Development. 2024 Jul 15:dev.202729. doi: 10.1242/dev.202729. Online ahead of print.

ABSTRACT

Many tissue-specific adult stem cell lineages maintain a balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase, Set1, regulates early-stage male germ cells in Drosophila. Early-stage germline-specific knockdown of set1 results in temporally progressed defects, arising as germ cell loss and developing into overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage non-cell-autonomously. Additionally, wild-type Set1, but not the catalytically inactive Set1, rescues the set1 knockdown phenotypes, highlighting the functional importance of the methyl-transferase activity of Set1. Further, RNA-seq experiments reveal key signaling pathway components, such as the JAK-STAT pathway stat92E and the BMP pathway mad genes that are upregulated upon set1 knockdown. Genetic interaction assays support the functional relationships between set1 and JAK-STAT or BMP pathways, as both stat92E and mad mutations suppress the set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The germ cell loss followed by over-proliferation phenotype when inhibiting a histone methyl-transferase also raise concerns about using their inhibitors in cancer therapy.

PMID:39007366 | DOI:10.1242/dev.202729

J Clin Invest. 2024 Jul 15;134(14):e168982. doi: 10.1172/JCI168982.

ABSTRACT

Copy number variation (CNV) at 7q11.23 causes Williams-Beuren syndrome (WBS) and 7q microduplication syndrome (7Dup), neurodevelopmental disorders (NDDs) featuring intellectual disability accompanied by symmetrically opposite neurocognitive features. Although significant progress has been made in understanding the molecular mechanisms underlying 7q11.23-related pathophysiology, the propagation of CNV dosage across gene expression layers and their interplay remains elusive. Here we uncovered 7q11.23 dosage-dependent symmetrically opposite dynamics in neuronal differentiation and intrinsic excitability. By integrating transcriptomics, translatomics, and proteomics of patient-derived and isogenic induced neurons, we found that genes related to neuronal transmission follow 7q11.23 dosage and are transcriptionally controlled, while translational factors and ribosomal genes are posttranscriptionally buffered. Consistently, we found phosphorylated RPS6 (p-RPS6) downregulated in WBS and upregulated in 7Dup. Surprisingly, p-4EBP was changed in the opposite direction, reflecting dosage-specific changes in total 4EBP levels. This highlights different dosage-sensitive dyregulations of the mTOR pathway as well as distinct roles of p-RPS6 and p-4EBP during neurogenesis. Our work demonstrates the importance of multiscale disease modeling across molecular and functional layers, uncovers the pathophysiological relevance of ribosomal biogenesis in a paradigmatic pair of NDDs, and uncouples the roles of p-RPS6 and p-4EBP as mechanistically actionable relays in NDDs.

PMID:39007270 | DOI:10.1172/JCI168982

Res Pharm Sci. 2024 Feb 6;19(1):73-82. doi: 10.4103/1735-5362.394822. eCollection 2024 Feb.

ABSTRACT

BACKGROUND AND PURPOSE: Treatment of malignancies with chemotherapy and surgery is often associated with disease recurrence and metastasis. Immunotherapy improves cancer treatment by creating an active response against tumor antigens. Various cancer cells express a large amount of glucose-regulated protein 78 (GRP78) protein on their surface. Stimulating the immune system against this antigen can expose cancer cells to the immune system. Herein, we investigated the effectiveness of a cGRP78-based vaccine against different cancer cells.

EXPERIMENTAL APPROACH: BALB/c mice were immunized with the cGRP78. The humoral immune response against different cancer cells was assessed by Cell-ELISA. The cellular immunity response was determined by splenocyte proliferation assay with different cancer antigens. The effect of vaccination on metastasis was investigated in vaccinated mice by injecting melanoma cancer cells into the tail of mice.

FINDINGS/RESULTS: These results indicated that the cGRP78 has acceptable antigenicity and stimulates the immune system to produce antibodies. After three injections, the amount of produced antibody was significantly different from the control group. Compared to the other three cell types, Hela and HepG2 showed the highest reaction to the serum of vaccinated mice. Cellular immunity against the B16F10 cell line had the best results compared to other cells. The metastasis results showed that after 30 days, the growth of B16F10 melanoma cancer cells was not noticeable in the lung tissue of vaccinated mice.

CONCLUSION AND IMPLICATIONS: Considering the resistance of vaccinated mice to metastasis, this vaccine offers a promising prospect for cancer treatment by inhibiting the spread of cancer cells.

PMID:39006979 | PMC:PMC11244710 | DOI:10.4103/1735-5362.394822

F1000Res. 2024 Jul 10;12:324. doi: 10.12688/f1000research.132628.2. eCollection 2023.

ABSTRACT

Sequestosome-1, encoded by the gene SQSTM1, functions as a bridge between ubiquitinated proteins and the proteasome or autophagosome, thereby regulating protein degradation pathways. Loss of Sequestosome-1 is hypothesized to enhance neurodegeneration progression in several diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal disorders (FTD). Sequestosome-1 reproducible research would be facilitated with the availability of well-characterized anti-Sequestosome-1 antibodies. In this study, we characterized seventeen Sequestosome-1 commercial antibodies for Western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs.

PMID:39006307 | PMC:PMC11240082 | DOI:10.12688/f1000research.132628.2

Heliyon. 2024 Jun 17;10(12):e33192. doi: 10.1016/j.heliyon.2024.e33192. eCollection 2024 Jun 30.

ABSTRACT

Gaze cues play a vital role in conveying critical information about objects and locations necessary for survival, such as food sources, predators, and the attentional states of conspecific and heterospecific individuals. During referential intentional communication, the continuous alternation of gaze between a communicative partner and a specific object or point of interest attracts the partner's attention towards the target. This behaviour is considered by many as essential for understanding intentions and is thought to involve mental planning. Here, we investigated the behavioural responses of seven bottlenose dolphins (Tursiops truncatus) that were given an impossible task in the presence of two experimenters (a 'commanding experimenter' and a 'non-commanding experimenter'), whose attentional state towards the dolphins varied. We found that the dolphins spontaneously displayed gaze alternation, specifically triadic referential pointing, only when the human commanding experimenter was facing them. However, they ceased to alternate their gaze between the impossible object and the commanding experimenter when the experimenter had their back turned. Notably, the dolphins' behaviour differed from general pointing and gaze, as their triadic sequence occurred within a narrow time window. These findings suggest that the dolphins were sensitive to human attentional cues and utilized their own gaze cue (pointing) as a salient signal to attract the attention of the commanding experimenter towards a specific location.

PMID:39005890 | PMC:PMC11239698 | DOI:10.1016/j.heliyon.2024.e33192

Iran J Pharm Res. 2024 Mar 30;23(1):e144368. doi: 10.5812/ijpr-144368. eCollection 2024 Jan-Dec.

ABSTRACT

BACKGROUND: The abnormal expression of microRNA (miRNA) influences RNA transcription and protein translation, leading to tumor progression and metastasis. Today, reliably identifying aberrant miRNA expression remains challenging, especially when employing quick, simple, and portable detection methods.

OBJECTIVES: This study aimed to diagnose and detect the miR-21 biomarker with high sensitivity and specificity.

METHODS: Our detection approach involves immobilizing ROX dye-labeled single-stranded DNA probes (ROX-labeled ssDNA) onto MWCNTs to detect target miRNA-21. Initially, adsorbing ROX-labeled ssDNA onto MWCNTs causes fluorescence quenching of ROX. Subsequently, introducing its complementary DNA (cDNA) forms double-stranded DNA (dsDNA), which results in the desorption and release from MWCNTs, thus restoring ROX fluorescence.

RESULTS: The study examined changes in fluorescence intensities before and after hybridization with miRNA-21. The fluorescence emission intensities responded linearly to increases in miR-21 concentration from 10-9 to 3.2 × 10-6 M. The developed fluorescence sensor exhibited a detection limit of 1.12 × 10-9 M.

CONCLUSIONS: This work demonstrates that using a nano-biosensor based on carbon nanotubes offers a highly sensitive method for the early detection of colorectal cancer (CRC), supplementing existing techniques.

PMID:39005737 | PMC:PMC11246647 | DOI:10.5812/ijpr-144368

Genome Biol Evol. 2024 Jul 15:evae151. doi: 10.1093/gbe/evae151. Online ahead of print.

ABSTRACT

New protein-coding genes can evolve from previously non-coding genomic regions through a process known as de novo gene emergence. Evidence suggests that this process has likely occurred throughout evolution and across the tree of life. Yet, confidently identifying de novo emerged genes remains challenging. Ancestral Sequence Reconstruction (ASR) is a promising approach for inferring whether a gene has emerged de novo or not, as it can enable us to inspect whether a given genomic locus ancestrally harbored protein-coding capacity. However, the use of ASR in the context of de novo emergence is still in its infancy and its capabilities, limitations, and overall potential are largely unknown. Notably, it is difficult to formally evaluate the protein-coding capacity of ancestral sequences, particularly when new gene candidates are short. How well-suited is ASR as a tool for the detection and study of de novo genes? Here, we address this question by designing an ASR workflow incorporating different tools and sets of parameters and by introducing a formal criterion that allows to estimate, within a desired level of confidence, when protein-coding capacity originated at a particular locus. Applying this workflow on ∼2,600 short, annotated budding yeast genes (<1,000 nucleotides), we found that ASR robustly predicts an ancient origin for most widely conserved genes, which constitute "easy" cases. For less robust cases, we calculated a randomization-based empirical P-value estimating whether the observed conservation between the extant and ancestral reading frame could be attributed to chance. This formal criterion allowed us to pinpoint a branch of origin for most of the less robust cases, identifying 49 genes that can unequivocally be considered de novo originated since the split of the Saccharomyces genus, including 37 S. cerevisiae-specific genes. We find that for the remaining equivocal cases, we cannot rule out different evolutionary scenarios including rapid evolution and multiple losses, or a recent de novo origin. Overall, our findings suggest that ASR is a valuable tool to study de novo gene emergence but should be applied with caution and awareness of its limitations.

PMID:39004885 | DOI:10.1093/gbe/evae151

J Theor Biol. 2024 Jul 12:111901. doi: 10.1016/j.jtbi.2024.111901. Online ahead of print.

ABSTRACT

Predictive models of signaling pathways have proven to be difficult to develop. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological signaling networks. Thus, there is a need to develop new approaches to create predictive mechanistic models of complex systems. To meet this need, we developed a method for generating artificial signaling networks that were reasonably realistic and thus could be treated as ground truth models. These synthetic models could then be used to generate synthetic data for developing and testing algorithms designed to recover the underlying network topology and associated parameters. We defined the reaction degree and reaction distance to measure the topology of reaction networks, especially to consider enzymes. To determine whether our generated signaling networks displayed meaningful behavior, we compared them with signaling networks from the BioModels Database. This comparison indicated that our generated signaling networks had high topological similarities with BioModels signaling networks with respect to the reaction degree and distance distributions. In addition, our synthetic signaling networks had similar behavioral dynamics with respect to both steady states and oscillations, suggesting that our method generated synthetic signaling networks comparable with BioModels and thus could be useful for building network evaluation tools.

PMID:39004118 | DOI:10.1016/j.jtbi.2024.111901

Eur J Med Chem. 2024 Jun 27;276:116613. doi: 10.1016/j.ejmech.2024.116613. Online ahead of print.

ABSTRACT

Cyclin-dependent kinase 7, along with cyclin H and MAT1, forms the CDK-activating complex (CAK), which directs cell cycle progression via T-loop phosphorylation of cell cycle CDKs. Pharmacological inhibition of CDK7 leads to selective anti-cancer effects in cellular and in vivo models, motivating several ongoing clinical investigations of this target. Current CDK7 inhibitors are either reversible or covalent inhibitors of its catalytic activity. We hypothesized that small molecule targeted protein degradation (TPD) might result in differentiated pharmacology due to the loss of scaffolding functions. Here, we report the design and characterization of a potent CDK7 degrader that is comprised of an ATP-competitive CDK7 binder linked to a CRL2VHL recruiter. JWZ-5-13 effectively degrades CDK7 in multiple cancer cells and leads to a potent inhibition of cell proliferation. Additionally, compound JWZ-5-13 displayed bioavailability in a pharmacokinetic study conducted in mice. Therefore, JWZ-5-13 is a useful chemical probe to investigate the pharmacological consequences of CDK7 degradation.

PMID:39004018 | DOI:10.1016/j.ejmech.2024.116613

Curr Opin Struct Biol. 2024 Jul 13;88:102886. doi: 10.1016/j.sbi.2024.102886. Online ahead of print.

ABSTRACT

Protein-protein interactions (PPIs) play a crucial role in cellular function and disease manifestation, with dysfunctions in PPI networks providing a direct link between stressors and phenotype. The dysfunctional Protein-Protein Interactome (dfPPI) platform, formerly known as epichaperomics, is a newly developed chemoproteomic method aimed at detecting dynamic changes at the systems level in PPI networks under stressor-induced cellular perturbations within disease states. This review provides an overview of dfPPIs, emphasizing the novel methodology, data analytics, and applications in disease research. dfPPI has applications in cancer research, where it identifies dysfunctions integral to maintaining malignant phenotypes and discovers strategies to enhance the efficacy of current therapies. In neurodegenerative disorders, dfPPI uncovers critical dysfunctions in cellular processes and stressor-specific vulnerabilities. Challenges, including data complexity and the potential for integration with other omics datasets are discussed. The dfPPI platform is a potent tool for dissecting disease systems biology by directly informing on dysfunctions in PPI networks and holds promise for advancing disease identification and therapeutics.

PMID:39003916 | DOI:10.1016/j.sbi.2024.102886

STAR Protoc. 2024 Jul 13;5(3):103002. doi: 10.1016/j.xpro.2024.103002. Online ahead of print.

ABSTRACT

Gene promoters filter transcription factor (TF) localization dynamics and changes in the DNA binding affinity of TFs. Here, we present a protocol to probe how promoters decode TF dynamics in Saccharomyces cerevisiae by combining optogenetic control with microscopy. We describe steps for preparing and characterizing a light delivery platform and light-controlled TF mutants. We then detail procedures for subjecting the TFs to light doses that generate defined patterns of localization while measuring fluorescent reporter gene activation via live-cell microscopy. For complete details on the use and execution of this protocol, please refer to Sweeney and McClean.1.

PMID:39003745 | DOI:10.1016/j.xpro.2024.103002

Cell Rep. 2024 Jul 13;43(7):114448. doi: 10.1016/j.celrep.2024.114448. Online ahead of print.

ABSTRACT

Noonan syndrome patients harboring causative variants in LZTR1 are particularly at risk to develop severe and early-onset hypertrophic cardiomyopathy. In this study, we investigate the mechanistic consequences of a homozygous variant LZTR1L580P by using patient-specific and CRISPR-Cas9-corrected induced pluripotent stem cell (iPSC) cardiomyocytes. Molecular, cellular, and functional phenotyping in combination with in silico prediction identify an LZTR1L580P-specific disease mechanism provoking cardiac hypertrophy. The variant is predicted to alter the binding affinity of the dimerization domains facilitating the formation of linear LZTR1 polymers. LZTR1 complex dysfunction results in the accumulation of RAS GTPases, thereby provoking global pathological changes of the proteomic landscape ultimately leading to cellular hypertrophy. Furthermore, our data show that cardiomyocyte-specific MRAS degradation is mediated by LZTR1 via non-proteasomal pathways, whereas RIT1 degradation is mediated by both LZTR1-dependent and LZTR1-independent pathways. Uni- or biallelic genetic correction of the LZTR1L580P missense variant rescues the molecular and cellular disease phenotype, providing proof of concept for CRISPR-based therapies.

PMID:39003740 | DOI:10.1016/j.celrep.2024.114448

Nat Commun. 2024 Jul 13;15(1):5911. doi: 10.1038/s41467-024-50172-9.

ABSTRACT

Robustness is the reproducible development of a phenotype despite stochastic noise. It often involves tradeoffs with other performance metrics, but the mechanisms underlying such tradeoffs were largely unknown. An Arabidopsis flower robustly develops four sepals from four precisely positioned auxin maxima. The development related myb-like 1 (drmy1) mutant generates noise in auxin signaling that disrupts robustness in sepal initiation. Here, we find that increased expression of CUP-SHAPED COTYLEDON1 (CUC1), a boundary specification transcription factor, in drmy1 underlies this loss of robustness. CUC1 surrounds and amplifies stochastic auxin noise in drmy1 to form variably positioned auxin maxima and sepal primordia. Removing CUC1 from drmy1 provides time for noisy auxin signaling to resolve into four precisely positioned auxin maxima, restoring robust sepal initiation. However, removing CUC1 decreases the intensity of auxin maxima and slows down sepal initiation. Thus, CUC1 increases morphogenesis speed but impairs robustness against auxin noise. Further, using a computational model, we find that the observed phenotype can be explained by the effect of CUC1 in repolarizing PIN FORMED1 (PIN1), a polar auxin transporter. Lastly, our model predicts that reducing global growth rate improves developmental robustness, which we validate experimentally. Thus, our study illustrates a tradeoff between speed and robustness during development.

PMID:39003301 | DOI:10.1038/s41467-024-50172-9

Int Immunopharmacol. 2024 Jul 12;139:112666. doi: 10.1016/j.intimp.2024.112666. Online ahead of print.

ABSTRACT

Immunotherapy has limited response rates in colorectal cancer (CRC) due to an immunosuppressive tumor microenvironment (TME). Combining transcriptome sequencing, clinical specimens, and functional experiments, we identified a unique group of CAF subpopulations (COX4I2 + ) with inhibited mitochondrial respiration and enhanced glycolysis. Through bioinformatics predictions and luciferase reporter assays, we determined that EBF1 can upstreamly regulate COX4I2 transcription. COX4I2 + CAFs functionally and phenotypically resemble myofibroblasts, are important for the formation of the fibrotic TME, and are capable of activating the M2 phenotype of macrophages. In vitro experiments demonstrated that COX4I2 + CAFs promote immunosuppressive TME by blocking CD8 + T cell infiltration and inducing CD8 + T cell dysfunction. Using multiple independent cohorts, we also found a strong correlation between the immunotherapy response rate of CRC patients and COX4I2 expression in their tumors. Our results identify a CAF subpopulation characterized by activation of the EBF1-COX4I2 axis, and this group of CAFs can be targeted to improve cancer immunotherapy outcomes.

PMID:39002521 | DOI:10.1016/j.intimp.2024.112666

STAR Protoc. 2024 Jul 11;5(3):103190. doi: 10.1016/j.xpro.2024.103190. Online ahead of print.

ABSTRACT

We present a protocol to generate highly multiplexed spatial data at cellular and subcellular resolutions using iterative indirect immunofluorescence imaging (4i). We describe streamlined steps for using 4i across fixed cultured cells, formalin-fixed paraffin-embedded (FFPE) tissue sections, and metaphase chromosome spreads. We detail procedures for sample preparation, antibody and DNA staining, immunofluorescence imaging, antibody elution, and image processing. This protocol is adapted for high-throughput analysis of fixed cultured cells and addresses sample-specific challenges such as intrinsic tissue autofluorescence and chromosome fragility. For complete details on the use and execution of this protocol for fixed cultured cells, please refer to Comandante-Lou et al.1.

PMID:39002133 | DOI:10.1016/j.xpro.2024.103190

Sci Rep. 2024 Jul 13;14(1):16170. doi: 10.1038/s41598-024-67222-3.

ABSTRACT

Increased urbanisation influences the morphometric traits of various species, often resulting in urban individuals being smaller than their non-urban counterparts. Urbanisation can affect fundamental eco-evolutionary patterns and impact species' ability to adapt to and occupy rapidly changing environments through morphological changes. We investigated the morphometric responses of two passerine species, the non-native house sparrow (Passer domesticus) and its native congener, the Cape sparrow (Passer melanurus), along gradients of spatial and temporal urbanisation in South Africa over a 52-year period. The house sparrow was significantly heavier, larger and in better condition with increasing urban infrastructure and lower urban vegetation cover, while the Cape sparrow showed opposing trends along these gradients. Temporally, the house sparrow's body mass increased consistently over the 52-year study period, suggesting changes in morphology were concomitant with increasing urbanisation over time. This study demonstrates distinct differences in the morphological responses of the non-native house sparrow and the native Cape sparrow to increasing urban development. These morphological responses may also underpin community-level changes caused by urbanisation, enhancing the capabilities of non-native species to thrive over their native counterparts in these environments.

PMID:39003406 | DOI:10.1038/s41598-024-67222-3

Neurobiol Dis. 2024 Jul 11:106604. doi: 10.1016/j.nbd.2024.106604. Online ahead of print.

ABSTRACT

Mitochondria are essential regulators of cellular energy metabolism and play a crucial role in the maintenance and function of neuronal cells. Studies in the last decade have highlighted the importance of mitochondrial dynamics and bioenergetics in adult neurogenesis, a process that significantly influences cognitive function and brain plasticity. In this review, we examine the mechanisms by which mitochondria regulate adult neurogenesis, focusing on the impact of mitochondrial function on the behavior of neural stem/progenitor cells and the maturation and plasticity of newborn neurons in the adult mouse hippocampus. In addition, we explore the link between mitochondrial dysfunction, adult hippocampal neurogenesis and genes associated with cognitive deficits in neurodevelopmental disorders. In particular, we provide insights into how alterations in the transcriptional regulator NR2F1 affect mitochondrial dynamics and may contribute to the pathophysiology of the emerging neurodevelopmental disorder Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS). Understanding how genes involved in embryonic and adult neurogenesis affect mitochondrial function in neurological diseases might open new directions for therapeutic interventions aimed at boosting mitochondrial function during postnatal life.

PMID:39002810 | DOI:10.1016/j.nbd.2024.106604

Virus Res. 2024 Jul 11:199437. doi: 10.1016/j.virusres.2024.199437. Online ahead of print.

ABSTRACT

The global monkeypox virus (MPXV) outbreak in 2022 emphasizes the urgent need for effective and accessible new-generation vaccines and neutralizing antibodies. Herein, we identified MPXV-neutralizing antibodies using high-throughput single-cell RNA and V(D)J sequencing of antigen-sorted B cells from patients with convalescent monkeypox. IgG1-expressing B cells were obtained from 34 paired heavy- and light-chain B cell receptor sequences. Subsequently, three potent neutralizing antibodies, MV127, MV128, and MV129, were identified and reacted with the MPXV A35 protein. Among these, MV129, which has a half-maximal inhibitory concentration of 2.68μg/mL against authentic MPXV, was considered to be the putative candidates for MPXV neutralization in response to monkeypox disease.

PMID:39002567 | DOI:10.1016/j.virusres.2024.199437

Dev Cell. 2024 Jul 9:S1534-5807(24)00389-7. doi: 10.1016/j.devcel.2024.06.011. Online ahead of print.

ABSTRACT

Keratin intermediate filaments confer structural stability to epithelial tissues, but the reason this simple mechanical function requires a protein family with 54 isoforms is not understood. During skin wound healing, a shift in keratin isoform expression alters the composition of keratin filaments. If and how this change modulates cellular functions that support epidermal remodeling remains unclear. We report an unexpected effect of keratin isoform variation on kinase signal transduction. Increased expression of wound-associated keratin 6A, but not of steady-state keratin 5, potentiated keratinocyte migration and wound closure without compromising mechanical stability by activating myosin motors to increase contractile force generation. These results substantially expand the functional repertoire of intermediate filaments from their canonical role as mechanical scaffolds to include roles as isoform-tuned signaling scaffolds that organize signal transduction cascades in space and time to influence epithelial cell state.

PMID:39002537 | DOI:10.1016/j.devcel.2024.06.011

Environ Int. 2024 Jul 8;190:108875. doi: 10.1016/j.envint.2024.108875. Online ahead of print.

ABSTRACT

Wastewater contains an extensive reservoir of genetic information, yet largely unexplored. Here, we analyzed by high-throughput sequencing total nucleic acids extracted from wastewater samples collected during a 17 month-period in Berlin, Germany. By integrating global wastewater datasets and applying a novel computational approach to accurately identify viral strains within sewage RNA-sequencing data, we demonstrated the emergence and global dissemination of a specific astrovirus strain. Astrovirus abundance and sequence variation mirrored temporal and spatial patterns of infection, potentially serving as footprints of specific timeframes and geographical locations. Additionally, we revealed more than 100,000 sequence contigs likely originating from novel viral species, exhibiting distinct profiles in total RNA and DNA datasets and including undescribed bunyaviruses and parvoviruses. Finally, we identified thousands of new CRISPR-associated protein sequences, including Transposase B (TnpB), a class of compact, RNA-guided DNA editing enzymes. Collectively, our findings underscore the potential of high-throughput sequencing of total nucleic acids derived from wastewater for a broad range of applications.

PMID:39002331 | DOI:10.1016/j.envint.2024.108875