A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record.

BACKGROUND: Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS: Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS: We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.

CDKN2A deletion remodels lipid metabolism to prime glioblastoma for ferroptosis.

Malignant tumors exhibit heterogeneous metabolic reprogramming, hindering the identification of translatable vulnerabilities for metabolism-targeted therapy. How molecular alterations in tumors promote metabolic diversity and distinct targetable dependencies remains poorly defined. Here we create a resource consisting of lipidomic, transcriptomic, and genomic data from 156 molecularly diverse glioblastoma (GBM) tumors and derivative models. Through integrated analysis of the GBM lipidome with molecular datasets, we identify CDKN2A deletion remodels the GBM lipidome, notably redistributing oxidizable polyunsaturated fatty acids into distinct lipid compartments. Consequently, CDKN2A-deleted GBMs display higher lipid peroxidation, selectively priming tumors for ferroptosis. Together, this study presents a molecular and lipidomic resource of clinical and preclinical GBM specimens, which we leverage to detect a therapeutically exploitable link between a recurring molecular lesion and altered lipid metabolism in GBM.

Co-pyrolysis of sewage sludge/cotton stalks with K2CO3 for biochar production: Improved biochar porosity and reduced heavy metal leaching.

The co-pyrolysis of sewage sludge and biomass is considered a promising technique for reducing the volume of sewage sludge, adding value, and decreasing the risk associated with this waste. In this study, sewage sludge and cotton stalks were pyrolyzed together with different amounts of K2CO3 to evaluate the potential of chemical activation using K2CO3 for improving the porosity of the biochar formed and immobilizing the heavy metals present in it. It was found that K2CO3 activation effectively improved the pore structure and increased the aromaticity of the biochar. Moreover, K2CO3 activation transformed the heavy metals (Cu, Zn, Pb, Ni, Cr, and Cd) into more stable forms (oxidizable and residual fractions). The activation effect became more pronounced with increasing amount of added K2CO3, eventually resulting in a significant reduction in the mobility and bioavailability of the heavy metals in the biochar. Further analysis revealed that, during the co-pyrolysis process, K2CO3 activation resulted in a reductive atmosphere, increased the alkalinity of the biochar, and led to the formation CaO, CaCO3, and aluminosilicates, which aided the immobilization of the heavy metals. K2CO3 activation also effectively reduced the leachability, and thus, the environmental risks of the heavy metals. Thus, K2CO3 activation can improve the porosity of the biochar derived from sewage sludge/cotton stalks and aid the immobilization of the heavy metals in it.

Circulating trophoblast cell clusters for early detection of placenta accreta spectrum disorders.

Placenta accreta spectrum (PAS) is a high-risk obstetrical condition associated with significant morbidity and mortality. Current clinical screening modalities for PAS are not always conclusive. Here, we report a nanostructure-embedded microchip that efficiently enriches both single and clustered circulating trophoblasts (cTBs) from maternal blood for detecting PAS. We discover a uniquely high prevalence of cTB-clusters in PAS and subsequently optimize the device to preserve the intactness of these clusters. Our feasibility study on the enumeration of cTBs and cTB-clusters from 168 pregnant women demonstrates excellent diagnostic performance for distinguishing PAS from non-PAS. A logistic regression model is constructed using a training cohort and then cross-validated and tested using an independent cohort. The combined cTB assay achieves an Area Under ROC Curve of 0.942 (throughout gestation) and 0.924 (early gestation) for distinguishing PAS from non-PAS. Our assay holds the potential to improve current diagnostic modalities for the early detection of PAS.

Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.

Characteristics of biochars prepared by co-pyrolysis of sewage sludge and cotton stalk intended for use as soil amendments.

The safe disposal and utilisation of sewage sludge can be challenging because of the potential environmental risks posed by heavy metals in the sludge. Conversion of sewage sludge and agriculture biomass into biochars that can be used to improve or remediate contaminated soils is a promising solution to this problem. In this study, biochars were produced via co-pyrolysis of sewage sludge and cotton stalk (1:1, w/w) at temperatures ranging from 300°C to 600°C. Then, the potential environmental risks of heavy metals and properties of the biochars were investigated. The addition of cotton stalk promoted the migration and transformation of heavy metals from bioavailable to stable fractions, which significantly reduced the potential environmental risks of heavy metals in biochars. Moreover, compared with biochars obtained via pyrolysis of sewage sludge alone, the pH values, C contents, and adsorption capacities of biochars increased, while the yields, ash contents, specific surface areas and molar H/C ratios decreased. In summary, co-pyrolysis of sewage sludge and cotton stalk is a feasible method for alleviating the potential environmental risks of heavy metals in biochars used to treat soils.

Co-pyrolysis of sewage sludge and cotton stalks.

Proper disposal of ever-increasing amounts sewage sludge and cotton stalks is a challenge around the world, and conversion of these wastes into biochars via co-pyrolysis may be a promising solution. In this study, biochars were prepared via co-pyrolysis of sewage sludge and cotton stalks with different mixing ratios (cotton stalks/sewage sludge, w/w) at 650 °C for 2.0 h, and then, biochars were characterized to identify their potential agronomic and environmental benefits as soil amendments. Biochars prepared with higher mixing ratios had higher C contents and lower H/C and N/C ratios, which suggests that this approach has potential for improving C storage in biochar-treated soils to help offset greenhouse gas emissions. All biochars were mesoporous materials with an average pore size of 3-4 nm. The specific surface area increases indicated that these biochars would have relatively high water holding capacities and heavy metal adsorption capacities in heavy metal contaminated soils. The high ash contents and cation exchange capacity values in biochars prepared with lower mixing ratios indicate that these products would be useful for enhancing the nutrient supply and nutrient retention capacity in degraded soils. Moreover, the addition of more cotton stalks efficiently decreased the mobility and bioavailability of heavy metals in the biochars. At a certain level, co-pyrolysis of sewage sludge and cotton stalks to produce biochars would have both economic and environmental benefits.

Dose-response relationships between dairy intake and chronic metabolic diseases in a Chinese population.

BACKGROUND: This study investigated associations between dairy intake and chronic metabolic diseases (CMDs), and evaluated possible dose-response relationships in Chinese. METHODS: This cross-sectional study included 6073 adults aged ≥18 years from China. General characteristics were gathered using a validated dietary questionnaire. Multivariable logistic regression analyses investigated associations between dairy intake and chronic metabolic diseases (CMDs) (overweight/obesity, obesity, central obesity, and hyperlipidemia). Restricted cubic spline models explored dose-response relationships between dairy intake and CMDs, and possible dairy intake in the prevention of CMDs. Structural equation modeling explored the potential mechanisms of the effects of dairy intake on CMDs. RESULTS: Significant inverse associations were found between dairy intake and overweight/obesity, obesity, central obesity, and hyperlipidemia, with odds ratios (ORs) of 0.66 (95% confidence interval [CI] 0.56-0.79), 0.63 (95% CI 0.47-0.85), 0.71 (95% CI 0.60-0.85), and 0.81 (95% CI 0.56-1.17), respectively (P < 0.05 for all). The intake of yogurt, milk, and total dairy to prevent CMDs differed according to age group (16-74, 29-187, and 159-269 mL/d, respectively, in the entire group; 69-110, 59-152, and 138-167 mL/d, respectively, in the young group, ≤ 44 years; 9-58, 57-149, and 117-145 mL/d, respectively, in the middle-aged group, 45-59 years; and 23-59 mL/d yogurt only in the old group, ≥ 60 years). Structural equation modeling showed that dairy intake could reduce body mass index and waist circumference by regulating carbohydrate, fat, protein, and total energy. CONCLUSIONS: Dairy intake was inversely associated with the prevalence of overweight, obesity, central obesity, and hyperlipidemia, and the optimal range of dairy intake differed with age. The beneficial effects of dairy intake in preventing CMDs could involve regulation of carbohydrate, fat, protein, and total energy.

Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds.

Virus ecology and evolution play a central role in disease emergence. However, their relative roles will vary depending on the viruses and ecosystems involved. We combined field studies, phylogenetics and experimental infections to document with unprecedented detail the stages that precede initial outbreaks during viral emergence in nature. Using serological surveys we showed that in the absence of large-scale outbreaks, horses in Mongolia are routinely exposed to and infected by avian influenza viruses (AIVs) circulating among wild birds. Some of those AIVs are genetically related to an avian-origin virus that caused an epizootic in horses in 1989. Experimental infections showed that most AIVs replicate in the equine respiratory tract without causing lesions, explaining the absence of outbreaks of disease. Our results show that AIVs infect horses but do not spread, or they infect and spread but do not cause disease. Thus, the failure of AIVs to evolve greater transmissibility and to cause disease in horses is in this case the main barrier preventing disease emergence.

Emergence and adaptation of H3N2 canine influenza virus from avian influenza virus: An overlooked role of dogs in interspecies transmission.

H3N2 canine influenza virus (CIV) originated from avian species and emerged in dogs in Asia around 2005 where it became enzootic before reaching the USA in 2015. To investigate the key aspects of the evolution of H3N2 CIV regarding its emergence and adaptation in the canine host, we conducted an extensive analysis of all publicly available H3N2 CIV sequences spanning a 10-year period. We believe that H3N2 AIVs transferred to canines around 2002-2004. Furthermore, H3N2 CIVs could be divided into seven major clades with strong geographic clustering and some changed sites evidence of adaptive evolution. Most notably, the dN/dS of each H3N2 CIVs segment was higher than the correspondent of H3N2 AIVs and the U content of HA and NA was increasing over time, suggesting the idea that this avian-origin virus may be gradually adapting to the host. Our results provide a framework to elucidate a general mechanism for emergence of novel influenza viruses.

Interspecies Transmission, Genetic Diversity, and Evolutionary Dynamics of Pseudorabies Virus.

BACKGROUND: Pseudorabies virus (PRV) causes Aujeszky's disease in pigs and can be transmitted to other mammals, including humans. In the current study, we systematically studied the interspecies transmission and evolutionary history of PRV. METHODS: We performed comprehensive analysis on the phylodynamics, selection, and structural biology to summarize the phylogenetic and adaptive evolution of PRV based on all available full-length and major glycoprotein sequences. RESULTS: PRV can be divided into 2 main clades with frequent interclade and intraclade recombination. Clade 2.2 (variant PRV) is currently the most prevalent genotype worldwide, and most commonly involved in cross-species transmission events (including humans). We also found that the population size of clade 2.2 has increased since 2011, and the effective reproduction number was >1 from 2011 to 2016, indicating that PRV may be still circulating in swine herds and is still a risk in relation with cross-species transmission in China. Of note, we identified amino acid sites in some important glycoproteins gB, gC, gD, and gE that may be associated with PRV adaptation to new hosts and immune escape to vaccines. CONCLUSIONS: Our study provides important genetic insight into the interspecies transmission and evolution of PRV within and between different hosts that warrant additional surveillance.

Origin, Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Circovirus 3.

Porcine circovirus 3 (PCV3) is a novel virus associated with acute PDNS (porcine dermatitis and nephropathy syndrome)-like clinical signs identified by metagenomic sequencing from swine. Its high occurrence may pose a potential threat to the swine industry worldwide. The processes resulting in the emergence and spread of PCV3 remain poorly understood. Herein, the possible origin, genotypes, and evolutionary dynamics of PCV3 based on available genomic sequences are determined. The closest ancestor of PCV3 is found to be within the clade 1 bat CVs. Using different phylogenetic methods, two major genotypes are identified, PCV3a and PCV3b. It is found that the effective population size of PCV3 increased rapidly during late 2013 to early 2014 and this is associated with the diversification of PCV3a and PCV3b. A relatively high effective reproductive number (Re) value and higher evolutionary rate were found compared to other single-stranded DNA viruses, and positive selection on codons 122 and 320 (24 of ORF2) is identified. It is hypothesized that this, together with the prediction of a potential change of an antigenic epitope at position 320, might have allowed PCV3 to escape from the host immune response. Overall, this study has important implications for understanding the ongoing PCV3 cases worldwide and will guide future efforts to develop effective preventive and control measures.

Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes.

The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.

Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus.

UNLABELLED: Influenza A viruses (IAVs) are maintained mainly in wild birds, and despite frequent spillover infections of avian IAVs into mammals, only a small number of viruses have become established in mammalian hosts. A new H3N2 canine influenza virus (CIV) of avian origin emerged in Asia in the mid-2000s and is now circulating in dog populations of China and South Korea, and possibly in Thailand. The emergence of CIV provides new opportunities for zoonotic infections and interspecies transmission. We examined 14,764 complete IAV genomes together with all CIV genomes publicly available since its first isolation until 2013. We show that CIV may have originated as early as 1999 as a result of segment reassortment among Eurasian and North American avian IAV lineages. We also identified amino acid changes that might have played a role in CIV emergence, some of which have not been previously identified in other cross-species jumps. CIV evolves at a lower rate than H3N2 human influenza viruses do, and viral phylogenies exhibit geographical structure compatible with high levels of local transmission. We detected multiple intrasubtypic and heterosubtypic reassortment events, including the acquisition of the NS segment of an H5N1 avian influenza virus that had previously been overlooked. In sum, our results provide insight into the adaptive changes required by avian viruses to establish themselves in mammals and also highlight the potential role of dogs to act as intermediate hosts in which viruses with zoonotic and/or pandemic potential could originate, particularly with an estimated dog population of ∼ 700 million. IMPORTANCE: Influenza A viruses circulate in humans and animals. This multihost ecology has important implications, as past pandemics were caused by IAVs carrying gene segments of both human and animal origin. Adaptive evolution is central to cross-species jumps, and this is why understanding the evolutionary processes that shape influenza A virus genomes is key to elucidating the mechanisms underpinning viral emergence. An avian-origin canine influenza virus (CIV) has recently emerged in dogs and is spreading in Asia. We reconstructed the evolutionary history of CIV and show that it originated from both Eurasian and North American avian lineages. We also identified the mutations that might have been responsible for the cross-species jump. Finally, we provide evidence of multiple reassortment events between CIV and other influenza viruses (including an H5N1 avian virus). This is a cause for concern, as there is a large global dog population to which humans are highly exposed.

Hippo pathway genes developed varied exon numbers and coevolved functional domains in metazoans for species specific growth control.

BACKGROUND: The Hippo pathway controls growth by mediating cell proliferation and apoptosis. Dysregulation of Hippo signaling causes abnormal proliferation in both healthy and cancerous cells. The Hippo pathway receives inputs from multiple developmental pathways and interacts with many tissue-specific transcription factors, but how genes in the pathway have evolved remains inadequately revealed. RESULTS: To explore the origin and evolution of Hippo pathway, we have extensively examined 16 Hippo pathway genes, including upstream regulators and downstream targets, in 24 organisms covering major metazoan phyla. From simple to complex organisms, these genes are varied in the length and number of exons but encode conserved domains with similar higher-order organization. The core of the pathway is more conserved than its upstream regulators and downstream targets. Several components, despite existing in the most basal metazoan sponges, cannot be convincingly identified in other species. Potential recombination breakpoints were identified in some genes. Coevolutionary analysis reveals that most functional domains in Hippo genes have coevolved with interacting functional domains in other genes. CONCLUSIONS: The two essential upstream regulators cadherins fat and dachsous may have originated in the unicellular organism Monosiga brevicollis and evolved more significantly than the core of the pathway. Genes having varied numbers of exons in different species, recombination events, and the gain and loss of some genes indicate alternative splicing and species-specific evolution. Coevolution signals explain some species-specific loss of functional domains. These results significantly unveil the structure and evolution of the Hippo pathway in distant phyla and provide valuable clues for further examination of Hippo signaling.