Life Sciences Commons^™

Optimization Of In-Vitro Tissue Culture And Transformation System For Sweet Sorghum Cultivars Using Immature Inflorescence, Logayn Abushal

Theses and Dissertations

Background: Sweet sorghum is a multi-purpose crop that can be used for human food, animal feed, and bio-fuel production. This crop is drought-tolerant and can therefore be grown in arid and semi-arid regions especially in marginal areas in Egypt. Nevertheless, production of Sweet sorghum cannot coup with the increasing demand in consumption as a food, and fuel due to a lag in scientific research regarding its genetic improvement. Therefore, genetic improvement of Sweet sorghum is innately required so that new traits of economic importance could be introduced; however, this can only be achieved through the establishment of a robust in-vitro …

Reproducibility Of Individual Dna Deposits Detected Through Cellular Fluorescence, Natalee Small-Davidson

Student Theses

Contact traces are an important part of DNA casework, but the probative value of any identified associations depends on the possibility of passive transfer. There is known individual variation in DNA left behind during contact, this DNA shedding propensity has an effect on whose DNA is detected. This study evaluated this variability using a cell staining approach. Volunteers were asked to deposit a fingerprint on a clean glass slide, then wash their hands and deposit a second fingerprint after a 30-minute wait without touching anything. Three sets of samples were collected over three consecutive weeks. Fingerprints were stained with a …

Rapid Land Assessment For Salt Farming Development In The Coastal Area Of The Special Region Of Yogyakarta, Indonesia, Malawani Mukhamad N., Marfai Muh Aris, Yoga Aldhila G. H., Handayani Tiara, Cahyadi Ahmad, Sadali Mohammad Isnaini, Mahasin Mohamad Zaki, Hendratmoro, Suadi, Wiyono Maryadi Budi

ASEAN Journal on Science and Technology for Development

The government of Indonesia has faced several challenges to its goal of achieving salt self-sufficiency, necessitating the formulation and implementation of strategic steps to increase salt production. Among its islands, Java has a great deal of potential for salt production, as does the Special Region of Yogyakarta, where the government has initiated salt farming development as part of its coastal community empowerment program. This study aimed to (1) evaluate the land suitability of existing salt farms and (2) identify potential sites and make a productivity estimation of salt farms in the Special Region of Yogyakarta, with the broad objective of …

Bcsa Rawmix Design: Correlation Between Chemical Constituents And Mineralogy, Palla Suresh, Vanguri Suresh, Ramakrishna S, Chaturvedi S. K, Mohapatra B. N

ASEAN Journal on Science and Technology for Development

The cement industry has been identified as one of the main contributors to climate change due to greenhouse gas emissions, mainly CO2. Therefore, to meet CO2 reduction targets, cement producers are working on different strategies of minimizing its emission, one of which is alternative clinkers. This study assessed the impact of variations of the raw mix design, concerning the type and proportions of materials, on the formation of calcium sulphoaluminate belite-type clinkers. Various materials were used to produce raw mixes for different percentages of belite, yeeliminite, and other minerals in resultant clinkers. Computer-based theoretical mixes were designed with different percentages …

Analyzing The Application Of Void Decks On High-Rise Affordable Housing In Jakarta, Indonesia, To Achieve Optimal Urban Ventilation, Ririhena Megan Afkasiga, Syafii Nedyomukti Imam

ASEAN Journal on Science and Technology for Development

Economic growth in ASEAN countries encourages significant urbanized growth. In line with the growth of urbanization, large swathes of residential buildings have been constructed in urban areas, especially, in the case of Indonesia, through the government's 1000 rusun (high-rise affordable housing) development program in Jakarta. In order to reduce energy consumption and create a sustainable rusun, a passive strategy is needed in the form of natural air conditioning through optimized natural ventilation in these buildings. In this study, testing was conducted on Rusun Rorotan in Jakarta, from two wind source directions (north and northwest) with five void decks configuration samples …

Dielectric Relaxation Studies Of Hydrogen Bonded Complexes Of Benzamide And Acetamide With Halogenated Phenols Using X-Band Microwave Frequency, Basha A. Aathif, Khan F. Liakath Ali

ASEAN Journal on Science and Technology for Development

At 308 K, using a 9.37 GHz dielectric relaxation setup, dielectric studies of hydrogen bonded complexes of benzamide and acetamide with 4-fluorophenol, 4-bromophenol, 4-chlorophenol, and 4-iodophenol in benzene were performed. Various dielectric parameters (such as ?', ?'', ?0, ??) were tested. The steric interactions of the proton donor determined the group rotation relaxation time t(2), whereas the significance of the single frequency method of Higasi et al. for multiple relaxation time t(1) was determined by the hydrogen bonding power of the phenolic hydrogen. The presence of a 1:1 complex system between the prepared samples, as well as a charge transfer …

Potential Of Three Taro (Colocasia Esculenta L.) Cultivars As Animal Feed, Setyawan Hidayat Bambang, Yulianto Roni, Zelin Oviaki, Purnamasari Listya

ASEAN Journal on Science and Technology for Development

The growth and yield of taro (Colocasia esculenta L.) plants are influenced by the planting material. The use of planting material derived from corms is expected to improve the quality and quantity of taro growth and yield. This research aimed to find the best type of planting material and cultivars for taro growth and the potential of taro plants as animal feed. The experiment was carried out in Jember, East Java ( elevation ±89 m asl). The experiment used the randomized completed block design method with two treatment factors, the type of planting material (B) as the first factor (B1: …

Study Of Microstructure And Mechanical Properties Of As-Built And Heat-Treated Additive Manufactured Inconel 718 Alloy, Maurya Ajay Kumar, Kumar Amit

ASEAN Journal on Science and Technology for Development

Additive manufacturing technology is becoming popular in the industry because it allows the manufacturer to fabricate cost-effective, strong, lightweight, and complex-shaped parts directly from 3D design data as compared with the conventional manufacturing method. Inconel 718 alloy is the most demanding material in aviation as well as in the automobile industry, in terms of manufacturing high-performance parts. In this study, Inconel 718 samples were built using the direct metal laser sintering process, and standard heat treatment was performed on the samples to improve their microstructure and mechanical properties. The as-built samples exhibited good grain structure with fine laves phases, but …

Deep Learning For Human Microrna Precursor Prediction: A Systematic Literature Review, Martina Ojonah

Master of Science in Information Technology Theses

The discovery of MicroRNA (miRNA) sparked medical breakthroughs, leading to the development of drugs/vaccines and biomarkers for some terminal diseases such as cancer. Due to the relatively short length of microRNAs, research has shown that discovering them on their own is a difficult task; thus, the focus has shifted to predicting precursor miRNAs, which are longer than miRNAs. Computational techniques evolve because of flaws discovered in existing designs, discoveries, and the desire to make the process as seamless as possible. Most researchers in recent studies indicated that the use of few input features and a lack of domain understanding of …

Identifying Micrornas Panel Associated With Hepatocellular Carcinoma In Serum Of Chronic Hepatitis C Patients, Areeg Dabbish

Theses and Dissertations

Introduction: early detection of hepatocellular carcinoma (HCC) will reduce morbidity and mortality rates of this poorly diagnosed widely-spread disease. Dysregulation in microRNA (miRNAs) expression is associated with HCC progression. Objective: Is to identify a panel of differentially expressed miRNAs (DE-miRNAs) to enhance HCC early prediction in hepatitis C virus (HCV) infected patients. Methodology: Candidate miRNAs were selected using bioinformatic analysis of microarray and RNA-sequencing datasets, resulting in nine DE- miRNAs (miR-142, miR-150, miR-183, miR-199a, miR-215, miR-217, miR-224, miR-424 and miR-3607). Their expressions were validated in the serum of 44 healthy individuals, 62 non-cirrhotic HCV patients, 67 cirrhotic-HCV and 72 HCV-associated …

Real-Time Monitoring Of Cell Death Progress Using Capacitance Spectroscopy, Suyang Wu

Electronic Theses and Dissertations

Biologics, including the monoclonal antibody (mAb), has experienced rapid development in the last decade. However, the price of biologics is often prohibitively high because of the low process efficiency. Delaying the inevitable cell death improves the productivity of upstream bioprocessing, whose success relies on monitoring the cell death onset that indicates the timing for preventive actions.

This study proposes to develop a real-time monitoring model that quantifies the dying cell percentage in lab-scale bioreactors using capacitance spectroscopy. The capacitance spectroscopy contains cell death-related information due to various physical properties changes during the cell death process, e.g., cytoplasmic conductivity change. The …

A Pkcα-Mediated Growth Suppressive Mek-Erk Signaling Axis In Intestinal Epithelial Cells, Navneet Kaur

Theses & Dissertations

Members of the protein kinase C (PKC) family of serine/threonine kinases are involved in regulation of fundamental cellular functions, including proliferation, differentiation, survival, migration, and transformation. Increasing evidence points to anti-proliferative and tumor suppressive role of PKCs. Our laboratory and others have reported that the classical PKC isozyme, PKCαnegatively regulates proliferation and tumorigenesis in the intestinal epithelium. Our laboratory has further determined that PKCα signaling induces a program of cell cycle withdrawal in intestinal epithelial cells that involves downregulation of the pro-proliferative proteins, cyclin D1 and Id1, and upregulation of the cyclin dependent kinase (CDK) inhibitor, p21^Cip1. Unexpectedly, …

Development Of Polymeric Cxcr4 Targeting Carriers For Sirna Delivery To Treat Acute Kidney Injury, Weimin Tang

Theses & Dissertations

Acute kidney injury (AKI) is a major kidney disease that is characterized by a sudden loss of renal function which manifests by a decrease in urine output and an increase in serum creatinine. AKI is a global healthcare burden associated with high morbidity, mortality, and increasing cost. Currently there are no effective pharmacological treatments available. Apoptosis induced by p53 has been demonstrated as an important pathological mechanism for the development of AKI. Meanwhile, CXCR4/SDF-1 axis has been associated with the inflammation during AKI, and CXCR4 is overexpressed on injured tubules. This dissertation hypothesized that polycations with CXCR4 targeting ability could …

A Link Between Methylglyoxal And Heart Failure During Hiv-1 Infection, Prasanta K. Dasg, Fadhel A. Alomar, Jesse L. Cox, Joellyn Mcmillan, Bryan T. Hackfort, Edward Makarov, Brenda Morsey, Howard S. Fox, Howard E. Gendelman, Santhi Gorantla, Keshore R. Bidasee

Department of Biochemistry: Faculty Publications

Early-onset heart failure (HF) continues to be a major cause of morbidity and mortality in people living with human immunodeficiency virus type one (HIV-1) infection (PLWH), yet the molecular causes for this remain poorly understood. Herein NOD.Cg- Prkdc^scidIl2rg^tm1Wjl/SzJ humanized mice (Hu-mice), plasma from PLWH, and autopsied cardiac tissues from deceased HIV seropositive individuals were used to assess if there is a link between the glycolysis byproduct methylglyoxal (MG) and HF in the setting of HIV-1 infection. At five weeks post HIV infection, Hu-mice developed grade III-IV diastolic dysfunction (DD) with an associated two-fold increase in plasma …

Modulation Of Effector Gene Expression In The Blood-Feeding Arthropods Cimex Lectularius Linnaeus, (Hemiptera: Cimicidae) And Aedes Albopictus Skuse, (Diptera: Culicidae), Travis C. Van Warmerdam

Theses and Dissertations

Hematophagy, or blood-feeding behavior, has independently evolved multiple times in the class Insecta and results in the transmission of vector-borne parasites, bacteria and viruses causing 17% of all infectious diseases and over 700,000 human deaths annually. One of the major challenges in studying the discrete mechanisms involved in host-response to hematophagy or the host seeking behavior of hematophagous insects, is the vast amount of signaling processes and genes that are inextricably tied to these interactions. These experiments used the clustered regularly interspersed short palindromic repeat (CRISPR)/CRISPR-associated (Cas) and dsRNA knock-down technologies to examine mechanisms of immunological reactivity and host-seeking behavior. …

Self-Extending Symbiosis In Symbiodinium Microadriaticum And The Effect Of Endosymbiotic / Horizontal Gene Transfer On Dinoflagellates And The Tree Of Life, Maha Kadry Ahmed Fathy

Archived Theses and Dissertations

Symbiodinium microadriaticum is a dinoflagellate that lives in a mutualistic relationship with the coral Stylophora pistillata in the Red Sea. Symbiodinium microadriaticum is divided into several clades and the A1 clade of Symbiodinium microadriaticum lives in shallow waters and is resilient to thermal stress. The association between Symbiodinium microadriaticum A1 and Stylophora pistillata enables Stylophora pistillata to tolerate the rise in the sea surface temperature caused by global warming and climate change. Here, the first completely sequenced dinoflagellate genome is explored to answer two questions: The first question is whether self-extending symbiosis has a role in the ability of Symbiodinium …

Enrichment Of Extremophilic Bacteria From Atlantis Ii Deep Brine Sediments Using Various Electron Donors & Acceptors, Nelly Abu Alkheir

Archived Theses and Dissertations

The Atlantis II Deep is the most studied and largest brine pool in the Red Sea. It is an active hydrothermal habitat with unique physical conditions. Its unique characteristics (70°C temperature, 26% salinity, pH 5.2) caused it to be a very attractive marine ecosystem for microbiological and metagenomics studies. Sediments of the Atlantis II Deep brine were investigated for the presence of extremophilic bacteria using a cultivation approach combined with phylogenetic analysis. Two different cultivation methods were utilized: substrate gradient cultures and minimal salts medium supplemented with various combinations of electron donors and acceptors. A bacterial culture enriched from the …

Metagenomic Assessment Of The Mobilomes Of Red Sea's Atlantis Ii, Discovery And Kebrit Deeps, Mohamed Mohamed El Rifai

Archived Theses and Dissertations

Mobile genetic elements in microbial communities are mainly composed of plasmids, transposons and viruses. They are collectively referred to as the mobilome and serve as agents that facilitate horizontal gene transfer, which plays an important role in evolution and adaptation of microorganisms. In order to study the abundance and distribution of mobile genetic elements in different marine environments and to clarify whether certain environmental conditions could explain such distribution, sequence similarity searches using protein family signatures against diverse marine metagenomic datasets were used to determine the relative frequency of coding sequences associated with transposases, integrases, plasmids and viruses, or phages. …

E2 Evolutionary Motif Prediction And Identification Of Drug Candidates To Prevent Hepatitis C Virus Cellular Entry, Shairy Azmy Danial

Archived Theses and Dissertations

Hepatitis C Virus (HCV) infection causes around three quarters of worldwide chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Interferon and ribavirin combination therapy is not effective with all HCV genotypes, and has serious side effects that may result in discontinuation of treatment. The aim of our work is to design inhibitors against HCV envelope glycoprotein E2 to prevent its binding to CD81 surface receptor and the consequent viral entry into hepatocytes. Currently, no crystal structure is constructed for E2. However, a model of E2 is available, Yagnik et al. model, which served as the starting point for the structure-based inhibitor …

Exploring The Aerobic Methanotrophs Community In The Red Sea Atlantis Ii Deep Brine Area, Rehab Abdallah

Archived Theses and Dissertations

Methane represents one of the most abundant hydrocarbons on earth and a powerful greenhouse gas. Methane oxidation by microbial consortia contributes positively to the environment by decreasing methane emission to the atmosphere from different ecosystems. Aerobic methanotrophic bacteria are considered one of the main groups involved in methane oxidation. Brine pools are dynamic habitats for microbial cycling of carbon. Atlantis II Deep is the largest brine pool in the Red Sea. The pool is well known for its elevated temperature, salinity and methane concentration. Methane seeps from the deep brine to the overlying brine seawater interface layer, providing a suitable …

Unique Biodiversity Of The Red Sea Brine Floor Revealed By Comparative Taxonomic Analysis Of Atlantis Ii And Discovery Deep Brine Sediments, Ghada Alaa El-Din Mustafa

Archived Theses and Dissertations

The sea floor is a unique and diverse ecosystem to investigate how geochemical processes affect the diversity of biological life. Red Sea brine pools are water bodies characterized by a unique multitude of extreme conditions, including high temperature, high salinity, and unusual high concentration of heavy metals. We performed a comparative metagenomic analysis of the microbial communities in the sea floor of the Atlantis II (2168 m; 68oC), Discovery Deep (2166 m; 48oC) brine pools and two non-brinesites (1,856 m; 21.93°C and 1,937 m; 31.87°C) in the Red Sea. Each brine core wasvertically dissected into seven distinct subsections. CHN&S profiles …

The Application Of Mathematical Optimization And Flavor-Detection Technologies For Modeling Aroma Of Hops, Yutong Liu

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In recent years, proprietary hops (Citra, Simcoe, and Mosaic) become the most sought-after hops among brewers due to their excellent aroma. However, they are restricted to the owners unless other growers purchase the costly licensing agreements. Many public hops are available to the growers without any additional costs, but their aroma is difficult to match to the proprietary hops. Although proprietary and public hop varieties are unique in their aroma profiles, all hops varieties contain similar volatile compounds, merely differ in the quantity of different individual compounds. The main objective of this thesis was to investigate the feasibility of matching …

Charting A New Frontier Integrating Mathematical Modeling In Complex Biological Systems From Molecules To Ecosystems, Katharine A. White, Kira D. Mcentire, Nicole R. Buan, Lecia Robinson, Elisar Barbar

Department of Biochemistry: Faculty Publications

Advances in quantitative biology data collection and analysis across scales (molecular, cellular, organismal, and ecological) have transformed how we understand, categorize, and predict complex biological systems. This surge of quantitative data creates an opportunity to apply, develop, and evaluate mathematical models of biological systems and explore novel methods of analysis. Simultaneously, thanks to increased computational power, mathematicians, engineers, and physical scientists have developed sophisticated models of biological systems at different scales. Novel modeling schemes can offer deeper understanding of principles in biology, but there is still a disconnect between modeling and experimental biology that limits our ability to fully realize …

Reintegrating Biology Through The Nexus Of Energy, Information, And Matter, Kim L. Hoke, Sara L. Zimmer, Adam B. Roddy, Mary Jo Ondrechen, Craig E. Williamson, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that compose this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, …

Prospecting For And Isolation Of Microalgae In South Texas, Mauricio Alejandro Peña

Theses and Dissertations

Microalgae is a very important microorganism that can be used for beneficial purposes for humans. One way to show the importance of algae in this planet is the contribution of Oxygen it provides to the atmosphere, which many organisms rely on (Medeiros et al., 2015). Carbon footprint has been one of the greatest causes for global warming and it is due to the use of fossils to create diesel. One of the ways to avoid contamination is to replace those fuels that are used on daily basis, such as for transportation. The microalgae are able to produce lipids that can …

Toward Lignin Valorization: Development Of Rhodococcus Opacus Pd630 As A Chassis For Triacylglycerol (Tag) Production From Recalcitrant Aromatic Feedstocks, Rhiannon R. Carr

McKelvey School of Engineering Theses & Dissertations

The advent of the industrial era was precipitated by the discovery of fossil fuels, and ushered in unprecedented changes for humanity included but not limited to the development of rapid transit and communications, improvements to food distribution and preservation, the mass production of goods, and a radical rearrangement of communities from relatively small enclaves to metropolises. With all the benefits, however, come considerable costs, especially to the global environment. Greenhouse gas emissions, built up over centuries of unregulated combustion, have precipitated a rate of global temperature change unparalleled in the 4.5 billion-year history of this planet. In order to preserve …

Bacterial Production Of Human Discoidin Domain Receptor 2 (Ddr2) Kinase And Its Gatekeeper Mutants To Assess Activation By Phosphorylation, Dina Allam Abdel Azeem

Archived Theses and Dissertations

Discoidin domain receptor 2 (DDR2) belongs to a subfamily of receptor tyrosine kinases (RTKs) known as discoidin domain receptors (DDRs). DDRs are characterized by an extracellular discoidin homology domain and being activated by collagen resulting in a delayed but sustained activation. DDR2 overexpression was reported in some tumors, atherosclerosis as well as a number of inflammatory and fibrotic conditions. Recently 3 kinase inhibitor drugs (imatinib, nilotinib and dasatinib) were reported to inhibit DDR2 kinase activity suggesting it might have a role in their therapeutic effect. However minimal information is available on DDR2 downstream signaling. Identification of DDR2 substrates is essential …

Isolation And Characterization Of A Novel Thermostable, Halotolerant L-Asparaginase Ii From The Metagenome Of The Red Sea; Atlantis Ii Brine Pool, Aya Medhat Saleh

Archived Theses and Dissertations

L-Asparaginases (E.C. 3.5.1.1) are group of enzymes which catalyze the hydrolysis of L-asparagine to L-aspartic acid and ammonia. Many microorganisms are known to produce two types of L-asparaginase. Considerable attention has been specifically drawn to type II L-asparaginases due to their potent tumor-inhibitory activity. Various limitations, such as high toxicity, poor stability and short half-life, are associated with the commercially available L-asparaginases used in cancer therapy. Additionally, L-asparaginases have a significant role in food industry owing to their ability to reduce the levels of acrylamide, which is a known neurotoxin and a potential carcinogen, in various food products. Knowing that …

Crispr Diversity In Brine Pools Of The Red Sea: A Comparative Study Of Clustered Regularly Interspaced Short Palindromic Repeats From The Red Sea Metagenomes, Mohamed Mohamed Lotaief

Archived Theses and Dissertations

Exploration of CRISPR/Cas systems in the unique Red sea Brine pools can provide insights into host-viral interactions in highly extremophile environments. 454 Metagenomic datasets from different strata of Atlantis II, Discovery deep and Kebrit deep brine pools were mined for CRISPR arrays, and Cas proteins and compared to one another. Overall composition of CRISPR types was inferred by Cas protein HMM data, together with Cas1 phylogenetic placement using RaxML and direct repeat typing. Spacerâ viral interaction was explored using local alignments of mined spacer data to local metagenomic prophage sequences, showing and comparing specific sample CRISPR affected viral occurrences as …

Mining And Identification Of A Potential Subtilisin-Like Serine Protease From The Lower Convective Layer Of The Atlantis Ii Brine Pool In The Red Sea, Ahmed Shibl

Archived Theses and Dissertations

The Red Sea harbors a number of deep-sea brine pools with diverse chemical, physical, and geological conditions. One of the environments, the Atlantis II Brine Pool, is unique to the Red Sea. The deepest part of Atlantis II Brine Pool â the Lower Convective Layer (LCL) â is 2060 meters below the sea surface water, with 26% salinity, and a temperature of about 68 °C. Moreover, it is almost anoxic, and contains a very high concentration of heavy metals. We are interested in identifying subtilisin-like serine proteases, which are an important group of proteolytic enzymes with a broad range of …