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.

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.

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.

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.

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.].

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.

Dyslexia associated gene KIAA0319 regulates cell cycle during human neuroepithelial cell development.

Dyslexia, also known as reading disability, is defined as difficulty processing written language in individuals with normal intellectual capacity and educational opportunity. The prevalence of dyslexia is between 5 and 17%, and the heritability ranges from 44 to 75%. Genetic linkage analysis and association studies have identified several genes and regulatory elements linked to dyslexia and reading ability. However, their functions and molecular mechanisms are not well understood. Prominent among these is KIAA0319, encoded in the DYX2 locus of human chromosome 6p22. The association of KIAA0319 with reading performance has been replicated in independent studies and different languages. Rodent models suggest that kiaa0319 is involved in neuronal migration, but its role throughout the cortical development is largely unknown. In order to define the function of KIAA0319 in human cortical development, we applied the neural developmental model of a human embryonic stem cell. We knocked down KIAA0319 expression in hESCs and performed the cortical neuroectodermal differentiation. We found that neuroepithelial cell differentiation is one of the first stages of hESC differentiation that are affected by KIAA0319 knocked down could affect radial migration and thus differentiation into diverse neural populations at the cortical layers.

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.

Expression of the transcription factor PU.1 induces the generation of microglia-like cells in human cortical organoids.

Microglia play a role in the emergence and preservation of a healthy brain microenvironment. Dysfunction of microglia has been associated with neurodevelopmental and neurodegenerative disorders. Investigating the function of human microglia in health and disease has been challenging due to the limited models of the human brain available. Here, we develop a method to generate functional microglia in human cortical organoids (hCOs) from human embryonic stem cells (hESCs). We apply this system to study the role of microglia during inflammation induced by amyloid-ß (Aß). The overexpression of the myeloid-specific transcription factor PU.1 generates microglia-like cells in hCOs, producing mhCOs (microglia-containing hCOs), that we engraft in the mouse brain. Single-cell transcriptomics reveals that mhCOs acquire a microglia cell cluster with an intact complement and chemokine system. Functionally, microglia in mhCOs protect parenchyma from cellular and molecular damage caused by Aß. Furthermore, in mhCOs, we observed reduced expression of Aß-induced expression of genes associated with apoptosis, ferroptosis, and Alzheimer's disease (AD) stage III. Finally, we assess the function of AD-associated genes highly expressed in microglia in response to Aß using pooled CRISPRi coupled with single-cell RNA sequencing in mhCOs. In summary, we provide a protocol to generate mhCOs that can be used in fundamental and translational studies as a model to investigate the role of microglia in neurodevelopmental and neurodegenerative disorders.

Tombul hazelnut (Corylus avellana L.) peptides with DPP-IV inhibitory activity: In vitro and in silico studies.

Cold press technology generates high quality value-added oil products along with highly stable oilseed cakes. Hazelnut cakes are characterized by high protein concentrations that can be industrially valorized. Here, using an aqueous extraction scheme along with enzymatic proteolysis and FPLC (fast protein liquid chromatography)-based fractionation, a variety of hazelnut peptide fractions with varying bioactive properties were manufactured and their sequences were determined based on mass spectrometry. DPP-IV inhibitory attributes were determined based on an in vitro DPP-IV assay and in silico techniques were administered for for the analysis of overall bioactive potential and DPP-IV inhibitory characteristics of peptides. Based on these investigations, 256 peptides were identified in 81 different fractions. The majority of fractions were characterized with low to moderate DPP-IV inhibitory activity possibly due to their dilute nature. Some hazelnut peptides were characterized by comparable IC50 values as the positive control (Diprotin-A). The most influential 7 peptides were shown to generate higher docking scores than the control. The main interaction mechanism between hazelnut peptides and DPP-IV possibly depended on hydrophobic interactions. While further concentration could enhance the DPP-IV inhibitory potential of hazelnut peptides, hazelnut cakes represent a sustainable resource of potentially antidiabetic peptides.

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.

Atrial fibrillation-related acute myocardial infarction and acute mesenteric ischemia.

Atrial fibrillation-related synchronous thromboembolism of the mesenteric and coronary arteries is a rare event. This case report is about an 82-year-old male patient who presented to the emergency department with epigastric pain and who was diagnosed with ST-elevated myocardial infarction accompanied with acute mesenteric ischemia. To our knowledge, this is the first report of angiographic evidence of synchronous thrombus in both the arteries.

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.

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.

Investigation of beta-lactoglobulin derived bioactive peptides against SARS-CoV-2 (COVID-19): In silico analysis.

The coronavirus disease of 2019 (COVID-19) outbreak caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which started in late 2019 in Wuhan, China spread to the whole world in a short period of time, and thousands of people have died due to this epidemic. Although scientists have been searching for methods to manage SARS-CoV-2, there is no specific medication against COVID-19 as of yet. Two main approaches should be followed in the treatment of SARS-CoV-2; one of which is to neutralize the virus, and the other is to inhibit the host cell membrane receptors, where SARS-CoV-2 will bind. In this study, peptides derived from beta-lactoglobulin, which inactivates both the virus and its receptors in the host cell, were identified using computer-based in silico analysis. The beta-lactoglobulin derived peptides used in this study were obtained by the treatment of goat milk whey fraction with trypsin. The structure of the peptides was characterized by the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF/MS), and six beta-lactoglobulin derived peptides were selected as candidate peptides. Subsequently, the effects of peptides on SARS-CoV-2 and host cells were identified using virtual screening. According to the results of this in silico analysis, Ala-Leu-Pro-Met-His-Ile-Arg (ALMPHIR) and Ile-Pro-Ala-Val-Phe-Lys (IPAVFK) peptides were evaluated as potential candidates to be used in the treatment of SARS-CoV-2 after the future in vitro and in vivo studies.

Generation of Regionally Specified Human Brain Organoids Resembling Thalamus Development.

Thalamus is a critical information relay hub in the cortex; its malfunction causes multiple neurological and psychiatric disorders. However, there are no model systems to study the development and function of human thalamus. Here, we present a protocol to generate regionally specified human brain organoids that recapitulate the development of the thalamus using human pluripotent stem cells (hPSCs). Thalamic organoids can be used to study human thalamus development, to model related diseases, and to discover potential therapeutics. For complete information on human thalamic organoids and their application, please refer to the paper by Xiang et al. (2019).

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.

Synthetic Analyses of Single-Cell Transcriptomes from Multiple Brain Organoids and Fetal Brain.

Human brain organoid systems offer unprecedented opportunities to investigate both neurodevelopmental and neurological disease. Single-cell-based transcriptomics or epigenomics have dissected the cellular and molecular heterogeneity in the brain organoids, revealing a complex organization. Similar but distinct protocols from different labs have been applied to generate brain organoids, providing a large resource to perform a comparative analysis of brain developmental processes. Here, we take a systematic approach to compare the single-cell transcriptomes of various human cortical brain organoids together with fetal brain to define the identity of specific cell types and differentiation routes in each method. Importantly, we identify unique developmental programs in each protocol compared to fetal brain, which will be a critical benchmark for the utility of human brain organoids in the future.