Biotechnology Commons^™

Ligand Binding And Signaling Of Hare/Stabilin-2, Edward N. Harris, Fatima Cabral

Department of Biochemistry: Faculty Publications

The Stabilin receptors are a two-member family in the type H class of scavenger receptors. These dynamic receptors bind and internalize multiple ligands from the cell surface for the purpose of clearing extracellular material including some synthetic drugs and for sensing the external environment of the cell. Stabilin-1 was the first receptor to be cloned, though the biological activity of Hyaluronic Acid Receptor for Endocytosis (HARE)/Stabilin-2 was observed about 10 years prior to the cloning of Stabilin-1. Stabilin-1 has a more diverse expression profile among the tissues than HARE/Stabilin-2. This review will focus on HARE/Stabilin-2 and its interactions with hyaluronan, …

Downregulation Of A Cyp74 Rubber Particle Protein Increases Natural Rubber Production In Parthenium Argentatum, Dante F. Placido, Niu Dong, Chen Dong, Von Mark V. Cruz, David A. Dierig, Rebecca E. Cahoon, Byung-Guk Kang, Trinh Huynh, Maureen Whalen, Grisel Ponciano, Colleen Mcmahan

Department of Biochemistry: Faculty Publications

We report functional genomics studies of a CYP74 rubber particle protein from Parthenium argentatum, commonly called guayule. Previously identified as an allene oxide synthase (AOS), this CYP74 constitutes the most abundant protein found in guayule rubber particles. Transgenic guayule lines with AOS gene expression down-regulated by RNAi (AOSi) exhibited strong phenotypes that included agricultural traits conducive to enhancing rubber yield. AOSi lines had higher leaf and stem biomass, thicker stembark tissues, increased stem branching and improved net photosynthetic rate. Importantly, the rubber content was significantly increased in AOSi lines compared to the wild-type (WT), vector control and …

การผลิตไบโอดีเซลจากกรดไขมันอิสระของน้ำมันปาล์มโดยปฏิกิริยาสองขั้นตอนโดยใช้ตัวเร่งปฏิกิริยาชีวภาพทั้งเซลล์, ฐนิสา หวั่งประดิษฐ์

Chulalongkorn University Theses and Dissertations (Chula ETD)

การผลิตไบโอดีเซลสามารถผลิตได้จากกรดไขมันอิสระของน้ำมันปาล์มโดยปฏิกิริยาสองขั้นตอนโดยใช้ตัวเร่งปฏิกิริยาชีวภาพทั้งเซลล์ ในการศึกษานี้ได้ใช้ยีสต์ Candida rugosa เป็นตัวเร่งปฏิกิริยาชีวภาพทั้งเซลล์ เนื่องจากเชื้อยีสต์ดังกล่าวมีความสามารถในการไฮโดรไลซ์น้ำมันปาล์มไปเป็นกรดไขมันอิสระ โดยพบว่าได้กรดไขมันอิสระสูงสุดเท่ากับ 82.61 เปอร์เซ็นต์ หลังจากทำการเพาะเลี้ยงเป็นเวลา 5 วัน จากนั้นกรดไขมันอิสระที่ผลิตโดย C. rugosa จะถูกนำไปใช้เป็นตัวเหนี่ยวนำในการผลิตเอนไซม์ลิเพสจากเชื้อ Aureobasidium pullulans var. melanogenum SRY 14-3 ซึ่งหลังจากการหาภาวะที่เหมาะสมพบว่าสามารถผลิตเอนไซม์ลิเพสที่มีค่าแอกทิวิตีและค่าแอกทิวิตีจำเพาะของเอนไซม์สูงสุด คือ 1.18 ยูนิตต่อมิลลิลิตร และ 17.28 ยูนิตต่อมิลลิกรัมโปรตีน ตามลำดับ โดยใช้ความเข้มข้นของกรดไขมันอิสระ 3 เปอร์เซ็นต์ ที่อุณหภูมิ 30 องศาเซลเซียส เป็นเวลา 120 ชั่วโมง การศึกษาการผลิตไบโอดีเซลจากปฏิกิริยาเอสเทอริฟิเคชันที่เร่งปฏิกิริยาด้วย A. pullulans var. melanogenum SRY 14-3 พบว่าสามารถผลิตไบโอดีเซลได้สูงสุดเท่ากับ 21.39 เปอร์เซ็นต์ เมื่อใช้อัตราส่วนโดยโมลของกรดไขมันอิสระต่อเมทานอลเท่ากับ 1:1 ที่อุณหภูมิ 30 องศาเซลเซียส เป็นเวลา 72 ชั่วโมง สำหรับการศึกษาตัวเร่งปฏิกิริยาชีวภาพทั้งเซลล์ด้วยการใช้เทคนิคการแสดงออกที่ผิวเซลล์ยีสต์ เอนไซม์ลิเพส 1 และเอนไซม์ลิเพส 3 จาก C. rugosa (CRL1 และ CRL3) และเอนไซม์ลิเพส จาก A. pullulans var. melanogenum SRY 14-3 (AML) ได้ถูกนำมาเชื่อมต่อกับโปรตีนฐาน PpPIR1 แล้วทำการโคลนเข้าสู่ยีสต์เจ้าบ้าน Pichia pastoris KM 71 ได้เป็นยีสต์ Pp-CRL1, Pp-CRL3 และ Pp-AML ตามลำดับ จากการศึกษาพบว่ายีสต์สายพันธุ์รีคอมบิแนนท์ Pp-CRL1 และ Pp-CRL3 สามารถผลิตเอนไซม์ลิเพสที่ผิวเซลล์สูงสุดเท่ากับ 1,499.9 มิลลิยูนิตต่อOD600 และ 181.96 มิลลิยูนิตต่อOD600 …

A 3d Bioprinter Platform For Mechanistic Analysis Of Tumoroids And Chimeric Mammary Organoids, John A. Reid, Xavier-Lewis Palmer, Peter A. Mollica, Nicole Northam, Patrick C. Sachs, Robert D. Bruno

School of Medical Diagnostics & Translational Sciences Publications

The normal mammary microenvironment can suppress tumorigenesis and redirect cancer cells to adopt a normal mammary epithelial cell fate in vivo. Understanding of this phenomenon offers great promise for novel treatment and detection strategies in cancer, but current model systems make mechanistic insights into the process difficult. We have recently described a low-cost bioprinting platform designed to be accessible for basic cell biology laboratories. Here we report the use of this system for the study of tumorigenesis and microenvironmental redirection of breast cancer cells. We show our bioprinter significantly increases tumoroid formation in 3D collagen gels and allows for precise …

Detection Of Sickle Cell Disease-Associated Single Nucleotide Polymorphism Using A Graphene Field Effect Transistor, Kandace Fung

CMC Senior Theses

Sickle Cell Disease (SCD) is a hereditary monogenic disorder that affects millions of people worldwide and is associated with symptoms such as stroke, lethargy, chronic anemia, and increased mortality. SCD can be quickly detected and diagnosed using a simple blood test as an infant, but as of now, there is currently limited treatment to cure an individual of sickle cell disease. Recently, there have been several promising developments in CRISPR-Cas-associated gene-editing therapeutics; however, there have been limitations in gene-editing efficiency monitoring, which if improved, could be beneficial to advancing CRISPR-based therapy, especially in SCD. The CRISPR-Chip, a three-terminal graphene-based field …

Phenogeneranker: A Tool For Gene Prioritization Using Complete Multiplex Heterogeneous Networks, Cagatay Dursun, Naoki Shimoyama, Mary Shimoyama, Michael Schläppi, Serdar Bozdag

Computer Science Faculty Research and Publications

Uncovering genotype-phenotype relationships is a fundamental challenge in genomics. Gene prioritization is an important step for this endeavor to make a short manageable list from a list of thousands of genes coming from high-throughput studies. Network propagation methods are promising and state of the art methods for gene prioritization based on the premise that functionally-related genes tend to be close to each other in the biological networks.

In this study, we present PhenoGeneRanker, an improved version of a recently developed network propagation method called Random Walk with Restart on Multiplex Heterogeneous Networks (RWR-MH). PhenoGeneRanker allows multi-layer gene and disease networks. …

Malate Dehydrogenase Allele Frequencies In Honeybee Populations And Its Correlation With Temperature, Thitipan Meemongkolkiat

Chulalongkorn University Theses and Dissertations (Chula ETD)

Temperature is one of the major factors that affect on the variation in honeybee in term of DNA and protein variants. The aim of this study is to investigate whether the three structural variants of the cytosolic malate dehydrogenase (cMDH) protein of the honeybee can explain clinal variation in allele frequencies. To test the hypothesis that there is a molecular basis to the temperature-dependent fitness of cMDH variation, the enzymic activity was determined across a range of temperatures in vitro. The F and S alleles have higher activity and are less sensitive to high temperatures than the M allele. Next, …

การตรวจสอบเอนไซม์ลิงค์อิมมูโนซอร์เบนต์แอสเสย์สำหรับการตรวจวัดสารตกค้างกลุ่มแรคโตพามีนและการประยุกต์, พลอยขวัญ พรหมพิทยายุทธ

Chulalongkorn University Theses and Dissertations (Chula ETD)

แรคโตพามีน (Ractopamine) เป็นสารในกลุ่มเบต้าอะโกนิสต์ (Beta-Agonist) ที่ถูกห้ามใช้ในประเทศไทย ดังนั้นงานวิจัยนี้จึงต้องการที่จะพัฒนาและทดสอบความใช้ได้ของวิธี Enzyme linked immunosorbent assay (ELISA) สำหรับตรวจวัดแรคโตพามีนตกค้างในเนื้อสัตว์ เครื่องในสัตว์และอาหารสัตว์ โดยได้เริ่มจากการพัฒนา ELISA 2 รูปแบบคือ indirect competitive ELISA และ direct competitive ELISA จากการทดสอบได้เลือก ELISA รูปแบบ direct competitive ELISA เนื่องจากมีค่าความไวที่สูงกว่าอีกรูปแบบ ค่า IC50 LOQ และ LOD เท่ากับ 0.57, 0.06 และ 0.02 นาโนกรัมต่อมิลลิลิตรตามลำดับ ทำการทดสอบความใช้ได้ของ direct competitive ELISA สำหรับนำไปตรวจวัดปริมาณแรคโตพามีนตกค้างในตัวอย่างกลุ่มเนื้อสัตว์ (เนื้อหมูและเนื้อโค) กลุ่มเครื่องในสัตว์ (ตับหมู ตับโคและไตหมู) และกลุ่มอาหารสัตว์ (อาหารหมูและอาหารโค) ทดสอบความไวของวิธี ELISA ในสารสกัดตัวอย่างต่างๆ พบว่า LOQ ของตัวอย่างอยู่ในช่วง 0.56-1.90 นาโนกรัมต่อกรัม และค่า LOD ของตัวอย่างอยู่ในช่วง 0.32-0.97 นาโนกรัมต่อกรัม ช่วงของการการตรวจวัดแรคโตพามีนในเนื้อหมูและไตหมูอยู่ที่ 0.4-6.25 นาโนกรัมต่อกรัม ในขณะที่ตัวอย่างอื่น ๆ มีช่วงของการตรวจวัดอยู่ที่ 0.8-12.5 นาโนกรัมต่อกรัม นอกจากนี้ได้ทดสอบการเกิดปฏิกิริยาข้ามพบว่าไม่เกิดปฏิกิริยาข้ามกับสารในกลุ่มเบต้าอะโกนิสต์ ความถูกต้อง (% recovery) และความแม่นยำ (%CV) มีค่าอยู่ในช่วง 64.06-109.80 % และ 6.26-28.87 % ตามลำดับ ค่าความสามารถในการตรวจวัด (CCβ) มีค่าอยู่ที่ 2 นาโนกรัมต่อกรัมสำหรับเนื้อหมูและไตหมู และ 3 นาโนกรัมต่อกรัมในตัวอย่างอื่นๆ โดยมีค่าความผิดพลาดผิดพลาดจากการตรวจวัดน้อยกว่าหรือเท่ากับ 5 % จากผลการทดสอบดังกล่าวพบว่าวิธี direct …

Therapeutic Delivery Technology And Its Economic Impact, Paul E. Savas Jr.

Senior Honors Theses

Therapeutic delivery technology is a current area of high interest in both university and industrial settings. These technologies are being developed in order to deliver therapeutic agents, such as genes, proteins, and drugs, to patients more efficiently. Nanoscale delivery vehicles have proven to be useful for these applications; these vehicles may either be naturally produced or chemically synthesized. The physical properties of these nanomaterials must be characterized correctly using instrumentation that evaluates their size, morphology, and potential for agglomeration. These technologies represent a high-growth economic area that fosters entrepreneurship and innovation. Because of this innovative spirit, research and economic interest …

Unraveling The Role Of Phenylethanolamine N-Methyltransferase (Pnmt+) Cells In-Vivo, Sanjana Manja

Electronic Theses and Dissertations

Phenylethanolamine N-methyltransferase (Pnmt) is the enzyme that N-methylates norepinephrine to produce the stress hormone/neurotransmitter, epinephrine, which is abundantly expressed in adrenal glands. Developmental studies have also identified Pnmt expression in the embryonic heart and several areas of the brain, including brainstem, cerebellum, and hypothalamus. Thus, we hypothesize that selective ablation of Pnmt+ cells will have detrimental effects on cardiovascular, neuromuscular, and metabolic processes. To uncover the importance of Pnmt+ cells in vivo, we generated a novel Diphtheria Toxin A (DTA) suicide model (Pnmt+/Cre; R26+/DTA) to selectively ablate Pnmt-expressing (Pnmt+) cells in mice. Appearing normal at birth, Pnmt-Cre/DTA mice began to …

Bone Morphogenetic Protein 7 Inhibits Pyroptotic Cell Death In Vascular Smooth Muscle Cells Of Atherosclerotic Apolipoprotein E -/- Mice, Kaley Garner

Electronic Theses and Dissertations

Atherosclerosis (ATH) is an inflammation-mediated disease in which cell death underlies the formation of lesions along the intima layer of vascular walls resulting in vessel narrowing, decreased blood flow, and increased risk of lesion rupture leading to myocardial infarction and stroke. The current study was undertaken to investigate whether inflammation in ATH can induce pyroptosis in vascular smooth muscle cells (SMC's). We therefore hypothesized that pyroptosis occurs and is inhibited by bone morphogenetic protein 7 (BMP7). We examined SMC pyroptosis at acute (D5) and midstage (D28) following disturbed flow-induced hemodynamic injury to the vascular wall using our partial left carotid …

Toward An Enzyme-Coupled, Bioorthogonal Platform For Methyltransferases: Probing The Specificity Of Methionine Adenosyltransferases, Tyler D. Huber

Theses and Dissertations--Pharmacy

Methyl group transfer from S-adenosyl-l-methionine (AdoMet) to various substrates including DNA, proteins, and natural products (NPs), is accomplished by methyltransferases (MTs). Analogs of AdoMet, bearing an alternative S-alkyl group can be exploited, in the context of an array of wild-type MT-catalyzed reactions, to differentially alkylate DNA, proteins, and NPs. This technology provides a means to elucidate MT targets by the MT-mediated installation of chemoselective handles from AdoMet analogs to biologically relevant molecules and affords researchers a fresh route to diversify NP scaffolds by permitting the differential alkylation of chemical sites vulnerable to NP MTs that are unreactive to …

Capital Efficiency For Development Stage Biotech-Based Firms: An Ipo Perspective, Mark J. Ahn, Amir Shaygan

Engineering and Technology Management Faculty Publications and Presentations

Access to multiple tranches of capital is critical for predominantly no revenue development stage biotech firms. While financing needs are monotonically increasing over multiple years in the product development approval cycle, the market for high risk, milestone driven biotech investment is significantly more volatile than the financial markets as a whole. In this paper, we analyzed the role and relative importance of global biotech IPOs, as well as other sources of capital such as strategic alliances, for research and development funding. We also explored and assessed the degree of mismatch between the access to capital, operational efficiencies, and how firms …

Mechanisms And Immunogenicity Of Nspef-Induced Cell Death In B16f10 Melanoma Tumors, Alessandra Rossi, Olga N. Pakhomova, Andrei G. Pakhomov, Samantha Weygandt, Anna A. Bulysheva, Len E. Murray, Peter A. Mollica, Claudia Muratori

Bioelectrics Publications

Accumulating data indicates that some cancer treatments can restore anticancer immunosurveillance through the induction of tumor immunogenic cell death (ICD). Nanosecond pulsed electric fields (nsPEF) have been shown to efficiently ablate melanoma tumors. In this study we investigated the mechanisms and immunogenicity of nsPEF-induced cell death in B16F10 melanoma tumors. Our data show that in vitro nsPEF (20-200, 200-ns pulses, 7 kV/cm, 2 Hz) caused a rapid dose-dependent cell death which was not accompanied by caspase activation or PARP cleavage. The lack of nsPEF-induced apoptosis was confirmed in vivo in B16F10 tumors. NsPEF also failed to trigger ICD-linked responses such …

Looking For Maize Genes Involved In Cold Response: Producing Knockouts For Arabidopsis Homologs Of Maize Candidate Genes Using A Crispr/Cas9 Approach, Katie Hillmann

Departmental Honors Projects

Most of today’s maize is cultivated outside its original climate zone, where yields are constrained by the changes in climate. Maize is especially vulnerable to high temperatures and drought stress, both of which negatively affect corn yields. An important strategy to combat this is early sowing, which avoids the effects of summer droughts and high temperatures in many places around the globe. However, maize is a cold sensitive species (Sanghera et al., 2011), making improvement to cold stress crucial for its adaption. The relatively new system CRISPR (Clustered regularly-interspaced short palindromic repeats)/Cas9 offers the potential to study cold-stress related …

Evaluation Of Brewer's Spent Grain Hydrolysate As A Substrate For Production Of Thermostable Α-Amylase By Bacillus Stearothermophilus, Rajeev Ravindran, Gwilym A. Williams, Amit Jaiswal

Articles

In the present study, BSG was hydrolysed using cellulolytic enzymes and used as a growth medium supplement for cultivation of the thermophilic bacterium, Bacillus stearothermophilus in the production of α-amylase. A central composite design involving five parameters and four levels viz. starch, peptone, KCl, and MgSO4 along with BSG hydrolysate was used to derive the optimal media composition. The fermentation was conducted using shake flasks for 36 h at a temperature of 50 °C and pH 7.0 at 220 rpm. Optimization trials revealed that maximal amylase production (198.09 U/ml) occurred with a medium composition of starch (0.2% w/v), peptone (0.2% …

Exploring The Efficacy Of Natural Products In Alleviating Alzheimer’S Disease Using Animal Models, Prajakta Deshpande, Neha Gogia, Amit Singh

Biology Faculty Publications

Alzheimer’s disease (hereafter AD) is a progressive neurodegenerative disorder that affects the central nervous system. There are multiple factors that cause AD, viz., accumulation of extracellular Amyloid-beta 42 plaques, intracellular hyper-phosphorylated Tau tangles, generation of reactive oxygen species due to mitochondrial dysfunction and genetic mutations. The plaques and tau tangles trigger aberrant signaling, which eventually cause cell death of the neurons. As a result, there is shrinkage of brain, cognitive defects, behavioral and psychological problems. To date, there is no direct cure for AD. Thus, scientists have been testing various strategies like screening for the small inhibitor molecule library …

Application Of Short Tandem Target Mimic (Sttm) Technique For Functional Analysis Of Micro-Rna396 In Transgenic Poplar Trees, Surattana Boonsai

Dissertations, Master's Theses and Master's Reports

Short Tandem Target Mimic (STTM) is a commonly technique used for functional studies of a number of genes in several plant model systems. However, very little is known about application of STTM technique in tree species. In this study, STTM was applied to knock down microRNA396 (miR396) in transgenic poplar trees for the first time. STTM396 expression resulted in dramatic decrease in miR396 expression levels leading to taller plants with larger leaves and larger leaf cell size. Additionally, an expression analysis of growth regulating factor genes (GRFs) that are members of miR396 target gene family showed up-regulation of GRF07 gene …

Effective Knowledge Transfer During Biopharmaceutical Technology Transfer - How Well Do We Do It?, Martin J. Lipa, Paige Kane, Anne Greene

Articles

Author’s Note: This is the author’s submitted manuscript which has subsequently been published in the Journal of Validation Technology (www.ivtnetwork.com, Volume 25, Issue 4 – August 2019).

While knowledge management (KM) has been widely applied in other sectors, the international biopharmaceutical sector has struggled with the meaningful and sustained application of effective KM practices. This is evident even though KM has been highlighted in regulatory guidance for over 10 years, and the positive business impact of KM is well recognized in other sectors. This paper focuses on the topic of KM as applied to biopharmaceutical technology transfer, introducing …

Enhancing Water Stress Tolerance In Floriculture Crops, Suejin Park

Graduate Theses, Dissertations, and Problem Reports (ETD)

Water deficit is one of the major constraints on plant growth and development, causing reduction of crop productivity. To minimize water loss, among many adaptation strategies, plants close their stomata to reduce transpiration. The stomatal closure is regulated by light, internal CO2 concentration, and plant hormones, mainly abscisic acid. Plants’ response mechanisms to water deficit are complex processes involving numerous genes and various signaling pathways. Floriculture crops are often exposed to water deficit during shipping and retailing, and these periods often result in damaged crops and profit loss. Understanding of plant responses to water deficit stress will provide us an …