Cell Genom. 2022 Nov 11;2(12):100213. doi: 10.1016/j.xgen.2022.100213. eCollection 2022 Dec 14.

ABSTRACT

The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.

PMID:36778052 | PMC:PMC9903846 | DOI:10.1016/j.xgen.2022.100213

Cell Genom. 2022 Nov 9;3(1):100215. doi: 10.1016/j.xgen.2022.100215. eCollection 2023 Jan 11.

ABSTRACT

Single-cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells; however, most genomic regions sequenced in single cells are non-informative. To overcome this issue, we developed a multi-patient-targeted (MPT) scDNA-seq method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 patients with triple negative-breast cancer (TNBC), which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From these data, we reconstructed mutational lineages and identified early mutational and copy-number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggest that MPT can overcome a major technical obstacle for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

PMID:36777188 | PMC:PMC9903705 | DOI:10.1016/j.xgen.2022.100215

Cell Genom. 2022 Jan 13;2(1):100083. doi: 10.1016/j.xgen.2021.100083. eCollection 2022 Jan 12.

ABSTRACT

DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlling their expression remain largely uncharacterized. To address this, we produced a multimodal resource and genomic regulatory map for the zebrafish community, which integrates single-cell combinatorial indexing assay for transposase-accessible chromatin with high-throughput sequencing (sci-ATAC-seq) with bulk histone PTMs and Hi-C data to achieve a genome-wide classification of the regulatory architecture determining transcriptional activity in the 24-h post-fertilization (hpf) embryo. We characterized the genome-wide chromatin architecture at bulk and single-cell resolution, applying sci-ATAC-seq on whole 24-hpf stage zebrafish embryos, generating accessibility profiles for ∼23,000 single nuclei. We developed a genome segmentation method, ScregSeg (single-cell regulatory landscape segmentation), for defining regulatory programs, and candidate CREs, specific to one or more cell types. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization and identified new regulatory principles between chromatin modalities prevalent during zebrafish development. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos identified novel cellular roles for this hematovascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work defines regulatory architecture and principles in the zebrafish embryo and establishes a resource of cell-type-specific genome-wide regulatory annotations and candidate CREs, providing a valuable open resource for genomics, developmental, molecular, and computational biology.

PMID:36777038 | PMC:PMC9903790 | DOI:10.1016/j.xgen.2021.100083

Cell Genom. 2022 Apr 13;2(4):100120. doi: 10.1016/j.xgen.2022.100120. eCollection 2022 Apr 13.

ABSTRACT

Tissue-tumor interactivity is the culmination of cell intrinsic features and their extrinsic interactions with the environment. Recently in Cell, Dhainaut and Rose et al. established a strategy to track pooled CRISPR-modified cells in vivo using protein barcodes (Pro-Codes) and measure their impact on the tumor microenvironment through multiplexed imaging and spatial transcriptomics of intact tissues.1.

PMID:36776528 | PMC:PMC9903767 | DOI:10.1016/j.xgen.2022.100120

Protein Sci. 2023 Feb 13:e4594. doi: 10.1002/pro.4594. Online ahead of print.

ABSTRACT

We describe the Predicting Protein Compound Interactions (PrePCI) database which comprises over 5 billion predicted interactions between nearly 7 million chemical compounds and 19,797 human proteins. PrePCI relies on a proteome-wide database of structural models based on both traditional modeling techniques and the AlphaFold Protein Structure Database. Sequence and structural similarity-based metrics are established between template proteins, T, in the Protein Data Bank that bind compounds, C, and query proteins in the model database, Q. When these metrics pass a sequence threshold value, it is assumed that C also binds to Q with a likelihood ratio derived from machine learning. If the relationship is based on structure, this LR is based on a scoring function that measures the extent to which C is compatible with the binding site of Q as described in the LT-scanner algorithm. For every predicted complex derived in this way, chemical similarity based on the Tanimoto coefficient identifies other small molecules that may bind to Q. A likelihood ratio for the binding of C to Q is obtained from Naïve Bayesian statistics. The PrePCI database can be queried by entering a UniProt ID or gene name for a protein to obtain a list of compounds predicted to bind to it along with associated LRs. Alternatively, entering an identifier for the compound outputs a list of proteins it is predicted to bind. Specific applications of the database to lead discovery, drug mechanism of action elucidation and biological function annotation are described. This article is protected by copyright. All rights reserved.

PMID:36776141 | DOI:10.1002/pro.4594

Sleep. 2023 Feb 13:zsad024. doi: 10.1093/sleep/zsad024. Online ahead of print.

NO ABSTRACT

PMID:36775897 | DOI:10.1093/sleep/zsad024

Eur J Pharmacol. 2023 Feb 10:175587. doi: 10.1016/j.ejphar.2023.175587. Online ahead of print.

ABSTRACT

BACKGROUND AND OBJECTIVES: Pharmacological treatments available for substance use disorder (SUD) focus on pharmacodynamics, agonizing or antagonizing the drug of abuse (DOA) on receptor level. Drawbacks of this approach include the reliance on long-term patient compliance, on-target off-site effects, perpetuation of addiction and unavailability for many DOAs. Newer, pharmacokinetic approaches are needed that restrict DOA's access to the brain or disrupt DOA-instated brain changes maintaining addiction. Biotechnology might be able to provide the right biopharmaceutical tools to deliver a fine-tuned solution with less side effects compared to currently available treatments.

METHODS: This review examines the available literature on biopharmaceuticals developed to treat SUD.

RESULTS: Active and passive immunization, metabolic enhancers that augment DOA metabolism and clearance, as well as genetic/epigenetic modulation are promising next generation SUD treatments. Active immunization relies on production of antidrug antibodies by means of vaccination, while passive immunization constitutes of exogenous administration of such antibodies. Metabolic enhancers include drug-specific metabolizing enzymes that can be administered or secreted by modified skin grafts, as well as catalytic antibodies that hasten DOA metabolism. Nanotechnological advances can also allow for brain delivery of siRNAs, mRNAs or DNA in order to modulate central, common in all addictions, genetic or epigenetic targets attenuating drug seeking behavior and reversing drug-induced brain changes.

CONCLUSIONS: and Scientific Significance: Biopharmaceuticals can in the future complement or even replace traditional pharmacodynamics approaches in SUD treatment. While passive and active immunization biopharmaceuticals have entered human clinical trials, metabolic enhancers and genetic approaches are at the preclinical level.

PMID:36775113 | DOI:10.1016/j.ejphar.2023.175587

Genomics Proteomics Bioinformatics. 2023 Feb 10:S1672-0229(23)00033-5. doi: 10.1016/j.gpb.2023.02.001. Online ahead of print.

ABSTRACT

Cyclocarya paliurus is a relict plant species that survived the last glacial period and shows a population expansion recently. Its leaves have been traditionally used to treat obesity and diabetes with the well-known active ingredient cyclocaric acid B (CA-B). Here, we present three C. paliurus genomes from two diploids with different flower morphs and one haplotype-resolved tetraploid assembly. Comparative genomic analysis revealed two rounds of recent whole-genome duplication events and identified 691 genes with dosage-effect that likely contribute to adaptive evolution through enhanced photosynthesis and increased accumulation of triterpenoids. Re-sequencing analysis of 45 C. paliurus accessions uncovered two bottlenecks, consistent with the known events of environmental changes, and many selectively swept genes involved in critical biological functions, including plant defense and secondary metabolite biosynthesis. We also proposed the biosynthesis pathway of CA-B based on multi-omics data and identified key genes, in particular gibberellin related genes, associated with heterodichogamy in C. paliurus species. Our study sheds light on evolutionary history and provides genomics resources to study the medicinal herb.

PMID:36775057 | DOI:10.1016/j.gpb.2023.02.001

Comput Biol Med. 2023 Feb 7;155:106630. doi: 10.1016/j.compbiomed.2023.106630. Online ahead of print.

ABSTRACT

Colorectal cancer (CRC) is a severe health concern that results from a cocktail of genetic, epigenetic, and environmental abnormalities. Because it is the second most lethal malignancy in the world and the third-most common malignant tumor, but the treatment is unavailable. The goal of the current study was to use bioinformatics and systems biology techniques to determine the pharmacological mechanism underlying putative important genes and linked pathways in early-onset CRC. Computer-aided methods were used to uncover similar biological targets and signaling pathways associated with CRC, along with bioinformatics and network pharmacology techniques to assess the effects of enzastaurin on CRC. The KEGG and gene ontology (GO) pathway analysis revealed several significant pathways including in positive regulation of protein phosphorylation, negative regulation of the apoptotic process, nucleus, nucleoplasm, protein tyrosine kinase activity, PI3K-Akt signaling pathway, pathways in cancer, focal adhesion, HIF-1 signaling pathway, and Rap1 signaling pathway. Later, the hub protein module identified from the protein-protein interactions (PPIs) network, molecular docking and molecular dynamics simulation represented that enzastaurin showed strong binding interaction with two hub proteins including CASP3 (-8.6 kcal/mol), and MCL1 (-8.6 kcal/mol), which were strongly implicated in CRC management than other the five hub proteins. Moreover, the pharmacokinetic features of enzastaurin revealed that it is an effective therapeutic agent with minimal adverse effects. Enzastaurin may inhibit the potential biological targets that are thought to be responsible for the advancement of CRC and this study suggests a potential novel therapeutic target for CRC.

PMID:36774894 | DOI:10.1016/j.compbiomed.2023.106630

Forensic Sci Int Genet. 2023 Feb 2;64:102841. doi: 10.1016/j.fsigen.2023.102841. Online ahead of print.

ABSTRACT

The human oral microbiome has primarily been studied in clinical settings and for medical purposes. More recently, oral microbial research has been incorporated into other areas of study. In forensics, research has aimed to exploit the variation in composition of the oral microbiome to answer forensic relevant topics, such as human identification and geographical provenience. Several studies have focused on the use of microbiome for continental, national, or ethnic origin evaluations. However, it is not clear how the microbiome varies between similar ethnic populations across different regions in a country. We report here a comparison of the oral microbiomes of individuals living in two regions of Italy - Lombardy and Piedmont. Oral samples were obtained by swabbing the donors' oral mucosa, and the V4 region of the 16S rRNA gene was sequenced from the extracted microbial DNA. Additionally, we compared the oral and the skin microbiome from a subset of these individuals, to provide an understanding of which anatomical region may provide more robust results that can be useful for forensic human identification. Initial analysis of the oral microbiota revealed the presence of a core oral microbiome, consisting of nine taxa shared across all oral samples, as well as unique donor characterising taxa in 31 out of 50 samples. We also identified a trend between the abundance of Proteobacteria and Bacteroidota and the smoking habits, and of Spirochaetota and Synergistota and the age of the enrolled participants. Whilst no significant differences were observed in the oral microbial diversity of individuals from Lombardy or Piedmont, we identified two bacterial families - Corynebacteriaceae and Actinomycetaceae - that showed abundance trends between the two regions. Comparative analysis of the skin and oral microbiota showed significant differences in the alpha (p = 0.0011) and beta (Pr(>F)= 9.999e-05) diversities. Analysis of skin and oral samples from the same donor further revealed that the skin microbiome contained more unique donor characterising taxa than the oral one. Overall, this study demonstrates that whilst the oral microbiome of individuals from the same country and of similar ethnicity are largely similar, there may be donor characterising taxa that might be useful for identification purposes. Furthermore, the bacterial signatures associated with certain lifestyles could provide useful information for investigative purposes. Finally, additional studies are required, the skin microbiome may be a better discriminant for human identification than the oral one.

PMID:36774834 | DOI:10.1016/j.fsigen.2023.102841

Sci Rep. 2023 Feb 11;13(1):2464. doi: 10.1038/s41598-023-29607-8.

ABSTRACT

Nicotinamide Adenine Dinucleotide (NAD+) plays an important role in energy metabolism and signaling pathways controlling crucial cellular functions. The increased interest in NAD+ metabolism and NAD+-boosting therapies has reinforced the necessity for accurate NAD+ quantification. To examine the published NAD(P)(H) measures across mammalian tissues, we performed a meta-analysis of the existing data. An Ovid MEDLINE database search identified articles with NAD(P)(H) quantification results obtained from mammalian tissues published between 1961 and 2021. We screened 4890 records and extracted quantitative data, as well as the quantification methods, pre-analytical conditions, and subject characteristics. The extracted physiological NAD(P)(H) concentrations in various tissues from mice, rats, and humans, revealed an important inter- and intra-method variability that extended to recent publications. This highlights the relatively poor potential for cross-experimental analyses for NAD(P)(H) quantitative data and the importance of standardization for NAD(P)(H) quantification methods and pre-analytical procedures for future preclinical and clinical studies.

PMID:36774401 | DOI:10.1038/s41598-023-29607-8

Nat Commun. 2023 Feb 11;14(1):785. doi: 10.1038/s41467-023-36336-z.

ABSTRACT

About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.

PMID:36774364 | DOI:10.1038/s41467-023-36336-z

Nat Commun. 2023 Feb 11;14(1):771. doi: 10.1038/s41467-023-36321-6.

ABSTRACT

Glioblastoma, the most common and aggressive primary brain tumor type, is considered an immunologically "cold" tumor with sparse infiltration by adaptive immune cells. Immunosuppressive tumor-associated myeloid cells are drivers of tumor progression. Therefore, targeting and reprogramming intratumoral myeloid cells is an appealing therapeutic strategy. Here, we investigate a β-cyclodextrin nanoparticle (CDNP) formulation encapsulating the Toll-like receptor 7 and 8 (TLR7/8) agonist R848 (CDNP-R848) to reprogram myeloid cells in the glioma microenvironment. We show that intravenous monotherapy with CDNP-R848 induces regression of established syngeneic experimental glioma, resulting in increased survival rates compared with unloaded CDNP controls. Mechanistically, CDNP-R848 treatment reshapes the immunosuppressive tumor microenvironment and orchestrates tumor clearing by pro-inflammatory tumor-associated myeloid cells, independently of T cells and NK cells. Using serial magnetic resonance imaging, we identify a radiomic signature in response to CDNP-R848 treatment and ultrasmall superparamagnetic iron oxide (USPIO) imaging reveals that immunosuppressive macrophage recruitment is reduced by CDNP-R848. In conclusion, CDNP-R848 induces tumor regression in experimental glioma by targeting blood-borne macrophages without requiring adaptive immunity.

PMID:36774352 | DOI:10.1038/s41467-023-36321-6

Adv Nutr. 2022 Sep;13(5):1450-1461. doi: 10.1093/advances/nmac075.

ABSTRACT

Humans often show variable responses to dietary, prebiotic, and probiotic interventions. Emerging evidence indicates that the gut microbiota is a key determinant for this population heterogeneity. Here, we provide an overview of some of the major computational and experimental tools being applied to critical questions of microbiota-mediated personalized nutrition and health. First, we discuss the latest advances in in silico modeling of the microbiota-nutrition-health axis, including the application of statistical, mechanistic, and hybrid artificial intelligence models. Second, we address high-throughput in vitro techniques for assessing interindividual heterogeneity, from ex vivo batch culturing of stool and continuous culturing in anaerobic bioreactors, to more sophisticated organ-on-a-chip models that integrate both host and microbial compartments. Third, we explore in vivo approaches for better understanding of personalized, microbiota-mediated responses to diet, prebiotics, and probiotics, from nonhuman animal models and human observational studies, to human feeding trials and crossover interventions. We highlight examples of existing, consumer-facing precision nutrition platforms that are currently leveraging the gut microbiota. Furthermore, we discuss how the integration of a broader set of the tools and techniques described in this piece can generate the data necessary to support a greater diversity of precision nutrition strategies. Finally, we present a vision of a precision nutrition and healthcare future, which leverages the gut microbiota to design effective, individual-specific interventions.

PMID:36774056 | DOI:10.1093/advances/nmac075

J Affect Disord. 2023 Feb 9:S0165-0327(23)00175-1. doi: 10.1016/j.jad.2023.02.023. Online ahead of print.

ABSTRACT

BACKGROUND: Maternal depressive symptoms are common in pregnancy and may extend to the perinatal period and beyond for some women. To date, few longitudinal studies have investigated maternal depressive symptoms from pregnancy to eleven years postpartum. Drawing data from a large population-based study cohort the aims of this study were to 1) identify distinct groups of mothers defined by their trajectories of depressive symptoms spanning from pregnancy to eleven years following the birth of the child, and 2) to identify psychosocial risk factors during pregnancy and in the first few postnatal years that are associated with these trajectories.

METHODS: Data were analyzed from 14,170 mothers who participated in Avon Longitudinal Study of Parents and Children (ALSPAC). The Edinburgh Postnatal Depression Scale (EPDS) was used to capture maternal depressive symptoms across 10 time points including two prenatal (18 and 32 weeks), and eight postnatal (2, 8, 21, 33, 61, 73, 97 and 134 months) time points. The latent growth model was created to describe the course of maternal depressive symptoms across the preceding time points followed by a latent growth mixture modelling (LGMM) to identify distinct trajectories of depressive symptoms over time within the overall sample. The predictors of maternal depressive symptoms trajectories were categorized into sociodemographic, child, and psychosocial factors. The multinomial regression analyses were conducted to explore associations between the risk factors and depressive symptoms trajectories.

RESULTS: LGMM identified four distinct trajectories of maternal depressive symptoms over time: minimal symptoms, increasing symptoms, persistent symptoms, and decreasing symptoms. Predictors of all patterns of depression - persistent, increasing and decreasing symptoms include smoking during pregnancy, and partner conflict. The strongest predictors of the persistent symptom trajectory included maternal history of depression and inadequate social support.

LIMITATIONS: The use of self-reported maternal mental health symptoms and under representation of ethnic minorities are our study's limitations.

CONCLUSIONS: The study findings highlight the importance of early identification and treatment for mothers experiencing depressive symptoms from pregnancy to the perinatal period and beyond.

PMID:36773763 | DOI:10.1016/j.jad.2023.02.023

Carbohydr Res. 2023 Jan 26;525:108747. doi: 10.1016/j.carres.2023.108747. Online ahead of print.

ABSTRACT

The clinically important anticoagulant heparin, a member of the glycosaminoglycan family of carbohydrates that is extracted predominantly from porcine and bovine tissue sources, has previously been shown to inhibit the β-site amyloid precursor protein cleaving enzyme 1 (BACE-1), a key drug target in Alzheimer's Disease. In addition, heparin has been shown to exert favourable bioactivities through a number of pathophysiological pathways involved in the disease processes of Alzheimer's Disease including inflammation, oxidative stress, tau phosphorylation and amyloid peptide generation. Despite the multi-target potential of heparin as a therapeutic option for Alzheimer's disease, the repurposing of this medically important biomolecule has to-date been precluded by its high anticoagulant potential. An alternative source to mammalian-derived glycosaminoglycans are those extracted from marine environments and these have been shown to display an expanded repertoire of sequence-space and heterogeneity compared to their mammalian counterparts. Furthermore, many marine-derived glycosaminoglycans appear to retain favourable bioactivities, whilst lacking the high anticoagulant potential of their mammalian counterparts. Here we describe a sulphated, marine-derived glycosaminoglycan extract from the Atlantic Sea Scallop, Placopecten magellanicus that displays high inhibitory potential against BACE-1 (IC50 = 4.8 μg.mL-1) combined with low anticoagulant activity; 25-fold less than that of heparin. This extract possesses a more favourable therapeutic profile compared to pharmaceutical heparin of mammalian provenance and is composed of a mixture of heparan sulphate (HS), with a high content of 6-sulphated N-acetyl glucosamine (64%), and chondroitin sulphate.

PMID:36773398 | DOI:10.1016/j.carres.2023.108747

Mol Ecol. 2023 Feb 11. doi: 10.1111/mec.16879. Online ahead of print.

ABSTRACT

Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in evolution of organisms. Metabolic models with different level of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relation of metabolic trade-offs to the classical black box Y-model that provides a conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.

PMID:36773330 | DOI:10.1111/mec.16879

Environ Microbiol. 2023 Feb 11. doi: 10.1111/1462-2920.16352. Online ahead of print.

ABSTRACT

The regular use of antimicrobials in livestock production selects for antimicrobial resistance. The potential impact of this practice on human health needs to be studied in more detail, including the role of the environment for the persistence and transmission of antimicrobial-resistant bacteria. During an investigation of a pig farm and its surroundings in Brandenburg, Germany, we detected abundant cephalosporin- and fluoroquinolone-resistant Escherichia coli in pig feces, sedimented dust, and house flies (Musca domestica). Genome sequencing of E. coli isolates revealed large phylogenetic diversity and plasmid-borne extended-spectrum beta lactamase (ESBL) genes CTX-M-1 and TEM-1 in multiple strains. Close genomic relationships indicated frequent transmission of antimicrobial-resistant E. coli between pigs from different herds and across buildings of the farm, and suggested dust and flies as vectors for dissemination of fecal pathogens. Strikingly, we repeatedly recovered E. coli from flies collected up to 2 km away from the source, whose genome sequences were identical or closely related to those from pig feces isolates, indicating the fly-associated transport of diverse ESBL-producing E. coli from the pig farm into urban habitation areas. The observed proximity of contaminated flies to human households poses a risk of transmission of antimicrobial-resistant enteric pathogens from livestock to man. This article is protected by copyright. All rights reserved.

PMID:36772962 | DOI:10.1111/1462-2920.16352

Polymers (Basel). 2023 Jan 18;15(3):511. doi: 10.3390/polym15030511.

ABSTRACT

The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these aggregates play important functional and regulatory roles within biological systems. However, the majority of studies focused on the behavior of pure systems in bulk solutions, thus neglecting confinement effects and the interplay between the numerous molecules present in cells. To better understand the physical mechanisms driving condensation in cellular environments, we perform molecular simulations of binary polymer mixtures in spherical droplets, considering both monodisperse and polydisperse molecular weight distributions for the longer polymer species. We find that confinement induces a spatial separation of the polymers by length, with the longer ones moving to the droplet center. This partitioning causes a distinct increase in the local polymer concentration near the droplet center, which is more pronounced in polydisperse systems. Consequently, the confined systems exhibit liquid-liquid phase separation at average polymer concentrations where bulk systems are still in the one-phase regime.

PMID:36771812 | DOI:10.3390/polym15030511

Plants (Basel). 2023 Feb 3;12(3):669. doi: 10.3390/plants12030669.

ABSTRACT

The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial-temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.

PMID:36771753 | DOI:10.3390/plants12030669