Double-stranded DNA Fragments Research Articles

Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors.

Biosensors based on endonuclease Cas12 provide high specificity in pathogen detection. Sensitive detection using Cas12-based assays can be achieved using trans-cleaved DNA probes attached to simply separated carriers, such as magnetic particles (MPs). The aim of this work was to compare polyA, polyC, and polyT single-stranded (ss) DNA with different lengths (from 10 to 145 nt) as trans-target probes were immobilized on streptavidin-covered MPs. Each ssDNA probe was labeled using fluorescein (5') and biotin (3'). To compare the probes, we used guide RNAs that were programmed for the recognition of two bacterial pathogens: Dickeya solani (causing blackleg and soft rot) and Erwinia amylovora (causing fire blight). The Cas12 was activated by targeting double-stranded DNA fragments of D. solani or E. amylovora and cleaved the MP-ssDNA conjugates. The considered probes demonstrated basically different dependencies in terms of cleavage efficiency. PolyC was the most effective probe when compared to polyA or polyT probes of the same length. The minimal acceptable length for the cleavage follows the row: polyC < polyT < polyA. The efficiencies of polyC and polyT probes with optimal length were proven for the DNA targets' detection of D. solani and E. amylovora. The regularities found can be used in Cas12a-based detection of viruses, bacteria, and other DNA/RNA-containing analytes.

P-053 Sperm aneuploidy and DNA integrity pre- and post-chemotherapy in men with testicular cancer

Abstract Study question Are fragmentation levels (single-double stranded DNA breaks) or aneuploidy frequencies in sperm increased in patients with testicular cancer who recovered spermatogenesis after chemotherapy (CT)? Summary answer Similar levels of sperm DNA fragmentation and sperm aneuploidy frequency are found in men with testicular cancer pre- and post-chemotherapy. What is known already Testicular cancer is the most frequent solid tumor among young men. Therefore, the restoration of fertility and achievement of fatherhood in survivors have become important concerns. The integrity of genetic material in sperm is crucial since some paternal genes are essential for early embryo development. Although previous studies analyzed the effect of CT on sperm DNA integrity, they did not differentiate single vs. double-stranded DNA breaks. Few data are available on aneuploidy in sperm from testicular cancer survivors, so it remains to be elucidated whether cancer treatments may lead to an increased risk of aneuploidy syndromes in offspring. Study design, size, duration Prospective multicenter study including 31 males with a history of testicular cancer who requested semen cryopreservation between 2007-2021. All patients included underwent CT and recovered spermatogenesis once treatment ended. Post-CT samples were collected and seminal parameters, single-double stranded DNA breaks and the proportion of sperm aneuploidies were compared with one aliquot of the initial ejaculate. The project was approved by an Institutional Review Board and written informed consent for participation was obtained from each subject. Participants/materials, setting, methods Patient´s age prior CT was 31.23yrs (IC 95%: 29.29-33.17). Mean interval time between 1st and 2nd samples was 4.53yrs (IC 95%: 3.42-5.64). TUNEL quantified overall sperm DNA fragmentation by flow cytometry analyzing at least 20,000 cells, while γH2AX staining was applied for double DNA fragmentation assessment. Sperm aneuploidies were calculated by using fluorescence in situ hybridization (FISH) probes for chromosomes 13, 18, 21, X, Y. A paired t-test was used to compare variables pre- and post-CT. Main results and the role of chance Similar results were found when sperm quality parameters were compared. Mean sperm concentration pre-CT was 33.03M/mL (IC 95%: 23.98-42.07) and 36.41 M/mL (IC 95%: 27.85-44.96) in post-CT ejaculates (N.S.). A comparable rate of motile spermatozoa was observed in pre-CT vs. post-CT samples [(43.81% (IC 95%: 38.42-49.19) vs. 44.73% (IC 95%: 38.95-50.51), N.S.]. Regarding TUNEL assay results, the sperm DNA fragmentation rate was 21.65% (IC 95%: 17.66-25.63) in pre-CT samples and 23.00% (IC 95%: 19.90-26.61) in post-CT samples (N.S.). Furthermore, similar results were obtained when double-stranded fragmentation levels (H2AX) were compared between pre and post-CT [10.2% (IC 95%: 6.45-13.96) vs. 12.44% (IC 95%: 8.75-16.13) N.S.]. Comparable sperm disomic proportions were found in PRE and POST-CT samples: [(Cr.13 =0.02%, Cr.18 =0.01%, Cr.21=0.30%, Cr.XY=0.84%) vs. (Cr.13 =0%, Cr.18 =0%, Cr.21=0%, Cr.XY=0.33%), N.S]. Results were also evaluated according to the time elapsed between the PRE and POST -CT samples. No significant differences were found for seminal values (sperm concentration, p = 0.26; motility, p = 0.68), overall sperm DNA fragmentation (p = 0.68), double-strand DNA fragmentation (p = 0.90) and the frequency of sperm disomies (Cr. 13 p = 0.79, Cr.18 p = 0.46, Cr. 21 p = 0.85, Cr.XY p = 0.05). Limitations, reasons for caution The main limitations of the present study are that we only recruited patients who recovered spermatogenesis and that our data evaluated a long-term effect of CT. Wider implications of the findings All men wishing to have their own children after gonadotoxic treatment should receive adequate counseling about the side effects of the therapy. Based on our results on sperm DNA integrity and euploidy, patients who recovered spermatogenesis should not be advised to use samples that were preserved before undergoing CT. Trial registration number na

P-250 The exclusive role of sperm DNA fragmentation on the clinical outcome of a sibling donor oocyte cohort

Abstract Study question Can sperm chromatin fragmentation (SCF) overwhelm the oocyte repair mechanism of healthy, young oocytes and impair embryo development and clinical outcome? Summary answer Elevated SCF, with its double-stranded DNA (dsDNA) component, remarkably impairs clinical outcome, despite oocyte repair mechanisms present in a sibling donor oocyte cohort. What is known already Despite a normal semen analysis, approximately 10-20% of males of reproductive age still have a subtle infertility. Therefore, conventional semen analysis is insufficient to identify the specific issues related to sperm function and its embryo developmental competence. Indeed, SCF with its dsDNA break component, is known to be associated with poor clinical outcome such as poor embryo development and pregnancy loss, by possibly increasing structural chromosomal abnormalities. Although a healthy oocyte may address certain levels of SCF, these oocyte repair mechanisms are incapable of repairing dsDNA breaks. Study design, size, duration Thirty-one couples were divided according to the degree and type of SCF, whether normal or abnormal, and shared the same sibling donor oocytes. The male partners in both groups had comparable semen parameters. Total SCF and dsDNA fragmentation were assessed in all men. Fertilization, implantation, clinical pregnancy (CPR; +FHB), delivery, and pregnancy loss rates were compared between the two cohorts. Participants/materials, setting, methods A total of 31 infertile couples underwent ICSI cycles utilizing split sibling donor oocytes due to advanced maternal age or premature ovarian insufficiency. Oocytes from the same donor were equally allocated among 2 couples. Semen analyses were performed according to WHO 6th edition. Overall SCF was assessed by TUNEL with a ≤ 15% normal threshold. Double-strand DNA (dsDNA) fragmentation was assessed by neutral comet assay with ≤3% considered normal. Main results and the role of chance A total of 18 male partners (44.3 ± 7yrs) with a normal SCF of 8.9 ± 2% had their spermatozoa injected into sibling donor oocytes, while 13 male partners with abnormal SCF at 25.4% ± 11 (P&amp;lt;0.001) had their spermatozoa injected into the remaining half. In the latter, the average dsDNA fragmentation rate was 3.6%, while in the former it was 0.3% (P&amp;lt;0.001). Sibling donor oocytes injected with normal SCF resulted in a fertilization of 87.4% (146/167), implantation of 56.4% (22/39), +bHCG of 69.0% (20/29), CPR of 62.1% (18/29), and delivery rate of 51.7% (15/29). The other half of the sibling oocytes, injected with spermatozoa with elevated SCF, resulted in a fertilization of 70.8% (97/137) (P&amp;lt;0.001), implantation of 15.4% (4/26) (P&amp;lt;0.01), +bHCG of 42.1% (8/19), CPR of 21.1% (4/19) (P&amp;lt;0.01), and delivery rate of 10.5% (2/19) (P&amp;lt;0.01). The pregnancy loss in cycles utilizing the oocyte cohort injected with spermatozoa with normal SCF was 8.7% (2/23), while the pregnancy loss in those injected with spermatozoa with elevated SCF was 50.0% (2/4). Limitations, reasons for caution This preliminary study indicates that SCF and dsDNA fragmentation negatively affects clinical outcome, overwhelming oocyte repair mechanisms. Nonetheless, the study has a limited number of observations and needs to be validated in a larger cohort. Wider implications of the findings SCF, with its dsDNA fragmentation component, seems to contribute a higher incidence of chromosomal abnormalities. The compounded aneuploidy of male and female gametes may explain the compromised embryo development and higher pregnancy loss rate observed in infertile couples with apparently normal semen parameters and younger oocytes. Trial registration number not applicable

STING is a prognostic factor related to tumor necrosis, sarcomatoid dedifferentiation, and distant metastasis in clear cell renal cell carcinoma

STING is a molecule involved in immune reactions against double-stranded DNA fragments, released in infective and neoplastic diseases, whose role in the interactions between immune and neoplastic cells in clear cell renal cell carcinoma has not been studied yet. We investigated the immunohistochemical expression of STING in a series of 146 clear-cell renal cell carcinomas and correlated it with the main pathological prognostic factors. Furthermore, tumoral inflammatory infiltrate was evaluated and studied for the subpopulations of lymphocytes. Expression of STING was observed in 36% (53/146) of the samples, more frequently in high-grade (G3–G4) tumors (48%,43/90) and recurrent/metastatic ones (75%, 24/32) than in low grade (G1–G2) and indolent neoplasms (16%, 9/55). STING staining correlated with parameters of aggressive behavior, including coagulative granular necrosis (p = 0.001), stage (p < 0.001), and development of metastases (p < 0.001). Among prognostic parameters, STING immune expression reached an independent statistical significance (p = 0.029) in multivariable analysis, along with the stage and the presence of coagulative granular necrosis. About tumor immune-environment, no significant statistical association has been demonstrated between tumor-infiltrating lymphocytes and STING. Our results provide novel insights regarding the role of STING in aggressive clear cell renal cell carcinomas, suggesting its adoption as a prognostic marker and a potentially targetable molecule for specific immunotherapies.

Abstract 998: A blood-based extracellular vesicles DNA methylation signature for colorectal cancer screening

Abstract Colorectal cancer (CRC) is the third most common cancer worldwide and the fourth leading cause of cancer related deaths, accounting for an estimated 1.8 million new cancer diagnoses and over 880,000 deaths in 2018. Furthermore, CRC patients who are diagnosed at the most advanced (metastatic) stage is estimated to have the 5-year survival rate of 14%. Dramatically, studies shows that if it can be detected at an early stage when surgical removal is feasible, the 5-year survival rate significantly increases to 90%. Therefore, early detection for CRC with curative treatment intent is crucially important to significantly reduce the mortality and morbidity and even cure CRC. Extracellular vesicles (EVs) are lipid-bilayer-enclosed vesicles of sub-micrometer size that are secreted by virtually all cell types. They contain hundreds of different proteins, thousands of intact RNA species, and double-stranded DNA (dsDNA) fragments that sample the entire human genome. Recent findings further corroborate the potential role of EVs in early cancer screening, cancer diagnosis, treatment selection and monitoring. In this study, we used lipid nanoprobe (LNP) for EV isolation and methylation-specific qPCR assay for detecting SEPT9 methylation to develop a minimal invasive CRC screening test. Firstly, we have successfully detected promoter methylation of cancer specific genes SEPT9 in EVs derived from both genomic DNA and EV DNA of the CRC cell line. Secondly, we isolated EV using LNP from plasma samples in a cohort of 19 CRC patients and 9 healthy donor controls. In parallel, we isolated circulating free DNA (cfDNA) from the same cohort of the plasma samples using commercially cfDNA isolation Kit. Then, SEPT9 methylation signature was analyzed by our quantitative real-time PCR assay in these 28 EV DNA samples and 28 cfDNA samples, respectively. In the 19 CRC samples, we identified 10 SEPT9 gene methylation samples from LNP-isolated EV DNA and cfDNA, respectively. In 9 healthy control samples, no SEPT9 methylation was detection in the EV-DNA samples, while one false-positive was detected with cfDNA. Thus, the sensitivity and specificity of EV-DNA in the detection of SEPT9 gene methylation from CRC were determined to be 53% and 100% respectively. In comparison, the sensitivity and specificity of cfDNA are 53% and 89%, respectively from this preliminary pilot study. This indicated that EV-DNA might be superior to cfDNA in detecting SEPT9 gene methylation for CRC screening. Citation Format: Sheng Zhang, Faming Wang, Mingxi Chen, Jeongyun Kim, Mengrou Lu, Hongzhang He, Siyang Zheng. A blood-based extracellular vesicles DNA methylation signature for colorectal cancer screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 998.

Tension Gauge Tethers as Tension Threshold and Duration Sensors.

Mechanotransduction, the process by which cells respond to tension transmitted through various supramolecular linkages, is important for understanding cellular behavior. Tension gauge tethers (TGTs), short fragments of double-stranded DNA that irreversibly break under shear-stretch conditions, have been used in live cell experiments to study mechanotransduction. However, our current understanding of TGTs' mechanical responses is limited, which limits the information that can be gleaned from experimental observations. In this study, we quantified the tension-dependent lifetime of TGTs to better understand their mechanical stability under various physiologically relevant stretching conditions. This work has broad applications for using TGTs as tension threshold and duration sensors and also suggests the need to revisit previous interpretations of experimental observations.

Tumor-Derived Extracellular Vesicles: Multifunctional Entities in the Tumor Microenvironment.

Tumor cells release extracellular vesicles (EVs) that can function as mediators of intercellular communication in the tumor microenvironment. EVs contain a host of bioactive cargo, including membrane, cytosolic, and nuclear proteins, in addition to noncoding RNAs, other RNA types, and double-stranded DNA fragments. These shed vesicles may deposit paracrine information and can also be taken up by stromal cells, causing the recipient cells to undergo phenotypic changes that profoundly impact diverse facets of cancer progression. For example, this unique form of cellular cross talk helps condition the premetastatic niche, facilitates evasion of the immune response, and promotes invasive and metastatic activity. These findings, coupled with those demonstrating that the number and content of EVs produced by tumors can vary depending on their tumor of origin, disease stage, or response to therapy, have raised the exciting possibility that EVs can be used for risk stratification, diagnostic, and even prognostic purposes. We summarize recent developments and the current knowledge of EV cargoes, their impact on disease progression, and implementation of EV-based liquid biopsies as tumor biomarkers.

Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin

The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.

Can a sperm selection technique improve embryo ploidy?

Spermatozoa with the highest motility retain a superior genomic integrity, and elevated sperm chromatin fragmentation (SCF) has been linked to a lower ability of the conceptus to develop and implant. Therefore, the utilization of a sperm selection method, such as microfluidic sperm selection (MFSS), is capable of reducing the SCF by yielding the most motile fraction of spermatozoa with the highest embryo developmental competence. What remains unclear, however, is the causal mechanism that linksSCF to an impaired embryo development. To identify a relationship between SCF and an unexpectedly high proportion of embryo aneuploidy, while addressing treatment options. We identified couples with a high incidence of embryo aneuploidy in a previous intracytoplasmic sperm injection (ICSI) cycle with pre-implantation genetic testing for aneuploidy (PGT-A), utilizing spermatozoa selected by density gradient (DG). Terminal deoxynucleotidyl dUTP transferase nick-end labeling (TUNEL) and neutral Comet assays were carried out on the semen specimens to assess total SCF and double-stranded DNA (dsDNA) fragmentation, respectively. These couples underwent subsequent ICSI/PGT-A cycles with MFSS. Total SCF and dsDNA fragmentation were compared between the two sperm selection methods. Embryo aneuploidy, implantation, clinical pregnancy, delivery,and pregnancy loss rates were compared between the couples' historical DG and subsequent MFSS cycles. In 57 couples undergoing 71 ICSI/PGT-A cycles, where DG sperm selection was carried out, a high incidence of aneuploid embryos (74.7%) resulted in poor implantation and no viable pregnancies. Testing for SCF, inclusive of dsDNA breaks, evidenced a SCF of 26.2% and dsDNA break of 3.6% in the raw specimen, that decreased to 18.0% (p < 0.001) and 3.1%, respectively, in the DG processed specimen. Following MFSS, total SCF and dsDNA fragmentation decreased to 1.9% and 0.3%, respectively (p<0.001). The embryo euploidy rate remarkable improved from 25.3% in the DG cycles to 42.9% in the MFSS cycles (p<0.001). The 6.7% implantation rate in the DG cycles increased to 65.5% in the MFSS cycles (p<0.001). Similarly, the clinical pregnancy rate rose from 10.5% (DG) to 64.6% (MFSS), resulting in a 62.5% delivery rate (p<0.001). In couples with a relatively young female partner with a negative infertility workup, and a male partner with semen parameters adequate for ICSI, presenting with a high rate of embryo aneuploidy, an additional subtle male factor component may be the culprit. Thus, it is crucial to assess the SCF and test for the dsDNA breaks, which can eventually contribute to embryo chromosomal abnormalities. Given the inverse relationship between SCF and motility, a selection of the most motile gamete by MFSS enhanced the proportion of spermatozoa with an intact genome, contributing to the generation of moreeuploid embryos that are capable of implanting and yielding increased term pregnancies.

Sperm DNA integrity does play a crucial role for embryo development after ICSI, notably when good-quality oocytes from young donors are used

Based on the inconsistent literature published thus far involving infertile patients, whether intracytoplasmic sperm injection (ICSI) allows overcoming total fertilization failure due to sperm DNA fragmentation is still unclear. Related to this, female factors, which may have a significant impact on assisted reproduction outcomes, can mask male infertility. In this scenario, evaluating ICSI outcomes following cycles using healthy donor gametes could shed light on this realm, as it would avoid the influence of (un)known confounding factors present in infertile individuals. The present work, therefore, aimed to address whether single- and double-stranded sperm DNA fragmentation leads to impaired ICSI outcomes in double gamete donation cycles. The study also compared these double-gamete donation cycles to cycles in which only sperm were donated and oocytes were obtained from infertile patients. Two cohorts were included: (a) the Donor-Donor (DD) cohort, which included 27 semen donor samples used in 49 ICSI cycles with young healthy oocyte donors; and (b) the Donor-Infertile (DI) cohort, which involved 34 semen donor samples used in 57 ICSI cycles with oocytes from patients. Single- and double-stranded sperm DNA breaks were determined with alkaline and neutral Comet assays, respectively; ICSI was conducted following standard protocols and embryos were monitored through time-lapse microscopy. In the DD cohort, the percentage of sperm with high overall DNA damage correlated with fertilization rates (Rs = − 0.666; P < 0.001) and with the percentage of blastocysts per injected oocyte (Rs = − 0.414; P = 0.040). In addition, sperm DNA damage delayed the first embryo division (Rs = 0.421; P = 0.036), and development from the 8-cell to the morula stage (Rs = 0.424; P = 0.034). In contrast, double-stranded DNA breaks had no effect in this cohort. As far as the DI cohort is concerned, while overall sperm DNA damage was not found to be correlated to fertilization or blastocyst rates, pronuclei formation following ICSI was delayed when the incidence of double-stranded DNA breaks was high (Rs = 0.485; P = 0.005). In conclusion, this study, which is the first involving double donation cycles (i.e., a donor-donor cohort), supports that sperm DNA damage has a detrimental impact on fertilization rates after ICSI, and delays embryo development. Moreover, the use of oocytes from infertile individuals is suggested to hide the male-factor effect.

Efficient modification and preparation of circular DNA for expression in cell culture

DNA plasmids are an essential tool for delivery and expression of RNAs and proteins in cell culture experiments. The preparation of plasmids typically involves a laborious process of bacterial cloning, validation, and purification. While the expression plasmids can be designed and ordered from the contract manufacturers, the cost may be prohibitive when a large number of plasmids is required. We have developed an efficient fully synthetic method and protocol that enables the production of circularized DNA containing expression elements ready for transfection in as little as 3 hours, thereby eliminating the bacterial cloning steps. The protocol describes how to take a linear double-stranded DNA fragment and efficiently circularize and purify this DNA fragment with minimal hands-on time. As proof of the principle, we applied Circular Vector expressing engineered prime editing guide RNA (epegRNA) in cell culture, and demonstrated matching and even exceeding performance of this method as compared to guides expressed by plasmids. The method’s speed of preparation, low cost, and ease of use will make it a useful tool in applications requiring the expression of short RNAs and proteins.

The New General Biological Property of Stem-like Tumor Cells (Part II: Surface Molecules, Which Belongs to Distinctive Groups with Particular Functions, Form a Unique Pattern Characteristic of a Certain Type of Tumor Stem-like Cells).

An ability of poorly differentiated cells of different genesis, including tumor stem-like cells (TSCs), to internalize extracellular double-stranded DNA (dsDNA) fragments was revealed in our studies. Using the models of Krebs-2 murine ascites carcinoma and EBV-induced human B-cell lymphoma culture, we demonstrated that dsDNA internalization into the cell consists of several mechanistically distinct phases. The primary contact with cell membrane factors is determined by electrostatic interactions. Firm contacts with cell envelope proteins are then formed, followed by internalization into the cell of the complex formed between the factor and the dsDNA probe bound to it. The key binding sites were found to be the heparin-binding domains, which are constituents of various cell surface proteins of TSCs-either the C1q domain, the collagen-binding domain, or domains of positively charged amino acids. These results imply that the interaction between extracellular dsDNA fragments and the cell, as well as their internalization, took place with the involvement of glycocalyx components (proteoglycans/glycoproteins (PGs/GPs) and glycosylphosphatidylinositol-anchored proteins (GPI-APs)) and the system of scavenger receptors (SRs), which are characteristic of TSCs and form functional clusters of cell surface proteins in TSCs. The key provisions of the concept characterizing the principle of organization of the "group-specific" cell surface factors of TSCs of various geneses were formulated. These factors belong to three protein clusters: GPs/PGs, GIP-APs, and SRs. For TSCs of different tumors, these clusters were found to be represented by different members with homotypic functions corresponding to the general function of the cluster to which they belong.

Host nucleases generate prespacers for primed adaptation in the E. coli type I-E CRISPR-Cas system.

CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In Escherichia coli, immunity is acquired upon integration of 33-bp spacers into CRISPR arrays. DNA targets complementary to spacers get degraded and serve as a source of new spacers during a process called primed adaptation. Precursors of such spacers, prespacers, are ~33-bp double-stranded DNA fragments with a ~4-nt 3' overhang. The mechanism of prespacer generation is not clear. Here, we use FragSeq and biochemical approaches to determine enzymes involved in generation of defined prespacer ends. We demonstrate that RecJ is the main exonuclease trimming 5' ends of prespacer precursors, although its activity can be partially substituted by ExoVII. The RecBCD complex allows single strand-specific RecJ to process double-stranded regions flanking prespacers. Our results reveal intricate functional interactions of genome maintenance proteins with CRISPR interference and adaptation machineries during generation of prespacers capable of integration into CRISPR arrays.

The new general biological property of stem-like tumor cells Part I. Peculiarities of the process of the double-stranded DNA fragments internalization into stem-like tumor cells.

Stem-like tumor cells of ascites carcinoma Krebs-2 and Epstein-Barr virus–induced B-lymphoma were shown to possess the innate capability of binding and internalizing the TAMRA-labeled double-stranded DNA (dsDNA) probe. The process of binding and internalizing is rather complicated and composed of the following successive stages: 1) initiating electrostatic interaction and contact of a negatively charged dsDNA molecule with a positively charged molecule(s) on the surface of a stem-like tumor cell; 2) binding of the dsDNA probe to a tumor stem cell surface protein(s) via the formation of a strong chemical/molecular bond; and 3) the very internalization of dsDNA into the cell. Binding of DNA to cell surface proteins is determined by the presence of heparin/polyanion-binding sites within the protein structure, which can be competitively blocked by heparin and/or dextran sulfate, wherein heparin blocks only the binding, while dextran sulfate abrogates both binding and internalization. The abrogation of internalization by dextran sulfate implies the role of scavenger receptors in this process. Cells were shown to uptake DNA in amounts constituting ∼0.008% of the haploid genome. Inhibitors of caveolae-dependent internalization abrogate the DNA uptake in Krebs-2 cells, and inhibitors of the clathrin/caveolar mechanism block the internalization in B-lymphoma cells. In the present report, it is shown for the first time that in contrast to the majority of committed tumor cells, stem-like tumor cells of Krebs-2 and B-lymphoma carry a general positive charge on their surface.

Seminal Microbiota of Idiopathic Infertile Patients and Its Relationship With Sperm DNA Integrity.

The development of new biomarkers for human male infertility is crucial to improve the diagnosis and the prognosis of this disease. Recently, seminal microbiota was shown to be related to sperm quality parameters, suggesting an effect in human fertility and postulating it as a biomarker candidate. However, its relationship to sperm DNA integrity has not been studied yet. The aim of the present study is to characterize the seminal microbiota of a western Mediterranean population and to evaluate its relationship to sperm chromatin integrity parameters, and oxidative stress. For that purpose, 14 samples from sperm donors and 42 samples from infertile idiopathic patients were obtained and were analyzed to assess the composition of the microbiota through full-length 16S rRNA gene sequencing (Illumina MiSeq platform). Microbial diversity and relative abundances were compared to classic sperm quality parameters (macroscopic semen parameters, motility, morphology and concentration), chromatin integrity (global DNA damage, double-stranded DNA breaks and DNA protamination status) and oxidative stress levels (oxidation-reduction potential). The seminal microbiota observed of these samples belonged to the phyla Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The most abundant genera were Finegoldia, Peptoniphilus, Anaerococcus, Campylobacter, Streptococcus, Staphylococcus, Moraxella, Prevotella, Ezakiella, Corynebacterium and Lactobacillus. To our knowledge, this is the first detection of Ezakiella genus in seminal samples. Two clusters of microbial profiles were built based on a clustering analysis, and specific genera were found with different frequencies in relation to seminal quality defects. The abundances of several bacteria negatively correlate with the sperm global DNA fragmentation, most notably Moraxella, Brevundimonas and Flavobacterium. The latter two were also associated with higher sperm motility and Brevundimonas additionally with lower oxidative-reduction potential. Actinomycetaceae, Ralstonia and Paenibacillus correlated with reduced chromatin protamination status and increased double-stranded DNA fragmentation. These effects on DNA integrity coincide in many cases with the metabolism or enzymatic activities of these genera. Significant differences between fertile and infertile men were found in the relative presence of the Propionibacteriaceae family and the Cutibacterium, Rhodopseudomonas and Oligotropha genera, which supports its possible involvement in male fertility. Our findings sustain the hypothesis that the seminal microbiome has an effect on male fertility.

Marker-free CRISPR-Cas9 based genetic engineering of the phytopathogenic fungus, Penicillium expansum

Filamentous fungi are prolific producers of secondary metabolites (SecMets), including compounds with antibiotic properties, like penicillin, that allows the producing fungus to combat competitors in a shared niche. However, the biological function of the majority of these small complex metabolites for the producing fungi remains unclear (Macheleidt et al., 2016). In an effort to address this lack of knowledge, we have chosen to study the microbial community of moldy apples in the hope of shedding more light on the role of SecMets for the dynamics of the microbial community. Penicillium expansum is one of the prevalent fungal species in this system, and in co-culture experiments with other apple fungal pathogens, we have observed up- and downregulation of several SecMets when compared to monocultures. However, molecular genetic dissection of the observed changes is challenging, and new methodologies for targeted genetic engineering in P. expansum are needed. In the current study, we have established a CRISPR-Cas9 dependent genetic engineering toolbox for the targeted genetic manipulation of P. expansum to allow for single-step construction of marker-free strains. The method and effect of different combinations of a Cas9-sgRNA expressing plasmids and repair template substrates in the NHEJ-proficient WT strain is tested by targeted deletion of melA, encoding a PKS responsible for pigment formation, which upon deletion resulted in white mutants. Co-transformation with a linear double-stranded DNA fragment consisting of two 2 kb homology arms flanking the PKS gene proved to be the most efficient strategy with 100% confirmed deletions by diagnostic PCR. Shorter homology arms (500–1000 bp) resulted in 20–30% deletion efficiency. Furthermore, we demonstrate the application of the CRISPR-Cas9 method for targeted deletion of biosynthetic genes without a visible phenotype, insertion of a visual reporter-encoding gene (mRFP), and overexpression of biosynthetic genes. Combined, these tools will advance in enabling the deciphering of SecMet biosynthetic pathways, provide in situ insight into when and where SecMets are produced, and provide an avenue to study the role of P. expansum SecMets in shaping the microbial community development on moldy apples via marker-free targeted genetic engineering of P. expansum.

Blunt-End Driven Re-entrant Ordering in Quasi Two-Dimensional Dispersions of Spherical DNA Brushes.

We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids coated with ultralong double-stranded DNA (dsDNA) fragments reveal nonmonotonic particle shrinking, aggregation, and re-entrant ordering. Theory and simulations show that aggregation and re-entrant ordering arise from the combined effect of shrinking, which is induced by the osmotic pressure exerted by the counterions absorbed in neighbor brushes and of a short-range attractive interaction competing with electrostatic repulsion. An unconventional mechanism gives origin to the short-range attraction: blunt-end interactions between stretched dsDNA fragments of neighboring brushes, which become sufficiently intense for dense and packed brushes. The attraction can be tuned by inducing free-end backfolding through the addition of monovalent salt. Our results show that base stacking is a mode parallel to hybridization to steer colloidal assembly in which attractions can be fine-tuned through salinity and, potentially, grafting density and temperature.

DOP46 Metabolic adaptation to ER stress licences STING signalling in intestinal epithelial cells

Abstract Background Chronic endoplasmic reticulum stress (ER) in the intestinal epithelium is a pathophysiological hallmark of IBD. cGAS/STING is an innate immune pathway involved in the detection of double stranded DNA fragments leading to the subsequent induction of type I IFN responses. We here tested the hypothesis that chronic ER stress impairs cGAS/STING signalling in the intestinal epithelium. Methods Mice with a conditional intestinal epithelial deletion of Xbp1 (Xbp1 ΔIEC, Xbp1fl/fl) were used to assess intestinal epithelial STING expression in-vivo. Small intestinal organoids (Xbp1ΔIEC, Xbp1fl/fl) and cell lines (Mode K, iCtrl and iXbp1) were used to assess cGAS/STING signalling in-vitro using STING agonist (dsDNA, DMXAA). Murine cytomegalovirus (mCMV) infection assays were performed in iCtrl and iXbp1cells and Xbp1ΔIEC, Xbp1fl/fl mice to functionally link impaired cGAS/STING to pathogen response. LC-MS profiling was performed in iCtrl and iXbp1cells to identify underlying metabolic programs affecting cGAS/STING responses in ER-stressed cells. IBD biopsy samples (cross-sectional, longitudinal therapy response cohort) were used to validate key molecular phenotypes in human IBD. Results Compared to Xbp1 fl/fl mice, Xbp1ΔIEC show completely abrogated STING expression in the basal crypt compartment of the small intestinal epithelium. In line with that iXbp1 ModeK cells displayed impaired pathway activation (TBK1) and interferon inducible gene expression (Cxcl10) in response to cGAS/STING stimulation and towards mCMV infection, leading to increased viral replication compared to iCtrl cells. In-vivo mCMV infection led to augmented small intestinal histopathological disease activity in Xbp1ΔIEC, but not Xbp1fl/fl mice. Using LC-MS, we show that ER-stress induces a metabolic adaptation towards increased serin/glycin metabolism, which is used to counterbalance reactive oxygen species (ROS) via glutathione (GSH) synthesis. Pharmacological interception of key pathways of GSH synthesis of deprivation of serin/glycin phenocopies ER-stress in abrogating STING signalling in IECs. Lastly, we show that key aspects of metabolic adaptation to ER-stress are present in intestinal biopsies of IBD patients. Conclusion Our data describe a novel mechanism of metabolic adaptation to compensate ER-stress and maintain intestinal epithelial cGAS/STING signalling. We therefore put forward a model of ER-stress driven immunodeficiency via cGAS/STING signalling which renders the intestinal mucosa susceptible towards CMV infection in the context of IBD.

DIRECT ELECTROCHEMICAL DETERMINATION OF MODIFIED DNA AMPLICONS CARRYING AROMATIC TYROSINE GROUPS FOR THE DETECTION OF DICKEYA SOLANI – THE CAUSATIVE AGENT OF POTATO BACTERIOSIS

Direct electrochemical determination of double-stranded DNA fragments obtained as a result of polymerase chain or recombinase polymerase reactions, using deoxyuridine triphosphates modified by the aromatic group of tyrosine as a substrate, was used to detect the causative agent of potato bacteriosis Dickeya solani.

A LAMP (loop-mediated isothermal amplification) test for rapid identification of Khapra beetle (Trogoderma granarium).

BACKGROUNDKhapra beetle (Trogoderma granarium Everts) is a significant pest of food products around the world, causing great losses of stored grain and produce, with export restrictions imposed on countries with established beetle populations. Khapra beetle is a high‐priority exotic invertebrate pest in many countries requiring a rapid quarantine/biosecurity response when incursions occur. To address this, we developed a novel Khapra LAMP (loop‐mediated isothermal amplification) assay using a portable real‐time fluorometer and an additional 18S ribosomal DNA (18S) insect control LAMP assay for confirmation of the presence of insect DNA. Both LAMP tests can be performed either in a portable real‐time fluorometer or using simple, visual colorimetric technique.RESULTSBoth the Khapra and 18S LAMP tests amplify positive samples within ≤ 25 min, with an anneal derivative temperature of 77.7 ± 0.7 °C for Khapra LAMP test and 88.0 ± 1.0 °C for 18S. The new Khapra LAMP assay is sensitive to very low levels of DNA (1.02 × 10 −6 ng μL−1). Additionally, we developed a gBlock double stranded DNA fragment for use as positive Khapra control with a different anneal derivative of 80 °C. Both assays are simple to use in the field and are capable of amplifying DNA from target beetles, even when samples are partially degraded which is typically found during surveillance activities. By screening a broad panel of Dermestidae species we demonstrate that our new assay is species‐specific, with no detections of false positives. Also, we evaluated multiple DNA extraction methods, with both QuickExtract and HotSHOT extraction methods proving suitable for in‐field use.CONCLUSIONThe novel Khapra and 18S LAMP assays should improve speed, accuracy and confidence of detection of Khapra beetle at incursion points and aid rapid biosecurity responses in any country affected, especially as the assays described here are portable and easy to implement in the field conditions where resources are limited. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.