Novel insights on the positive correlation between sense and antisense pairs on gene expression.

A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

Controlled Photooxidation via Singlet Oxygen Generation by Triplet Harvesting in a Heavy Atom Free Pure Organic Dithienylethene-Naphthalene Diimide.

Noninvasive control over the reversible generation of singlet oxygen (1O2) has found the enormous practical implications in the field of biomedical science. However, metal-free pure organic emitters, connected with a photoswitch, capable of generating "on-demand" 1O2 via triplet harvesting remain exceedingly rare; therefore, the utilization of these organic materials for the reversible control of singlet oxygen production remains at its infancy. Herein, an ambient triplet mediated emission in quinoline-dithienylethene (DTE)-core-substituted naphthalene diimide (cNDI) derivative is unveiled via delayed fluorescence. The quinoline-DTE-cNDI triad displayed enhanced photoswitching efficiency via double FRET mechanism.  It was found to have direct utilization in controlled photosensitized organic transformations via efficient generation of singlet oxygen (yield ΦΔ ~ 0.73). The designed molecule exhibits a long-lived emission (τ ∼ 1.1 µs) and very small singlet-triplet splitting (ΔSET) of 0.13 eV empowering it to display delayed fluorescence. Comprehensive steady state and time-resolved emission spectroscopy (TRES) analyses along with DFT calculations offer detailed understandings into the excited-state manifolds of organic compound and energy transfer (ET) pathways involved in 1O2 generation.

Surface functionalized perovskite nanocrystals: a design strategy for organelle-specific fluorescence lifetime multiplexing.

Fluorescent molecules or materials with high photoluminescence quantum yields and stability towards photobleaching are ideally suited for multiplex imaging. Despite complying with such properties, perovskite nanocrystals (Pv-NCs) are rarely used for bioimaging owing to their toxicity and limited stability in aqueous media and towards human physiology. We aim to address these deficiencies by designing core-shell structures with Pv-NCs as the core and surface-engineered silica as the shell (SiO2@Pv-NCs) since silica is recognized as a biologically benign carrier material and is known to be excreted through urine. The post-grafting methodology is adopted for developing [SiO2@Pv-NCs]tpm and [SiO2@Pv-NCs]tsy (tpm: triphenylphosphonium ion, tsy: tosylsulfonamide) for specific imaging of mitochondria and endoplasmic reticulum (ER) of the live HeLa cell, respectively. A subtle difference in their average fluorescence decay times ([SiO2@Pv-NCs]tpm: tpm τ av = 3.1 ns and [SiO2@Pv-NCs]tsy: tsy τ av = 2.1 ns) is used for demonstrating a rare example of perovskite nanocrystals in fluorescence lifetime multiplex imaging.

Imidazolium and Pyridinium-based Ionic Porous Organic Polymers: Advances in Transformative Solutions for Oxoanion Sequestration and Non-redox CO2 Fixation.

The rapid pace of industrialization has led to a multitude of detrimental environmental consequences, including water pollution and global warming. Consequently, there is an urgent need to devise appropriate materials to address these challenges. Ionic porous organic polymers (iPOPs) have emerged as promising materials for oxoanion sequestration and non-redox CO2 fixation. Notably, iPOPs offer hydrothermal stability, structural tunability, a charged framework, and readily available nucleophilic counteranions. This review explores the significance of pores and charged functionalities alongside design strategies outlined in existing literature, mainly focusing on the incorporation of pyridinium and imidazolium units into nitrogen-rich iPOPs for oxoanion sequestration and non-redox CO2 fixation. The present review also addresses the current challenges and future prospects, delineating the design and development of innovative iPOPs for water treatment and heterogeneous catalysis.

WITHDRAWN: Supinoxin blocks Small Cell Lung Cancer Progression by Inhibiting Mitochondrial Respiration through the RNA Helicase DDX5.

The authors have requested that this preprint be removed from Research Square.

Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer.

Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay for triple-negative breast cancer (TNBC). The epithelial-to-mesenchymal transition (EMT) is a developmental program co-opted by cancer cells that promotes metastasis and chemoresistance. There are no therapeutic strategies specifically targeting mesenchymal-like cancer cells. We report that the US Food and Drug Administration (FDA)-approved chemotherapeutic eribulin induces ZEB1-SWI/SNF-directed chromatin remodeling to reverse EMT that curtails the metastatic propensity of TNBC preclinical models. Eribulin induces mesenchymal-to-epithelial transition (MET) in primary TNBC in patients, but conventional chemotherapy does not. In the treatment-naive setting, but not after acquired resistance to other agents, eribulin sensitizes TNBC cells to subsequent treatment with other chemotherapeutics. These findings provide an epigenetic mechanism of action of eribulin, supporting its use early in the disease process for MET induction to prevent metastatic progression and chemoresistance. These findings warrant prospective clinical evaluation of the chemosensitizing effects of eribulin in the treatment-naive setting.

Arbuscular mycorrhizal fungal contribution towards plant resilience to drought conditions.

Climate changes cause altering rainfall patterns resulting in an increase in drought occurrences globally. These events are disrupting plants and agricultural productivity. To evade droughts, plants try to adapt and modify in the best capacities possible. The plants have adapted by structurally modifying roots, stems, and leaves, as well as modifying functions. Lately, the association of microbial communities with plants has also been proven to be an important factor in aiding resilience. The fungal representatives of the microbial community also help safeguard the plants against drought. We discuss how these fungi associate with plants and contribute to evading drought stress. We specifically focus on Arbuscular mycorrhizal fungi (AMF) mediated mechanisms involving antioxidant defenses, phytohormone mediations, osmotic adjustments, proline expressions, fungal water absorption and transport, morphological modifications, and photosynthesis. We believe understanding the mechanisms would help us to optimize the use of fungi in agricultural practices. That way we could better prepare the plants for the anticipated future drought events.

A Case Report on Clotrimazole-Induced Localized Erythema.

Clotrimazole, a commonly used antifungal agent, is employed in the treatment of otomycosis and other ear infections. However, its use can lead to adverse drug reactions (ADRs), occasionally manifesting as local irritation or allergic responses. This abstract presents a case study of a patient exhibiting an adverse reaction to clotrimazole ear drops, highlighting the clinical presentation, management, and resolution of the ADR. The patient, a 73-year-old male, presented with itching and erythema over the left pinna extending up to the middle of the sternum following clotrimazole ear drop application. Immediate cessation of the medication and symptomatic treatment led to rapid resolution of symptoms. This case emphasizes the importance of recognizing potential ADRs associated with clotrimazole ear drops and the necessity of prompt intervention to mitigate adverse effects, thereby ensuring optimal patient care.

Unveiling autophagy and aging through time-resolved imaging of lysosomal polarity with a delayed fluorescent emitter.

Detecting the lysosomal microenvironmental changes like viscosity, pH, and polarity during their dynamic interorganelle interactions remains an intriguing area that facilitates the elucidation of cellular homeostasis. The subtle variation of physiological conditions can be assessed by deciphering the lysosomal microenvironments during lysosome-organelle interactions, closely related to autophagic pathways leading to various cellular disorders. Herein, we shed light on the dynamic lysosomal polarity in live cells and a multicellular model organism, Caenorhabditis elegans (C. elegans), through time-resolved imaging employing a thermally activated delayed fluorescent probe, DC-Lyso. The highly photostable and cytocompatible DC-Lyso rapidly labels the lysosomes (within 1 min of incubation) and exhibits red luminescence and polarity-sensitive long lifetime under the cellular environment. The distinct variation in the fluorescence lifetime of DC-Lyso suggests an increase in local polarity during the lysosomal dynamics and interorganelle interactions, including lipophagy and mitophagy. The lifetime imaging analysis reveals increasing lysosomal polarity as an indicator for probing the successive development of C. elegans during aging. The in vivo microsecond timescale imaging of various cancerous cell lines and C. elegans, as presented here, therefore, expands the scope of delayed fluorescent emitters for unveiling complex biological processes.

Immunological Assessment of Recent Immunotherapy for Colorectal Cancer.

Colorectal cancer (CRC) is the third most prevalent malignancy with increased incidence and mortality rates worldwide. Traditional treatment approaches have attempted to efficiently target CRC; however, they have failed in most cases, owing to the cytotoxicity and non-specificity of these therapies. Therefore, it is essential to develop an effective alternative therapy to improve the clinical outcomes in heterogeneous CRC cases. Immunotherapy has transformed cancer treatment with remarkable efficacy and overcomes the limitations of traditional treatments. With an understanding of the cancer-immunity cycle and tumor microenvironment evolution, current immunotherapy approaches have elicited enhanced antitumor immune responses. In this comprehensive review, we outline the latest advances in immunotherapy targeting CRC and provide insights into antitumor immune responses reported in landmark clinical studies. We focused on highlighting the combination approaches that synergistically induce immune responses and eliminate immunosuppression. This review aimed to understand the limitations and potential of recent immunotherapy clinical studies conducted in the last five years (2019-2023) and to transform this knowledge into a rational design of clinical trials intended for effective antitumor immune responses in CRC.

Unveiling the Long-Lived Emission of Copper Nanoclusters Embedded in a Protein Scaffold.

Protein-conjugated coinage metal nanoclusters have become promising materials for optoelectronics and biomedical applications. However, the origin of the photoluminescence, especially the long-lived excited state emission in these metal nanoclusters, is still elusive. Here, we unveiled the underlying mechanism of long-lived emission in albumin protein-conjugated copper nanoclusters (Cu NCs) using steady state and time-resolved spectroscopic techniques. Our findings reveal room-temperature phosphorescence (RTP) in protein-conjugated Cu NCs. Time-resolved area-normalized spectra distinguished short- and long-lived components, where the former arises from the singlet state and the latter from the triplet state, thus resulting in RTP. The similarity of the emission spectra at room (298 K) and cryogenic (77 K) temperature ascertains the RTP phenomenon by harvesting the higher-lying triplet states. Time-gated bioimaging of A549 cells using the long-lived emission not only supports RTP emission in the cellular environment but also provides exciting avenues in long-term bioimaging using bovine serum albumin-conjugated Cu NCs.

Kimura Disease-A Case Report.

Kimura Disease, an eosinophilic hyperplastic granulomatous disease of idiopathic origin is most commonly seen in young males. It mostly presents with deep subcutaneous tissue swelling along with enlargement of salivary glands and regional lymphadenopathy. Diagnosis is mainly based on histopathological findings and raised serum IgE and hypereosinophilia. The radiological investigation of choice is Magnetic Resonance Imaging. Management strategy includes surgery and steroid therapy. Chemotherapeutic agents are also frequently used by some centres. Relapse and recurrence stands to be a common problem with management of this disease process. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-023-03817-y.

The genomic region of the 3' untranslated region (3'UTR) of PHO84, rather than the antisense RNA, promotes gene repression.

PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense pairs in a dbp2Δ strain and found over 700 sense/antisense pairs, including PHO84, to be positively correlated, contrasting the prevailing model. To define what mechanism regulates the PHO84 gene and how this regulation could have been originally attributed to repression by the antisense transcript, we conducted a series of molecular biology and genetics experiments. We now report that the 3' untranslated region (3'UTR) of PHO84 plays a repressive role in sense expression, an activity not linked to the antisense transcripts. Moreover, we provide results of a genetic screen for 3'UTR-dependent repression of PHO84 and show that the vast majority of identified factors are linked to negative regulation. Finally, we show that the PHO84 promoter and terminator form gene loops which correlate with transcriptional repression, and that the RNA-binding protein, Tho1, increases this looping and the 3'UTR-dependent repression. Our results negate the current model for antisense non-coding transcripts of PHO84 and suggest that many of these transcripts are byproducts of open chromatin.

Fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy for deciphering the morphological evolution of supramolecular self-assembly.

The properties and functions of non-covalent interaction-driven fluorescent supramolecular self-assembly depend greatly on their evolution dynamics. Electron microscopy, atomic force microscopy, and confocal laser scanning microscopy have been used to elucidate the formation of molecular self-assembly. However, some pertinent issues, such as the drying or freezing of the sample for electron microscopy, the influence of the interactions between the tip and the sample in atomic force microscopy imaging, and the low spatial resolution of confocal laser scanning microscopy images, often impede the real-time analysis and exploration of the dynamics of molecular self-assembly processes. In this context, fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy have recently been explored to unravel the physical picture of the in situ growth dynamics and stimuli-induced morphological transformation of luminescent self-assembled structures. The current highlight article demonstrates the need for fluorescence correlation spectroscopy and fluorescence lifetime imaging microscopy to acquire precise information on the dynamics and morphological evolution of fluorescent self-assembled architectures using a few remarkable recent studies. In addition to the current status and challenges, the future directions for the further exploration of dynamic self-assembly processes towards developing next-generation functional materials have been delineated.

Histidine-Containing Amphiphilic Peptide-Based Non-Cytotoxic Hydrogelator with Antibacterial Activity and Sustainable Drug Release.

A histidine-based amphiphilic peptide (P) has been found to form an injectable transparent hydrogel in phosphate buffer solution over a pH range from 7.0 to 8.5 with an inherent antibacterial property. It also formed a hydrogel in water at pH = 6.7. The peptide self-assembles into a nanofibrillar network structure which is characterized by high-resolution transmission electron microscopy, field-emission scanning electron microscopy, atomic force microscopy, small-angle X-ray scattering, Fourier-transform infrared spectroscopy, and wide-angle powder X-ray diffraction. The hydrogel exhibits efficient antibacterial activity against both Gram-positive bacteria Staphylococcus aureus (S. aureus) and Gram-negative bacteria Escherichia coli (E. coli). The minimum inhibitory concentration of the hydrogel ranges from 20 to 100 µg/mL. The hydrogel is capable of encapsulation of the drugs naproxen (a non-steroidal anti-inflammatory drug), amoxicillin (an antibiotic), and doxorubicin, (an anticancer drug), but, selectively and sustainably, the gel releases naproxen, 84% being released in 84 h and amoxicillin was released more or less in same manner with that of the naproxen. The hydrogel is biocompatible with HEK 293T cells as well as NIH (mouse fibroblast cell line) cells and thus has potential as a potent antibacterial and drug releasing agent. Another remarkable feature of this hydrogel is its magnification property like a convex lens.

Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression.

The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no therapeutic avenues specifically targeting cells that have acquired mesenchymal traits. We show that treatment of mesenchymal-like triple-negative breast cancer (TNBC) cells with the microtubule-destabilizing chemotherapeutic eribulin, which is FDA-approved for the treatment of advanced breast cancer, leads to a mesenchymal-epithelial transition (MET). This MET is accompanied by loss of metastatic propensity and sensitization to subsequent treatment with other FDA-approved chemotherapeutics. We uncover a novel epigenetic mechanism of action that supports eribulin pretreatment as a path to MET induction that curtails metastatic progression and the evolution of therapy resistance.

Rice (Oryza sativa) alleviates photosynthesis and yield loss by limiting specific leaf weight under low light intensity.

The physiological mechanisms of shade tolerance and trait plasticity variations under shade remain poorly understood in rice (Oryza sativa L.). Twenty-five genotypes of rice were evaluated under open and shade conditions. Various parameters to identify variations in the plasticity of these traits in growth irradiance were measured. We found wide variations in specific leaf weight (SLW) and net assimilation rate measured at 400µmolm-2 s-1 photosynthetic photon flux density (PPFD; referred to as A 400 ) among the genotypes. Under shade, tolerant genotypes maintained a high rate of net photosynthesis by limiting specific leaf weight accompanied by increased intercellular CO2 concentration (C i ) compared with open-grown plants. On average, net photosynthesis was enhanced by 20% under shade, with a range of 2-30%. Increased accumulation of biomass under shade was observed, but it showed no correlation with photosynthetic plasticity. Chlorophyll a /b ratio also showed no association with photosynthetic rate and yield. Analysis of variance showed that 11%, 16%, and 37% of the total variance of A 400 , SLW, and C i were explained due to differences in growth irradiance. SLW and A 400 plasticity in growth irradiance was associated with yield loss alleviation with R 2 values of 0.37 and 0.16, respectively. Biomass accumulation was associated with yield loss alleviation under shade, but no correlation was observed between A 400 and leaf-N concentration. Thus, limiting specific leaf weight accompanied by increased C i rather than leaf nitrogen concentration might have allowed rice genotypes to maintain a high net photosynthesis rate per unit leaf area and high yield under shade.

Molecular to Supramolecular Self-Assembled Luminogens for Tracking the Intracellular Organelle Dynamics.

Deciphering the dynamics of intracellular organelles has gained immense attention due to their subtle control over diverse, complex biological processes such as cellular metabolism, energy homeostasis, and autophagy. In this context, molecular materials, including small-organic fluorescent probes and their supramolecular self-assembled nano-/microarchitectures, have been employed to explore the diverse intracellular biological events. However, only a handful of fluorescent probes and self-assembled emissive structures have been successfully used to track different organelle's movements, circumventing the issues related to water solubility and long-term photostability. Thus, the water-soluble molecular fluorescent probes and the water-dispersible supramolecular self-assemblies have emerged as promising candidates to explore the trafficking of the organelles under diverse physiological conditions. In this review, we have delineated the recent progress of fluorescent probes and their supramolecular self-assemblies for the elucidation of the dynamics of diverse cellular organelles with a special emphasis on lysosomes, lipid droplets, and mitochondria. Recent advancement in fluorescence lifetime and super-resolution microscopy imaging has also been discussed to investigate the dynamics of organelles. In addition, the fabrication of the next-generation molecular to supramolecular self-assembled luminogens for probing the variation of microenvironments during the trafficking process has been outlined.

Mycobacterium Species on the Cutaneous Microbiome of Very Preterm Neonates.

The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harboring on an infant's skin. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead to pathological disease. This study was conducted to understand the neonatal skin microbiome of very preterm neonates (under 32 weeks) admitted to the Neonatal Intensive Care Unit(NICU) at a tertiary healthcare setting before and after kangaroo mother care (KMC), using next-generation sequencing (NGS). Skin swabs were collected on two different occasions and analyzed using the NGS technique after amplification via polymerase chain reaction. The results showed relative abundance for Mycobacterium tuberculosis in 83.33% and 66.67% (p = 0.29) and Mycobacteroides abscessus in 100% and 93.33% (p = 0.30) of the very preterm neonates on the skin microbiome before and after KMC, respectively as an incidental finding. The mere presence of these bacilli as commensals or as potential pathogens is alarming due to the risk of early exposure and incidence of tuberculosis from birth. These findings, in our view, are the first findings to be established in such a setting.

Three in One: Stimuli-Responsive Fluorescence, Solid-State Emission, and Dual-Organelle Imaging Using a Pyrene-Benzophenone Derivative.

Small organic luminogens, owing to their contrasting stimuli-responsive fluorescence in solution along with strong emission in aggregated and solidstates, have been employed in optoelectronic devices, sensors, and bioimaging. Pyrene derivatives usually exhibit strong fluorescence and concentration-dependent excimer/aggregate emission in solution. However, the impacts of microenvironments on the monomer and aggregate emission bands and their relative intensities in solution, solid, and supramolecular aggregates are intriguing. The present study delineates a trade-off between the monomer and aggregate emissions of a pyrene-benzophenone derivative (ABzPy) in solution, in the solid-state, and in nanoaggregates through a combined spectroscopic and microscopic approach. The impact of external stimuli (viscosity, pH) on the aggregate emission was demonstrated using steady-state and time-resolved spectroscopy, including fluorescence correlation spectroscopy and fluorescence anisotropy decay analysis. The aggregate formation was noticed at a higher concentration (>10 µM) in solution, at 77 K (5 µM), and in the solid-state due to the π-π stacking interactions (3.6 Å) between two ABzPy molecules. In contrast, no aggregate formation was observed in the viscous medium as well as in a micellar environment even at a higher concentration of ABzPy (50 µM). The crystal structure analysis further shed light on the intermolecular hydrogen-bonding-assisted solid-state emission, which was found to be highly sensitive toward external stimuli like pH and mechanical forces. The broad emission band comprising both monomer and aggregate in the aqueous dispersion of nanoaggregates was used for the specific cellular imaging of lysosomes and lipid droplets, respectively.