Biotechnology Commons^™

Sbml Level 3: An Extensible Format For The Exchange And Reuse Of Biological Models, Sarah M. Keating, Dagmar Waltemath, Tomáš Helikar, Michael Hucka, 50 Additional Co-Authors

Department of Biochemistry: Faculty Publications

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraintbased models, reaction-diffusion models, logical network models, and rule-based models. The format leverages …

Photosynthetic Efficiency And Mesophyll Conductance Are Unaffected In Arabidopsis Thaliana Aquaporin Knock-Out Lines, Johannes Kromdijk, Katarzyna Głowacka, Stephen P. Long

Department of Biochemistry: Faculty Publications

Improving photosynthetic efficiency is widely regarded as a major route to achieving much-needed yield gains in crop plants. In plants with C₃ photosynthesis, increasing the diffusion conductance for CO₂ transfer from substomatal cavity to chloroplast stroma (g_m) could help to improve the efficiencies of CO₂ assimilation and photosynthetic water use in parallel. The diffusion pathway from substomatal cavity to chloroplast traverses cell wall, plasma membrane, cytosol, chloroplast envelope membranes, and chloroplast stroma. Specific membrane intrinsic proteins of the aquaporin family can facilitate CO₂ diffusion across membranes. Some of these aquaporins, such as PIP1;2 …

Development Of A Novel Highly-Sensitive Brucellosis Sensor Based On Surface Plasmon Resonance Spectroscopy, Amal Kasry, Ihab Adly, Asharf Sayour, Hossam Sayour

Nanotechnology Research Centre

Brucellosis is considered a significant health threat, it is an infectious disease caused by the bacteria Brucella, which can spread from animals to humans causing severe diseases. Through this project, we aim to develop a very highly sensitive biosensor to detect Brucella early before spreading. This sensor is based on surface plasmon resonance (SPR) technique, which is used to analyze kinetics of interaction between biomolecules. It can detect down to picomolar concentrations of some proteins.

Brassinosteroids Inhibit Autotropic Root Straightening By Modifying Filamentous-Actin Organization And Dynamics, Louise De Bang, Ana Paez-Garcia, Ashley E. Cannon, Sabrina Chin, Jaydeep Kolape, Fuqi Liao, J. Alan Sparks, Qingzhen Jiang, Elison B. Blancaflor

Nebraska Center for Biotechnology: Faculty and Staff Publications

When positioned horizontally, roots grow down toward the direction of gravity. This phenomenon, called gravitropism, is influenced by most of the major plant hormones including brassinosteroids. Epi-brassinolide (eBL) was previously shown to enhance root gravitropism, a phenomenon similar to the response of roots exposed to the actin inhibitor, latrunculin B (LatB). This led us to hypothesize that eBL might enhance root gravitropism through its effects on filamentous-actin (F-actin). This hypothesis was tested by comparing gravitropic responses of maize (Zea mays) roots treated with eBL or LatB. LatB- and eBL-treated roots displayed similar enhanced downward growth compared with controls …

Functional Characterization Of Petiolule-Like Pulvinus (Plp) Gene In Abscission Zone Development In Medicago Truncatula And Its Application To Genetic Improvement Of Alfalfa, Juan Du, Shaoyun Lu, Maofeng Chai, Chuanen Zhou, Liang Sun, Yuhong Tang, Jin Nakashima, Jaydeep Kolape, Zhaozhu Wen, Marjan Behzadirad, Tianxiu Zhong, Juan Sun, Yunwei Zhang, Zeng-Yu Wang

Nebraska Center for Biotechnology: Faculty and Staff Publications

Alfalfa (Medicago sativa L.) is one of the most important forage crops throughout the world. Maximizing leaf retention during the haymaking process is critical for achieving superior hay quality and maintaining biomass yield. Leaf abscission process affects leaf retention. Previous studies have largely focused on the molecular mechanisms of floral organ, pedicel and seed abscission but scarcely touched on leaf and petiole abscission. This study focuses on leaf and petiole abscission in the model legume Medicago truncatula and its closely related commercial species alfalfa. By analysing the petiolule-like pulvinus (plp) mutant in M. truncatula at phenotypic level (breakstrength and …

The Balancing Act Of Cytokinin In Environmental Stress Tolerance, Sumudu Sandeepani Karunadasa

Theses and Dissertations--Plant and Soil Sciences

Cytokinin, long known as a phytohormone that regulates plant growth and development, has been recently recognized as an important regulator of stress responses. However, our current knowledge about the mechanisms by which cytokinin regulates stress responses is fragmentary, as many of the studies in this field yielded conflicting results. Most of the work described here has focused on analyses of the molecular mechanisms of cytokinin-dependent regulation of growth and development under stress conditions, with an emphasis on the role of cytokinin-dependent regulation of protein synthesis in development and stress tolerance.

One of the important contributions of this study is the …

Production Of Biodegradable Uv Protection Film Using Cellulose And Lignin Extracted From Oil Palm Empty Fruit Bunch, Muhammad Taufiq Haqiqi

Chulalongkorn University Theses and Dissertations (Chula ETD)

The optimized process for cellulose extraction from oil palm empty fruit bunch (EFB) consisting of acid pretreatment (0.5% (v/v) H2SO4), alkaline extraction (15% (w/w) NaOH), and chlorine-free bleaching (10% (w/v) H2O2) yielded pulp with the highest cellulose content at 83.42%. The EFB cellulose was then etherified into carboxymethyl cellulose (CMC) which was readily water-soluble (81.32%). The EFB CMC (2.5% (w/v)) was blended with glycerol (0.5 % (w/v)) to produce a composite film by a solution casting method. Lignin obtained from acid precipitation of the EFB black liquor was added into the film at different concentrations, and its influence on the …

A Cloning Strategy For Expression Of Fungal Hemicellulases In Plant Systems, Amer Alrudayan

Masters Theses

Lignocellulosic biomass is notoriously difficult to deconstruct into lignin, hemicellulose, and cellulose fractions without the use of biochemical, chemical, and/or mechanical pretreatments. These pretreatment strategies add operational cost and in some cases produce hazardous waste that poses health and safety risks. Direct biological pretreatment from biomass-degrading bacteria and fungi may significantly reduce the costs and risks associated with these traditional strategies due to the innate ability of these organisms to modify plant cell walls. An additional measure that could further reduce the expenses associated with lignocellulosic biomass fractionation is genetic modification of the lignocellulosic feedstocks, which can be accomplished by …

The Transcriptome Response Of The White-Rot Fungus Trametes Versicolor To Wild-Type And Lignin-Modified Hybrid Poplar, Anbarah Alzabaidi

Masters Theses

Plant biomass is a renewable and sustainable feedstock for biofuel production that can reduce societal dependence on fossil fuels. However, the production of liquid biofuels from the non-starch (i.e. lignocellulosic) material through fermentation technology is limited due to the complexity of the cell wall structure. This necessitates the use of chemical, thermal, and/or mechanical pretreatment technologies, which adds significant capital, operational, and environmental costs. Biological pretreatment strategies have the potential to mitigate these expenses by harnessing the innate ability of specialized bacteria and fungi to deconstruct lignocellulose. White-rot fungi (e.g. Trametes versicolor) have been shown to be …

Cu(Ii) Phenanthroline-Phenazine Complexes Dysregulate Mitochondrial Function And Stimulate Apoptosis, Garret Rochford, Zara Molphy, Kevin Kavanagh, Malachy Mccann, Michael Devereux, Andrew Kellett, Orla L. Howe

Articles

Herein we report an in-depth study on the cytotoxic mechanism of action of four developmental cytotoxic copper(II) complexes: [Cu(phen)2]2+ (Cu-Phen); [Cu(DPQ)(Phen)]2+ (Cu-DPQ-Phen); [Cu(DPPZ)(Phen)]2+; and [Cu(DPPN)(Phen)]2+ (where Phen = 1,10-phenanthroline, DPQ = dipyrido[3,2-f:20,30-h]quinoxaline, DPPZ = dipyrido[3,2-a:20,30-c]phenazine, and DPPN = benzo[i]dipyrido[3,2-a:20,30-c]phenazine). This complex class is known for its DNA intercalative properties and recent evidence—derived from an in vivo proteomic study—supports the potential targeting of mitochondrial function. Therefore, we focused on mitochondrial-mediated apoptosis related to cytotoxic activity and the potential impact these agents have on mitochondrial function. The Cu(II) complexes demonstrated superior activity regardless of aromatic extension within the phenazine ligand to the …

Neurodegenerative Modeling: Tau Protein, Degradative Pathways, And Gene Expression Profiling Of Human Ipsc-Derived Neural Precursors And Differentiated 3-D Neural Sphere Versus 2-D Monolayer Cultures, Kyle H. Anthoney

Cal Poly Humboldt theses and projects

Human induced pluripotent stem cells offer a model for human brain development and disease by differentiation into brain organoids; however, current neural culture systems lack the microenvironment, neuronal circuits and connectivity, vascular circulation, and immune system that exist in vivo. After differentiation and development of neuronal and non-neuronal cell types within two formats of cell cultures, we can visualize and recapitulate in vivo protein accumulation, gene expression, and degradative processes such as autophagy. Using RNA extraction, purification methods and reverse transcription I compared traditional monolayer cultures and novel 3-D neural sphere cultures via gene expression analysis. This analysis indicated …

Inhibitory Activity Of Metabolites From Mangosteen Roots Garcinia Mangostana L. On Hepatocellular Carcinoma And Colon Cancer Cell Growth, Kedkran Koopklang

Chulalongkorn University Theses and Dissertations (Chula ETD)

Liver cancer is one of the most common deadliest diseases both worldwide and in Thailand. Because of its rich and dual blood supply, malignant tumors in the liver could grow proliferative and rapidly spread to another organ. This process was called Metastasis, the major cause of human death. Mangosteen (Garcinia mangostana L.) generally known as a queen of fruits, has been widely studied in medicinal applications for many decades, due to plenty of bioactive metabolites such as xanthones as a major component. Nonetheless, reports about bioactivities of minor components were barely known. In this study, metabolites isolated from mangosteen roots …

Potential Of Antimicrobial Peptides Against Bacterial Pathogens Causing Bovine Mastitis, Kwantida Popitool

Chulalongkorn University Theses and Dissertations (Chula ETD)

Bovine mastitis is a common disease in dairy cows. The majority causes of bovine mastitis disease is an intramammary bacterial infection via the teat orifice. In general, antibiotics are used for bovine mastitis treatment, its inappropriate usage leads to antibiotic-resistance problem and residue in meat and dairy products. One of the alternative ways against pathogen to reduce antibiotic usage is antimicrobial peptides which are innate immune of life. Three cationic peptides as Pm11, Pep64, and L10 peptides were evaluated for an antimicrobial activity to gram-positive and gram-negative bacteria. Pm11 has shown the best potent antimicrobial activity with minimum bactericidal concentration …

Effects Of Valproic Acid On Fatty Acid Production In Microorganisms And Bioactive Compounds From Feroniella Lucida (Scheff.) Swingle And Termite-Associated Fungus Isfb10, Prapassorn Poolchanuan

Chulalongkorn University Theses and Dissertations (Chula ETD)

Valproic acid or valproate (VPA) is a drug for the treatment of epilepsy, bipolar disorder, migraine headaches and neuropathic pain. Unfortunately, VPA has many side effects. In this work, it was found that productions of some fatty acids were significantly affected by VPA at the concentration of 100 μM. Further exploration of VPA on fatty acid production in microorganisms including fungi, yeast, and bacteria, as well as representative gut microbiome. This work showed that VPA could enhance, reduce or completely inhibit the production of some fatty acids. VPA could induce the production of trans-9-elaidic acid that was previously found to …

Phytoalexin And Biomarker Peptide Detection Using Mass Spectrometry, Sasikarn Komkleow

Chulalongkorn University Theses and Dissertations (Chula ETD)

Mass spectrometry (MS) has been one of the scientific techniques most commonly used in different areas. Therefore, the current research was carried out in order to investigate the role of MS in biological analysis. This study is divided into two main parts. The first part used MS imaging to reveal the ability of the technique for imaging metabolites directly from plant tissue. Thai rice varieties were used to investigate the production and distribution of diterpenoid phytoalexins using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Results revealed the successfully detection of 5 types of diterpenoid phytoalexins on RD6 rice leaf tissue, …

Drought Tolerant Gene Identification By Rice Genome Comparison And Gene Characterization In Arabidopsis Plant Model, Chutarat Punchkhon

Chulalongkorn University Theses and Dissertations (Chula ETD)

Abiotic stresses, especially drought and salt stresses can affect plant growth and productivity. 'Kao Dawk Mali 105' ('KDML105') rice is one of the crops which has to face both drought and salt stresses as it is grown in rain-fed saline soil in the northeastern region of Thailand, where the irrigation is limited. CSSL104, a chromosome substitution line with 'KDML105' genetic background, was developed in order to improve drought tolerant ability of 'KDML105' rice by transferring the drought tolerant (DT)-QTL region from double haploid line, DH103. Photosynthesis parameters of CSSL104 and its parental lines, 'KDML105' and DH103, were investigated, when they …

Quantitative Trait Loci Analysis For Antioxidant Traits In Rice Oryza Sativa L., Saranyu Thaworn

Chulalongkorn University Theses and Dissertations (Chula ETD)

This research was conducted to study the antioxidant traits that contained the total phenolic content (TPC), total flavonoid content (TFC), and the antioxidant capacity (AC), by ABTS assay in the seed of 174 Thai rice cultivars, comprising 152 white, 10 red, and 12 purple pericarp cultivars. The hierarchical cluster analysis was evaluated, and the rice cultivars were classified into four clusters based on the antioxidant. Cluster I comprised of 72 white pericarp cultivars and had the lowest TPC, TFC, and AC. Cluster II contained 80 white cultivars and showed higher TFC values than cluster I. Cluster III consisted of 6 …

Spectral Reflectance Analysis For Genome-Wide Association Of Thali Rice Oryza Sativa L. Under Phosphorus-Deficient Condition, Sompop Pinit

Chulalongkorn University Theses and Dissertations (Chula ETD)

The goals of this research have three main points: (i) to develop a rapid method for inorganic phosphorus quantification, (ii) to investigate spectral reflectance indices representing phosphorus deficiency in rice, and (iii) to determine SNPs associated with phosphorus deficiency tolerance in Thai rice via genome-wide association study (GWAS). The punching method was developed to enhance the high throughput performance of the conventional Pi extraction and molybdate blue assay. Pi content can be extracted using equally small leaf areas without leaf grinding, balancing, and tedious transferring steps. The punching method provided comparable results to the conventional grinding method with a strong …

การพัฒนาชุดตรวจที่ง่ายต่อการใช้งานสำหรับวัณโรคในช้างโดยอินเตอร์เฟียรอนแกมมารีลีส, จิตสุดา พงษ์มา

Chulalongkorn University Theses and Dissertations (Chula ETD)

วัณโรค เป็นโรคติดต่อจากสัตว์สู่คนหรือจากคนสู่สัตว์ที่เป็นปัญหาด้านสาธารณสุขที่สำคัญระดับโลก รวมถึงในประเทศไทย เนื่องจากเชื้อ Mycobacterium tuberculosis (M. tb) complex (MTBC) ซึ่งเป็นเชื้อสาเหตุของวัณโรค สามารถพบการติดเชื้อได้ในสัตว์หลายกลุ่ม ทั้งสัตว์เท้ากีบ สัตว์ตระกูลลิง สัตว์เลี้ยงลูกด้วยนมรวมถึงช้าง การวินิจฉัยวัณโรคในช้างทำได้ยาก เนื่องจากช้างเป็นสัตว์ที่มีขนาดใหญ่ จึงไม่สามารถวินิจฉัยได้ด้วยวิธีเดียวกับมนุษย์ เช่น การเอกซเรย์ปอด และการทดสอบทางผิวหนัง นอกจากนี้ วิธีมาตรฐานโดยการเพาะเลี้ยงเชื้อจากน้ำล้างงวงช้างมีความไวต่ำ ใช้เวลานาน และตรวจได้เฉพาะระยะที่แสดงอาการเท่านั้น ดังนั้น การตรวจวินิจฉัยที่แม่นยำ ครอบคลุมทุกระยะการติดเชื้อ M. tb จึงเป็นสิ่งจำเป็น นำมาสู่การประยุกต์ใช้เทคนิค Interferon gamma release assay (IGRA) สำหรับเป็นวิธีทางเลือกในการวินิจฉัยวัณโรค ซึ่งเป็นวิธีตรวจหาอินเตอร์เฟียรอนแกมมา (IFN) ที่มีการหลั่งออกมาจากทีลิมโฟไซต์ชนิด memory หลังถูกกระตุ้นด้วยแอนติเจนจำเพาะของ M.tb งานวิจัยนี้จึงมีวัตถุประสงค์ที่จะพัฒนาวิธี IGRA ให้ใช้งานได้ง่ายกว่าที่มีอยู่เดิม โดยการคัดกรองเพปไทด์สังเคราะห์ของโปรตีน early secreted antigenic target 6 kDa (ESAT6) และ culture filtrate protein 10 kDa (CFP10) ที่สามารถกระตุ้นการหลั่ง eIFN ของเซลล์เม็ดเลือดขาวของช้าง และพัฒนาวิธีการตรวจโดยการกระตุ้นแบบ whole blood culture โดยเริ่มทำการตรวจการติดเชื้อของช้างด้วยวิธี IGRA เดิม (IGRA โดยใช้เซลล์เม็ดเลือดขาว PBMCs) ในตัวอย่างเลือดจากช้าง 20 เชือก โดยมีโปรตีนทั้งสายเป็นแอนติเจน พบว่าช้างมีการติดเชื้อ MTBC 50% ของตัวอย่างทั้งหมด ไม่ติดเชื้อ 30% และ 20% มีการติดเชื้อกลุ่ม Non tuberculous mycobacterium (NTM) จากนั้นทำการคัดกรองเพปไทด์สังเคราะห์ของโปรตีน ESAT6 และ CFP10 ในช้างทั้ง 20 เชือก พบว่าเพปไทด์สังเคราะห์ของโปรตีน …

การเตรียมไมโครแคปซูลของแคลเซียมอัลจิเนตเคลือบด้วย เจลาติน และ คัปปาคาราจีแนนเพื่อเพิ่มอัตราการรอดชีวิตของแบคทีเรียที่มีศักยภาพเป็นโปรไบโอติกในน้ำมะเกี๋ยง Cleistocalyx Nervosum Var. Paniala, ภัสริน หัทยาภิชาติ

Chulalongkorn University Theses and Dissertations (Chula ETD)

งานวิจัยนี้มีจุดประสงค์ศึกษาการเพิ่มอัตราการรอดชีวิตของแบคทีเรียที่มีศักยภาพเป็นโปรไบโอติกในน้ำมะเกี๋ยง Cleistocalyx nervosum var. paniala ที่มีกรด และ ฟีนอลิคเป็นองค์ประกอบในปริมาณมาก โดยคัดเลือกจุลินทรีย์ที่ผ่านการปรับตัว(Adaptation) ในเมี่ยงหมัก Camellia sinensis (L.) Kuntze var. assamica.ที่มีสภาวะ ฟีนอลิคสูง และ มีคุณสมบัติเป็นโปรไบโอติก โดยพบว่าแบคทีเรียที่คัดแยกได้จากเมี่ยงหมัก ซึ่งสามารถคัดแยกได้ 6 ไอโซเลท เมื่อนำมาเพิ่มจำนวนยีสต์เป้ามายด้วย 16S ribosomal RNA และ หาลำดับนิวคลีโอไทด์ พบว่าคล้ายคลึงกับแบคทีเรียโปรไบโอติกสายพันธุ์ Lactobacillus plantarum ในฐานข้อมูล GenBank โดยมีความคล้ายคลึงที่ 98-100% ซึ่งทำการศึกษา การลดลงของเซลล์ที่มีชีวิต ในน้ำมะเกี๋ยง ของแบคทีเรียที่เป็นเซลล์อิสระ 2 กลุ่ม ได้แก่ แบคทีเรียกลุ่ม LAB-MF ที่คัดแยกได้จากเมี่ยงหมัก และ กลุ่ม Lactobacillus sp. ทั้ง 6 สายพันธุ์ พบว่าในเวลา 24 ชั่วโมง L. plantarum KC332 (LAB-MF 105) มีอัตราการลดลงของเชื้อ 20.10% ซึ่ง แบคทีเรียในกลุ่ม Lactobacillus sp. พบว่า แบคทีเรียสายพันธุ์ L. plantarum TISTR2074 มีอัตรากาลดลงของเชื้อ 61.41% จึงนำมาศึกษาการยืดอายุโดยการห่อหุ้มในไมโครแคปซูล โดยเตรียมไมโครแคปซูล ทั้งหมด 5 ชนิด ได้แก่ 2% อัลจิเนตบีด (2% Al) 2% อัลจิเนตบีดเคลือบด้วยเจลาตินชั้นเดี่ยว(ACG) 2% อัลจิเนตบีดเคลือบด้วยเจลาตินชั้นคู่ (ACGD) 2% อัลจิเนตบีดเคลือบด้วยคัปปาคาราจีแนนชั้นเดี่ยว (ACC) และ 2% อัลจิเนตบีดเคลือบด้วยคัปปาคาราจีแนนชั้นคู่ (ACCD) จากการศึกษาการเปลี่ยนแปลงของลักษณะทางกายภาพ และ ทางเคมี ของเม็ดบีด …