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Öğe A novel in-vitro digestion model designed by integration of microbiome associated enzymes(Çanakkale Onsekiz Mart Üniversitesi, Lisansüstü Eğitim Enstitüsü, 2022) Kaplan, Merve; Karav, Sercanİnsan mikrobiyotası, milyonlarca sayıda mikroorganizma içermektedir ve bu mikroorganizmalar beyin bağırsak etkileşimi ve enerji metabolizması gibi birçok önemli biyolojik fonksiyonda görev almaktadır. Özellikle, birçok komensal bakteri sahip oldukları özel enzim sistemi ile sindirim işleminde önemli roller oynamaktadır. Glikan diye isimlendirilen prebiyotik bileşenler, insan enzimleri tarafından sindirilemediklerinden bağırsağa kadar denatürasyona uğramadan ulaşmaktadırlar. Bağırsakta ise bazı bakteriler sahip oldukları enzimler (glikozidazlar vb.) sayesinde glikanları karbon kaynağı olarak kullanabilmektedir. Glikanlar gibi prebiyotiklerin sindirilme mekanizmasını daha iyi anlamak için in-vitro sindirim modelleri kullanılmaktadır. Fakat, kullanılan in-vitro sindirim modellerinde sadece insan kaynaklı enzimlerin yer alması bu modellerin mikroorganizmaların sindirimdeki etkisini inceleyen çalışmalarda kullanılmasını engellemektedir. Bu yüzden, mikrobiyal enzimlerin yer aldığı yeni sindirim modellerinin tasarımı glikan çalışmaları için kritik öneme sahiptir. Bu tez kapsamında, öncelikle insan sindirim sisteminin farklı bölgelerinde baskın olarak bulunan mikroorganizmalar ve bu mikroorganizmalara ait glikozidaz enzimleri biyoinformatik yöntemler kullanılarak belirlenmiştir. Belirlenen ve seçilen 32 glikozidaz rekombinant olarak uygun bir moleküler klonlama sistemi ile klonlanmış ve üretilmiştir. Üretilen rekombinant enzimler, sadece insan kökenli sindirim enzimlerini içeren standart bir in-vitro sindirim modeline entegre edilmiştir ve bir glikoprotein kaynağı olan whey üzerinde test edilmiştir.Öğe Benefits of A2 Milk for Sports Nutrition, Health and Performance(Frontiers Media Sa, 2022) Kaplan, Merve; Baydemir, Baris; Gunar, Bilgetekin Burak; Arslan, Aysenur; Duman, Hatice; Karav, SercanBovine milk is one of the best pre-and pro-workout sources for athletes owing to its rich nutritional content. Even though bovine milk consumption significantly benefits athletes' health and performance, many athletes cannot consume bovine milk since they struggle with gastrointestinal problems caused after milk consumption. Especially, the consumption of regular milk, which contains A1 beta -casein, is associated with a variety of diseases ranging from gastrointestinal discomfort to ischemic heart diseases. The main reason behind this is related to beta -casomorphine 7 (BCM-7), which is derived from A1 beta -casein during the digestion of A1 milk. A1 beta -casein is formed as a result of a point mutation in the position of 67(th) in the amino acid sequence A2 beta -casein by changing proline to histidine. Therefore, this mutated form of beta -casein in regular milk cannot easily be digested by the human-associated digestion enzymes. A2 milk, which includes A2 beta -casein instead of A1 beta -casein, is the best substitute for regular milk with the same nutritional content. This natural form of milk positively affects the athlete's health as well as performance without causing any gastrointestinal discomfort or more serious problems which are seen in the consumption of regular milk. In this review, A2 milk and its potential health effects in comparison to diseases related to A1 milk consumption are discussed.Öğe Bovine Colostrum and Its Potential for Human Health and Nutrition(Frontiers Media S.A., 2021) Arslan, Ayşenur; Kaplan, Merve; Duman, Hatice; Bayraktar, Ayşe; Karav, Sercan; Ertürk, Melih; Henrick, Bethany M.; Frese, Steven A.Colostrum is the first milk produced post-partum by mammals and is compositionally distinct from mature milk. Bovine colostrum has a long history of consumption by humans, and there have been a number of studies investigating its potential for applications in human nutrition and health. Extensive characterization of the constituent fractions has identified a wealth of potentially bioactive molecules, their potential for shaping neonatal development, and the potential for their application beyond the neonatal period. Proteins, fats, glycans, minerals, and vitamins are abundant in colostrum, and advances in dairy processing technologies have enabled the advancement of bovine colostrum from relative limitations of a fresh and unprocessed food to a variety of potential applications. In these forms, clinical studies have examined bovine colostrum as having the substantial potential to improve human health. This review discusses the macro-and micronutrient composition of colostrum as well as describing well-characterized bioactives found in bovine colostrum and their potential for human health. Current gaps in knowledge are also identified and future directions are considered in order to elevate the potential for bovine colostrum as a component of a healthy diet for a variety of relevant human populations.Öğe Climate change and the ocean economy: A review on OECD's ocean economy(IGI Global, 2023) Yildirim, Seda; Kaplan, Merve; Yildirim, Durmus CagriThe ocean economy is directly linked to the biodiversity of the ocean. Biodiversity is under great threat as a result of the effects of climate change and global warming. Therefore, the ocean economy and the marine economy are among the economies that will be most affected by the effects of climate change. Each change in ocean and sea levels causes changes in biodiversity. Considering its importance in terms of food health, economic and social development, the sustainability of the marine economy is an important issue. The aim of this study is to present indicators of ocean economy among OECD countries and show the importance of ocean and marine economy in the long term. © 2023, IGI Global.Öğe Determining Total Protein and Bioactive Protein Concentrations in Bovine Colostrum(Journal of Visualized Experiments, 2021) Arslan, Ayşenur; Duman, Hatice; Kaplan, Merve; Uzkuç, Hasan; Bayraktar, Ayşe; Erturk, Melih; Alkan, Merve; Karav, SercanColostrum is a complex biological fluid produced by mammals immediately after parturition. It meets all the nutritional requirements for neonates as a good source of macro-and micronutrients, bioactive peptides, and growth factors. Bovine colostrum is also a potential source of nutrition and bioactive because of its rich protein content that includes immunoglobulin G (IgG) and lactoferrin. However, the level of lactoferrin and IgG in bovine colostrum changes markedly during the lactation period. Therefore, monitoring the concentration of IgG and lactoferrin for the use of bovine colostrum as a protein source is an important question to study. Methods in this article describe how to determine protein content, as well as specific concentrations of lactoferrin and IgG. These methods include the following steps: Isolation of bovine colostrum proteins, Determination of protein concentration via Bicinchoninic acid assay (BCA), Visualization of proteins via SDS-PAGE, Determination of lactoferrin, and IgG concentration using an ELISA Assay.Öğe Immobilization of a Bifidobacterial Endo-ss-N-Acetylglucosaminidase to Generate Bioactive Compounds for Food Industry(Frontiers Media Sa, 2022) Pekdemir, Burcu; Duman, Hatice; Arslan, Aysenur; Kaplan, Merve; Karyelioglu, Melda; ozer, Tolgahan; Kayili, Haci MehmetConjugated N-glycans are considered next-generation bioactive prebiotic compounds due to their selective stimulation of beneficial microbes. These compounds are glycosidically attached to proteins through N-acetylglucosamines via specific asparagine residue (AsN-X-Ser/Thr). Certain bacteria such as Bifidobacterium longum subspecies infantis (B. infantis) have been shown to be capable of utilizing conjugated N-glycans, owing to their specialized genomic abilities. B. infantis possess a unique enzyme, Endo-ss-N-acetylglucosaminidase (EndoBI-1), which cleaves all types of conjugated N-glycans from glycoproteins. In this study, recombinantly cloned EndoBI-1 enzyme activity was investigated using various immobilization methods: 1) adsorption, 2) entrapment-based alginate immobilization, 3) SulfoLink-, and 4) AminoLink-based covalent bonding immobilization techniques were compared to develop the optimum application of EndoBI-1 to food processes. The yield of enzyme immobilization and the activity of each immobilized enzyme by different approaches were investigated. The N-glycans released from lactoperoxidase (LPO) using different immobilized enzyme forms were characterized using MALDI-TOF mass spectrometry (MS). As expected, regardless of the techniques, the enzyme activity decreased after the immobilization methods. The enzyme activity of adsorption and entrapment-based alginate immobilization was found to be 71.55% +/- 0.6 and 20.32% +/- 3.18, respectively, whereas the activity of AminoLink- and SulfoLink-based covalent bonding immobilization was found to be 58.05 +/- 1.98 and 47.49% +/- 0.30 compared to the free form of the enzyme, respectively. However, extended incubation time recovery achieved activity similar to that of the free form. More importantly, each immobilization method resulted in the same glycan profile containing 11 different N-glycan structures from a model glycoprotein LPO based on MALDI-TOF MS analysis. The glycan data analysis suggests that immobilization of EndoBI-1 is not affecting the enzyme specificity, which enables full glycan release without a limitation. Hence, different immobilization methods investigated in this study can be chosen for effective enzyme immobilization to obtain bioactive glycans. These findings highlight that further optimization of these methods can be a promising approach for future processing scale-up and commercialization of EndoBI-1 and similar enzymes.Öğe Lactoferrin for COVID-19 prevention, treatment, and recovery(Frontiers Media Sa, 2022) Bolat, Ecem; Eker, Furkan; Kaplan, Merve; Duman, Hatice; Arslan, Aysenur; Saritas, Suemeyye; Sahutoglu, Arif SercanSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), a unique beta-coronavirus, has caused the most serious outbreak of the last century at the global level. SARS-CoV-2 infections were firstly reported in the city of Wuhan in China in 2019 and this new disease was named COVID-19 by World Health Organization (WHO). As this novel disease can easily be transmitted from one individual to another via respiratory droplets, many nations around the world have taken several precautions regarding the reduction in social activities and quarantine for the limitation of the COVID-19 transmission. SARS-CoV-2 is known to cause complications that may include pneumonia, acute respiratory distress syndrome (ARDS), multi-organ failure, septic shock, and death. To prevent and treat COVID-19, some significant studies have been conducted since the outbreak. One of the most noticeable therapeutic approaches is related to a multifunctional protein, lactoferrin. Lactoferrin (Lf) is an 80 kDa cationic glycoprotein that has a great range of benefits from improving the immunity to antiviral effects due to its unique characteristics such as the iron-binding ability. This review summarizes the characteristics of SARS-CoV-2 and the potential applications of Lf for the prevention, treatment, and recovery of COVID-19.Öğe Lactoferrin: A Promising Therapeutic Molecule against Human Papillomavirus(Mdpi, 2024) Kaplan, Merve; Baktiroglu, Merve; Kalkan, Arda Erkan; Canbolat, Ahmet Alperen; Lombardo, Mauro; Raposo, Antonio; Alves, Jose Luiz de BritoLactoferrin is a multifunctional glycoprotein naturally found in mammalian secretions, predominantly in colostrum and milk. As a key component of dairy foods, lactoferrin enhances viral protection and boosts human health, owing to its fundamental properties including antiviral, anti-inflammatory, and immune-modulatory effects. Importantly, the antiviral effect of lactoferrin has been shown against a range of viruses causing serious infections and threatening human health. One of the viruses that lactoferrin exerts significant antiviral effects on is the human papillomavirus (HPV), which is the most prevalent transmitted infection affecting a myriad of people around the world. Lactoferrin has a high potential to inhibit HPV via different mechanisms, including direct binding to viral envelope proteins or their cell receptors, thereby hindering viral entry and immune stimulation by triggering the release of some immune-related molecules through the body, such as lymphocytes. Along with HPV, lactoferrin also can inhibit a range of viruses including coronaviruses and hepatitis viruses in the same manner. Here, we overview the current knowledge of lactoferrin and its effects on HPV and other viral infections.Öğe N-glycans from human milk glycoproteins are selectively released by an infant gut symbiont in vivo(Elsevier, 2019) Karav, Sercan; Casaburi, Giorgio; Arslan, Aysenur; Kaplan, Merve; Sucu, Berfin; Frese, StevenComplex, indigestible free oligosaccharides as well as conjugated glycans are found in milk that shape the gut microbiome of infants. The activity of an endo-beta-N-acetylglucosaminidase from B. longum subsp. infantis (B. infantis) is known to release N-glycans from native milk glycoproteins under physiological conditions. We investigated whether this enzyme is active in vivo in breastfed infants fed B. infantis EVC001. Using mass spectrometry, we found 19 N-glycans related to human milk glycoproteins increased in abundance, similar to previous work using bovine milk glycoproteins, and these 19 N-glycans matched unique specificities of this enzyme. Twenty N-glycans were unique to infants fed B. infantis EVC001. Bifidobacteriaceae were correlated with these glycans, confirming the relationship between B. infantis and released N-glycans. This suggests that this enzyme is active in vivo and releases N-glycans from milk glycoproteins, and may play a role in B. infantis EVC001 colonization of the gut microbiome.Öğe Phage-encoded carbohydrate-interacting proteins in the human gut(Frontiers Media S.A., 2023) Rothschild-Rodriguez, Daniela; Hedges, Morgen; Kaplan, Merve; Karav, Sercan; Nobrega, Franklin L.In the human gastrointestinal tract, the gut mucosa and the bacterial component of the microbiota interact and modulate each other to accomplish a variety of critical functions. These include digestion aid, maintenance of the mucosal barrier, immune regulation, and production of vitamins, hormones, and other metabolites that are important for our health. The mucus lining of the gut is primarily composed of mucins, large glycosylated proteins with glycosylation patterns that vary depending on factors including location in the digestive tract and the local microbial population. Many gut bacteria have evolved to reside within the mucus layer and thus encode mucus-adhering and -degrading proteins. By doing so, they can influence the integrity of the mucus barrier and therefore promote either health maintenance or the onset and progression of some diseases. The viral members of the gut – mostly composed of bacteriophages – have also been shown to have mucus-interacting capabilities, but their mechanisms and effects remain largely unexplored. In this review, we discuss the role of bacteriophages in influencing mucosal integrity, indirectly via interactions with other members of the gut microbiota, or directly with the gut mucus via phage-encoded carbohydrate-interacting proteins. We additionally discuss how these phage-mucus interactions may influence health and disease states.Öğe Potential Applications of Endo-beta-N-Acetylglucosaminidases From Bifidobacterium longum Subspecies infantis in Designing Value-Added, Next-Generation Infant Formulas(Frontiers Media S.A., 2021) Duman, Hatice; Kaplan, Merve; Arslan, Ayşenur; Şahutoglu, Arif Sercan; Karav, Sercan; Kayılı, Hacı Mehmet; Frese, Steven A.Human milk is the optimal source of infant nutrition. Among many other health benefits, human milk can stimulate the development of a Bifidobacterium-rich microbiome through human milk oligosaccharides (HMOs). In recent years, the development of novel formulas has placed particular focus on incorporating some of the beneficial functional properties of human milk. These include adding specific glycans aimed to selectively stimulate the growth of Bifidobacterium. However, the bifidogenicity of human milk remains unparalleled. Dietary N-glycans are carbohydrate structures conjugated to a wide variety of glycoproteins. These glycans have a remarkable structural similarity to HMOs and, when released, show a strong bifidogenic effect. This review discusses the biocatalytic potential of the endo-β-N-acetylglucosaminidase enzyme (EndoBI-1) from Bifidobacterium longum subspecies infantis (B. infantis), in releasing N-glycans inherently present in infant formula as means to increase the bifidogenicity of infant formula. Finally, the potential implications for protein deglycosylation with EndoBI-1 in the development of value added, next-generation formulas are discussed from a technical perspective.Öğe Production of Bovine Colostrum for Human Consumption to Improve Health(Frontiers Media Sa, 2022) Kaplan, Merve; Arslan, Aysenur; Duman, Hatice; Karyelioglu, Melda; Baydemir, Baris; Guenar, Bilgetekin Burak; Alkan, MerveColostrum contains all essential nutrients for the neonate during the first days of life, with impacts that continue far beyond these first days. Bovine colostrum has been used for human consumption due to the high concentrations of bioactive proteins, vitamins, minerals, growth factors, as well as free and conjugated oligosaccharides. Processes involved in the preparation of bovine colostrum for human consumption play a pivotal role in preserving and maintaining the activity of the bioactive molecules. As bovine colostrum is a multifunctional food that offers a myriad of benefits for human health, assessing the main processes used in preparing it with both advantages and disadvantages is a crucial point to discuss. We discuss major processes effects for colostrum production on the nutritional value, some advanced technologies to preserve processed bovine colostrum and the end-product forms consumed by humans whether as dairy products or dietary supplements.Öğe Recombinant Production of Bifidobacterial Endoglycosidases for N-glycan Release(Journal of Visualized Experiments, 2021) Sucu, Berfin; Bayraktar, Ayşe; Duman, Hatice; Arslan, Ayşenur; Kaplan, Merve; Karyelioğlu, Melda; Ntelitze, Eda; Taştekin, Taner; Yetkin, Seray; Karav, SercanProtein glycosylation is a diverse and common post-translational modification that has been associated with many important roles such as protein function, including protein folding, stability, enzymatic protection, and biological recognition. N-glycans attached to glycoproteins (such as lactoferrin, lactadherin, and immunoglobulins) cannot be digested by the host and reach the large intestine, where they are consumed by certain beneficial microbes. Therefore, they are considered next-generation prebiotic compounds that can selectively stimulate the gut microbiome's beneficial microorganisms. However, the isolation of these new classes of prebiotics requires novel enzymes. Here, we describe the recombinant production of novel glycosidases from different Bifidobacteria strains (isolated from infants, rabbits, chicken, and bumblebee) for improved N-glycan isolation from glycoproteins. The method presented in this study includes the following steps: molecular cloning of Bifidobacterial genes by an in vivo recombinational cloning strategy, control of transformation success, protein induction, and protein purification.Öğe Release of bifidogenic N-glycans from native bovine colostrum proteins by an endo-?-N-acetylglucosaminidase(Elsevier Inc., 2023) Bunyatratchata, Apichaya; Parc, Annabelle Le; de Moura Bell, Juliana Maria Leite Nobrega; Cohen, Josh L.; Duman, Hatice; Arslan, Ayşenur; Kaplan, Merve; Barile, Daniela; Karav, SercanMilk glycoproteins play various biological roles including antibacterial, antiviral activities, modulating immune responses in living organisms. Released N-glycans from milk glycoproteins act as growth substrates for infant-associated bifidobacteria, which are key members of the breastfed infant's gut. To date, the mechanisms, and contributions of glycans to the biological activities of glycoproteins remain to be elucidated. Only by testing both the released glycans and the deglycosylated protein in their native (i.e., non-denatured) form, can the individual contribution to the biological activity of glycoproteins be elucidated. However, for conventional enzymatic and chemical deglycosylation strategies to work efficiently, glycoprotein denaturation is required, which alters the protein native shape, hindering further investigations of its biological roles. An endo-β-N-acetylglucosaminidase (EndoBI-1) from Bifidobacterium longum subsp. infantis ATCC 15697 (B. infantis) was characterized as having the ability to release N-glycans from bovine milk glycoproteins efficiently, without the denaturation. In this study, the activity of EndoBI-1 was compared to a commercial enzyme to release N-glycans, the peptide-N-glycosidase F (PNGase F), using dairy glycoproteins as the substrate. The kinetic evaluation showed that EndoBI-1 displayed higher activity on native glycoproteins than PNGase F, with 0.036 mg/mL×min and 0.012 mg/mL×min glycan release, respectively. EndoBI-1 released a broader array of glycan structures compared to PNGase F from native glycoproteins. Thirty-two and fifteen distinct compositions were released from the native glycoproteins by EndoBI-1 and PNGase F, respectively, as characterized by advanced mass spectrometry. EndoBI-1 can be considered a promising enzyme for the release of N-glycans and their protein backbone in the native form, which will enable effective glycan release and will facilitate subsequent investigations to reveal their contribution to glycoproteins’ biological roles.Öğe Role of milk glycome in prevention, treatment, and recovery of COVID-19(Frontiers Media Sa, 2022) Kaplan, Merve; Sahutoglu, Arif Sercan; Saritas, Sumeyye; Duman, Hatice; Arslan, Aysenur; Pekdemir, Burcu; Karav, SercanMilk contains all essential macro and micro-nutrients for the development of the newborn. Its high therapeutic and antimicrobial content provides an important function for the prevention, treatment, and recovery of certain diseases throughout life. The bioactive components found in milk are mostly decorated with glycans, which provide proper formation and modulate the biological functions of glycosylated compounds. The glycome of milk consists of free glycans, glycolipids, and N- and O- glycosylated proteins. Recent studies have shown that both free glycans and glycan-containing molecules have antiviral characteristics based on different mechanisms such as signaling, microbiome modulation, natural decoy strategy, and immunomodulatory action. In this review, we discuss the recent clinical studies and potential mechanisms of free and conjugated glycans' role in the prevention, treatment, and recovery of COVID-19.
