Earing Prediction of AA5754-H111 (Al-Alloy) with Linear Transformation-Based Anisotropic Drucker Yield Function under Non-Associated Flow Rule (Non-AFR).

The yield behavior of aluminum alloy 5754-H111 under different stress conditions for three kinds of plastic work is studied using an anisotropic Drucker model. It is found that when the plastic work is 30 MPa, the anisotropic Drucker model has the most accurate prediction. Comparing the Hill48 and Yld91 models with the Drucker model, the results show that both the anisotropic Drucker and Yld91 models can accurately predict the yield behavior of the alloy. Cylinder drawing finite element analysis is performed under the AFR, but it is not possible to accurately predict the position and height of earing appearance. The anisotropic Drucker model is used to predict the earing behavior under the non-AFR, which can accurately predict the earing phenomenon. Numerical simulation is conducted using three different combinations of yield functions: the anisotropic yield function and the anisotropic plastic potential function (AYAPP), the anisotropic yield function and the isotropic plastic potential function (AYIPP), and the isotropic yield function and the anisotropic plastic potential function (IYAPP). It is concluded that the influence of the plastic potential function on predicting earing behavior is more critical than that of the yield function.

Mix-match synthesis of nanosynbiotics from probiotics and prebiotics to counter gut dysbiosis via AI integrated formulation profiling.

Antibiotics, improper food, and stress have created a dysbiotic state in the gut and almost 81% of the world's population has been affected due to the pandemic of COVID-19 and the prevalence of dengue virus in the past few years. The main intent of this study is to synthesize nanosynbiotics as nu traceuticals by combining probiotics, and prebiotics with nanoformulation. The effectiveness of the nanosynbiotics was evaluated using a variety of Nutra-pharmacogenetic assays leading to an AI-integrated formulation profiling was assessed by using machine learning methods. Consequently, Acetobacter oryzoeni as a probiotic and inulin as a prebiotic has been chosen and iron-mediated nanoformulation of symbiotic is achieved. Nanosynbiotics possessed 89.4, 96.7, 93.57, 83.53, 88.53% potential powers of Nutra-pharmacogenetic assays. Artificial intelligent solid dispersion formulation of nanosynbiotics has high dissolution, absorption, distribution, and synergism, in addition, they are non-tox, non-allergen and have a docking score of - 10.83 kcal/mol, implying the best interaction with Pregnane X receptor involved in dysbiosis. The potential of nanosynbiotics to revolutionize treatment strategies through precise targeting and modulation of the gut microbiome for improved health outcomes and disease management is promising. Their transformational influence is projected to be powered by integration with modern technology and customized formulas. Further in-vivo studies are required for the validation of nanosynbiotics as nutraceuticals.

Enhancing chromium resistance and bulb quality in onion (Allium cepa L.) through copper nanoparticles and possible health risk.

Chromium (Cr) is a toxic metal in soil-plant system, hence causing possible health risks prominently in the areas with forgoing industrial activities. Copper nanoparticles (Cu NPs) have been reported as an excellent adsorbent for pollutants. Therefore, this study investigates how copper nanoparticles enhance onion growth while decreasing chromium uptake in onion plants. Additionally, it examines the potential health risks of consuming onion plants with elevated chromium levels. The results demonstrated that the addition of CuNPs at 15 mg kg-1 significantly improved the plant height (48%), leaf length (37%), fresh weight of root (61%), root dry weight (70%), fresh weight of bulb (52%), bulb dry weight (59%), leaves fresh weight (52%) and dry weight of leaves (59%), leaf area (72%), number of onion leaves per plant (60%), Chl. a (42%), chl. b (36%), carotenoids (40%), total chlorophyll (40%), chlorophyll contents SPAD value (56%), relative water contents (35%), membrane stability index (16%), total sugars (25%), crude protein (21%), ascorbic acid (19%) and ash contents (64%) at 10 mg kg-1 Cr. Whereas, maximum decline of Cr by 46% in roots, 68% in leaves and 92% in bulb was found with application of 15 mg kg-1 of Cu NPs in onion plants under 10 mg kg-1 Cr toxicity. The health risk assessment parameters of onion plants showed minimum values 0.0028 for average daily intake (ADI), 0.001911 for Non-cancer risk (NCR), and 0.001433 for cancer risk (CR) in plants treated with Cu NPs at 15 mg kg-1 concentration grown in soil spiked with 10 mg kg-1 chromium. It is concluded that Cu NPs at 15 mg kg-1 concentration improved growth of plants in control as well as Cr contaminated soil. Therefore, use of Cu NPs at 15 mg kg-1 concentration is recommended for improving growth of plants under normal and metal contaminated soils.

Designing an mRNA Vaccine against P. jirovecii Involved in Fatal Pneumonia Infections via Comparative Proteomics and Reverse Vaccinology Approaches.

BACKGROUND: Pneumocystis jirovecii is the most emerging life-threating health problem that causes acute and fatal pneumonia infection. It is rare and more contagious for patients with leukemia and immune-deficiency disorders. Until now there is no treatment available for this infection therefore, it is needed to develop any treatment against this pathogen. METHODS: In this work, we used comparative proteomics, robust immune-informatics, and reverse vaccinology to create an mRNA vaccine against Pneumocystis jirovecii by targeting outer and transmembrane proteins. Using a comparative subtractive proteomic analysis of two Pneumocystis jirovecii proteomes, a distinct non-redundant Pneumocystis jirovecii (strain SE8) proteome was chosen. Seven Pneumocystis jirovecii transmembrane proteins were chosen from this proteome based on hydrophilicity, essentiality, virulence, antigenicity, pathway interaction, protein-protein network analysis, and allergenicity. OBJECTIVE: The reverse vaccinology approach was used to predict the immunogenic and antigenic epitopes of major histocompatibility complex (MHC) I, II and B-cells from the selected proteins on the basis of their antigenicity, toxicity and allergenicity. These immunogenic epitopes were linked together to construct the mRNA-based vaccine. To enhance the immunogenicity, suitable adjuvant, linkers (GPGPG, KK, and CYY), and PRDRE sequences were used. RESULTS: Through predictive modeling and confirmation via the Ramachandran plot, we assessed secondary and 3D structures. The adjuvant RpfE was incorporated to enhance the vaccine construct's immunogenicity (GRAVY index: -0.271, instability index: 39.53, antigenicity: 1.0428). The physiochemical profiling of vaccine construct was predicted it an antigenic, efficient, and potential vaccine. Notably, strong interactions were observed between the vaccine construct and TLR-3/TLR-4 (-1301.7 kcal/mol-1 and -1374.7 kcal/mol-1). CONCLUSIONS: The results predicted that mRNA-based vaccines trigger a cellular and humoral immune response, making the vaccine potential candidate against Pneumocystis jirovecii and it is more suitable for in-vitro analysis and validation to prove its effectiveness.

Revolutionizing the probiotic functionality, biochemical activity, antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H via in-vitro and in-silico approaches.

This study presents a comprehensive genomic exploration, biochemical characterization, and the identification of antibiotic resistance and specialty genes of Pediococcus acidilactici BCB1H strain. The functional characterization, genetic makeup, biological activities, and other considerable parameters have been investigated in this study with a prime focus on antibiotic resistance and specialty gene profiles. The results of this study revealed the unique susceptibility patterns for antibiotic resistance and specialty genes. BCB1H had good in vitro probiotic properties, which survived well in simulated artificial gastrointestinal fluid, and exhibited acid and bile salt resistance. BCB1H didn't produce hemolysis and had certain antibiotic sensitivity, making it a relatively safe LAB strain. Simultaneously, it had good self-coagulation characteristics and antioxidant activity. The EPS produced by BCB1H also had certain antioxidant activity and hypoglycemic function. Moreover, the genome with a 42.4 % GC content and a size of roughly 1.92 million base pairs was analyzed in the genomic investigations. The genome annotation identified 192 subsystems and 1,895 genes, offering light on the metabolic pathways and functional categories found in BCB1H. The identification of specialty genes linked to the metabolism of carbohydrates, stress response, pathogenicity, and amino acids highlighted the strain's versatility and possible uses. This study establishes the groundwork for future investigations by highlighting the significance of using multiple strains to investigate genetic diversity and experimental validation of predicted genes. The results provide a roadmap for utilizing P. acidilactici BCB1H's genetic traits for industrial and medical applications, opening the door to real-world uses in industries including food technology and medicine.

Redefining a new frontier in alkaptonuria therapy with AI-driven drug candidate design via in- silico innovation.

A rare metabolic condition called alkaptonuria (AKU) is caused by a decrease in homogentisate 1,2 dioxygenase (HGO) activity due to a mutation in homogentisate dioxygenase (HGD) gene. Homogentisic acid is a byproduct of the catabolism of tyrosine and phenylalanine that darkens the urine and accumulates in connective tissues which causes an agonizing arthritis. Employing the use of deep learning artificial intelligence (AI) drug design, this study aims to alleviate the current toxicity of the AKU drugs currently in use, particularly nitisinone, by utilizing the natural flavanol kaempferol molecule as a 4-hydroxyphenylpyruvate dioxygenase inhibitor. Kaempferol was employed to generate three effective de novo drug candidates targeting the enzyme 4-hydroxyphenylpyruvate dioxygenase using an AI drug design tool. We present novel AIK formulations in the present study. The AIK's (Artificial Intelligence Kaempferol) examination of drug-likeliness among the three led to its choice as a possible target. The toxicity assessment research of AIK demonstrates that it is not only safer to use than other treatments, but also more efficient. The docking of the AIGT with 4-hydroxyphenylpyruvate dioxygenase, which revealed a binding affinity of around -9.099 kcal/mol, highlights the AIK's potential as a therapeutic candidate. An innovative approach to deal with challenging circumstances is thus presented in this study by new formulations kaempferol that have been meticulously designed by AI. The results of the in vitro tests must be confirmed in vivo, even though AI-designed AIK is effective and sufficiently safe as computed.

Unlocking the potential of biofilm-forming plant growth-promoting rhizobacteria for growth and yield enhancement in wheat (Triticum aestivum L.).

Plant growth-promoting rhizobacteria (PGPR) boost crop yields and reduce environmental pressures through biofilm formation in natural climates. Recently, biofilm-based root colonization by these microorganisms has emerged as a promising strategy for agricultural enhancement. The current work aims to characterize biofilm-forming rhizobacteria for wheat growth and yield enhancement. For this, native rhizobacteria were isolated from the wheat rhizosphere and ten isolates were characterized for plant growth promoting traits and biofilm production under axenic conditions. Among these ten isolates, five were identified as potential biofilm-producing PGPR based on in vitro assays for plant growth-promoting traits. These were further evaluated under controlled and field conditions for their impact on wheat growth and yield attributes. Surface-enhanced Raman spectroscopy analysis further indicated that the biochemical composition of the biofilm produced by the selected bacterial strains includes proteins, carbohydrates, lipids, amino acids, and nucleic acids (DNA/RNA). Inoculated plants in growth chamber resulted in larger roots, shoots, and increase in fresh biomass than controls. Similarly, significant increases in plant height (13.3, 16.7%), grain yield (29.6, 17.5%), number of tillers (18.7, 34.8%), nitrogen content (58.8, 48.1%), and phosphorus content (63.0, 51.0%) in grains were observed in both pot and field trials, respectively. The two most promising biofilm-producing isolates were identified through 16 s rRNA partial gene sequencing as Brucella sp. (BF10), Lysinibacillus macroides (BF15). Moreover, leaf pigmentation and relative water contents were significantly increased in all treated plants. Taken together, our results revealed that biofilm forming PGPR can boost crop productivity by enhancing growth and physiological responses and thus aid in sustainable agriculture.

Optimizing the resveratrol fragments for novel in silico hepatocellular carcinoma de novo drug design.

Hepatocellular carcinoma (HCC) incidence varies widely around the world and is impacted by factors such as the prevalence of chronic hepatitis B and C infections, alcohol intake, and access to healthcare. The proteins (BRAF_human, VGFR3_human, EGFR_human and UFO_human) play a vital role in hepatocellular carcinoma prognosis, which involves cell proliferation, cell growth, transmission of extracellular signals to the cell nucleus and consequently regulating many other cellular processes. Fostamatinib has been studied for its possible use in the treatment of hepatocellular cancer because it is a more convenient therapy choice for patients and has minor side effects on the human body. However, resveratrol phytochemical has been investigated for its potential use in the prevention and treatment of a wide range of disorders, including cancer, cardiovascular disease, diabetes, and neurological problems due to its frequently antioxidant, anti-inflammatory, and immune-modulating characteristics, which can aid in the prevention of chronic illnesses. This study developed de novo-based fragment-optimized resveratrol (FOR), enhancing therapeutic potential and lowering toxicity. The docking study was performed with four target proteins, and the findings reveal that the vascular endothelial growth factor receptor 3 protein possessed the highest binding energy values of -7.6 kcal/mol with FOR. Additionally, it completely fulfills the criteria of drug-likeliness rules. Thus, FOR proves to be an efficient drug candidate for future in-vivo studies against hepatocellular carcinoma.

Follicular, luteal dynamics and effect of synchronization methods on reproductive responses in Cholistani cows.

The Cholistani cow is considered one of the milch breeds of Zebu cattle. Despite being heat and tick-resistant, it has not yet gained much popularity among Pakistan dairy farmers due to its long calving interval. This study aimed to understand the basic reproductive physiology of Cholistani cows using sonography and reproductive biotechnologies such as estrus synchronization and timed artificial insemination to improve reproductive efficiency. In experiment 1, six Cholistani cows with mixed parity 3.20 ± 1.30 and weighing 400 kg were selected to monitor ovarian dynamics on alternate days by the same sonographer from the onset of heat through ovulation until the next ovulation. Experiment 2 measured the effect of estrus synchronization methods, controlled internal drug release-gonadotropin-releasing hormone (CIDR-GnRH, n = 31) and Ovsynch (OVS, n = 32) on various reproductive parameters. The mean estrous cycle length was 19.81 ± 0.56 days with two follicular waves. The mean inter-ovulatory interval was 20.80 ± 0.52 days, with a preovulatory follicular size of 13.83 ± 2.37 mm. Estrus response was higher (p > 0.05) in controlled internal drug release (CIDR)-GnRH (93.54%) than in OVS (84.37%) cows. Similarly, ovulation and conception rates were higher in CIDR-GnRH (91.66% vs. 68.42%) than in OVS cows (41.37% vs. 33.33%), respectively. In conclusion, CIDR-GnRH results in a better estrus response, higher ovulation rate, and subsequently greater conception rate than OVS in Bos indicus dairy cows.

Urinary polycyclic aromatic hydrocarbons and adult obesity among the US population: NHANES 2003-2016.

Polycyclic aromatic hydrocarbons (PAHs) are naturally occurring environmental pollutants that may contribute to obesity in the adult population. To investigate the relationship between the urinary concentrations of PAH metabolites and adult obesity among the US population, the National Health and Nutritional Examination Survey (NHANES, 2003-2016) was used as a data source for this study. As many as 4464 participants in the NHANES 2003-2016 were included in the final analyses. We used logistic regression to look at the link between urinary PAH metabolites and obesity, using odds ratios (ORs) and 95% confidence intervals (CIs). The study sample comprised 4464 individuals aged ≥18 years, 2199 were male and 2265 were female. The study characteristics for four different quartiles were analyzed, and the average ages of the four urinary PAH quartiles were 49.61 ± 20.01, 46.63 ± 20.33, 44.28 ± 19.19, and 43.27 ± 17.68 years, respectively. In the quartile analysis of all participants, the third quartile was significantly associated with an increased prevalence of obesity (OR = 1.33, 95% CI = 1.12-1.59) with p-values <.05. In addition, females, but not males, had a strong link between the second, third, and fourth quartiles of urinary PAH and a higher risk of obesity (OR = 1.27, 95% CI = 1.00-1.61; OR = 1.52, 95% CI = 1.19-1.94; and OR = 1.39, 95% CI = 1.09-1.78). In conclusion, the study observed that urinary PAH metabolites were associated with the prevalence of obesity among the US population.

Green extraction and application of yellow natural curcumin colorant from Curcuma aromatica rhizomes for silk dyeing.

Green products such as plant tints are becoming more and more well-known worldwide due to their superior biological and ayurvedic properties. In this work, colorant from Amba Haldi (Curcuma aromatica) was isolated using microwave (MW), and bio-mordants were added to produce colorfast shades. Response surface methodology was used to develop a central composite design (CCD), which maximizes coloring variables statistically. The findings from 32 series of experiments show that excellent color depth (K/S = 12.595) was established onto MW-treated silk fabric (RS = 4 min) by employing 65 mL of radiated aqueous extract (RE = 4 min) of 5 pH cutting-edge the existence of 1.5 g/100 mL used sodium chloride at 75 °C for 45 min. It was discovered that acacia (keekar) extract (1%), pomegranate extract (2%), and pistachio extract (1.5%) were present before coloring by the use of bio-mordants. On the other hand, upon dyeing, acacia extract (1.5%), pomegranate extract (1.5%), and pistachio extract (2%) have all shown extremely strong colorfast colors. Comparatively, before dyeing, salts of Al3+ (1.5%), Fe2+ (2%), and TA (1.5%) gave good results; after dyeing, salts of Al3+ (1%) and Fe2+ (1.5%) and TA (2%) gave good results. When applied to silk fabric, MW radiation has increased the production of dyes recovered from rhizomes. Additionally, the right amount of chemical and biological mordants have been added, resulting in color fastness ratings ranging from outstanding to good. Therefore, the natural color extracted from Amba Haldi can be a sustainable option for the dyeing of silk fabric in the textile dyeing and finishing industries.

Evaluating the MDCK cell permeability of greenly synthesize bimetallic Ag/Zn Nanoparticles using leaf extract of Vallaris solanacea as a potential antipesticide-resistant agent.

Bimetallic nanoparticles, particularly Ag/Zn bimetallic nanoparticles, have gained increasing attention due to their unique properties, making them suitable for a variety of applications such as catalysis, water treatment, and environmental remediation. This study aimed to elucidate the use of bimetallic nanoparticles of Ag/Zn as an alternative to resistant pesticides for pest control. Furthermore, this research demonstrates that BNPs can target specific pollutants and degrade them through various mechanisms. BNP docking with the Nilaparvata lugens cytochrome P450 (CYP6ER1) protein exhibited the lowest binding energy of -7.5 kcal/mol. The cell permeability analysis of BNP in plant cells reveals that the BNP has 0 % permeability towards any cell at -10 kcal/mol energy, which is the lowest free energy translocation pathway. The harmful leftover residues of the pesticides have a higher chance of degradability in case of interaction with BNP validated by chemical-chemical interaction analysis. Additionally, MDCK permeability coefficient of small molecules based on the regression model was calculated for BNP which authenticated the efficiency of BNP. Moreover, Swiss ADMET simulated absorption using a boiled egg model with no blood-brain barrier and gastrointestinal crossing for the expected BNP molecule has been observed. Significantly, the findings indicate that employing bimetallic nanoparticles like Ag/Zn is a crucial strategy for bioremediation because they proficiently decompose pesticides while posing no risk to humans. Our results will facilitate the design of novel BNPs materials for environmental remediation and pest control ensuring human health safety that are predicated on bimetallic nanoparticles.

Integrating 16S rRNA profiling and in-silico analysis for an epitope-based vaccine strategy against Achromobacter xylosoxidans infection.

Achromobacter xylosoxidans is an aerobic, catalase-positive, non-pigment-forming, Gram-negative, and motile bacterium. It potentially causes a wide range of human infections in cystic fibrosis and non-cystic fibrosis patients. However, developing a safe preventive or therapeutic solution against A. xylosoxidans remains challenging. This study aimed to construct an epitope-based vaccine candidate using immunoinformatic techniques. A. xylosoxidans was isolated from an auto workshop in Lahore, and its identification was confirmed through 16S rRNA amplification and bioinformatic analysis. Two protein targets with GenBank accession numbers AKP90890.1 and AKP90355.1 were selected for the vaccine construct. Both proteins exhibited antigenicity, with scores of 0.757 and 0.580, respectively and the epitopes were selected based on the IC50 value using the ANN 4.0 and NN-align 2.3 epitope prediction method for MHC I and MHC II epitopes respectively and predicted epitopes were analyzed for antigenicity, allergenicity and pathogenicity. The vaccine construct demonstrated structural stability, thermostability, solubility, and hydrophilicity. The vaccine produced 250 B-memory cells per mm3 and approximately 16,000 IgM + IgG counts, indicating an effective immune response against A. xylosoxidans. Moreover, the vaccine candidate interacted stably with toll-like receptor 5, a pattern recognition receptor, with a confidence score of 0.98. These results highlight the potency of the designed vaccine candidate, suggesting its potential to withstand rigorous in vitro and in vivo clinical trials. This epitope-based vaccine could serve as the first preventive immunotherapy against A. xylosoxidans infections, addressing this bacterium's health and financial burdens. The findings demonstrate the value of employing immunoinformatic tools in vaccine development, paving the way for more precise and tailored approaches to combating microbial threats.

Naringin: Cardioprotective properties and safety profile in diabetes treatment.

Flavonoids derived from plants offer a broad spectrum of therapeutic potential for addressing metabolic syndrome, particularly diabetes mellitus (DM), a prevalent non-communicable disease. Hyperglycemia in DM is a known risk factor for cardiovascular diseases (CVDs), which substantially impact global mortality rates. This review examines the potential effects of naringin, a citrus flavonoid, on both DM and its associated cardiovascular complications, including conditions like diabetic cardiomyopathy. The safety profile of naringin is summarized based on various pre-clinical studies. The data for this review was gathered from diverse electronic databases, including Medline, PubMed, ScienceDirect, SpringerLink, Google Scholar, and Emerald Insight. Multiple pre-clinical studies have demonstrated that naringin exerts hypoglycemic and cardioprotective effects by targeting various vascular mechanisms. Specifically, research indicates that naringin down-regulates the renin-angiotensin and oxidative stress systems while concurrently upregulating ß-cell and immune system functions. Clinical trial outcomes also support the therapeutic potential of naringin in managing hyperglycemic states and associated cardiovascular issues. Moreover, toxicity studies have confirmed the safety of naringin in animal models, suggesting its potential for safe administration in humans. In conclusion, naringin emerges as a promising natural candidate for both antidiabetic and cardioprotective purposes, offering potential improvements in health outcomes. While naringin presents a new avenue for therapies targeting DM and CVDs, additional controlled and long-term clinical trials are necessary to validate its efficacy and safety for human use.

Designing a Multiepitope Vaccine against the Foodborne Pathogenic Bacteria Listeria monocytogenes Using Subtractive Immunoinformatics Approaches.

BACKGROUND: Listeria monocytogenes, a Gram-positive bacterium, is a prominent foodborne pathogen that causes listeriosis and poses substantial health hazards worldwide. The continuing risk of listeriosis outbreaks underlies the importance of designing an effective prevention strategy and developing a robust immune response by reverse vaccinology approaches. This study aimed to provide a critical approach for developing a potent multiepitope vaccine against this foodborne disease. METHODS: A chimeric peptide construct containing 5 B-cell epitopes, 16 major histocompatibility complex I (MHC-I) epitopes, and 18 MHC-II epitopes were used to create a subunit vaccination against L. monocytogenes. The vaccine safety was evaluated by several online methods, and molecular docking was performed using ClusPro to determine the binding affinity. Immune simulation was performed using the C-ImmSimm server to demonstrate the immune response. RESULTS: The results validated the antigenicity, non-allergenicity, and nontoxicity of the chimeric peptide construct, confirming its suitability as a subunit vaccine. Molecular docking showed a good score of 1276.5 and molecular dynamics simulations confirmed the construct's efficacy, demonstrating its promise as a good candidate for listeriosis prophylaxis. The population coverage was as high as 91.04% with a good immune response, indicating good antigen presentation with dendritic cells and production of memory cells. CONCLUSIONS: The findings of this study highlight the potential of the designed chimeric peptide construct as an effective subunit vaccine against Listeria, paving the way for future advances in preventive methods and vaccine design.

Untacking small RNA profiling and RNA fragment footprinting: Approaches and challenges in library construction.

Small RNAs (sRNAs) with sizes ranging from 15 to 50 nucleotides (nt) are critical regulators of gene expression control. Prior studies have shown that sRNAs are involved in a broad range of biological processes, such as organ development, tumorigenesis, and epigenomic regulation; however, emerging evidence unveils a hidden layer of diversity and complexity of endogenously encoded sRNAs profile in eukaryotic organisms, including novel types of sRNAs and the previously unknown post-transcriptional RNA modifications. This underscores the importance for accurate, unbiased detection of sRNAs in various cellular contexts. A multitude of high-throughput methods based on next-generation sequencing (NGS) are developed to decipher the sRNA expression and their modifications. Nonetheless, distinct from mRNA sequencing, the data from sRNA sequencing suffer frequent inconsistencies and high variations emanating from the adapter contaminations and RNA modifications, which overall skew the sRNA libraries. Here, we summarize the sRNA-sequencing approaches, and discuss the considerations and challenges for the strategies and methods of sRNA library construction. The pros and cons of sRNA sequencing have significant implications for implementing RNA fragment footprinting approaches, including CLIP-seq and Ribo-seq. We envision that this review can inspire novel improvements in small RNA sequencing and RNA fragment footprinting in future. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.

Investigating the anti-cancer compounds from Calliandra harrisii for precision medicine in pancreatic cancer via in-silico drug design and GC-MS analysis.

Pancreatic cancer is a fatal illness caused by mutations in multiple genes. Pancreatic cancer damages the organ that helps in digestion, resulting in symptoms including fatigue, bloating, and nausea. The use of medicinal plants has been crucial in the treatment of numerous disorders. The medicinal plant Calliandra Harrisi has been widely exploited for its possibilities in biology and medicine. The current study aimed to assess the biopotential of biologically active substances against pancreatic cancer. The GC-MS data of these phytochemicals from Calliandra Harrisi were further subjected to computational approaches with pancreatic cancer genes to evaluate their potential as therapeutic candidates. Molecular docking analysis revealed that N-[Carboxymethyl] maleamic acid is the leading molecule responsible for protein denaturation inhibition, having the highest binding affinity of 6.8 kJ/mol among all other compounds with KRAS inflammatory proteins. Furthermore, ADMET analysis and Lipinski's rule validation were also performed revealing its higher absorption in the gastrointestinal tract. The results of the hepatotoxicity test demonstrated that phytochemicals are non-toxic, safe to use, and do not cause necrosis, fibrosis, or vacuolar degeneration even at excessive levels. Calliandra Harrisi has phytoconstituents that have a variety of pharmacological uses in consideration.

Comparative analysis among the degradation potential of enzymes obtained from Escherichia coli against the toxicity of sulfur dyes through molecular docking.

The common bacterium Escherichia coli has demonstrated potential in the field of biodegradation. E. coli is naturally capable of biodegradation because it carries a variety of enzymes that are essential for the breakdown of different substances. The degradation process is effectively catalyzed by these enzymes. The collaborative effects of E. coli's aryl sulfotransferase, alkanesulfonate moonoxygenase, and azoreductase enzymes on the breakdown of sulfur dyes from industrial effluents are investigated in this work. ExPASY ProtParam was used to confirm the stability of the enzyme, showing an instability index less than 40. We determined the maximum binding affinities of these enzymes with sulfur dye pollutants - 1-naphthalenesulfonic acid, sulfogene, sulfur green 3, sulfur red 6, sulfur red 1, sulfur yellow 2, thianthrene, thiazone, and thional - using comparative molecular docking. Significantly, the highest binding affinity was shown by monooxygenase (-12.1), whereas aryl sulfotransferase and azoreductase demonstrated significant energies of -11.8 and -11.4, respectively. The interactions between proteins and ligands in the docked complexes were examined. To evaluate their combined effects, co-expression analysis of genes and enzyme bioengineering were carried out. Using aryl sulfotransferase, alkanesulfonate monooxygenase, and azoreductase, this study investigates the enzymatic degradation of sulfur dye pollutants, thereby promoting environmentally friendly and effective sulfur dye pollutant management.

Characterizations of biogenic selenium nanoparticles and their anti-biofilm potential against Streptococcus mutans ATCC 25175.

INTRODUCTION: S. mutans has been identified as the primary pathogenic bacterium in biofilm-mediated dental caries. The biogenic selenium nanoparticles (SeNPs) produced by L. plantarum KNF-5 were used in this study against S. mutans ATCC 25175. OBJECTIVES: The aims of this study were: (1) the biosynthesis of SeNPs by L. plantarum KNF-5, (2) the characterization of SeNPs, (3) the investigation of the inhibitory effect of biogenic SeNPs against S. mutans ATCC 25175, and (4) the determination of the anti-biofilm potential of SeNPS against S. mutans ATCC 25175. METHODOLOGY: 3 mL of the culture was added to 100 mL of MRS medium and incubated. After 4 h, Na2SeO3 solution (concentration 100 µg/mL) was added and incubated at 37 °C for 36 h. The color of the culture solution changed from brownish-yellow to reddish, indicating the formation of SeNPs. The characterization of SeNPs was confirmed by UV-Vis spectrophotometry, FTIR, SEM-EDS and a particle size analyzer. The antibacterial activity was determined by the disk diffusion method, the MIC by the micro-double dilution method, and the biofilm inhibitory potential by the crystal violet method and the MTT assay. The effect of SeNPs on S. mutans ATCC 25175 was determined using SEM and CLSM spectrometry techniques. The sulfate-anthrone method was used to analyze the effect of SeNPs on insoluble extracellular polysaccharides. The expression of genes in S. mutans ATCC 25175 was analyzed by real-time quantitative polymerase chain reaction (RT-qPCR). PREPARATION OF NANOPARTICLES: SeNPs produced by probiotic bacteria are considered a safe method. In this study, L. plantarum KNF-5 (probiotic strain) was used for the production of SeNPs. RESULTS: The biogenic SeNPs were spherical and coated with proteins and polysaccharides and had a diameter of about 270 nm. The MIC of the SeNPs against S. mutans ATCC 25175 was 3.125 mg/mL. Biofilm growth was also significantly suppressed at this concentration. The expression of genes responsible for biofilm formation (GtfB, GtfC, BrpA and GbpB,) was reduced when S. mutans ATCC 25175 was treated with SeNPs. CONCLUSION: It was concluded that the biogenic SeNPs produced by L. plantarum KNF-5 was highly effective to inhibit the growth of S. mutans ATCC 25175. NOVELTY STATEMENT: The application of biogenic SeNPs, a natural anti-biofilm agent against S. mutans ATCC 25175. In the future, this study will provide a new option for the prevention and treatment of dental caries.