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

Genetic diversity of gluten protein pattern of wheat cultivars and their importance in dough making properties of flour

Ph.D. - Doctoral Progra

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

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

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

The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain

Access to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.This research was supported by funds provided by the Ege University Scientific Research Projects Coordination Department (BAP) under project number FBG-2020-22532 > and TUBITAK (Scientific and Technological Research Council of Turkiye) under project number 222Z189 >. Financial support by TUBITAK and BAP is gratefully acknowledged.TUBITAK; BAP; Ege University Scientific Research Projects Coordination Department (BAP) [FBG-2020-22532]; TUBITAK (Scientific and Technological Research Council of Turkiye) [222Z189