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The gas-phase fragmentation reactions of the a(7) ions derived from glutamine (Q) containing model heptapeptides have been studied in detail with low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). Specifically, the positional effect of the Q residue has been investigated on the fragmentation reactions of a(7) ions. The study involves two sets of permuted isomers of the Q containing model heptapeptides. The first set contains the QAAAAAA sequence, and the second set involves of QYAGFLV sequence, where the position of the Q residue is changed from N- to C-terminal gradually for both peptide series. An intense loss of ammonia from the a7 ions followed by internal amino acid eliminations strongly supports forming the imine-amides structure via cyclization/rearrangement reaction for all studied a(7) ions. This is in agreement with the pioneering study reported by Bythell et al. (2010, 10.1021/ja101556g). A novel rearrangement reaction is detected upon fragmentation of imine-amide structure, which yields a protonated C-terminal amidated hexapeptide excluding the Q residue. A possible fragmentation mechanism was proposed to form the protonated C-terminal amidated hexapeptide, assisted via nucleophilic attack of the side chain amide nitrogen of the Q residue on its N-protonated imine carbon atom of the rearranged imine-amide structure. Highlights The gas-phase fragmentation reactions of a(7) ions obtained from protonated model peptides containing glutamine residue were studied by ESI-MS/MS. A rearranged imine-amide structure is the predominant even for a(7) ions. Novel rearrangement reaction is observed which forms a protonated C-terminal amidated hexapeptide excluding Q residue upon fragmentation of the imine-amide structure.

Characterization of ε-N-acetylated lysine containing peptides, one of the most prominent post-translational modifications of proteins, is an important goal for tandem mass spectrometry experiments. A systematic study for the fragmentation reactions of b ions derived from ε-N-acetyllysine containing model octapeptides (KAcYAGFLVG and YAKAcGFLVG) has been examined in detail. Collision-induced dissociation (CID) mass spectra of bn (n=4-7) fragments of ε-N-acetylated lysine containing peptides are compared with those of N-terminal acetylated and doubly acetylated (both ε-N and N-terminal) peptides, as well as acetyl-free peptides. Both direct and nondirect fragments are observed for acetyl-free and singly acetylated (ε-N or N-terminal) peptides. In the case of ε-N-acetylated lysine containing peptides, however, specific fragment ions (m/z 309, 456, 569 and 668) are observed in CID mass spectra of bn (n=4-7) ions. The CID mass spectra of these four ions are shown to be identical to those of selected protonated C-terminal amidated peptides. On this basis, a new type of rearrangement chemistry is proposed to account for the formation of these fragment ions,which are specific for ε-N-acetylated lysine containing peptides. Consistent with the observation of nondirect fragments, it is proposed that the b ions undergo head-to-tail macrocyclization followed by ring opening. The proposed reaction pathway assumes that bn (n=4-7) of ε-N-acetylated lysine containing peptides has a tendency to place the KAc residue at the C-terminal position after macrocyclization/reopening mechanism. Then, following the loss of CO, it is proposed that the marker ions are the result of the loss of an acetyllysine imine as a neutral fragment., Scientific and Technological Research Council of Turkey (113Z172); State Planning Organization, DPT; Reseau National de Spectrometrie de Masse FT - ICR a tres haut champ (FR3624)

Boron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley. © TÜBITAK., Bor, bitkiler ve hayvanlar için gerekli olan mikrolementlerdendir. Ancak yüksek konsantrasyonlarda toksik etki göstermektedir. Bu çalışmada bora dayanıklı Anadolu arpa (Hordeum vulgare) genotipindeki bor tolerans mekanizmasının anlaşılması amaçlanmıştır. Kontrol ve bor stresi uygulanmış ve Anadolu genotipi arasındaki farklı seviyede ekspres olan proteinleri taramak için 2 boyutlu elektroforez tekniği uygulanmıştır. İki boyutlu elektroforez deneyi sonucu ekspresyon seviyesi artan yedi protein bulunmuştur: ribuloz 1,5-bifosfat karboksilaz/oksijenaz büyük zincir, thaumatin benzeri protein TLP5, patojenaz benzeri protein PR5, RNaz S benzeri protein, PSI tipi III a/bbağlayıcı protein, ışık toplayan kompleks protein I LHC I ve vakuol proton translokasyon ATPaz alt birim E. V-ATPaz alt birim E geni tarafından kodlanan proteinin seviyesinin bor uygulaması ile artmasına rağmen, genin transkript seviyesi azalmıştır. Arpa V-ATPaz alt birim E geninin maya hücrelerinde ifadenlenmesi maya hücrelerine bora karşı dayanıklılık sağlamıştır. Bu sonuçlar, V-ATPaz alt birim E geninin mayada fonksiyonel olduğunu ve maya hücrelerine, toksik bor seviyelerine karşı dayanıklılık sağladığını ve de arpada bor toleransında bir rolü olabileceğini göstermektedir., TUBITAK 104T213; TUBITAK TBAG-2354; IYTE-BAP20

Boron is an essential micronutrient for plants and animals; however, it can be toxic when present at high concentrations. The purpose of this study was to understand the mechanisms of boron tolerance in the Turkish barley (Hordeum vulgare) Anadolu cultivar. For this purpose, 2-dimensional electrophoresis (2-DE) was used to screen differentially expressed proteins for both control and boron-stressed Anadolu barley genotypes. Seven proteins were revealed by 2-DE: 1) ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo large chain), 2) TLP5, a thaumatin-like protein, 3) PR5, a basic pathogenesis-related protein, 4) a RNase S-like protein, 5) a PSI type III chlorophyll a/b-binding protein, 6) a light-harvesting complex I LHC I, and 7) the vacuolar proton-translocating ATPase subunit E protein. These were found to be upregulated in response to boron treatment. Even though the protein encoded by the V-ATPase subunit E gene was overexpressed, its transcript level was downregulated by boron treatment. Heterologous expression of the barley V-ATPase subunit E gene in yeast provided boron resistance to yeast cells. These results indicated that the V-ATPase subunit E gene was functional and conferred tolerance to toxic boron levels in yeast and might play a role in the overall boron tolerance of barley.

Bu tez düşük-enerjili çarpışmayla-indüklenmiş ayrışma (CID) altında peptit b iyonlarının gaz-fazı parçalanma mekanizmalarının detaylı çalışmalarını göstermektedir. b iyonlarının gaz-fazı yapılarının ve parçalanma mekanizmalarının anlaşılması özellikle peptit kütle spektrumlarının yorumlanması için önemlidir. Son zamanlarda, büyük bn (n = 5, 6, 7...) iyonlarının makrohalkalı yapı oluşturduğu ve bu yapının bilinmeyen peptitlerin sekanslanmasında hataya yol açabileceği gösterilmiştir. Bu nedenle, tezin ilk bölümünde çeşitli hepta- ve oktapeptiler kullanılarak asidik amino asitin (glutamik veya aspartik asit) makrohalkalı yapının oluşmasına olan etkisi araştırılmıştır. Sonuçlar göstermiştir ki, peptitlerdeki ne asidik amino asitlerin varlığı ne de pozisyonları b iyonlarının makrohalkalaşmasını engellemiştir. Buna ek olarak, asidik amino asitlerin tercihli bölünmesinin uygulanan çarpışma enerjisine olan bağlılığı makrohalkalı b iyonları için incelenmiştir.İkinci bölümde, peptinin N-ucu asetillenmiş olsa bile lizin amino asitinin yan zincirindeki ?-amin grubun b iyonlarının makrohalkalaşmalasına olan etkisi incelenmiştir. Elde edilen sonuçlar, makrohalkalaşmanın N-ucu asetillenmiş olan peptitteki lizinin ?-amin grubu ile okzazolon yapısı arasında gerçekleştiği ortaya koymuştur. Diğer taraftan, N-ucu asetillenmiş peptitlerdeki lizinin pozisyonu b iyonlarının makrohalkalaşma için önemli bir parametredir.Tezin üçünçü ve dördüncü bölümlerinde ise, asetillenmiş lizin veya yan zincirlerinde hidroksil grubu içeren model peptitlerden elde edilen b iyon serilerinin CID kütle spektrumlarında yeni parçalanma iyonlarının varlığı saptanmıştır. Bu yeni oluşan iyonların gaz-fazı yapıları ve parçalanma mekanizmaları çok-aşamalı ikili kütle spektrometresi (MS4) deneyleri ile çalışılmıştır.Sonuç olarak, bu çalışmalarda gösterilen sonuçlar peptit sekanslarının doğru ve güvenilir bir şekilde açıklamak için kullanılabilinir ve bu durum proteomik çalışmalar için gerekli olan protein tanımlama stratejilerini geliştirebilir. This dissertation presents detailed studies of gas-phase fragmentation mechanism of peptide b ions under low-energy collision-induced dissociation (CID). Understanding the gas-phase structures and fragmentation mechanisms of the b ions is especially important for interpretation of peptide mass spectra. Recently, larger bn (n = 5, 6, 7...) ions are shown to form macrocyclic structures which can lead to erroneous in sequencing of unknown peptides. Therefore, in the first part of thesis, the effect of acidic amino acid residues (glutamic or aspartic acid) on the formation of macrocyclic structure is probed using various model hepta- and octapeptides. The results indicate that neither the presence nor the positions of acidic residues in peptides prevents macrocyclization of b ions. In addition, the dependence of preferential cleavage of acidic residues on applied collision energy is investigated for macrocyclic b ions.In the second part, the effect of ?-amine group of lysine residue is examined for the macrocyclization of b ions even if the N-terminal of the peptide is acetylated. The obtained results reveal that the macrocyclization is accomplished between ?-amine group of lysine and the oxazolone structure in the N-terminal acetylated peptide. Moreover, the lysine position is important parameter for the macrocyclization of b ions for N-terminal acetylated peptide.In the third and fourth parts of the thesis, the novel rearranged fragment ions are detected in the CID mass spectra of b ion series of acetylated lysine and side chain hydroxyl group containing model peptides, respectively. The gas-phase structures and fragmentation mechanisms of these novel fragment ions are investigated via multi-stage tandem mass spectrometry (MS4) experiments.In conclusions, the results presented in this dissertation can be used to elucidate the correct and reliable peptide sequences, and this improve protein identification strategies which is required for high-throughput proteomic studies. 164

Olfaktör sistem anatomisi ve beyin içerisinde ilişkili olduğu yapılar son 10 yıla kadar üzerinde diğer beyin bölgeleri kadar çalışma olmayan bir bölgeydi. Yakın zamanda hücresel düzeydeki tekniklere paralel olarak gelişen ileri radyolojik yöntemler sayesinde bu duyunun beyin içerisindeki organizasyonuna dair çalışmalar da hız kazanmıştır. İnsan olfaktör sisteminin memeliler arasında en az gelişmiş sistemlerden biri olması sebebiyle daha çok fareler ve diğer memeliler üzerinde bu çalışmalar yapılagelmiştir. Bu laboratuar çalışmasında koyun beynindeki olfaktör sistem'in anatomik ilişkileri anlaşılmaya çalışılmıştır. İnsana göre daha belirgin bir olfaktör bulb,, koku yolakları ve koku merkezine sahip olan bu canlılardaki yolakların ortaya çıkarılması için Klingler'in beyaz cevher disseksiyon tekniği uygulanmıştır. Daha önce herhangi bir memelide beyaz cevher disseksiyonu yöntemi ile olfaktör sistem anatomisi ortaya konulmamıştır. İnsanda diğer kafa çiftleri üzerine yapılmış radyolojik çalışmalar olmakla birlikte traktları hakkında bir veri elde edilemeyen tek kafa çifti de birinci kafa çifti olan Olfaktör sinirdir.Bu çalışma Marmara Üniversitesi Prof.Rhoton Nöroanatomi laboratuarında on adet koyun beyni ile gerçekleştirilmiştir. Olfaktör bulb ve bunu takip eden ana olfaktör trakt üç ana yola ayrılmıştır. Bu yolaklar lateral, orta ve medyal olfaktör traktlar olarak isimlendirilmiştir. Adı geçen yolakların koyun koku korteksi olarak çalıştığı bilinen piriform lob ve koku duyusu ile ilişkili olan Amigdala, Nükleus Akkümbens, Anterior komissür, gibi beyin bölgeleri ile olan bağlantıları ortaya konulmaya çalışılmıştır.Bu çalışma ile koyun beynindeki olfaktör sistem beyaz cevher anatomisi ortaya konulmakla birlikte, subkortikal nükleuslar ve limbik sistem ile olan ilişkilerinin net açıklanabilmesi için ileri laboratuar çalışmalarına ihtiyaç vardır.Memelilerin beyin anatomisinin büyük oranda benzer olması nedeniyle bu çalışmada ortaya çıkarılan yolaklar insan beyni olfaktör sistem anatomisini anlama konusunda yardımcı olabilecektir. Olfactory system has very complex relationship with limbic system and cortical areas. These structures were not anatomically well defined until last 10 years. Recent developments at ''in vitro'' studies and radiologic explorations suggested new methods for olfactory system research. Most of previous researches were being made on either mice or other mammals which olfactory system is more sophisticated than human. A white matter dissection study for olfactory system on mammals has never been reported. However there are many other studies to understand structural design of other cranial nerves radiologically and anatomically.10 fresh sheep brains were used for this study. The specimens were processed according to Klingler's technique. Dissection were carried out at the basal surface of brains, ventral to caudal direction.We found that main olfactory tract divides in three pathways; Lateral, middle and medial olfactory pathways. We demonstrated courses of pathways and their relations with cortical areas and subcortical nuclei . These structures include pyriform lobe, amygdala, nucleus accumbens and anterior commissure.Sheep brain has advantage of olfactory system maturity but applying Klingler's technique to these small brains need smaller devices, equipments and larger magnification. We can name it as ''Micro-White Matter Dissection''.In this study we aimed to understand basic structural design of olfactory system. Eventhough this study reveals the pathways of olfactory system in sheep, further studies are needed to clearly understand connections between nuclei system and targeted cortical areas. We believe this anatomical knowledge can help scientists to better understand the organization of complex relations of olfactory system. 74

Thesis (Master)--İzmir Institute of Technology, Chemistry, İzmir, 2008, Includes bibliographical references (leaves: 78-87), Text in English; Abstract: Turkish and English, xi, 87 leaves, Boron is an essential micro-nutrient for plants. However, when boron is present at high concentrations in the soil or ground water, healthy plant growth and development can be affected by boron toxicity. Turkey constitutes about 72 % of the total boron reserves in the world. In Turkey, barley (Hordeum vulgare) is the second widely grown cereal after wheat. Boron toxicity is one of the major factors limiting the yield of barley in Central Anatolia of Turkey. In the present study, proteomic approach was used to investigate the boronstress tolerant proteins in Anadolu barley genotype (boron-tolerant). Eight-day-old barley plants were treated with 10 mM H3BO3 for seven days. Control plants received no boron treatment during this period. Total proteins of leaves were extracted and separated by two-dimensional polyacrylamide gel electrophoresis. Control and borontreated Anadolu genotype.s proteome maps were compared and the novel proteins were fragmented into peptides using in-gel digestion technique. Liquid chromatographytandem mass spectrometry (LC-MS/MS) analysis and database searching gave way to identify ten spots representing seven different proteins. Two spots were identified as the same protein and one protein could not identified. The identified seven proteins are namely, ribulose 1,5-bisphosphate carboxylase/oxygenase large chain (RuBisCo largechain), thaumatin-like protein TLP5, basic pathogenesis-related protein PR5, RNase Slikeprotein, vacuolar proton-translocating ATPase subunit E, PSI type III chlorophyll a/b-binding protein, and light-harvesting complex I; LHC I. Among the identified seven proteins, vacuolar proton-translocating ATPase (VATPase) subunit E is the important one for boron tolerance in tolerant barley genotype. It is shown that the accumulation of excess boron in the vacuolar compartment of the plant cell by the help of V-ATPase subunit E protein. This is the known as internal tolerance mechanisms for Anadolu genotype of barley to survive under boron stress. It was proposed that, this might be the defense mechanism in boron-tolerant barley genotype under toxic boron concentrations.

Bor bitkiler için gerekli bir mikro-besindir. Topraktaki veya yer altı suyundaki fazla miktardaki bor, bor toksikliğine yol açarak bitkinin sağlıklı bir şekilde büyümesi ve gelişmesini etkiler. Türkiye'de bulunan bor kaynakları dünya toplam bor rezervinin yaklaşık olarak %72'sini oluşturmaktadır. Arpa (Hordeum vulgare) Türkiye'de buğdaydan sonra en çok üretilen tahıldır. Bor toksikliği Türkiye'nin Orta Anadolu'sunda yapılan arpa tarımında verimi sınırlayan bir faktördür.Bu çalışmada, Anadolu (bora karşı dirençli) arpa genotipinde bor-stresine toleranslı proteinler proteomik yaklaşım kullanılarak incelenmiştir. Sekiz-günlük arpa bitkileri yedi gün boyunca 10 mM borik asite maruz bırakılmıştır. Kontrol bitkilerine bu süre içinde bor uygulanmamıştır. Yapraktaki toplam proteinler izole edilmiştir ve iki boyutlu poli akrilamit jel elektroforezi kullanılarak birbirlerinden ayrılmışlardır. Kontrol ve bora maruz bırakılmış Anadolu genotipinin proteom haritaları karşılaştırılmış ve bor stresi altında oluşan yeni proteinler jelden kesilip çıkartılmıştır. Jel içinde parçalama tekniği kullanılarak proteinler peptitlere parçalanmıştır. Sıvı kromatografisi-ikili kütle spektrometresi (LC-MS/MS) analizi ve veritabanı taraması yedisi farklı olan on tane proteinin tanımlanmasını sağlamıştır. İki tane protein aynı protein olarak tanımlanmıştır ve bir protein tanımlanamamıştır. Tanımlanan yedi tane proteinin isimleri şöyledir: ribuloz 1,5-bifosfat karboksilaz/oksijenaz büyük zincir (RuBisCo büyük zincir), thaumatin-benzer proteini TLP5, bazik patogenez-ilgili protein PR5, RNaz S-benzer protein, koful proton-translokasyon ATPaz alt birim E proteini, PSI tipi III klorofil a/b-bağlayıcı protein, ve ışık-toplayan komleks protein I; LHC I.Tanımlanan yedi tane protein içinde, bora karşı dirençli arpa genotipinin bor toleransını sağladığı düşünülen koful proton-translokasyon ATPaz (V-ATPaz) alt birim E proteini en önemli olanıdır. V-ATPaz alt birim E protein sayesinde hücre içindeki fazla miktardaki bor hücrenin kofulunda biriktirildiği gösterilmiştir. Anadolu arpa genotipindeki dahili dayanıklılık mekanizması olarak bilinen bu mekanizma bor stresi altında bitkinin yaşamasını sağlamıştır ve bora karşı dirençli arpa genotipinin toksik bor konsantrasyonuna dayanıklılık mekanizması olarak önerilmiştir. Boron is an essential micro-nutrient for plants. However, when boron is present at high concentrations in the soil or ground water, healthy plant growth and development can be affected by boron toxicity. Turkey constitutes about 72 % of the total boron reserves in the world. In Turkey, barley (Hordeum vulgare) is the second widely grown cereal after wheat. Boron toxicity is one of the major factors limiting the yield of barley in Central Anatolia of Turkey.In the present study, proteomic approach was used to investigate the boron-stress tolerant proteins in Anadolu barley genotype (boron-tolerant). Eight-day-old barley plants were treated with 10 mM H3BO3 for seven days. Control plants received no boron treatment during this period. Total proteins of leaves were extracted and separated by two-dimensional polyacrylamide gel electrophoresis. Control and boron-treated Anadolu genotype?s proteome maps were compared and the novel proteins were excised from gels which were newly expressed under boron stress. The proteins were fragmented into peptides using in-gel digestion technique. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and database searching gave way to identify ten spots representing seven different proteins. Two spots were identified as the same protein and one protein could not identified. The identified seven proteins are namely, ribulose 1,5-bisphosphate carboxylase/oxygenase large chain (RuBisCo large chain), thaumatin-like protein TLP5, basic pathogenesis-related protein PR5, RNase S-like protein, vacuolar proton-translocating ATPase subunit E, PSI type III chlorophyll a/b-binding protein, and light-harvesting complex I; LHC I.Among the identified seven proteins, vacuolar proton-translocating ATPase (V-ATPase) subunit E is the important one for boron tolerance in tolerant barley genotype. It is shown that the accumulation of excess boron in the vacuolar compartment of the plant cell by the help of V-ATPase subunit E protein. This is the known as internal tolerance mechanisms for Anadolu genotype of barley to survive under boron stress. It was proposed that, this might be the defense mechanism in boron-tolerant barley genotype under toxic boron concentrations. 98

ÖZET Doktora Tezi NİKSAR OVASINDA TARIMSAL ÜRETİM YAPAN AİLELERDE YARDIMLAŞMA DÜZEYLERİ VE BUNU ETKİLEYEN FAKTÖRLER ÜZERİNE BİR ARAŞTIRMA A. Ahmet YÜCER Ankara Üniversitesi Fen Bilimleri Enstitüsü Tarım Ekonomisi Anabilim Dalı Danışman : Prof. Dr. Nurettin YILDIRAK Jurj : Prof. Dr. Gülcan ERAKTAN Jurj : Prof. Dr. Ayhan TUFAN Jurj : Prof. Dr. Ö. Faruk YALÇIN Jurj : Prof. Dr. Mustafa SOYSAL Bu araştırma, Niksar Ovasında tarımsal üretim yapan ailelerde yardımlaşma düzeyleri ve bunu etkileyen faktörlerin saptanarak yerel önderlere ışık tutması amacı ile yapılmıştır. Bu amaçla 113 çiftçi ailesinden anket yoluyla elde edilen veriler Khi-Kare testine ve Korelasyon analizine tabi tutulmuştur. Araştırma sonucunda aile başkanlarının yaşı, eğitim düzeyi, aile işgücü varlığı, yabancı işgücü gereksinimi, göç ve makine varlığı ile yardımlaşma düzeyi arasında olumlu bir ilişki görülmüştür. Yöre köylerinin ortalama yardımlaşma düzeyi, köy halkının aynı etnik yapıya veya mezhebe sahip olmasına bağlı olarak da artmaktadır. Kırsal kesimin örgütlenmesinde yerel yöneticiler yerine, tabandan işbirliği talebinin oluşturulması başarının ön şartlarındandır. Yardımlaşma ile ilgili Köy Kanunu, Çiftçi Malları Koruma Kanunu ve Tabii Afetlerden Zarar Görenlere Yapılacak Yardımlarla ilgili mevzuat, fonksiyonlarını ve etkinliklerini kaybetmişlerdir. Yörede en önemli alt yapı eksiklikleri olarak; kanalizasyon, köy yollarının asfaltlanması ve içme suyu yetersizliği olarak saptanmıştır. Aile başkanları, kırsal alt yapı eksikliklerinin giderilmesini devletten bekleme eğilimindedirler. 1985-1990 yılları arasında yapılan köylü-devlet işbirliğinden olumlu sonuçlar alınmış ise de, zorlayıcı nedenlerle yeni işbirliği talepleri oluşmamıştır. Aile başkanlarının % 54.9'u tarımsal girdilerin alımı ve ürünlerin satımında işbirliği eğilimi göstermektedir. Bu eğilimi patates, karpuz ve domates üreticilerinin formal örgütlenmelerinde potansiyel olarak kullanmak olasıdır. Aile başkanları ev işlerinde eşlerine çok düşük düzeyde (%13.3) yardım etmektedir. Komşu kadınlar arasında yardımlaşmaya ekmek yapımında, pancar ve patates çapasında rastlanmaktadır. 1999, 124 sayfa ANAHTAR KELİMELER : Karşılıklı yardımlaşma, işbirliği, dayanışma, kırsal sosyoloji, kırsal kalkınma, toplum kalkınması ABSTRACT Ph. D. Thesis A RESARCH ON THE LEVELS OF COOPERATION AT THE FARM FAMILIES IN NİKSAR PLAIN AND THE EFFECTING FACTORS A. Ahmet YÜCER Ankara Universty Graduate School of Natural and Applied Sciences Department of Agricultural Economics Supervisor : Prof. Dr. Nurettin YILDIRAK Jurj : Prof. Dr. Gûlcan ERAKTAN Jurj : Prof. Dr. Ayhan TUFAN Jurj : Prof. Dr. Ö. Faruk YALÇIN Jurj : Prof. Dr. Mustafa SOYSAL In this resarch the main goal was to determine the levels of cooperation at the farm families in Niksar plain and enligten of local leaders by the effecting factors. The data have been obtained by survey from 113 farm families and these have been analysed with Khi-square test and correlation analysis. At the results of the resarch were seemed that the level of cooperation is related to the age of family head, education level of family head, family labour, foreing labour requirement, immigration and existence of machine. Level of cooperation average at the villages have been changed according to same ethnic structure and denomination of villagers. The contruction of demand for cooperation from villagers at the organization of rural sector is the perior circumstances of the success instead of local managers. The Law of Village, the Law of Farmer Proporties Protection and The Law of Harm Natural disaster related to the cooperation have been lost their real functions and efficecy. The lack of important infrastructure such as sewerage, asphalt of roads and drinking water have been determined in the area. Family heads have been expecting the solution of these problems Turkish government. The positive result between 1985 and 1990 were obtained from cooperation between government and villagers. But new cooperations didn't occure due to forces majeures. In addition, 54.9 % of the family head were found in the tendency of cooperation on buying of agricultural inputs and selling of products. It is possible to use of this tendency on formal organization of potato, tomato and watermelon producers. Family heads have been helping their wives in a very small (13.3 %) at the house work. Besides in this resarch cooperation was obtained bamong neighbour women in the preparing of bread and the digging of the potatoes and sugar beets in the field. 1999, 124 pages Key Words : Mutual aid, cooperation, solidarity, rural sociology, rural development, community development 124

O-methylation of the side chains of glutamic acid (E) and aspartic acid (D) residues is generally observed modification when an acidified methanol/water (MeOH/dH2O) mixture is used as a solvent system during sample preparation for proteomic research. This chemical modification may result misidentification with endogenous protein methylation; therefore, a special care should be taken during sample handling prior to mass spectrometric analysis. In the current study, we systematically examined the extent of E/D methylation and C-terminus carboxyl group of synthetic model peptides in terms of different incubation temperatures, storage times, and added acid types as well as its percentages. To monitor these effects, C-terminus amidated and free acid forms of synthetic model peptides comprised of E or D residue(s) have been analyzed by electrospray ionization-mass spectrometry (ESI-MS). Additionally, LC–MS/MS experiments were performed to confirm the formation of methylated peptide product. The results showed that the rate of methylation was increased as the temperature increases along with prolong incubation times. Moreover, the extent of methylation was remarkably high when formic acid (FA) used as a protonation agent instead of acetic acid (AA). In addition, it was found that the degree of methylation was significantly decreased by lowering acid percentages in ESI solution. More than one acidic residue containing model peptides have been also used to explore the extent of multiple methylation reaction. Lastly, the ethanol (EtOH) and isopropanol (iPrOH) have been substituted separately with MeOH in sample preparation step to investigate the extent of esterification reaction under the same experimental conditions. However, in the positive perspective of view, this method can be used as a simple, rapid and cheap method for methylation of acidic residues under normal laboratory conditions., The State Planning Orga-nization (DPT) of Turkey; Izmir Institute of Technology; TUBITAK (113Z172-COST 1306)

In this study, we investigated the effect of the second amino acid identity of hexapeptides on gas-phase structures and the proton affinities of N-terminal proline containing b2 + ions produced from the fragmentation of b6 + ions under low-energy collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). It should be noted that, among all other fragments, the b2 + and nominally b4 + (AAAA) ions ([M+H]+ → b6 + → b2 + (PX+) + b4 + (AAAA+) were mainly considered in this study. This is a unique example of consecutive cleavage of b6 + ions which fragments to b2 + and nominal b4 + ions. All structural and proton affinity calculations for b2 + ions were carried out with the B3LYP/6-31+G(d,p) level of theory. The study utilized C-terminal amidated model peptides consisting of PAAAAA-NH2 and PXAAAA-NH2 where X is phenylalanine (F), glutamic acid (E), tryptophan (W), and histidine (H) residue. Two main structural isomers of b2 + ions, namely oxazolone and diketopiperazine, have been considered for the computations. The results demonstrated that the proton affinities of oxazolone isomers of PX are greater than its diketopiperazine isomers. Higher correlation coefficient is calculated if the structure of PX is considered as oxazolone rather than diketopiperazine isomer. Additionally, a linear fit is observed between intensity ratio (PX/AAAA) and calculated proton affinities of PX ions. Additionally, MS/MS results revealed that the relative intensities of b2 +-PA, PF, and PE- ions are lower compared to the relative intensity of AAAA fragment ion. In contrast, b2 +-PW and PH- ions have higher relative intensities compared to the AAAA ion. This behavior is explained by the proton affinities of fragment ions computationally., Scientific and Technological Research Council of Turkey (111T935/112T558); State Planning Organization, DPT