Important structural features of antimicrobial peptides towards specific activity: Trends in the development of efficient therapeutics.

Proteins and peptides, as polypeptide chains, have usually got unique conformational structures for effective biological activity. Antimicrobial peptides (AMPs) are a group of bioactive peptides, which have been increasingly studied during recent years for their promising antibacterial, antifungal, antiviral and anti-inflammatory activity, as well as, other esteemed bioactivities. Numerous AMPs have been separated from a wide range of natural resources, or produced in vitro through chemical synthesis and recombinant protein expression. Natural AMPs have had limited clinical application due to several drawbacks, such as their short half-life due to protease degradation, lack of activity at physiological salt concentrations, toxicity to mammalian cells, and the absence of suitable methods of delivery for the AMPs that are targeted and sustained. The creation of synthetic analogs of AMPs would both avoid the drawbacks of the natural analogs and maintain or even increase the antimicrobial effectiveness. The structure-activity relationship of discovered AMPs or their derivatives facilitates the development of synthetic AMPs. This review discovered that the relationship between the activity of AMPs and their positive net charge, hydrophobicity, and amino acid sequence and the relationship between AMPs' function and other features like their topology, glycosylation, and halogenation.

Modifying lignin: A promising strategy for plant disease control.

Lignin is a complex polymer found in the cell walls of plants, providing structural support and protection against pathogens. By modifying lignin composition and structure, scientists aim to optimize plant defense responses and increase resistance to pathogens. This can be achieved through various genetic engineering techniques which involve manipulating the genes responsible for lignin synthesis. By either up regulating or down regulating specific genes, researchers can alter the lignin content, composition, or distribution in plant tissues. Reducing lignin content in specific tissues like leaves can improve the effectiveness of defense mechanisms by allowing for better penetration of antimicrobial compounds. Overall, Lignin modification through techniques has shown promising results in enhancing various plants resistance against pathogens. Furthermore, lignin modification can have additional benefits beyond pathogen resistance. It can improve biomass processing for biofuel production by reducing lignin recalcitrance, making the extraction of sugars from cellulose more efficient. The complexity of lignin biosynthesis and its interactions with other plant components make it a challenging target for modification. Additionally, the potential environmental impact and regulatory considerations associated with genetically modified organisms (GMOs) require careful evaluation. Ongoing research aims to further optimize this approach and develop sustainable solutions for crop protection.

Inadequate Niacin Intake Disrupts Growth and Retinol Homeostasis Resulting in Higher Liver and Lower Serum Retinol Concentrations in Male Rats.

BACKGROUND: Niacin-derived nicotinamide adenine dinucleotide is an essential cofactor for many dehydrogenase enzymes involved in vitamin A (VA) metabolism. Several countries with high prevalence of VA deficiency rely on maize, a poor source of available niacin, as a dietary staple. OBJECTIVES: This study evaluated the interaction of dietary niacin on VA homeostasis using male Sprague-Dawley rats, aged 21 d (baseline body weight 88.3 ± 6.6 g). METHODS: After 1 wk of acclimation, baseline samples were collected (n = 4). Remaining rats (n = 54) were split into 9 groups to receive low tryptophan, VA-deficient feed with 3 different amounts of niacin (0, 15, or 30 mg/kg) and 3 different oral VA doses (50, 350, or 3500 nmol/d) in a 3 × 3 design. After 4 wk, the study was terminated. Serum, livers, and small intestine were analyzed for retinoids using high-performance liquid chromatography. Niacin and metabolites were evaluated with nuclear magnetic resonance. Plasma pyridoxal-P (PLP) was measured with high-performance liquid chromatography. RESULTS: Niacin intake correlated with serum retinol concentrations (r = 0.853, P < 0.001). For rats receiving the highest VA dose, liver retinol concentrations were lower in the 30-mg/kg niacin group (5.39 ± 0.27 µmol/g) than those in the 0-mg/kg and 15-mg/kg groups (9.18 ± 0.62 and 8.75 ± 0.07 µmol/g, respectively; P ≤ 0.05 for both). This phenomenon also occurred in the lower VA doses (P ≤ 0.05 for all). Growth and tissue weight at endline were associated with niacin intake (P ≤ 0.001 for all). Plasma PLP correlated with estimated niacin intake (r = 0.814, P < 0.001). CONCLUSIONS: Optimal niacin intake is associated with lower liver VA and higher serum retinol and plasma PLP concentrations. The extent to which vitamin B intake affects VA homeostasis requires further investigation to determine if the effects are maintained in humans.

Design and Evaluation of a Novel Anti-microbial Peptide from Cathelicidin-2: Selectively Active Against Acinetobacter baumannii.

Background: Infections caused by pathogenic microorganisms have increased the need for hospital care and have thus represented a public health problem and a significant financial burden. Classical treatments consisting of traditional antibiotics face several challenges today. Anti-microbial peptides (AMPs) are a conserved characteristic of the innate immune response among different animal species to defend against pathogenic microorganisms. Objectives: In this study, a new peptide sequence (mCHTL131-140) was designed using the in silico approach. Methods: Cathelicidin-2 (UniprotID: Q2IAL7) was used as a potential antimicrobial protein, and a novel 10 - 12 amino acids sequence AMP was designed using bioinformatics tools and the AMP databases. Then, the anti-bacterial, anti-biofilm, and anti-fungal properties of the peptide, as well as its hemolytic activity and cytotoxicity towards human fibroblast (HDF) cells, were investigated in vitro. Results: Online bioinformatics tools indicated that the peptide sequence could have anti-bacterial, anti-viral, anti-fungal, and anti-biofilm properties with little hemolytic properties. The experimental tests confirmed that mCHTL131-140 exhibited the best anti-bacterial properties against Acinetobacter baumannii and had fair anti-fungal properties. Besides, it did not cause red blood cell lysis and showed no cytotoxicity towards HDF cells. Conclusions: In general, the designed peptide can be considered a promising AMP to control hospital-acquired infections by A. baumannii.

Anti-Microbial Peptides: Strategies of Design and Development and Their Promising Wound-Healing Activities.

BACKGROUND: Current approaches used to overcome microbial infections are becoming inefficient due to the overuse or misuse of antibiotics. Antimicrobial peptides (AMPs) are one of the most promising substitutional candidates for commercial antibiotics. METHODS AND RESULTS: The publications in the field of in silico design of AMPs with focus on the wound-healing AMPs were searched though SCOPUS and PubMed. Through publications, it was reported that a number of AMPs approved for clinical use have also showed efficient wound-healing activity. Todays, the design and production of synthetic types of AMPs have attracted attention in order to expand their applications and to cope with their limitations and adverse effects. In this paper, the currently published researches in the field of AMPs and their wound-healing features were summarized and the strategies used in AMPs design and development have been reviewed. Moreover, different databases and online servers used in this regard were summarized. CONCLUSION: Design and development of active AMPs, especially those with wound-healing activity, can be performed using bioinformatics servers and software, regarding AMPs structure-activity relationships.

Microencapsulation of a Pseudomonas Strain (VUPF506) in Alginate-Whey Protein-Carbon Nanotubes and Next-Generation Sequencing Identification of This Strain.

Alginate is a common agent used for microencapsulation; however, the formed capsule is easily damaged. Therefore, alginate requires blending with other biopolymers to reduce capsule vulnerability. Whey protein is one polymer that can be incorporated with alginate to improve microcapsule structure. In this study, three different encapsulation methods (extrusion, emulsification, and spray drying) were tested for their ability to stabilize microencapsulated Pseudomonas strain VUPF506. Extrusion and emulsification methods enhanced encapsulation efficiency by up to 80% and gave the best release patterns over two months. A greenhouse experiment using potato plants treated with alginate-whey protein microcapsules showed a decrease in Rhizoctonia disease intensity of up to 70%. This is because whey protein is rich in amino acids and can serve as a resistance induction agent for the plant. In this study, the use of CNT in the ALG-WP system increased the rooting and proliferation and reduced physiological complication. The results of this study showed that the technique used in encapsulation could have a significant effect on the efficiency and persistence of probiotic bacteria. Whole genome sequence analysis of strain VUPF506 identified it as Pseudomonas chlororaphis and revealed some genes that control pathogens.

Screening of Altered Metabolites and Metabolic Pathways in Celiac Disease Using NMR Spectroscopy.

BACKGROUND: Celiac disease (CeD) is an autoimmune intestinal disorder caused by gluten protein consumption in genetically predisposed individuals. As biopsy sampling is an invasive procedure, finding novel noninvasive serological markers for screening of at-risk CeD population is a priority. Metabolomics is helpful in monitoring metabolite changes in body fluids and tissues. In the present study, we evaluated serum metabolite levels of CeD patients relative to healthy controls with the aim of introducing new biomarkers for population screening. METHOD: We compared the serum metabolic profile of CeD patients (n = 42) and healthy controls (n = 22) using NMR spectroscopy and multivariate analysis. RESULT: 25 metabolites were identified by serum metabolic profiling. Levels of 3-hydroxyisobutyric acid and isobutyrate showed significant differences in CeD patients' samples compared with healthy controls (p < 0.05). According to pathway analysis, our data demonstrated that changes in nine metabolic pathways were significantly disrupted/affected in patients with CeD. These enriched pathways are involved in aminoacyl-tRNA biosynthesis; primary bile acid biosynthesis; nitrogen metabolism; glutamine and glutamate metabolism; valine, leucine, and isoleucine biosynthesis and degradation; taurine and hypotaurine metabolism; glyoxylate and dicarboxylate metabolism; glycine, serine, and threonine metabolism; and arginine biosynthesis. CONCLUSION: In summary, our results demonstrated that changes in the serum level of 25 metabolites may be useful in distinguishing CeD patients from healthy controls, which have the potential to be considered candidate biomarkers of CeD.

Survivability and controlled release of alginate-microencapsulated Pseudomonas fluorescens VUPF506 and their effects on biocontrol of Rhizoctonia solani on potato.

Preserving the efficacy of plant probiotic bacteria in soil is a major challenge to the biological control of plant diseases. The microencapsulation technique is an important step in preserving the viability and activity of probiotics in adverse environmental conditions. The main objective of this study was to choose an appropriate coating for probiotic encapsulation. For this purpose, the survivability and controlled release of Pseudomonas fluorescens VUPF506 encapsulated with alginate (Alg) combined with whey protein concentrate (WPC), carboxymethyl cellulose (CMC), and peanut butter (PB) were evaluated. Moreover, the encapsulated cells were evaluated to control for Rhizoctonia solani in potato plants under in vivo conditions. The results showed that all tested wall material maintained more than 80% of the bacterial cells. The Alg-WPC microcapsules provided a better controlled release over two months. Interestingly, the greenhouse experiment also revealed that the treatment of potato plants with Alg-WPC microcapsules was the most effective treatment, suppressing 90% of the pathogen. The results showed that Alg-WPC is the most promising combination to improve the survivability of P. fluorescens VUPF506. Moreover, it can be used as a fertilizer due to its content of valuable amino acids.

In vitro and in vivo evaluation of antibacterial and anti-biofilm properties of five ethnomedicinal plants against oral bacteria by TEM.

OBJECTIVE: The aim of the present study was to investigate antibacterial and antibiofilm activity of a few medicinal plants against oral bacteria. MATERIALS AND METHODS: Salvia officinalis, Lippie citriodora, Mentha piperita, Echinacea purpurea and Matricaria chamomilla were extracted. Isolates from oral cavity were identified by microbiological and molecular methods. Minimum inhibitory concentration and minimum bactericidal concentration were determined by Broth microdilution method. The anti-biofilm activity of essential oils and extracts investigated and as a mixture by Broth dilution method. Toxicity of the herbal mixture was assayed by in Wistar rats treated with intradermal injection. Wound healing properties of the herbal mixture against infected wounds on the back of the rats were investigated. Anti-biofilm activity was investigated on tooth surfaces. Bacterial structure changes and fine- structure study were performed by light microscopy and Transmission electron microscopy. RESULTS: The lowest MIC and MBC for the plant mixtures was 0.0002 mg/ml belonged to Streptococcus pyogenes and the highest values (0.025 mg/ml) belonged to Eikenella corrodens. The essential oils of S.officinalis, L.citriodora and M.piperita, but not E.purpurea and M.chamomilla extracts, were able to remove the biofilms created by the studied bacteria. The herbal mixture was able to completely heal the wound skin of rats in 21 days (p<0.05 compared to control). The mixture was able to decompose the teeth biofilm in 45 seconds. The results of light and electron microscopy showed that the bacterial structure exposed to the herbal mixture was deformed. CONCLUSION: It was concluded that the essential oils of S.officinalis, L.citriodora and M.piperita had significant effects on inhibition of oral bacteria biofilm formation.

Metabolic Changes in Synaptosomes in an Animal Model of Schizophrenia Revealed by 1H and 1H,13C NMR Spectroscopy.

Synaptosomes are isolated nerve terminals that contain synaptic components, including neurotransmitters, metabolites, adhesion/fusion proteins, and nerve terminal receptors. The essential role of synaptosomes in neurotransmission has stimulated keen interest in understanding both their proteomic and metabolic composition. Mass spectrometric (MS) quantification of synaptosomes has illuminated their proteomic composition, but the determination of the metabolic composition by MS has been met with limited success. In this study, we report a proof-of-concept application of one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy for analyzing the metabolic composition of synaptosomes. We utilize this approach to compare the metabolic composition synaptosomes from a wild-type rat with that from a newly generated genetic rat model (Disc1 svΔ2), which qualitatively recapitulates clinically observed early DISC1 truncations associated with schizophrenia. This study demonstrates the feasibility of using NMR spectroscopy to identify and quantify metabolites within synaptosomal fractions.

NMR-Based Identification of Metabolites in Polar and Non-Polar Extracts of Avian Liver.

Metabolites present in liver provide important clues regarding the physiological state of an organism. The aim of this work was to evaluate a protocol for high-throughput NMR-based analysis of polar and non-polar metabolites from a small quantity of liver tissue. We extracted the tissue with a methanol/chloroform/water mixture and isolated the polar metabolites from the methanol/water layer and the non-polar metabolites from the chloroform layer. Following drying, we re-solubilized the fractions for analysis with a 600 MHz NMR spectrometer equipped with a 1.7 mm cryogenic probe. In order to evaluate the feasibility of this protocol for metabolomics studies, we analyzed the metabolic profile of livers from house sparrow (Passer domesticus) nestlings raised on two different diets: livers from 10 nestlings raised on a high protein diet (HP) for 4 d and livers from 12 nestlings raised on the HP diet for 3 d and then switched to a high carbohydrate diet (HC) for 1 d. The protocol enabled the detection of 52 polar and nine non-polar metabolites in ¹H NMR spectra of the extracts. We analyzed the lipophilic metabolites by one-way ANOVA to assess statistically significant concentration differences between the two groups. The results of our studies demonstrate that the protocol described here can be exploited for high-throughput screening of small quantities of liver tissue (approx. 100 mg wet mass) obtainable from small animals.

NMR spectroscopy-based metabolomic study of serum in sulfur mustard exposed patients with lung disease.

Sulfur mustard (SM) is a vesication chemical warfare agent for which there is currently no antidote. Despite years of research, there is no common consensus about the pathophysiological basis of chronic pulmonary disease caused by this chemical warfare agent. In this study, we combined chemometric techniques with nuclear magnetic resonance (NMR) spectroscopy to explore the metabolic profile of sera from SM-exposed patients. A total of 29 serum samples obtained from 17 SM-injured patients, and 12 healthy controls were analyzed by Random Forest. Increased concentrations of seven amino acids, glycerol, dimethylamine, ketone bodies, lactate, acetate, citrulline and creatine together with the decreased very low-density lipoproteins (VLDL) levels were observed in patients compared with control subjects. Our study reveals the metabolic profile of sera from SM-injured patients and indicates that NMR-based methods can distinguish these patients from healthy controls.

NMR- and GC/MS-based metabolomics of sulfur mustard exposed individuals: a pilot study.

Sulfur mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and healthy controls are observed are related to lipid metabolism, ketogenesis, tricarboxylic acid (TCA) cycle and amino acid metabolism.

A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.

The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(ß) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type.

A targeted metabolomics approach toward understanding metabolic variations in rice under pesticide stress.

Diazinon insecticide is widely applied throughout rice (Oryza sativa L.) fields in Iran. However, concerns are now being raised about its potential adverse impacts on rice fields. In this study, a time-course metabolic change in rice plants was investigated after diazinon treatment using gas chromatography-mass spectrometry (GC-MS), and subsequently the statistical strategy of random forest (RF) was performed in order to find the stress-associated effects. According to the results, a wide range of metabolites were dynamically varied as a result of the plant response to diazinon such as biosynthesis and metabolism of sugars, amino acids, organic acids, and phenylpropanoids, all correlating with the exposure time. Plant response was involved in multiple metabolic pathways, most of which were correlated with the exposure time. In this study, RF was explored as a potential multivariate method for GC-MS analysis of metabolomics data of rice (O. sativa L.) plants under diazinon stress; more than 31 metabolites were quantitatively determined, and time-course metabolic response of the plant during different days after treatment was measured. Results demonstrated RF as a potential multivariate method for GC-MS analysis of changes in plant metabolome under insecticide stress.

1H NMR based metabolic profiling in Crohn's disease by random forest methodology.

The present study was designed to search for metabolic biomarkers and their correlation with serum zinc in Crohn's disease patients. Crohn's disease (CD) is a form of inflammatory bowel disease that may affect any part of the gastrointestinal tract and can be difficult to diagnose using the clinical tests. Thus, introduction of a novel diagnostic method would be a major step towards CD treatment. Proton nuclear magnetic resonance spectroscopy ((1)H NMR) was employed for metabolic profiling to find out which metabolites in the serum have meaningful significance in the diagnosis of CD. CD and healthy subjects were correctly classified using random forest methodology. The classification model for the external test set showed a 94% correct classification of CD and healthy subjects. The present study suggests Valine and Isoleucine as differentiating metabolites for CD diagnosis. These metabolites can be used for screening of risky samples at the early stages of CD diagnoses. Moreover, a robust random forest regression model with good prediction outcomes was developed for correlating serum zinc level and metabolite concentrations. The regression model showed the correlation (R(2)) and root mean square error values of 0.83 and 6.44, respectively. This model suggests valuable clues for understanding the mechanism of zinc deficiency in CD patients.

A metabonomics investigation of multiple sclerosis by nuclear magnetic resonance.

Multiple sclerosis (MS) is a nervous system disease that affects the fatty myelin sheaths around the axons of the brain and spinal cord, leading to demyelination and a broad range of signs and symptoms. MS can be difficult to diagnose because its signs and symptoms may be similar to other medical problems. To find out which metabolites in serum are effective for the diagnosis of MS, we utilized metabolic profiling using proton nuclear magnetic resonance spectroscopy ((1)H-NMR). Random forest (RF) was used to classify the MS patients and healthy subjects. Atomic absorption spectroscopy was used to measure the serum levels of selenium. The results showed that the levels of selenium were lower in the MS group, when compared with the control group. RF was used to identify the metabolites that caused selenium changes in people with MS by building a correlation model between these metabolites and serum levels of selenium. For the external test set, the obtained classification model showed a 93% correct classification of MS and healthy subjects. The regression model of levels of selenium and metabolites showed the correlation (R(2)) value of 0.88 for the external test set. The results indicate the suitability of NMR as a screen for identifying MS patients and healthy subjects. A novel model with good prediction outcomes was constructed between serum levels of selenium and NMR data.

The concentration of serum zinc in celiac patients compared to healthy subjects in Tehran.

AIM: This study evaluated serum levels of zinc in patient with CD compare to healthy subjects. BACKGROUND: Celiac disease (CD) is characterized by small intestinal malabsorption of nutrients as a consequence of ingestion of wheat gluten. Zinc is an essential trace element that it has vital biological functions. PATIENTS AND METHODS: Sera of 30 celiac cases and 30 healthy normal cohorts as control group were obtained. Atomic absorption spectrophotometer was employed for estimating serum zinc level. RESULTS: Zinc concentrations in patients diagnosed with CD were significantly lower than healthy subjects (75.97±12 compared with 92.83±18, P-value < 0.0001). CONCLUSION: The result of this study shows that serum zinc concentration is decreased in celiac patients compare to healthy controls. Serum zinc may thus be a marker of CD in adults presenting with gastrointestinal symptoms.

NMR based metabonomics study on celiac disease in the blood serum.

AIM: The aim of this study is to look for the proper methods that would be a major step towards untreated CD diagnosis and seek the metabolic biomarkers causes of CD and compare them to control group. BACKGROUND: Celiac disease (CD) is a common autoimmune disorder that is not easily diagnosed using the clinical tests. PATIENTS AND METHODS: Thirty cases and 30 controls were entered into this study. Metabolic profiling was obtained using proton nuclear magnetic resonance spectroscopy ((1)HNMR) to seek metabolites that are helpful for the detection of CD. Classification of CD and healthy subject was done using random forest (RF). RESULTS: The obtained classification model showed an 89% correct classification of CD and healthy subject for the external test set. The metabolites that caused changes in people with CD were identified using RF; these metabolites include lactate, valine and lipid. CONCLUSION: The findings of the present study reveal serum lactate, valin and lipid levels in CD patient are lower than healthy cohorts. This metabolite may provide diagnostic tools as well as insight into potential targets for disease therapy.

Metabonomics exposes metabolic biomarkers of Crohn's disease by (1)HNMR.

Metabonomics and other "omics" fields are essential science in analytical chemistry. Modern analytical instruments such as proton nuclear magnetic resonance ((1)H NMR) can be provided the great quantity of analytical information. In order to assign unknown samples, chemometrics methods recognition build classification model based on experimental data. Firstly some current strategies for regarding disease diagnosis are exhibited in metabonomics studies. Some disease such as crohn's disease can be difficult to diagnosis since its signs and symptoms may be similar to other medical problems or often mimic other symptoms. Applications of NMR and supervised pattern recognition in the field of metabonomics are also reviewed in recent years. The aim of present study was to review the assessment of (1)HNMR to investigate a metabolic profile of crohn's disease.