Cell wall engineering for better conversion of lignocellulosic biomass

The objective of our research was to use the flexibility of the cell wall to its extremes by modifying its composition while avoiding deleterious effects on plant physiology. One of the strategies to achieve this is the heterologous expression of genes coding for cell wall degrading (CWD) enzymes in plants. These can alter the cell wall structure during plant growth and might improve saccharification yield of the lignocellulosic biomass. In this PhD study 29 genes coding for cell wall degrading enzymes (66 different constructs) were introduced in Arabidopsis and one of the enzymes (a galactanase) was studied in detail. Interestingly, galactanase expression improved the saccharification efficiency without causing a dramatic yield penalty. In parallel, an attempt was made to modify cell wall properties by the expression of the A. caulinodans NodC gene in Arabidopsis. The obtained transgenic lines accumulated GlcNAc mono- and oligosaccharides in their apoplast, which influenced the overall cell wall architecture and modified the cell wall properties. Furthermore, since lignin is major limiting factor that affect saccharification yield, reducing lignin content became a potential strategy to improve the saccharification yield. Here, we have generated Arabidopsis lines with an altered PIRIN2 and PIRIN4 expression. The lines had an altered lignin composition, reduced lignin content and an improved saccharification yield. Despite their modified cell wall, no dramatic effect on plant growth and development was detected

Investigation of combustion potential of tea pruning waste biomass mixed with lignite coal

Hayat standartlarının artmasına paralel olarak artan enerji gereksinimi enerjide dışa bağımlı olan ülkeler için önemli bir sorundur. Artan enerji talebini karşılarken çevreye verilecek olan zararın en aza indirgenmesi öncelikli hedefler arasında yer almaktadır. Kömür ile ile çalışan termik santrallerden elde edilen enerji ülkemizin enerji ihtiyacının %32’sini karşılamaktadır. Kullanılan kömürün büyük bir kısmı ithal kömür ve taşkömürüdür. Ülkemizde son yıllarda yapılan çalışmalar sonucunda linyit kömür rezervimiz 16 milyar tonun üzerine çıkmıştır. Fakat bu linyit kömür çoğunlukla düşük kalorili olup, yüksek oranda kükürt, nem ve kül içeriklidir. Bu tür ısıl değeri düşük çevresel etkisi fazla olan kömür kaynaklarının verimli bir şekilde kullanımı için ileri teknolojilerin geliştirilmesi ulusal ve uluslararası düzeyde bir gerekliliktir. Diğer yandan, ülkemizin sahip olduğu biyokütle enerjisi potansiyeli verimli bir şekilde değerlendirilememektedir. Doğu Karadeniz bölgesinin önemli tarımsal atığı olan çay budama atıkları linyit kömür ile belirli oranlarda harmanlanarak karışımın ısıl değeri, kül içeriği, kükürt ve uçucu madde içeriği tespit edilmiştir. Çay budama atığının ısıl değeri linyit kömüründen yaklaşık olarak %30 az olmasına rağmen, linyit kömür ile %50 oranında harmanlandığında kül içeriği %12’lerden %6’lara, kükürt içeriği ise %1.15’lerden %0.69’lara düşmüştür. Atık olarak kullanılan ve ekonomiye kazandırılmayan bu tarımsal atıkların, linyit kömürü ile uygun karışım değerleri ile homojen şekilde harmanlandığında enerji potansiyellerinin yüksek olduğu ve çevreci bir yakıt olduğu belirlenmiştir.The growing energy requirement in parallel with the increase in living standards is a major problem for countries which are dependent on foreign sources for energy. Reducing the damage effect to the environment while meeting increasing energy demand is among the priority targets. The energy obtained from coal-fired thermal power plants accounts for 32%of our country's energy needs. Most of the used coal are imported coal and hard coal in our country. The lignite reserves that have been known in recent years by exploration studies have exceeded 16 billion tons in our country. However, these lignite’s are generally low calorie, high sulfur, moisture and ash content. The development of unique designs and / or technologies for the effective evaluation of such coal at national and international level are needed. On the other hand, there is an important biomass potential in our country; this potential is still not being assessed effectively and efficiently. Tea pruning wastes, which are important agricultural wastes of the Eastern Black Sea region, were blended with lignite coal at certain ratios and the content of the mixture was determined for colorimetric value, ash content, sulfur content and volatile matter content. Although the tea pruning waste thermal value was approximately 30% lower than the lignite, 50% blended biomass with lignite coal, ash content decreased from 12% to 6% and sulfur content decreased from 1.15% to 0.69%. It was determined that these agricultural wastes, which were used as waste and not used in industry, have a high energy potential and an environmentally friendly fuel when they are homogeneously blended with lignite coal

The phenolic composition and antioxidant activity of tea with different parts of Sideritis condensate at different steeping conditions

Tea with different parts (flower, leaf, seed) of Sideritis condensate infused at different temperatures (60 and 100°C) and times (5, 10 and 30 minutes) were assessed for their phenolic composition and antioxidant activities. Leaf tea had the highest total phenolic content where as seed tea had the lowest.Leaves soaked at 100°C for 10 minutes had the highest total phenolic content. Total phenolic content of flower tea increased with increase in extraction temperature and time. Radical scavenging activities of leaves infused at 60°C for 5, 10 and 30 minutes were statistically in the same group but lower than those of leaves soaked at 100°C for 5, 10 and 30 min. The major phenolic compound identified from almost all aqueous infusions was the p-coumaric acid. The conditions of tea prepared from leaves of the Sideritis condensata at 100°C for 5, 10 and 30 minutes are the most appropriate conditions in regard to extraction of the highest total phenolics and the strongest antioxidant activity

Biological activities and DNA interactions of aqueous extract of Phlomis linearis (Boiss. & Bal.)

Phlomis linearis Boiss. & Bal. of the Lamiaceae family is one of the endemic species in Turkey, i.e., growing in the east, central, and southeast parts of Anatolia and used for herbal tea. This study was designed to identify the biochemical and bioactivity properties of this endemic species by DPPH scavenging activity, metal chelating activity, total phenolic content, HPLC-DAD analysis, and MTT assay. Furthermore, the plant extract was evaluated for its antimicrobial activity against bacteria and fungi by using the microdilution method. The interactions between extract and plasmid DNA and their restriction endonuclease reactions were investigated by agarose gel electrophoresis. To support our hypothesis, we performed a molecular docking analysis. The DPPH scavenging activity of the plant extract was 53.86 ± 0.50 µg/ml in terms of IC50 value. The IC50 value of the plant extract was determined as 14.71 ± 4.01 mg/ml for metal chelating assay. The phenolic content of the extract was 231.55 ± 2.11 mg/g dry weight expressed as gallic acid equivalents (GAE). HPLC-DAD results revealed that the phenolic compounds were mainly derivatives of rosmarinic acid, chlorogenic acid, luteolin, luteolin-7-glycoside, luteolin derivatives, rutin derivatives, and apigenin derivatives. Besides, the cytotoxic activity of the plant extract against L929 fibroblast, H1299 non-small-cell lung carcinoma, and Caco-2 colorectal adenocarcinoma cell lines was determined by MTT assay. Phenolic content and molecular docking results correlated with each other

High-throughput screening of inhibitory effect of medicinal plants on bacterial DNA polymerases

European Biotechnology Conference -- MAY 05-07, 2016 -- LATVIAWOS: 000380240300080[No abstract available

Elucidation of Bioactive compounds in flower extracts of Camellia sinensis by HPLC-DAD-MS/MS and their inhibitory effects on replicative bacterial DNA polymerases

Camellia sinensis L. (C. sinensis) is an economically valuable crop whose leaves are used to produce tea. Tea flowers extracts (TFE) have been tested for their DNA polymerase inhibitory effect experimentally and in silico. Antioxidant capacities of TFE were determined by their DPPH radical scavenging activities (RSA), total phenolic acid, and flavonoid contents. While methanol extract and its fractions, except the aqueous fraction, showed strong inhibition on Gram (-) DNA polymerase DnaE, ethyl acetate, and butanol fractions showed strong inhibition on Gram (+) DNA polymerase PolC. The fractions had varying degrees of inhibition in tested microorganisms, except Enterococcus faecalis. Bacillus subtilis was the most inhibited microorganism. The binding energies of compounds for both polymerases varied between 5.5 kcal/mol (polC) and - 9.7 kcal/mol (DnaE). Some compounds especially interact with the catalytic aspartic acid amino acids (D973, D975, and D1098) of polC. The ethyl acetate fraction had the best DPPH RSA and the highest total phenolic content. According to HPLC-DADMS/MS analysis, tea catechins corresponded to 58.1% of all phenolics, which comprised 17.9% of the methanol extract. All these results might support the hypothesis of the use of TFE for a potential candidate as a functional food and beverage

Correlation between phenolic compounds and antioxidant activity of Anzer tea (Thymus praecox Opiz subsp. caucasicus var. caucasicus)

Sahin, Huseyin/0000-0002-6018-1494WOS: 000332189200091Phenolic compounds of Thymus praecox Opiz subsp. caucasicus var. caucasicus were analyzed by high performance liquid chromatography equipped with an ultraviolet detector (HPLC-UV). Quercetin (co-eluting with luteolin) and caffeic acid were among the most abundant compounds identified. in addition syringic, ferulic, p-coumaric, protocatechuic,p-hydroxybenzoic and vanillic acid as well as the flavonoids catechin, epicatechin, and kaempferol were identified and quantified in the plant extracts. Acidic hydrolysis was used to gain additional information on the glycosylation state of the phenolics. Although chromatographic profiles changed considerable upon hydrolysis, quercetin and caffeic acid remained among the most abundant compounds identified. in addition the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging activities of different tissues were determined and correlations were found between phenolic or flavonoid content and antioxidant property with strongest radical scavenging activity in hydrolyzed flower extracts. Crown Copyright (C) 2013 Published by Elsevier B.V. All rights reserved.RIZEBAPRecep Tayyip Erdogan University; TUBITAK BIDEBTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK)Authors would like to thank RIZEBAP for the financial support given to this work. We also thank Prof. Salih Terzioglu for identifying the Thymus genus, Recep Tayyip Erdogan University for supporting us HPLC-UV device and thank to Mustafa Lezgioglu for collecting fresh Thymus praecox Opiz subsp. caucasicus var. caucasicus. the authors (H. Sahin and H. Turumtay) would like to thank TUBITAK BIDEB for the financial support given to them

Paeoniflorigenone purified from Paeonia daurica roots potently inhibits viral and bacterial DNA polymerases: investigation by experimental validation and docking simulation

emirik, mustafa/0000-0001-9489-9093WOS: 000496324100012The methanolic extracts from fruit, leaf, stem and roots of Paeonia daurica subsp. macrophylla (P. daurica) were investigated for inhibitory effect on replicative bacterial (PolC and DnaE2) and viral (MMLV-RT from Moloney Murine Leukemia Virus) DNA polymerases by primer extension assay. While all plant parts showed inhibition effect on bacterial and viral DNA polymerases, roots of the plant was focused to purify inhibitory compound(s). the chemical structures of compounds were completely elucidated using a combination of NMR, MS and FT-IR analyses. Five molecules with tree monoterpene glycosides, paeoniflorin (PD-2), paeoniflorigenone (PD-4), benzoyl paeoniflorin (PD-5), and benzoic acid (PD-3) with its derivate 2,4,6-trihydroxy-1-methyl benzoate (PD-1) were purified and identified. Both DNAdependent and RNA-dependent polymerase activity of MMLV-RT was strongly inhibited by these five molecules. on the other hand, bacterial polymerases PolC and DnaE2 were strongly inhibited by only paeoniflorigenone (PD-4). Molecular modeling result suggested that paeoniflorigenone (PD-4) interacts with the important residues at active site (palm, fingers and thumb domains) of three polymerases which support our experimental result. Ethyl acetate fraction had smallest SC50 value against DPPH and ABTS radicals. It showed also higher scavenging activity than quercetin, trolox and ascorbic acid since its quite high total phenolic content. We proposed that the parts of P. daurica might be used to find new antimicrobial agents and generate supplementary material for foods. Furthermore, the isolated molecules with inhibitory effect may be used as new scaffold for the further modification in order to develop novel inhibitors against DNA polymerization

M-MLV reverse transcriptase was strongly inhibited by essential oil extract of paeonia daurica subsp. macrophylla

Paconia species arc known for their rich chemical content and their compounds exhibit different medicinal properties. In this study, we firtly investigated the essential oil (EO) content of the root, scape, fruit and fruit bark of Paeonia daurica Andrews subsp, Macrophylla Albow (P, daurica) by using gas chromatography-mass spectrometry (GC-MS). Both solid-phase micro-extraction (SPME) and hydro-distillation (HD) were used to prepare EO extracts for each plant sample. While fifty-two compounds were identified in SPME-EO extract, sixty-eight compounds were identified in HD-EO extract and eighteen compounds were jointly found in both extract. Major constituents of the EOs were salicylaldehyde (100-65%), myrtanal (3.10-45%), palmitic acid (2.1%-40.4%), methyl salicylate (3.1%-37.5%) and myrtenal (3%-35.1%). Fruit bark had the richest identified EOs among plant parts. Furthermore, the total SPME-EO and HD-EO extracts were evaluated for their inhibition on Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV-RT) by using primer extension assay (measuring of single dATP nucleotide addition). M-MLV-RT could not add a single nucleotide to the 14-mer primer in the presence of both EO extracts and it revealed that both SPME and HD total EO extracts had strong inhibition effect on M-MLV-RT. alpha-bisabolol, beta-bisabolol and benzoic acid-ethylester (a derivate of benzoic acid) in HD-fruit extract were evaluated as potential compounds responsible for the inhibitory effect according to literature, To the best of our knowledge, this is the first detailed report about EO compositions and its inhibition effect against M-MLV-RT of the root. scape. fruit and fruit bark of P. daurica. We propose the EOs of P. daurica might have potential of therapeutic candidate for preventing viral diseases.Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) TUBITAK-113Z05