SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana.

Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases such as Friedreich's ataxia in humans. The molecular mechanisms underlying repeat expansion-induced epigenetic silencing remain largely unknown. Using a plant model with a temperature-sensitive phenotype, we have previously shown that expanded repeats can induce small RNAs, which in turn can lead to epigenetic silencing through the RNA-dependent DNA methylation pathway. Here, using a genetic suppressor screen and yeast two-hybrid assays, we identified novel components required for epigenetic silencing caused by expanded repeats. We show that FOURTH ULP GENE CLASS 1 (FUG1)-an uncharacterized SUMO protease with no known role in gene silencing-is required for epigenetic silencing caused by expanded repeats. In addition, we demonstrate that FUG1 physically interacts with ALFIN-LIKE 3 (AL3)-a histone reader that is known to bind to active histone mark H3K4me2/3. Loss of function of AL3 abolishes epigenetic silencing caused by expanded repeats. AL3 physically interacts with the chromodomain protein LIKE HETEROCHROMATIN 1 (LHP1)-known to be associated with the spread of the repressive histone mark H3K27me3 to cause repeat expansion-induced epigenetic silencing. Loss of any of these components suppresses repeat expansion-associated phenotypes coupled with an increase in IIL1 expression with the reversal of gene silencing and associated change in epigenetic marks. Our findings suggest that the FUG1-AL3-LHP1 module is essential to confer repeat expansion-associated epigenetic silencing and highlight the importance of post-translational modifiers and histone readers in epigenetic silencing.

Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics.

The interior of a living cell is an active, fluctuating, and crowded environment, yet it maintains a high level of coherent organization. This dichotomy is readily apparent in the intracellular transport system of the cell. Membrane-bound compartments called endosomes play a key role in carrying cargo, in conjunction with myriad components including cargo adaptor proteins, membrane sculptors, motor proteins, and the cytoskeleton. These components coordinate to effectively navigate the crowded cell interior and transport cargo to specific intracellular locations, even though the underlying protein interactions and enzymatic reactions exhibit stochastic behavior. A major challenge is to measure, analyze, and understand how, despite the inherent stochasticity of the constituent processes, the collective outcomes show an emergent spatiotemporal order that is precise and robust. This review focuses on this intriguing dichotomy, providing insights into the known mechanisms of noise suppression and noise utilization in intracellular transport processes, and also identifies opportunities for future inquiry. Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Deterministic early endosomal maturations emerge from a stochastic trigger-and-convert mechanism.

Endosomal maturation is critical for robust and timely cargo transport to specific cellular compartments. The most prominent model of early endosomal maturation involves a phosphoinositide-driven gain or loss of specific proteins on individual endosomes, emphasising an autonomous and stochastic description. However, limitations in fast, volumetric imaging long hindered direct whole cell-level measurements of absolute numbers of maturation events. Here, we use lattice light-sheet imaging and bespoke automated analysis to track individual very early (APPL1-positive) and early (EEA1-positive) endosomes over the entire population, demonstrating that direct inter-endosomal contact drives maturation between these populations. Using fluorescence lifetime, we show that this endosomal interaction is underpinned by asymmetric binding of EEA1 to very early and early endosomes through its N- and C-termini, respectively. In combination with agent-based simulation which supports a 'trigger-and-convert' model, our findings indicate that APPL1- to EEA1-positive maturation is driven not by autonomous events but by heterotypic EEA1-mediated interactions, providing a mechanism for temporal and population-level control of maturation.

Complication profile in a cochlear implantation- surgical audit in a large study population of low socio-economic status in a developing country.

OBJECTIVES: To audit surgical complications and their management in cochlear implant (CI) recipients in a tertiary care referral otorhinolaryngology center in South India. MATERIALS AND METHODS: Hospital data on 1,250 CI surgeries performed from June 2013 to December 2020 was reviewed. This is an analytical study with data collected from medical records. The demographic details, complications, management protocols and relevant literature were reviewed. Patients were divided into the following five age groups: 0-3 years, 3-6 years, 6-13 years, 13-18 years and above 18 years. Complications were divided into major and minor and complication occurrence was divided into peri-operative, early post-operative, and late post-operative, and the results were analyzed. RESULTS: The overall major complication rate was 9.04% (including 6.0% due to device failure). If the device failure rate was excluded, the major complication rate was 3.04%. The minor complication rate was 6%. DISCUSSION: CI is the gold standard in the management of patients with severe to profound hearing loss with minimal benefit from conventional hearing aids. Experienced tertiary care CI referral and teaching centers manage complicated implantation cases. Such centers typically audit their surgical complications, providing important reference data for young implant surgeons and newer centers. CONCLUSION: Although not bereft of complications, the list of complications and its prevalence is sufficiently low to warrant the advocacy of CI worldwide, including developing countries with low socio-economic status.

Termination of STING responses is mediated via ESCRT-dependent degradation.

cGAS-STING signalling is induced by detection of foreign or mislocalised host double-stranded (ds)DNA within the cytosol. STING acts as the major signalling hub, where it controls production of type I interferons and inflammatory cytokines. Basally, STING resides on the ER membrane. Following activation STING traffics to the Golgi to initiate downstream signalling and subsequently to endolysosomal compartments for degradation and termination of signalling. While STING is known to be degraded within lysosomes, the mechanisms controlling its delivery remain poorly defined. Here we utilised a proteomics-based approach to assess phosphorylation changes in primary murine macrophages following STING activation. This identified numerous phosphorylation events in proteins involved in intracellular and vesicular transport. We utilised high-temporal microscopy to track STING vesicular transport in live macrophages. We subsequently identified that the endosomal complexes required for transport (ESCRT) pathway detects ubiquitinated STING on vesicles, which facilitates the degradation of STING in murine macrophages. Disruption of ESCRT functionality greatly enhanced STING signalling and cytokine production, thus characterising a mechanism controlling effective termination of STING signalling.

Tuning of MgO's base characteristics by blending it with amphoteric ZnO facilitating the selective glucose isomerization to fructose for bioenergy development.

Fructose serves as an important intermediate in the preparation of liquid fuel compounds. Herein, we report its selective production via a chemical catalysis method over ZnO/MgO nanocomposite. The blending of an amphoteric ZnO with MgO reduced the latter's unfavorable moderate/strong basic sites that can influence the side reactions in the sugar interconversion, reducing fructose productivity. Of all the ZnO/MgO combinations, a 1 : 1 ratio of ZnO and MgO showed a 20% reduction in moderate/strong basic sites in MgO with ∼2-2.5 times increase in weak basic sites (overall), which is favorable for the reaction. The analytical characterizations affirmed that MgO settles on the surface of ZnO by blocking the pores. The amphoteric ZnO undertakes the neutralization of the strong basic sites and improves the weak basic sites (cumulative) by the Zn-MgO alloy formation. Therefore, the composite afforded as high as 36% fructose yield and 90% selectivity at 90 °C; especially, the improved selectivity can be accounted for by the effect of both basic and acidic sites. The favorable action of acidic sites in controlling the unwanted side reactions was maximum when an aqueous medium contained 1/5th methanol. However, ZnO's presence regulated the glucose's degradation rate by up to 40% compared to the kinetics of pristine MgO. From the isotopic labelling experiments, the proton transfer pathway (or LdB-AvE mechanism by the formation of 1,2-enediolate) is dominant in the glucose-to-fructose transformation. The composite exhibited a long-lasting ability based on the good recycling efficiency of up to 5 cycles. The insights into the fine-tuning of the physicochemical characteristics of widely available metal oxides would help develop a robust catalyst for sustainable fructose production for biofuel production (via a cascade approach).

Assessment of Oral Hygiene Status and Prevalence of Dental Caries and Traumatic Injuries to Anterior Teeth among Visually Impaired Children in Chennai City.

Aim: To assess the oral hygiene status and prevalence of dental caries and trauma to anterior teeth among visually impaired children in Chennai city. Settings and design-a cross-sectional study was conducted in institutionalized blind schoolchildren. Materials and methods: A total of 130 children from two blind schools were selected based on the inclusion and exclusion criteria. Oral hygiene status was assessed using the oral hygiene index-simplified (OHI-S). Dental caries were assessed using decayed-missing-filled teeth (DMFT) and decayed, extracted due to carries, filled teeth (deft) index for permanent and primary dentition, respectively. Trauma to anterior teeth was assessed using Ellis and Davey classification. Statistical analysis used-all the data were analyzed using the Statistical Package for the Social Sciences (SPSS) software 20.0. Results: The assessment of oral hygiene status showed that 54.6% of children had good oral hygiene, 45.4% had fair oral hygiene, and none had poor oral hygiene. The prevalence of dental caries in permanent and primary dentition was found to be 40 and 63.1%, respectively. The prevalence of trauma to anterior teeth was found to be 35.4%. Conclusion: Primary prevention approaches should be taught to parents and school teachers for early intervention of oral health problems. How to cite this article: Kannappan J, Srinivasan D, Chiriyankandath JL, et al. Assessment of Oral Hygiene Status and Prevalence of Dental Caries and Traumatic Injuries to Anterior Teeth among Visually Impaired Children in Chennai City. Int J Clin Pediatr Dent 2023;16(1):93-96.

Carbon credit reduction: A techno-economic analysis of "drop-in" fuel production.

The current study elucidates the fundamentals of technical, financial, and environmental viability of the processes used for sustainable "drop-in" fuel generation. At present, the price of producing "drop-in" fuels is around two times as costly (5-6 USD/gallon) as the cost of fossil fuels (3 USD/gallon), especially when using second-generation feedstocks. Hence, this necessitates a comprehensive techno-economic understanding of the current technologies with respect to "drop-in"-fuel. This entitles technical-economic viability, and environmental sustainability to make the processes involved commercially viable. In this context, the present review addresses unique contrasts among the various processes involved in "drop-in" fuel production. Furthermore, principles and process flow of techno-economic analysis as well as environmental implications in terms of reduced carbon footprint and carbon credit are elucidated to discuss fundamentals of techno-economic analysis in terms of capital and operational expenditure, revenue, simulation, cash flow analysis, mass and energy balances with respect to evidence-based practices. Case specific techno-economic studies with current developments in this field of research with emphasis on software tools viz., Aspen Plus, Aspen HYSIS, Aspen Plus Economic Analyser (APEC) Aspen Icarus Process Evaluator (AIPE) are also highlighted. The study also emphasis on the carbon foot print of biofuels and its carbon credits (Carbon Offset Credits (COCs) and Carbon Reduction Credits (CRCs)) by leveraging a deep technical and robust business-oriented insights about the techno-economic analysis (TEA) exclusively for the biofuel production.

Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy.

Autophagy depends on the repopulation of lysosomes to degrade intracellular components and recycle nutrients. How cells co-ordinate lysosome repopulation during basal autophagy, which occurs constitutively under nutrient-rich conditions, is unknown. Here, we identify an endosome-dependent phosphoinositide pathway that links PI3Kα signaling to lysosome repopulation during basal autophagy. We show that PI3Kα-derived PI(3)P generated by INPP4B on late endosomes was required for basal but not starvation-induced autophagic degradation. PI(3)P signals were maintained as late endosomes matured into endolysosomes, and served as the substrate for the 5-kinase, PIKfyve, to generate PI(3,5)P2 . The SNX-BAR protein, SNX2, was recruited to endolysosomes by PI(3,5)P2 and promoted lysosome reformation. Inhibition of INPP4B/PIKfyve-dependent lysosome reformation reduced autophagic clearance of protein aggregates during proteotoxic stress leading to increased cytotoxicity. Therefore under nutrient-rich conditions, PI3Kα, INPP4B, and PIKfyve sequentially contribute to basal autophagic degradation and protection from proteotoxic stress via PI(3,5)P2 -dependent lysosome reformation from endolysosomes. These findings reveal that endosome maturation couples PI3Kα signaling to lysosome reformation during basal autophagy.

The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology?

Modern biology and biomedicine are undergoing a big data explosion, needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome Project: a framework and approach for creating, sharing, and using biophysics-based computational models of single-cell physiology. Using examples in calcium signaling, bioenergetics, and endosomal trafficking, we highlight the need for spatially detailed, biophysics-based computational models to uncover new mechanisms underlying cell biology. We review progress and challenges to date toward creating cell physiome models. We then introduce bond graphs as an efficient way to create cell physiome models that integrate chemical, mechanical, electromagnetic, and thermal processes while maintaining mass and energy balance. Bond graphs enhance modularization and reusability of computational models of cells at scale. We conclude with a look forward at steps that will help fully realize this exciting new field of mechanistic biomedical data science.

Highly selective and sensitive 'on-off' fluorescent chemosensor for Fe3+ ions crafted by benzofuran moiety in both experimental and theoretical methods.

A benzofuran glycinamide-based chemosensor, 3-(2-([4-fluorobenzyl]amino)acetamido)benzofuran-2-carboxamide (BGA) was developed and synthesized for the selective and sensitive detection of Fe3+ ions. The photophysical properties of the probe BGA were studied using UV-visible light absorption and fluorescence spectrophotometers. The chemosensor BGA showed a marked 'on-off' fluorescence response towards Fe3+ ions in the presence of other metal ions in DMSO/H2 O solution (9/1, v/v). The very low limits of detection (LOD) were calculated to be 10 nM and 43 nM using UV-visible light absorption and fluorescence spectrophotometers, respectively. Job's plot analysis revealed the formation of a BGA-Fe3+ complex with a 1:1 binding stoichiometry ratio using UV-visible light spectroscopy. The sensing mechanism was also demonstrated using density functional theory calculation.

ßIII-Tubulin Structural Domains Regulate Mitochondrial Network Architecture in an Isotype-Specific Manner.

ßIII-tubulin is a neuronal microtubule protein that is aberrantly expressed in epithelial cancers. The microtubule network is implicated in regulating the architecture and dynamics of the mitochondrial network, although the isotype-specific role for ß-tubulin proteins that constitute this microtubule network remains unclear. High-resolution electron microscopy revealed that manipulation of ßIII-tubulin expression levels impacts the volume and shape of mitochondria. Analysis of the structural domains of the protein identifies that the C-terminal tail of ßIII-tubulin, which distinguishes this protein from other ß-tubulin isotypes, significantly contributes to the isotype-specific effects of ßIII-tubulin on mitochondrial architecture. Mass spectrometry analysis of protein-protein interactions with ß-tubulin isotypes identifies that ßIII-tubulin specifically interacts with regulators of mitochondrial dynamics that may mediate these functional effects. Advanced quantitative dynamic lattice light sheet imaging of the mitochondrial network reveals that ßIII-tubulin promotes a more dynamic and extended reticular mitochondrial network, and regulates mitochondrial volume. A regulatory role for the ßIII-tubulin C-terminal tail in mitochondrial network dynamics and architecture has widespread implications for the maintenance of mitochondrial homeostasis in health and disease.

Role of Immediate Pre-Operative Tympanometry in Cochlear Implantation: MERF Protocol and Experience.

(1) To study the association between an immediate pre-operative tympanometric profile in patients undergoing cochlear implantation with their intraoperative findings. (2) To analyse the intraoperative middle ear findings that require a staged cochlear implantation in patients presenting with a B-type tympanogram. (3) To study the complications in this group of patients during the 1-year follow-up. This retrospective non-interventional cohort study is done over a period of 6 years. Bilaterally profound deaf children, less than 6 years of age, and no history of otitis media with effusion were included in the study. Children who met the inclusion criteria were divided into 4 groups based on their tympanometric profiles that are A, As, B, and C type tympanogram and, their intraoperative findings were categorized as normal, mild oedema, minimal granulation with mild oedema, moderate to extensive granulation with or without oedematous mucosa and glue. Then finally, depending on the intraoperative middle ear and mastoid finding, a single-stage surgery or a two stage surgery was decided upon. A total of 1025 patients were implanted during the study period, 975 patients met our inclusion criteria. In our series, we found a statistically significant difference (p < 0.0001) between the tympanograms and their respective intra-operative middle ear findings. A statistically significant difference was seen (p < 0.0001) between patients who underwent a single-stage cochlear implant and those who underwent a two-staged surgery, regarding their intraoperative middle ear findings. No statistical significance was seen in the occurrence of complications between the groups undergoing a single stage and a two-staged surgery (p > 0.5). This study showcases the importance of immediate pre-operative tympanometry in cochlear implant surgeries. Two-stage surgery is a decision taken on the operating table, depending on the extent of pathology and visibility of the round window niche.