Biology subjects

Ghosh, A.

Publications and source records attributed to Ghosh, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Enzyme-driven phase separation of synthetic condensates enables self-organizing compartments and protective microenvironments

Compartmentalization via phase separation is increasingly recognized as a dynamic regulator of cellular biochemistry, yet the consequences of coupling enzymatic reactions to compartmentalization remain poorly understood. We combine a minimal, cell-free expression system with kinetic modeling to show how coupling enzymatic activity to biomolecular condensates drives emergent self-regulation via droplet formation and dissolution. In-vitro mRNA transcription induces phase separation with an intrinsically disordered protein (mutant G3BP1), forming condensates that modulate transcription and degradation kinetics. Our kinetic model shows that phase separation reduces rate constants, with slower degradation within condensates than in the mRNA-protein-poor phase. This leads to more mRNA with a prolonged lifetime of mRNA relative to the case without condensates. Extending the model to sustained and oscillatory resource supply reveals that condensates elevate mean mRNA levels and buffer deviations from the mean compared to the non-condensate scenario. These findings provide a general mechanism of cross-regulation and feedback between phase separation and enzymatic networks, highlighting condensates as active regulators of biochemical flux rather than as passive organizers. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=172 SRC="FIGDIR/small/696465v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@d48750org.highwire.dtl.DTLVardef@ffc9eeorg.highwire.dtl.DTLVardef@1222de6org.highwire.dtl.DTLVardef@f36701_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

RNA methyltransferase CMTR-1 inhibition activates a GATA transcription factor-mediated protective immune response

Organisms can activate innate immunity not only by detecting pathogens but also by sensing disturbances to essential cellular processes. Such damage-based surveillance provides a means to identify cellular disruptions that prime host immunity even in the absence of infection. To uncover pathways that enhance immunity, we perform a forward genetic screen in Caenorhabditis elegans for mutants with elevated intestinal immune activation. This screen identifies a hypomorphic allele of the conserved mRNA cap 2-O-methyltransferase cmtr-1, which strongly induces immune effector expression. Transcriptomic profiling reveals the broad activation of innate immune responses, and functional analyses demonstrate that this response requires the GATA transcription factor ELT-2. Notably, loss of cmtr-1 increases resistance to Pseudomonas aeruginosa, indicating that reduced RNA cap methylation can elicit protective immunity. Together, these findings reveal a previously unrecognized mechanism of immune surveillance and demonstrate that perturbation of CMTR-1 serves as a danger signal, triggering an ELT-2-dependent protective immune response.

immunology↗

bioRxiv2025

Deubiquitinase USP-14 controls intestinal distension-induced immune activation in Caenorhabditis elegans via Wnt/β-catenin signaling

Pathogen infections disrupt multiple host cellular processes, and hosts have consequently evolved mechanisms to detect these perturbations and initiate appropriate immune responses. In Caenorhabditis elegans, gut distension caused by bacterial colonization is known to activate innate immunity, yet the molecular mechanisms linking intestinal distension to immune activation remain poorly understood. Here, we perform a forward genetic screen to identify suppressors of intestinal distension-induced immune activation in C. elegans. This screen identifies a loss-of-function mutation in the gene encoding the deubiquitinase (DUB) USP-14 as a potent suppressor of immune activation triggered by gut distension. We show that usp-14 knockout mutants exhibit increased sensitivity to the bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. Global transcriptomic profiling further demonstrates that USP-14 modulates innate immune responses induced by intestinal distension. Epistasis analyses establish that USP-14 functions through the Wnt/{beta}-catenin signaling pathway to regulate these immune responses. Together, our findings reveal a previously unrecognized role for the conserved DUB USP-14 in host immunity, providing a foundation for future studies investigating how USP-14 modulates immune signaling.

immunology↗

bioRxiv2025

A non-canonical AKT1-TERT pathway coordinates autophagy and ERphagy

The retinal pigment epithelium (RPE) sustains lifelong proteostasis under chronic stress, yet how post-mitotic cells activate autophagy when canonical kinase pathways suppress it remains unresolved. Here we demonstrate that AKT1, conventionally regarded as an autophagy suppressor, drives autophagy through a non-canonical transcriptional mechanism triggered by isoform imbalance. In RPE and age-related macular degeneration (AMD) models, AKT2 hyperactivation destabilizes mTORC2 and engages S6K-mediated IRS-1 inhibition, creating a feedforward autophagic arrest. Compensatory AKT1 activation via mTORC2 phosphorylates telomerase reverse transcriptase (TERT) at Serine 824, driving nuclear translocation that is independent of telomere maintenance. In the nucleus, TERT assembles with FOXO3 and MYC into a tripartite transcriptional complex that occupies the EIF2AK3 promoter, enabling PERK transcriptional activation. This activity converts the unfolded protein response from pro-apoptotic to cytoprotective: PERK-ATF4 signaling drives biogenesis of core autophagy machinery while simultaneously inducing selective ERphagy through the receptors TEX264 and CCPG1, which prevents pathological PERK clustering and preserves tubular ER architecture in diseased RPE. Using C. elegans phosphorylation-deficient mutants, mouse models and AMD patient induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE), we establish that AKT1-mediated TERT phosphorylation is an evolutionarily conserved prerequisite for FOXO/DAF-16 nuclear function and lysosomal homeostasis in post-mitotic cells. Pharmacologic targeting of AKT2 with a first-in-class dual-pocket allosteric inhibitor selectively enhances AKT1 compensation, restoring macroautophagic and ERphagy flux across disease models. These findings reveal a kinase-to-transcription axis that reprograms organelle quality control and identify the AKT1-TERT-PERK-ATF4 pathway as a therapeutic target in proteostasis-driven disease.

cell biology↗

bioRxiv2025

Integrated host phage RNA seq analysis of Mycobacteriophage D29 infection reveals dual arm balanced phage genome expression and inhibited expression of host transporter and VapC target genes.

The Mycobacteriophage D29 infects Mycobacterium species. Many of these are deadly human pathogens. In earlier studies, we performed proteomic analyses using a temperature-sensitive variant of D29, called D29ts12. This work indicated that a regulatory mechanism controls the expression of the phages right arm genes. In this study, we executed a transcriptomic analysis. We gained further insight into how phage infection affects gene expression, both in its genome and in the host genome. We identified several novel non-coding RNA contigs spanning the cos site junction. This finding indicates that this region is expressed. In addition, we observed two areas of intense transcriptional activity. One is located downstream of Pleft, in the right arm, and coincides with a major noncoding RNA species. This RNA species is essential for lytic growth, as reported earlier for mycobacteriophages of the A2 family. The other area of transcriptional activity was gene 17, which encodes the major coat protein. By comparing TPM values, we found that thermal inactivation of phage D29ts12 growth significantly decreased right-arm gene expression. Interestingly, an accompanying sharp increase in left-arm gene expression was observed. Therefore, a mechanism ensures balanced expression from the two arms. We also analysed the impact of phage infection on host gene expression. The results indicate significant changes in the expression levels of genes encoding transporters and genes regulated by the toxin VapC. This investigation is the first to use a mycobacteriophage to examine the combined transcriptome of the phage and its host.

microbiology↗

bioRxiv2025

Germline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques

Germline-targeting-(GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a germline-targeting trimer immunogen Q23-APEX-GT2 that primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated V2-apex-specific B cells in humanized knock-in mice and consistently elicited immunofocused antibody responses in rhesus macaques, priming multiple long CDRH3-loop bnAb-B cell lineages. Monoclonal antibodies from immunized macaques exhibited broad heterologous HIV trimer binding and cross-neutralization. Atomic-level structural studies confirmed precise epitope targeting and revealed CDRH3-paratope configurations that mirrored those of human V2-apex bnAbs. This study provides proof-of-principle for successful priming and maturation of authentic V2-apex bnAb precursors in outbred macaques, underscoring the potential of V2-apex-targeted vaccines. HIGHLIGHTSO_LIEngineered Q23-APEX-GT2 trimer to stimulate diverse V2-apex bnAb B cell precursors C_LIO_LIQ23-APEX-GT2 primed rare V2-apex bnAb B cells in mice and outbred rhesus macaques C_LIO_LIQ23-APEX-GT2 elicited immunofocused antibody responses and diverse V2-apex B cell lineages with desirable long-CDRH3 paratope properties C_LIO_LIQ23-APEX-GT2 alone induced V2-apex antibodies with broad HIV trimer binding and modest neutralization breadth C_LIO_LIStructural analysis confirmed bnAb site targeting, mirroring human and rhesus V2-apex bnAbs C_LI

immunology↗

bioRxiv2025

The Mitochondrial F-box protein 1 and DJ-1 homolog HSP31 support cellular proteostasis during mitochondrial protein import clogging

Mitochondrial biogenesis requires the import of [~]1,000-1,500 nuclear-encoded proteins across the Translocase of Outer Membrane (TOM) and the Translocase of Inner Membrane (TIM) 22 or 23 complexes. Protein import defects cannot only impair mitochondrial respiration but also cause mitochondrial Precursor Overaccumulation Stress (mPOS) in the cytosol. Recent studies showed that specific mutations in the nuclear-encoded Adenine Nucleotide Translocase 1 (ANT1) cause musculoskeletal and neurological diseases by clogging TOM and TIM22 and inducing mPOS. Here, we found that overexpression of MFB1, encoding the mitochondrial F-box protein 1, suppresses cell growth defect caused by a clogger allele of AAC2, the yeast homolog of Ant1. Disruption of MFB1 synergizes with a clogger allele of aac2 to inhibit cell growth. This is accompanied by increased retention of mitochondrial proteins in the cytosol, suggesting exacerbated defect in mitochondrial protein import. Proximity-dependent biotin identification (BioID) suggested that Mfb1 interacts with several mitochondrial surface proteins including Tom22, a component of the TOM complex. Loss of MFB1 under clogging conditions activates genes encoding cytosolic chaperones including HSP31. Interestingly, disruption of HSP31 creates a synthetic lethality with protein import clogging under respiring conditions. We propose that Mfb1 functions to maintain mitochondrial protein import competency under clogging conditions, whereas Hsp31 plays an important role in protecting the cytosol against mPOS. Mutations in DJ-1, the human homolog of Hsp31, and mitochondria-associated F-box proteins (eg., Fbxo7) are known to cause early-onset Parkinsons disease. Our work may help to better understand how these mutations affect cellular proteostasis and cause neurodegeneration.

genetics↗

bioRxiv2025

Smartphone behavior is suppressed during bursts of wake slow wave

Real-world behavior unfolds as a continuous flow of actions over time. One possibility is that this continuous flow is enabled by a seamless stream of cortical activity. However, emerging evidence suggests that even during ongoing behaviors, cortical neural populations undergo brief periods of silence. This off-state can be detected as wake slow waves in EEG, similar to the slow waves characterizing deep sleep. Here, we leveraged the spontaneously occurring fluctuations in smartphone touchscreen interactions in combination with EEG to investigate the dynamics of slow waves during behavior. We find that slow waves occur in bursts - characterized by short consecutive intervals - interleaved with longer periods of absent slow waves. During smartphone use, the probability of bursts increased compared to rest, and the duration of burst-absent periods was lower. During the bursts, however, the likelihood of generating smartphone interactions was substantially diminished. Conversely, the periods of absent slow waves were more permissive to the behavioral output. We propose that slow wave burst dynamics are state-dependent, configured to create temporal windows permissive to action generation. This configuration, in turn, allows behavioral outputs to leverage the windows of opportunity that emerge between slow wave bursts. Our study, combining smartphone behavior with EEG, reveals how brief cortical silencing events structure the computations underlying everyday actions.

neuroscience↗

bioRxiv2025

Beyond P-values: A Multi-Metric Framework for Robust Feature Selection and Predictive Modeling

High-dimensional biomedical datasets routinely contain sparse signals embedded among vast, correlated features, making variable selection central to building models that generalize. Although significance-based selection is widely used across modalities (e.g., imaging, EHR, multi-omics), statistical significance does not guarantee predictive utility, and vice versa. Yet few methods unify inferential and predictive evidence within a single selection framework. We introduce MIXER (Multi-metric Integration for eXplanatory and prEdictive Ranking), a domain-agnostic approach that integrates multiple selection metrics into one consensus model via adaptive weighting that quantifies each criterions contribution. Through simulation studies, we demonstrate that different selection metrics identified markedly different feature sets whose over-laps depended on the underlying feature distributions and signal strength. Applied to Alzhemiers disease in UK Biobank, MIXER outperformed every individual criterion, including statistical significance, and generalized to an external disease-specific cohort, Alzheimers Disease Sequencing Project, yielding higher discrimination and stronger risk stratification. The MIXER framwork is also modular and readily extends to other selection criteria and data modalities, providing a practical route to more accurate, interpretable, and transportable predictive models.

bioinformatics↗

bioRxiv2025

Myoglobin leaching into the serum of IDA mice is driven by the high activation of sGC under anemic conditions which induces myoglobin expression

Our study reveals that status of the sGC heterodimer or its subsequent activation aligns with active erythropoiesis, and this heterodimer also correlates with the expression of myoglobin (Mb) or HO1. In this study we found that Mb expression which is driven by iron restriction and high sGC activation in iron deficiency anemia (IDA) leaches out more into the serum relative to non-anemic WTs. Tissues from IDA mice of both models developed either by nutritional iron deprivation or by ablation of ferroportin (Fpn) gene or from iron refractory iron deficiency anemia (IRIDA) mice found that Mb expression follows a variable pattern in different tissues but always correlates to the status of the sGC heterodimer or its subsequent activation. Here higher Mb expression happening in anemic (IDA, Fe<5 ppm or IDA, Fpn) or non-anemic WT mice is both due to iron restriction and an elevated sGC heterodimer that corroborated with greater sGC activation. More importantly we find significant leaching of Mb into the serum of these anemic (IDA) mice from both models and our spectral data suggests that this Mb is heme-free. This Mb leaching in anemia is a cumulative impact of Mb secreting out from various tissues including lungs, spleen, skeletal or cardiac muscles where Mb is expressed and not just in the skeletal muscles where Mb expression is low. Based on these findings we construct a working model of anemia, where high activation of sGC under anemic conditions (Fpn ablation or restricted Fe diet) induces Apo-Mb or heme-free Mb expression which can then leach out into the serum. Our findings of Mb leaching are novel and can find further application as a diagnostic strategy in anemia.

biochemistry↗

bioRxiv2025

Absolute Quantification of Fluorescent Protein Fusions by Proteomics

Fusions with fluorescence proteins (FPs) play a pivotal role in experimental biology because of their sensitive and spatially precise visualization by spectroscopy. However, observed fluorescence is not always proportional to their molar abundance. Only a fraction of the fusion protein containing the mature fluorescence chromophore is detectable by spectroscopy and there is no generic method for estimating its molar abundance. We developed a fluorescence-independent mass-spectrometry based approach for accurate absolute sub-femtomole quantification of FP-fusions that also estimates the protein faction having fully matured chromophore. The method exploits an isotopically labelled 68 kDa recombinant protein standard containing peptide proxies for 6 prototypical FPs (mCherry, mScarlet-I, mKate2, EGFP, mNeonGreen and Dendra2) and two self-labelling (Halo- and SNAP-) tags. It enables quantification of proteins fused to any of more than 70 FPs or self-labelling tags. It is versatile, robust, precise and can be used broadly for the absolute quantification of fluorescent fusions in in-vivo and in-vitro cellular systems. As case study we combined mass spectrometry with fluorescence spectroscopy to study expression kinetics of FP fusions in cell-free systems. Molar concentrations of the expressed fusion protein, its fraction containing the mature fluorescent chromophore and of the fluorescent protein were integrated into a mathematical model to obtain kinetic rates of translation, chromophore maturation and folding.

biochemistry↗

bioRxiv2025

TDP-43 pathology triggers SRRM4-dependent cryptic splicing of G3BP1 in ALS/FTD

Loss of nuclear TDP-43 is a defining feature of the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet how this leads to selective neuronal vulnerability is poorly understood. Here, using human iPSC-derived neurons and a large multi-omics dataset of ALS/FTD patients, we demonstrate that TDP-43 pathology induces the inclusion of an in-frame cryptic exon in human G3BP1. The resulting CRYPTIC G3BP1 protein contains an additional 10-amino acids within the highly conserved NTF2L domain, which acts as a dominant negative and disrupts stress granule dynamics. We further show that cryptic exon inclusion in G3BP1 upon TDP-43 loss is enriched in neurons. Mechanistically, the loss of TDP-43 unmasks a binding site for the neuron-specific splicing regulator SRRM4 within intron 2 of G3BP1, enabling the inclusion of the cryptic exon. Collectively, our findings reveal that neuron-specific regulatory mechanisms intersect with TDP-43 -mediated splicing and suggest a mechanistic basis for the increased neuronal vulnerability observed in ALS/FTD.

neuroscience↗

bioRxiv2025

Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles

Anatomic location of white adipose tissue is a determinant of cardiometabolic risk. To understand differences within/between adipose depots, we generated 65,668 single-nucleus transcriptomes from human subcutaneous or intraabdominal adipose tissue (SAT/IAT). Unsupervised analysis revealed 26 adipose-resident cell clusters including two subpopulations of mature adipocytes, characterized by high vs. low expression of adipocyte maturation genes (ADIPOMAThi vs. ADIPOMATlo). ADIPOMATlo adipocytes demonstrate a low-differentiation, pro-inflammatory, and pro-fibrotic transcriptome. IAT-resident ADIPOMATlo were more abundant in higher BMI donors, while SAT-resident ADIPOMATlo associated with impaired glycemia. TSHZ3 was identified as a candidate regulator of ADIPOMATlo transcriptome. TSHZ3 knockdown in adipogenic progenitors inhibited differentiation, with downregulation of early adipogenic regulators (e.g. CEBPA/B, PPARG) and mature adipocyte genes. Heterozygous deletion of Tshz3 in mice reduced SAT and IAT weight. Here, we show that adipocyte subsets with distinct transcriptomic signature reside in human WAT; altered TSHZ3-mediated transcriptional regulation may contribute to low-maturation subpopulation linked to metabolic disease.

cell biology↗

bioRxiv2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide vari- ants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alter- ations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational frame- work for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by indepen- dent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

genomics↗

bioRxiv2025

Comparative genome analysis of tea rhizosphere dwelling Paenarthrobacter nicotinovorans AB444: Uncovering Physiological Resilience and Ecological Adaptability

Plant growth-promoting rhizobacteria (PGPR) can be considered a promising tool for sustainable agriculture. The recent scenario of growing demand for higher crop yields, with declining soil fertility and impacts of climate change, promotes the global shift towards eco-friendly agricultural practices, emphasising the significance of PGPR as a sustainable solution. In this study, a PGPR Paenarthrobacter sp. AB444 was isolated from the rhizosphere of tea plants at the Longview and Makaibari tea estates in the Darjeeling District of West Bengal. Based on the draft genome sequence along with comprehensive chemotaxonomic analyses, strain AB444 was identified as Paenarthrobacter nicotinovorans. The pangenomic analysis with phylogenetically close strains revealed the gene clusters that are common and unique to the isolate. The plant growth-promoting attributes of AB444 were explored with different assays like phosphate solubilisation, IAA and siderophore production, ACC deaminase, nitrogen fixation, and protease activity. The colonization of the isolate to the plant root and in-planta growth were also assessed. The presence of biosynthetic gene clusters of AB444 related to plant growth was also extensively studied, highlighting the unmapped disposition of Paenarthrobacter nicotinovorans.

microbiology↗

bioRxiv2025

Bursts of regional cortical inhibition during smartphone use

Transient burst of beta ({beta}) oscillations - brief neural events lasting only a fraction of a second - are increasingly recognised for their role in functional inhibition that may support cognitive processes and motor timing underlying goal-directed behaviour. Smartphone behaviour, which involves sustained engagement across diverse cognitive processes provides a fresh avenue to examine these bursts. In this study, we used EEG to measure {beta}-bursts as participants freely interacted with their smartphones using their right hand for [~] 80 min. Bursts were detected across the scalp, with bilateral sensorimotor electrodes accumulating more periods with bursts than the rest of the electrodes. There was a brain-wide reduction in the probability of bursts preceding a touchscreen touch, followed by an increase, with the strongest modulation in the left sensorimotor electrodes. Interestingly, touchscreen touches sometimes occurred during the bursts. We further examined the intra-burst touch rate across the scalp and found that the rate was lower over the left sensorimotor cortex than the rest of electrodes. Finally, we characterised the diverse behaviours in terms of the interval between touchscreen interactions to find that the behaviours with bursts were typically longer than the behaviours without bursts. We propose that the apparently continuous stream of smartphone touches is supported by brief, spatially localised transient bursts of inhibition. These transients may help support the computational flexibility in distributed neural networks needed for processing continuous motor output and integrating the rich sensory information.

neuroscience↗

bioRxiv2025

A new dual-affinity peptide nucleic acid for targeting miRNA-21 precursor rescues tumor repressor PTEN expression

MicroRNAs (miRNAs) have multiple functions in cells and are related to many diseases including cancer by regulating posttranscriptional gene expression. The microRNA precursors (pre-miRs), which can be cleaved by Dicer endonuclease to produce mature miRNAs, often have a cleavage site consisting of both double-stranded (ds) and single-stranded (ss) RNA structures. Peptide nucleic acid (PNA) is a kind of analogue of DNA which can hybridize to DNA or RNA through Watson-Crick and Hoogsteen pairing. We previously reported a novel dual-affinity PNA (daPNA) platform that can simultaneously form a duplex and a triplex with a target RNAs ssRNA-dsRNA junction region. The PNA-RNA complex structure is stabilized by forming antisense PNA (asPNA)-ssRNA duplex immediately adjacent to a chemically modified dsRNA-binding PNA (dbPNA)-dsRNA triplex. In this study, we further explored the application of the daPNA platform to target the precursor of miR-21, which is considered an oncogene. We have designed a set of PNAs including asPNAs, dbPNAs, and daPNAs. The nondenaturing polyacrylamide gel electrophoresis (PAGE) and biolayer interferometry (BLI) data reveal that daPNA-21-10 can strongly bind to pre-miR-21 with high specificity. The data show that pre-miR-21 is easily targeted by traditional antimir, asPNA or dbPNA and optimization of the dsRNA-ssRNA junction position is needed for identifying a tightly binding daPNA. Furthermore, daPNA-21-10 not only inhibits the Dicer activity on pre-miR-21 in cell-free assays, but also down-regulates the expression of miR-21, rescuing PTEN protein expression in cells. Taken together, the biofunction and programmability of daPNA make it a promising platform for probing and regulating miRNA biogenesis and many other RNA-involved biological processes. HighlightsO_LISimultaneous recognition of dsRNA and ssRNA regions C_LIO_LIRNA targeting by dividing and conquering through a dsRNA-ssRNA junction construction C_LIO_LISubstrate-specific inhibition of Dicer acting on pre-miR-21 C_LIO_LIDerepressing PTEN expression by inhibiting miR-21 maturation C_LI O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/668835v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@c8af64org.highwire.dtl.DTLVardef@172d2bdorg.highwire.dtl.DTLVardef@1698ea1org.highwire.dtl.DTLVardef@112fa16_HPS_FORMAT_FIGEXP M_FIG C_FIG eToc BlurbLian et al. show that the miR-21 precursor structure containing the Dicer cleavage site can be targeted by a new type of dual-affinity peptide nucleic acids (daPNAs) through the creation of a dsRNA-ssRNA junction, energetically optimized for the simultaneous duplex and triplex formation. Pre-miR-21 structure, which is hardly accessible to traditional antisense strategies and triplex formation alone, can be targeted by a daPNA with high sequence/structure specificity and strong binding affinity. daPNA platform has a great potential in probing many other RNA structures and broad therapeutic applications.

molecular biology↗

bioRxiv2025

Furrow tillage reduces soil carbon loss and enhances microbial metabolism

With increasing global carbon loss from agricultural fields, agricultural practices should be monitored with proper regulatory measures. To address three problems of minimising carbon loss, optimising soil fertility and enhancing soil microbiota together, this study has developed a new innovative "Furrow tillage" approach that affords a balance between conventional and conservative tillage. Based on two years of trials in rice fields at multiple sites, this practice has justifications from agronomy, geochemistry, crop physiology, and molecular microbiology. Furrow tillage illustrated low carbon loss, similar to no-tillage, while retaining high nutrient bioavailability, similar to deep tillage. Microbial diversity, molecular responses and metabolic activities showed that furrow tillage induced microbial interactions while allowing a better entrapment of carbon dioxide in the soil. The study used CO2 flux, spatial distribution, total and available elemental analysis, plant ultra-structural observations, microbial metagenomics, high-throughput sequencing and molecular modelling to establish an optimal soil-crop quality, microbial maintenance and reduce carbon loss through furrow tillage practice.

ecology↗