Biotechnology Commons^™

Transcriptomic Analysis On Hepatocellular Carcinoma Model In Response To Safranal Treatment, Badriya Mahmood Ahmed Baig

Biology Theses

Unsolved riddle of cancer remains a major global health concern particularly in hepatocellular carcinoma (HCC) which is among the leading causes of cancer related death worldwide. Saffron (Crocus sativus L.) and its bioactive phytochemicals possess promising anti-cancer activities. One of these phytochemicals, safranal, has demonstrated potent anti-cancer activities against different types of cancers. Yet, its association with liver cancer remains under documented. This study investigated HCC response to safranal’s treatment via transcriptomic approach. Safranal was found to be involved in mitochondrial dysfunction, induced oxidative stress and increased reactive oxygen species (ROS) production leading to cell death. Interestingly, safranal has …

Anti-Colon Cancer Effect Of Origanum Majorana Essential Oil, Asma Nasser Rashed Alrashedi

Biology Theses

Plants have been shown to be an excellent source of new drugs, including anticancer agents. Origanum majorana commonly known as marjoram is a plant that is known to possess different therapeutic values including antioxidant andantimicrobial activities.

Our research team has previously tested the ethanolic extract of O. majorana on triple negative breast cancer and published the findings. The ethanolic extract promoted mitotic arrest at G2/M phase, induced apoptosis as well as inhibition of migration and metastasis. The promising potential of the ethanolic extract encouraged us to test the effects of O. majorana essential oil on human colon cancer cell lines. …

Characterization Of A Morphogenetic Furrow Specific Gal4 Driver In The Developing Drosophila Eye, Ankita Sarkar, Neha Gogia, Kevin Farley, Lydia C. Payton, Amit Singh

Biology Faculty Publications

The ability to express a gene of interest in a spatio-temporal manner using Gal4-UAS system has allowed the use of Drosophila model to study various biological phenomenon. During Drosophila eye development, a synchronous wave of differentiation called Morphogenetic furrow (MF) initiates at the posterior margin resulting in differentiation of retinal neurons. This synchronous differentiation is also observed in the differentiating retina of vertebrates. Since MF is highly dynamic, it can serve as an excellent model to study patterning and differentiation. However, there are not any Gal4 drivers available to observe the gain- of- function or loss- of- function of a …

Prediction Of Lncrna-Disease Associations Based On Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA–disease associations, especially for novel lncRNAs, remains challenging.

Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA– disease associations based on inductive matrix completion. We compute Gaussian interaction profile kernel of lncRNAs from known lncRNA–disease interactions and functional similarity of diseases based on disease–gene and gene–gene onotology …

Designer Babies: A Paired Analysis Of The Technological Advances And Ethical Implications Of Genetic Selection, Alexandra Schmerge 18

Honor Scholar Theses

No abstract provided.

Molecular Cloning And Functional Analysis Of Salt Overly Sensitive (Sos) Pathway Genes From Local Plants Of The United Arab Emirates, Mariam Obaid Saeed Abdalla Alzaabi

Biology Theses

Salinity is one of the major abiotic stresses that lead to extreme reduction in crop productivity worldwide. Increased soil and water salinity is a major issue in UAE’s agriculture. Some plants however have adapted to grow in high saline conditions, i.e. halophytes. Unfortunately, most crops are glycophytes and cannot tolerate high salinity. During salinity stress, expression of numerous genes is altered to protect the plants. Understanding the differences in gene structure between halophytes and glycophytes could provide insights into developing transgenic crops that can thrive in salinity conditions. The Salt Overly Sensitive (SOS) pathway is a key mechanistic cascade controlling …

Structural Determinants For The Interactions Of Chemically Modified Nucleic Acids With The Stabilin‑2 Clearance Receptor, Hans Gaus, Colton M. Miller, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

The Stabilin receptors are systemic clearance receptors for some classes of chemically modified nucleic acid therapeutics. In this study, the recombinant human secreted ecto-domain of the small isoform of Stabilin-2 (s190) was purified from cell culture and evaluated for direct binding with a multitude of antisense oligonucleotides (ASOs) using a fluorescence polarizationbased assay. The tested ASOs varied in their backbone composition, modification of the ribose 2′ position, overall length of the oligo, and sequence of the nucleotide bases. A fully phosphorothioate (PS) ASO with a 5−10−5 pattern of flanking 2′-O-methoxyethyl modifications was then used to test the effects …

Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov

Biological Sciences Faculty Research

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family …

Correlation Of Structure, Function And Protein Dynamics In Gh7 Cellobiohydrolases From Trichoderma Atroviride, T. Reesei And T. Harzianum, Anna S. Borisova, Elena V. Eneyskaya, Suvamay Jana, Silke F. Badino, Jeppe Kari, Antonella Amore, Magnus Karlsson, Henrik Hansson, Mats Sandgren, Michael E. Himmel, Peter Westh, Christina M. Payne, Anna A. Kulminskaya, Jerry Ståhlberg

Chemical and Materials Engineering Faculty Publications

Background: The ascomycete fungus Trichoderma reesei is the predominant source of enzymes for industrial conversion of lignocellulose. Its glycoside hydrolase family 7 cellobiohydrolase (GH7 CBH) TreCel7A constitutes nearly half of the enzyme cocktail by weight and is the major workhorse in the cellulose hydrolysis process. The orthologs from Trichoderma atroviride (TatCel7A) and Trichoderma harzianum (ThaCel7A) show high sequence identity with TreCel7A, ~ 80%, and represent naturally evolved combinations of cellulose-binding tunnel-enclosing loop motifs, which have been suggested to influence intrinsic cellobiohydrolase properties, such as endo-initiation, processivity, and off-rate.

Results: The TatCel7A, ThaCel7A, …

Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABC transporters are essential for cellular transport; contribute to maintain the homeostasis of the cells. Generally, ABC transporters are multi-subunit; contain essential cytoplasmic factors which are critical to ATP hydrolysis activity. In this paper, we would like to take a closer look to Mrub_1283, Mrub_1284 and Mrub_1285, three consecutive genes in Meiothermus ruber genome. We hypothesize that these genes are in the same operon and encode for ABC glycine/ betaine transporters. To confirm our hypothesis, we utilizes several bioinformatics tools to predict the potential function of Mrub_1283, Mrub_1284 and Mrub_1285 and to search for their orthologs in Escherichia coli genome. …

Chitosan Biopolymer Promotes Yield And Stimulates Accumulation Of Antioxidants In Strawberry Fruit, Mosaddiqur Rahman, Julakha Akter Mukta, Abdullah As Sabir, Dipall Rani Gupta, Mohammed Mohi-Ud-Din, Mirza Hasanuzzaman, Md. Giashuddin Miah, Mahfuzur Rahman, Md Tofazzai Islam

Faculty & Staff Scholarship

Strawberry is a well-known source of natural antioxidants with excellent free radical scav- enging capacity. This study determined the effects of chitosan application in field condition on plant growth, fruit yield and antioxidant activities in strawberry fruit. Foliar applications of chitosan on strawberry significantly increased plant growth and fruit yield (up to 42% higher) compared to untreated control. Increased fruit yield was attributed to higher plant growth, individual fruit weight and total fruit weight/plant due to the chitosan application. Surprisingly, the fruit from plants sprayed with chitosan also had significantly higher contents (up to 2.6- fold) of carotenoids, anthocyanins, flavonoids …

Quantum Confined Peptide Assemblies With Tunable Visible To Near-Infrared Spectral Range, Kai Tao, Zhen Fan, Leming Sun, Pandeeswar Makam, Zhen Tian, Mark Ruegsegger, Shira Shaham-Niv, Derek Hansford, Ruth Aizen, Zui Pan, Scott Galster, Jianjie Ma, Fan Yuan, Mingsu Si, Songnan Qu, Mingjun Zhang, Ehud Gazit, Junbai Li

Faculty & Staff Scholarship

Quantum confined materials have been extensively studied for photoluminescent applica- tions. Due to intrinsic limitations of low biocompatibility and challenging modulation, the utilization of conventional inorganic quantum confined photoluminescent materials in bio- imaging and bio-machine interface faces critical restrictions. Here, we present aromatic cyclo-dipeptides that dimerize into quantum dots, which serve as building blocks to further self-assemble into quantum confined supramolecular structures with diverse morphologies and photoluminescence properties. Especially, the emission can be tuned from the visible region to the near-infrared region (420 nm to 820 nm) by modulating the self-assembly process. Moreover, no obvious cytotoxic effect is observed for …

Pleiotropic And Epistatic Network-Based Discovery: Integrated Networks For Target Gene Discovery, Deborah Weighill, Piet Jones, Manesh Shah, Priya Ranjan, Wellington Muchero, Jeremy Schmutz, Avinash Sreedasyam, David Macaya-Sanz, Robert Sykes, Nan Zhao, Madhavi Z. Martin, Stephen Difazio, Timothy J. Tschaplinski, Gerald Tuskan, Daniel Jacobson

Faculty & Staff Scholarship

Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant’s sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use …

Macrophage Sensing Of Single- Walled Carbon Nanotubes Via Toll- Like Receptors, Sourav P. Mukherjee, Olesja Bondarenko, Pekka Kohonen, Fernando T. Andon, Tana Brzicova, Isabel Gessner, Sanjay Mathur, Massimo Bottini, Paolo Calligari, Lorenzo Stella, Elena Kisin, Anna Shvedova, Reija Autio, Heli Salminen-Mankonen, Ritta Lahesmaa, Bengt Fadeel

Faculty & Staff Scholarship

Carbon-based nanomaterials including carbon nanotubes (CNTs) have been shown to trigger

inflammation. However, how these materials are ‘sensed’ by immune cells is not known. Here we compared the effects of two carbon-based nanomaterials, single-walled CNTs (SWCNTs) and graphene oxide (GO), on primary human monocyte-derived macrophages. Genome-wide transcriptomics assessment was performed at sub-cytotoxic doses. Pathway analysis of the microarray data revealed pronounced effects on chemokine-encoding genes in macrophages exposed to SWCNTs, but not in response to GO, and these results were validated by multiplex array-based cytokine and chemokine profiling. Conditioned medium from SWCNT-exposed cells acted as a chemoattractant for dendritic cells. …

Structure Of The Ambrosia Beetle (Coleoptera: Curculionidae) Mycangia Revealed Through Micro-Computed Tomography, You Li, Yongying Ruan, Matthew T. Kasson, Edward L. Stanley, Conrad P.D.T Gillett, Andrew J. Johnson, Mengna Zhang, Jiri Hulcr

Faculty & Staff Scholarship

Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) rely on a symbiosis with fungi for their nutrition. Symbiotic fungi are preserved and transported in specialized storage structures called mycangia. Although pivotal in the symbiosis, mycangia have been notoriously difficult to study, given their minute size and membranous structure. We compared the application of novel visualization methods for the study of mycangia, namely micro-computed tomography (micro-CT) and laser ablation tomography (LATscan) with traditional paraffin sectioning. Micro-CT scanning has shown the greatest promise in new organ discovery, while sectioning remains the only method with sufficient resolution for cellular visualization. All three common types …

Spontaneous Dna Damage To The Nuclear Genome Promotes Senescence, T Redox Imbalance And Aging, Andria R. Robinson, Matthew J. Yousefzadeh, Tania A. Rozgaja, Jin Wang, Xuesen Li, Jeremy S. Tilstra, Chelsea H. Feldman, Siobhan Q. Gregg, Caroline H. Johnson, Erin M. Skoda, Marie-Celine Frantz, Harris Bell-Temin, Hannah Pope-Varsalona, Aditi U. Gurkar, Luigi A. Nasto, Rena A.S. Robinson, Heike Fuhrmann-Stroissnigg, Jolanta Czerwinska, Sara J. Mcgowan, Nadiezhda Cantu-Madellin, Jamie B. Harris, Salony Maniar, Mark A. Ross, Christy E. Trussoni, Nicholas F. Larusso, Eugenia Cifuentes-Pagano, Patrick J. Pagano, Barbara Tudek, Nam V. Vo, Lora H. Rigatti, Patricia L. Opresko, Donna B. Stolz, Simon C. Watkins, Christin E. Burd, Claudette M. St, Croix, Gary Siuzdak, Nathan A. Yates, Paul D. Robbins, Yinsheng Wang, Peter Wipf, Eric E. Kelley, Laura J. Neidernhofer

Faculty & Staff Scholarship

Accumulation of senescent cells over time contributes to aging and age-related diseases. However, what drives senescence in vivo is not clear. Here we used a genetic approach to determine if spontaneous nuclear DNA damage is sufficient to initiate senescence in mammals. Ercc1-/Δ mice with reduced expression of ERCC1-XPF endonuclease have impaired capacity to repair the nuclear genome. Ercc1-/Δ mice accumulated spontaneous, oxidative DNA damage more rapidly than wild-type (WT) mice. As a consequence, senescent cells accumulated more rapidly in Ercc1-/Δ mice compared to repair-competent animals. However, the levels of DNA damage and senescent cells in Ercc1-/Δ mice never exceeded that …

Real-Time Assessment And Visual Feedback For Patient Rehabilitation Using Inertial Sensors, Deepa Adinarayanan

ETD Archive

Rehabilitation exercises needs have been continuously increasing and have been projected to increase in future as well based on its demand for aging population, recovering from surgery, injury and illness and the living and working lifestyle of the people. This research aims to tackle one of the most critical issues faced by the exercise administers-Adherence or Non-Adherence to Home Exercise problems especially has been a significant issue resulting in extensive research on the psychological analysis of people involved. In this research, a solution is provided to increase the adherence of such programs through an automated real-time assessment with constant visual …

Stabilization Of Hypoxia Inducible Factor By Cobalt Chloride Can Alter Renal Transepithelial, Subhra Sankar Nag

ETD Archive

Kidney cyst expansion, stagnant fluid accumulation, and insufficient vascular supply can result in localized chronic ischemia-hypoxia in kidney cysts, as well as in normal renal epithelia adjacent to a cyst. We hypothesize that in normal epithelia near a cyst, the stabilization of Hypoxia Inducible Factor 1a (HIF1a), a major regulator of cellular response to hypoxia, can cause altered paracellular and transcellular transport, transforming a normal absorptive phenotype to a secretory and paracellularly leaky phenotype, leading to cyst expansion. Using 100 µmol/L cobalt chloride (CoCl2), HIF1a was stabilized in cellular nucleus of a mouse cortical collecting duct cell line (mCCD 1296 …

Biosynthetic Mechanism Of The Antibiotic Capuramycin, Erfu Yan

Theses and Dissertations--Pharmacy

A-102395 is a member of the capuramycin family of antibiotics which was isolated from the culture broth of Amycolatopsis sp. SANK 60206. A-102339 is structurally classified as a nucleoside antibiotic, which like all members of the capuramycin family, inhibits bacterial MraY (translocase I) with IC₅₀ of 11 nM which is the lowest among the capuramycin family. A semisynthetic derivative of capuramycin is currently in clinical trials as an antituberculosis antibiotic, suggesting high potential for using A-102395 as a starting point for new antibiotic discovery. In contrast to other capuramycins, A-102395 has a unique arylamine-containing polyamide side chain. The biosynthetic …

Lignocellulosic Biorefineries In Europe: Current State And Prospects, Shady S. Hassan, Gwilym A. Williams, Amit Jaiswal

Articles

Lignocellulosic biorefining processes plant-derived biomass into a range of bio-based products. Currently, more than 40 lignocellulosic biorefineries are operating across Europe. Here, we address the challenges and future opportunities of this nascent industry by elucidating key elements of the biorefining sector, including feedstock sourcing, processing methods, and the bioproducts market.