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FEBS Letters May 2024Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize...
Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development. In conclusion, PATs exhibit both specific and redundant functions during different plant growth stages and our observations underpin the selective regulation of the mRNA decay machinery for proper development.
Topics: Arabidopsis; Arabidopsis Proteins; RNA, Messenger; Gene Expression Regulation, Plant; Mutation; RNA Stability
PubMed: 38605280
DOI: 10.1002/1873-3468.14872 -
RSC Advances Apr 2024A difficult issue in chemistry and materials science is to create metal compounds with well-defined components. Metal nanoclusters, particularly those of coinage groups... (Review)
Review
A difficult issue in chemistry and materials science is to create metal compounds with well-defined components. Metal nanoclusters, particularly those of coinage groups (Cu, Ag, and Au), have received considerable research interest in recent years owing to the availability of atomic-level precision joint experimental and theoretical methods, thus revealing the mechanisms in diverse nano-catalysts and functional materials. The textile sector significantly contributes to wastewater containing pollutants such as dyes and chemical substances. Textile and fabric manufacturing account for about 7 × 10 tons of wastewater annually. Approximately one thousand tons of dyes used in textile processing and finishing has been recorded as being discharged into natural streams and water bodies. Owing to the widespread environmental concerns, research has been conducted to develop absorbents that are capable of removing contaminants and heavy metals from water bodies using low-cost technology. Considering this idea, we reviewed coinage metal nanoclusters for azo and cationic dye degradation. Fluorometric and colorimetric techniques are used for dye degradation using coinage metal nanoclusters. Few reports are available on dye degradation using silver nanoclusters; and some of them are discussed in detailed herein to demonstrate the synergistic effect of gold and silver in dye degradation. Mostly, the Rhodamine B dye is degraded using coinage metals. Silver nanoclusters take less time for degradation than gold and copper nanoclusters. Mostly, HO is used for degradation in gold nanoclusters. Still, all coinage metal nanoclusters have been used for the degradation due to suitable HOMO-LUMO gap, and the adsorption of a dye onto the surface of the catalyst results in the exchange of electrons and holes, which leads to the oxidation and reduction of the adsorbed dye molecule. Compared to other coinage metal nanoclusters, Ag/g-CN nanoclusters displayed an excellent degradation rate constant with the dye Rhodamine B (0.0332 min). The behavior of doping transition metals in coinage metal nanoclusters is also reviewed herein. In addition, we discuss the mechanistic grounds for degradation, the fate of metal nanoclusters, anti-bacterial activity of nanoclusters, toxicity of dyes, and sensing of dyes.
PubMed: 38595712
DOI: 10.1039/d4ra00931b -
Annual Review of Biochemistry Apr 2024DEAD- and DExH-box ATPases (DDX/DHXs) are abundant and highly conserved cellular enzymes ubiquitously involved in RNA processing. By remodeling RNA-RNA and RNA-protein... (Review)
Review
DEAD- and DExH-box ATPases (DDX/DHXs) are abundant and highly conserved cellular enzymes ubiquitously involved in RNA processing. By remodeling RNA-RNA and RNA-protein interactions, they often function as gatekeepers that control the progression of diverse RNA maturation steps. Intriguingly, most DDX/DHXs localize to membraneless organelles (MLOs) such as nucleoli, nuclear speckles, stress granules, or processing bodies. Recent findings suggest not only that localization to MLOs can promote interaction between DDX/DHXs and their targets but also that DDX/DHXs are key regulators of MLO formation and turnover through their condensation and ATPase activity.In this review, we describe the molecular function of DDX/DHXs in ribosome biogenesis, messenger RNA splicing, export, translation, and storage or decay as well as their association with prominent MLOs. We discuss how the enzymatic function of DDX/DHXs in RNA processing is linked to DDX/DHX condensation, the accumulation of ribonucleoprotein particles and MLO dynamics. Future research will reveal how these processes orchestrate the RNA life cycle in MLO space and DDX/DHX time.
PubMed: 38594920
DOI: 10.1146/annurev-biochem-052521-121259 -
BioRxiv : the Preprint Server For... Mar 2024Subgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3'-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay...
Subgenomic flavivirus RNAs (sfRNAs) are structured RNA elements encoded in the 3'-UTR of flaviviruses that promote viral infection by inhibiting cellular RNA decay machinery. Herein, we analyze the production of sfRNAs using single-molecule RNA fluorescence hybridization (smRNA-FISH) and super-resolution microscopy during West Nile virus, Zika virus, or Dengue virus serotype 2 infection. We show that sfRNAs are initially localized diffusely in the cytosol or in processing bodies (P-bodies). However, upon activation of the host antiviral endoribonuclease, Ribonuclease L (RNase L), nearly all sfRNAs re-localize to antiviral biological condensates known as RNase L-induced bodies (RLBs). RLB-mediated sequestration of sfRNAs reduces sfRNA association with RNA decay machinery in P-bodies, which coincides with increased viral RNA decay. These findings establish a role of RLBs in promoting viral RNA decay, demonstrating the complex host-pathogen interactions at the level of RNA decay and biological condensation.
PubMed: 38585896
DOI: 10.1101/2024.03.25.586660 -
Journal of Environmental Management Apr 2024While phosphorus fertilizers contribute to food security, part of the introduced phosphorus dissipates into water bodies leading to eutrophication. At the same time,...
While phosphorus fertilizers contribute to food security, part of the introduced phosphorus dissipates into water bodies leading to eutrophication. At the same time, conventional mineral phosphorus sources are increasingly scarce. Therefore, closing phosphorus cycles reduces pollution while decreasing trade dependence and increasing food security. A major part of the phosphorus loss occurs during food processing. In this article, we combine a systematic literature review with investment and efficiency analysis to investigate the financial feasibility of recovering phosphorus from dairy processing wastewater. This wastewater is particularly rich in phosphorus, but while recovery technologies are readily available, they are rarely adopted. We calculate the Net Present Value (NPV) of investing in phosphorus recycling technology for a representative European dairy processing company producing 100,000 tonnes of milk per year. We develop sensitivity scenarios and adjust the parameters accordingly. Applying struvite precipitation, the NPV can be positive in two scenarios. First, if the phosphorus price is high (1.51 million EUR) or second if phosphorus recovery is a substitute for mandatory waste disposal (1.48 million EUR). However, for a variety of methodological specifications, the NPV is negative, mainly because of high input costs for chemicals and energy. These trade-offs between off-setting pollution and reducing energy consumption imply, that policy makers and investors should consider the energy source for phosphorus recovery carefully.
Topics: Wastewater; Phosphorus; Struvite; Refuse Disposal; Agriculture; Waste Disposal, Fluid; Phosphates
PubMed: 38583387
DOI: 10.1016/j.jenvman.2024.120606 -
Analytical and Bioanalytical Chemistry May 2024Inclusion bodies (IBs) are protein aggregates formed as a result of overexpression of recombinant protein in E. coli. The formation of IBs is a valuable strategy of...
Inclusion bodies (IBs) are protein aggregates formed as a result of overexpression of recombinant protein in E. coli. The formation of IBs is a valuable strategy of recombinant protein production despite the need for additional processing steps, i.e., isolation, solubilization and refolding. Industrial process development of protein refolding is a labor-intensive task based largely on empirical approaches rather than knowledge-driven strategies. A prerequisite for knowledge-driven process development is a reliable monitoring strategy. This work explores the potential of intrinsic tryptophan and tyrosine fluorescence for real-time and in situ monitoring of protein refolding. In contrast to commonly established process analytical technology (PAT), this technique showed high sensitivity with reproducible measurements for protein concentrations down to 0.01 g L . The change of protein conformation during refolding is reflected as a shift in the position of the maxima of the tryptophan and tyrosine fluorescence spectra as well as change in the signal intensity. The shift in the peak position, expressed as average emission wavelength of a spectrum, was correlated to the amount of folding intermediates whereas the intensity integral correlates to the extent of aggregation. These correlations were implemented as an observation function into a mechanistic model. The versatility and transferability of the technique were demonstrated on the refolding of three different proteins with varying structural complexity. The technique was also successfully applied to detect the effect of additives and process mode on the refolding process efficiency. Thus, the methodology presented poses a generic and reliable PAT tool enabling real-time process monitoring of protein refolding.
Topics: Inclusion Bodies; Protein Refolding; Spectrometry, Fluorescence; Recombinant Proteins; Tryptophan; Escherichia coli; Tyrosine; Fluorescence; Protein Folding
PubMed: 38573344
DOI: 10.1007/s00216-024-05249-1 -
Signal Transduction and Targeted Therapy Apr 2024RNA-binding proteins (RBPs)-RNA networks have contributed to cancer development. Circular RNAs (circRNAs) are considered as protein recruiters; nevertheless, the...
RNA-binding proteins (RBPs)-RNA networks have contributed to cancer development. Circular RNAs (circRNAs) are considered as protein recruiters; nevertheless, the patterns of circRNA-protein interactions in colorectal cancer (CRC) are still lacking. Processing bodies (PBs) formed through liquid-liquid phase separation (LLPS) are membrane-less organelles (MLOs) consisting of RBPs and RNA. Previous evidence suggests a connection between PBs dynamics and cancer progression. Despite the increasingly acknowledged crucial role of RBPs and RNA in the accumulation and maintenance of MLOs, there remains a lack of specific research on the interactions between PBs-related RBPs and circRNAs in CRC. Herein, we identify that MEX-3 RNA binding family member A (MEX3A), frequently upregulated in CRC tissues, predicts poorer patient survival. Elevated MEX3A accelerates malignance and inhibits autophagy of CRC cells. Importantly, MEX3A undergoes intrinsically disordered regions (IDRs)-dependent LLPS in the cytoplasm. Specifically, circMPP6 acts as a scaffold to facilitate the interaction between MEX3A and PBs proteins. The MEX3A/circMPP6 complex modulates PBs dynamic and promotes UPF-mediated phosphodiesterase 5A (PDE5A) mRNA degradation, consequently leading to the aggressive properties of CRC cells. Clinically, CRC patients exhibiting high MEX3A expression and low PDE5A expression have the poorest overall survival. Our findings reveal a collaboration between MEX3A and circMPP6 in the regulation of mRNA decay through triggering the PBs aggregation, which provides prognostic markers and/or therapeutic targets for CRC.
Topics: Humans; Autophagy; Colorectal Neoplasms; Family; Phosphoproteins; Proteins; RNA; RNA, Circular; RNA-Binding Proteins
PubMed: 38565536
DOI: 10.1038/s41392-024-01787-3 -
The Journal of Neuroscience : the... May 2024Coordinated neuronal activity has been identified to play an important role in information processing and transmission in the brain. However, current research...
Coordinated neuronal activity has been identified to play an important role in information processing and transmission in the brain. However, current research predominantly focuses on understanding the properties and functions of neuronal coordination in hippocampal and cortical areas, leaving subcortical regions relatively unexplored. In this study, we use single-unit recordings in female Sprague Dawley rats to investigate the properties and functions of groups of neurons exhibiting coordinated activity in the auditory thalamus-the medial geniculate body (MGB). We reliably identify coordinated neuronal ensembles (cNEs), which are groups of neurons that fire synchronously, in the MGB. cNEs are shown not to be the result of false-positive detections or by-products of slow-state oscillations in anesthetized animals. We demonstrate that cNEs in the MGB have enhanced information-encoding properties over individual neurons. Their neuronal composition is stable between spontaneous and evoked activity, suggesting limited stimulus-induced ensemble dynamics. These MGB cNE properties are similar to what is observed in cNEs in the primary auditory cortex (A1), suggesting that ensembles serve as a ubiquitous mechanism for organizing local networks and play a fundamental role in sensory processing within the brain.
Topics: Animals; Rats, Sprague-Dawley; Female; Rats; Neurons; Geniculate Bodies; Acoustic Stimulation; Auditory Pathways; Action Potentials; Auditory Cortex; Thalamus; Evoked Potentials, Auditory
PubMed: 38561224
DOI: 10.1523/JNEUROSCI.1729-23.2024 -
Journal of Dentistry Jun 2024The aim of the present in vitro study was to evaluate the effect of a novel auxiliary geometric device (AGD) on the accuracy of full-arch scans captured with 3 different...
OBJECTIVES
The aim of the present in vitro study was to evaluate the effect of a novel auxiliary geometric device (AGD) on the accuracy of full-arch scans captured with 3 different intraoral scanners (IOS).
METHODS
An edentulous maxillary model with four internal connection implant replicas was scanned using 3 different IOS: iTero Element 5D (ITERO) (Align Technology, Tempe, AZ, USA), Trios 4 (TRIOS) (3Shape A/S, Copenhagen, Denmark), and Carestream 3700 (CS) (Carestream Dental, Atlanta, USA). Thirty-six scans were taken with each IOS, 18 with the AGD in place, and 18 without the AGD. A digital master model was created using an industrial optical scanner (ATOS compact Scan 5M, GOM GmbH, Braunschweig, Germany). The master and IOS models were aligned using the scan bodies as a reference area. A surface comparison was performed, and deviation labels were exported for each scan body to evaluate the linear and angular deviation. Total body, platform and angular deviations were measured.
RESULTS
The use of AGD resulted in a statistically significant increase of angular deviation: 0.87° (SD=0.21) in the AGD group versus 0.64° (SD=0.46) in the no AGD group (p-value=0.005). The difference between the AGD and no AGD groups was not statistically significant for total body and platform deviation values (p-value=0.051 and 0.302 respectively). Using AGD, ITERO showed a statistically significant increase in angular deviation (mean difference=-0.46 µm, p-value=0.002) and a decrease in mean platform deviation (mean difference=63.19 µm, p-value<0.001). No statistically significant differences were found for the other IOS.
CONCLUSIONS
The use of AGD did not add benefit on CS and TRIOS. On ITERO, there was an improvement in platform deviation, that was outweighed by the worsening of the angular deviation.
CLINICAL SIGNIFICANCE
In vitro data suggest that intraoral scans can be successfully used in full-arch cases. The use of AGD has no additional benefit on CS and TRIOS. On ITERO there was an improvement in platform deviation that was outweighed by the worsening of the angular deviation. Translational application to clinical practice deserves further investigation, taking into account patient-related and anatomical variables.
Topics: Humans; Dental Prosthesis, Implant-Supported; Dental Implants; Models, Dental; Maxilla; Computer-Aided Design; Imaging, Three-Dimensional; Jaw, Edentulous; In Vitro Techniques; Dental Arch; Image Processing, Computer-Assisted; Dental Prosthesis Design
PubMed: 38556193
DOI: 10.1016/j.jdent.2024.104979 -
Journal of Alzheimer's Disease Reports 2024The prodromal stage of Lewy body dementia includes a mild cognitive impairment with visual processing and/or attention-executive deficits. A clinical presentation with...
The prodromal stage of Lewy body dementia includes a mild cognitive impairment with visual processing and/or attention-executive deficits. A clinical presentation with progressive visual loss is indeed seldom reported and can be misleading with a posterior cortical atrophy disease. While the neurodegeneration at the occipital cortex can only partially explain the visual disturbances of Lewy body dementia, more recently a retinal dysfunction has been suggested by preliminary optical coherence tomography and autoptic findings. Herein, we present a case of a mild cognitive impairment with Lewy bodies, who presented initially with visual disturbances and signs of both retinal and cortical visual processing dysfunction. A complete neuropsychological, neurophysiological and brain imaging assessment highlighted a prominent ventral visual pathway involvement. This report provides first that the prodromal stage of Lewy body dementia can manifest as a primarily progressive visual loss, second that the involvement of visual pathway, particularly the ventral stream, can be detectable from the retinal to the cortical level.
PubMed: 38549630
DOI: 10.3233/ADR-230176