CDKL5 regulates p62-mediated selective autophagy and confers protection against neurotropic viruses

Virophagy, the selective autophagosomal engulfment and lysosomal degradation of viral components, is crucial for neuronal cell survival and antiviral immunity. However, the mechanisms leading to viral antigen recognition and capture by autophagic machinery remain poorly understood. Here, we identified cyclin-dependent kinase-like 5 (CDKL5), known to function in neurodevelopment, as an essential regulator of virophagy. Loss-of-function mutations in CDKL5 are associated with a severe neurodevelopmental encephalopathy. We found that deletion of CDKL5 or expression of a clinically relevant pathogenic mutant of CDKL5 reduced virophagy of Sindbis virus (SINV), a neurotropic RNA virus, and increased intracellular accumulation of SINV capsid protein aggregates and cellular cytotoxicity. Cdkl5-knockout mice displayed increased viral antigen accumulation and neuronal cell death after SINV infection and enhanced lethality after infection with several neurotropic viruses. Mechanistic studies demonstrated that CDKL5 directly binds the canonical selective autophagy receptor p62 and phosphorylates p62 at T269/S272 to promote its interaction with viral capsid aggregates. We found that CDKL5-mediated phosphorylation of p62 facilitated the formation of large p62 inclusion bodies that captured viral capsids to initiate capsid targeting to autophagic machinery. Overall, these findings identify a cell-autonomous innate immune mechanism for autophagy activation to clear intracellular toxic viral protein aggregates during infection.

Wnt16 Promotes Vascular Smooth Muscle Contractile Phenotype and Function via Taz (Wwtr1) Activation in Male LDLR-/- Mice

Wnt16 is expressed in bone and arteries, and maintains bone mass in mice and humans, but its role in cardiovascular physiology is unknown. We show that Wnt16 protein accumulates in murine and human vascular smooth muscle (VSM). WNT16 genotypes that convey risk for bone frailty also convey risk for cardiovascular events in the Dallas Heart Study. Murine Wnt16 deficiency, which causes postnatal bone loss, also reduced systolic blood pressure. Electron microscopy demonstrated abnormal VSM mitochondrial morphology in Wnt16-null mice, with reductions in mitochondrial respiration. Following angiotensin-II (AngII) infusion, thoracic ascending aorta (TAA) dilatation was greater in Wnt16-/- vs Wnt16+/+ mice (LDLR-/- background). Acta2 (vascular smooth muscle alpha actin) deficiency has been shown to impair contractile phenotype and worsen TAA aneurysm with concomitant reductions in blood pressure. Wnt16 deficiency reduced expression of Acta2, SM22 (transgelin), and other contractile genes, and reduced VSM contraction induced by TGFβ. Acta2 and SM22 proteins were reduced in Wnt16-/- VSM as was Ankrd1, a prototypic contractile target of Yap1 and Taz activation via TEA domain (TEAD)-directed transcription. Wnt16-/- VSM exhibited reduced nuclear Taz and Yap1 protein accumulation. SiRNA targeting Wnt16 or Taz, but not Yap1, phenocopied Wnt16 deficiency, and Taz siRNA inhibited contractile gene upregulation by Wnt16. Wnt16 incubation stimulated mitochondrial respiration and contraction (reversed by verteporfin, a Yap/Taz inhibitor). SiRNA targeting Taz inhibitors Ccm2 and Lats1/2 mimicked Wnt16 treatment. Wnt16 stimulated Taz binding to Acta2 chromatin and H3K4me3 methylation. TEAD cognates in the Acta2 promoter conveyed transcriptional responses to Wnt16 and Taz. Wnt16 regulates cardiovascular physiology and VSM contractile phenotype, mediated via Taz signaling.

Analyzing and simulating heat transfer and designing a shell and tube heat exchanger for the pasteurization process of tomato paste: A CFD study

Pasteurization is a vital process to destroy harmful enzymes. This process is very critical to obtain quality tomato paste. In this study, Computational Fluid Dynamics (CFD) has been used to design a shell and tube heat exchanger on an industrial scale and to simulate heat transfer in order to visualize this process and present it to the industry. In this research, a three-dimensional CFD model was simulated using ANSYS FLUENT commercial software. Also, using the Herschel-Bulkley model, the behavior of viscosity in the pasteurization process of tomato paste has been explained. In this stage of the production line, the tomato paste enters a shell and tube heat exchanger at 65 °C and reaches 80 °C at the outlet. Compared with the experimental data, the output temperature of tomato paste predicted by CFD simulation reached 79 °C. In addition, thermophysical properties of tomato paste were measured, and these exact values were used for simulation. Also, the evaluation of this heat exchanger with three hot water inlet mass flow rates has been done in order to provide the results to the factory to avoid spending more energy. And the simulation results showed that the output temperature of tomato paste at three different mass flow rates did not change less than the mass flow rates measured in the factory, and also the output visualizations from this research can be suitable for presenting to the industry and benefiting from them.

A Large Sublingual Dermoid Cyst Causing Dysphagia and Dysphonia: A Case Review Study

A seventeen-year-old girl was referred to the emergency department with dysphagia and dyspnea due to large swelling in the floor of the mouth after 20 days of evaluation. Magnetic resonance imaging shows a well-defined sublingual mass measuring 70 mm × 74 mm × 46 mm, causing severe oral and oropharyngeal space narrowing. The surgical excision of the lesion was performed through an intraoral approach under general anesthesia. Moreover, the pathologist reported a dermoid cyst. A dermoid cyst rapidly enlarging can lead to a life-threatening condition, particularly if they grow near main upper airway structures, so their resection in golden time has an especially clinical importance.

Global protein-protein interaction networks in yeast saccharomyces cerevisiae and helicobacter pylori

Understanding many biological processes relies heavily on accurately predicting protein-protein interactions (PPIs). In this study, we propose a novel method for predicting PPIs that is based on LogitBoost with a binary bat feature selection algorithm. Our approach involves the extraction of an initial feature vector by combining pseudo amino acid composition (PseAAC), pseudo-position-specific scoring matrix (PsePSSM), reduced sequence and index-vectors (RSIV), and autocorrelation descriptor (AD). Subsequently, a binary bat algorithm is applied to eliminate redundant features, and the resulting optimal features are fed into the LogitBoost classifier for the identification of PPIs. To evaluate the proposed method, we test it on two databases, Saccharomyces cerevisiae and Helicobacter pylori, using 10-fold cross-validation, and achieve accuracies of 94.39% and 97.89%, respectively. Our results showcase the significant potential of our pipeline in accurately predicting protein-protein interactions (PPIs), thereby offering a valuable resource to the scientific research community.

An overview of recent advances in isatin-based multicomponent reactions

Abstract:

Isatin has been widely deployed in multicomponent reactions to prepare diverse heterocyclic compounds, which have garnered the attention of organic chemists considering their anti-inflammatory, anti-microbial, and antiviral activities, among others. This review discusses the applications of isatin in multicomponent reactions from 2019 to 2022. Isatin has been used as a raw material in multicomponent reactions due to its diverse biological and therapeutic activities. This overview may help stimulate the readers to exploit such convergent strategies in their synthetic endeavors.

A Novel Anticoagulation Method Based on Electrochemical Characteristics of Blood: An in vitro Study

This in vitro experimental investigation aimed to provide a novel method for preventing blood clotting based on the electrochemical characteristics of blood. Using this method in cases such as dialysis can minimize the risk of blood clots and also avoid hemorrhagic risk for patients. Blood samples were collected from 13 sheep (45 kg) (25 mL), and the clotting time (CT) was measured using a 20-min cutoff after they were separated into control and experimental samples. The test blood sample was put in a cell designed with two aluminum electrodes (positive pole/anode) located in a container containing 0.9% sodium chloride (as a salt bridge) and a platinum (negative pole/cathode) linked to a power supply (-3.5 V, 1 mA/cm2). Biochemical and hematological tests to check blood damage and clotting were performed. The control sample coagulated after 8 min, while the electrified blood did not, even at the end of the cutoff time. Among hematologic and biochemical tests, the average time of prothrombin time (PT) and partial thromboplastin time (PTT) was significantly different between the control and test samples (p = 0.001). Our findings on electrified blood with expanding CT, PT, and PTT times revealed that the electric current passing through the blood enhanced the CT. Furthermore, no change in biochemical or hematological factors demonstrated that this current had no detrimental effect on the blood.

Abstract P3049: Age-independent Cardiac Protection By Pharmacological Activation Of Beclin-1 During Endotoxemia And Its Association With Energy Metabolic Reprogramming In Myocardium-A Targeted Metabolomics Study

Background: We previously showed that Beclin-1-dependent autophagy is cardiac protective in a rodent model of endotoxemia using young adult mice. In this report, we compared the potential therapeutic effects of pharmacological Beclin-1 activating peptide, TB-peptide, on the cardiac outcomes of young adult and aged mice during endotoxemia. We further examined alterations in myocardial metabolism induced by lipopolysaccharide (LPS) challenge with and without the TB-peptide treatment.

Methods: C57BL/6J mice of 10-week and 24-month-old were challenged by LPS at doses at which cardiac dysfunction occurred. Following the treatment of TB-peptide or control vehicle, heart contractility, circulating cytokines, and myocardial autophagy were evaluated. A targeted metabolomics assay was applied to analyze cardiac metabolism.

Results: TB-peptide boosted autophagic response, attenuated cytokine production, and improved cardiac performance in both young and aged mice during endotoxemia. A targeted metabolomics assay was designed to detect a pool of 361 known metabolites, of which 156 were detected in at least one of the heart tissue samples. LPS-induced impairments were found in glucose and amino acid (AA) metabolisms in mice of all ages, and TB-peptide provided ameliorative effects to rescue these alterations. However, lipid metabolites were upregulated in the young group but moderately downregulated in the aged by LPS, suggesting an age-dependent response. TB-peptide mitigated LPS-mediated trend of lipids in the young mice but provided little effect on the aged ones.

Conclusion: Pharmacological activation of Beclin-1 by TB-peptide protects the heart in both young and aged population during endotoxemia, suggest a therapeutic potential for sepsis-induced cardiomyopathy. Metabolomics analysis suggests that this age-independent protection by TB-peptide is associated with reprograming of energy production via glucose and AA metabolisms.

Age-Independent Cardiac Protection by Pharmacological Activation of Beclin-1 During Endotoxemia and Its Association With Energy Metabolic Reprograming in Myocardium-A Targeted Metabolomics Study

Background We showed that Beclin-1-dependent autophagy protects the heart in young and adult mice that underwent endotoxemia. Herein, we compared the potential therapeutic effects of Beclin-1 activating peptide, TB-peptide, on endotoxemia-induced cardiac outcomes in young adult and aged mice. We further evaluated lipopolysaccharide (lipopolysaccharide)-induced and TB-peptide treatment-mediated alterations in myocardial metabolism. Methods and Results C57BL/6J mice that were 10 weeks and 24 months old were challenged by lipopolysaccharide using doses at which cardiac dysfunction occurred. Following the treatment of TB-peptide or control vehicle, heart contractility, circulating cytokines, and myocardial autophagy were evaluated. We detected that TB-peptide boosted autophagy, attenuated cytokines, and improved cardiac performance in both young and aged mice during endotoxemia. A targeted metabolomics assay was designed to detect a pool of 361 known metabolites, of which 156 were detected in at least 1 of the heart tissue samples. Lipopolysaccharide-induced impairments were found in glucose and amino acid metabolisms in mice of all ages, and TB-peptide ameliorated these alterations. However, lipid metabolites were upregulated in the young group but moderately downregulated in the aged by lipopolysaccharide, suggesting an age-dependent response. TB-peptide mitigated lipopolysaccharide-mediated trend of lipids in the young mice but had little effect on the aged. (Study registration: Project DOI: https://doi.org/10.21228/M8K11W). Conclusions Pharmacological activation of Beclin-1 by TB-peptide is cardiac protective in both young and aged population during endotoxemia, suggest a therapeutic potential for sepsis-induced cardiomyopathy. Metabolomics analysis suggests that an age-independent protection by TB-peptide is associated with reprograming of energy production via glucose and amino acid metabolisms.

RBM33 directs the nuclear export of transcripts containing GC-rich elements

Although splicing is a major driver of RNA nuclear export, many intronless RNAs are efficiently exported to the cytoplasm through poorly characterized mechanisms. For example, GC-rich sequences promote nuclear export in a splicing-independent manner, but how GC content is recognized and coupled to nuclear export is unknown. Here, we developed a genome-wide screening strategy to investigate the mechanism of export of NORAD, an intronless cytoplasmic long noncoding RNA (lncRNA). This screen revealed an RNA binding protein, RBM33, that directs the nuclear export of NORAD and numerous other transcripts. RBM33 directly binds substrate transcripts and recruits components of the TREX-NXF1/NXT1 RNA export pathway. Interestingly, high GC content emerged as the feature that specifies RBM33-dependent nuclear export. Accordingly, RBM33 directly binds GC-rich elements in target transcripts. These results provide a broadly applicable strategy for the genetic dissection of nuclear export mechanisms and reveal a long-sought nuclear export pathway for transcripts with GC-rich sequences.

Abstract 562: Altered Hippo Pathway Activity And Impaired Smooth Muscle Contractile Phenotype In Wnt16-Deficient Mice Worsens Ascending Aortic Aneurysm

Wnt16 is expressed in mouse & human vascular smooth muscle (VSM). We assessed the impact of Wnt16 deficiency on angiotensin-II (AngII) -induced aneurysmal remodeling. AngII infusion for 4 weeks increased aortic Wnt16 2-fold & ascending thoracic aorta diameter by 60% (p = 1.5E-4, ANOVA p = 3E-6) in male LDLR-/- mice. Wnt16-/-;LDLR-/- cohorts exhibited worsened aorta dilatation (by 20%; Holm-Sidak p =0.03), indicating a protective role for Wnt16. Wnt16 deficiency reduced both pulse wave velocity & systolic blood pressure (Wnt16-null = 132+/- 3 vs. 146 +/- 6 mmHg, p < 0.05, n =11/genotype), suggesting altered contractile function. Since hypomorphic alleles encoding contractile proteins predispose to ascending aortic aneurysms, we studied the impact of Wnt16 on the contractile phenotype. VSM from Wnt16-null thoracic aorta exhibited reductions in Acta2 & SM22 (protein, mRNA; down 50%, p < 0.05), Myh11 (down 60%; p < 0.05), & Myocardin ( Myocd ; by 65%; p =0.0002). Inhibitory H3K27me3 histone methylation was selectively increased 3-fold in chromatin of genes encoding contractile proteins in Wnt16-/- VSM (p = 3E-5). DNA fragmentation was increased 22% in Wnt16-null VSM (p < 0.01). Label-free quantitative proteomic analyses of aorta revealed (a) upregulation of 14 mechanosensitive LIM proteins in Wnt16-null mice, with (b) > 90% reduction in Ankrd1 - a wound contraction protein & a prototypic target of Yap1-Taz/Wwtr1 activity in the Hippo pathway. Wnt16 deficiency significantly increased VSM cytoplasmic Yap1-Taz protein accumulation while reducing nuclear Yap1-Taz. siRNA targeting Taz, but not Yap1, reduced contractile gene expression, phenocopying the actions of Wnt16 siRNA or genetic deficiency. Antagonism of Lats1/2, Hippo pathway kinases that inhibit Yap1-Taz cytoplasmic-nuclear shuttling, upregulated VSM Myocd (4.4x), Acta2 (1.6x), Ankrd1 (2.5x; p < 0.01), mimicking actions of 8 nM Wnt16 treatment. Dosing mice with Wnt16 (0.25 mg/kg/day, 2 days) upregulated aortic contractile gene expression 1.6- to 1.8-fold (all p < 0.05). Wnt16 limits thoracic aortic remodeling & preserves the VSM contractile phenotype in part via the Hippo - Taz/Wwtr1 signal relay. Strategies that augment Wnt16 activity may mitigate enlargement of ascending aortic aneurysms.

Abstract 130: Wnt16 Deficiency Worsens Angiotensin Ii - Induced Aneurysmal Remodeling Of Ascending Thoracic Aorta

Wnt16 controls bone strength via paracrine osteoblast-osteoclast remodeling interactions. Wnt16 mRNA is highly expressed in both aorta & bone, & immunofluorescence (IF) localized Wnt16 to vascular smooth muscle (VSM). Paracrine VSM - monocyte/macrophage (M/MAC) interactions control arterial remodeling, resembling osteoblast-osteoclast interactions in bone. We assessed the impact of Wnt16 deficiency on aneurysmal remodeling (6-7/group). Angiotensin II infusion for 4 weeks increased ascending thoracic aorta diameter by 60% (Holm-Sidak p = 1.5E-4, ANOVAp = 2.7E-6) in male LDLR-/- mice. Wnt16-/-;LDLR-/- cohorts exhibited worsened ascending aorta dilatation (by 20%; Holm-Sidak p = 0.03), indicating a protective role for Wnt16. Mass spectrometry of thoracic aorta proteins from Wnt16-/-;LDLR-/- vs. LDLR-/-mice revealed a 9-fold increase in MMP12 (p = 0.008; n=3/group) — a M/MAC protease key to aneurysmal remodeling. IF confirmed enhanced adventitial MMP12 in aortas of Wnt16-null mice. Treatment of M/MACs with Wnt16 (8 nM) down-regulated Mmp12 mRNA (78%; p < 0.001), with increased IL10 (2-fold; p < 0.05) & Arg1 (6-fold; p =0.001). Hypomorphic alleles encoding contractile proteins predispose to hereditary thoracic aortic aneurysm; thus, we studied the impact of Wnt16 deficiency on the contractile phenotype. VSM from Wnt16-null thoracic aorta exhibited reductions in Myh11 (down 60%; p < 0.05), Acta2 (by 35%, p <0.05), & the VSM transcriptional co-activator Myocardin ( by 65%; p = 0.0002), while Axin2 was increased 1.7-fold (p = 0.01). Acute siRNA-mediated knockdown of Wnt16 in VSM -M/MAC admixtures (95% VSM, 5% M/MAC) also downregulated contractile genes & upregulated Mmp12 . This was phenocopied by siRNA targeting Taz/Wwtr1 — a transcriptional collaborator of Myocd we identified as exhibiting impaired nuclear localization in Wnt16-null VSM. In vivo dosing with Wnt16 (0.25 mg/kg/day, 2 days) upregulated aortic contractile gene expression 1.6- to 1.8-fold, with Mmp12 reduced 50% (p < 0.05), as consistent with the reciprocal changes upon Wnt16 deficiency. Wnt16 limits thoracic aortic remodeling, preserves the VSM contractile phenotype, & reduces Mmp12. Strategies that augment Wnt16 signaling may mitigate enlargement of thoracic aortic aneurysms.

Resveratrol: A New Potential Therapeutic Agent for Melanoma?

Melanoma is the most life-threatening and aggressive class of skin malignancies. The incidence of melanoma has steadily increased. Metastatic melanoma is greatly resistant to standard antimelanoma treatments such as chemotherapy, and the 5-year survival rate of cases with melanoma who have a metastatic form of the disease is less than 10%. The contributing role of apoptosis, angiogenesis and autophagy in the pathophysiology of melanoma has been previously demonstrated. Thus, it is extremely urgent to search for complementary therapeutic approaches that could enhance the quality of life of subjects and reduce treatment resistance and adverse effects. Resveratrol, known as a polyphenol component present in grapes and some plants, has anti-cancer properties due to its function as an apoptosis inducer in tumor cells, and anti-angiogenic agent to prevent metastasis. However, more clinical trials should be conducted to prove resveratrol efficacy. Herein, for the first time, we summarize the current knowledge of anti-cancerous activities of resveratrol in melanoma.

Improvement of quantitative structure-retention relationship models for chromatographic retention prediction of peptides applying individual local partial least squares models

In Reversed-Phase Liquid Chromatography, Quantitative Structure-Retention Relationship (QSRR) models for retention prediction of peptides can be built, starting from large sets of theoretical molecular descriptors. Good predictive QSRR models can be obtained after selecting the most informative descriptors. Reliable retention prediction may be an aid in the correct identification of proteins/peptides in proteomics and in chromatographic method development. Traditionally, global QSRR models are built, using a calibration set containing a representative range of analytes. In this study, a strategy is presented to build individual local Partial Least Squares (PLS) models for peptides, based on selected local calibration samples, most similar to the specific query peptide to be predicted. Similar local calibration peptides are selected from a possible calibration set. The calibration samples with the lowest Euclidian distances to the query peptide are considered as most similar. Two Euclidian distances are investigated as similarity parameter, (i) in the autoscaled descriptor space and, (ii) in the PLS factor space of the global calibration samples, both after variable selection by the Final Complexity Adapted Models (FCAM) method. The predictive abilities of individual local QSRR PLS models for peptides, developed with both Euclidian distances, are found significantly better than those of two global models, i.e. before and after FCAM variable selection. The predictive abilities of the local models, developed with distances calculated in the PLS factor space, were best.

PTH/PTHrP Receptor Signaling Restricts Arterial Fibrosis in Diabetic LDLR-/- Mice by Inhibiting Myocardin-Related Transcription Factor Relays

RATIONALE

The PTH1R (PTH [parathyroid hormone]/PTHrP [PTH-related protein] receptor) is expressed in vascular smooth muscle (VSM) and increased VSM PTH1R signaling mitigates diet-induced arteriosclerosis in LDLR^-/- mice.

OBJECTIVE

To study the impact of VSM PTH1R deficiency, we generated mice SM22-Cre:PTH1R(fl/fl);LDLR^-/- mice (PTH1R-VKO) and Cre-negative controls.

METHODS AND RESULTS

Immunofluorescence and Western blot confirmed PTH1R expression in arterial VSM that was reduced by Cre-mediated knockout. PTH1R-VKO cohorts exhibited increased aortic collagen accumulation in vivo, and VSM cultures from PTH1R-VKO mice elaborated more collagen (2.5-fold; P=0.01) with elevated Col3a1 and Col1a1 expression. To better understand these profibrotic responses, we performed mass spectrometry on nuclear proteins extracted from Cre-negative controls and PTH1R-VKO VSM. PTH1R deficiency reduced Gata6 but upregulated the MADS (MCM1, Agamous, Deficiens, and Srf DNA-binding domain)-box transcriptional co-regulator, Mkl-1 (megakaryoblastic leukemia [translocation] 1). Co-transfection assays (Col3a1 promoter-luciferase reporter) confirmed PTH1R-mediated inhibition and Mkl-1-mediated activation of Col3a1 transcription. Regulation mapped to a conserved hybrid CT(A/T)₆GG MADS-box cognate in the Col3a1 promoter. Mutations of C/G in this motif markedly reduced Col3a1 transcriptional regulation by PTH1R and Mkl-1. Upregulation of Col3a1 and Col1a1 in PTH1R-VKO VSM was inhibited by small interfering RNA targeting Mkl1 and by treatment with the Mkl-1 antagonist CCG1423 or the Rock (Rho-associated coiled-coil containing protein kinase)-2 inhibitor KD025. Chromatin precipitation demonstrated that VSM PTH1R deficiency increased Mkl-1 binding to Col3a1 and Col1a1, but not TNF, promoters. Proteomic studies of plasma extracellular vesicles and VSM from PTH1R-VKO mice identified C1r (complement component 1, r) and C1s (complement component 1, s), complement proteins involved in vascular collagen metabolism, as potential biomarkers. VSM C1r protein and C1r message were increased with PTH1R deficiency, mediated by Mkl-1-dependent transcription and inhibited by CCG1423 or KD025.

CONCLUSIONS

PTH1R signaling restricts collagen production in the VSM lineage, in part, via Mkl-1 regulatory circuits that control collagen gene transcription. Strategies that maintain homeostatic VSM PTH1R signaling, as reflected in extracellular vesicle biomarkers of VSM PTH1R/Mkl-1 action, may help mitigate arteriosclerosis and vascular fibrosis.

PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD

NORAD is a conserved long noncoding RNA (lncRNA) that is required for genome stability in mammals. NORAD acts as a negative regulator of PUMILIO (PUM) proteins in the cytoplasm, and we previously showed that loss of NORAD or PUM hyperactivity results in genome instability and premature aging in mice (Kopp et al., 2019). Recently, however, it was reported that NORAD regulates genome stability through an interaction with the RNA binding protein RBMX in the nucleus. Here, we addressed the contributions of NORAD:PUM and NORAD:RBMX interactions to genome maintenance by this lncRNA in human cells. Extensive RNA FISH and fractionation experiments established that NORAD localizes predominantly to the cytoplasm with or without DNA damage. Moreover, genetic rescue experiments demonstrated that PUM binding is required for maintenance of genomic stability by NORAD whereas binding of RBMX is dispensable for this function. These data provide an important foundation for further mechanistic dissection of the NORAD-PUMILIO axis in genome maintenance.

Inert and seed-competent tau monomers suggest structural origins of aggregation

Tauopathies feature progressive accumulation of tau amyloids. Pathology may begin when these amplify from a protein template, or seed, whose structure is unknown. We have purified and characterized distinct forms of tau monomer—inert (M_i) and seed-competent (M_s). Recombinant M_s triggered intracellular tau aggregation, induced tau fibrillization in vitro, and self-assembled. M_s from Alzheimer’s disease also seeded aggregation and self-assembled in vitro to form seed-competent multimers. We used crosslinking with mass spectrometry to probe structural differences in M_i vs. M_s. Crosslinks informed models of local peptide structure within the repeat domain which suggest relative inaccessibility of residues that drive aggregation (VQIINK/VQIVYK) in M_i, and exposure in M_s. Limited proteolysis supported this idea. Although tau monomer has been considered to be natively unstructured, our findings belie this assumption and suggest that initiation of pathological aggregation could begin with conversion of tau monomer from an inert to a seed-competent form.

When doctors perform autopsies to look at the brain tissue of people with Alzheimer’s disease, they find toxic buildups of certain proteins – in particular, a protein called tau – in structures called ‘aggregates’. People with more severe dementia have more tau aggregates in their brain. Aggregates form when individual proteins stick together in repetitive patterns, much like the way a single Lego block might attach to another identical one. Like all proteins, tau is built from a string of amino acids that folds into a specific shape. Normally folded tau proteins do not form aggregates. It was not clear that an individual tau protein had two distinct forms—structures associated with health (“good”) or disease (“bad”).

Mirbaha et al. have now studied the folding pattern of purified tau proteins with a sophisticated technology called mass spectrometry. This technique can measure changes in tiny amounts of protein. Some of the purified proteins had been extracted from human brains (from people with and without Alzheimer’s). To detect which of the proteins were toxic, Mirbaha et al. also grew simple human cells in a dish that were designed to react specifically to the bad forms of tau. This allowed the good and bad forms of tau to be isolated.

Mirbaha et al. discovered that in the good form of tau the parts of the protein that allow it to stick to itself are hidden, folded inside. By contrast, the bad form of tau exposes the parts that allow it to aggregate, enabling the protein to build upon itself to form a large, toxic assembly.

The shape-shifting concept established by Mirbaha et al. might apply to other proteins that form toxic aggregates. This could help us to better understand how many other neurodegenerative diseases develop and progress. Recognizing that the shapes that tau forms can be categorized as either ‘good’ or ‘bad’ may also help to develop new treatments for Alzheimer’s disease. Drugs could be designed to stabilize the good form of tau, or to help remove the bad form from the brain. Furthermore, if the shape-shift described by Mirbaha et al. can be measured early enough in patients, it may allow treatments for Alzheimer’s before people have developed any detectable symptoms.

Prevalence of Apical Periodontitis in Different Communities: A Meta-Analysis

Introduction

The aim of this study was to perform a meta-analysis on the prevalence of apical periodontitis (AP) in different communities to obtain accurate data on its prevalence.

Methods and Materials

The prevalence of AP in different communities based on the number of individuals, teeth and root-filled teeth was searched using electronic databases of ISI Web of Knowledge, PubMed, Scopus and also ProQuest and Springer. The Metaprop meta-analysis was done using the software R version 3.3.0 with Meta package. The Logit transformation method and random-effects model were used to calculate the pooled prevalence. Heterogeneity was tested by the Q-test (P<0.1 represented statistical significance), I² statistics (25%, 50% and 75% represented low, medium and high heterogeneity, respectively) and 2τ (2τ was calculated by DerSimonian-Laird estimator method).

Results

A total of 77 studies were identified to qualify for inclusion into this meta-analysis. The prevalence of AP based on the number of individuals, teeth and root-filled teeth with the pooled prevalence was 0.519, 0.0498 and 0.3828, respectively.

Conclusions

The results of the present study can be helpful for policy makers to monitor the dental public health demographically and compare it to other communities; they may be able find the strengths and drawbacks of their oral and dental health program.

Hydralazine induces stress resistance and extends C. elegans lifespan by activating the NRF2/SKN-1 signalling pathway

Nuclear factor (erythroid-derived 2)-like 2 and its Caenorhabditis elegans ortholog, SKN-1, are transcription factors that have a pivotal role in the oxidative stress response, cellular homeostasis, and organismal lifespan. Similar to other defense systems, the NRF2-mediated stress response is compromised in aging and neurodegenerative diseases. Here, we report that the FDA approved drug hydralazine is a bona fide activator of the NRF2/SKN-1 signaling pathway. We demonstrate that hydralazine extends healthy lifespan (~25%) in wild type and tauopathy model C. elegans at least as effectively as other anti-aging compounds, such as curcumin and metformin. We show that hydralazine-mediated lifespan extension is SKN-1 dependent, with a mechanism most likely mimicking calorie restriction. Using both in vitro and in vivo models, we go on to demonstrate that hydralazine has neuroprotective properties against endogenous and exogenous stressors. Our data suggest that hydralazine may be a viable candidate for the treatment of age-related disorders.

GC-MS based metabolomics used for the identification of cancer volatile organic compounds as biomarkers

A biomarker can be a metabolite, coming from a metabolic pathway or cell process, which might be employed in the diagnostic of diseases, predict patient response towards chemical therapies and/or monitor disease recurrences. Biomarkers, e.g. aldehydes or hydrocarbons, are often identified from different body fluids such as blood, urine, serum, saliva or from various tissues samples, and their concentration can vary from one sample to the other. However, the detection and the action of these biomarkers for diseases is a complicated process. Cancer is one of the main cause of death worldwide. The main characteristic of cancerous tumor is the uncontrolled growing of cells inside the organism. Likely, these uncontrolled growths are as consequence changes in the metabolism that could be analytically monitored. Depending on where the cancer cells are located, they provide different characteristics profiles. These profiles as fingerprints are used for differentiation in a comparison to normal cells. This critical study aimed at highlighting the latest progress in this area, especially in the employment of gas chromatography for the monitoring of volatile organic compounds (VOCs) and the identification of possible molecules used as biomarkers for cancer therapy.

State of the art in microRNA as diagnostic and therapeutic biomarkers in chronic lymphocytic leukemia

Early diagnostic is one of the most important steps in cancer therapy which helps to design and choose a better therapeutic approach. The finding of biomarkers in various levels including genomics, transcriptomics, and proteomics levels could provide better treatment for various cancers such as chronic lymphocytic leukemia (CLL). The CLL is the one of main lymphoid malignancies which is specified by aggregation of mature B lymphocytes. Among different biomarkers (e.g., CD38, chromosomes abnormalities, ZAP-70, TP53, and microRNA [miRNA]), miRNAs have appeared as new diagnostic and therapeutic biomarkers in patients with the CLL disease. Multiple lines of evidence indicated that deregulation of miRNAs could be associated with pathological events which are present in the CLL. These molecules have an effect on a variety of targets such as Bcl2, c-fos, c-Myc, TP53, TCL1, and STAT3 which play critical roles in the CLL pathogenesis. It has been shown that expression of miRNAs could lead to the activation of B cells and B cell antigen receptor (BCR). Moreover, exosomes containing miRNAs are one of the other molecules which could contribute to BCR stimulation and progression of CLL cells. Hence, miRNAs and exosomes released from CLL cells could be used as potential diagnostic and therapeutic biomarkers for CLL. This critical review focuses on a very important aspect of CLL based on biomarker discovery covers the pros and cons of using miRNAs as important diagnostics and therapeutics biomarkers for this deadly disease.

Green tea and its anti-angiogenesis effects

The development of new blood vessels from a pre-existing vasculature (also known as angiogenesis) is required for many physiological processes including embryogenesis and post-natal growth. However, pathological angiogenesis is also a hallmark of cancer and many ischaemic and inflammatory diseases. The pro-angiogenic members of the VEGF family (vascular endothelial growth factor family), VEGF-A, VEGF-B, VEGF-C, VEGF-D and placental growth factor (PlGF), and the related receptors, VEGFR-1, VEGFR-2 and VEGFR-3 have a central and decisive role in angiogenesis. Indeed, they are the targets for anti-angiogenic drugs currently approved. Green tea (from the Camellia sinensis plant) is one of the most popular beverages in the world. It is able to inhibit angiogenesis by different mechanisms such as microRNAs (miRNAs). Green tea and its polyphenolic substances (like catechins) show chemo-preventive and chemotherapeutic features in various types of cancer and experimental models for human cancers. The tea catechins, including (-)-epigallocatechin-3-gallate (EGCG), have multiple effects on the cellular proteome and signalome. Note that the polyphenolic compounds from green tea are able to change the miRNA expression profile associated with angiogenesis in various cancer types. This review focuses on the ability of the green tea constituents to suppress angiogenesis signaling and it summarizes the mechanisms by which EGCG might inhibit the VEGF family. We also highlighted the miRNAs affected by green tea which are involved in anti-angiogenesis.

Diagnostic and Therapeutic Potential of Exosomes in Cancer: The Beginning of a New Tale?

Exosomes have emerged as one of the main players in intercellular communication. These small nano-sized particles have many roles in various physiological pathways in normal and abnormal cells. Exosomes can carry various cargos such as proteins, mRNAs, and miRNAs to recipient cells. Uptake of exosomes and their cargo can induce and/or inhibit different cellular and molecular pathways that lead to the alteration of cell behavior. Multiple lines of evidence have indicated that exosomes released from cancer cells can effect development of cancer in different stages. These particles and their cargo could regulate different processes such as tumor growth, metastasis, drug resistance, angiogenesis, and immune system functioning. It has been observed that exosomes can be used as potential diagnostic biomarkers in various cancer types. Moreover, some studies have used these particles as biological vehicles for delivery of various drugs such as doxorubicin, siRNAs, and miRNAs. Here, we summarized the findings on the role of exosomes in different pathological processes involved in cancer. Moreover, application of these particles as diagnostic and therapeutic biomarkers in different types of cancers is discussed. J. Cell. Physiol. 232: 3251-3260, 2017. © 2016 Wiley Periodicals, Inc.

Analysis of Volatile Compounds by Advanced Analytical Techniques and Multivariate Chemometrics

Smelling is one of the five senses, which plays an important role in our everyday lives. Volatile compounds are, for example, characteristics of food where some of them can be perceivable by humans because of their aroma. They have a great influence on the decision making of consumers when they choose to use a product or not. In the case where a product has an offensive and strong aroma, many consumers might not appreciate it. On the contrary, soft and fresh natural aromas definitely increase the acceptance of a given product. These properties can drastically influence the economy; thus, it has been of great importance to manufacturers that the aroma of their food product is characterized by analytical means to provide a basis for further optimization processes. A lot of research has been devoted to this domain in order to link the quality of, e.g., a food to its aroma. By knowing the aromatic profile of a food, one can understand the nature of a given product leading to developing new products, which are more acceptable by consumers. There are two ways to analyze volatiles: one is to use human senses and/or sensory instruments, and the other is based on advanced analytical techniques. This work focuses on the latter. Although requirements are simple, low-cost technology is an attractive research target in this domain; most of the data are generated with very high-resolution analytical instruments. Such data gathered based on different analytical instruments normally have broad, overlapping sensitivity profiles and require substantial data analysis. In this review, we have addressed not only the question of the application of chemometrics for aroma analysis but also of the use of different analytical instruments in this field, highlighting the research needed for future focus.

QSAR of Antioxidants

Antioxidants are substances that protect cells from the damaging effects of oxygen radicals, which are chemicals that play a part in some diseases such as cancer and others. Antioxidants are expected to be promising drugs in the management of these diseases by removing oxidative stress. Most of the modeling approaches involved in designing new antioxidants is based on Quantitative Structure-Activity Relationship (QSAR). A number of QSAR studies have been conducted to elucidate the structural requirements of antioxidants for their activities in order to predict the potency of these compounds with regard to the targeted activity and to direct the synthesis of more potent analogues. The main focus of this chapter is on the QSAR modeling of antioxidant compounds. The authors provide different QSAR studies of antioxidant compounds and try to compare between them in terms of the best models obtained and their use in designing potential new drugs.

Glioblastoma: exosome and microRNA as novel diagnosis biomarkers

Glioblastoma (GBM) is known as a tumor type, which arises from astrocytes. Several studies indicated that GBM tumor cells are malignant. This is because of the fact that they consist of different cell types, which are reproducing very quickly and are also supported by a large network of blood vessels. The correct identification of various stages of GBM could help to better treat the patients with this disease. Therefore, new biomarkers such as exosomes and microRNAs (miRNAs) may help us to learn more about GBM and they may also lead to a more effective treatment for patients with GBM. Exosomes have emerged as biological vehicles, which can perform various tasks in carcinogenesis pathways such as PI3K/AKT, SOX2, PTEN, ERK, and STAT3. The miRNAs are known as small noncoding RNAs that are involved in several GBM pathogenic events. These molecules have key roles in various biological processes such as angiogenesis, metastasis and tumor growth. In this study, we highlighted various exosomes and miRNAs that could be used for diagnosis and/or prognosis biomarkers in patients with GBM.

Application of quantitative structure-property relationship analysis to estimate the vapor pressure of pesticides

The application of molecular descriptors in describing Quantitative Structure Property Relationships (QSPR) for the estimation of vapor pressure (VP) of pesticides is of ongoing interest. In this study, QSPR models were developed using multiple linear regression (MLR) methods to predict the vapor pressure values of 162 pesticides. Several feature selection methods, namely the replacement method (RM), genetic algorithms (GA), stepwise regression (SR) and forward selection (FS), were used to select the most relevant molecular descriptors from a pool of variables. The optimum subset of molecular descriptors was used to build a QSPR model to estimate the vapor pressures of the selected pesticides. The Replacement Method improved the predictive ability of vapor pressures and was more reliable for the feature selection of these selected pesticides. The results provided satisfactory MLR models that had a satisfactory predictive ability, and will be important for predicting vapor pressure values for compounds with unknown values. This study may open new opportunities for designing and developing new pesticide.

Hemoglobin fructation promotes heme degradation through the generation of endogenous reactive oxygen species

Protein glycation is a cascade of nonenzymatic reactions between reducing sugars and amino groups of proteins. It is referred to as fructation when the reducing monosaccharide is fructose. Some potential mechanisms have been suggested for the generation of reactive oxygen species (ROS) by protein glycation reactions in the presence of glucose. In this state, glucose autoxidation, ketoamine, and oxidative advance glycation end products (AGEs) formation are considered as major sources of ROS and perhaps heme degradation during hemoglobin glycation. However, whether fructose mediated glycation produces ROS and heme degradation is unknown. Here we report that ROS (H2O2) production occurred during hemoglobin fructation in vitro using chemiluminescence methods. The enhanced heme exposure and degradation were determined using UV-Vis and fluorescence spectrophotometry. Following accumulation of ROS, heme degradation products were accumulated reaching a plateau along with the detected ROS. Thus, fructose may make a significant contribution to the production of ROS, glycation of proteins, and heme degradation during diabetes.

Binary classification of chalcone derivatives with LDA or KNN based on their antileishmanial activity and molecular descriptors selected using the Successive Projections Algorithm feature-selection technique

Chalcones are naturally occurring aromatic ketones, which consist of an α-, β-unsaturated carbonyl system joining two aryl rings. These compounds are reported to exhibit several pharmacological activities, including antiparasitic, antibacterial, antifungal, anticancer, immunomodulatory, nitric oxide inhibition and anti-inflammatory effects. In the present work, a Quantitative Structure-Activity Relationship (QSAR) study is carried out to classify chalcone derivatives with respect to their antileishmanial activity (active/inactive) on the basis of molecular descriptors. For this purpose, two techniques to select descriptors are employed, the Successive Projections Algorithm (SPA) and the Genetic Algorithm (GA). The selected descriptors are initially employed to build Linear Discriminant Analysis (LDA) models. An additional investigation is then carried out to determine whether the results can be improved by using a non-parametric classification technique (One Nearest Neighbour, 1NN). In a case study involving 100 chalcone derivatives, the 1NN models were found to provide better rates of correct classification than LDA, both in the training and test sets. The best result was achieved by a SPA-1NN model with six molecular descriptors, which provided correct classification rates of 97% and 84% for the training and test sets, respectively.

Using experimental data designs and multivariate modeling to assess the effect of glycated serum protein concentration on glucose prediction from near-infrared spectra of human serum

Near-infrared (NIR) spectra of human blood serum consist of overlapping strong absorption bands of water and serum proteins, which affect the ability of multivariate calibration models to predict glucose. Furthermore, serum proteins such as albumin and globulins undergo a glycation reaction by forming covalent bonds with freely available glucose molecules in the serum. In diabetic individuals with poor glucose control, more and more serum protein molecules react with glucose, resulting in a high glycated protein concentration. The glucose molecules covalently bonded to serum proteins might contribute to the overall glucose signal acquired by NIR spectroscopy. This might affect the prediction ability of multivariate calibration models such as partial least squares regression (PLSR). In this study, we investigated the effect of total protein concentration and the glycated protein concentration in blood serum on the prediction ability of PLSR calibration models. Serum samples were subjected to ultra-filtration, and the PLSR model was built using NIR spectra of filtered serum solutions. Prediction performance was found to improve by 39-42% in absence of serum protein molecules. Various experimental data set designs were generated by carefully varying the glycated serum protein concentration in calibration and test sets of PLSR models. This investigation revealed that the impact of varying glycated protein concentration on the root mean square error of prediction was not drastic. To test the statistical significance of the prediction results, a multiple linear regression model was built. The glycated serum protein concentration was found to be statistically insignificant (p = 0.86) in predicting glucose concentration. Overall, it was concluded that the glycated serum proteins do not affect the glucose prediction accuracy of PLSR models using NIR spectra of human serum.