Commun Biol. 2023 Mar 28;6(1):334. doi: 10.1038/s42003-023-04708-2.

ABSTRACT

CRISPR/Cas13 systems are increasingly used for programmable targeting of RNAs. While Cas13 nucleases are capable of degrading both target RNAs and bystander RNAs in vitro and in bacteria, initial studies fail to detect collateral degradation of non-target RNAs in eukaryotic cells. Here we show that RfxCas13d, also known as CasRx, a widely used Cas13 system, can cause collateral transcriptome destruction when targeting abundant reporter RNA and endogenous RNAs, resulting in proliferation defect in target cells. While these results call for caution of using RfxCas13d for targeted RNA knockdown, we demonstrated that the collateral activity can be harnessed for selective depletion of a specific cell population defined by a marker RNA in an in vitro setting.

PMID:36977923 | DOI:10.1038/s42003-023-04708-2

Metabolomics. 2023 Mar 29;19(4):27. doi: 10.1007/s11306-023-02000-2.

NO ABSTRACT

PMID:36977802 | DOI:10.1007/s11306-023-02000-2

Nat Commun. 2023 Mar 28;14(1):1733. doi: 10.1038/s41467-023-37254-w.

ABSTRACT

Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

PMID:36977673 | DOI:10.1038/s41467-023-37254-w

Curr Biol. 2023 Mar 24:S0960-9822(23)00263-4. doi: 10.1016/j.cub.2023.02.073. Online ahead of print.

ABSTRACT

Neurons modify their transcriptomes in response to an animal's experience. How specific experiences are transduced to modulate gene expression and precisely tune neuronal functions are not fully defined. Here, we describe the molecular profile of a thermosensory neuron pair in C. elegans experiencing different temperature stimuli. We find that distinct salient features of the temperature stimulus, including its duration, magnitude of change, and absolute value, are encoded in the gene expression program in this single neuron type, and we identify a novel transmembrane protein and a transcription factor whose specific transcriptional dynamics are essential to drive neuronal, behavioral, and developmental plasticity. Expression changes are driven by broadly expressed activity-dependent transcription factors and corresponding cis-regulatory elements that nevertheless direct neuron- and stimulus-specific gene expression programs. Our results indicate that coupling of defined stimulus characteristics to the gene regulatory logic in individual specialized neuron types can customize neuronal properties to drive precise behavioral adaptation.

PMID:36977417 | DOI:10.1016/j.cub.2023.02.073

Curr Biol. 2023 Mar 27;33(6):R228-R230. doi: 10.1016/j.cub.2023.02.052.

ABSTRACT

Many disease-causing mutations can have mild or no effects in some people. This incomplete phenotype penetrance phenomenon is still poorly understood, but model animal studies now show that it is stochastic, with the outcome akin to flipping a coin. These findings can affect how genetic diseases are understood and treated.

PMID:36977385 | DOI:10.1016/j.cub.2023.02.052

Mar Drugs. 2023 Feb 21;21(3):135. doi: 10.3390/md21030135.

ABSTRACT

Two phenylspirodrimanes, never isolated before, stachybotrin J (1) and new stachybocin G (epi-stachybocin A) (2), along with the already reported stachybotrin I (3), stachybotrin H (4), stachybotrylactam (5), stachybotrylactam acetate (6), 2α-acetoxystachybotrylactam acetate (7), stachybotramide (8), chartarlactam B (9), and F1839-J (10) were isolated from the sponge-associated fungus Stachybotrys chartarum MUT 3308. Their structures were established based on extensive spectrometric (HRMS) and spectroscopic (1D and 2D NMR) analyses. Absolute configurations of the stereogenic centers of stachybotrin J (1), stachybocin G (2), and stachybotrin I (3), were determined by comparison of their experimental circular dichroism (CD) spectra with their time-dependent density functional theory (TD-DFT) circular dichroism (ECD) spectra. The putative structures of seventeen additional phenylspirodrimanes were proposed by analysis of their respective MS/MS spectra through a Feature-Based Molecular Networking approach. All the isolated compounds were evaluated for their cytotoxicity against five aggressive cancer cell lines (MP41, 786, 786R, CAL33, and CAL33RR), notably including two resistant human cancer cell lines (786R, CAL33RR), and compounds 5, 6, and 7 exhibited cytotoxicity with IC50 values in the range of 0.3-2.2 µM.

PMID:36976184 | DOI:10.3390/md21030135

Insects. 2023 Mar 21;14(3):305. doi: 10.3390/insects14030305.

ABSTRACT

Invasive insects pose an increasing risk to global agriculture, environmental stability, and public health. Giant pine scale (GPS), Marchalina hellenica Gennadius (Hemiptera: Marchalinidae), is a phloem feeding scale insect endemic to the Eastern Mediterranean Basin, where it primarily feeds on Pinus halepensis and other Pinaceae. In 2014, GPS was detected in the southeast of Melbourne, Victoria, Australia, infesting the novel host Pinus radiata. An eradication program was unsuccessful, and with this insect now established within the state, containment and management efforts are underway to stop its spread; however, there remains a need to understand the insect's phenology and behaviour in Australia to better inform control efforts. We documented the annual life cycle and seasonal fluctuations in activity of GPS in Australia over a 32 month period at two contrasting field sites. Onset and duration of life stages were comparable to seasons in Mediterranean conspecifics, although the results imply the timing of GPS life stage progression is broadening or accelerating. GPS density was higher in Australia compared to Mediterranean reports, possibly due to the absence of key natural predators, such as the silver fly, Neoleucopis kartliana Tanasijtshuk (Diptera, Chamaemyiidae). Insect density and honeydew production in the Australian GPS population studied varied among locations and between generations. Although insect activity was well explained by climate, conditions recorded inside infested bark fissures often provided the weakest explanation of GPS activity. Our findings suggest that GPS activity is strongly influenced by climate, and this may in part be related to changes in host quality. An improved understanding of how our changing climate is influencing the phenology of phloem feeding insects such as GPS will help with predictions as to where these insects are likely to flourish and assist with management programs for pest species.

PMID:36975990 | DOI:10.3390/insects14030305

Elife. 2023 Mar 28;12:e82364. doi: 10.7554/eLife.82364. Online ahead of print.

ABSTRACT

Biological age, distinct from an individual's chronological age, has been studied extensively through predictive aging clocks. However, these clocks have limited accuracy in short time-scales. Here we trained deep learning models on fundus images from the EyePACS dataset to predict individuals' chronological age. Our retinal aging clocking, 'eyeAge', predicted chronological age more accurately than other aging clocks (mean absolute error of 2.86 and 3.30 years on quality-filtered data from EyePACS and UK Biobank, respectively). Additionally, eyeAge was independent of blood marker-based measures of biological age, maintaining an all-cause mortality hazard ratio of 1.026 even when adjusted for phenotypic age. The individual-specific nature of eyeAge was reinforced via multiple GWAS hits in the UK Biobank cohort. The top GWAS locus was further validated via knockdown of the fly homolog, Alk, which slowed age-related decline in vision in flies. This study demonstrates the potential utility of a retinal aging clock for studying aging and age-related diseases and quantitatively measuring aging on very short time-scales, opening avenues for quick and actionable evaluation of gero-protective therapeutics.

PMID:36975205 | DOI:10.7554/eLife.82364

Mol Plant Pathol. 2023 Mar 28. doi: 10.1111/mpp.13327. Online ahead of print.

ABSTRACT

Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.

PMID:36975024 | DOI:10.1111/mpp.13327

Curr Zool. 2022 Feb 15;69(1):41-49. doi: 10.1093/cz/zoac009. eCollection 2023 Feb.

ABSTRACT

Indris Indri indri are group-living lemurs that occupy stable territories over several years and perform remarkable long-distance vocal displays. Vocal exchanges between long-term territory neighbors may contribute to assessing reciprocal resource-holding potentials, thus adaptively reducing the costs of territorial defense by limiting aggressive escalation. Previous work showed that indris' songs show distinctive acoustic features at individual and group level. However, the possibility that indris use such cues for individual or group-level recognition has never been investigated experimentally. We conducted a playback experiment to test whether indris discriminate between familiar and nonfamiliar songs. Our rationale lies in the hypothesis of the dear enemy phenomenon, which predicts that territorial animals will show reduced aggression levels toward familiar neighbors compared with novel rivals. We played back stimulus recordings to wild indris from their territory boundaries and examined their responses in terms of vocal and behavioral indicators of willingness to engage in a fight. In line with our predictions, focal animals responded more rapidly and approached more often the speaker in response to playback stimuli of nonfamiliar individuals than to stimuli of neighboring groups. These results indicate that indris can discriminate between different classes of intruders based on distinctive acoustic features of their song choruses. We suggest that increased aggression directed toward unfamiliar intruders may be explained by higher threat levels associated with dispersal and group formation dynamics. We further discuss the relevance of these findings in a strepsirrhine primate model for comparative studies of vocal communication and sociality.

PMID:36974154 | PMC:PMC10039182 | DOI:10.1093/cz/zoac009

Curr Zool. 2022 Feb 23;69(1):50-58. doi: 10.1093/cz/zoac013. eCollection 2023 Feb.

ABSTRACT

Dogs engage in play behavior at every age and the play bow is their most iconic playful posture. However, the function of this posture is still under debate. Here, we selected the Czechoslovakian Wolfdog (CWD) as a model breed to clarify the function of the play bow. We analyzed frame-by-frame 118 sessions of 24 subjects and recorded 76 play bow events. We found that all the play bows were performed in the visual field of the playmate suggesting that the sender takes into account the attentional state of the receiver when releasing the signal. By drawing survival curves and using log-rank test we found that play bow was mainly performed during a short pause in an ongoing session and that its performance triggered the playmate's reaction again. These findings show that play bow functions in restoring the partner motivation to play. Finally, by using a sequential analysis and a generalized mixed model, we found no evidence supporting the metacommunicative function of the play bow. The signal did not necessarily precede a contact offensive behavior (e.g., play biting and play pushing) and it was not affected by the level of asymmetry of the play session. In conclusion, in CWDs play bow can be considered a visual signal useful to maintain the motivation to play in the receiver. Therefore, we suggest that the mismatched number of play bows emitted by the 2 players in a given session can be predictive of their different motivations to play.

PMID:36974148 | PMC:PMC10039175 | DOI:10.1093/cz/zoac013

Virus Evol. 2023 Mar 27;9(1):vead024. doi: 10.1093/ve/vead024. eCollection 2023.

ABSTRACT

Adenoviruses (AdVs) are important human and animal pathogens and are frequently used as vectors for gene therapy and vaccine delivery. Surprisingly, there are only scant data regarding primate AdV origin and evolution, especially in the most basal primate hosts. We detect and sequence AdVs from faeces of two Madagascan lemur species. Complete genome sequence analyses define a new AdV species with a particularly large gene encoding a protein of unknown function in the early gene region 3. Unexpectedly, the new AdV species is not most similar to human or other simian AdVs but to bat adenovirus C. Genome characterisation shows signals of virus-host codivergence in non-structural genes, which show lower diversity than structural genes. Outside a lemur species mixing zone, recombination less frequently separates structural genes, as in human adenovirus C. The evolutionary history of lemur AdVs likely involves both a host switch and codivergence with the lemur hosts.

PMID:37091898 | PMC:PMC10121206 | DOI:10.1093/ve/vead024

iScience. 2023 Mar 27;26(4):106502. doi: 10.1016/j.isci.2023.106502. eCollection 2023 Apr 21.

ABSTRACT

RNA-binding protein muscleblind-like1 (MBNL1) was recently identified as a central regulator of cardiac wound healing and myofibroblast activation. To identify putative MBNL1 targets, we integrated multiple genome-wide screens with a fibroblast network model. We expanded the model to include putative MBNL1-target interactions and recapitulated published experimental results to validate new signaling modules. We prioritized 14 MBNL1 targets and developed novel fibroblast signaling modules for p38 MAPK, Hippo, Runx1, and Sox9 pathways. We experimentally validated MBNL1 regulation of p38 expression in mouse cardiac fibroblasts. Using the expanded fibroblast model, we predicted a hierarchy of MBNL1 regulated pathways with strong influence on αSMA expression. This study lays a foundation to explore the network mechanisms of MBNL1 signaling central to fibrosis.

PMID:37091233 | PMC:PMC10119756 | DOI:10.1016/j.isci.2023.106502

J Inflamm (Lond). 2023 Mar 27;20(1):12. doi: 10.1186/s12950-023-00335-0.

ABSTRACT

BACKGROUND: Modifying the acute inflammatory response has wide clinical benefits. Current options include non-steroidal anti-inflammatory drugs (NSAIDs) and therapies that may resolve inflammation. Acute inflammation involves multiple cell types and various processes. We, therefore, investigated whether an immunomodulatory drug that acts simultaneously at multiple sites shows greater potential to resolve acute inflammation more effectively and with fewer side effects than a common anti-inflammatory drug developed as a small molecule for a single target. In this work, we used time-series gene expression profiles from a wound healing mouse model to compare the effects of Traumeel (Tr14), a multicomponent natural product, to diclofenac, a single component NSAID on inflammation resolution.

RESULTS: We advance previous studies by mapping the data onto the "Atlas of Inflammation Resolution", followed by in silico simulations and network analysis. We found that Tr14 acts primarily on the late phase of acute inflammation (during resolution) compared to diclofenac, which suppresses acute inflammation immediately after injury.

CONCLUSIONS: Our results provide new insights how network pharmacology of multicomponent drugs may support inflammation resolution in inflammatory conditions.

PMID:36973809 | DOI:10.1186/s12950-023-00335-0

Microbiome. 2023 Mar 28;11(1):60. doi: 10.1186/s40168-023-01500-6.

ABSTRACT

BACKGROUND: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.

RESULTS: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.

CONCLUSIONS: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.

PMID:36973750 | DOI:10.1186/s40168-023-01500-6

BMC Genomics. 2023 Mar 27;24(1):152. doi: 10.1186/s12864-023-09246-z.

ABSTRACT

BACKGROUND: The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown.

RESULTS: This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways.

CONCLUSION: Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

PMID:36973662 | DOI:10.1186/s12864-023-09246-z

Nat Biotechnol. 2023 Mar 27. doi: 10.1038/s41587-023-01716-9. Online ahead of print.

ABSTRACT

Metacells are cell groupings derived from single-cell sequencing data that represent highly granular, distinct cell states. Here we present single-cell aggregation of cell states (SEACells), an algorithm for identifying metacells that overcome the sparsity of single-cell data while retaining heterogeneity obscured by traditional cell clustering. SEACells outperforms existing algorithms in identifying comprehensive, compact and well-separated metacells in both RNA and assay for transposase-accessible chromatin (ATAC) modalities across datasets with discrete cell types and continuous trajectories. We demonstrate the use of SEACells to improve gene-peak associations, compute ATAC gene scores and infer the activities of critical regulators during differentiation. Metacell-level analysis scales to large datasets and is particularly well suited for patient cohorts, where per-patient aggregation provides more robust units for data integration. We use our metacells to reveal expression dynamics and gradual reconfiguration of the chromatin landscape during hematopoietic differentiation and to uniquely identify CD4 T cell differentiation and activation states associated with disease onset and severity in a Coronavirus Disease 2019 (COVID-19) patient cohort.

PMID:36973557 | DOI:10.1038/s41587-023-01716-9

Cell Mol Immunol. 2023 Mar 27. doi: 10.1038/s41423-023-01006-z. Online ahead of print.

NO ABSTRACT

PMID:36973487 | DOI:10.1038/s41423-023-01006-z

Commun Biol. 2023 Mar 27;6(1):327. doi: 10.1038/s42003-023-04652-1.

ABSTRACT

Bone regeneration after fracture is a complex process with high and dynamic energy demands. The impact of metabolism on bone healing progression and outcome, however, is so far understudied. Our comprehensive molecular profiling reveals that central metabolic pathways, such as glycolysis and the citric acid cycle, are differentially activated between rats with successful or compromised bone regeneration (young versus aged female Sprague-Dawley rats) early in the inflammatory phase of bone healing. We also found that the citric acid cycle intermediate succinate mediates individual cellular responses and plays a central role in successful bone healing. Succinate induces IL-1β in macrophages, enhances vessel formation, increases mesenchymal stromal cell migration, and potentiates osteogenic differentiation and matrix formation in vitro. Taken together, metabolites-here particularly succinate-are shown to play central roles as signaling molecules during the onset of healing and in steering bone tissue regeneration.

PMID:36973478 | DOI:10.1038/s42003-023-04652-1

Nat Genet. 2023 Mar 27. doi: 10.1038/s41588-023-01349-3. Online ahead of print.

ABSTRACT

Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can produce immunogenic antigens. We performed a comprehensive screen for these TE exaptation events in 33 TCGA tumor types, 30 GTEx adult tissues and 675 cancer cell lines, and identified 1,068 TE-exapted candidates with the potential to generate shared tumor-specific TE-chimeric antigens (TS-TEAs). Whole-lysate and HLA-pulldown mass spectrometry data confirmed that TS-TEAs are presented on the surface of cancer cells. In addition, we highlight tumor-specific membrane proteins transcribed from TE promoters that constitute aberrant epitopes on the extracellular surface of cancer cells. Altogether, we showcase the high pan-cancer prevalence of TS-TEAs and atypical membrane proteins that could potentially be therapeutically exploited and targeted.

PMID:36973455 | DOI:10.1038/s41588-023-01349-3