Extracellular nucleic acids

DNA-Directed Activation of Photocatalytic Labeling at Cell-Cell Contact Sites

Cell-cell interactions govern diverse biological activities, necessitating molecular tools for understanding and regulating these interactions. Photoredox chemistry can detect cell-cell interactions by anchoring photocatalysts on cellular membranes to generate reactive species that tag closely contacting cells. However, the activation of photocatalysts lacks precise spatial resolution for selectively labeling intercellular interfaces. Herein, we report a DNA-based approach to selectively activate photocatalytic reactions at cell-cell contacts. Two cell populations are coated with distinct DNA strands, which interact at intercellular contacts, mediating the site-specific turn-on of a Ru(bpy)3-type photocatalyst. We demonstrate high spatial specificity for intercellular chemical labeling in cultured mammalian cells. Furthermore, as a proof of concept, we activate the dynamic DNA catalyst at cell-cell contacts in response to customized DNA triggers. This study lays the foundation for designing versatile chemical tools with high spatial precision and programmable responsiveness, along with the temporal resolution afforded by photoirradiation, to investigate and manipulate cell-cell interactions.

Is cross-species horizontal gene transfer responsible for gallbladder carcinogenesis

BACKGROUND

Cross-species horizontal gene transfer (HGT) involves the transfer of genetic material between different species of organisms. In recent years, mounting evidence has emerged that cross-species HGT does take place and may play a role in the development and progression of diseases.

METHODS

Transcriptomic data obtained from patients with gallbladder cancer (GBC) was assessed for the differential expression of antisense RNAs (asRNAs). The Basic Local Alignment Search Tool (BLAST) was used for cross-species analysis with viral, bacterial, fungal, and ancient human genomes to elucidate the evolutionary cross species origins of these differential asRNAs. Functional enrichment analysis and text mining were conducted and a network of asRNAs targeting mRNAs was constructed to understand the function of differential asRNAs better.

RESULTS

A total of 17 differentially expressed antisense RNAs (asRNAs) were identified in gallbladder cancer tissue compared to that of normal gallbladder. BLAST analysis of 15 of these asRNAs (AFAP1-AS1, HMGA2-AS1, MNX1-AS1, SLC2A1-AS1, BBOX1-AS1, ELFN1-AS1, TRPM2-AS, DNAH17-AS1, DCST1-AS1, VPS9D1-AS1, MIR1-1HG-AS1, HAND2-AS1, PGM5P4-AS1, PGM5P3-AS1, and MAGI2-AS) showed varying degree of similarities with bacterial and viral genomes, except for UNC5B-AS1 and SOX21-AS1, which were conserved during evolution. Two of these 15 asRNAs, (VPS9D1-AS1 and SLC2A1-AS1) exhibited a high degree of similarity with viral genomes (Chikungunya virus, Human immunodeficiency virus 1, Stealth virus 1, and Zika virus) and bacterial genomes including (Staphylococcus sp., Bradyrhizobium sp., Pasteurella multocida sp., and, Klebsiella pneumoniae sp.), indicating potential HGT during evolution.

CONCLUSION

The results provide novel evidence supporting the hypothesis that differentially expressed asRNAs in GBC exhibit varying sequence similarity with bacterial, viral, and ancient human genomes, indicating a potential shared evolutionary origin. These non-coding genes are enriched with methylation and were found to be associated with cancer-related pathways, including the P53 and PI3K-AKT signaling pathways, suggesting their possible involvement in tumor development.

Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers

Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56% and 4-45% of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

New prospects of environmental RNA metabarcoding research in biological diversity, ecotoxicological monitoring, and detection of COVID-19: a critical review

Ecosystems are multifaceted and complex systems and understanding their composition is crucial for the implementation of efficient conservation and management. Conventional approaches to biodiversity surveys can have limitations in detecting the complete range of species present. In contrast, the study of environmental RNA (eRNA) offers a non-invasive and comprehensive method for monitoring and evaluating biodiversity across different ecosystems. Similar to eDNA, the examination of genetic material found in environmental samples can identify and measure many species, including ones that pose challenges to traditional methods. However, eRNA is degraded quickly and therefore shows promise in detection of living organisms closer to their actual location than eDNA methods. This method provides a comprehensive perspective on the well-being of ecosystems, facilitating the development of focused conservation approaches to save at-risk species and uphold ecological equilibrium. Furthermore, eRNA has been recognized as a valuable method for the identification of COVID-19 in the environment, besides its established uses in biodiversity protection. The SARS-CoV-2 virus, which is accountable for the worldwide epidemic, releases RNA particles into the surrounding environment via human waste, providing insights into the feasibility of detecting it in wastewater and other samples taken from the environment. In this article, we critically reviewed the recent research activities that use the eRNA method, including its utilization in biodiversity conservation, ecological surveillance, and ecotoxicological monitoring as well as its innovative potential in identifying COVID-19. Through this review, the reader can understand the recent developments, prospects, and challenges of eRNA research in ecosystem management and biodiversity conservation.

Brain alarm by self-extracellular nucleic acids: from neuroinflammation to neurodegeneration

Neurological disorders such as stroke, multiple sclerosis, as well as the neurodegenerative diseases Parkinson's or Alzheimer's disease are accompanied or even powered by danger associated molecular patterns (DAMPs), defined as endogenous molecules released from stressed or damaged tissue. Besides protein-related DAMPs or "alarmins", numerous nucleic acid DAMPs exist in body fluids, such as cell-free nuclear and mitochondrial DNA as well as different species of extracellular RNA, collectively termed as self-extracellular nucleic acids (SENAs). Among these, microRNA, long non-coding RNAs, circular RNAs and extracellular ribosomal RNA constitute the majority of RNA-based DAMPs. Upon tissue injury, necrosis or apoptosis, such SENAs are released from neuronal, immune and other cells predominantly in association with extracellular vesicles and may be translocated to target cells where they can induce intracellular regulatory pathways in gene transcription and translation. The majority of SENA-induced signaling reactions in the brain appear to be related to neuroinflammatory processes, often causally associated with the onset or progression of the respective disease. In this review, the impact of the diverse types of SENAs on neuroinflammatory and neurodegenerative diseases will be discussed. Based on the accumulating knowledge in this field, several specific antagonistic approaches are presented that could serve as therapeutic interventions to lower the pathological outcome of the indicated brain disorders.

PANoptosome signaling and therapeutic implications in infection: central role for ZBP1 to activate the inflammasome and PANoptosis

The innate immune response provides the first line of defense against infection and disease. Regulated cell death (RCD) is a key component of innate immune activation, and RCD must be tightly controlled to clear pathogens while preventing excess inflammation. Recent studies have highlighted a central role for the innate immune sensor Z-DNA-binding protein 1 (ZBP1) as an activator of a form of inflammatory RCD called PANoptosis, which is regulated by a multifaceted cell death complex called the PANoptosome. In response to influenza A virus infection, ZBP1 activates the nucleotide-binding oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome, which then acts as an integral component of the ZBP1-PANoptosome to drive inflammatory cell death, PANoptosis. In this context, the NLRP3 inflammasome is critical for caspase-1 activation and proinflammatory cytokine interleukin (IL)-1β and IL-18 maturation, but dispensable for cell death due to functional redundancies between PANoptosome molecules. Similarly, ZBP1 is also central to the absent in melanoma 2 (AIM2)-PANoptosome; this PANoptosome forms in response to Francisella novicida and herpes simplex virus 1 infection and incorporates the AIM2 inflammasome as an integral component. In this review, we will discuss the critical roles of ZBP1 in mediating innate immune responses through inflammasomes, PANoptosomes, and PANoptosis during infection. An improved understanding of the molecular mechanisms of innate immunity and cell death will be essential for the development of targeted modalities that can improve patient outcomes by mitigating severe disease.

Environmental risks of antibiotic resistance genes released from biological laboratories and its control measure

Antibiotic resistance genes (ARGs) are a growing global threat to public health. Biological laboratory wastewater contains large amounts of free ARGs. It is important to assess the risk of free ARGs from biological laboratories and to find appropriate treatments to control their spread. The fate of plasmids in the environment and the effect of different thermal treatments on their persistence activity were tested. The results showed that untreated resistance plasmids could exist in water for more than 24 h (the special 245 bp fragment). Gel electrophoresis and transformation assays showed that the plasmids boiled for 20 min retained 3.65% ± 0.31% transformation activity of the intact plasmids, while autoclaving for 20 min at 121 °C could effectively degrade the plasmids and that NaCl, bovine serum albumin, and EDTA-2Na affected the degradation efficiency of the plasmids during boiling. In the simulated aquatic system, using 10⁶ copy/μL of plasmids after autoclaving, only 10² copies/μL of the fragment after only 1-2 h could be detected. By contrast, boiled plasmids for 20 min were still detectable after plunging them into water for 24 h. These findings suggest that untreated and boiled plasmids can remain in the aquatic environment for a certain time resulting in the risk of disseminating ARGs. However, autoclaving is an effective way of degrading waste free resistance plasmids.

Effect of pH on the mitigation of extracellular/intracellular antibiotic resistance genes and antibiotic resistance pathogenic bacteria during anaerobic fermentation of swine manure

Effects of various initial pH values (i.e., 3, 5, 7, 11) during anaerobic fermentation of swine manure on intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) and ARG-carrying potential microbial hosts were investigated. The abundance of almost all iARGs and eARGs decreased by 0.1-1.7 logs at pH 3 and pH 5. The abundance of only three iARGs and eARGs decreased by 0.1-0.9 logs at pH 7 and pH 11. Under acidic initial fermentation conditions (pH 3 and pH 5), the ARG removal effect was more pronounced. Acidic conditions (pH 3 and pH 5) significantly reduced the diversity and abundance of the microbial community, thereby eliminating many potential ARG hosts and antibiotic-resistant pathogenic bacteria (ARPB). Therefore, the study results contribute to the investigation of the effects of swine manure anaerobic fermentation on the removal and risk of contamination of ARGs and ARPB.

Profiling of intracellular and extracellular antibiotic resistance genes in municipal wastewater treatment plant and their effluent-receiving river

The presence of antibiotic resistance genes (ARGs) and heavy metal resistance genes (MRGs) in extracellular and intracellular DNA (eDNA and iDNA) has received considerable attention in recent years owing to the potential threat to human health and the ecosystem. As a result, we investigated six ARGs, three MRGs, and two mobile genetic elements (MGEs) in the municipal wastewater treatment plant (MWWTP) and its adjacent environments. Results revealed that the absolute abundances of eARGs and eMRGs were lower than iARGs and iMRGs in MWWTP. By contrast, eARGs and eMRGs were higher in river sediments. Among ARGs, aminoglycoside resistance genes (aadA) was the most abundant gene (3.13 × 10² to 2.31 × 10⁶ copies/mL in iDNA; 1.27 × 10³ to 7.23 × 10⁵ copies/mL in eDNA) in MWWTP, while zntA gene (9.4 × 10² to 3.97 × 10⁶ copies/mL in iDNA; 3.2 × 10³ to 6 × 10⁵ copies/mL in eDNA) was amongst the MRGs. Notably, intI1 was enriched and positively correlated with iDNA (tetA, sul1, blaCTX-M, ermB, and merA) and eDNA (blaCTX-M, ermB, and merA), demonstrating its function in the proliferation of resistance genes. This widespread distribution of ARGs, MRGs, and MGEs in MWWTP and its adjacent river sediments will help clarify the transmission routes within these environments and provide a theoretical basis for better monitoring and mitigation of such dissemination.

Microplastisphere may induce the enrichment of antibiotic resistance genes on microplastics in aquatic environments: A review

Microplastics have been proven to be hotspots of bacterial pathogens and antibiotic resistance genes (ARGs). The enrichment of ARGs in microplastisphere, the specific niche for diverse microbial communities attached to the surface of microplastic, has attracted worldwide attention. By collecting 477 pairs of ARG abundance data belonging to 26 ARG types, based on the standardized mean difference (SMD) under the random effect model, we have performed the first meta-analysis of the ARG enrichment on microplastics in aquatic environments in order to quantitatively elucidate the enrichment effect, with comparison of non-microplastic materials. It was found that ARGs enriched on the microplastics were more abundant than that on the inorganic substrates (SMD = 0.26) and natural water environments (SMD = 0.10), but lower abundant than that on the natural organic substrates (SMD = -0.52). Furthermore, microplastics in freshwater tended to have a higher degree of ARG enrichment than those in saline water and sewage. The biofilm formation stage, structure, and component of microplastisphere may play a significant role in the enrichment of ARGs.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome

Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.

The Influence of Proteins on Fate and Biological Role of Circulating DNA

Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA's fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.

Escherichia coli Can Eat DNA as an Excellent Nitrogen Source to Grow Quickly

Is DNA or RNA a good nutrient? Although scientists have raised this question for dozens of years, few textbooks mention the nutritional role of nucleic acids. Paradoxically, mononucleotides are widely added to infant formula milk and animal feed. Interestingly, competent bacteria can bind and ingest extracellular DNA and even integrate it into their genome. These results prompt us to clarify whether bacteria can “eat” DNA as food. We found that Escherichia coli can grow well in the medium with DNA as carbon and nitrogen sources. More interestingly, in the presence of glucose and DNA, bacteria grew more rapidly, showing that bacteria can use DNA as an excellent nitrogen source. Surprisingly, the amount of DNA in the culture media decreased but its length remained unchanged, demonstrating that E. coli ingested long DNA directly. The gene expression study shows that E. coli mainly ingests DNA before digestion and digests it in the periplasm. Bifidobacterium bifidum can also use DNA as the nitrogen source for growth, but not efficiently as E. coli. This study is of great significance to study DNA metabolism and utilization in organisms. It also lays a foundation to understand the nutritional function of DNA in intestinal flora and human health.

Extracellular polymeric substances (EPS) associated extracellular antibiotic resistance genes in activated sludge along the AAO process: Distribution and microbial secretors

Wastewater treatment plants (WWTPs) are important sources of antibiotic resistance genes (ARGs). Increasing attention has been paid to extracellular ARGs in cell-free form due to their horizontal gene transfer via transformation. However, the fate of the adsorbed form of extracellular ARGs that exist in extracellular polymeric substances (EPS) of activated sludge in WWTP remains largely unknown. Herein, seven EPS-associated ARGs along the anaerobic-anoxic-aerobic (AAO) process were quantified using quantitative polymerase chain reaction. Results show that the absolute abundances of EPS-associated ARGs were 0.69-4.52 logs higher than those of cell-free ARGs. There was no significant difference in the abundances of EPS-associated ARGs along the AAO process. Among these target genes, the abundances of EPS-associated sul genes were higher than those of EPS-associated tet and bla genes. Proteobacteria and Bacteroidetes were identified as the major secretors of EPS-associated ARGs, and they may play an important role in the proliferation of extracellular ARGs. Moreover, the transformation efficiencies of EPS-associated ARGs were 3.55-4.65 logs higher than those of cell-free ARGs, indicating that EPS-associated ARGs have higher environmental risks. These findings have advanced our understanding of EPS-associated ARGs and are useful for the control and risk assessment of ARGs in WWTPs.

Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids

Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.

Toward Sensitive and Reliable Surface-Enhanced Raman Scattering Imaging: From Rational Design to Biomedical Applications

Early specific detection through indicative biomarkers and precise visualization of lesion sites are urgent requirements for clinical disease diagnosis. However, current detection and optical imaging methods are insufficient for these demands. Molecular imaging technologies are being intensely studied for reliable medical diagnosis. In the past several decades, molecular imaging with surface-enhanced Raman scattering (SERS) has significant advances from analytical chemistry to medical science. SERS is the inelastic scattering generated from the interaction between photons and substances, presenting molecular structure information. The outstanding SERS virtues of high sensitivity, high specificity, and resistance to biointerference are highly advantageous for biomarker detection in a complex biological matrix. In this work, we review recent progress on the applications of SERS imaging in clinical diagnostics. With the assistance of SERS imaging, the detection of disease-related proteins, nucleic acids, small molecules, and pH of the cellular microenvironment can be implemented for adjuvant medical diagnosis. Moreover, multimodal imaging integrates the high penetration and high speed of other imaging modalities and imaging precision of SERS imaging, resulting in final complete and accurate imaging outcomes and exhibiting robust potential in the discrimination of pathological tissues and surgical navigation. As a promising molecular imaging technology, SERS imaging has achieved remarkable performance in clinical diagnostics and the biomedical realm. It is expected that this review will provide insights for further development of SERS imaging and promote the rapid progress and successful translation of advanced molecular imaging with clinical diagnostics.

Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area

Aquaculture is the productive activity that will play a crucial role in the challenges of the millennium, such as the need for proteins that support humans and the respect for the environment. Aquaculture is an important economic activity in the Mediterranean basin. A great impact is presented, however, by aquaculture practices as they involve the use of antibiotics for treatment and prophylaxis. As a consequence of the use of antibiotics in aquaculture, antibiotic resistance is induced in the surrounding bacteria in the column water, sediment, and fish-associated bacterial strains. Through horizontal gene transfer, bacteria can diffuse antibiotic-resistance genes and mobile resistance genes further spreading genetic determinants. Once triggered, antibiotic resistance easily spreads among aquatic microbial communities and, from there, can reach human pathogenic bacteria, making vain the use of antibiotics for human health. Climate change claims a significant role in this context, as rising temperatures can affect cell physiology in bacteria in the same way as antibiotics, causing antibiotic resistance to begin with. The Mediterranean Sea represents a 'hot spot' in terms of climate change and aspects of antibiotic resistance in aquaculture in this area can be significantly amplified, thus increasing threats to human health. Practices must be adopted to counteract negative impacts on human health, with a reduction in the use of antibiotics as a pivotal point. In the meantime, it is necessary to act against climate change by reducing anthropogenic impacts, for example by reducing CO2 emissions into the atmosphere. The One Health type approach, which involves the intervention of different skills, such as veterinary, ecology, and medicine in compliance with the principles of sustainability, is necessary and strongly recommended to face these important challenges for human and animal health, and for environmental safety in the Mediterranean area.

The Role of Exosomes in Breast Cancer Diagnosis

The importance of molecular re-characterization of metastatic disease with the purpose of monitoring tumor evolution has been acknowledged in numerous clinical guidelines for the management of advanced malignancies. In this context, an attractive alternative to overcome the limitations of repeated tissue sampling is represented by the analysis of peripheral blood samples as a 'liquid biopsy'. In recent years, liquid biopsies have been studied for the early diagnosis of cancer, the monitoring of tumor burden, tumor heterogeneity and the emergence of molecular resistance, along with the detection of minimal residual disease. Interestingly, liquid biopsy consents the analysis of circulating tumor cells, circulating tumor DNA and extracellular vesicles (EVs). In particular, EVs play a crucial role in cell communication, carrying transmembrane and nonmembrane proteins, as well as metabolites, lipids and nucleic acids. Of all EVs, exosomes mirror the biological fingerprints of the parental cells from which they originate, and therefore, are considered one of the most promising predictors of early cancer diagnosis and treatment response. The present review discusses current knowledge on the possible applications of exosomes in breast cancer (BC) diagnosis, with a focus on patients at higher risk.

Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine

Simple Summary

Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed.

Abstract

Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants

Serious concerns have been raised regarding antibiotic resistance genes (ARGs) with respect to their potential threat to human health. Wastewater treatment plants (WWTPs) have been considered to be hotspots for ARGs. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) was used to profile size-dependent ARGs and mobile genetic elements (MGEs) divided by particle-associated (PA) assemblages (>3.0-μm), free-living (FL) bacteria (0.2 - 3.0-μm) and cell-free (CF) DNA (< 0.2-μm) in two full-scale WWTPs (plants A and B) and a receiving stream. The results revealed that FL-ARGs were predominant in WWTPs and the receiving stream, especially in the final effluent of both plants. More than 40 types of CF-ARGs and CF-MGEs were detected with absolute abundances ranging from 6.0 ± 0.7 × 10⁵ to 1.0 ± 0.2 × 10⁸ copies/mL in wastewater, and relatively high abundances were also detected in the final effluent of the two plants, suggesting that CF-ARGs were important sources spreading from the WWTPs to the receiving environment. Plant A exhibited higher log-removal of size-fractionated ARGs and MGEs than was observed for plant B, which was attributed to the enhanced settleability of PA assemblages and FL bacteria by additional macrophytes and chemical coagulants. Ultraviolet disinfection had limited effects on ARGs and MGEs of the PA and FL fractions, which was probably ascribed to the protective matrices of the particles and cell walls. The bacterial communities of the two plants were significantly different among the size fractions (p < 0.01). The variation partitioning analysis (VPA) indicated that the microbial community structures and MGEs contributed a variation of 68.2% in total to the relative abundance changes of size-fractionated ARGs. Procrustes analyses and Mantel tests showed that the relative abundances of ARGs were significantly correlated with bacterial community structures. These results suggested that the bacterial community structures and MGEs might have been the main drivers of the size-fractionated ARG disseminations. This study provides novel insights into size-fractionated ARGs and MGEs in full-scale WWTPs and may lead to the identification of key targets to control the spread of ARGs.

Extracellular DNA builds and interacts with vibrio polysaccharide in the biofilm matrix formed by Vibrio cholerae

Vibrio cholerae form biofilm, which is essential for their survival under harsh environmental conditions. The eDNA produced during biofilm formation and interaction with other components like vibrio polysaccharide is less studied in Vibrio cholerae despite its importance in biofilm structure and stability. In this study, we selected two strains of V. cholerae, which produced sufficient extracellular DNA in the biofilm, for characterization and studied its interaction with vibrio polysaccharide. Our data demonstrate that eDNA is present in the biofilm and interacts with VPS in V. cholerae. Our findings suggest that eDNA contributes to biofilm integrity by interacting with VPS and provides strength to the biofilm. Moreover, it might interact with other components of biofilm, which need further study.

The environmental contribution to the dissemination of carbapenem and (fluoro)quinolone resistance genes by discharged and reused wastewater effluents: The role of cellular and extracellular DNA

Wastewater treatment plants (WWTPs) are major reservoirs and sources for the dissemination of antibiotic resistance into the environment. In this study, the population dynamics of two full-scale WWTPs was characterized along different sampling points, including the reused effluents, in both cellular and extracellular DNA samples. The analysis was performed by high throughput sequencing targeting the 16S rRNA V4 gene region and by three in-house TaqMan multiplex qPCR assays that detect and quantify the most clinically relevant and globally distributed carbapenem (bla) and (fluoro)quinolone (qnr) resistance genes. The obtained results identify the biological treatment as the crucial step on tailoring the wastewater bacterial community, which is thereafter maintained in both discharged and reused effluents. The influent bacterial community does not alter the WWTP core community, although it clearly contributes for the introduction and spread of antibiotic resistance to the in-house bacteria. The presence of high concentrations of bla and qnr genes was not only detected in the wastewater influents and discharged effluents, but also in the reused effluents, which therefore represent another gateway for antibiotic resistant bacteria and genes into the environment and directly to the human populations. Moreover, and together with the study of the cellular DNA, it was described for the first time the role of the extracellular DNA in the dissemination of carbapenem and (fluoro)quinolone resistance, as well as the impact of the wastewater treatment process on this DNA fraction. Altogether, the results prove that the current wastewater treatments are inefficient in the removal of antibiotic resistant bacteria and genes and reinforce that targeted treatments must be developed and implemented at full-scale in the WWTPs for wastewater reuse to become a safe and sustainable practice, able to be implemented in areas such as agricultural irrigation.

Minimizing extracellular DNA improves the precision of microbial community dynamic analysis in response to thermal hydrolysis

Extracellular DNA (exDNA) can induce bias when evaluating the microbiota in wastewater treatment systems, particularly when cell lysis caused by thermal hydrolysis pretreatment (THP) releasing abundant DNA. However, the influence of such exDNA is still unknown. Accordingly, this study applied a pretreatment strategy for DNA extraction with proteinase K and DNase Ⅰ to minimize the influence of exDNA when evaluating the sludge microbiota. Lactobacillus and Peptostreptococcus were confirmed as the main THP-resistant microorganisms. Gram-positive bacteria were more resistant to THP, implying that the presence of a cell wall could promote THP resistance in bacteria. Moreover, the ability to form spores did not affect the resistance of bacteria to THP. These findings showed that resistant microbiota could be effectively evaluated by excluding exDNA, which can provide important insights into the understanding of microbiota dynamic and the effects of pretreatment on the precision of microbiota analysis in sludge.

Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential

Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion-dependent manner. However, a few metal ion-independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion-independent nucleases are presented and discussed.Key Points • Bacterial phospholipases (PLD-family) exhibit nucleolytic activity. • Bacterial nucleases of the PLD-family are metal ion-independent. • NSNs can be used in downstream processing approaches.

The discrepant mobility of antibiotic resistant genes: Evidence from their spatial distribution in sewage sludge flocs

The present study stratified excess activated sludge from six municipal wastewater treatment plants into four extracellular fractions including supernatant, slime, slightly-bond extracellular polymeric substances (LB-EPS) and tightly-bond EPS (TB-EPS) and one intracellular fraction (pellet) according to their different degrees of tight binding to sludge microbial aggregates and determined the abundance of seven antibiotic resistance genes (ARGs) (sul-I, sul-II, tet-C, tet-X, blaTEM, mefA and cat) and one mobile genetic elements (MGEs) (IntI-1) in each fraction. Extracellular ARGs were found to make up 0.1% - 74.2% of total ARGs, while the ratio of extracellular DNA to total DNA was only 1.2% - 4.2%, implying that EPS was a major ARG reservoir in sewage sludge. The genes of sul-I, tet-C and mefA have the highest mobility owing to a large proportion ranging from 0.5% to 32.7% in the fractions of LB-EPS, slime and supernatant, which indicates an increased risk of mediating the transfer of ARGs to environment. Comparatively, the proportion of blaTEM in the TB-EPS of sludge accounted for 0.3%-34.9% and caused limited-mobility. Sul-II, tet-X and cat and IntI-1, made up approximately 82.6% - 99.6% proportion in the cells, and were thus less mobile. This study proposes that ARGs and MGEs can have different mobilities. Those located in the outermost layers of sludge have a higher mobility potential of propagation into the natural environment during wastewater treatment and sludge utilization, leading to an increased risk of transferability.

Fates of intracellular and extracellular antibiotic resistance genes and microbial community structures in typical swine wastewater treatment processes

Swine wastewater is an important reservoir of spread antibiotic resistance to the environment. Intra- and extracellular antibiotic resistance genes (iARGs and eARGs) were quantified during two typical swine wastewater treatment processes including a sequencing membrane bioreactor (SMBR) at pilot-scale and anaerobic-anoxic-oxic (A²O) at full-scale. The concentrations of iARGs and eARGs in raw wastewater were 3.42E+09 and 3.79E+07 copies/mL, respectively. The compositions were different between iARGs and eARGs. SMBR showed 0.63 log higher removals in the concentrations of iARG than A²O, while similar removal effects (3.01-3.44 log copies/mL) of eARGs were performed by the two processes. It suggested that membrane separation had advantages in the concentration removals of iARG rather than eARG. sul1 took the dominance in eARGs in effluent and had positive correlations with intI1, which indicated the risk of horizontal gene transfer of eARGs after wastewater discharge. Microbial community structures were estimated by 16S rRNA gene sequencing with both intra- and extracellular DNA (iDNA and eDNA). Compared between the effluent samples of the two treatment processes, microbial community structures estimated by iDNA had great differences, however which were similar for eDNA. Microbial community and water-quality parameters were the major influencing factors on ARG occurrences during swine wastewater treatment.

Extracellular DNA: A Nutritional Trigger of Mycoplasma bovis Cytotoxicity

Microbial access to host nutrients is a key factor of the host-pathogen interplay. With their nearly minimal genome, wall-less bacteria of the class Mollicutes have limited metabolic capacities and largely depend on host nutrients for their survival. Despite these limitations, host-restricted mycoplasmas are widely distributed in nature and many species are pathogenic for humans and animals. Yet, only partial information is available regarding the mechanisms evolved by these minimal pathogens to meet their nutrients and the contribution of these mechanisms to virulence. By using the ruminant pathogen Mycoplasma bovis as a model system, extracellular DNA (eDNA) was identified as a limiting nutrient for mycoplasma proliferation under cell culture conditions. Remarkably, the growth-promoting effect induced by supplementation with eDNA was associated with important cytotoxicity for actively dividing host cells, but not confluent monolayers. To identify biological functions mediating M. bovis cytotoxicity, we produced a library of transposon knockout mutants and identified three critical genomic regions whose disruption was associated with a non-cytopathic phenotype. The coding sequences (CDS) disrupted in these regions pointed towards pyruvate metabolism as contributing to M. bovis cytotoxicity. Hydrogen peroxide was found responsible for eDNA-mediated M. bovis cytotoxicity, and non-cytopathic mutants were unable to produce this toxic metabolic compound. In our experimental conditions, no contact between M. bovis and host cells was required for cytotoxicity. Further analyses revealed important intra-species differences in eDNA-mediated cytotoxicity and H₂O₂ production, with some strains displaying a cytopathic phenotype despite no H₂O₂ production. Interestingly, the genome of strains PG45 and HB0801 were characterized by the occurrence of insertion sequences (IS) at close proximity to several CDSs found disrupted in non-cytopathic mutants. Since PG45 and HB0801 produced no or limited amount of H₂O₂, IS-elements might influence H₂O₂ production in M. bovis. These results confirm the multifaceted role of eDNA in microbial communities and further identify this ubiquitous material as a nutritional trigger of M. bovis cytotoxicity. M. bovis may thus take advantage of the multiple sources of eDNA in vivo to modulate its interaction with host cells, a way for this minimal pathogen to overcome its limited coding capacity.

Occurrence of antibiotic resistance genes in extracellular and intracellular DNA from sediments collected from two types of aquaculture farms

The occurrence and quantities of ARGs in extracellular and intracellular DNA (eARGs and iARGs) from sediments collected in two different types of aquaculture farms were investigated. A total of 20 ARG subtypes associated with 7 categories of commonly used antibiotics (e.g., aminoglycosides, beta-lactams, sulfonamides, tetracyclines) were identified, and some of these subtypes were not related to the antibiotics used. ARGs are mainly present in the iDNA form with the ratio of the total iARGs to eARGs being in the range of 7.9-45.5. The ratio of eARG to iARGs varies greatly with ARG subtypes, probably due to their differences in persistence as a part of eDNA. Significant correlation between int1 and ARGs was observed for both eDNA and iDNA in sediments from the aquaculture farms. Moreover, ARG pollution was more serious in bullfrog ponds than polyculture ponds due to the more frequent use of antibiotics in bullfrog rearing operations.

Marine Purple Photosynthetic Bacteria as Sustainable Microbial Production Hosts

Photosynthetic microorganisms can serve as the ideal hosts for the sustainable production of high-value compounds. Purple photosynthetic bacteria are typical anoxygenic photosynthetic microorganisms and are expected to be one of the suitable microorganisms for industrial production. Purple photosynthetic bacteria are reported to produce polyhydroxyalkanoate (PHA), extracellular nucleic acids and hydrogen gas. We characterized PHA production as a model compound in purple photosynthetic bacteria, especially focused on marine strains. PHA is a family of biopolyesters synthesized by a variety of microorganisms as carbon and energy storage materials. PHA have recently attracted attention as an alternative to conventional petroleum-based plastics. Production of extracellular nucleic acids have been studied in Rhodovulum sulfidophilum, a marine purple non-sulfur bacterium. Several types of artificial RNAs have been successfully produced in R. sulfidophilum. Purple photosynthetic bacteria produce hydrogen via nitrogenase, and genetic engineering strategies have been investigated to enhance the hydrogen production. This mini review describes the microbial production of these high-value compounds using purple photosynthetic bacteria as the host microorganism.

Characterization of Vibrio cholerae's Extracellular Nuclease Xds

The Gram-negative bacterium Vibrio cholerae encodes two nucleases, Dns and Xds, which play a major role during the human pathogen's lifecycle. Dns and Xds control three-dimensional biofilm formation and bacterial detachment from biofilms via degradation of extracellular DNA and thus contribute to the environmental, inter-epidemic persistence of the pathogen. During intestinal colonization the enzymes help evade the innate immune response, and therefore promote survival by mediating escape from neutrophil extracellular traps. Xds has the additional function of degrading extracellular DNA down to nucleotides, which are an important nutrient source for V. cholerae. Thus, Xds is a key enzyme for survival fitness during distinct stages of the V. cholerae lifecycle and could be a potential therapeutic target. This study provides detailed information about the enzymatic properties of Xds using purified protein in combination with a real time nuclease activity assay. The data define an optimal buffer composition for Xds activity as 50 mM Tris/HCl pH 7, 100 mM NaCl, 10 mM MgCl2, and 20 mM CaCl2. Moreover, maximal activity was observed using substrate DNA with low GC content and ambient temperatures of 20-25°C. In silico analysis and homology modeling predicted an exonuclease domain in the C-terminal part of the protein. Biochemical analyses with truncated variants and point mutants of Xds confirm that the C-terminal region is sufficient for nuclease activity. We also find that residues D787 and H837 within the predicted exonuclease domain are key to formation of the catalytic center.

Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG

The emergence and spread of antibiotic resistance has pose a huge threat to both human health and environmental ecosystem. However, little is known regarding the pool of ARGs in extracellular DNA (eDNA). In this study ten ARGs (sul1, sul2, tetW, tetX, ermA, ermB, bla_TEM, ampC, cat and cmr) and class I integron (intI1) in the sludge from hospital, pharmaceutical industry, wastewater treatment plant (WWTP), and swine manure, and sediment in urban lake in the form of both eDNA and intracellular DNA (iDNA) were evaluated by quantitative polymerase chain reaction (qPCR). The results showed that every gram of sludge dry weight contained from 7.31 × 10³ to 1.16 × 10¹⁰ copies of extracellular ARGs (eARGs) and from 1.04 × 10⁵ to 2.74 × 10¹² copies of intracellular ARGs (iARGs). The sludge from hospital with the highest ratio of eARGs to total ARGs (11.02-89.63%), followed by the sediment from urban lake, implying that most of the ARGs in these regions were contributed by eARGs. The relative abundance of eARGs were higher than iARGs in sludge from WWTP and pharmaceutical industry, moreover, 1/3 and 5/9 detected eARGs were higher than the ARGs in the iDNA extracted from sludge of hospital and sediment from urban lake, respectively. Furthermore, the transforming ability of eARGs suggesting that adsorbed eARG is more preferentially coupled to the competent cells than free eARG. These findings highlight the need to focus attention on the contribution of eARGs to the dissemination of antibiotic resistance into environment, and also future needs in mitigating the spread of eARGs in the environment.

Optimal small-molecular reference RNA for RT-qPCR-based body fluid identification

MicroRNA (miRNA) -based body fluid identification (BFID) plays a prominent role in a forensic practice, and the selected reference RNA is indispensable for a robust normalization in BFID performed using reverse transcription-quantitative PCR. In this study, we first examined sample quality using RNA integrity number, then evaluated the consistency of expression of candidate reference RNAs in 4 forensically relevant body fluids using NormFinder and BestKeeper, and lastly used each rank and index output from these tools for selecting the optimal reference RNA and the combination of the multiple RNAs using the RankAggreg package of R. We found that RNA integrity number was small in our samples, despite the use of pristine body fluids; 5S-rRNA was the optimal reference RNA for the identification of forensically relevant body fluids; and the combination of 5S-rRNA and miR-92a-3p and/or miR-484 enhanced the normalization quality. Our findings enable us to perform stringent normalization of the expression of body fluid-specific RNAs, and thus, can contribute to the development of small RNA-based BFID systems.

Characterization of ExeM, an Extracellular Nuclease of Shewanella oneidensis MR-1

Bacterial extracellular nucleases have multiple functions in processes as diverse as nutrient acquisition, natural transformation, biofilm formation, or defense against neutrophil extracellular traps (NETs). Here we explored the properties of ExeM in Shewanella oneidensis MR-1, an extracellular nuclease, which is widely conserved among species of Shewanella, Vibrio, Aeromonas, and others. In S. oneidensis, ExeM is crucial for normal biofilm formation. In vitro activity measurements on heterologously produced ExeM revealed that this enzyme is a sugar-unspecific endonuclease, which requires Ca²⁺ and Mg²⁺/Mn²⁺ as co-factors for full activity. ExeM was almost exclusively localized to the cytoplasmic membrane fraction, even when a putative C-terminal membrane anchor was deleted. In contrast, ExeM was not detected in medium supernatants. Based on the results we hypothesize that ExeM predominantly interacts with DNA in close proximity to the cell, e.g., to promote biofilm formation and defense against NETs, or to control uptake of DNA.

The abundance and diversity of antibiotic resistance genes in the atmospheric environment of composting plants

Composting is considered to reduce the introduction of antimicrobial resistance genes (ARGs) into the environment through land application of manure; however, the possible pollution of ARGs in the atmospheric environment of composting plants is unknown. In this study, 29 air samples including up- and downwind, composting, packaging, and office areas from 4 composting plants were collected. Dynamic concentrations of 22 subtypes of ARGs, class 1 integron (intl1), and 2 potential human pathogenic bacteria (HPB), and bacterial communities were investigated using droplet digital PCR and 16S rRNA gene sequencing, respectively. In this study, intl1 and 22 subtypes of ARGs (except tetQ) were detected in air of composting, packaging, office, and downwind areas. The highest concentration of 15 out of 22 subtypes of ARGs was detected in the packaging areas, and intl1 also had the maximum average concentration of 10⁴ copies/m³, with up to (1.78 ± 0.49) × 10^-2 copies/16S rRNA copy. Non-metric multi-dimensional scaling of ARGs, potential HPBs, and bacterial components all indicated that the bioaerosol pollutant pattern in packaging areas was most similar to that in composting areas, followed by office, downwind, and upwind areas. The co-occurrence between ARGs and bacterial taxa assessed by Procrustes test, mantel test, and network analysis implied that aerosolized ARG fragments from composting and packaging areas contributed to the compositions of ARG aerosols in office and downwind areas. The results presented here show that atmoshperic environments of composting plants harbor abundant and diverse ARGs, which highlight the urgent need for comprehensive evaluation of potential human health and ecological risks of composts during both production as well as land application.

Involvement of the response regulator CtrA in the extracellular DNA production of the marine bacterium Rhodovulum sulfidophilum

The marine bacterium Rhodovulum sulfidophilum is a nonsulfur phototrophic bacterium, which is known to produce extracellular nucleic acids in soluble form in culture medium. In the present paper, constructing the response regulator ctrA-deficient mutant of R. sulfidophilum, we found that this mutation causes a significant decrease in the extracellular DNA production. However, by the introduction of a plasmid containing the wild type ctrA gene into the mutant, the amount of extracellular DNA produced was recovered. This is the first and clear evidence that the extracellular DNA production is actively controlled by the CtrA in R. sulfidophilum.

Kinetics of circulating cell-free DNA for biomedical applications: critical appraisal of the literature

Circulating cell-free DNA is considered as one of the major breakthroughs in the field of innovative diagnosis, used as a liquid biopsy. The kinetic parameters of a biomarker are mandatory to assess its usefulness as a diagnostic tool. Obtaining precise mathematical values for the kinetic parameters (e.g., half-life) is then crucial because it could be used for therapeutic monitoring as a prognostic factor. However, little is known about the intrinsic properties of circulating cell-free DNA, more especially, its kinetic properties within the organism. We summarized the basic principles that may affect the kinetics of circulating cell-free DNA within the organism in the light of biological and clinical evidence. We also meta-analyzed the reported data in the literature and the methodologies that have been used to study the kinetic parameters of human circulating cell-free DNA in vivo.

Circulating cell-free DNA as a biomarker was a major breakthrough in the field of diagnostics. Understanding the kinetic parameters of a biomarker is mandatory to assess its usefulness as a diagnostic tool, especially for therapeutic monitoring. However, at the present time little is known about its kinetic properties within the organism. This review provides an overview of the basic principles that may impact the kinetics of cell-free DNA within the organism and analyzes the reported data thus far.

Cell-free DNA: A Neglected Source for Antibiotic Resistance Genes Spreading from WWTPs

Cell-associated ARGs in wastewater treatment plants (WWTPs) has been concerned, however, cell-free ARGs in WWTPs was rarely studied. In this study, the abundances of four representative ARGs, sulII, tetC, bla_PSE-1, and ermB, in a large municipal WWTP were investigated in both cell-associated and cell-free fractions. Cell-associated ARGs was the dominant ARGs fraction in the raw wastewater. After biological treatment, sludge settling, membrane filtration, and disinfection, cell-associated ARGs were substantially reduced, though the ratios of ARG/16S rRNA gene were increased with disinfection. Cell-free ARGs persisted in the WWTP with a removal of 0.36 log to 2.68 logs, which was much lower than the removal of cell-associated ARGs (3.21 logs to 4.14 logs). Therefore, the abundance ratio of cell-free ARGs to cell-associated ARGs increased from 0.04-1.59% to 2.00-1895.08% along the treatment processes. After 25-day-storage, cell-free ARGs in both biological effluent and disinfection effluent increased by 0.14 log to 1.99 logs and 0.12 log to 1.77 logs respectively, reflecting the persistence and low decay rate of cell-free ARGs in the discharge water. Therefore, cell-free ARGs might be a kind of important but previously neglected pollutant from WWTPs, which added potential risks to the effluent receiving environments.

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes

Molecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of "diversity," and consequently that neither is entirely superior to the other when investigating environmental protists.

Dissipation of double-stranded RNA in aquatic microcosms

Silencing genes of a pest with double-stranded RNA (dsRNA) is a promising new pest management technology. As part of the environmental risk assessment for dsRNA-based products, the environmental fate and the potential for adverse effects to on-target organisms should be characterized. In the present study, a nonbioactive dsRNA was spiked into the water column of a water and sediment microcosm to mimic drift from a spray application run off of unbound dsRNA or transport of plant tissues. Dissipation of dsRNA in the water column and partitioning into sediment was determined. The dsRNA rapidly dissipated in the water column and was below the limit of detection after 96 h. The levels detected in the sediment were not significant and may indicate rapid degradation in the water column prior to partitioning to sediment. Environ Toxicol Chem 2017;36:1249-1253. © 2016 SETAC.

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H₂S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River

The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on an Illumina MiSeq platform. Up to 1.8 × 10⁷ bp (4.5× mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices, this study provides a 'proof of concept' on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments.

Origins, structures, and functions of circulating DNA in oncology

While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.

Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles

The biological relevance of extracellular vesicles (EV) in intercellular communication has been well established. Thus far, proteins and RNA were described as main cargo. Here, we show that EV released from human bone marrow derived mesenchymal stromal cells (BM-hMSC) also carry high-molecular DNA in addition. Extensive EV characterization revealed this DNA mainly associated with the outer EV membrane and to a smaller degree also inside the EV. Our EV purification protocol secured that DNA is not derived from apoptotic or necrotic cells. To analyze the relevance of EV-associated DNA we lentivirally transduced Arabidopsis thaliana-DNA (A.t.-DNA) as indicator into BM-hMSC and generated EV. Using quantitative polymerase chain reaction (qPCR) techniques we detected high copy numbers of A.t.-DNA in EV. In recipient hMSC incubated with tagged EV for two weeks we identified A.t.-DNA transferred to recipient cells. Investigation of recipient cell DNA using quantitative PCR and verification of PCR-products by sequencing suggested stable integration of A.t.-DNA. In conclusion, for the first time our proof-of-principle experiments point to horizontal DNA transfer into recipient cells via EV. Based on our results we assume that eukaryotic cells are able to exchange genetic information in form of DNA extending the known cargo of EV by genomic DNA. This mechanism might be of relevance in cancer but also during cell evolution and development.