Alteration of boza microbiota in the fermentation process

Boza is a fermented beverage containing beneficial microorganisms for human health. In our study, microbiota present in raw materials used boza production (corn flour, wheat flour, and mayşe), 1st day, 3rd day of boza fermentation and 4th day final product of boza, has been identified by Next Generation DNA Sequencing and metagenomic analysis. As a result of genus-level analysis directly from corn flour and wheat flour samples contained dominantly Streptophyta and Pleomorphobacterium, while in the 1st day, 3rd day, the final product of boza and boza ferment the dominant bacteria were Leuconostoc and Lactococcus at genus level. In the analysis of the pre-enriched samples, the dominant bacteria in corn flour were Enterococcus, Klebsiella, and Micromonospora and in wheat flour were Pantoea and Bacillus. Boza ferment, boza on the 1st day, boza on the 3rd day and the final product of boza dominantly contained Lactococcus. The bacterial diversity, similarity and differences among samples were analyzed by Principal Coordinate Analysis and dendrogram construction. The contribution of raw materials used in the production of boza change to the products at the fermentation stage and to the microbiota during the fermentation process and their contribution to the final product were determined by metagenomic analysis at DNA level.Boza, insan sağlığı için yararlı mikroorganizmaları içeren fermente bir içecektir. Çalışmamızda boza üretiminde ham madde olarak kullanılan (mısır unu, buğday unu, mayşe) ve boza fermantasyonunun 1. günü, 3. günü ve 4. gün son ürün boza’nın içerdiği mikrobiyota Yeni Nesil DNA Dizileme yöntemi ve metagenomik analiz ile ortaya çıkarılmıştır. Örneklerden doğrudan cins düzeyinde yapılan analiz sonucunda, mısır unu ve buğday ununda dominant olarak Streptophyta ve Pleomorphobacterium bulunurken; bozanın 1. gün, 3. gün ve son ürün ile boza mayasında dominant bakterilerin Leuconostoc ve Lactococcus cinsine ait olduğu tespit edilmiştir. Ön zenginleştirme yapılan örneklerin analizinde, mısır ununda dominant bakteriler Enterococcus, Klebsiella ve Micromonospora, buğday ununda ise Pantoea ve Bacillus olduğu, boza mayası, 1. gün boza, 3. gün boza ve satışa sunulan son üründe dominant bakteri Lactococcus olarak belirlenmiştir. Çalışmamızda örnekler arasındaki bakteriyel çeşitlilik, benzerlik ve farklılıklar Principal Coordinate Analiz ve dendrogram oluşturulması ile ortaya konmuştur. Boza üretiminde kullanılan ham maddelerin bozanın fermantasyon aşamalarındaki ürünler ile fermantasyon sürecinde mikrobiyotasına nasıl değiştiği ve son ürüne olan katkıları, DNA düzeyinde yapılan metagenomik analizler ile belirlenmiştir

Nükleik asit kapaklı nanogözenekli antibiyotik taşınımı.

Discovery of new strategies in administration of antimicrobial agents are essential in the ongoing battle against pathogens due to rapidly emerging antimicrobial resistance. Nanotechnology provide unique opportunities in this respect for the development of targeted drug delivery solutions for effective usage of current antibiotics. Mesoporous silica particles are micrometer-sized particles with nanometer-sized porous surface structure. They are advantageous molecules due to small size, biocompatibility, well-defined pore size and modifiable surface. Functional nucleic acids have potential to target the drug loaded nanoparticles. From this perspective, affinity capabilitiy of aptamers and enzymatic cleavage of capability of nucleic acid oligos, targeting of nanoparticles was experimented in this study. Incorporation of Staphylococcus aureus aptamer and an oligo sequence specific to micrococcal nuclease were analysed against the hypothesis that, sealing of drug loaded nanopores with nucleic acids having a function to release the drug in the presence of a specific target, thus increasing the efficiency of drug and decreasing the risk of antibiotic resistance. Staphylococcus epidermidis was used as control organisms and vancomycin was used as antimicrobial drug for proving the specifity of the system. Nanoparticles with cleavega-oriented oligo sealing mechanism decreased the MIC of vancomycin against S. aures strain from 1.061µg/mL to 0.332µg/mL, while affinity-oriented aptamer sealing mechanism functioned with a decreased MIC for S. aures strain from 1.168µg/mL to 0.420µg/mL. In both mechanisms, MIC against Staphylococcus epidermidis increased proving the specifity of antibiotic delivery. The inhibitory performance of proposed targeted drug delivery mechanism proved its potential for further applications and developments.Ph.D. - Doctoral Progra

Pestisitlerin belirlenmesi için asetilkolinesteraz biyosensörünün geliştirilmesi.

Pesticides are natural or artificial molecules aimed to kill, or mitigate any harmful organism. Although their use in agriculture provides us with an increased crop yield, remains of chemicals on the products creates health concerns in society. Organophosphates and carbamates are two groups of insecticides. Although they are far more lethal against insects and small animals, they can also cause poisoning in humans through the inhibition of acetylcholinesterase enzyme (AChE) that plays an important role in human nervous system. Therefore, the detection of these compounds is crucial. The conventional methods for the detection of these compounds are expensive, time-consuming and need expertise. In this study, a fast, disposable, cheap and accurate acetylcholinesterase biosensor was developed to detect organophosphate and carbamate-based pesticide residues. By means of adsorption method, AChE, the chromophore 5,5'-Dithio-bis(2-nitrobenzoic acid) (DTNB) and artificial substrate acetylthiocholine (ATCh) were immobilized on the supporting material. In optimization studies; from 3 to 15U/mL concentrations were experimented for AChE, 1 to 5mM DTNB and 1 to 5mM ATCh concentration gradients were used. v As a result of the optimization studies 12U/mL ACHE concentration, 5mM DTNB concentration and 5mM ATCh concentration were determined for constructing a pesticide biosensor. Detection limit of malathion, an organophosphate-based insecticide was found as 2.5ppm in 5% methanol solution. The biosensor conserved its integrity between pH 4 and 8, and gave false positive results after pH 10. Stability studies showed that, biosensor retained its activity for at least 60 days at 4°C to discrimnate between positive and negative controls.M.S. - Master of Scienc

FEN BİLİMLERİ ENSTİTÜSÜ/LİSANSÜSTÜ TEZ PROJESİ

APTAMERLERİN MİKROKÜRE KULLANILARAK SEÇİMİ İÇİN YÖNTEM GELİŞTİRİLMES

In Silico Evaluation of Antimicrobial Potential of Amaranth, Chia and Quinoa Peptides Released During the Simulated Gastric Digestion and Their Effects on Helicobacter pylori: In silico antimicrobial potential study of amaranth, chia and quinoa peptid

Helicobacter pylori is the most common cause of peptic ulcers and gastroduodenal pathologies and has been identified by the World Health Organization as a serious threat to human health. The increasing antibiotic resistance of H. pylori necessitates prevention and early intervention, as well as the discovery of novel drugs. Amaranth, chia, and quinoa are classified as pseudocereals and are known as superfoods because of their nutritional density. The effect of consuming these pseudocereals at the onset of H. pylori infection was investigated using in silico methods. 34 proteins from amaranth, chia, and quinoa were subjected to in silico pepsin digestion, and antimicrobial, antibiofilm, and cell-penetrating activities of the released peptides were analyzed. Peptides predicted to be cell-penetrating were further used for peptide-protein docking. 58 peptides were predicted to have antimicrobial activity whereas 76 were predicted to have antibiofilm activity. A total of 116 peptides were classified as cell-penetrating peptides, and those with the highest scores were used for peptide-protein docking with shikimate dehydrogenase, type II dehydroquinase, and D-alanine-D-alanine ligase of H. pylori to evaluate their enzyme inhibition potential. A peptide released from the chia seed proteins A0A1Z1EC55 and A0A1Z1EC46 with the sequence SWKYSHRRHHSNTGSL gave the highest docking energy scores for all three enzymes. To the best of our knowledge, this is the first work concerning the effect of ingested food on H. pylori infection. We believe our results will provide valuable data and a new point of view for the scientists interested in this topic. HIGHLIGHTS H. pylori is a common infection and the leading cause of gastroduodenal pathologies. Gastric digestion of amaranth, chia, and quinoa proteins with pepsin revealed antimicrobial and antibiofilm peptides that may be effective against H. pylori growth. One particular peptide SWKYSHRRHHSNTGSL had high docking energy scores when docked to the three enzymes of H. pylori

Portable Bioactive Paper-Based Sensor for Quantification of Pesticides

A paper-based biosensor was developed for the detection of the degradation products of organophosphorus pesticides. The biosensor quantifies acetylcholine esterase inhibitors in a fast, disposable, cheap, and accurate format. We specifically focused on the use of sugar or protein stabilizer to achieve a biosensor with long shelf-life. The new biosensor detected malathion with a detection limit of 2.5 ppm in 5 min incubation time. The operational stability was confirmed by testing 60 days storage at 4°C when glucose was used as stabilizer

KBRN Ajanlarına Yönelik Nükleik Asit Tabanlı Tespit Yöntemlerinin Geliştirilmesi

Eski çağlarından beri bulaşıcı hastalığa sebep olan mikroorganizmalar, mantarlar yada mikrobiyal toksinler savaş sırasında insan, hayvan ve bitkilere zarar vermek için kullanılmıştır. Günümüzde ise bilgi ve teknolojiye erişimin geniş kitlelere yayılması ile doğru orantılı olarak kitle imha silahı olarak kullanılma olasılıkları da artmıştır. Biyolojik ajanların yarattığı tehlikeler sadece terörist saldırılarla da sınırlı değildir. Artan küresel ticaret ve yolcu taşımacılığı doğal yollarla ortaya çıkan bulaşıcı hastalıkların hızla yayılmalarına ve çok sayıda insanı etkilemelerine yol açmaktadır. Tüm bu sebeplerden KBRN ajanlarının yüksek doğruluk, kesinlik ve hassasiyetle belirlenmesine yönelik uygun yöntemlerin geliştirilmesi büyük önem taşımaktadır. Biyolojik ajanların tespiti için birçok teknik mevcuttur. Nükleik asit tabanlı tespit sistemleri hassasiyet ve tanı konusunda immüno tabanlı yeni nesil tanı sistemlere göre çok daha üstündür. Ayrıca konvansiyonel mikrobiyoloji yöntemlerine göre daha kısa sürede sonuç vermektedir. Önerilen projede KBRN kapsamında kullanılabilecek biyolojik ajanların tespitine yönelik nükleik asit tabanlı tespit sistemlerinin geliştirilmesi amaçlanmaktadır. Projemiz kapsamında çeşitli biyolojik ajanların uygun bir şekilde saflaştırılması ve saflaştırılan DNA’lardan ajanlara özgün bölgelerin çoğaltılması üzerinde Ar-Ge çalışmalarının gerçekleştirilmesi hedeflenmektedir

Antimicrobial aptamers for detection and inhibition of microbial pathogen growth

Discovery of alternative sources of antimicrobial agents are essential in the ongoing battle against microbial pathogens. Legislative and scientific challenges considerably hinder the discovery and use of new antimicrobial drugs, and new approaches are in urgent demand. On the other hand, rapid, specific and sensitive detection of airborne pathogens is becoming increasingly critical for public health. In this respect affinity oligonucleotides, aptamers, provide unique opportunities for the development of nanotechnological solutions for such medical applications. In recent years, aptamers specifically recognizing microbial cells and viruses showed great potential in a range of analytical and therapeutic applications. This article describes the significant advances in the development of aptamers targeting specific pathogens. Therapeutic application of aptamers as neutralizing agents demonstrates great potential as a future source of antimicrobial agent

Aptamers: molecular tools for medical diagnosis

WOS:000353246400006PubMed:25866272Aptamers have been increasingly applied in biomedical field as a class of biorecognition elements that possess many advantages such as high specificity and binding affinity, easy synthesis, easy modification, small size, non-toxicity and good stability. Many diseases like cancer exhibit cellular aberrations at morphological and molecular levels. Medical diagnosis based on molecular features can be highly specific and extremely sensitive when proper recognition molecule and an efficient signal transduction system are employed. However, bioanalysis of human diseases at the molecular level is an extremely challenging field because effective probes to identify and recognize biomarkers of diseases are not readily available. Traditional bio-recognition molecule, antibody has been exploited to develop excellent diagnosis assays in many formats, but antibodies are insufficient to match the requirements of fast and portable biosensors for point-of-care applications, which are at high demand in pathogenic bacteria detection as well as other diseases like cancer. Aptamers are short single-stranded oligonucleotides, which can be selected from random combinatorial library by SELEX in vitro. This relatively new biorecognition agent has superior intrinsic characteristics for biosensor development. In this review, we first present major aptamer selection technologies and the main formats of biosensors, which were frequently employed in aptasensor development. Then, the current state of aptamers as applied to medical diagnosis was discussed for specifically cancer and pathogen diagnosis. Finally, an overview of aptamer-nanomaterials conjugates was presented in many applications such as diagnosis, bioimaging, and theranostics.TUBITAK ProjectTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [213M315]This review has been written as part of the TUBITAK Project 213M315