First Barnacle (Amphibalanus amphitrite) Adhesion Strength Data on the Self-Polishing Coatings Off the Aegean Sea.

The aim of this work is to study the adhesion strength of Amphibalanus amphitrite in the Izmir Bay and compare the results with the pseudobarnacle adhesion test. Normally, adhesion tests are performed to evaluate the performance of the antifouling coatings, but the test results can also be used to predict biofouling cleaning process efficacy. The biofouling process is highly dependent on environmental conditions. For this reason, laboratory tests are required to perform the performance tests on self-polishing coatings in cases where living organisms cannot be reached. For this purpose, different self-polishing antifouling coatings have been formulated. Field tests for the coatings were carried out in the Aegean Sea for 10 weeks. After 10 weeks, barnacle and pseudobarnacle adhesion tests were conducted on coatings. When the results were compared, similarity was observed between the adhesion strength of barnacles and pseudobarnacles with 10 mm diameter on coating with the rosin/xylene/BaSO4 (40:40:20 w/w %). The adhesion strength of barnacles and pseudobarnacles on the coating 12 was found to be 0.46 and 0.45 MPa, respectively. In conclusion, the present study exhibits the first data related to the adhesion strength of A. amphitrite on rosin-based self-polishing coatings in the Aegean Sea. Moreover, based on field tests, a pseudobarnacle adhesion test methodology was developed to mimic barnacles and the correlation between barnacle and pseudobarnacle tests was examined.

A Sample Guideline for Reverse Vaccinology Approach for the Development of Subunit Vaccine Using Varicella Zoster as a Model Disease.

For the development of multi-peptide vaccine, identification of antigenic epitopes is crucial. If it is done using wet lab techniques, the identification process can be time-consuming, laborious, and cost-intensive. In silico tools, on the other hand, enable researchers to predict potential epitopes with little to no cost for further in vivo and in vitro testing. The rapid identification process using in silico tools helps in responding to health emergencies faster. Developing an efficient and high coverage vaccine is one of the ways to reduce morbidity and mortality rates of the diseases and protect the affected populations. In this chapter, we introduce the necessary tools and methodology for the identification and characterization of antigenic epitopes to design a multi-epitope vaccine using varicella-zoster virus as an example vector model.

Biohydrogen production via green silver nanoparticles synthesized through biomass of Ulva lactuca bloom.

Ulva lactuca is a marine green seaweed. Its bloom based biomass accumulated in the Izmir bay and is collected by local authorities. In this investigation, an alternative solution was proposed to utilize the biomass of U. lactuca to produce biohydrogen via green synthesized silver nanoparticles. According to the results, the optimum conditions related to silver nanoparticle production such as pH, temperature, biomass concentration, silver nitrate concentrations, and incubation time were determined to be 11, 25 °C, 10 mg/mL, 4 mM, and 3 days, respectively. Effective conditions for biohydrogen production such as pH, temperature, agitation rate, and sodium borohydride concentration were found to be 7, 50 °C, 250 rpm and 150 mM, respectively. These parameters are also modelled with an artificial neural network. The data presented here provide recommendations for producing biohydrogen from waste algae and helping reduce carbon emissions for better environment and future.

In-silico molecular interactions among the secondary metabolites of Caulerpa spp. and colorectal cancer targets.

Caulerpa spp. secrete more than thirty different bioactive chemicals which have already been used in cancer treatment research since they play a pivotal role in cancer metabolism. Colorectal cancer is one of the most common cancer types, thus using novel and effective chemicals for colorectal cancer treatment is crucial. In the cheminformatics pipeline of this study, ADME-Tox and drug-likeness tests were performed for filtering the secondary metabolites of Caulerpa spp. The ligands which were selected from the ADME test were used for in silico molecular docking studies against the enzymes of the oxidative branch of the pentose phosphate pathway (glucose-6-phosphate dehydrogenase and 6-phosphoglutarate dehydrogenase), which is of great importance for colorectal cancer, by using AutoDock Vina. Pharmacophore modeling was carried out to align the molecules. Molecular dynamic simulations were performed for each target to validate the molecular docking studies and binding free energies were calculated. According to the ADME test results, 13 different secondary metabolites were selected as potential ligands. Molecular docking studies revealed that vina scores of caulerpin and monomethyl caulerpinate for G6PDH were found as -10.6 kcal mol-1, -10.5 kcal mol-1, respectively. Also, the vina score of caulersin for 6PGD was found as -10.7 kcal mol-1. The highest and the lowest binding free energies were calculated for monomethyl caulerpinate and caulersin, respectively. This in silico study showed that caulerpin, monomethyl caulerpinate, and caulersin could be evaluated as promising marine phytochemicals against pentose phosphate pathway enzymes and further studies are recommended to investigate the detailed activity of these secondary metabolites on these targets.

An Efficient and Quick Analytical Method for the Quantification of an Algal Alkaloid Caulerpin Showed In-Vitro Anticancer Activity against Colorectal Cancer.

Biological invasion is the successful spread and establishment of a species in a novel environment that adversely affects the biodiversity, ecology, and economy. Both invasive and non-invasive species of the Caulerpa genus secrete more than thirty different secondary metabolites. Caulerpin is one of the most common secondary metabolites in genus Caulerpa. In this study, caulerpin found in invasive Caulerpa cylindracea and non-invasive Caulerpa lentillifera extracts were analyzed, quantified, and compared using high-performance thin layer chromatography (HPTLC) for the first time. The anticancer activities of caulerpin against HCT-116 and HT-29 colorectal cancer (CRC) cell lines were also tested. Caulerpin levels were found higher in the invasive form (108.83 ± 5.07 µg mL-1 and 96.49 ± 4.54 µg mL-1). Furthermore, caulerpin isolated from invasive Caulerpa decreased cell viability in a concentration-dependent manner (IC50 values were found between 119 and 179 µM), inhibited invasion-migration, and induced apoptosis in CRC cells. In comparison, no cytotoxic effects on the normal cell lines (HDF and NIH-3T3) were observed. In conclusion, HPTLC is a quick and novel method to investigate the caulerpin levels found in Caulerpa extracts, and this paper proposes an alternative utilization method for invasive C. cylindracea due to significant caulerpin content compared to non-invasive C. lentillifera.

Effects of currently used marine antifouling paint biocides on green fluorescent proteins in Anemonia viridis.

Some of the antifouling booster biocides affects the marine ecosystem negatively. The booster biocides that are resistant to degradation are accumulated in the sediment of the oceans. One of the sedentary organisms in the Mediterranean Sea is Anemonia viridis. This study aims at showing the toxicities of common biocides such as irgarol, seanine-211, zinc omadine, and acticide on the fluorescence by GFPs of A. viridis. The decreases in the fluorescence intensities of the GFP were measured within different booster biocide concentrations. The results show that fluorescent intensities of GFP proteins decrease more than 50% when they are exposed to different concentrations of irgarol, zinc omadine, acticide. In conclusion, ecosystem health should be prioritized when new antifouling paint compositions are proposed. From the results, it seems that A. viridis can be considered as a vulnerable organism and it is sensitive to booster biocides within self-polishing antifouling paint formulations.

Characterization of siderophores from Escherichia coli strains through genome mining tools: an antiSMASH study.

Although urinary tract infections (UTIs) affect many people, they are usually a disease observed in women. UTIs happen when exogenous and endogenous bacteria enter the urinary tract and colonize there. Cystitis and pyelonephritis occur when bacteria infect the bladder and the kidneys, respectively. UTIs become much serious if the bacteria causing the infection are antibiotic resistant. Since the pathogenic microorganisms have been adopted to current antibiotics via genetic variations, UTIs have become an even more severe health problem. Therefore, there is a great need for the discovery of novel antibiotics. Genome mining of nonpathogenic and pathogenic Escherichia coli strains for investigating secondary metabolites were conducted by the antiSMASH analysis. When the resulting secondary metabolites were examined, it was found that some of the siderophores are effective in UTIs. In conclusion, since the siderophore production in E. coli is directly related to UTIs, these molecules can be a good target for development of future pharmaceutical approaches and compounds. Siderophores can also be used in industrial studies due to their higher chelating affinity for iron.

Semi-Purified Saponins of Holothuria poli Associated Antiproliferation in Tumor Cell Lines.

The incidence of cancer has exhibited an increasing trend in recent years because of many reasons such as environmental and nutritional factors. There is a great need for the development of new and natural molecules with lower side effects in the therapy of cancer. It was aimed to evaluate the antiproliferative effect of semi-purified triterpene glycosides of Holothuria poli on different human cancer cell lines. The body walls of H. poli as the main sources of saponins were used and the saponin content of the extract was characterized by MALDI-TOF/MS. The antiproliferation activity of the characterized extract was tested on cancer cell lines. The extract showed antiproliferative effect on the studied cancer cell lines. The mass analysis results reveal that Holothurin A is one of the saponins within the extract. The measured IC50 values were found as 31.41 ± 2.20, 77.45 ± 0.23, and 34.79 ± 0.90 µg mL-1 for HT-29, UPCI-SCC-131, and T84 cell lines, respectively. H. poli secretes not only specific saponins but also a cocktail of them. Specific versus. cocktails of the saponins and by also applying organic modification must be studied in further research to understand their mechanisms in the antiproliferation studies since this paper reveals promising results.

Modelling of multilinear gradient retention time of bio-sweetener rebaudioside A in HPLC analysis.

Artificial neural network (ANN), as one of the artificial intelligence methods, has been widely using in HPLC studies for modelling purposes. Stevia rebaudiana is an important industrial plant due to its bio-sweetener molecule, rebaudioside-a, in its leaves. Although rebaudioside-a is up to 300-fold sweeter than sucrose, its calorie is almost zero. In this study, HPLC optimization of rebaudioside-a was studied and the optimization data based on multilinear gradient retention times were modelled by ANN. The input parameters were selected as concentrations, column temperatures, initial acetonitrile percentage for the first step of gradient elution, initial acetonitrile percentage for the second step of gradient elution, slope of acetonitrile, wavelengths, flow rates. The retention time was the output. Also, dried S. rebaudiana leaves were extracted and the concentrations were evaluated by HPLC. According to the ANN results, the most effective parameters on the prediction of non-linear gradient retention time for rebaudioside-a were found as flow rate and initial acetonitrile percentage for the second step of gradient. The best back propagation was selected as Levenberg-Marquardt algorithm. The highest rebaudioside-a level was found as 96.53 ± 6.36 µg mL-1. ANN modelling methods can be used in preparative HPLC applications to estimate the retention time of steviol glycosides.

Identification of Kiwellin-like Proteins in Fruits by Using In Silico Tools.

Identification of allergen proteins by using wet-lab technology is a time-consuming and also costly process. In recent years, thanks to the developments in the field of bioinformatics, it is now possible to estimate the allergen proteins by using in silico tools. In the present study, it is aimed to find kiwellin-like proteins from different fruits samples by using bioinformatics tools. According to the results of the study, six proteins from Corchorus olitorius, Cucumis sativus, Capsicum chinense, Carica papaya, Morus notabilis and Jatropha curcas were defined as the allergens. In conclusion, in silico tools developed under the field of bioinformatics can provide a big contribution to the estimation of unknown allergen proteins in different fruits. Based on the in silico results, physicians can suggest people who have allergenicity to kiwellin not to consume the fruits that contain kiwellin-like proteins.

In Silico Analysis of Bioactive Peptides in Invasive Sea Grass Halophila stipulacea.

Halophila stipulacea is a well-known invasive marine sea grass in the Mediterranean Sea. Having been introduced into the Mediterranean Sea via the Suez Channel, it is considered a Lessepsian migrant. Although, unlike other invasive marine seaweeds, it has not demonstrated serious negative impacts on indigenous species, it does have remarkable invasive properties. The present in-silico study reveals the biotechnological features of H. stipulacea by showing bioactive peptides from its rubisc/o protein. These are features such as antioxidant and hypolipideamic activities, dipeptidyl peptidase-IV and angiotensin converting enzyme inhibitions. The reported data open up new applications for such bioactive peptides in the field of pharmacy, medicine and also the food industry.

Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds.

Siphonous green seaweeds, such as Caulerpa, are among the most morphologically complex algae with differentiated algal structures (morphological niches). Caulerpa is also host to a rich diversity of bacterial endo- and epibionts. The degree to which these bacterial communities are species-, or even niche-specific remains largely unknown. To address this, we investigated the diversity of bacteria associated to different morphological niches of both native and invasive species of Caulerpa from different geographic locations along the Turkish coastline of the Aegean sea. Associated bacteria were identified using the 16S rDNA marker gene for three morphological niches, such as the endobiome, epibiome, and rhizobiome. Bacterial community structure was explored and deterministic factors behind bacterial variation were investigated. Of the total variation, only 21.5% could be explained. Pronounced differences in bacterial community composition were observed and variation was partly explained by a combination of host species, biogeography and nutrient levels. The majority of the explained bacterial variation within the algal holobiont was attributed to the micro-environments established by distinct morphological niches. This study further supports the hypothesis that the bacterial assembly is largely stochastic in nature and bacterial community structure is most likely linked to functional genes rather than taxonomy.

Neural Network Modeling of AChE Inhibition by New Carbazole-Bearing Oxazolones.

Acetylcholine esterase (AChE) is one of the targeted enzymes in the therapy of important neurodegenerative diseases such as Alzheimer's disease. Many studies on carbazole- and oxazolone-based compounds have been conducted in the last decade due to the importance of these compounds. New carbazole-bearing oxazolones were synthesized from several carbazole aldehydes and p-nitrobenzoyl glycine as AChE inhibitors by the Erlenmeyer reaction in the present study. The inhibitory effects of three carbazole-bearing oxazolone derivatives on AChE were studied in vitro and the experimental results were modeled using artificial neural network (ANN). The developed ANN provided sufficient correlation between several dependent systems, including enzyme inhibition. The inhibition data for AChE were modeled by a two-layered ANN architecture. High correlation coefficients were observed between the experimental and predicted ANN results. Synthesized carbazole-bearing oxazolone derivatives inhibited AChE under in vitro conditions, and further research involving in vivo studies is recommended. An ANN may be a useful alternative modeling approach for enzyme inhibition.

The Topology Prediction of Membrane Proteins: A Web-Based Tutorial.

There is a great need for development of educational materials on the transfer of current bioinformatics knowledge to undergraduate students in bioscience departments. In this study, it is aimed to prepare an example in silico laboratory tutorial on the topology prediction of membrane proteins by bioinformatics tools. This laboratory tutorial is prepared for biochemistry lessons at bioscience departments (biology, chemistry, biochemistry, molecular biology and genetics, and faculty of medicine). The tutorial is intended for students who have not taken a bioinformatics course yet or already have taken a course as an introduction to bioinformatics. The tutorial is based on step-by-step explanations with illustrations. It can be applied under supervision of an instructor in the lessons, or it can be used as a self-study guide by students. In the tutorial, membrane-spanning regions and α-helices of membrane proteins were predicted by internet-based bioinformatics tools. According to the results achieved from internet-based bioinformatics tools, the algorithms and parameters used were effective on the accuracy of prediction. The importance of this laboratory tutorial lies on the facts that it provides an introduction to the bioinformatics and that it also demonstrates an in silico laboratory application to the students at natural sciences. The presented example education material is applicable easily at all departments that have internet connection. This study presents an alternative education material to the students in biochemistry laboratories in addition to classical laboratory experiments.

Sulfation mediates activity of zosteric acid against biofilm formation.

Zosteric acid (ZA), a metabolite from the marine sea grass Zostera marina, has attracted much attention due to its attributed antifouling (AF) activity. However, recent results on dynamic transformations of aromatic sulfates in marine phototrophic organisms suggest potential enzymatic desulfation of metabolites like ZA. The activity of ZA was thus re-investigated using biofilm assays and simultaneous analytical monitoring by liquid chromatography/mass spectrometry (LC/MS). Comparison of ZA and its non-sulfated form para-coumaric acid (CA) revealed that the active substance was in all cases the non-sulfated CA while ZA was virtually inactive. CA exhibited a strong biofilm inhibiting activity against Escherichia coli and Vibrio natriegens. The LC/MS data revealed that the apparent biofilm inhibiting effects of ZA on V. natriegens can be entirely attributed to CA released from ZA by sulfatase activity. In the light of various potential applications, the (a)biotic transformation of ZA to CA has thus to be considered in future AF formulations.

Caulerpenyne and related bis-enol esters are novel-type inhibitors of human 5-lipoxygenase.

Caulerpenyne (CYN) is a sesquiterpene from green algae with known inhibitory properties against soybean lipoxygenase. Here we introduce a detailed structure-activity study elucidating the inhibitory effects of CYN and a library of six synthetic CYN analogues on isolated human 5-lipoxygenase (5-LO) and cellular 5-LO in polymorphonuclear leukocytes. Essential structural elements are identified and a structurally simplified inhibitor is introduced. The modes of 5-LO inhibition by CYN and the synthetic inhibitors cannot be assigned to any of the known categories of lipoxygenase inhibitors. These compounds clearly interfere directly with 5-LO and represent rather small and flexible molecules, with unique structures among 5-LO inhibitors identified thus far.

Synthesis of new ibuprofen derivatives with their in silico and in vitro cyclooxygenase-2 inhibitions.

Cyclooxygenase-2 (COX-2) is one of the important targets for treatment of inflammation related diseases. In the literature, most of drug candidates are first synthesized and then their COX-2 inhibitory activities are tested by in vitro and in vivo experiments. However, synthesis of dozens of drug analogues without any interpretations on their inhibitory activity can result in loss of time and chemicals. Therefore, synthetic drug designs with molecular modeling are of importance to synthesize selective drug candidates against inflammatory diseases. The synthesis of the novel ibuprofen derivatives through their in silico and in vitro COX-2 inhibitory activities were investigated in the present study. Starting from ibuprofen, ibuprofen amide and ibuprofen acyl hydrazone derivatives were synthesized. According to the results of the in silico molecular docking and in vitro enzyme inhibition studies, the synthesized novel ibuprofen derivatives have selective COX-2 inhibition, and molecule 3a and 3c were showed higher inhibition compared to ibuprofen. In conclusion, the newly synthesized ibuprofen derivatives can be used in model in vivo studies.

Molecular analysis of the KIT gene in gastrointestinal stromal tumors with novel mutations.

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. KIT gene mutations have great importance for GISTs. This study evaluated the relationship between KIT mutations and GIST clinicopathologic features to define region-specific and population-specific differences. Genomic DNA was extracted from 60 GISTs, and polymerase chain reaction was performed for KIT gene exons 9, 11, 13, and 17. Polymerase chain reaction amplicons were sequenced in both directions. This study represents the first mutation data of the KIT gene in GISTs from a Turkish population and reports novel mutations. The mutation rate in exon 11 (46.7%) was remarkably higher than those of the other exons (8.3% for exon 9; 11.7% for exon 13; 1.7% for exon 17). There was an association between malignancy potential and the presence of KIT mutations (odds ratio=3.18). Cases with mutations in codons W557-K558 in exon 11 had 11-fold greater risk of malignancy when compared with those without a mutation in this exon (odds ratio=11). We report different mutations than those previously reported, which emphasizes the importance of personalized medicine that could be empowered by the use of bioinformatics tools in the diagnostic process and therapeutic approaches.

The sesquiterpene caulerpenyne from Caulerpa spp. is a lipoxygenase inhibitor.

Many algae contain secondary metabolites with the potential to gain importance as pharmaceutically active secretions. Caulerpa racemosa var. cylindracea and Caulerpa prolifera are very abundant on the Mediterranean coastlines. The methanolic extracts of C. racemosa and C. prolifera were tested for inhibitory effects on soybean lipoxygenase. The extract of C. prolifera showed potent inhibitory effect in a lipoxygenase enzyme activity assay. HPLC comparison revealed that C. racemosa extract contained less caulerpenyne, the major secondary metabolite of both algae. In accordance with these findings, purified caulerpenyne inhibited lipoxygenase with an IC(50) of 5.1 µM. The enzyme kinetic studies indicated that both K (M) and V (max) decreased from 0.041 to 0.019 mM and 312.5 to 151.5 U mL(-1) in the presence of 5 µM caulerpenyne, revealing an un-competitive type of inhibition kinetics. The major secondary metabolite of Caulerpa species, caulerpenyne, is thus a novel lipoxygenase inhibitor that can be easily obtained in high quantities from the abundant algae.