the 3′ α,β-unsaturated aldehyde and 3′ phosphate products was modulated by DNA structure. Although these cell-free reactions revealed that mitoxantrone can generate 3′ phosphates, cells lacking polynucleotide kinase phosphatase did not show increased sensitivity to mitoxantrone treatment. Consistent with its ability to inhibit APE1 activity on DNAs containing either an AP site or a 3′ α,β-unsaturated aldehyde, combined exposures to clinically-relevant concentrations of mitoxantrone and a small molecule APE1 inhibitor revealed additive cytotoxicity. These data suggest that in a cellular context, mitoxantrone may interfere with APE1 DNA repair functions.

Condensed DNA Nanosphere for DNA Origami Cryptography

Maintaining the confidentiality and integrity of the messages during a transmission is one of the most important aims of encrypted communication systems. Many achievements were made using biomolecules to improve the quality of the messages in communication. At the same time, it is still a challenge to construct cooperative communications based on the interactions between biomolecules to achieve the confidentiality and integrity of the transmitted messages. DNA-based encrypted communications have been developed, and in particular, DNA-origami-based message encryption can combine steganography and pattern encryption and exhibits extremely high confidentiality. Nevertheless, limited by biological characteristics, encrypted messages based on DNA require a strict storage environment in the process of transmission. The integrity of the message encoded in the DNA may be damaged when the DNA is in an unfriendly and hard environment. Therefore, it is particularly significant to improve the stability of DNA when it is exposed to a harsh environment during transmission. Here, we encoded the information into the DNA strands that were condensed for encryption to form a nanosphere covered with a shell of SiO2, which brings high-density messages and exhibits higher stability than separated DNA. The solid shell of SiO2 could prevent DNA from contacting the harsh environment, thereby protecting the DNA structure and maintaining the integrity of the information. At the same time, DNA nanospheres can achieve high throughput input and higher storage density per unit volume, which contribute to confusing the message strand (M-strand) with the interference strand in the stored information. Condensing DNA into the nanosphere that is used for DNA origami cryptography has the potential to be used in harsh conditions with higher confidentiality and integrity for the transmitted messages.

Metaproteomic and Metagenomic-Coupled Approach to Investigate Microbial Response to Electrochemical Conditions in Microbial Fuel Cells.

MFCs represent a promising sustainable biotechnology that enables the direct conversion of organic matter from wastewater into electricity using bacterial biofilms as biocatalysts. A crucial aspect of MFCs is how electroactive bacteria (EAB) behave and their associated mechanisms during extracellular electron transfer to the anode. A critical phase in the MFC start-up process is the initial colonization of the anode by EAB. Two MFCs were operated with an external resistance of 1000 ohms, one with an applied electrical voltage of 500 mV during the initial four days of biofilm formation and the other without any additional applied voltage. After stabilization of electricity production, total DNA and protein were extracted and sequenced from both setups. The combined metaproteomic/metagenomic analysis revealed that the application of voltage during the colonization step predominantly increased direct electron transfer via cytochrome c, mediated primarily by Geobacter sp. Conversely, the absence of applied voltage during colonization resulted in a broader diversity of bacteria, including Pseudomonas and Aeromonas, which participated in electricity production via mediated electron transfer involving flavin family members.

Recombinant VAR2CSA malaria protein-targeted exosome-mediated DACT2 gene therapy for effective glioma treatment

A good non-viral vector is the key to the success of gene delivery and therapy; hence, modified exosomes may overcome the physiological barrier in the delivery in vivo. This study aims to design a novel non-viral vector and verify its gene delivery function in vitro and in vivo for dapper homolog 2 (DACT2) genes. In this study, amphipathicity cationic exosomes with receptor targeted function and DACT2 gene loading function were constructed by exosomes, PEG, glycidyl hexadecyl dimethylammonium chloride, and recombinant VAR2CSA malaria protein (RVP) antibody. Characterizations of RVP antibody and PEG modified cationic lipid exosome (RVP-CL) nanocomplexes were evaluated by dynamic light scattering, atomic force microscopy, FTIR, and so on. The DNA condensation ability and stability were assessed by agarose gel electrophoresis. Cellular uptake efficiency and cytotoxicity in glioma cells were investigated. Furthermore, the tumor suppressive effect was evaluated in vitro and in vivo. The results indicated that RVP-CL had a uniform size of 100–200 nm and positive zeta potential. With high uptake efficiency, RVP-CL can rapidly target, recognize, and enter the glioma cell (KNS-42 and U118 mg) and release the gene. Moreover, RVP-CL/DACT2 can effectively inhibit the growth of glioma cells in vitro and in vivo. The modified cationic exosomes may offer a promising strategy for gene delivery in the treatment of RVP-positive gliomas or other tumors.

Evaluation of accumulation and translocation of Pb and Cr in Vigna unguiculata by hydroponic phytoremediation model and assess it genetic stability

In this study, the phytoremediation (accumulation and translocation) competence of Pb and Cr by Vigna unguiculata under metal supplemented hydrophonic medium was investigated. Moreover, analyzed the genomic DNA stability of V. unguiculata under different dosages of Pb and Cr was analyzed through RAPD analysis. To assess the phytoextraction along with tolerance of V. unguiculata under Pb and Cr metal stress circumstances, a number of investigations were performed. The dosages of these metals reached maximum values (Pd: root 4685.8 ± 8.57 mg kg−1 & shoot 956.63 ± 3.9 mg kg−1, and Cr: root 5157.62 ± 11.56 mg kg−1 & 1243.51 ± 10.2 mg kg−1) in plant tissues in 1500 mg L−1 treatment. The Bioconcentration factors (BCF) for Pb as well as Cr demonstrated that V. unguiculata possess phytoextraction competence and the translocation factors (TCF) revealed that these metals were slightly translocated. This study indicates that, V. unguiculatais more appropriate for the phytoremediation of Pb and Cr polluted soil. However, the total soluble protein (TSP) and RAPD analysis revealed the occurrent of metal toxicity on TSP and plant genomic DNA. As a result of these findings, this V. unguiculata may be used for phytoremediation purposes; however, cultivation for edible purposes should be avoided in metal-contaminated soil because it adsorbs toxic metals that can spread to the food web while using this plant yield.

4mC-CGRU: Identification of N4-Methylcytosine (4mC) sites using convolution gated recurrent unit in Rosaceae genome

An epigenetic modification is DNA N4-methylcytosine (4mC) that affects several biological functions without altering the DNA nucleotides, including DNA conformation, cell development, replication, stability, and DNA structural changes. To prevent restriction enzyme from damaging self-DNA, 4mC performs a critical role in restriction–modification functions. Existing studies mainly focused on finding hand-crafted features to identify 4mC locations, but these methods are inefficient due to high time consuming and high costs. In our research work, we propose a 4mC-CGRU which is a deep learning-based computational model with a standard encoding method to identify the 4mC sites from DNA sequences that learned autonomous feature selection in the Rosaceae genome, particularly in Rosa chinensis (R. chinensis) and Fragaria vesca (F. vesca). The proposed model consists of a convolutional neural network (CNN) and a gated recurrent unit network (GRU)-based model for identifying 4mC sites from Fragaria vesca and Rosa chinensis in the genomes. The CNN model extracts useful features from the datasets and the GRU classifies the DNA sequences. Thus, our approach can automatically extract important features to detect relative sites from DNA sequence. The performance analysis shows that the proposed model consistently outperforms over the state-of-the-art works in detecting 4mC sites.

DNA Hairpins and Stabilization of Gold Nanoparticles: Effect of Stem Length and Toehold Composition.

This study investigates the effect of DNA hairpins on the stabilization of gold nanoparticles (AuNPs) against salt-induced aggregation (SIA) in label-free colorimetric biosensors. AuNPs were incubated with DNA hairpins of varying stem lengths and toehold sequences, followed by the addition of NaCl, before being subjected to ultraviolet-visible (UV-vis) measurement. Results showed that hairpins with longer stems generally provide better stabilization of AuNPs (18-bp >14-bp >10-bp). No improvement was observed for 14- and 18-bp hairpins with a toehold beyond 8A, which may be attributed to saturated adsorption of hairpins on the gold surface. For 14-bp hairpins with an 8-mer homopolymeric toehold, we observed a stabilization trend of A > C > G > T, similar to the reported trend of ssDNA. For variants containing ≥50% adenine as terminal bases, introducing cytosine or guanine as preceding bases could also result in strong stabilization. As the proportion of adenine decreases, variants with guanine or thymine provide less protection against SIA, especially for guanine-rich hairpins (≥6G) that could form G-quadruplexes. Such findings could serve as guidelines for researchers to design suitable DNA hairpins for label-free AuNP-based biosensors.

Impact of Cell-Debris and Room-Temperature Storage on Urine Circulating Tumor DNA from Hepatocellular Carcinoma

This study evaluated the impact of cell debris and 7-day room temperature storage on the quality and yield of transrenal DNA. Archived urine specimens collected from five hepatocellular carcinoma (HCC) patients and two pregnant women carrying male fetuses were used to assess the impact of cell debris on urine cell-free DNA (ucfDNA) isolation as measured by quantitative PCR for Y-chromosome DNA, or HCC-associated mutation and methylation markers, and by capillary electrophoresis. Prospectively collected urine from 21 HCC patients was aliquoted after collection for paired immediate freezing versus 7-day room temperature storage followed by freezing for further analysis. Cell debris contained more Y-chromosome DNA than supernatant in three of the six urine specimens tested from pregnant women, suggesting that cell debris can be associated with 20.6% to 84.9% of transrenal ucfDNA. Ninety-five percent (20 of 21) of frozen and room temperature urine pairs had overlapping DNA size distribution. ucfDNA quantity determined by quantitative PCR for TP53, CTNNB1, TERT, and HCC-associated urine circulating tumor DNA markers were statistically similar between room temperature and frozen samples. This suggests no significant difference in DNA degradation between the groups. The association of transrenal ucfDNA with cell debris and HCC circulating DNA stability at room temperature is significant to further the understanding of transrenal circulating tumor DNA pre-analytical handling for HCC screening.

Spectroscopy evidence of interaction of 1,5 disubstituted piperidino-amido anthraquinone derivative with human telomeric G-quadruplex DNA: Basis of anticancer action

The binding of ligands to G-quadruplex (G4) structures at the ends of human telomeric DNA induces thermal stabilization, which interferes with telomere maintenance by disrupting the association of telomeres with the telomerase enzyme—an important marker for cancer. Understanding the binding mode of the ligand-G quadruplex DNA complex is imperative for evaluating the relative efficacy and specificity of their interaction. We focused on the interaction of 1,5-Bis(3-piperidino propionamido) anthracene-9,10-dione with human telomeric DNA sequences using surface plasmon resonance, absorbance, fluorescence (steady-state and lifetime), and circular dichroism spectroscopy techniques. The ligand binding with HTel22 (Kb = 8.4 × 105 M−1) induced cell toxicity with an IC50 value of ∼ 8.64 µM in MCF-7 cancer cell lines. Significant hypochromism (59 %), fluorescence quenching (97 %), no change in fluorescence lifetime and absence of induced Circular Dichroism (CD) band upon addition of G4 DNA to ligand, suggest a groove/external binding mode. CD spectral changes reflect rearrangement in parallel and antiparallel strands to accommodate the ligand. Docking results reveal specific short contacts of the ligand's side chain, including 9CO, 13N, 14NH, and 11CO, with the grooves of the G4 DNA, without making any contact with the loops, favoring an energetically more favorable conformation. Thermal denaturation profiles, obtained by Differential Scanning Calorimetry and CD, show the stabilization of wHTel26 and HTel22 G4 DNA in K+ and Na+ rich solutions by 21.2 and 17.6 °C, respectively, which may restrict the access of telomerase to telomeres. The findings indicate the potential of modifying anthraquinone substituent groups for therapeutic applications.

Tau protein modulates an epigenetic mechanism of cellular senescence in human SH-SY5Y neuroblastoma cells.

Introduction: Progressive Tau deposition in neurofibrillary tangles and neuropil threads is the hallmark of tauopathies, a disorder group that includes Alzheimer's disease. Since Tau is a microtubule-associated protein, a prevalent concept to explain the pathogenesis of tauopathies is that abnormal Tau modification contributes to dissociation from microtubules, assembly into multimeric β-sheets, proteotoxicity, neuronal dysfunction and cell loss. Tau also localizes in the cell nucleus and evidence supports an emerging function of Tau in DNA stability and epigenetic modulation. Methods: To better characterize the possible role of Tau in regulation of chromatin compaction and subsequent gene expression, we performed a bioinformatics analysis of transcriptome data obtained from Tau-depleted human neuroblastoma cells. Results: Among the transcripts deregulated in a Tau-dependent manner, we found an enrichment of target genes for the polycomb repressive complex 2. We further describe decreased cellular amounts of the core components of the polycomb repressive complex 2 and lower histone 3 trimethylation in Tau deficient cells. Among the de-repressed polycomb repressive complex 2 target gene products, IGFBP3 protein was found to be linked to increased senescence induction in Tau-deficient cells. Discussion: Our findings propose a mechanism for Tau-dependent epigenetic modulation of cell senescence, a key event in pathologic aging.