Biotechnology Commons^™

Valorising Urban Organic Waste Streams Through Agrochemical Extraction And Organic Acid Production Via Cascading Biorefinery Approach, Shon Shiju Mr

ORBioM (Open Research BioSciences Meeting)

The CircBioCityWaste project is based on the vital principle of the ‘circular bioeconomy’ focusing on the sustainable, resource-efficient valorisation of anaerobic digestate, from urban waste streams (mainly, wastewater treatment plants, dairy processed sludge (DPS), food waste, and organic fraction of municipal solid waste (OFMSW)) to produce bio-based agrochemicals (biostimulants and biofertilisers) and organic acids via the cascading biorefinery concept. The project focuses on an ‘end-of-waste’ approach to producing deliverables for sustainable agriculture, promoting plant growth, and improving soil health while keeping circular bio-economy aspects in the focus. The biorefinery starts with digestate collection, characterisation, development of pre-treatment methods, and novel …

Prediction Of Central Visual Field Measures From Macular Oct Volume Scans With Deep Learning, Vahid Mohammadzadeh, Arvind Vepa, Chuanlong Li, Sean Wu, Leila Chew, Golnoush Mahmoudinezhad, Evan Maltz, Serhat Sahin, Apoorva Mylavarapu, Kiumars Edalati, Jack Martinyan, Dariush Yalzadeh, Fabien Scalzo, Joseph Caprioli, Kouros Nouri-Mahdavi

All Faculty Open Access Publications

Purpose: Predict central 10° global and local visual field (VF) measurements from macular optical coherence tomography (OCT) volume scans with deep learning (DL). Methods: This study included 1121 OCT volume scans and 10-2 VFs from 289 eyes (257 patients). Macular scans were used to estimate 10-2 VF mean deviation (MD), threshold sensitivities (TS), and total deviation (TD) values at 68 locations. A three-dimensional (3D) convolutional neural network based on the 3D DenseNet121 architecture was used for prediction. We compared DL predictions to those from baseline linear models. We carried out 10-fold stratified cross-validation to optimize generalizability. The performance of the …

Anti Cancer Activity Of Rhus Coriaria (Sumac) Against 5-Fluorouracil-Resistant Colorectal Cancer Cells, Zohra Nausheen Nizami

Theses

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, both worldwide and in the UAE. 5-Fluorouracil (5-FU), a pyrimidine analogue, is a chemotherapeutic agent that is an integral component of chemotherapy regimens for CRC treatment. However, 5-FU resistance (intrinsic and/or acquired) inhibits their clinical efficacy. In recent years, there has been a growing popularity for plant-based cancer therapeutics, specifically using phytochemical compounds. Rhus coriaria (Sumac) is a Mediterranean plant whose fruits are used as a spice and medicinal herb. Extracts of Rhus coriaria fruits (RCE) have been reported to exhibit anti-cancer activity against breast cancer and CRC. In …

Association Of Human Leukocyte Antigen (Hla) Alleles With Atopic Dermatitis In The Uae Population, Suhib Ziad Abu Jwayed

Theses

In the face of the increasing global prevalence of Atopic Dermatitis (AD), a chronic inflammatory skin condition, this thesis seeks to elucidate the genetic underpinnings of AD within the UAE population. Previous literature has underscored the ethnic-specific involvement of Human Leukocytes Antigen (HLA) genetic variations, especially within HLA-A and HLA-DRB1 genes, in the pathogenesis of various skin diseases, including AD. Leveraging this knowledge, our research specifically aimed to investigate the association between these HLA variants and AD in the UAE. Utilizing a comparative approach, the frequencies of HLA-A and HLA-DRB1 variants were assessed in AD patients vis-à-vis a control group. …

Development And Application Of Sem/Eds In Biological, Biomedical & Nanotechnological Research, Aniruddha Acharya

Faculty Publications - Biological Sciences

This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high resolution imaging of surface or topography, the technology is coupled with analytical techniques such as energy dispersive spectroscopy for elemental mapping. Since the commercialization of the technology, it has developed manifold and currently very high-resolution nano scale imaging is possible by this technology. The development of FIB-SEM has allowed three-dimensional imaging of materials while the development of cryostage allows imaging of hydrated biological samples. Though variable pressure or …

Shedding Light On Cellular Glycolysis Pathway Kinetics: Combining Kinetic, Mechanistic Modelling Approaches With Label Free Microspectroscopic Imaging. (Cytomechspec), Nitin Patil

Articles

Glycolysis pathway kinetics in cells are known to be modulated for several disorders (cancers, neurodegenerative disorders, diabetes, etc.) and are currently been targeted as a biomarker for disease diagnostics and therapy. Although there are several approaches for monitoring the pathway kinetics, ranging from simple kinetic biochemical assays to sophisticated omics techniques, there remains a significant gap in the field, as there is a noticeable compromise between the extent of insights achievable from approaches which are destructive to the sample, and the real-time, kinetic analysis of a system.

Vibrational spectroscopy is a powerful, label-free, non-invasive tool capable of sub-cellular resolution, the …

Changes In Lipid Profiles Of Epileptic Mouse Model, Alicia Johnson, Ryan A. Grove, Deepak Madhavan, Cory Honsinger Thomas Boone, Camila Pereira Braga, Hannah Kyllo, Kaeli Samson, Timothy Simeone, Tomáš Helikar, Corrine K. Hanson, Jiri Adamec

Department of Biochemistry: Faculty Publications

Introduction—Approximately 1% of the world’s population is impacted by epilepsy, a chronic neurological disorder characterized by seizures. One-third of epileptic patients are resistant to AEDs, or have medically refractory epilepsy (MRE). One non-invasive treatment that exists for MRE includes the ketogenic diet, a high-fat, low-carbohydrate diet. Despite the KD’s success in seizure attenuation, it has a few risks and its mechanisms remain poorly understood. The KD has been shown to improve metabolism and mitochondrial function in epileptic phenotypes. Potassium channels have implications in epileptic conditions as they have dual roles as metabolic sensors and control neuronal excitation.

Objectives—The …

Liposome Synthesis And Evaluation In The Hek-293 Cell Line, Christine Skibinski

Harrisburg University Research Symposium: Highlighting Research, Innovation, & Creativity

Liposomes were synthesized using the thin film method. A lyophilized power of egg-derived phosphatidylcholine, stearylamine, and cholesterol were added to ethanol and dried under argon to form a lipid cake. The lipid cake was rehydrated with dPBS and sonicated at 60°C forming a heterogenous batch of liposomes. Our results revealed the average size of the liposomes, determined by Dynamic Light Scattering, was approximately 223.1nm, while demonstrating a weakly positive zeta-potential of 1.9± 8.07mv. Next, we tested the antitumor action of the liposomes in the HEK-293 cell line via an MTT assay. We observed that the liposomes were able to inhibit …

Bola3 And Nfu1 Link Mitoribosome Iron–Sulfur Cluster Assembly To Multiple Mitochondrial Dysfunctions Syndrome, Hui Zhong, Alexandre Janer, Oleh Khalimonchuk, Hana Antonicka, Eric A. Shoubridge, Antoni Barrientos

Department of Biochemistry: Faculty Publications

The human mitochondrial ribosome contains three [2Fe–2S] clusters whose assembly pathway, role, and implications for mitochondrial and metabolic diseases are unknown. Here, structure-function correlation studies show that the clusters play a structural role during mitoribosome assembly. To uncover the assembly pathway, we have examined the effect of silencing the e xpression of Fe–S cluster biosynthetic and delivery factors on mitoribosome stability. We find that the mitoribosome receives its [²Fe–2S] clusters from the GLRX5-BOLA3 node. Additionally, the assembly of the small subunit depends on the mitoribosome biogenesis factor METTL17, recently reported containing a [⁴Fe–4S] cluster, which we …

Plasmid Midiprep: A Method To Purify Plasmids For Recombinant Dna Studies, Adithya Anilkumar, Kyle Doxtater, Samantha Lopez, Sudhir Kotnala, Justin Wendel, Manish Tripathi

Research Colloquium

A fundamental aspect of molecular biology involves exploring the properties and functions of specific genes. The rise of recombinant DNA technology has vastly improved and simplified functional studies by allowing scientists to isolate specific genes using restriction enzymes and plasmids providing greater precision. Plasmids take great significance in downstream studies, which is why quantity and quality of the plasmids purified is important. In this study, we isolated and purified recombinant plasmids in microgram quantities to confirm the yield, quantity, and quality using spectral and size fractionation methods. We also assessed the plasmids for application in downstream studies. We found the …

Early Development Of C3ar1-Targeting Chimeric Antigen Receptor T Cells For The Treatment Of Glioblastoma Multiforme, Cameron Fraser

Electronic Theses, Projects, and Dissertations

Glioblastoma multiforme is the most aggressive type of glioma, demonstrating extremely low long-term survival despite modern therapies. Chimeric antigen receptor T cells have shown extreme levels of success in the treatment of B cell lymphomas through persistent anti-tumor activity. Prior research has demonstrated the therapeutic potential in targeting the C3a-C3aR1 pathway as it acts in an autocrine loop, maintaining the proliferation and survival of cancer stem cells within the tumor. Here, we reorient the treatment to target C3aR1 for the treatment of glioblastoma multiforme. In order to achieve this, Jurkat immortalized T cells will express various chimeric antigen receptor designs …

Factors Influencing Instructors’ Adoption And Continued Use Of Computing Science Technologies: A Case Study In The Context Of Cell Collective, Changsoo Song, Resa M. Helikar, Wendy Smith, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Acquiring computational modeling and simulation skills has become ever more critical for students in life sciences courses at the secondary and tertiary levels. Many modeling and simulation tools have been created to help instructors nurture those skills in their classrooms. Understanding the factors that may motivate instructors to use such tools is crucial to improve students’ learning, especially for having authentic modeling and simulation learning experiences. This study designed and tested a decomposed technology acceptance model in which the perceived usefulness and perceived ease of use constructs are split between the teaching and learning sides of the technology to examine …

Targeting Cellular Signaling Pathways In Cancer By Lactobacilli, Varish Ahmad, Aftab Ahmad, Quazi Muhammad Sajid Jamal

Research Symposium

Purpose: Presenting lactobacilli therapy for cancer treatment targeting cancer signaling Lactobacilli as Probiotic lactic acid bacteria (LAB) are a group of fermentative gram-positive and gram-negative bacteria that produces a large number of intracellular and extracellular metabolites used in the food manufacture industry as well as complementary and alternative medicines against many diseases including cancer.

Description: Some LAB has been found to have inhibitory activity against colon liver cancer, cancer, colorectal cancer, breast cancer, and lung cancer in vivo or in vitro. These fermentative bacteria induced the autophagy cell death either by GRP78 and Beclin-1 or by induction of Bak …

Precise Method To Identify Kinase Drug Targets In Complex Diseases: The First Step Towards Sustainable And Effective Treatment, Hasbanny Irisson, Marzieh Ayati

Research Symposium

Background: Kinases are enzymes that have proven to be important drug targets due to their role in critical biological mechanisms such as phosphorylation. Phosphorylation happens when a kinase catalyzes the transfer of a phosphate group to a protein in a phosphorylated site, which then becomes known as the substrate of the kinase. Any dysregulation of protein phosphorylation causes a wide range of complex diseases including cancer. Thus, discovering the links between kinases and their substrates (i.e. predicting kinase-substrate associations (KSAs)) is crucial in developing effective and sustainable treatments. Presently, less than 5% of phosphorylated sites have an associated kinase, and …

Piperine Encourages Apoptosis In Human Cervical Adenocarcinoma Cells Through Ros Generation, Dna Fragmentation, Caspase-3 Activation And Cell Cycle Arrest, Asif Jafri, Juhi Rais, Sudhir Kumar, Md Arshad

Research Symposium

Background: Cancer is one of the most common destructive diseases and the second leading cause of death in humans. Among cancer, cervical cancer is the second most common malignancy among women globally. Thus, there is a continuous need to search for chemotherapeutic chemicals or naturally occurring drugs to resolve this global health problem. Piperine (1-piperoylpeperdine) is present in the fruits of black pepper (Piper nigrum Linn.) and long pepper (Piper longum Linn.). It possesses several pharmacological properties and in the present study we have evaluated its anti-cancer potential on human cervical adenocarcinoma (HeLa) cells.

Methods: The anti-proliferative effect …

Novel Nanoparticle Formulation Of Sabizabulin (Veru-111) For Pancreatic Cancer Treatment, Vivek K. Kashyap, Godwin P. Darkwah, Neeraj Chauhan, Prashanth Kb Nagesh, Anupam Dhasmana, Swati Dhasmana, Qinghui Wang, Duane D. Miller, Wei Li, Bilal B. B. Hafeez, Murali M. Yallapu, Meena Jaggi, Subhash C. Chauhan

Research Symposium

Background: Pancreatic cancer (PanCa) is one of the leading causes of cancer-related mortality in the United States due to very limited therapeutic options. Thus, developing novel therapeutic strategies will help for the management of this disease. We recently identified VERU-111, a novel synthetic molecule which showed potent anti-cancer effect against PanCa via targeting clinically important βIII and βIV tubulin isoforms. In this study, we synthesized and characterized its novel nanoformulation (MNP-VERU) and evaluated its therapeutic effects in vitro and xenograft mouse model.

Methods: MNPs were prepared by chemical precipitation method and loaded with VERU-111 using diffusion method. This formulation was …

Mortaparibplus- A Novel Anticancer Small Molecule Abrogating Mortalin-P53 Interaction In Cancer Cells, Anissa N. Sari, Ahmed Elwakeel, Jaspreet K. Dhanjal, Vipul Kumar, Durai Sundar, Sunil C. Kaul, Renu Wadhwa

Research Symposium

Background. The cessation of tumor cell growth through cell cycle arrest and apoptosis is determined by p53, a tumor suppressor protein. However, the interaction between mortalin-p53 within cytoplasm/nucleus leads to the inactivation of p53 transcriptional activation function. The disruption of mortalin-p53 complex has been suggested as an approach for developing a potential anticancer drug.

Methods. A screening of a high-content chemical library was performed to determine a molecule with mortalin-p53-interaction disrupting characteristics. After four-rounds of visual assays, we discovered a triazole derivative (4-[(1E)-2-(2-phenylindol-3-yl)-1-azavinyl]-1,2,4-triazole, named Mortaparib^Plus) with a potential ability of disrupting mortalin-p53-complex. In this study, we recruited …

Development Of An Antibiotic Resistance Breaker To Combat Staphylococcus Aureus Pathogenesis Skin Infections Ssis A Multidisciplinary, Gopalakrishnan T Mr

Theses and Dissertations

Problem Statement: Staphylococcus aureus is a highly adaptable and tenacious pathogen known to cause a wide range of infections. The survival characteristics of the pathogen in different host niches are due to their ability to produce various pathogenic determinants. Although there lies the first line of treatment regimens with antibiotics, the pathogen defends at various levels to cause the waves of resistance - a silent pandemic “AMR”.

Notable strategies are through the protective layer, biofilm that enables the inter-/intra species communication (Quorum Sensing; QS) and emerges as a battleground to withstand host-immune response and antibiotic pressure. In parallel, several research …

Hiv-1 Vpu Protein Forms Stable Oligomers In Aqueous Solution Via Its Transmembrane Domain Self-Association, Saman Majeed, Lan Dang, Md Majharul Islam, Olamide Ishola, Peter P Borbat, Steven J Ludtke, Elka R Georgieva

Faculty, Staff and Students Publications

We report our findings on the assembly of the HIV-1 protein Vpu into soluble oligomers. Vpu is a key HIV-1 protein. It has been considered exclusively a single-pass membrane protein. Previous observations show that this protein forms stable oligomers in aqueous solution, but details about these oligomers still remain obscure. This is an interesting and rather unique observation, as the number of proteins transitioning between soluble and membrane embedded states is limited. In this study we made use of protein engineering, size exclusion chromatography, cryoEM and electron paramagnetic resonance (EPR) spectroscopy to better elucidate the nature of the soluble oligomers. …

Transcriptional Pausing Factor M1bp Regulates Cellular Homeostasis By Suppressing Autophagy And Apoptosis In Drosophila Eye, Anuradha Venkatakrishnan Chimata, Hannah Darnell, Akanksha Raj, Madhuri Kango-Singh

Biology Faculty Publications

During organogenesis cellular homeostasis plays a crucial role in patterning and growth. The role of promoter proximal pausing of RNA polymerase II, which regulates transcription of several developmental genes by GAGA factor or Motif 1 Binding Protein (M1BP), has not been fully understood in cellular homeostasis. Earlier, we reported that M1BP, a functional homolog of ZKSCAN3, regulates wingless (wg) and caspase-dependent cell death (apoptosis) in the Drosophila eye. Further, blocking apoptosis does not fully rescue the M1BP^RNAi phenotype of reduced eye. Therefore, we looked for other possible mechanism(s). In a forward genetic screen, members of the Jun-amino-terminal-(NH2)-Kinase (JNK) pathway …