Biotechnology Commons^™

Optimization Of Recombinant Adeno-Associated Virus (Aav) Vector Production In Saccharomyces Cerevisiae, Juan Aponte

KGI Theses and Dissertations

Recombinant adeno-associated viral vectors (rAAV) are emerging drugs for gene therapy applications. Their non-pathogenic status, low inflammatory potential, availability of viral serotypes with different tissue tropisms, and prospective long-lasting gene expression are important attributes that make rAAVs safe and efficient therapeutic options. One of the main limitations for bringing rAAV gene therapy to the market is the difficulty in supplying enough rAAV vector product. The high vector doses suggested by early clinical data infer the need to scale up production at high volumes in order to satisfy patient demand. Current production platforms such as HEK293 or Sf9 cells are very …

Reversible Heparin Molecules And Methods Of Making And Using The Same, Jian Liu, Yongmei Xu, Robert J. Linhardt, Edward Harris

Department of Biochemistry: Faculty Publications

Methods and systems for synthesizing heparin compounds are provided . The chemoenzymatic synthesis of structurally homogeneous low molecular weight heparins that have a reversible anticoagulant activity is provided . Also disclosed are heparin compounds having anticoagulant activity , including a binding affinity to antithrombin and an anti - Xa activity , but no detectable anti - lla activity . Additionally , provided are synthetic , low - molecular weight heparin com pounds with reversible anticoagulant activity , where the anticoagulant activity is reversible by protamine.

Restoration Of Phage Growth On A Non-Permissive Host By Bypassing Transcription Termination Signals, Millicent Ronkainen

Mahurin Honors College Capstone Experience/Thesis Projects

RNA polymerase is the central enzyme in all gene expression. The rpoCY75N mutation in the zinc-binding domain of the β’ subunit of E. coli RNA polymerase blocks a unique RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022 and its relatives. Here, we describe the characterization of mutant phage, orc0368, which overcomes the rpoCY75N mutation. The orc0368 genome varies from the wild type phage genome by 4 single base pair mutations. Three of these mutations were not characterized because they occur in intergenic regions but the fourth was chosen for study because of its location between a series …

Algal Biofuel: The Future Of Green Jet Fuel In Air Transportation, Rajee Olaganathan

Publications

The aviation industry is one of the major contributors for the greenhouse gases. As air travel has become inevitable in this modern era, and fossil fuel usage is not sustainable, it is essential to produce renewable fuel and commercialize it to reduce the greenhouse gas emissions. In order to produce an alternate aviation biofuel a lot of industrial and academic collaborations have been developed worldwide. The main concern of this collaborative research is to produce aviation biofuel from renewable resources with low environmental impacts, and which is sustainable at an economically viable price. This mini-review briefly discusses the biotechnological approaches …

Keragaan Tiga Jenis Planlet Anggrek Phalaenopsis Asal Protocorm Yang Diinduksi Ethyl Methyl Sulfonate (Ems) Secara In Vitro, Romiyadi, Ai Komariah, Suseno Amien

Jurnal Kultivasi

This research was conducted to determine the effect of concentration of Ethyl Methyl Sulfonate (EMS) to performance of three types of Phalaenopsis Planlets and to know the optimum concentration of EMS on any type of Phalaenopsis orchids. The experiment was conduc-ted at Tissue Culture Laboratory of the Faculty of Agriculture, Winaya Mukti University, Sumedang. It used a completely randomized design (CRD) with factorial pattern, that consisted of two factors and replicated twice.The first factor was the type of Phalaenopsis that resulted form hybridization which consisted of v1 (Phalaenopsis 717 X Phalae-nopsis Fire Bird), v2 (Phalaenopsis Tianong Rose X Sibling), and …

Effect Of Vitrification On Epigenetic Modifications And The Meiotic Spindle Of Bovine Oocytes, Emilio Jose Gutierrez-Castillo

LSU Master's Theses

While oocyte vitrification has become a common practice, it still faces some challenges such as the low survival rates after warming, probably related to cryoinjuries and cryoprotectant (CPA) toxicity. Evidence suggests that vitrification might have an effect on the patterns of some epigenetic marks including DNA methylation and histone acetylation. During fertilization and embryogenesis, key events for healthy and adequate embryo development take place, not only governed by the information contained within the DNA sequence, but also by epigenetic mechanisms.

This study was aimed at determining the effect of vitrification and CPA exposure, using a combination of ethylene glycol (EG) …

Intellectual Property, Surrogate Licensing, And Precision Medicine, Jacob S. Sherkow, Jorge L. Contreras

IP Theory

The fruits of the biotechnology revolution are beginning to be harvested. Recent regulatory approvals of a variety of advanced therapies—Keytruda (pembrolizumab), Kymriah (tisagenlecleucel), and patisiran—have ushered in an age of “precision medicine” treatments that target patients’ specific genetic, physiological, and environmental profiles rather than generalized diagnoses of disease. Therapies like these may soon be supplemented by gene editing technologies such as CRISPR, which could enable the targeted eradication of deleterious genetic variants to improve human health. But the intellectual property (IP) surrounding precision therapies and their foundational technology remain controversial. Precision therapies ultimately rely—and are roughly congruent with—basic scientific information …

Adsorption And Diffusion Characteristics Of 2-Naphthol From Aqueous Media By Chitosan-Enr Biocomposites, Gunasunderi R., Mas Haris M. R. H.

ASEAN Journal on Science and Technology for Development

Chitosan entrapped ENR-50 (CTS-t-ENR) biocomposites developed were studiedfor the absorption and desorption of 2-naphthol in aqueous media. Biocomposites comprising chitosan (CTS) immobilized or trapped in a partially crosslinked ENR (designated as CTS-t-ENR) was prepared by homogenising CTS in ENR-50 latex with curative agents in the presence of acetic acid. It was found that absorption increased with the increase in the initial 2-naphthol concentrations. Chitosan powder was found to be a poor absorbent compared CTS-t-ENR biocomposites. Desorption studyrevealed that the 2-naphthol diffusedslowly in water. The biocomposites exhibited a good slow-release properties and this was proven by the kinetic studyusing zero order, …

Quantitative Analysis Of Microcystin-Lr In Drinking Water Comparing On-Line Solid Phase Extraction And Direct Injection Lc/Ms/Ms, Malarvili R., Low Y.Y., Zaiton A.

ASEAN Journal on Science and Technology for Development

An efficienmethod for microcystin-LRin drinking water at the sub-ng/l level applying on-line solid phase extraction (SPE) with LC/MS/MS detection and comparing it to direct injection LC/MS/MS is presented. The performance of the method of direct injection did not signifiantly deviate from the SPE approach. However, the direct injection method used less sample volume (100 µl) in shorter analysis time (4 min) and allowed more sample throughput. Conversely, the uncertainty of measurement could be reduced using SPE.

Influence Of Tespt On Tensile And Tear Strengths Of Vulcanized Silica-Filled Natural Rubbe, Norizah A.K., Azemi S.

ASEAN Journal on Science and Technology for Development

The effectof coupling agent on tensile and tear strengthsof vulcanized NR filledwith 50 pphr of precipitated silica (VN3) was investgated. The amount of coupling agent was varied from 0,1,2,3,4,5 to 8 pphr. In the absence of coupling agent bis[3-(triethoxysilyl)propyl] tetrasulphide (TESPT), the tensile strengthof silica-fille vulcanized NR was lower than the tensile strengthof unfilledvulcanized NR. The enhancement in the tensile strengthwas achieved only when TESPT was incorporated into the rubber compound. The dependence of tensile strengthon the amount of TESPT showed a similar trend as the dependence of tensile strengthon the crosslink concentration. This might imply that varying the amount …

Preparation And Characterisation Of Crosslinked Natural Rubber (Smr Cv 60) And Epoxidised Natural Rubber (Enr-50) Blends, Sasitaran M., Manroshan S., Lim C.S., Veni B. N. Krishna, Ong S.K., Gunasunderi R.

ASEAN Journal on Science and Technology for Development

In this sudy, the influenceof di(tert-butylperoxyisopropyl)benzene (DTBPIB) on the properties of natural rubber (NR) blend with epoxidized natural rubber (ENR) was determined. Fourier transform infrared spectroscopy with attenuated total refletance analysis and gel content confired crosslinking occurred in the rubber blends in the presence of peroxide DTBPIB percentage. Studies including tensile properties, dynamic mechanical properties, thermogravimetric analysis (TGA) and water absorptivity showed the changes in properties of the crosslinked NR/ENR blends. Tensile properties analysis disclosed the improvements in the modulus at 300% elongation and tensile stength with increasing NR ratios. Dynamic mechanical analysis revealed the blends to be incompatible and …

Assessment Of Natural Radioactivity Level And Radiological Index In The Vicinity Of Lynas Rare-Earth Processing Plants, Zal U’Yun W.M., Yii M.W., Ashhar K. Mohd, Khairuddin M.K., Kadir I. Abdul, Wahab Y. Mohd Abd

ASEAN Journal on Science and Technology for Development

The findingsof the sudy on assessment of natural radioactivity level and radiation hazard parameters in the vicinity of Lynas rare-earth processing plants are reported. This studyaims to quantify the environmental levels of natural radionuclides in soil collected in the vicinity of Lynas rare-earth processing plants and thereby to assess potential radiological hazards to the environment. About 31 terrestrialsampling locations were chosen for collection of the soil samples. The activity concentrations of the naturally occurring radioactive material (NORM) members, i.e. 226Ra, 228Ra, 238U, 232Th and 40K were measured using HpGe gamma spectrometer after reaching 30 days of secular equilibrium with their …

Thermal Efficient Design Of Distributed Memorgenerator For Dual-Port Ram Using Unidirectional High-Performance Io Standard, Das B., Abdullah M.F.L.

ASEAN Journal on Science and Technology for Development

he distributeddual-port RAM offersthe high-speed data rate transmission for differentmemory access modes such as: busy mode; interrupt mode; JTAG mode; maser mode; slave mode; and sleep mode, at high-frequency operation. The execution of these modes at high-frequency operation increases the on-chip temperature of distributeddual-port RAM. It might short the distribute dual-port RAM forever. Currently, differenttechniques have been reported, but significanton-chip temperature consumption is not reduced for distributeddual-port RAM. In this paper, the thermal-efficiendesign for disributed dual-port RAM was achieved using IO sandard technique. The distributeddual-port RAM was designed using differentIO standardssuch as; LVTTL IO standardand Mobile_DDR IO standard.It was determined …

Ediorial Board, Board Editorial

ASEAN Journal on Science and Technology for Development

No abstract provided.

Intraperitoneal Nanotherapy For Metastatic Ovarian Cancer Based On Sirna-Mediated Suppression Of Dj-1 Protein Combined With A Low Dose Of Cisplatin, Canan Schumann, Stephanie Chan, Jess A. Miller, Yuliya Bortnyak, Katherine Carey, Alex Fedchyk, Leon Wong, Tetiana Korzun, Abraham S. Moses, Anna Lorenz, Delany Shea, Olena Taratula, Oleh Khalimonchuk, Oleh Taratula

Department of Biochemistry: Faculty Publications

Herein, we report an efficient combinatorial therapy for metastatic ovarian cancer based on siRNA-mediated suppression of DJ-1 protein combined with a low dose of cisplatin. DJ-1 protein modulates, either directly or indirectly, different oncogenic pathways that support and promote survival, growth, and invasion of ovarian cancer cells. To evaluate the potential of this novel therapy, we have engineered a cancer-targeted nanoplatform and validated that DJ-1 siRNA delivered by this nanoplatform after intraperitoneal injection efficiently downregulates the DJ-1 protein in metastatic ovarian cancer tumors and ascites. In vivo experiments revealed that DJ-1 siRNA monotherapy outperformed cisplatin alone by inhibiting tumor growth …

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 …

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 …

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 …

The Role Of Vitamin D Receptors In Gastric Epithelial Homeostasis, Ifrah Ismail Ali

Biology Theses

The gastric epithelium consists of different types of cells, which are involved in gastric homeostasis by balancing cell proliferation and differentiation. This process involves several signaling molecules such as growth factors, hormones and vitamins. Vitamin D3 (VD3) is engaged in several biological activities. It plays a role in cell differentiation, cell proliferation, immune response and also regulates calcium homeostasis. The biological activities of VD3 are mediated by vitamin D receptor (VDR). Target tissues of VD3 in the gastrointestinal tract were identified earlier in intestine, colon and gastric cancer tissues; however, the normal expression of VDR in stomach is poorly studied. …

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. …

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 …

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. …