Proteases catalyse irreversible posttranslational modifications that often alter a biological function of the substrate. The protease dipeptidyl peptidase 4 (DPP4) is a pharmacological target in type 2 diabetes therapy primarily because it inactivates glucagon-like protein-1. DPP4 also has roles in steatosis, insulin resistance, cancers and inflammatory and fibrotic diseases. In addition, DPP4 binds to the spike protein of MERS virus, causing it to be the human cell surface receptor for that virus. DPP4 has been identified as a potential binding target of SARS-CoV-2 spike protein, so this question requires experimental investigation. Understanding protein structure and function requires reliable protocols for production and purification. We developed such strategies for baculovirus generated soluble recombinant human DPP4 (residues 29-766) produced in insect cells. Purification used differential ammonium sulphate precipitation, hydrophobic interaction chromatography, dye affinity chromatography in series with immobilised metal affinity chromatography, and ion exchange chromatography. The binding affinities of DPP4 to the SARS-CoV-2 full-length spike protein and its receptor binding domain (RBD) were measured using surface plasmon resonance and ELISA. This optimised DPP4 purification procedure yielded 1 to 1.8 mg of pure fully active soluble DPP4 protein per litre of insect cell culture with specific activity >30 U/mg, indicative of high purity. No specific binding between DPP4 and CoV-2 spike protein was detected by surface plasmon resonance or ELISA. In summary, a procedure for high purity high yield soluble human DPP4 was achieved and used to show that, unlike MERS-CoV, SARS-CoV-2 does not bind human DPP4.

Wild game consumption has been associated with health benefits, but the influence on protein metabolism remains unknown. We compared the feeding-induced response to 2 oz of free-range reindeer (FR) versus commercial beef (CB) using stable isotope methodology. Seven male and female participants (age: 38±12 years; body mass index: 24±3 kg/m2) completed two studies using a randomized, crossover design in which they ingested 2 oz of FR or CB. L-[ring 2H5]phenylalanine & L-[ring 2H2]tyrosine were delivered via primed, continuous intravenous infusion. Blood samples were collected during the basal period and following consumption of FR or CB. Feeding-induced changes in whole body protein synthesis (PS), protein breakdown (PB), and net protein balance (NB) were determined via analysis of plasma samples for phenyalanine and tyrosine enrichment by gas chromatography mass spectrometry; plasma essential amino acid concentrations were determined by liquid chromatography-electrospray ionization-mass spectrometry. Plasma post-prandial essential amino acid (EAA) concentrations were higher with the ingestion of FR compared to CB (P=0.02). The acute feeding-induced response in PS was not different in either trial, but PB was reduced with the ingestion of FR compared to CB (P<0.0001). The difference in PB contributed to a superior level of NB (P<0.0001). When protein kinetics were normalized relative to the amino acids ingested, PB/EAAs and total amino acids ingested were reduced (P<0.01 and 0.001, respectively) in FR compared to CB; contributing to greater NB/total amino acid ingested (P<0.0001) between FR and CB. We conclude that the nutrient profiles of FR may have a more favorable benefit on protein metabolism compared to CB. These data support the potential health benefits of wild game in the preservation of whole-body protein.

The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made on complex multicellular organisms, and then modified to fit a DNA-centric view. In this article, I argue that, based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that: i) natural selection plays a dominant role in evolution, and ii) the probability of mutations is independent of the generated phenotype. I will show that the adaptation of a phenotype to an environment does not correspond to organism fitness but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome, and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype, the phenotype ensuring the stability of the genotype in a cellular and environment physicochemical parameter-depending manner.

A model of the early RNA world is proposed. Nearly self-complementary sequences that could adopt double-stranded, smallhairpin-like (shRNA), structures would be selected for due to their greater hydrolytic stability. These would be phosphorylated attheir 5' ends. We suppose that dehydrating conditions arise (perhaps intermittently) in the early environment allowing amino acidsto condense with these RNA molecules. The resulting phosphate-amino acid anhydrides would play the role of early, charged,tRNAs. A crude genetic code could emerge owing to the greater resistance of some amino acid-shRNA pairings to hydrolysisrelative to others. Early on there is no division of labor between mRNAs and tRNAs; the same molecules perform both functions.But the first systems would have encoded little in the way of protein sequence information. Rather they would have served as catalysts for the random polymerization of amino acids. It is speculated that the selective advantage inhering in such systems lay intheir ability to supply raw materials for the formation of coacervates within which the various molecules essential to proto-lifecould be concentrated. This would greatly facilitate the necessary chemistries. The evolution of homochiral protein and RNA populations is discussed. An appealing feature of this model is its ability to explain the transition from phosphorylated amino acids to the 3' ester-linked aminoacyl-tRNAs employed by modern life.

This study was conducted to investigate the effect of supplementing different types of methionine (L and D-type) and its precursor (HMBi) on milk protein synthesis using immortalized bovine mammary epithelial cell line (MAC-T Cell); D-methionine (D-Met), L-methionine (L-met) and 2-hydroxy-4-methylthiobutanoic acid I (HMBi), an isopropyl ester of the hydroxy analogue precursor of methionine. The underlying mechanism of milk protein synthesis by adding D- and L-type amino acid as well as HMBi was elucidated through omics analysis to verify the metabolism pathway. Results showed that HMBi group showed the highest beta casein mRNA expression levels compared to D- and L-Met groups and highest medium protein although not different with the L-Met treatment. The observed upregulated (>2 protein expression vs. control) and downregulated (<0.5 protein expression vs. control) proteins in L-Met, D-Met and HMBi treated groups were: 39, 77; 46, 68; and 40, 78, respectively. Interestingly, based on protein pathway analysis, L-Met treated group stimulated the ATP synthesis, PI3 kinase and pyruvate metabolism. On the other hand, the D-Met group stimulated fructose-galactose metabolism, glycolysis pathway, PI3 kinase and pyruvate metabolism. And lastly HMBi-treated group stimulated pentose phosphate pathway and glycolysis pathway. Metabolite analysis revealed that L-Met treated group resulted in the increase in 11 metabolites. On the other hand, D-Met treated group showed increase in 7 metabolites and decreased of uridine monophosphate (UMP). HMBi supplementation caused increases of 3 metabolites and decreased of UMP and N-acetyl-L-glutamate Addition of different isoforms of Met stimulated the production of intermediate metabolites for energy production. Addition of L-Met stimulated the production of energy metabolites such as pyruvate, malate, and fumarate, well-known as intermediates of Krebs cycle. On the other hand, HMBi supplementation resulted in increases of energy metabolite glucose 1-phosphate and 6-phosphogluconate. Results showed that HMBi-treated group exhibited highest expression of β-casein mRNA expression by stimulating proteins and metabolites as well as protein and metabolic pathways involved in protein and energy synthesis. As a result, HMBi-treated group resulted in highest protein concentration but not significantly different with L-Met. Both the D- and L-isoforms has considerably the same medium protein concentration and β-casein mRNA expression higher than the control. So, D- and L-Met isoforms can be used alternatively without any significant change in protein synthesis efficiency in bovine mammary epithelial cells.

Abnormal filamentous aggregates formed by tangled tau protein turn out to be classic amyloid fibrils, meeting all criteria defined under the fuzzy oil drop model in the context of amyloid characterization. The model recognizes amyloids as linear structures where local hydrophobicity minima and maxima propagate in an alternating manner along the fibril’s long axis. This distribution of hydrophobicity differs greatly from the classic monocentric hydrophobic core observed in globular proteins. Rather than becoming a globule, the amyloid instead forms a ribbonlike (or cylindrical) structure, which can be thought of as a distorted spherical micelle, which in limit form appears to be the ribbon-like micelle.

The mitochondrial network is a dynamic organization within eukaryotic cells that participates in a variety of essential cellular processes, such as ATP synthesis, central metabolism, apoptosis and inflammation. The mitochondrial network is balanced between rates of fusion and fission that respond to pathophysiologic signals to coordinate appropriate mitochondrial processes. Mitochondrial fusion and fission are regulated by proteins that either reside or translocate to the inner or outer mitochondrial membranes or are soluble in the inter-membrane space. Mitochondrial fission and fusion are performed by GTPases on the outer and inner mitochondrial membranes with the assistance of other mitochondrial proteins. Due to the essential nature of mitochondrial function for cellular homeostasis regulation of mitochondrial dynamics is under strict control. Some of the mechanisms used to regulate the function of these proteins are post-translational proteolysis and/or turnover and this review will discuss these mechanisms required for correct mitochondrial network organization.

Glioblastoma multiforme (GBM) is the most frequent and aggressive primary brain tumor. GBM is formed by a very heterogeneous astrocyte population, neurons, neovascularization and infiltrating myeloid cells (microglia and monocyte derived macrophages). The IQGAP1 scaffold protein interacts with components of the cytoskeleton, cell adhesion molecules, and several signaling molecules to regulate cell morphology and motility, cell cycle and other cellular functions. IQGAP1 overexpression and delocalization has been observed in several tumors, suggesting a role for this protein in cell proliferation, transformation and invasion. IQGAP1 has been identified as a marker of amplifying cancer cells in GBMs. To determine the involvement of IQGAP1 in the onco-biology of GBM, we performed immunohistochemical confocal microscopic analysis of the IQGAP1 protein in human GBM tissue samples using cell type-specific markers. IQGAP1 immunostaining and subcellular localization was heterogeneous; the protein was located in the plasma membrane and, at variable levels, in nucleus and/or cytosol. Moreover, IQGAP1 positive staining was found in podosome/invadopodia-like structures. IQGAP1⁺ staining was observed in neurons (Map2⁺ cells), in cancer stem cells (CSC; nestin⁺) and in several macrophages (CD31⁺ or Iba1⁺). Our results indicate that the IQGAP1 protein is involved in normal cell physiology as well as oncologic processes.

In tissue engineering scaffolds take the place of the natural extra cellular matrix (ECM). The natural ECM is the extracellular part of animal tissue that usually provides structural support to the animal cells in addition to performing various other important functions. The design aspect along with the choice of the material for the artificial scaffold is very crucial to cell differentiation, adhesion, proliferation, and the transport of the growth factors or other bio molecular signals. In addition to the material and design of the scaffolds, it is necessary to replicate the normal physiological situation if the scaffold has to function as an implant. The cells have to be located in the porous scaffold to form a three dimensional assembly. The article discusses the important factors to be considered while designing a scaffold for tissue engineering and regenerative medicine.

Yeast two-hybrid approaches, which are based on fusion proteins that must co-localise to the nucleus to reconstitute the transcriptional activity of GAL4 have greatly contributed to understand the nitrogen interaction network of cyanobacteria, whose main hubs are the trimeric PII and the monomeric PipX regulators. The bacterial two-hybrid system, based on the reconstitution in the E. coli cytoplasm of the adenylate cyclase of Bordetella pertussis, should provide a relatively faster and presumably more physiological assay for cyanobacterial proteins than the yeast system. Here we use the bacterial two-hybrid system to gain additional insights into the cyanobacterial PipX interaction network while simultaneously assessing the advantages and limitations of the two most popular two-hybrid systems. Comprehensive mutational analysis of PipX and bacterial two-hybrid assays were performed to compare outcomes between yeast and bacterial systems. We detected interactions previously recorded in the yeast two-hybrid system as negative as well as a “false positive”, the self-interaction of PipX, which is rather an indirect interaction dependent on PII homologs from the E. coli host, a result confirmed by Western analysis with relevant PipX variants. This is, to our knowledge, the first report of the molecular basis of a false positive in the bacterial two-hybrid system.

Replication protein A (RPA) is a heterotrimeric protein complex and the main single-stranded DNA (ssDNA) binding protein in eukaryotes. RPA has key functions in most of the DNA-associated metabolic pathways and DNA damage signalling. Its high affinity for ssDNA helps to stabilise ssDNA structures and prevents the DNA sequence from nuclease attacks. RPA consists of multiple DNA-binding domains which are oligonucleotide/oligosaccharide-binding (OB)-folds, responsible for DNA binding, and interactions with proteins. These RPA-ssDNA and RPA-protein interactions are crucial for DNA replication, DNA repair, DNA damage signalling, and the conversation of the genetic information of cells. Proteins such as ATR use RPA to locate to regions of DNA damage for DNA damage signalling. Recruitment of nucleases and DNA exchange factors to sites of double strand breaks are also an important RPA function to ensure effective DNA recombination to correct these DNA lesions. Due to its high affinity to ssDNA, RPA’s removal from ssDNA is of central importance to allow these metabolic pathway to proceed and processes to exchange RPA against downstream factors are established in all eukaryotes. These facetted and multi-layered functions of RPA will be discussed in detail in the review. RPA is also a major player in a variety of human diseases, which will be discussed.

Polycystic ovary syndrome (PCOS) is an insulin resistant state, compensated by hyperinsulinemia. More than 50% of the women with PCOS are obese, and/or have metabolic syndrome. Weight loss improves both metabolic and reproductive outcomes. Not only the energy content, but also the nutrient composition of a diet may be important. This article will present a series of studies from our research comparing effects of dietary protein vs. simple-carbohydrates (CHO). Results of the acute challenge studies demonstrate that simple-CHO intake causes reactive hypoglycemia in one third of the women with PCOS, especially among obese and insulin resistant individuals. Symptoms of hypoglycemia are associated with secretion of cortisol and adrenal androgens. Simple-CHO suppresses the hunger signal ghrelin for a shorter period. During weight loss, women who receive protein supplementation achieve larger amounts of weight- and fat-mass losses. Amino acid compositions of the protein supplements do not affect the improvements in weight and insulin resistance. It is plausible that simple-CHO intake leads to weight gain, or interferes with weight-loss, by causing reactive hypoglycemia, triggering adrenal steroid secretion, and leading to snacking. Since obese women with PCOS are more susceptible to reactive hypoglycemia, a vicious cycle establishes. Restriction of simple-CHO may break this cycle.

Chronic Kidney Disease (CKD) is a major public health concern with an increasing proportion of sufferers progressing to renal replacement therapy (RRT). Early identification of those at risk of disease progression could be key in improving outcomes. We hypothesise that urinary liver-type fatty acid binding protein (uL-FABP) may be a suitable biomarker for CKD progression and can add value to currently established biomarkers such as urinary protein to creatinine ratio (uPCR) 583 participants with CKD 1-5 (not receiving renal replacement therapy) entered a 2-yr prospective longitudinal study. UPCR and uL-FABP were measured at baseline and CKD progression was defined as either i) a decline in eGFR of >5ml/min/1.73m2 or an increase in serum creatinine by 10% at 1-yr or ii) a decline in eGFR of >6 ml/min/1.73m2, or an increase in serum creatinine by 20% at 2-yrs or iii) the initiation of RRT. A combined outcome of initiating RRT or death was also included. Approximately 40% of participants showed CKD progression. UL-FABP predicted CKD progression at both years 1 and 2 (OR 1.01, p<0.01). Sensitivity and specificity were comparable to those of uPCR (AUC 0.623 v 0.706) and heat map analysis suggested that uL-FABP in the absence of significant proteinuria can predict an increase in serum creatinine of 10% at 1yr and 20% at 2yr. The risk of the combined outcome of initiating RRT or death was 23% higher in those with high uL-FABP (p<0.01) independent of uPCR. UL-FABP appears to be a highly sensitive and specific biomarker of CKD progression. The use of this biomarker could enhance the risk stratification of CKD and its progression and should be assessed further.

The expression of the Fasciola hepatica Carboxylesterase type B (CestB) gene is induced in response to the anthelmintic triclabendazole (TCBZ), resulting in a significant increase in enzymatic specific activity. Furthermore, the amino acid sequence of CestB exhibits variations that could lead to substantial amino acid substitutions at the ligand-binding site. These substitutions have the potential to affect the interaction between the ligand and the protein, as well as the catalytic properties of the enzyme. The objective of this study was to identify new CestB polymorphisms in TCBZ-resistant parasites using 3D modeling against the metabolically oxidized form of the anthelmintic TCBZSOX. Our aim was to observe the formation of TCBZSOX-specific binding pockets that could potentially explain the resistance to anthelmintic agents. We identified a CestB polymorphism in a TCBZ-resistant strain of parasites exhibiting three radical amino acid substitutions at positions 147, 215, and 243, resulting in the formation of a TCBZSOX-affinity pocket capable of binding the anthelmintic drug. Additionally, our 3D modeling analysis revealed that these amino acid substitutions also had an impact on the configuration of the CestB catalytic site, affecting the enzyme's interaction with chromogenic carboxylic ester substrates and altering its catalytic properties; however, the identified TCBZSOX-binding pocket was located far from the enzyme's catalytic site, making the enzymatic hydrolysis of TCBZSOX theoretically impossible. Nonetheless, the increased affinity for the anthelmintic may explain a drug-sequestration type of anthelmintic resistance and lays the foundation for the development of a molecular diagnostic tool for identifying anthelmintic resistance in F. hepatica.

Begomoviruses, which belong to the Geminiviridae family, are intracellular parasites transmitted by whiteflies to dicotyledonous plants, significantly damaging agronomically relevant crops. These nucleus-replicating DNA viruses need to move intracellularly from the nucleus to the cytoplasm and then, like other plant viruses, spread systemically throughout the plant to cause dis-ease. The transport proteins of begomoviruses play a crucial role in recruiting host components for the movement of viral DNA within and between cells while exhibiting functions that suppress the host's immune defense. Pioneering studies on species of the Begomovirus genus have identified specific viral transport proteins involved in intracellular transport, cell-to-cell movement, and systemic spread. Recent research has primarily focused on viral movement proteins and their interaction with the cellular host transport machinery, significantly expanding our understanding of viral infection pathways. This review focuses on three main aspects: (i) the role of viral transport proteins, specifically movement proteins (MPs) and nuclear shuttle proteins (NSPs), (ii) their ability to recruit host factors for intra- and intercellular viral movement, and (iii) suppress antiviral immunity, with a particular emphasis on bipartite begomoviral movement proteins.

Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the ”rule of five (RO5).” Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is difficult. In this study, we propose a molecule generation model based on deep reinforcement learning, specialized for generating PPI inhibitors. By introducing a scoring function that can represent the properties of PPI inhibitors, we successfully generated potential PPI inhibitor compounds. The generated virtual compounds possess the desired properties for PPI inhibitors, and show similarity to commercially available PPI libraries. These generated virtual compounds are freely available as a virtual library.

Directed evolution methods are becoming increasingly popular, as they are extremely powerful toward developing new biomolecules with altered/novel activities, e.g., proteins with new catalytic functions or substrate specificities, and nucleic acids that recognize an intended target. Especially useful are systems that have incorporated continuous evolution, where the protein to be evolved undergoes continuous mutagenesis to evolve a desired trait with little to no input from the researcher once the system is started. However, continuous evolution methods can be challenging to implement in the lab and daunting for researchers to invest time and resources. Our intent is to provide basic information and helpful suggestions that we have gained from our experience with bacterial phage-assisted continuous evolution (PACE). Specifically, we review factors to consider before adopting PACE for a given evolution scheme, different types of selection circuits that can be utilized with particular focus on the PACE-B1H selection system, what optimization of a PACE selection circuit may look like using directed evolution of ME47 as a case study, and additional techniques that may be incorporated into a PACE experiment. With this information, researchers will be better equipped to determine if PACE is a valid strategy to use to evolve their proteins and how to set up a valid selection circuit.

Lung cancer is one of the most important health risks worldwide for human. Non-small cell lung cancer (NSCLC) is the most common cause of premature death from malignant disease. This study provides in-depth insights from systems biology analyses to identify molecular to inform systemic drug targeting in NSCLC. Gene expression profiles from non small cell lung cancer were analyzed with genome-scale biomolecular networks (I,e., protein-protein interaction, transcriptional and post transcriptional regulatory networks). The aim of the study was to determine the pathways and expression profile of the genes to discover molecular signature at RNA and protein levels which could serve as potential drug targets for therapeutics innovation and the identification of novel targets. Eight proteins, six TFs and seven miRNAs came into prominence as potential drug targets. The differential expression profiles of these reporter biomolecules were cross-validated by independent RNA-Seq and miRNA-Seq. Risk discrimination performance of the reporter biomolecules NPR3, JUN, PPARG, TP53, CKMT1A, SP3 and TFAP2A were also evaluated. Total 213 drugs and 7 proteins were found for non small cell lung cancer through dgidb. Among these identified drugs seven drugs such as- Gemcitabine, Carboplatin, paclitaxel, Docetaxel, Crizotinib, Bevacizumab and Gemcitabine is used for NSCLC which is approved by National Cancer Institute. The molecular signatures and repurposed drugs presented here permit further attention for experimental studies which are offer significant potential as biomarkers and candidate therapeutics for precision medicine approaches to clinical management of NSCLC.

The regulation of hepatic very-low-density lipoprotein (VLDL) secretion plays an important role in the pathogenesis of dyslipidemia and fatty liver diseases. VLDL is controlled by hepatic microsomal triglyceride transfer protein (MTTP). Mttp is regulated by carbohydrate response element binding protein (ChREBP) and small heterodimer partner (SHP). However, it is unclear whether both coordinately regulate Mttp expression and VLDL secretion. Here, adenoviral overexpression of ChREBP and SHP in rat primary hepatocytes induced and suppressed Mttp mRNA, respectively. However, Mttp induction by ChREBP was much more potent than suppression by SHP. Promoter assays of Mttp and the liver type pyruvate kinase gene revealed that SHP and ChREBP did not affect the transactivity of each other. Mttp mRNA and protein levels of Shp^/– mice were similar to those of wild-type; however, those of Chrebp^–/–Shp^–/– and Chrebp^–/– mice were much lower. Consistent with this, the VLDL particle number and VLDL secretion rates in Shp^–/–- mice were similar to wild-type, but were much lower in Chrebp^–/– and Chrebp^–/–Shp^–/–- mice. These findings suggested that ChREBP rather than SHP regulates VLDL secretion and that ChREBP and SHP do not affect the transactivities of each other.

This work aims to explore the impact of side loads, drill-pipe tool-joint (DP-TJ) speed (RPM), and mud type on the austenitic stainless steel SM2535-110 casing wear characteristics. Actual field drill pipe tool joints, casings, and drilling muds are used in this study. The results of the study show that under both types of lubrication, the wear volume increased with radial load and DP-TJ speed. SM2535-110 casing specimens tested under oil-based mud (OBM) lubrication had higher casing wear volumes than those obtained under water-based mud (WBM) lubrication. This unexpected behavior is mainly due to the increase in the surface hardness of the casing specimens tested under WBM. The results also show that the specific wear factor (K) values of specimens tested under WBM are in general 2 to 4 times higher than those obtained under OBM. While K values under WBM increase with both the side load and RPM, those under OBM show a sharp decrease with RPM. This behavior under OBM is due to this lubricant’s higher viscosity and the change of lubrication regime from thin film to thick film lubrication at higher RPM. Scanning electron microscopy (SEM) and the digital microscopic imaging (DMI) of SM235-110 casing specimens show that an aggressive combination of adhesive, abrasive, and plastic deformation was observed under WBM, while the dominant wear mechanism under OBM is abrasive wear.

Financial markets require a great deal of decision making from the investors and market makers. One metric that can help ease the process of decision making is investment risk which can be measured in two parts; systematic risk and idiosyncratic risk. Clear understanding of the volatilities in each risk component can be a powerful signal in recognizing the right assets to maximize the investment returns. In this paper, we focus on the idiosyncratic volatility values and pre-calculate the idiosyncratic volatility values for 31,198 members of NYSE, Amex and Nasdaq markets for the trades occurring between January 1963 and December 2019. Utilizing a subset of dataset, limited to Nasdaq100 index, we consider the application of machine learning techniques in predicting the idiosyncratic volatility values using the raw trade data to explore a data extension option for the future market trade records that have not yet occurred. We offer a deep learning based regression model and compare it with traditional tree-based methods on a small subset of our per-calculated idiosyncratic volatility dataset. Our analytical results show that the performance of the deep learning techniques is much more robust in comparison to that of the traditional tree-based baselines.

This study compares the effects of lecture-based instruction and process-oriented guided inquiry learning (POGIL)-based instruction on the self-efficacy performance of Grade 12 students. A quasi-experimental, pretest-posttest design was adopted to investigate and assess the impact of POGIL-based instruction versus lecture-based instruction on students’ performance as measured by three types of cognitive outcomes; Knowing, Applying and Reasoning (KAR). Two government high schools in Alain were selected as research sites, one for the boys and one for the girls. The total number of participants was approximately 110 students (N=110); 54 were assigned to treatment groups (25 girls and 29 boys), and 56 were assigned to control groups (27 girls and 29 boys). The treatment group was taught a circular motion unit in physics using POGIL-based instruction, while the control group was taught the unit using lecture-based instruction. The study's findings showed statistically significant differences between students of the control group and the treatment group in favour of the latter regarding their science performance, self-efficacy and science-related attitudes. Moreover, positive correlations were found between participants’ performance at the KAR test, self-efficacy and scientific attitudes towards scientific inquiry after the intervention. In conclusion, it is recommended to shift teaching towards POGIL-based instruction due to its positive impact on students’ performance and self-efficacy. It is also suggested to replicate the study to include government and private schools, elementary and high schools, teachers and advisors.

This review article focuses on the current state-of-the-art in the area of cellular and molecular biotechnology for over-production of clinically relevant therapeutic and anabolic growth factors. We discuss how the currently available tools and emerging technologies can be used for the regenerative treatment of osteoarthritis (OA). Transfected protein packaging cell lines such as GP-293 cells may be used as “cellular factories” for large-scale production of therapeutic proteins and pro-anabolic growth factors, particularly in the context of cartilage regeneration. However, when irradiated with gamma or x-rays, these cells lose their capacity for replication, which actually makes them safe for use as a live cell component of intra-articular injections. This innovation is already here, in the form of TissueGene-C, a new biological drug which consists of normal allogeneic primary chondrocytes combined with transduced GP2-293 cells that overexpress the growth factor transforming growth factor β1 (TGF-β1). TissueGene-C has revolutionized the concept of cell therapy, allowing drug companies to develop live cells as biological drug delivery systems for direct intra-articular injection of growth factors whose half-lives are in the order of minutes. Therefore, in this paper, we discuss the potential for new innovations in regenerative medicine for degenerative diseases of synovial joints using mammalian protein production platforms, specifically protein packaging cell lines, for over-producing growth factors for cartilage tissue regeneration and give recent examples. Mammalian protein production platforms that incorporate protein packaging eukaryotic cell lines are superior to prokaryotic bacterial expression systems and are likely to have a significant impact on the development of new humanized biological growth factor therapies for treating focal cartilage defects and more generally for the treatment of degenerative joint diseases such as OA, especially when injected directly into the joint.

Cancer is one of the most dreaded illnesses of the 20th century, cancer is continuing to spread and is becoming more common in the 21 st century.As of right now, breast cancer seems to be the most common cancer worldwide and the leading cause of cancer-related fatalities.In present study we used different network pharmacology tools for identification of target that involved in breast cancer that network pharmacology tool used target identification and validation process in drug discovery.In present study we used UniprotKB as text mining tool for identification of breast cancer gene in that we got the 2,658 gene in that we take the 165 in study the we done the GO and KEGG enrichment analysis in that we take pathways related to the breast cancer further we used STRING for determination protein-protein interaction in that we got the interaction between NDUFA1 with NDUFA3 and EREG,MYO1B with ACTN4 and XRCC3 with XRCC2.The interaction network was drawn and the network was analyzed by Cytoscape.

Pre-mRNA splicing is an essential process orchestrated by the spliceosome, a dynamic complex assembled stepwise on pre-mRNA. We have previously identified that USH1G protein SANS regulates pre-mRNA splicing by mediating the intra-nuclear transfer of the spliceosomal U4/U6.U5 tri-snRNP complex. During this process, SANS interacts with the U4/U6 and U5 snRNP-specific proteins PRPF31 and PRPF6 and regulates splicing, which is disturbed by variants of USH1G/SANS causative for human Usher syndrome (USH) the most common form of hereditary deaf-blindness.Here, we aimed to gain further insight into the molecular interaction of the splicing molecules PRPF31 and PRPF6 to the CENTn domain of SANS using fluorescence resonance energy transfer assays in cells and in silico deep learning-based protein structure predictions. This demonstrates that SANS directly binds via two distinct conserved regions of its CENTn to the two PRPFs. In addition, we provide evidence that these interactions occur sequentially and a conformational change of an intrinsically disordered region to a short α-helix of SANS CENTn2 is triggered by binding of PRPF6. Furthermore, we found that pathogenic variants of USH1G/SANS perturb the binding of SANS to both PRPFs implying a significance for the USH1G pathophysiology.

Intrinsic disorder accounts for the flexibility of protein loops, molecular building blocks that are largely responsible for the processes and molecular functions of the living world. While loops likely represent early structural forms that served as intermediates in the emergence of protein structural domains, their origin and evolution remains poorly understood. Here, we conduct a phylogenomic survey of disorder in loop prototypes sourced from the ArchDB classification. Tracing prototypes associated with protein fold families along an evolutionary chronology revealed ancient prototypes tended to be more disordered than their derived counterparts, with ordered prototypes developing later in evolution. This highlights the central evolutionary role of disorder and flexibility. While mean disorder increased with time, a minority of ordered prototypes exist that emerged early in evolutionary history, possibly driven by the need to preserve specific molecular functions. We also revealed percolation of evolutionary constraints from higher to lower levels of organization. Percolation resulted in trade-offs between flexibility and rigidity that impacted prototype structure and geometry. Our findings provide a deep evolutionary view of the link between structure, disorder, flexibility and function, as well as insights into the evolutionary role of intrinsic disorder in loops and their contribution to protein structure and function.

Three isoenergetic diets differing on their fishmeal/ soy protein concentrate (SPC) ratio were assessed on tissue growth and energy budget of juvenile crabs Scylla serrata in postmolt stages (PMolt) and in intermolt stages (IMolt). The average growth rate on dry matter basis, were 2.064 ± 0.324% and 0.492 ± 0.08% initial BW.day-1 during PMolt and IMolt stages respectively. The efficiency in feed conversion (FCE, %), protein retention (PRE, %) and energy retention (ERE, %) were similar for the 3 experimental diets. However, FCE, PRE and ERE in PMolt stages were 4 to 5 times higher than in IMolt stages. Feed intake, energy and protein required for growth in PMolt stages were obviously higher than in IMolt stages. The energy budgets (%total energy intake) were marginally affected by diet but were significantly affected by the molt stage. Maintenance energy was lower in PMolt stages (49.84 ± 4.9%) than in IMolt stages (83.33 ± 2.45%). The excess of maintenance energy in IMolt stages represents the portion set aside for next molt: shell energy content (4.97 ± 0.31%) and energy for ecdysis (± 28%). Conversely, recovery energy was significantly higher in PMolt stages (34.39 ± 0.99%) than in IMolt stages (8.33 ± 1.7%). In conclusion SPC sustained good tissue growth and good feed utilization and can be used as a main source of dietary protein for crab juveniles in captivity.

Tick-borne encephalitis virus (TBEV) is a pathogenic, enveloped, positive-stranded RNA virus in the family Flaviviridae. Structural studies of flavivirus virions have primarily focused on mosquito-borne species with only one cryo-electron microscopy (cryo-EM) structure of a tick-borne species published. Here, we present a 3.3 Å cryo-EM structure of the TBEV virion of the Kuutsalo-14 isolate, confirming the overall organisation of the virus. We observe conformational switching of the peripheral and transmembrane helices of M protein, which can explain the quasi-equivalent packing of the viral proteins and highlights their importance in stabilizing the membrane protein arrangement in the virion. The residues responsible for the M protein inter-actions are highly conserved in TBEV but not in the structurally studied Hypr strain, nor in mosquito-borne flaviviruses. These interactions may compensate for the lower number of hydrogen bonds between E proteins in TBEV compared to the mosquito-borne flaviviruses. The structure reveals two lipids bound in the E protein, which are important for virus assembly. The lipid pockets are comparable to those recently described in mosquito-borne Zika, Spondweni, Dengue, and Usutu viruses. Our results thus advance the understanding of tick-borne flavivirus architecture and virion-stabilising interactions.

Influenza virus transcription is catalyzed by the viral RNA-polymerase (FluPol) through a cap-snatching activity. The snatching of the cap of cellular mRNA by FluPol is preceded by its binding to the flexible C-terminal domain (CTD) of the RPB1 subunit of RNA-polymerase II (Pol II). To better understand how FluPol brings the 3’-end of the genomic RNAs in close proximity to the host-derived primer, we hypothesized that FluPol may recognize additional Pol II subunits/domains to ensure cap-snatching. Using binary complementation assays between the Pol II and FluPol subunits and their structural domains, we revealed an interaction between the N-third domain of PB2 and RPB4. This interaction was confirmed by a co-immunoprecipitation assay and found to occur with the homologous domains of influenza B and C FluPols. Residues [1-72] of RPB4 were found critical in this interaction. Numerous punctual mutants generated at conserved positions between influenza A, B and C FluPols in the N-third domain of PB2 exhibited strong transcriptional activity defect. These results suggest that FluPol interacts with several domains/subunits of Pol II, the CTD to bind Pol II initiating host transcription and a second on RPB4 to locate FluPol at the proximity of the 5’-end of nascent host mRNA.

During its first month, the recently emerged 2019 Wuhan novel coronavirus (SARS-CoV-2) has already infected many thousands of people in mainland China and worldwide and took hundreds of lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge we leverage the data about the related coronaviruses that is readily available in public databases, and integrate these data into a single computational pipeline. As a result, we provide a comprehensive structural genomics and interactomics road-maps of SARS-CoV-2 and use these information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community at http://korkinlab.org/wuhan .

To date, Cartesian (x, y, z) coordinate system (CCS) has been the default approach to geometrically specify atomic spatial positions in protein structures since the launch of Protein Data Bank (PDB) in 1971. To this end, this paper proposes a local spherical coordinate system (SCS) approach as an alternative to the default approach and a previously reported global SCS approach. The local SCS approach here requires only two parameters (θ and φ), instead of x, y and z as required by the default CCS approach. Essentially, CCS and SCS are like the two sides of one coin, i.e., geometric coordinate system for three-dimensional position specification. Therefore, this paper furthermore argues that it is time to flip the coin over, and have a look at the other side of the coin, e.g., the local SCS approach, which possesses an intrinsically lower degree of descriptional complexity than that of the default CCS approach, and constitutes a potentially useful alternative perspective for all protein structural research field.

More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae, which turn out to be an effective barcode gene for these corals. However, its function remains unknown. Recently, this gene revealed the existence of a hybrid Stylophora lineage (RS_LinA) inhabiting in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C) with its parental species (RS_LinB). Furthermore, in RS_LinB, the mtORF uncovered phylogeographic patterns that were strongly correlated with environmental variations. This was similar to the patterns unraveled by hsp70, suggesting that mtORF too might be involved in thermal adaptation. Here we used computational approaches to characterize the mtORF and to identify its potential role. Results showed that this gene encodes a transmembrane protein (0.97<P< 1.00) involved in transport (0.80<P< 0.87), regulation of metabolic processes (0.70<P<0.85), and likely in the cell-surface receptor signaling pathway (0.56<P<0.80). Predicted protein functions differed among Stylophora lineages and interestingly, in RS_LinB only, the protein was intrinsically disordered and displayed domains involved in cellular complexes and stress response (0.0001< P <0.001). These characteristics, exclusive of an endemic lineage adapted to extreme environmental fluctuations, support a role of the mtORF in stress response, speciation and adaptation.

Background and objectives: Colorectal cancer (CRC) is the second most common cause of cancer-related death in the world, but early diagnosis ameliorates the survival of CRC. This report directed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) from Gene Expression Omnibus (GEO) to identify mutual differentially expressed genes (DEGs). We integrated DEGs with protein-protein interaction and transcriptional/post-transcriptional regulatory networks to identify reporter signaling and regulatory molecules; utilized functional overrepresentation and pathway enrichment analyses to elucidate their roles in biological processes and molecular pathways; performed survival analyses to evaluate their prognostic performance; and applied drug repositioning analyses through Connectivity map (CMap) and geneXpharma tools to hypothesize possible drug candidates targeting reporter molecules. Results: A total of 727 up-regulated and 99 down-regulated DEGs were detected. The PI3K-Akt signaling, Wnt signaling, ECM-interaction, and cell cycle were identified as significantly enriched pathways. Ten hub proteins (ADNP, CCND1, CD44, CDK4, CEBPB, CENPA, CENPH, CENPN, MYC, and RFC2), 10 transcription factors (ETS1, ESR1, GATA1, GATA2, GATA3, AR, YBX1, FOXP3, E2F4, and PRDM14) and 2 miRNAs (miR-193b-3p and miR-615-3p) were detected as reporter molecules. The survival analyses through Kaplan Meier curves indicated remarkable performance of reporter molecules in estimation of survival probability in CRC patients. In addition, several drug candidates including anti-neoplastic and immunomodulating agents were repositioned. Conclusions: This study presents biomarker signatures at protein and RNA levels with prognostic capability in CRC. We think that the molecular signatures and candidate drugs presented in this study might be useful in future studies indenting development of accurate diagnostic and/or prognostic biomarker screens and efficient therapeutic strategies in CRC.

The potential advantages of plant-based interventions in decreasing the incidence and lessening the morbidity and mortality of COVID-19 are yet to be widely acknowledged. Nevertheless, recent publications propose that these interventions could be effective. Our cardiology center conducted an interventional study in which we incorporated plant-based foods and provided supplementation to 3470 elderly COVID-19 patients with multiple comorbidities. We pay close attention to the precise selection of food items, the application of appropriate processing methods, and the provision of nourishing meals to our patients. Our outcome was highly successful as we achieved a zero mortality rate, and none of our patients experienced worsening conditions or required hospitalization. In this review article we present the mechanisms how plant-based and supplement interventions can mitigate COVID-19 disease severity and mortality. And experts have validated our hypotheses very recently. The measures and methods used to address the ongoing SARS-CoV-2 pandemic through plant-based interventions and supplements are effective and may help prevent or manage future pandemics.

Abstract: This study aims to evaluate the effectiveness of plant-based diets and supplement interventions in mitigating the severity and mortality of COVID-19 patients. Observational research suggests that a diet high in plant-based foods may decrease the likelihood and severity of SARS-CoV-2 infection. However, several studies have faced criticism regarding the accuracy of obtaining dietary questionnaires and the insufficient intake of essential vitamins and minerals in such diets. To address these issues, this study employed a prospective interventional design that strictly controlled the quality, quantity, and processing of plant-based foods provided. Furthermore, the study incorporated supplementation, which enhanced the anti-viral, anti-inflammatory, antioxidant, antithrombotic, and immunomodulatory properties of a plant-based diet against the SARS-CoV-2 virus. Of the 3,470 COVID-19 elderly patients, half already followed a plant-based diet, and the other half new patients, both with various comorbidities, were intervened with a plant-based diet and supplementation. The results showed that the participants in the non-plant-based diet group were twice as likely to have experienced moderate disease (with 95% confidence limit: 1.42-3.12) and 2.4 times more likely to have experienced severe disease (with 95% confidence limit: 1.2-5.0) with a significant p-value of less than 0.0005 and 0.016 respectively, compared to those in the PBD group. During the interventions, none of the participants experienced disease progression or hospitalization, and there were no reported deaths by the end of the study. The outcome was highly favorable and aligned with the researchers' expectations, as COVID-19 morbidity and mortality rates in Indonesia were among the highest in Asia. This research may provide significant insights into the prevention and management of COVID-19 and aid in better preparation for future pandemics.

Chitosan is a copolymer of β-glucosamine and N-acetylglucosamine. Recent experiments showed that the degree and pattern of acetylation along the chitosan chain modulate the biological and physicochemical properties; however, the molecular mechanism is unknown. Here we apply the de novo all-atom molecular dynamics (MD) simulations to study chitosan’s self-assembly process at different degrees of acetylation and two different acetylation patterns. The simulations revealed that the 10-mer chitosan chains with 50% acetylation in either block or alternating patterns associate to form ordered nanofibrils comprised of mainly antiparallel chains in agreement with the fiber diffraction data of deacetylated chitosan. Surprisingly, regardless of the acetylation pattern, the same intermolecular hydrogen bonds mediate the fibril sheet formation while water-mediated interactions stabilize the sheet-sheet stacking. Moreover, the acetylated units are involved in forming the strong intermolecular hydrogen bonds (NH–O6 and O6H–O7), which offers an explanation for the experimental observation that increased acetylation lowers chitosan’s solubility. Taken together, the present study provides the atomic-level understanding the role of acetylation plays in modulating chitosan’s physiochemical properties, contributing to the rational design of chitosan-based materials with the ability to tune by its degree and pattern of acetylation. Additionally, we disseminate the improved molecular mechanics parameters that can be applied in MD studies to further understand chitosan-based materials.

The process of Targeted Opinion Word Extraction (TOWE), a critical component of aspect-based sentiment analysis (ABSA), revolves around identifying opinionated words linked to specific aspect-terms within sentences. Existing deep learning approaches, while effective, often overlook the syntactic structure of sentences, a factor that previous studies have identified as beneficial for TOWE. In this study, we introduce the Syntactic-Enhanced Deep Learning Model (SEDLM) that integrates syntactic structures into deep learning frameworks for TOWE. Our approach leverages syntax-driven opinion potential scores and syntactic inter-word connections, enhancing model performance. Additionally, we introduce an innovative regularization strategy aimed at distinguishing word representations in TOWE tasks. Our comprehensive analysis reveals that SEDLM sets new benchmarks in performance across multiple standard datasets.

The implementation of Boolean functions using Nano crossbar- based switching lattices has been suggested as a substitute for conventional CMOS-based approaches in digital circuits . This alternative may satisfy the needs of future electronic designs, con- sidering the expected end of Moore’s law. This study introduces CVM, a Crossbar-based circuit Verification through Modeling tech- nique

Castor oil may be differentiated from other non-edible vegetable oils because of its main composition of hydroxylated fatty acids. Ricinoleic acid comprises 80–90% wt. of fatty acids in castor oil (Ricinus communis). In this study, the thermo-oxidative stability and tribological behavior of bio-based lubricant samples synthesized from castor oil using isoamyl alcohol were evaluated. Initially, the compositional and physicochemical properties of the obtained samples were assessed using 1H NMR, FTIR, and ASTM methods. Oxidative stability of the samples was evaluated using Rancimat method at 110 °C under air flow. The final biolubricant sample (BL2), obtained after esterification, epoxidation, and oxirane rings opening reactions, presented an oxidation stability time (OST) of 14.3 h. The thermal stability was also evaluated by thermogravimetry (TG) from the mass variations under inert and oxidative atmosphere. BL2 showed higher thermal stability compared to the other samples, demonstrating higher decomposition temperatures in both inert (339.04 °C) and oxidative (338.47 °C) atmospheres, for a mass loss of 50%. The tribological properties of the samples were evaluated using a four-ball tribometer configuration. The BL1 and BL2 samples exhibited lower friction coefficients than the mineral oil sample (MOS) by 21.5% and 43.1%, respectively. Regarding wear, the observed wear scar diameter (WSD) was also lower in BL1 and BL2 compared to MOS by 5.2% and 40.4%, respectively. The results of the tribological evaluation suggest that both samples obtained in this study have promising potential for applications in lubricating machines and mechanical systems.

As formally is known, nanozymes are the nanomaterials or nanoscale materials which reveal enzyme-like properties. These nanomaterilas can be utilzied instead of the natural enzymes for simulation of enzymatic reactions in harsh environmental conditions. Among different nanoscale enzyme-like materials, the majority of them reveal peroxidase-like activity, due to the high catalytic efficiency and stability of peroxidase-like nanozymes, they had been widely utilized for sensing and detection via constructing the colorimetric and fluorescence-based analytical and bioanalytical sensors. There are several high impact nanozymatic sensors which reported in the literature. Although the review articles published in this field, however, the current reviews focus on the introducing nanozyme field not description on the best articles published in this filed. Hence, this article aimed to present a brief introduction on the nanozyme-based chemistry with emphasizing on the historical overview of recent nanozymatic sensors. In this regard the best nanozymatic sensors which published over 2016-2023 were briefly described and overviewed.

Waste management is a significant issue that Indonesia must face. The presence of waste will always exist as long as life continues. One of the main challenges in waste management is the proper separation of organic and inorganic waste. As a solution to address this issue, the Ministry of Environment has made efforts to develop Waste Banks. However, it also creates new problems related to manual data collection, lack of monitoring by the community in implementing waste management activities, and a lack of specific reports regarding waste management conducted by officers. We propose the creation of a website using the Agile Development SDLC method. This website involve several steps and incorporate functions for data digitalization and expedited data collection, such as the addition of QR Code functionality, Monthly Reporting Function, and enhanced data security. The method used in this research is Agile Development. The application has been developed with a user-friendly interface and the latest web development technologies to ensure smooth performance. Overall, the web-based application for organic and inorganic waste using Laravel is an important step to promoting sustainable waste management practices.

In this work, the inhibition properties of new bio-based lignine ILs on the corrosion of mild steel in an aqueous solution of 0.01 M NaCl were investigated by Potentiostatic Electrochemical Impedance Spectroscopy (PEIS), Cyclic Potentiodynamic Polarization (CPP). Moreover, the surface was characterized using SEM, EDS, and optical profilometry. The influence of cation and anion on the inhibitor properties and a possible synergistic effect were investigated. The IL choline syringate showed a promising performance, reducing the corrosion current after 24-hour immersion in 0.01 M sodium chloride, from 1.66 µA/cm2 for the control to 0.066 µA/cm2 with 10 mM of the IL present. In addition to the performance as a corrosion inhibitor, both components of this IL also meet or exceed current additional desired properties of such compounds, being readily available, economically efficient, and well tolerated in organisms and the environment.

Paper-based analytical devices have been substantially developed in recent decades. Many fabrication techniques for paper-based analytical devices have been demonstrated and reported. Herein we report a relatively rapid, simple, and inexpensive method for fabricating paper-based analytical devices using parafilm hot pressing. We studied and optimized the effect of the key fabrication parameters, namely pressure, temperature, and pressing time. We discerned the optimal conditions, including pressure of 3.8 MPa (3 tons), temperature of 80oC, and 3 minutes of pressing time, with the smallest hydrophobic barrier size (821 µm) being governed by laminate mask and parafilm dispersal from pressure and heat. Physical and biochemical properties were evaluated to substantiate the paper functionality for analytical devices. Wicking speed in the fabricated paper strips was slightly slower than that of non-processed paper, resulting from reducing paper pore size. A colorimetric immunological assay was performed to demonstrate the protein binding capacity of the paper-based device after exposure to pressure and heat from the fabrication. Moreover, mixing in two-dimensional paper-based device and flowing in a three-dimensional counterpart were thoroughly investigated, demonstrating that the paper device from this fabrication process is potentially applicable as analytical devices for biomolecule detection. Fast, easy, and inexpensive parafilm hot press fabrication presents an opportunity for researchers to develop paper-based analytical devices in resource-limited environments.

Abstract: Calcium-based catalysts are of a high interest for glycerol polymerization due to their high catalytic activity and large availability. However, their poor stability under reaction conditions is an issue. In the present study, we investigated the stability and catalytic activity of Ca-hydroxyapatites (HAps) as one of the most abundant Ca-source in nature. A stochiometric, a Ca-deficient and a Ca-rich HAps have been synthetized and tested as catalysts in the glycerol polymerization reaction. Deficient and stochiometric HAps exhibited a remarkable 100% selectivity to triglycerol at 15 % of glycerol conversion at 245 °C after 8 h of reaction in the presence 0.5 mol.% of catalyst. Moreover, under the same reaction conditions, Ca-rich HAp showed a high selectivity (88 %) to di- and triglycerol at a glycerol conversion of 27 %. Most importantly, these catalysts were unexpectedly stable towards leaching under the reaction conditions based on the ICP-OES results. However, based on the catalytic tests and characterization analysis performed by XRD, XPS, IR, TGA-DSC and ICP-OES, we found that HAps can be deactivated by the presence of the reaction products themselves, i.e., water and polymers.

A project-based module on Sustainable Development Goal number 5, Gender Equality, was im-plemented on 5 different groups of Business English students consisting of a total number of 62 students in higher education. The main purpose of this project was to raise awareness of this goal by means of a flipped method in which students were required to carry out some research on specific areas of the aforementioned goal and work in teams to elaborate oral presentations. Once their findings were shared in class, students were expected to answer a written questionnaire of open-ended questions which were part of a qualitative analysis. Results of this survey showed that not only 90% of the students gained in depth knowledge of this goal, but also 85% had built a positive attitude to take initiative and 80% were optimistic about future gender equality. Finally, 70% of students suggested further social action to curb the problem of gender discrimination. On the whole, the flipped classroom method of learning combined with project-based group work have proven to be an effective way to raise awareness of this goal, create a more positive attitude, in-crease their willingness to take action as well as widening their English lexical resources.

Object-Based Image Analysis (OBIA) has been successfully used to map slums. In general, the occurrence of uncertainties in producing geographic data is inevitable. However, most studies concentrated solely on assessing the classification accuracy and neglecting the inherent uncertainties. Our research analyses the impact of uncertainties in measuring the accuracy of OBIA-based slum detection. We selected Jakarta as our case study area, because of a national policy of slum eradication, which is causing rapid changes in slum areas. Our research comprises of four parts: slum conceptualization, ruleset development, implementation, and accuracy and uncertainty measurements. Existential and extensional uncertainty arise when producing reference data. The comparison of a manual expert delineations of slums with OBIA slum classification results into four combinations: True Positive, False Positive, True Negative and False Negative. However, the higher the True Positive (which lead to a better accuracy), the lower the certainty of the results. This demonstrates the impact of extensional uncertainties. Our study also demonstrates the role of non-observable indicators (i.e., land tenure), to assist slum detection, particularly in areas where uncertainties exist. In conclusion, uncertainties are increasing when aiming to achieve a higher classification accuracy by matching manual delineation and OBIA classification.

Web-Based GIS is a platform that deals with the representation, management and storage of locational information for real-time online retrieval, viewing and manipulations. Web-based GIS incorporate all the functions of information systems: gathering, storing, retrieving, visualizing and dissemination of spatial information on the Internet. In modern-day GIS serve as vital means to not only geo-referenced locational information that are been retrieved but also the development in web-based technologies as well as there involvements in decision making processes. In recent time the increased used of GIS on the Internet have totally transformed and made three distinct changes across our GIS environment. These are: (i) how are GIS data being accessed (ii) what are modes of its transmission and (iii) what available GIS functionalities are within the environment for analysis. This paper examines the applications and technologies associated with web-based GIS architectures with an emphasis on the internet GIS based structure and case studies of GIS Web-based applications in MapInfo, Microsoft Silverlight Technology and the ArcGIS Server using ArcGIS JavaScript API.

Mitochondrial pyruvate dehydrogenase complex (PDHC) is essential for the brain glucose and neurotransmitter metabolism, dysregulated in many pathologies. Using specific inhibitors of PDHC in vivo, we determine biochemical and physiological responses to PDHC dysfunction. Dose dependence of the responses to membrane-permeable dimethyl acetylphosphonate (Ac-PMe2) is non-monotonous. Primary decreases in glutathione and its redox potential, methionine and ethanolamine are alleviated with increasing PDHC inhibition, the alleviation accompanied by physiological changes. Comparison of 39 brain biochemical parameters after administration of four phosphinate and phosphonate analogs of pyruvate at a fixed dose of 0.1 mmol/kg reveals no primary, but the secondary changes, such as activation of 2-oxoglutarate dehydrogenase complex (OGDHC) and decreased levels of glutamate, isoleucine and leucine. The accompanying decreases in RMSSD of ECG and freezing time are most pronounced after administration of me-thyl acetylphosphinate and dimethyl acetylphosphonate. The levels of PDHA1 expression and phosphorylation, sirtuin 3 and total protein acetylation are not significantly changed by the PDHC inhibitors that affect the brain protein succinylation and glutarylation. Thus, decreased production of the tricarboxylic acid cycle substrate acetyl-CoA by inhibited PDHC is compen-sated by increased degradation of amino acids through the cycle with activated OGDHC, increas-ing total protein succinylation and decreasing anxiety indicators.

A significant number and range of challenges besetting sustainability can be traced to the actions and interactions of multiple autonomous agents (people mostly) and the entities they create (e.g., institutions, policies, social network) in the corresponding social-environmental systems (SES). To address these challenges, we need to understand decisions made and actions taken by agents, the outcomes of their actions, including the feedbacks on the corresponding agents and environment. The science of Agent-based Complex Systems—ACS science—has a significant potential to handle such challenges. The advantages of ACS science for sustainability are addressed by way of identifying the key elements and challenges in sustainability science, the generic features of ACS, and the key advances and challenges in modeling ACS. Artificial intelligence and data science promise to improve understanding of agents’ behaviors, detect SES structures, and formulate SES mechanisms.

Wearable assistant devices play an important role in daily life for people with disabilities. Those who are hearing impaired may face dangers while walking or driving on the road. The major danger is their inability to hear warning sounds from cars or ambulances. Thus, the goal of this study is to develop a wearable assistant device for the hearing impaired to recognize emergency vehicle sirens on the road using edge computing. An EfficientNet-based fuzzy rank-based ensemble model was proposed to classify seven audio sounds, including human vocalizations and emergency vehicle sirens. This model was embedded in an Arduino Nano 33 BLE Sense development board. The audio files were respectively obtained from the CREMA-D dataset and Large Scale Audio dataset of emergency vehicle sirens on the road, with a total number of 8756 files. The seven audio sounds included neutral vocalization, anger vocalization, fear vocalization, happy vocalization, car horn sound, siren sound, and ambulance siren sound. The audio signal was converted into a spectrogram by the short-time Fourier transform as the feature. When one of the car horns, sirens, or ambulance sirens was detected, the wearable assistant device presented alarms through vibration and messages on the OLED panel. The performances of the EfficientNet-based fuzzy rank-based ensemble model in offline computing achieved an accuracy of 97.1%, precision of 97.79%, sensitivity of 96.8%, and specificity of 97.04%. In edge computing, the results were an accuracy of 95.2%, precision of 93.2%, sensitivity of 95.3%, and specificity of 95.1%. Thus, the proposed wearable assistant device has the potential benefit of helping the hearing impaired avoid traffic accidents.

Graphene-based nanomaterials (GNMs), including graphene, graphene oxide, reduced graphene oxide, and graphene quantum dots, may have direct anticancer activity or be used as nanocarri-ers for antitumor drugs. GNMs usually enter tumor cells by endocytosis and can accumulate in lysosomes. This accumulation prevents drugs bound to GNMs from reaching their targets, sup-pressing their anticancer effects. A number of chemical modifications are made to GNMs to facili-tate the separation of anticancer drugs from GNMs at low lysosomal pH and to enable lysosomal escape of drugs. Lysosomal escape may be associated with oxidative stress, permeabilization of the unstable membrane of cancer cell lysosomes, release of lysosomal enzymes into the cytoplasm, and cell death. GNMs can prevent or stimulate tumor cell death by inducing protective autopha-gy or suppressing autolysosomal degradation, respectively. Furthermore, because GNMs prevent bound fluorescent agents from emitting light, their separation in lysosomes may enable tumor cell identification and therapy monitoring. In this review, we explain how the characteristics of the lysosomal microenvironment and the unique features of tumor cell lysosomes can be exploited for GNM-based cancer therapy.

This study was designed to extend the literature on multicomponent interventions for the children of deaf adults (CODA) population. This study used two evidence-based behavior intervention strategies: pre-session pairing (PSP) and independent group contingency (GC). These strategies have been successfully used to decrease off-task behavior in elementary school children with various abilities and diverse backgrounds. However, the research on multicomponent interventions has yet to examine their effects on the CODA population in inclusive classrooms. This study used a concurrent multiple baseline design across participants with an ABC sequence to examine teacher-implemented PSP with independent GC in reducing the off-task behavior of three CODAs in an inclusive classroom at a public elementary school. The results show that the intervention successfully decreased off-task behavior for all participating CODAs. The results suggest that CODAs can adapt to classroom rules and expectations when PSP and independent GC are systematically applied to them in classrooms.

Event-based vision is an emerging field of computer vision that offers unique properties such as asynchronous visual output, high temporal resolutions, and dependence on brightness changes to generate data. These properties can enable robust high-temporal-resolution object detection and tracking when combined with frame-based vision. In this paper, we present a hybrid, high-temporal-resolution, object detection and tracking approach, that combines learned and classical methods using synchronized images and event data. Off-the-shelf frame-based object detectors are used for initial object detection and classification. Then, event masks, generated per each detection, are used to enable inter-frame tracking at varying temporal resolutions using the event data. Detections are associated across time using a simple low-cost association metric. Moreover, we collect and label a traffic dataset using the hybrid sensor DAVIS 240c. This dataset is utilized for quantitative evaluation using state-of-the-art detection and tracking metrics. We provide ground truth bounding boxes and object IDs for each vehicle annotation. Further, we generate high-temporal-resolution ground truth data to analyze the tracking performance at different temporal rates. Our approach shows promising results with minimal performance deterioration at higher temporal resolutions (48 – 384 Hz) when compared with the baseline frame-based performance at 24 Hz.

The recent covid crisis has proven important lessons for academia and industry regarding digital reorganization. Among fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and over. Moreover, drug development is a costly and time-consuming business, and only a minority of approved drugs return the revenue that exceeds the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper will review the most significant research on artificial intelligence in the de novo drug design for COVID-19 pharmaceutical research.

Maternal-child care is one of the foundations of primary health care. Nurses’ competency skills they have been taught. Community awareness is an important part of preventive healthcare, and nurses must be aware of the factors that impact the health of the community. This study examines the effectiveness of lecture-based instructions in maternal and child care and its implications to students' social competency skills and community awareness in Nursing Colleges in Nueva Ecija, Philippines. The researcher uses survey questionnaire and employed the descriptive design where fifteen (15) nursing students and five (5) teachers were purposively selected. The findings revealed that the weighted mean for the effectiveness of lecture based instruction in maternal and child care is 3.91 with verbal description of “Effective”, the effects of lecture based instruction in maternal and childcare to students’ social competency skills and community awareness got the weighted mean of 3.87 and interpreted as “very satisfactory” and the effectiveness of actual community-based instruction is very effective with weighted mean of 4.25 and is higher compare to lecture based instruction. The results also revealed that students and teachers were challenged in lecture-based instruction in maternal and chi8ldcare during distance learning. Recommendations for the enhancement of lecture-based instruction in maternal and childcare in social competency skills and community awareness were also made.

Over the last decade, a significant literature has emerged that advocates the potential of different Additive manufacturing (AM) technologies and printable polymeric materials. Nevertheless, large scale printing and complex geometric shapes, with curvatures and non-planar layer deposition, are a challenging process for the traditional gantry-based machine. The 3 degrees of freedom cartesian configuration restricted their capability to planar layered printing and restricted part dimensions. To date, many researchers have used industrial robots to overcomes this limitation. This review gives the reader a good overview of the FDM technique due to its scalability, cost efficiency and a wide range of material printability. A strong emphasis is laid on the PLA and PLA-based composites as promising materials for the FDM process applications. The second part of this paper links the successful use of these materials in the traditional printing process to large scale printing using the robot-based FDM process. This survey presents representative setups for robot-based AM and works that have been used these setups for non-planar material deposition. Finally, we conclude this paper by identifying opportunities for realizing new functional capabilities by exploiting robot-based AM, and we also present the future trends in this area.

Saccharomyces cerevisiae are a phenotypically diverse species that adapt to a wide variety of environments by exploiting standing genetic diversity and selecting for advantageous mutations. Glyphosate and copper-based herbicides/ fungicides affect non-target organisms, these incidental exposures can impact microbial populations. In this study, glyphosate resistance was found in the historical collection of yeast which was collected over the last century, but only in yeast isolated after the introduction of glyphosate. The highest glyphosate-resistant yeasts were isolated from agricultural sites. However, herbicide application at these sites was not recorded. In an effort to assess glyphosate resistance and impact on non-target microorganisms, yeast were harvested from 15 areas with known herbicidal histories, including an organic farm, conventional farm, remediated coal mine, suburban locations, state park, and a national forest. Yeast representing 23 genera were isolated from 237 samples of plant, soil, spontaneous fermentation, nut, flower, fruit, feces, and tree material samples. Saccharomyces, Candida, Metschnikowia, Klyveromyces, Hanseniaspora, and Pichia were other genera commonly found across our sampled environments. Managed areas had less species diversity and at the brewery, only Saccharomyces and Pichia were isolated. A conventional farm growing RoundUp Ready™ corn had the lowest phylogenetic diversity and the highest glyphosate resistance. The mine was sprayed with multiple herbicides including a commercial formulation of glyphosate; however, the yeast did not have elevated glyphosate resistance. In contrast to the conventional farm, the mine was exposed to glyphosate only one year prior to sample isolation. Glyphosate resistance is an example of the anthropogenic selection of nontarget organisms.

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins and carbohydrates in their seeds, distinctly dominate modern agronomic practice. Indeed, these plants play an essential role in the food industry and fuel production. Therefore, the seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, not only seed development and germination, but also age- and stress-related alterations in seed vigor, longevity, nutritional value and safety can be addressed by a broad panel of analytical, biochemical and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes, accompanying plant development, senescence and response to biotic or environmental stress. Among individual methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. Here we discuss the main methodological approaches employed by seed proteomics in the context of physiological changes related to seed development, ageing and response to environmental stress.

Salmonella sp. is a globally prevalent organism responsible for causing salmonellosis, a foodborne illness. Salmonella Typhimurium represents a type of Salmonella sp. not associated with typhoid fever but capable of causing stomach and intestinal inflammation or severe infection. In the present study, 150 uncharacterized proteins of S. Typhimurium were randomly selected from UniProtKB and analyzed using TMHMM, PROSITE, STRING, DEG, and BLASTp. Results indicated that 32 uncharacterized proteins (21%) were predicted to be transmembrane proteins involved in various biological pathways. Among them, 30 transmembrane proteins were predicted to be essential and non-host homologous. This study's findings suggest their potential as drug targets against salmonellosis.

Proteins have the ability to adsorb on the surface of materials, such as soft contact lenses (SCLs), and can affect the hydrophobicity, roughness and surface properties of the contact lenses (CLs), which, in turn, can influence the friction between the lenses and the ocular surface. Excessive friction between contact lenses and the ocular surface can lead to discomfort for the wearer and may cause irritation or inflammation of the cornea, better known as corneal ulcers (keratitis). Bovine serum albumin (BSA) is often used as a standard protein in biocompatibility testing of materials, including contact lenses. One standard commercial contact lenses was tested under lubricated conditions to access the coefficient of friction (CoF), being the contact lubricated with a tear like fluid (TLF) solution containing six different concentrations of BSA. In all cases, a good linearity of the results of the friction force was verified, so the first friction law can be applied to determine the value of the coefficient of friction. It was found that friction increases with increasing protein concentration.

Enteroviruses (EV) are important pathogens causing human disease with various clinical manifestations. To date, treatment of enteroviral infections is mainly supportive since no vaccination or antiviral drugs are approved for their prevention or treatment. Here, we describe the antiviral properties and mechanisms of action of leucoverdazyls - novel heterocyclic compounds with antioxidant potential. The lead compound, 1a, demonstrated low cytotoxicity along with high antioxidant and virus-inhibiting activity. A viral strain resistant to 1a was selected, and the development of resistance was shown to be accompanied by mutation of virus-specific non-structural protein 2C. This resistant virus had lower fitness when grown in cell culture. Taken together, our results demonstrate high antiviral potential of leucoverdazyls as novel inhibitors of enterovirus replication and support previous evidence of an important role of 2C proteins in EV replication.

Recent advancements in artificial intelligence (AI) and deep learning have revolutionized the field of protein engineering, particularly in the area of de novo protein design. This review article explores the impact of AI-driven approaches on protein design, with a specific focus on the role of structure prediction neural networks, such as AlphaFold and RoseTTAFold. The article discusses the paradigm shift brought about by these networks, which have enabled the design of proteins with unique structures and functions that are not found in nature. The review covers various aspects of AI-driven protein design, including the use of protein language models to harness evolutionary information, the development of de novo protein design workflows utilizing deep learning, and the application of generative models like RFdiffusion and RoseTTAFold All-Atom. The article also highlights the successes and applications of AI-driven protein design across diverse domains, such as enzyme engineering, antibody design, and vaccine development. Additionally, the review identifies current challenges and future directions in the field, emphasizing the need to address limitations in modeling conformational dynamics and designing proteins for in vivo functionality. The article concludes by underscoring the potential of AI-driven protein design to transform various aspects of science and technology, while also acknowledging the importance of interdisciplinary collaboration and the development of robust pipelines for the validation and optimization of designed proteins. Overall, this comprehensive review serves as a valuable resource for researchers and practitioners interested in understanding the current state and future prospects of AI-driven protein design.

Peas are among the most widely consumed legumes and are of great benefit for human nutrition. Sowing and cultivation techniques are known to affect the yield and the quality of the seeds. Existing studies investigating the nutritional properties of the seeds from plants cultivated using different methods are continue to be of significant value. However, changes in the climate in recent years are presumed to have affected the optimum sowing dates for grain yield and quality. This study in-vestigates the effects of sowing peas at different sowing dates on the yield of the seed and on its nutrient content, as determined by certain quality traits (parameters). The experiment was con-ducted at the Aydin Adnan Menderes University Faculty of Agriculture in Turkey during the 2021-2022 and 2022-2023 pea production seasons. Specifically, it examined the yield of the seed (fresh/dry), its saponin and phenolic matter content and its amino acid composition in the case of five pea cultivars (Deren, Misya, Irmak, Karina, Local) sown at three different sowing times (November 15, November 30, December 15). The study found that the effects of sowing date on grain yield and quality characteristics were significant. However, the varieties' reactions to sowing dates were found to be different. The highest fresh seed yield (3.27 t ha-1) was obtained from samples sown at the second sowing date, while the highest dry yield (1.85 t ha-1) came from samples sown at the third sowing date. The cultivars also had a statistically significant effect on the yields. The highest fresh seed yields were obtained from the Misya (2.88 t ha-1) and Local (2.81 t ha-1) varieties, while the highest dry yields were obtained from samples of Local (1.76 t ha-1) and Irmak (1.73 t ha-1). In terms of sowing dates, the highest protein (27.75%) was obtained from the first sowing date, and the protein content decreased in the following dates. Misya was the cultivar from which the highest protein content (28.77%) was obtained. In the study, higher yields were obtained from the second and third sowing dates, while the first sowing time resulted in higher protein and amino acid composition. Similar to the protein content, the composition of almost all amino acids increased on the first sowing date. In addition, it was established that the saponin and phenolic substance contents of seeds varied with the sowing date.

Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantify the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was adopted for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, B-factor, beta structure proportion, roughness, and disordered regions proportion. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments.

PIM1is involved in critical cellular processes, playing a key role in the regulation of the cell cycle, apoptosis, transcriptional activation, and broader signal transduction pathways . The exploration of PIM1inhibitors, such as small molecules or antibodies, represents a promising avenue in cancer research for developing novel treatment strategiess. Its significance in oncogenic signaling has led to extensive research on PIM1 as a target in cancer studies. Docking studies have revealed a robust interaction between hypericin and PIM1, suggesting a strong binding affinity (-12.5 kcal/mol). This research aims to explore the molecular dynamics of the hypericin-PIM1 interaction, identifying potential binding sites and elucidating the impact on PIM1-mediated cellular processes, such as cell cycle regulation and apoptosis. The findings may contribute valuable insights into developing hypericin-based therapies targeting PIM1, paving the way for novel and effective strategies in cancer research.

Peptidoglycan hydrolases are enzymes that cleave the peptidoglycan of the bacterial cell wall, facilitating cell growth, cell division, and peptidoglycan turnover. Xanthomonas citri subsp. citri (X. citri), the causal agent of citrus canker, encodes an Escherichia coli M23 peptidase EnvC homolog. EnvC is a LytM factor required for septal peptidoglycan splitting and daughter cell separation. In this study we investigate how EnvC contributes to the virulence and cell separation of X. citri. We observed that disruption of the X. citri envC gene (ΔenvC) led to a reduction in virulence. Upon inoculation into leaves of Rangpur lime (Citrus limonia Osbeck), the X. citri ΔenvC mutant showed a delay in causing citrus canker symptoms compared with the wild-type X. citri strain. Mutant complementation restored the X. citri wild type phenotype. Subcellular localization confirmed that X. citri EnvC is a periplasmic protein. Moreover, the X. citri ΔenvC mutant exhibited elongated cells, indicative of a cell division defect. These findings support the role of EnvC in regulating virulence, cell wall organization, and cell division in X. citri.

Protein malnutrition is present in developing countries but also in developed ones, due by the actual eating habits with insufficient protein intake, in addition to this it is estimated by the Food and Agricultural Organization of the United Nations an increase of world population of 9.1 billion people in less those 30 years, posing the challenge of nourish the mankind. There are different strategies to afford this challenge, one of the most promising ones is to approach novel protein sources like plants, microorganisms, and insects from dry lands.

Cows produce saliva in very large quantities to lubricate and facilitate food processing. Estimates indicate an amount of 50-150 liter per day. Human saliva has previously been found to contain numerous antibacterial components, such as lysozyme, histatins, members of the S-100 family and lactoferrin to limit pathogen colonization. Cows are dependent of a complex microbial community in their digestive system for food digestion. We wondered how this would influence the content of their saliva. We therefore sampled saliva from five humans and both nose secretions and saliva from six cows and separated the saliva on SDS-PAGE gradient gels and analyzed the major protein bands by LC-MS/MS. The cow saliva was found to be dominated by a few major proteins only, the carbonic anhydrase 6, a pH stabilizing enzyme, and the short palate, lung and nasal epithelium carcinoma-associated protein 2A (SPLUNC2A), also named bovine salivary protein 30kDa (BSP30). This latter protein has been proposed to play a role in local antibacterial response by binding bacterial lipopolysaccharide (LPS) and inhibit bacterial growth, but may instead according to more recent data instead have primarily surfactant activity. Numerous peptide fragments of mucin-5B were also detected in the MS analysis. However, mucins stain poorly by the gel staining solution and they are large and have difficult to enter regular gels why their presence easily are overseen. Interestingly, no major band on gel was detected representing any of the antibacterial proteins indicating that cows may produce them at very low levels not to harm the microbial flora of their digestive system. The nose secretions of the cows primarily contained the odorant protein, a protein thought to be involved in enhancing the sensing of smell by the olfactory receptors to enhance the possibility to quickly sense potential poisonous food components. High levels of secretory IgA was also found in one sample of cow mouth drippings indicating a strong upregulation during an infection. The human saliva we more complex containing both secretory IgA, amylase, carbonic anhydrase 6, lysozyme, histatins and a number of other less abundant proteins.

Autophagy is a highly conserved self-degradation process involving the degradation and recycling of cellular components and organelles. Although the involvement of autophagy in metabolic changes during fruit ripening has been preliminarily demonstrated, the variations in autophagic flux and specific functional roles in fruit ripening remain to be elucidated. In this study, we analyzed the occurrence of autophagy during tomato fruit ripening. The results revealed differential expression of SlATG8 family member during tomato fruit ripening. Transmission electron microscopy observations and dansylcadaverine (MDC) staining confirmed the presence of autophagy at the cellular level in tomato fruits. Furthermore, the overexpression of SlATG8f induced the formation of autophagosomes, increased autophagic flux within tomato fruits, effectively enhanced the expression of ATG8 proteins during the color transition phase of fruit ripening, thereby promoting tomato fruit maturation. This overexpression also led to the accumulation of vitamin C (VC) and soluble solids while reducing acidity in the fruit. Collectively, our findings highlight the pivotal role of SlATG8f in enhancing tomato fruit ripening, providing insights into the mechanistic involvement of autophagy in this process. This research contributes to a better understanding of key factors regulating tomato fruit quality and offers a theoretical basis for tomato variety improvement.

The collective considerations presented here lead to a crucial question: What truly constitutes the primary public health challenge posed by SARSCoV-2 infection and its variants?The findings of Bowen et al.(1) and Noé et al.(4) have offered us new insights into the actual repercussions of SARSCoV-2 virus infections on public health. They unmistakably point to the late sequelae and complications arising as secondary effects of the viral infection, causing severe and long-term damage to global public health. Rather than the acute infection which has a very low mortality rate in the general population, as initially and commonly believed.

Lipases have tremendous potential for industrial use, particularly, those mostly active against water-insoluble substrates, such as triglycerides composed of long-chain fatty acids. However, in most cases, mutants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases, or through lid domain swapping. Here, we have improved the lipase character of a lipase, retrieved from the Marine Metagenomics MarRef Database and assigned to the Actinoalloteichus genus (WP_075743487.1), through site-directed mutagenesis and by substituting its lid domain (FRGTEITQIKDWLTDA) by the one of Rhizopus delemar (previously Rhizopus oryzae) lipase (FRGTNSFRSAITDIVF). Results demonstrated that the redesigned mutants gain activity against bulkier triglycerides such as glyceryl tridecanoate and tridodecanoate, olive oil, coconut oil, and palm oil. The absence of a residue in the new lid, present in the original lid, appears to be a key aspect to the increase in lipase character, although full activity recovery is only obtained with lid swapping.

Is HSP-27 an emerging marker of good prognosis in septic shock patients – a pilot study Objective To estimate the value of serum changes of C-reactive protein, procalcitonin, presepsin, heat shock protein 27 (HSP27) and neutrophil to lymphocyte ratio in assessing the prognosis in patients with septic shock (SS) treated in intensive care unit. Methods The SS was diagnosed and treated in accordance with the guidelines of the Surviving Sepsis Campaign. 37 selected adult patients with SS were included. Serum concentrations of biomarkers were measured at admission and daily for 4 consecutive days (time points T0,T1, T2, T3 and T4 respectively). The mortality rate was determined 28 days after admission. Patients were divided into survivor and non-survivor groups according to their mortality. The differences between the levels of biomarkers at the T0 and T4 time points were analyzed. Results The mean value of the SOFA score on admission was 11.7 ± 2.7, and the APACHE II scale 29.9 ± 6.85. Nine patients died. Univariate logistic analysis revealed that changes between T0 and T4 time points of presepsin, procalcytonin, and HSP27 were associated with prognosis. A multivariate Cox analysis showed that an increase in HSP27 on T4 was the only independent predictor of good prognosis in SS patients. The area under the receiver operating characteristics curve for HSP27 was 0.785. Kaplan–Meier analysis showed that the mortality was lower (p=0.014) in patients who had an increase in HSP27 on T4 compared to those whose serum HSP27 did not increase on T4. Conclusions The increase of HSP27 level on the 4th day predicts favorable outcome in SS patients.

Conclusive evidence that speci c long-term memory formation relies on den- dritic growth and structural synaptic changes has proven elusive. Connec- tionist models of memory based on this hypothesis are confronted with the so-called plasticity stability dilemma or catastrophic interference. Other fun- damental limitations of these models are the feature binding problem, the speed of learning, the capacity of the memory, the localisation in time of an event and the problem of spatio-temporal pattern generation. This paper suggests that the generalisation and long-term memory mechanisms are not correlated. Only the development and the improvement of the feature ex- tractors in the cortex involves structural synaptic changes. We suggest the long-term memory has a separate mechanism which involves protein synthe- sis to encode the information into the structure of these proteins. A model of memory should be capable of explaining the dierence between memorisation and learning. Learning has in our approach two dierent mechanisms. The generalisation in the brain is handled by the proper development of the links between neurons via synapses. The Hebbian learning rule could be applied only for this part of learning. Storing an internal ring pattern involves, in our approach, a new mechanism which puts the information regarding this ring pattern into the structure of special proteins in such a way that it can be retrieved later. The hypotheses introduced in this article includes a physiological assumption which has not been yet verifi ed because it is not currently experimentally accessible. Keywords: Waves, Protein Synthesis, Resonance, Long Term Memory Preprint submitted to Neural Networks

Duckweeds are the smallest flowering plants on Earth. They grow fast on water's surface and produce large amounts of biomass. Further, duckweeds display high adaptability, and species are found around the globe growing under different environmental conditions. In this work, we report the composition of 21 ecotypes of fourteen species of duckweeds belonging to the two sub-families of the group (Lemnoideae and Wolffioideae). It is reported the presence of starch and the composition of soluble sugars, cell walls, amino acids, phenolics, and tannins. These data were combined with literature data recovered from 85 publications to produce a compiled analysis that affords the examination of duckweeds as possible food sources for human consumption. We compare duckweeds compositions with some of the most common food sources and conclude that duckweed, which is already in use as food in Asia, can be an interesting food source anywhere in the world.

Cells that experience high levels of oxidative stress respond with the induction of antioxidant proteins through the activation of the transcription factor Nrf2. Nrf2 is negatively regulated by Keap1 which binds to Nrf2 to facilitate its ubiquitination and ensuing proteasomal degradation under basal conditions. Here, we study protein folding and misfolding in Nrf2 and Keap1 in yeast, mammalian cells, and purified proteins under oxidative stress conditions. Both Nrf2 and Keap1 are susceptible to protein misfolding and inclusion formation upon oxidative stress. We propose that the intrinsically disordered regions within Nrf2 and the high cysteine content of Keap1 contribute to their oxidation and the ensuing misfolding. Our work reveals previously unexplored aspects of Nrf2 and Keap1 regulation and dysregulation by oxidation-induced protein misfolding.

Nuclear protein of testis (NUT), a protein product of the NUTM1 gene (located on the long arm of chromosome 15) with highly restricted physiologic expression in post-meiotic spermatids, is the oncogenic driver of a group of emerging neoplasms when fused with genes involved in transcription regulation. Although initially identified in a group of lethal midline carcinomas in which NUT forms fusion proteins with bromodomain proteins, NUTM1-rearrangement has since been identified in tumors at non-midline locations, with non-bromodomain partners and with varied morphology. The histologic features of these tumors have also expanded to include sarcoma, skin adnexal tumors, and hematologic malignancies that harbor various fusion partners and are associated with markedly different clinical courses varying from benign to malignant. Most of these tumors have nondescript primitive morphology and therefore should be routinely considered in any undifferentiated neoplasm. The diagnosis is facilitated by the immunohistochemical use of the monoclonal C52 antibody, fluorescence in situ hybridization (FISH), and, recently, RNA-Sequencing. The pathogenesis is believed to be altered expression of oncogenes or tumor suppressor genes by NUT-mediated genome-wide histone modification. NUTM1-rearranged neoplasms respond poorly to classical chemotherapy and radiation therapy. Targeted therapies such as bromodomain and extraterminal domain inhibitor (BETi) therapy are being developed. This current review provides an update of NUTM1-rearranged neoplasms, focusing on the correlation between basic sciences and clinical aspects.

Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of the structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein-DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build in the nanoscale. This review focuses on the strategies deployed to create hybrid protein-DNA nanostructures. Here, we will discuss strategies such as polymerization, spatial directing and organizing, coating, rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein-DNA nanotechnology will open new avenues in the fabrication of nano-assemblies with unique functional applications and enrich the toolbox of bionanotechnology.

There are currently worldwide efforts to reduce sugar intake due to the various adverse health effects linked with the overconsumption of sugars. Artificial sweeteners have been used as an alternative to nutritive sugars in numerous applications; however, their long-term effects on human health remain controversial. This led to a shift in consumer preference towards non-caloric sweeteners from natural sources. Thaumatins are a class of intensely sweet proteins found in arils of the fruits of the West-African plant Thaumatococcus danielli. Thaumatins’ current production method through aqueous extraction from this plant and uncertainty of the harvest from tropical rainforests limits its supply while the demand is increasing. Despite successful recombinant expression of the protein in several organisms, no large-scale bioproduction facilities exist. We present preliminary process design, process simulation, and economic analysis for a large-scale (50 metric tons/year) production of thaumatin II variant by several different molecular farming platforms.

The experiment was conducted in three locations Jari, Chefa and Sirinka of Eastern Amhara to select the best performing varieties, in terms of biomass yield, chemical composition, haulm yield, seed yield and other agronomic characteristics of Glycine max (L.) Merrill grown under the rain- fed condition of lowland areas of Eastern Amhara in a randomized complete block design with tree replications. Twelve released soybean varieties were Afgat ,Belesa-95, Boshe , Cheri , Dhidhessa, Gishama , Gizo, Korme, Pawe-03, katta, Wegayen and Wollo were used as a treatments. The seeds were planted in 40 cm between rows and 10 cm between plants on a plot size of 3.2m*4m. Spacing between blocks and plots were 1 and 0.5m, respectively. The seed rate was 60 kg/ha and a fertilizer rate 100 kg/ha NPS was applied during seed planting. The combined analysis of variance over two years at location Jari for dry matter yield of varieties Afgat, Gizo, Pawe-03, Wogayen and Wollo were significantly higher as compared to other soybean varieties. The combined analysis across locations at Jari and Sirinka (2019-second year) showed that varieties Afgat, Gishama, Gizo, Pawe-03, Wogayen and Wollo had higher dry matter yield and varieties Gishama (3.97 t/ha), Gizo (3.60 t/ha), Pawe-03 (4.04 t/ha) and Wogayen (3.36 t/ha) had higher haulm yield as compared with other varieties. The combined analysis across locations at Jari and Sirinka (2019) showed that varieties Pawe-03(2951 kg/ha), Gizo (2862 kg/ha), Afgat (2859 kg/ha), Gishama (2654 kg/ha),Wollo (2461 kg/ha) and Wogayen (2404 kg/ha) had higher seed yield as compared with other varieties. The variety Wollo gave higher crud protein content in two locations (Jari and Sirinka) .Therefore, varieties Afgat, Pawe-03 and Wollo were recommends for the given areas of Jari , Chefa, Sirinka and could be produced in similar environments for the best of produced optimal amount of dry matter, haulm and seed yield and good protein supplement for production of ruminants.Thus, further researches will be needed to investigate on the utilization of livestock.

In this paper, the effects of different food-grade enzymes on the antigenicity of casein (CN), β- lactoglobulin (β-LG) and ɑ-lactalbumin (ɑ-LA) in natural cow milk were studied. The degree of hydrolysis (DH), SDS-PAGE and molecular mas (MW) distribution of cow milk (CM) hydrolysates was assessed. Additionally, the residual antigenicity of CM hydrolysates was evaluated by using ELISA and western blotting with anti-CN, anti-β-LG and anti-ɑ-LA rabbit polyclonal antibody. The results showed that Alcalase and Protamex hydrolysis could efficiently reduce the antigenicity of CN, β-LG, ɑ-LA, showed a higher DH and the loss of density of CM proteins, as indicated by SDS-PAGE. The increasing of the low MW (<3 kDa) in CM hydrolysates was also presented. It was also found that Protamex, Alcalase could be more efficiently hydrolyzed major allergenic of CM than other enzymes for the development of hypoallergenic cow milk. Our research will lay a theoretical foundation for the study of hypoallergenic cow milk.

For its microtubule-binding properties, the expression level of the neurodegeneration-associated protein Tau is pondered as a potential modifier of cancer resistance to chemotherapy since decades. Indeed, Tau binds microtubules at the same site as taxanes, a class of chemotherapeutic drugs designed to stabilize the microtubule network in order to stall cell division and to induce tumor cell death. Whilst independent studies report the association between low Tau expression and superior taxane response, the data were refused by a meta-analysis, suggesting interference of other parameters. Unpredictably, Tau expression level was identified as a prognostic cancer marker, whereby its positive or negative predictive value for survival depended on the cancer type. With recent experimental evidence linking Tau to P53 signaling, DNA stability and protection and to the implication of Tau in cancer is strengthened. The identification of a role of Tau at the interface between two major aging-related disorder families, neurodegeneration and cancer, offers clues for the epidemiological observation inversely correlating these disorders. Elucidating how Tau is mechanistically implicated in cellular pathways common to these devastating illnesses may extend the Tau-targeting therapeutic opportunities to cancer.

Single cell proteins are the dead dried cells of microorganisms or purified protein isolated from microorganism’s cell culture, used as a food supplement to humans’ food and animals feed. World suffer from malnutrition particularly developing countries, due to rapid increase in population, increased the demand for protein and nutrients requirement. Bacteria is potential microorganism for SCP production due to high protein content, fast generation time, bio-active secondary metabolites production and can grow on various substrates. Actinobacteria species and strain have capability to produce biological active compounds, produced about two-thirds of antibiotics available in the market, actively used as antibiotics, antiprotozoal, antifungal, antiviral, anticancer, anticholesterol, antihelminth and immunosuppressant. Actinomycetes can be used as probiotic as well as single cell protein that will deal with antibiotic as well as protein source.

Purpose: Pandemic Novel Coronavirus (SARS-CoV-2) has emerger centered from wuhan, China. Structurally homologous spike protein of SARS-CoV-2 receptor is taxonomically homologous with SARS-Cov and SARS associated bat coronavirus. Still now scientists are trying to find out proper vaccine and treatments for this disease. Methods: Systematically we modeled and compared the structure of SARS-CoV-2 spike protein along with Bat Cov, Bat SARS Cov and SARS Cov Urbani. S1 and S2 unit of the coronavirus (SARS-CoV-2) are attached with ACE2 and furin, here we docked 5 Ca+ chelating drugs with these two proteins. Results: Structural comparison with all these spike proteins revealed that less significant but not negligible difference exists among them. Inserted stable nucleotide sequences and corresponding surface exposed peptidal region may be considered as epitope. Docking result with Toxicokinetics and half life of Penicillamine can effectly inhibit the attachment site of spike protein of coronavirus (SARS-CoV-2). Conclusions: Docking summery and the pharmacokinetics with toxicokinetics index recommend that Penicillamine can able to inhibit the infection of SARS-CoV-2.

Both in lung adenocarcinoma (LUAD) and severe acute respiratory syndromes (SARS) uncontrolled inflammation could be detected in lung tissue. Whether the similarity mechanism exists is still unknown. PDZ-binding motif (PBM) in SARS-CoV E protein has been demonstrated as virulence factor induce inflammation storm. Study function of PBM in LUAD is significant for mechanism exploration of carcinogenesis mediated by SARS-CoV. To identify gene expression fluctuation induced by PBM, a microarray sequencing data of lung tissue infected by wild type (SARS-CoV-E-wt) and recombinant virus (SARS-CoV-E-mutPBM) was analysis followed by functional enrichment analysis. To understand the role of screened specific genes in LUAD, overall survival and immune correlation were calculated. A total of 12 genes (MAPK1, PRKCA, FGFR4, KDR, PTPRD, BCL2L15, UBD, MAMDC2, LTBP4, PTPRB, LGI3 and ITGA8) might participate in initial and development stage of LUAD through expression variation and mutation. Meanwhile, a total of 12 genes (CARHSP1, EIF4E2, HMGA1, IL1R2, MAGOHB, PVR, ADCY9, ELF5, ESYT3, SCML4, SECL14L4 and THRA) could lead to poorer prognosis via dysregulation. In addition, MAMDC2 and ITGA8 down-regulated by PBM could also alter prognosis. Though the conservative PBM (-D-L-L-V-) could be found at the end of carboxyl terminal in multi E proteins of coronaviruses, the specific function of each one depend on the whole amino acid sequence simultaneously. In conclusion, PBM of SARS-CoV E protein could promote carcinogenesis of LUAD by dysregulating important gene expression profiles followed by influence immune response and overall prognosis. The results in present study also provided reference for the therapy of SARS-CoV-2 in LUAD patients.

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Considering its broad modeling capabilities, Rosetta consistently ranks highly when compared to other leading methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of scientists at more than 60 institutions, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss the methods developed in the last five years, involving the latest protocols for structure prediction, protein–protein and protein–small molecule docking, protein structure and interface design, loop modeling, the incorporation of various types of experimental data, and modeling of peptides, antibodies and other proteins in the immune system, nucleic acids, non-standard amino acids, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the ­­software. Rosetta is available at www.rosettacommons.org.

Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that was used in the current study. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB and p38 indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein-ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave an insight of cyclosaplin as a potential apoptosis inducer and protein kinase inhibitor.

Proper regulation of microtubules (MTs) is critical for the execution of diverse cellular processes, including mitotic spindle assembly and chromosome segregation. There are a multitude of cellular factors that regulate the dynamicity of MTs and play critical roles in mitosis. Members of the Kinesin-8 family of motor proteins act as MT-destabilizing factors to control MT length in a spatially and temporally regulated manner. In this review, we focus on recent advances in our understanding of the structure and function of the Kinesin-8 motor domain, and the emerging contributions of the C-terminal tail of Kinesin-8 proteins to regulate motor activity and localization.

The study was done to determine the effect of supplementing different forms of L-methionine (L-Met) and acetate on protein synthesis in immortalized bovine mammary epithelial cell line (MAC-T Cell): Control, L-Met, conjugated L-Met and acetate (CMA), and non-conjugated L-Met and Acetate (NMA). Protein synthesis mechanism was determined by omics method. NMA group had the highest protein content in the media and β-casein mRNA expression levels (P < 0.05). The number of upregulated and downregulated proteins observed were 77 and 62 in CMA group and 50 and 81 in NMA group from 448 proteins, respectively (P < 0.05). NMA and CMA treatments stimulated pathways related to protein and energy metabolism (P < 0.05). Metabolomic analysis also revealed CMA and NMA treatments resulted in increases of several metabolites (P < 0.05). In conclusion, NMA treatment increased protein concentration and expression level of β-casein mRNA in MAC-T cells compared to CMA.

Sub-micron o/w emulsions coated with chitosan have been used for drug delivery, quorum sensing inhibition and vaccine development. To study interactions with biological systems, nanocapsules have been fluorescently labelled in previous works, but it is often difficult to distinguish the released label from intact nanocapsules. In this study, we present advanced labelling strategies based on FRET measurements for chitosan-coated nanocapsules and investigate their dissolution and degradation. We used FRET measurements of nanocapsules loaded with equimolar concentrations of two fluorescent dyes in their oily core and correlated them with DLS count rate measurement and absorbance measurements during their disintegration by dissolution. Using count rate measurements, we also investigated the enzymatic degradation of nanocapsules using pancreatin and how protein corona formation influences their degradation. Of note, nanocapsules dissolved in ethanol, where FRET decreased simultaneously with count rate, and absorbance caused by nanocapsule turbidity, indicating increased distance between dye molecules after their release. Nanocapsules were degradable by pancreatin in a dose dependent manner, and showed a delayed enzymatic degradation after protein corona formation. We present here novel labelling strategies for nanocapsules that allow us to judge their status and an in vitro method to study nanocapsule degradation and the influence of surface characteristics.

Brevibacillus laterosporus (Bl) is a Gram-positive and spore-forming bacterium belonging to the Brevibacillus brevis phylogenetic cluster. Globally, insect pathogenic strains of the bacterium have been isolated, characterised, and some activities patented. Two isolates, Bl 1821L and Bl 1951, exhibiting pathogenicity against the diamondback moth and mosquitoes, are under development as a biopesticide in New Zealand. However, due to the suspected activity of putative antibacterial proteins (ABPs), the endemic isolates often grow erratically. Various purification methods including size exclusion chromatography, sucrose density gradient centrifugation, polyethylene glycol precipitation, and ammonium sulphate precipitation employed in this study enabled the isolation of two putative antibacterial proteins of ~30 kD and ~48 kD from Bl 1821L and one putative antibacterial protein of ~30 kD from Bl 1951. Purification of the uninduced cultures of Bl 1821L and Bl 1951 also yielded the protein bands of ~30 kD and ~48 kD on SDS-PAGE which indicated their spontaneous induction. Disc diffusion assay was used to determine the antagonistic activities of the putative ABPs. Subsequent transmission electron microscope (TEM) examination of purified putative antibacterial protein-containing solution showed the presence of encapsulin (~30 kD) and polysheath (~48 kD) like structures. Although only the ~30 kD protein was purified from Bl 1951, both structures were seen in this strain under TEM. Furthermore, while assessing the antibacterial activity of some fractions of Bl 1951 against Bl 1821L in size exclusion chromatography method, population of Bl 1821L persister cells was noted. Overall, this work added a wealth of knowledge for the purification of the HMW proteins (bacteriocins) of the Gram-positive bacteria including Bl.

The pharmaceutical market consists mainly of chemical and biological drugs. These drugs act on different types of targets and have distinct pharmacological properties. Generally, chemical drugs bind to the active site of target enzymes and easily penetrate the cell membrane owing to their small size; however, biological drugs can bind to the protein–protein interaction site but are less stable due to their protein properties. Cyclic peptides possess the pharmacological merits of both chemical and biological drugs, such as the ability to bind to the protein–protein interaction site and penetrate cell membranes. In this study, we developed a simple two-step system to generate a cyclic peptide library using the split intein of Npu DnaE and Gateway cloning. The first step is the PCR of Ready-to-use(R) template DNA having the coding sequences of random cyclic peptides between two split intein elements NpuC and NpuN and the recombination recognition site of Gateway cloning. The second step is the transformation of the PCR products via Gateway cloning to produce colonies with expression vectors to produce cyclic peptides comprising random amino acid sequences. The expression vectors in randomly chosen transformed colonies were confirmed to have random cyclic peptide sequences and all the clones, except ones having a stop codon in the cyclic peptide coding region, showed the expected protein splicing result. This simple two-step system for bacterial expression systems may be modified to suit various expression systems for cell-based assays.

Acetylcholine (ACh) is the best one characterized neurotransmitter. Its central roles in the cholinergic areas and central nervous system (CNS) and peripheral (PNS) synapses are well known. It was the first molecule identified as a neurotransmitter and appears to be phylogenetically the oldest one signaling molecules. ACh was detected in bacteria, protozoa, fungi, algae and primitive plants, indicating that the cholinergic system was widely distributed in living organisms before its appearance in the nervous system. The autonomous nervous system (ANS) is an integral part animal kingdom history. It determines fight-escape reactions as well as outlining the vital and cognitive functions bio-organization rhythms. The virus (Covid-19) extraneous effects acting on it could help to better understand its functions. The Blast results show some factors like protein that can be implicated such as bungaro-toxins, phospholipase A2 and the similar prothrombin activator protein. A positive correlation with different toxins is obtained and the Covid-19 double pathogenic mechanism theory is proposed. The process allows us to outline the possibility about toxic-like factors presence.

Myocardial infarction, more commonly known as heart attack, is a huge health problem around the world. It is a result of inadequate blood supply to certain parts of the heart and death of heart muscle cells in that region. Although it has been around for a long time, newer and newer ways of probing myocardial infarction is being followed. Bioinformatics and Systems Biology are relatively recent fields to try to give new insights into myocardial infarction. Following the footsteps of others, this in silico study has tried to chime in on the investigation into myocardial infarction. The study began with the gene expression omnibus dataset uploaded to the NCBI from a whole-genome gene expression analysis carried out at Mayo Clinic in Rochester, Minnesota. From the dataset, differentially expressed genes following first-time myocardial infarction were identified and classified into up-regulated and down-regulated ones. Gene Set Enrichment Analysis (GSEA) was carried out on the up-regulated genes which were statistically significant and corresponded with the NCBI generated annotations. Protein-Protein Interaction Network for these genes was constructed. GSEA revealed 5 transcription factors, 5 microRNAs and 3 pathways significantly associated with them. From the Protein-Protein Interaction Network, 6 key proteins (hub nodes) have been identified. These 6 proteins may open a new window of opportunity for the discovery/design of new drugs for mitigating the damage caused by myocardial infarction.

At the molecular level, aging is often accompanied by dysfunction of stress-induced membrane-less organelles (MLOs) and changes in their material state. In this work, we analyzed the proteins included in the proteome of stress granules (SGs) and P-bodies for their tendency to transform the material state of these MLOs. Particular attention was paid to proteins whose gene expression changes during replicative aging. It was shown that the proteome of the studied MLOs practically does not differ in the analyzed characteristics and consists of completely or partially intrinsically disordered proteins, 30 - 40% of which are potentially capable of liquid-liquid phase separation (LLPS). At the same time, the proportion of proteins capable of spontaneous LLPS is relatively small, which indicates the leading role of nucleic acids in the biogenesis of these membrane-less organelles. Proteins whose gene expression changes during the transition of human cells to a senescent state make up about 20% of the studied proteomes. There is a statistically significant increase in the number of positively charged proteins in both datasets studied compared to the complete proteomes of these organelles. An increase in the relative content of DNA-, but not RNA-binding proteins, was also found in the stress-granules dataset with senescence-related processes. Among SG proteins potentially involved in senescent processes, there is an increase in the abundance of potentially amyloidogenic proteins compared to the whole proteome. The hnRPDL protein has the highest degree of disorder and highest propensity for LLPS among such proteins, which allows us to consider it as “potentially dangerous.” Proteins common to SGs and P bodies, potentially involved in processes associated with senescence, form clusters of interacting proteins. The largest cluster is represented by RNA-binding proteins involved in RNA processing and translation regulation. These data indicate that SG proteins, but not proteins of P-bodies, are more likely to transform the material state of MLOs. Furthermore, these MLOs can participate in processes associated with aging in a coordinated manner.

This paper presents an in-depth contextualized tutorial on Agricultural IoT (Agri-IoT), covering the fundamental concepts, assessment of routing architectures and protocols, and performance optimization techniques via systematic survey and synthesis of related literature. The negative impacts of climate change and the increasing global population on food security and unemployment threats have motivated the adoption of the wireless sensor network (WSN)-based Agri-IoT as an indispensable underlying technology in precision agriculture and greenhouses to improve food production capacities and quality. However, most related Agri-IoT testbed solutions have failed to achieve their performance expectations due to the lack of an in-depth and contextualized reference tutorial that provides a holistic overview of communication technologies, routing architectures, and performance optimization modalities based on users’ expectations. Thus, although IoT applications are founded on a common idea, each use case (e.g., Agri-IoT) varies based on specific performance and users expectations as well as its technological, architectural, and deployment requirements. Likewise, the agricultural setting is a unique and hostile area where conventional IoT technologies do not apply, hence the need for this tutorial. Consequently, this tutorial addresses these via the following contributions: (1) a systematic overview of the fundamental concepts, technologies, and architectural standards of WSN-based Agri-IoT, (2) an evaluation of the technical design requirements of a robust, location-independent, and affordable Agri-IoT, (3) a comprehensive survey of the benchmarking fault tolerance techniques, communication standards, routing and medium access control (MAC) protocols, and WSN-based Agri-IoT testbed solutions, and (4) an in-depth case study on how to design a self-healing, energy-efficient, affordable, adaptive, stable, autonomous, and cluster-based WSN-specific Agri-IoT from a proposed taxonomy of multi-objective optimization (MOO) metrics that can guarantee an optimized network performance. Furthermore, this tutorial established new taxonomies of faults, architectural layers, and MOO metrics for cluster-based Agri-IoT (CA-IoT) networks and a 3-tier objective framework with remedial measures for designing an efficient associated supervisory protocol for cluster-based Agri-IoT networks.

Driven by environmental sustainability concerns, the integration of biobased components in curtain wall systems is gaining traction in both research and the construction market. This paper explores the development and validation of a bio-based façade system within the Basajaun H2020 project. The project aimed to demonstrate the feasibility of introducing environmentally friendly bio-based components into the mature curtain wall façade industry. The paper focuses on identifying technological solutions for replacing key components such as profiles, insulation, and the tightness system with bio-based and less environmental impact alternatives presenting the results achieved in the façade system design of the Basajaun project funded by European Union. These solutions aimed at creating a bio-composite-based curtain wall façade that adheres to current building envelope standards and normative; to implement diverse façade typologies for vision panels, opaque sections, and integrated windows; to engineer the prefabrication process for industrialization, enabling wider market replication and simplified transport and installation. The results demonstrate that the Basajaun façade successfully integrates selected components and meets the performance requirements set by regulations. However, questions remain regarding the workability of bio-based profiles as a commercially viable, ready-to-market solution that can replace traditional aluminum profiles in the curtain wall façade industry.

This review aims to consolidate varied information regarding Port Scanning, and examine the tools, techniques, and detection algorithms used. It explores TCP SYN, Full TCP, UDP, and stealth scans, and shows their functions and abilities. Paired with these techniques, it also shows the tools that they can be used by, such as NMap, Zmap, and MASSCAN. It discusses the various detection techniques such as Signature and Anomaly based detection, and discusses the real world impact of this technology, while commenting on the legal and ethical issues posed.

This study reports the synthesis and characterization of novel per-fluorinated organic polymers with azo- and azomethine-based linkers using nucleophilic aromatic substitution. The polymers reveal variations in the fluorine content via the incorporation of decafluorobiphenyl and hexafluorobenzene linkers, which enhanced their hydrophobic nature. The rich fluorine polymers were slightly soluble in THF and have shown molecular weights between 4886 to 11948 g/mol. All polymers exhibit thermal stability in the range of 350-500°C, with varying thermal stability depending on the fluorine and nitrogen content. Conjugation of the polymers was confirmed through changes in the UV-Vis spectra, with a hypsochromic shift observed in all cases, more pronounced in azo-based fluorinated chains due to H-bonding on the nitrogen sites, chain conformations, and planarity. The optical band gap (Eg) of the polymers was determined from the UV-Vis data, with the Eg values of the azo-based fluorinated polymers being 1 eV higher than those of their corresponding linkers. The cross-linking formation was characterized by porosity measurements, with the azo-based polymer exhibiting the highest surface area of 770 m²/g with a pore volume of 0.35 cm³/g, while the open-chain azomethine-based polymer exhibited the lowest surface area of 285 m²/g with a pore volume of 0.0872 cm³/g. Porous structures with varied hydrophobicities were investigated as adsorbents for separating water-benzene and water-phenol mixtures and selectively binding methane/carbon dioxide gases from the air. The most hydrophobic polymers containing the decafluorbiphenyl linker were suitable for benzene separation, while the best methane uptake values were 6.14 and 3.46 mg/g for DAB-Z-1O and DAB-A-1O, respectively. DAB-Z-1h, with the highest surface area and rich in nitrogen sites, exhibited the highest CO₂ uptake at 298 K (17.25).

G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. 3D pharmacophore models are powerful computational tools in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and elucidation of ligand-receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning will be highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.

To delve into the structure-function relationship of transmembrane proteins (TMPs), robust protocols are needed to produce them in a pure, stable, and functional state. Among all hosts that express heterologous TMPs, E. coli has the lowest cost and fastest turnover. However, many of the expressed in E. coli TMPs are misfolded. Several strategies have been developed to either direct the foreign TMPs to E. coli’s membrane or retain them in a cytosolic soluble form to overcome this deficiency. Here, we summarize protein engineering methods to produce chimera constructs of the desired TMPs fused to either signal peptide or precursor maltose binding protein (pMBP) to direct the entire construct to the periplasm, therefore depositing the fused TMP in the plasma membrane. We further describe strategies to produce TMPs in soluble form by utilizing N-terminally fused MBP without signal peptide. Depending on its N- or C-terminus location, a fusion to apolipoprotein A-I can either direct the TMP to the membrane or shield the hydrophobic regions of the TMP, maintaining the soluble form. Strategies to produce G-protein coupled receptors, TMPs of Mycobacterium tuberculosis, HIV-1 Vpu, and other TMPs are discussed. This knowledge could increase the scope of TMPs’ expression in E. coli.