Desiccated cat spermatozoa retain DNA integrity and developmental potential after prolonged storage and shipping at non-cryogenic temperatures.

PURPOSE: To evaluate the DNA integrity and developmental potential of microwave-dehydrated cat spermatozoa after storage at - 20 °C for different time periods and/or overnight shipping on dry ice. METHODS: Epididymal spermatozoa from domestic cats were microwave-dehydrated on coverslips after trehalose exposure. Dried samples were either assessed immediately, stored for various duration at - 20 °C, or shipped internationally on dry ice before continued storage. Dry-stored spermatozoa were rehydrated before assessing DNA integrity (TUNEL assays) or developmental potential (injection into in vitro matured oocytes followed by in vitro embryo culture for up to 7 days). RESULTS: Percentages of dried-rehydrated spermatozoa with intact DNA was not significantly affected (P > 0.05) by desiccation and short-term storage (range, 78.9 to 80.0%) but decreased (P < 0.05) with storage over 5 months (range, 71.0 to 75.2%) compared to fresh controls (92.6 ± 2.2%). After oocyte injection with fresh or dried-rehydrated spermatozoa (regardless of storage time), percentages of activation, pronuclear formation, and embryo development were similar (P > 0.05). Importantly, spermatozoa shipped internationally also retained the ability to support embryo development up to the morula stage. CONCLUSION: Results demonstrated the possibility to sustain DNA integrity and developmental potential of spermatozoa by dry-preservation, even after long-term storage and long-distance shipment at non-cryogenic temperatures. While further studies are warranted, present results demonstrate that dry preservation can be a reliable approach for simple and cost-effective sperm biobanking or shipment.

Electrostatic Drivers of GPx4 Interactions with Membrane, Lipids, and DNA.

Glutathione peroxidase 4 (GPx4) serves as the only enzyme that protects membranes through the reduction of lipid hydroperoxides, preventing membrane oxidative damage and cell death through ferroptosis. Recently, GPx4 has gained attention as a therapeutic target for cancer through inhibition and as a target for inflammatory diseases through activation. In addition, GPx4 isoforms perform several distinct moonlighting functions including cysteine cross-linking of protamines during sperm cell chromatin remodeling, a function for which molecular and structural details are undefined. Despite the importance in biology, disease, and potential for drug development, little is known about GPx4 functional interactions at high resolution. This study presents the first NMR assignments of GPx4, and the electrostatic interaction of GPx4 with the membrane is characterized. Mutagenesis reveals the cationic patch residues that are key to membrane binding and stabilization. The cationic patch is observed to be important in binding headgroups of highly anionic cardiolipin. A novel lipid binding site is observed adjacent to the catalytic site and may enable protection of lipid-headgroups from oxidative damage. Arachidonic acid is also found to engage with GPx4, while cholesterol did not display any interaction. The cationic patch residues were also found to enable DNA binding, the first observation of this interaction. Electrostatic DNA binding explains a mechanism for the nuclear isoform of GPx4 to target DNA-bound protamines and to potentially reduce oxidatively damaged DNA. Together, these results highlight the importance of electrostatics in the function of GPx4 and illuminate how the multifunctional enzyme is able to fill multiple biological roles.

EFFECT OF ADENYLATE KINASE 1 ON THE GROWTH AND DEVELOPMENT OF SCHISTOSOMA JAPONICUM SCHISTOSOMULUM.

We investigated the effect of Schistosoma japonicum adenylate kinase 1 (Sjak1) on the growth and development of schistosomula. Quantitative real-time PCR showed that Sjak1 mRNA was expressed in 3-, 10-, 14-, 18-, and 21-day-old schistosomula, and its levels increased gradually with the development of S. japonicum. Using immunohistochemical techniques, ak1 protein was found to be mainly distributed in the tegument and some parenchymal tissues of the schistosomula. Double-stranded RNA-mediated knockdowns of ak1 decreased ak1 mRNA transcripts by more than 90%, and western blot results showed that expression of ak1 protein was decreased by 66%. Scanning electron microscopy following the RNA-mediated ak1 knockdown showed that the sensory papillae did not develop. Transmission electron microscopy showed a lower mean thickness of the tegument in the Sjak1 interference group than in the negative control group. Terminal deoxynucleotidyl transferase dUTP nick-end labeling suggested higher apoptosis in the interference group than the negative control group. These results showed that ak1 may be involved in the growth and development of S. japonicum schistosomula and especially in the development of the integument. Consequently, ak1 may be a potential target in developing prevention methods for schistosomiasis in the future.

A role for condensin in mediating transcriptional adaptation to environmental stimuli.

Nuclear organisation shapes gene regulation; however, the principles by which three-dimensional genome architecture influences gene transcription are incompletely understood. Condensin is a key architectural chromatin constituent, best known for its role in mitotic chromosome condensation. Yet at least a subset of condensin is bound to DNA throughout the cell cycle. Studies in various organisms have reported roles for condensin in transcriptional regulation, but no unifying mechanism has emerged. Here, we use rapid conditional condensin depletion in the budding yeast Saccharomyces cerevisiae to study its role in transcriptional regulation. We observe a large number of small gene expression changes, enriched at genes located close to condensin-binding sites, consistent with a possible local effect of condensin on gene expression. Furthermore, nascent RNA sequencing reveals that transcriptional down-regulation in response to environmental stimuli, in particular to heat shock, is subdued without condensin. Our results underscore the multitude by which an architectural chromosome constituent can affect gene regulation and suggest that condensin facilitates transcriptional reprogramming as part of adaptation to environmental changes.

From RNA to DNA: Insights about the transition of informational molecule in the biological systems based on the structural proximity between the polymerases.

Structural relations in an evolutionary context of polymerases is crucial to gain insights into the transition from an RNA world to a Ribonucleoprotein world. Herein, we present a structural proximity tree for the polymerases, from which we observe that the enzymes that have RNA as substrate are more homogeneous than the group with DNA as substrate. The homogeneity observed in enzymes with RNA as a substrate, may be because they performed all steps in information processing. In this sense, the emergence of the DNA molecule posed new challenges to the biological systems, where several parts of the informational flow were individualized by the emergence of enzymes for each step. From the data presented, we propose a polymerase diversification model, in which we have RNA-dependent RNA polymerases as an ancestor and all other polymerases diverged directly from this group by a radiation process.

In vitro ameliorative effects of ellagic acid on vitality, motility and DNA quality in human spermatozoa.

Oxidative stress (OS) plays a significant role in the etiology of male infertility, resulting in the impairment of male reproduction. This condition, characterized by an imbalance in the levels of oxidizing and antioxidant species in the seminal fluid, has a harmful impact on sperm functions and DNA integrity. The present study aimed to evaluate the anti-genotoxic action of ellagic acid, a polyphenolic molecule of natural origin having a powerful antigenotoxic, anti-inflammatory and antiproliferative role. An OS condition was induced in vitro by incubating normozoospermic human semen samples in benzene for 45, 60 and 90 min. DNA integrity was evaluated by terminal deoxynucleotidyl transferase dUTP nick end labeling assay, RAPD-PCR was performed to calculate the genome template stability, while the percentage of intracellular reactive oxygen species (ROS) was assessed by the 2', 7'-dichlorofluorescein assay. Our results showed that ellagic acid has a consistent protective effect on DNA integrity, as well as on sperm vitality and motility, by counteracting generation of intracellular ROS. The results of this study suggest ellagic acid as a suitable molecule to protect sperm DNA from oxidative stress, with a potentially significant translational impact on the management of the male infertility.

Multivalent molecular tension probes as anisotropic mechanosensors: concept and simulation.

Cells use protein-based mechanosensors to measure the physical properties of their surroundings. Synthetic tension sensors made of proteins, DNA, and other molecular building blocks have recently emerged as tools to visualize and perturb the mechanics of these mechanosensors. While almost all synthetic tension sensors are designed to exhibit orientation-independent force responses, recent work has shown that biological mechanosensors often function in a manner that is highly dependent on force orientation. Accordingly, the design of synthetic mechanosensors with orientation-dependent force responses can provide a means to study the role of orientation in mechanosensation. Furthermore, the process of designing anisotropic force responses may yield insight into the physical basis for orientation-dependence in biological mechanosensors. Here, we propose a DNA-based molecular tension sensor design wherein multivalency is used to create an orientation-dependent force response. We apply chemomechanical modeling to show that multivalency can be used to create synthetic mechanosensors with force response thresholds that vary by tens of pN with respect to force orientation.

Exploiting replicative stress in gynecological cancers as a therapeutic strategy.

Elevated levels of replicative stress in gynecological cancers arising from uncontrolled oncogenic activation, loss of key tumor suppressors, and frequent defects in the DNA repair machinery are an intrinsic vulnerability for therapeutic exploitation. The presence of replication stress activates the DNA damage response and downstream checkpoint proteins including ataxia telangiectasia and Rad3 related kinase (ATR), checkpoint kinase 1 (CHK1), and WEE1-like protein kinase (WEE1), which trigger cell cycle arrest while protecting and restoring stalled replication forks. Strategies that increase replicative stress while lowering cell cycle checkpoint thresholds may allow unrepaired DNA damage to be inappropriately carried forward in replicating cells, leading to mitotic catastrophe and cell death. Moreover, the identification of fork protection as a key mechanism of resistance to chemo- and poly (ADP-ribose) polymerase inhibitor therapy in ovarian cancer further increases the priority that should be accorded to the development of strategies targeting replicative stress. Small molecule inhibitors designed to target the DNA damage sensors, such as inhibitors of ataxia telangiectasia-mutated (ATM), ATR, CHK1 and WEE1, impair smooth cell cycle modulation and disrupt efficient DNA repair, or a combination of the above, have demonstrated interesting monotherapy and combinatorial activity, including the potential to reverse drug resistance and have entered developmental pipelines. Yet unresolved challenges lie in balancing the toxicity profile of these drugs in order to achieve a suitable therapeutic index while maintaining clinical efficacy, and selective biomarkers are urgently required. Here we describe the premise for targeting of replicative stress in gynecological cancers and discuss the clinical advancement of this strategy.

Emerging strategies to target cancer metabolism and improve radiation therapy outcomes.

Cancer-specific metabolic changes support the anabolic needs of the rapidly growing tumor, maintain a favorable redox balance, and help cells adapt to microenvironmental stresses like hypoxia and nutrient deprivation. Radiation is extensively applied in a large number of cancer treatment protocols but despite its curative potential, radiation resistance and treatment failures pose a serious problem. Metabolic control of DNA integrity and genomic stability can occur through multiple processes, encompassing cell cycle regulation, nucleotide synthesis, epigenetic regulation of gene activity, and antioxidant defenses. Given the important role of metabolic pathways in oxidative damage responses, it is necessary to assess the potential for tumor-specific radiosensitization by novel metabolism-targeted therapies. Additionally, there are opportunities to identify molecular and functional biomarkers of vulnerabilities to combination treatments, which could then inform clinical decisions. Here, we present a curated list of metabolic pathways in the context of ionizing radiation responses. Glutamine metabolism influences DNA damage responses by mechanisms such as synthesis of nucleotides for DNA repair or of glutathione for ROS detoxification. Repurposed oxygen consumption inhibitors have shown promising radiosensitizing activity against murine model tumors and are now in clinical trials. Production of 2-hydroxy glutarate by isocitrate dehydrogenase1/2 neomorphic oncogenic mutants interferes with the function of α-ketoglutarate-dependent enzymes and modulates Ataxia Telangiectasia Mutated (ATM) signaling and glutathione pools. Radiation-induced oxidative damage to membrane phospholipids promotes ferroptotic cell loss and cooperates with immunotherapies to improve tumor control. In summary, there are opportunities to enhance the efficacy of radiotherapy by exploiting cell-inherent vulnerabilities and dynamic microenvironmental components of the tumor.

Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation.

BACKGROUND: Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo. RESULTS: As a basis for comparing lncRNAs and cellular properties among different cell types, we screened lncRNAs in human pluripotent stem cells (hPSCs) that were differentiated to an atlas of cell lineages. We found that paraspeckles, which form by aggregation of the lncRNA NEAT1, are scaled by the size of the nucleus, and that small DNA-binding molecules promote the disintegration of paraspeckles and other lncRNA condensates. Furthermore, we found that paraspeckles regulate the differentiation of hPSCs. CONCLUSIONS: Positive correlation between the size of the nucleus and the number of paraspeckles exist in numerous types of human cells. The tethering and structure of paraspeckles, as well as other lncRNAs, to the genome can be disrupted by small molecules that intercalate in DNA. The structure-function relationship of lncRNAs that regulates stem cell differentiation is likely to be determined by the dynamics of nucleus size and binding site accessibility.

Investigation of thermal properties of DNA structure with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches.

BACKGROUND AND OBJECTIVE: Thermal conductivity of Deoxyribonucleic acid molecules is important for nanotechnology applications. Theoretical simulations based on simple models predict thermal conductivity for these molecular structures. METHODS: In this work, we calculate the thermal properties of Deoxyribonucleic acid with precise atomic arrangement via equilibrium and non-equilibrium molecular dynamics approaches. In these methods, each Deoxyribonucleic acid molecule is represented by C, N, O, and P atoms and implemented dreidng potential to describe their atomic interactions. RESULTS: Our calculated rate for thermal conductivity via equilibrium and non-equilibrium molecular dynamics methods is 0.381 W/m K and 0.373 W/m K, respectively. By comparing results from these two methods, it was found that the results from equilibrium and non-equilibrium molecular dynamics methods are identical, approximately. On the other hand, the number of DNA molecules and the equilibrium temperature of the simulated structures were important factors in their thermal conductivity rates, and their thermal conductivity was calculated at 0.323 W/m K-0.381 W/m K intervals for equilibrium and 0.303 W/m K-0.373 W/m K interval for non-equilibrium calculations. CONCLUSIONS: These results are in good agreement with thermal conductivity calculation with other research groups.

Pyridoxine/pyridoxamine 5'-phosphate oxidase (Sgll/PNPO) is important for DNA integrity and glucose homeostasis maintenance in Drosophila.

Pyridoxine/pyridoxamine 5'-phosphate oxidase (PNPO) and pyridoxal kinase (PDXK) cooperate to produce pyridoxal 5'-phosphate (PLP), the active form of vitamin B6. PDXK phosphorylates pyridoxine, pyridoxamine, and pyridoxal by producing PNP, PMP, and PLP, whereas PNPO oxidizes PNP, PMP, into PLP. We previously demonstrated that PDXK depletion in Drosophila and human cells impacts on glucose metabolism and DNA integrity. Here we characterized sgll, the Drosophila ortholog of PNPO gene, showing that its silencing by RNA interference elicits chromosome aberrations (CABs) in brains and induces diabetic hallmarks such as hyperglycemia and small body size. We showed that in sgllRNAi neuroblasts CABs are largely produced by the genotoxic effect of the advanced glycation end products triggered by high glucose. As in sgllRNAi cells, part of PLP is still produced by PDXK activity, these data suggest that PLP dosage need to be tightly regulated to guarantee glucose homeostasis and DNA integrity.

Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability.

BACKGROUND: Denaturants, namely, urea and guanidinium chloride (GdmCl) affect the stability as well as structure of DNA. Critical assessment of the role of hydrogen bonding of these denaturants with the different regions of DNA is essential in terms of its stability and structural aspect. However, the understanding of the mechanistic aspects of structural change of DNA induced by the denaturants is not yet well understood. METHODS: In this study, various spectroscopic along with molecular dynamics (MD) simulation techniques were employed to understand the role of hydrogen bonding of these denaturants with DNA bases in their stability and structural change. RESULTS AND CONCLUSION: It has been found that both, GdmCl and urea intrude into groove region of DNA by striping surrounding water. The hydrogen bonding pattern of Gdm+ and urea with DNA bases in its groove region is multimodal and distinctly different from each other. The interaction of GdmCl with DNA is stabilized by electrostatic interaction whereas electrostatic and Lennard-Jones interactions both contribute for urea. Gdm+ forms direct hydrogen bond with the bases in the minor groove of DNA whereas direct and water assisted hydrogen bond takes place with urea. The hydrogen bond formed between Gdm+ with bases in the groove region of DNA is stronger than urea due to strong electrostatic interaction along with less self-aggregation of Gdm+ than urea. The distinct hydrogen bonding capability of Gdm+ and urea with DNA bases in its groove region affects its width differently. The interaction of Gdm+ decreases the width of the minor and major groove which probably increases the strength of hydrogen bond between the Watson-Crick base pairs of DNA leading to its stability. In contrast, the interaction of urea does not affect much to the width of the grooves except the marginal increase in the minor groove width which probably decreases the strength of hydrogen bond between Watson Crick base pairs leading to the destabilization of DNA. GENERAL SIGNIFICANCE: Our study clearly depicts the role of hydrogen bonding between DNA bases and denaturants in their stability and structural change which can be used further for designing of the guanidinium based drug molecules.

Influence of the age of the individual on the stability of boar sperm genetic material.

Routine evaluation of the sperm of livestock animals involves detection of morphological abnormalities. However, most sperm defects that reduce fertilizing capacity are a result of anomalies in spermatogenesis. The aim of the study was to evaluate the effect of a boar's age on the stability of the genetic material of its sperm. The age of the boar was found to have a significant effect on sperm DNA stability and chromatin structure. The highest percentage of spermatozoa with DNA fragmentation was found in the oldest group of boars (0,61%), while the highest proportion of spermatozoa with abnormal histone retention (8,01%) and protamination (9,78%) was found in the youngest group of boars. Aniline blue (AB), chromomycin A3 (CMA3) and acridine orange (AO) staining should be routinely used in individuals used for artificial insemination especially young animals at the start of their exploitation for breeding, as well as older individuals with an age-related decrease in the stability of genetic material. Earlier diagnosis based on additional tests would allow for stricter selection and elimination of males with fertility disorders from breeding, to be replaced by breeders of full value. It was also demonstrated that all three staining methods mentioned above can be used in classical morphological analysis, because they clearly distinguish the sperm head from the background of the slide. Chromomycin staining clearly reveals the midpiece and thus can be used as a specific staining method for its evaluation. Staining with aniline blue is a fast and simple test whose result can be analysed under a light microscope. This staining technique can be recommended for use at insemination stations.

An Acidic-Microenvironment-Driven DNA Nanomachine Enables Specific ATP Imaging in the Extracellular Milieu of Tumor.

Extracellular ATP is an emerging target for cancer treatment because it is a key messenger for shaping the tumor microenvironment (TME) and regulating tumor progression. However, it remains a great challenge to design biochemical probes for targeted imaging of extracellular ATP in the TME. A TME-driven DNA nanomachine (Apt-LIP) that permits spatially controlled imaging of ATP in the extracellular milieu of tumors with ultrahigh signal-to-background ratio is reported. It operates in response to the mild acidity in the TME with the pH (low) insertion peptide (pHLIP) module, thus allowing the specific anchoring of the structure-switching signaling aptamer unit to the membrane of tumor cells for "off-on" fluorescence imaging of the extracellular ATP. Apt-LIP allows for acidity driven visualization of different extracellular concentrations of exogenous ATP, as well as the monitoring of endogenous ATP release from cells. Furthermore, it is demonstrated that Apt-LIP represents a promising platform for the specific imaging of the extracellular ATP in both primary and metastatic tumors. Ultimately, since diverse aptamers are obtained through in vitro selection, this design strategy can be further applied for precise detection of various extracellular targets in the TME.

The many length scales of DNA packaging.

This collection of reviews focuses on the most exciting areas of DNA packaging at the current time. Many of the new discoveries are driven by the development of molecular or imaging techniques, and these are providing insights into the complex world of chromatin. As these new techniques continue to improve, we will be able to answer many of the questions we have now, while likely raising many new ones.

DAMPs and sterile inflammation in drug hepatotoxicity.

Drug hepatotoxicity is the leading cause of acute liver failure (ALF) in the developed countries. The early diagnosis and treatment are still problematic, and one important reason is the lack of reliable mechanistic biomarkers and therapeutic targets; therefore, searching for new biomarkers and therapeutic targets is urgent. Drug hepatotoxicity induces severe liver cells damage and death. Dead and damaged cells release endogenous damage-associated molecular patterns (DAMPs). Increased circulating levels of DAMPs (HMGB1, histones and DNA) can reflect the severity of drug hepatotoxicity. Elevated plasma HMGB1 concentrations can serve as early and sensitive mechanistic biomarker for clinical acetaminophen hepatotoxicity. DAMPS significantly contribute to liver injury and inhibiting the release of DAMPs ameliorates experimental hepatotoxicity. In addition, HMGB1 mediates 80% of gut bacterial translocation (BT) during acetaminophen toxicity. Gut BT triggers systemic inflammation, leading to multiple organ injury and mortality. Moreover, DAMPs can trigger and extend sterile inflammation, which contributes to early phase liver injury but improves liver regeneration at the late phase of acetaminophen overdose, because anti-inflammatory treatment reduces liver injury at early phase but impairs liver regeneration at late phase of acetaminophen toxicity, whereas pro-inflammatory therapy improves late phase liver regeneration. DAMPs are promising mechanistic biomarkers and could also be the potential therapeutic targets for drug hepatotoxicity. DAMPs-triggered sterile inflammation contributes to liver injury at early phase but improves liver regeneration at later phase of acetaminophen hepatotoxicity; therefore, anti-inflammatory therapy would be beneficial at early phase but should be avoided at the late phase of acetaminophen overdose.

DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins.

Recognition and repression of RNA targets by Argonaute proteins guided by small RNAs is the essence of RNA interference in eukaryotes. Argonaute proteins with diverse structures are also found in many bacterial and archaeal genomes. Recent studies revealed that, similarly to their eukaryotic counterparts, prokaryotic Argonautes (pAgos) may function in cell defense against foreign genetic elements but, in contrast, preferably act on DNA targets. Many crucial details of the pAgo action, and the roles of a plethora of pAgos with non-conventional architecture remain unknown. Here, we review available structural and biochemical data on pAgos and discuss their possible functions in host defense and other genetic processes in prokaryotic cells.

ClpAP protease is a universal factor that activates the parDE toxin-antitoxin system from a broad host range RK2 plasmid.

The activity of type II toxin-antitoxin systems (TA), which are responsible for many important features of bacterial cells, is based on the differences between toxin and antitoxin stabilities. The antitoxin lability results from bacterial protease activity. Here, we investigated how particular Escherichia coli cytosolic proteases, namely, Lon, ClpAP, ClpXP, and ClpYQ, affect the stability of both the toxin and antitoxin components of the parDE system from the broad host range plasmid RK2. The results of our in vivo and in vitro experiments show that the ParD antitoxin is degraded by the ClpAP protease, and dsDNA stimulates this process. The ParE toxin is not degraded by any of these proteases and can therefore cause growth inhibition of plasmid-free cells after an unequal plasmid distribution during cell division. We also demonstrate that the ParE toxin interaction with ParD prevents antitoxin proteolysis by ClpAP; however, this interaction does not prevent the ClpAP interaction with ParD. We show that ClpAP protease homologs affect plasmid stability in other bacterial species, indicating that ClpAP is a universal activator of the parDE system and that ParD is a universal substrate for ClpAP.