Dysregulation of BRD4 Function Underlies the Functional Abnormalities of MeCP2 Mutant Neurons.

Rett syndrome (RTT), mainly caused by mutations in methyl-CpG binding protein 2 (MeCP2), is one of the most prevalent intellectual disorders without effective therapies. Here, we used 2D and 3D human brain cultures to investigate MeCP2 function. We found that MeCP2 mutations cause severe abnormalities in human interneurons (INs). Surprisingly, treatment with a BET inhibitor, JQ1, rescued the molecular and functional phenotypes of MeCP2 mutant INs. We uncovered that abnormal increases in chromatin binding of BRD4 and enhancer-promoter interactions underlie the abnormal transcription in MeCP2 mutant INs, which were recovered to normal levels by JQ1. We revealed cell-type-specific transcriptome impairment in MeCP2 mutant region-specific human brain organoids that were rescued by JQ1. Finally, JQ1 ameliorated RTT-like phenotypes in mice. These data demonstrate that BRD4 dysregulation is a critical driver for RTT etiology and suggest that targeting BRD4 could be a potential therapeutic opportunity for RTT.

Deconstructing and reconstructing the human brain with regionally specified brain organoids.

Brain organoids, three-dimensional neural cultures recapitulating the spatiotemporal organization and function of the brain in a dish, offer unique opportunities for investigating the human brain development and diseases. To model distinct parts of the brain, various region-specific human brain organoids have been developed. In this article, we review current approaches to produce human region-specific brain organoids, developed through the endeavor of many researchers. We highlight the applications of human region-specific brain organoids, especially in reconstructing regional interactions in the brain through organoid fusion. We also outline the existing challenges to drive forward further the brain organoid technology and its applications for future studies.

Analysis of Conocurvone, Ganoderic acid A and Oleuropein molecules against the main protease molecule of COVID-19 by in silico approaches: Molecular dynamics docking studies.

Traditional medicines against COVID-19 have taken important outbreaks evidenced by multiple cases, controlled clinical research, and randomized clinical trials. Furthermore, the design and chemical synthesis of protease inhibitors, one of the latest therapeutic approaches for virus infection, is to search for enzyme inhibitors in herbal compounds to achieve a minimal amount of side-effect medications. Hence, the present study aimed to screen some naturally derived biomolecules with anti-microbial properties (anti-HIV, antimalarial, and anti-SARS) against COVID-19 by targeting coronavirus main protease via molecular docking and simulations. Docking was performed using SwissDock and Autodock4, while molecular dynamics simulations were performed by the GROMACS-2019 version. The results showed that Oleuropein, Ganoderic acid A, and conocurvone exhibit inhibitory actions against the new COVID-19 proteases. These molecules may disrupt the infection process since they were demonstrated to bind at the coronavirus major protease's active site, affording them potential leads for further research against COVID-19.

Retraction notice to "Analysis of Conocurvone, Ganoderic acid A and Oleuropein molecules against the main protease molecule of COVID-19 by in silico approaches: Molecular dynamics docking studies" [Engineering Analysis with Boundary Elements volume 150 (2023) Pages 583-598].

[This retracts the article DOI: 10.1016/j.enganabound.2023.02.043.].

Sequence alterations affect the antidiabetic attributes of hazelnut peptide fractions during the industrial manufacture and simulated digestion of hazelnut paste.

Press cakes are by-products of cold press oil manufacture and are characterized by significant protein concentrations. Our group has previously demonstrated potential bioactive attributes of hazelnut protein hydrolysates including their antidiabetic activities. Here, an effort was made to utilize DPP-IV (Dipeptidyl peptidase-IV)-inhibitory hazelnut peptides in industrial food manufacture. Hazelnut protein isolates (approx. 95% protein) were obtained via an alkali extraction-isoelectric precipitation method. Papain, bromelain and pepsin were used in the enzymatic hydrolysis and hydrolysates were fractionated via Fast Protein Liquid Chromatography. As a general observation, although fractionation lead to dilution of the samples, fractions were observed to be more bioactive than the total hydrolysates. In vitro antidiabetic activities of the fractions were tested and 3 antidiabetic fractions were added to hazelnut paste. Afterwards simulated gastrointestinal digestion and antidiabetic activity assays were performed. DPP-IV inhibition was the major antidiabetic mechanism in the fractions and digested paste, while some fractions were characterized by comparable IC50 values as the positive controls. Alpha-glucosidase inhibition was limited by digestion trials, whereas alpha-amylase inhibition was only slight in the digested paste (< %6). In silico analyses predicted partial degradation of the peptides, whereas the interactions between DPP-IV or alpha-glucosidase and hazelnut peptides were predicted to be significant (p < 0.05). Consequently hazelnut press cakes were regarded as a potential source of antidiabetic peptides that can be used in industrial manufacture of functional foods, while food processing conditions or gastrointestinal digestion could largely affect peptide bioactivity. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-022-05601-2.

Engineering of human brain organoids with a functional vascular-like system.

Human cortical organoids (hCOs), derived from human embryonic stem cells (hESCs), provide a platform to study human brain development and diseases in complex three-dimensional tissue. However, current hCOs lack microvasculature, resulting in limited oxygen and nutrient delivery to the inner-most parts of hCOs. We engineered hESCs to ectopically express human ETS variant 2 (ETV2). ETV2-expressing cells in hCOs contributed to forming a complex vascular-like network in hCOs. Importantly, the presence of vasculature-like structures resulted in enhanced functional maturation of organoids. We found that vascularized hCOs (vhCOs) acquired several blood-brain barrier characteristics, including an increase in the expression of tight junctions, nutrient transporters and trans-endothelial electrical resistance. Finally, ETV2-induced endothelium supported the formation of perfused blood vessels in vivo. These vhCOs form vasculature-like structures that resemble the vasculature in early prenatal brain, and they present a robust model to study brain disease in vitro.

Potential anticarcinogenic effect of goat milk-derived bioactive peptides on HCT-116 human colorectal carcinoma cell line.

Novel food-derived anti cancerogenic bioactive peptides were characterized by goat milk pepsin hydrolysate. Pepsin treated casein fraction of goat milk caused an apoptotic cell death on the HCT116 cell lines. These bioactive peptides are encrypted in the protein structure in the inactive form and can become active during gastrointestinal digestion in the body. In this study, the possible therapeutic effect of goat milk-based bioactive peptides on human colorectal cancer cell lines was investigated. Goat milk-derived bioactive peptides were extracted from the casein and whey protein fractions using trypsin, pepsin, and papain enzymes. The bioactive peptides were characterized by the liquid chromatography quadrupole time of flight mass spectrometry. Both enzyme-treated casein and whey fractions were incubated with the HCT116 cell lines, and then the cell cytotoxicity was evaluated using MTT assay. The type of cell death was analyzed by flow cytometry using Annexin V and propidium iodide. Among all applications, the pepsin-treated casein fraction was the highest potential peptides that cause 80.92% apoptotic cell death. In conclusion, pepsin treated casein fraction exhibited antiproliferative activity against HCT116 cells. The bioactive peptides of this fraction can be considered as a potential source for the development of new anti cancerogenic agents.

Influence of Maillard reaction conditions and solvent extraction on the surface activity and foaming characteristics of black cumin protein concentrates.

Cold press manufacture of black cumin (BC) oil leads to the formation of BC press cakes that contain significant amounts of protein. Here, an attempt was made to enhance the functionality of BC protein concentrates obtained from cakes based on Maillard conjugation using 3 different of carbohydrates. Molecular weight distribution of the conjugates was determined via electrophoretic techniques. The extent of carbohydrate binding was measured by RP-HPLC-RID. Surface activity and elasticity was studied using drop shape tensiometry. The extent of glucose binding accounted for up to 85% for a protein:glucose ratio of 1:2. Foaming capabilities were moderately enhanced due to Maillard conjugation in the absence of solvent extraction, while due to solvent induced partial denaturation, further enhancement of foaming performance took place. Furthermore, sugar binding capabilities were enhanced upon solvent treatment, while surface pressure and foaming capacity were not necessarily improved. Adsorption rate at the air-water surface and dilational elasticity was highly dependent on molecular size of reacting sugars. In addition, oil remaining in the samples also had a bearing on the extent of Maillard conjugation. Consequently, tailoring of processing conditions could enhance foaming characteristics of BC proteins and ensure their utilization in food foams and other food dispersions.

Re-programming of gene expression in the CS8 rice line over-expressing ADPglucose pyrophosphorylase induces a suppressor of starch biosynthesis.

The CS8 transgenic rice (Oryza sativa L.) lines expressing an up-regulated glgC gene produced higher levels of ADPglucose (ADPglc), the substrate for starch synthases. However, the increase in grain weight was much less than the increase in ADPglc levels suggesting one or more downstream rate-limiting steps. Endosperm starch levels were not further enhanced in double transgenic plants expressing both glgC and the maize brittle-1 gene, the latter responsible for transport of ADPglc into the amyloplast. These studies demonstrate that critical processes within the amyloplast stroma restrict maximum carbon flow into starch. RNA-seq analysis showed extensive re-programming of gene expression in the CS8 with 2073 genes up-regulated and 140 down-regulated. One conspicuous gene, up-regulated ~15-fold, coded for a biochemically uncharacterized starch binding domain-containing protein (SBDCP1) possessing a plastid transit peptide. Confocal microscopy and transmission electron microscopy analysis confirmed that SBDCP1 was located in the amyloplasts. Reciprocal immunoprecipitation and pull-down assays indicated an interaction between SBDCP1 and starch synthase IIIa (SSIIIa), which was down-regulated at the protein level in the CS8 line. Furthermore, binding by SBDCP1 inhibited SSIIIa starch polymerization activity in a non-competitive manner. Surprisingly, artificial microRNA gene suppression of SBDCP1 restored protein expression levels of SSIIIa in the CS8 line resulting in starch with lower amylose content and increased amylopectin chains with a higher degree of polymerization. Collectively, our results support the involvement of additional non-enzymatic factors such as SBDCP in starch biosynthesis.

Identification of Novel Proteins from Black Cumin Seed Meals Based on 2D Gel Electrophoresis and MALDI-TOF/TOF-MS Analysis.

The amount of cold press oil manufacture is globally rising, which in turn leads to the accumulation of deoiled plant seeds at significant quantities and consequent manufacture of plant protein products. In this study, we made an attempt to analyze the protein profile of black cumin seed protein concentrates prepared by the alkali extraction-acid precipitation technique (AE-IP). The analytical strategy relied on gel-based proteome mapping which included two-dimensional gel electrophoresis followed by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF/TOF). 14 different protein bands were identified, and in gel-trypsinolysis was carried out for the corresponding gel spots. Using the MASCOT database, current findings on 10 proteins were compared with the existing data. The highest similarity was 46 which was obtained between the highest pI black cumin protein observed here and the cyclin dependent kinase inhibitor of Arabidopsis thaliana. The molecular mass of the intact protein was determined by linear MALDI-TOF/TOF-MS as 23,711.2186 Da. The peptide constructs of this protein have been further studied in order to identify potential biological activity. Matching sequences generated bioactive peptides in silico such as IR, AL, and SL dipeptides during sequential enzymatic digestion with pepsin and trypsin. Since the majority of bioactivity investigations on black cumin seeds have been related to black cumin oil and its oil soluble components, the structure and bioactivities of black cumin proteins deserve further research.

Analysis of the Rice ADP-Glucose Transporter (OsBT1) Indicates the Presence of Regulatory Processes in the Amyloplast Stroma That Control ADP-Glucose Flux into Starch.

Previous studies showed that efforts to further elevate starch synthesis in rice (Oryza sativa) seeds overproducing ADP-glucose (ADPglc) were prevented by processes downstream of ADPglc synthesis. Here, we identified the major ADPglc transporter by studying the shrunken3 locus of the EM1093 rice line, which harbors a mutation in the BRITTLE1 (BT1) adenylate transporter (OsBt1) gene. Despite containing elevated ADPglc levels (approximately 10-fold) compared with the wild-type, EM1093 grains are small and shriveled due to the reduction in the amounts and size of starch granules. Increases in ADPglc levels in EM1093 were due to their poor uptake of ADP-[(14)C]glc by amyloplasts. To assess the potential role of BT1 as a rate-determining step in starch biosynthesis, the maize ZmBt1 gene was overexpressed in the wild-type and the GlgC (CS8) transgenic line expressing a bacterial glgC-TM gene. ADPglc transport assays indicated that transgenic lines expressing ZmBT1 alone or combined with GlgC exhibited higher rates of transport (approximately 2-fold), with the GlgC (CS8) and GlgC/ZmBT1 (CS8/AT5) lines showing elevated ADPglc levels in amyloplasts. These increases, however, did not lead to further enhancement in seed weights even when these plant lines were grown under elevated CO2. Overall, our results indicate that rice lines with enhanced ADPglc synthesis and import into amyloplasts reveal additional barriers within the stroma that restrict maximum carbon flow into starch.

The plastidial starch phosphorylase from rice endosperm: catalytic properties at low temperature.

MAIN CONCLUSION: Consistent with its essential role in starch biosynthesis at low temperatures, the plastidial starch phosphorylase from rice endosperm is highly active at low temperature. Moreover, contrary to results on other higher plant phosphorylases, the L80 peptide, a domain unique to plant phosphorylases and not present in orthologous phosphorylases from other organisms, is not involved in enzyme catalysis. Starch phosphorylase (Pho) is an essential enzyme in starch synthesis in developing rice endosperm as the enzyme plays a critical role in both the early and maturation phases of starch granule formation especially at low temperature. In this study, we demonstrated that the rice Pho1 maintains substantial enzyme activity at low temperature (<20 °C) and its substrate affinities for branched α-glucans and glucose-1-phosphate were significantly increased at the lower reaction temperatures. Under sub-saturating substrate conditions, OsPho1 displayed higher catalytic activities at 18 °C than at optimal 36 °C, supporting the prominent role of the enzyme in starch synthesis at low temperature. Removal of the highly charged 80-amino acid sequence L80 peptide, a region found exclusively in the plastidial Pho1 of higher plants, did not significantly alter the catalytic and regulatory properties of OsPho1 but did affect heat stability. Our kinetic results support the low temperature biosynthetic role of OsPho1 in rice endosperm and indicate that its L80 region is unlikely to have a direct enzymatic role but provides stability of the enzyme under heat stress.

The rice endosperm ADP-glucose pyrophosphorylase large subunit is essential for optimal catalysis and allosteric regulation of the heterotetrameric enzyme.

Although an alternative pathway has been suggested, the prevailing view is that starch synthesis in cereal endosperm is controlled by the activity of the cytosolic isoform of ADPglucose pyrophosphorylase (AGPase). In rice, the cytosolic AGPase isoform is encoded by the OsAGPS2b and OsAGPL2 genes, which code for the small (S2b) and large (L2) subunits of the heterotetrameric enzyme, respectively. In this study, we isolated several allelic missense and nonsense OsAGPL2 mutants by N-methyl-N-nitrosourea (MNU) treatment of fertilized egg cells and by TILLING (Targeting Induced Local Lesions in Genomes). Interestingly, seeds from three of the missense mutants (two containing T139I and A171V) were severely shriveled and had seed weight and starch content comparable with the shriveled seeds from OsAGPL2 null mutants. Results from kinetic analysis of the purified recombinant enzymes revealed that the catalytic and allosteric regulatory properties of these mutant enzymes were significantly impaired. The missense heterotetramer enzymes and the S2b homotetramer had lower specific (catalytic) activities and affinities for the activator 3-phosphoglycerate (3-PGA). The missense heterotetramer enzymes showed more sensitivity to inhibition by the inhibitor inorganic phosphate (Pi) than the wild-type AGPase, while the S2b homotetramer was profoundly tolerant to Pi inhibition. Thus, our results provide definitive evidence that starch biosynthesis during rice endosperm development is controlled predominantly by the catalytic activity of the cytoplasmic AGPase and its allosteric regulation by the effectors. Moreover, our results show that the L2 subunit is essential for both catalysis and allosteric regulatory properties of the heterotetramer enzyme.

Systemic immune inflammation index and its implication on in-stent restenosis among patients with acute coronary syndrome.

OBJECTIVE: This study aims to assess the predictive value of the Systemic Immune Inflammation Index (SII) in determining in-stent restenosis (ISR) likelihood in patients with acute coronary syndrome (ACS) who have undergone percutaneous coronary intervention (PCI). METHODS: The study enrolled 903 ACS patients undergoing PCI, categorized into ISR (+) and ISR (-) groups based on control coronary angiography results. Demographic, clinical, laboratory, and angiographic-procedural characteristics were systematically compared. RESULTS: The ISR (+) group encompassed 264 individuals (29.2%), while the ISR (-) group comprised 639 individuals (70.8%). Patients had a mean age of 55.8 ±â€…10.2 years, with 69% being male. The ISR (+) group had higher diabetes and smoking prevalence and notably larger stent dimensions. Lab parameters showed significantly elevated creatinine, total cholesterol, red cell distribution width, white blood cell and neutrophil counts, SII index and C-reactive protein (CRP) in the ISR (+) group, while lymphocyte levels were lower. Binary logistic regression identified stent diameter (odds ratio [OR]: 0.598, 95% confidence interval [CI]: 0.383-0.935; P  = 0.024), stent length (OR: 1.166, 95% CI: 1.132-1.200; P  < 0.001), creatinine (OR: 0.366, 95% CI: 0.166-0.771; P  = 0.003), CRP (OR: 1.075, 95% CI: 1.042-1.110; P  = 0.031), and SII index (OR: 1.014, 95% CI: 1.001-1.023; P  < 0.001) as independent ISR predictors. CONCLUSION: The SII index exhibits potential as a predictive marker for ISR in ACS patients post-PCI, indicating systemic inflammation and heightened restenosis risk. Integrating the SII index into risk models could identify high-risk patients for targeted interventions.

Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis.

The transmembrane death receptor Fas transduces apoptotic signals upon binding its ligand, FasL. Although Fas is highly expressed in cancer cells, insufficient cell surface Fas expression desensitizes cancer cells to Fas-induced apoptosis. Here, we show that the increase in Fas microaggregate formation on the plasma membrane in response to the inhibition of endocytosis sensitizes cancer cells to Fas-induced apoptosis. We used a clinically accessible Rho-kinase inhibitor, fasudil, that reduces endocytosis dynamics by increasing plasma membrane tension. In combination with exogenous soluble FasL (sFasL), fasudil promoted cancer cell apoptosis, but this collaborative effect was substantially weaker in nonmalignant cells. The combination of sFasL and fasudil prevented glioblastoma cell growth in embryonic stem cell-derived brain organoids and induced tumor regression in a xenograft mouse model. Our results demonstrate that sFasL has strong potential for apoptosis-directed cancer therapy when Fas microaggregate formation is augmented by mechano-inhibition of endocytosis.

Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations.

Three-dimensional (3D) genomics shows immense promise for studying X chromosome inactivation (XCI) by interrogating changes to the X chromosomes' 3D states. Here, we sought to characterize the 3D state of the X chromosome in naïve and primed human pluripotent stem cells (hPSCs). Using chromatin tracing, we analyzed X chromosome folding conformations in these cells with megabase genomic resolution. X chromosomes in female naïve hPSCs exhibit folding conformations similar to the active X chromosome (Xa) and the inactive X chromosome (Xi) in somatic cells. However, naïve X chromosomes do not exhibit the chromatin compaction typically associated with these somatic X chromosome states. In H7 naïve human embryonic stem cells, XIST accumulation observed on damaged X chromosomes demonstrates the potential for naïve hPSCs to activate XCI-related mechanisms. Overall, our findings provide insight into the X chromosome status of naïve hPSCs with a single-chromosome resolution and are critical in understanding the unique epigenetic regulation in early embryonic cells.

Generation of ventralized human thalamic organoids with thalamic reticular nucleus.

Human brain organoids provide unique platforms for modeling several aspects of human brain development and pathology. However, current brain organoid systems mostly lack the resolution to recapitulate the development of finer brain structures with subregional identity, including functionally distinct nuclei in the thalamus. Here, we report a method for converting human embryonic stem cells (hESCs) into ventral thalamic organoids (vThOs) with transcriptionally diverse nuclei identities. Notably, single-cell RNA sequencing revealed previously unachieved thalamic patterning with a thalamic reticular nucleus (TRN) signature, a GABAergic nucleus located in the ventral thalamus. Using vThOs, we explored the functions of TRN-specific, disease-associated genes patched domain containing 1 (PTCHD1) and receptor tyrosine-protein kinase (ERBB4) during human thalamic development. Perturbations in PTCHD1 or ERBB4 impaired neuronal functions in vThOs, albeit not affecting the overall thalamic lineage development. Together, vThOs present an experimental model for understanding nuclei-specific development and pathology in the thalamus of the human brain.

Getting the right cells.

Fusing brain organoids with blood vessel organoids leads to the incorporation of non-neural endothelial cells and microglia into the brain organoids.

Advanced in vitro models: Microglia in action.

In the central nervous system (CNS), microglia carry out multiple tasks related to brain development, maintenance of brain homeostasis, and function of the CNS. Recent advanced in vitro model systems allow us to perform more detailed and specific analyses of microglial functions in the CNS. The development of human pluripotent stem cells (hPSCs)-based 2D and 3D cell culture methods, particularly advancements in brain organoid models, offers a better platform to dissect microglial function in various contexts. Despite the improvement of these methods, there are still definite restrictions. Understanding their drawbacks and benefits ensures their proper use. In this primer, we review current developments regarding in vitro microglial production and characterization and their use to address fundamental questions about microglial function in healthy and diseased states, and we discuss potential future improvements with a particular emphasis on brain organoid models.

Hazelnut peptide fractions preserve their bioactivities beyond industrial manufacture and simulated digestion of hazelnut cocoa cream.

Cold press hazelnut cakes represent a concentrated source of proteins that can be industrially exploited. Previously, bioactive attributes of hazelnut protein hydrolysates including antihypertensive and antidiabetic activities were documented. Here, we made an attempt to utilize bioactive hazelnut protein hydrolysates (1 % w/w) in the manufacture of industrial hazelnut cocoa cream and investigate their stability through processing and simulated gastrointestinal digestion. The inclusion of bioactive peptide fractions was a safe practice in the microbiological sense. Proteolysis lowered the potential allergenicity of hazelnut proteins in the cocoa cream products up to about 20 %. In silico trypsinolysis predicted partial degradation for 51.8 % of the peptide sequences (i.e., 43/83) that were present in the hydrolysates. However, partial degradation and mixing of degraded vs non-degraded peptides preserved and/or further elevated bioactive attributes in the digested cocoa cream products in terms of Angiotensin converting enzyme (ACE)-inhibitory (up to about 92 %) and antidiabetic activities (between 7.5 and 44.4 %). In most cases, however, antioxidative activity was < 10 %. While simulated in vitro digestion potentially influenced the bioactive attributes of protein hydrolysates, the influence of cocoa cream processing and food matrix were relatively limited for hydrolysate fractions and more pronounced for protein isolates. Hazelnut press cakes represent a significant resource for the generation and industrial utilization of bioactive peptides, which could preserve their bioactivity beyond industrial manufacture and digestion and lead to slightly reduced allergenicity.