Biotechnology Commons^™

Analyzing The Characteristics Of Domestic Wastes In Belik River, The Special Region Of Yogyakarta, Indonesia, Suprayogi Slamet, Marfai Muh Aris, Cahyadi Ahmad, Latifah Reviana, Fatchurohman Hendy

ASEAN Journal on Science and Technology for Development

The multiplying number of population in the City of Yogyakarta has resulted in a larger volume of wastes in the region. People living on the riverbanks are unfortunately in the habit of discarding domestic waste directly to the river channel, worsening the already polluted water. This study was intended to analyze the characteristics of the municipal wastewater contaminating Belik River. During the water quality test, a rapid investigation method and laboratory analysis were employed. The sampling in the field was based on river segments and travel time of river water. Based on the laboratory test results, the concentrations of phosphate, …

Fenton Oxidation Using Easily Recoverable Catalyst Of Magnetite (Fe3o4) As An Efficient Approach To Treatment Of Rhodamine B Dyeing Effluent In Traditional Fabrics Industry, Prasetyo Imam, Akbar Febry, Prabandari Anindya Widi, Ariyanto Teguh

ASEAN Journal on Science and Technology for Development

A direct release of dye wastewater to a water environment without pre-treatment could cause negative impacts. To solve them, an effective method for degrading wastewater contaminants is needed. In this research, the Fenton reaction using Fe3O4 catalyst for removal of wastewater contaminants taken from a traditional fabrics industry was studied. For this purpose, reaction temperature was varied in the range of 27–90°C. Furthermore, catalyst concentration was also varied in the range of 2–6 g/L solution. The results showed that increasing both temperature and catalyst concentration will increase the performance of the Fenton reaction in degrading wastewater contaminants. The contaminant degradation …

Singv – The Convective-Scale Numerical Weather Prediction System For Singapore, Huang Xiang-Yu, Barker Dale, Webster Stuart, Dipankar Anurag, Lock Adrian, Mittermaier Marion, Sun Xiangming, North, Darvell Rob, Boyd Douglas, Lo Jeff, Liu Jianyu, Macpherson Bruce, Heng Peter, Maycock Adam, Pitcher Laura, Tubbs Robert, Mcmillan Martin, Zhang Sijin, Hagelin Susanna, Porson Aurore, Song Guiting, Beckett Becky, Cheong Wee Kiong, Semple Allison, Gordon Chris

ASEAN Journal on Science and Technology for Development

Extreme rainfall is one of the primary meteorological hazards in Singapore, as well as elsewhere in the deep tropics, and it can lead to significant local flooding. Since 2013, the Meteorological Service Singapore (MSS) and the United Kingdom Met Office (UKMO) have been collaborating to develop a convective-scale Numerical Weather Prediction (NWP) system, called SINGV. Its primary aim is to provide improved weather forecasts for Singapore and the surrounding region, with a focus on improved short-range prediction of localized heavy rainfall. This paper provides an overview of the SINGV development, the latest NWP capabilities at MSS and some key results …

Temporary Shelter Simulation Towards Effectiveness Value Of Ottv And Thermal Comfort, Ayu Dyah Puspa, Prayitno Budi, Hariyadi Agus

ASEAN Journal on Science and Technology for Development

Indonesia is prone to a variety of natural disasters, one of which is earthquakes. Earthquakes are detrimental to human life, causing among other things a loss of shelter. As such, victims of earthquakes need basic assistance in the form of shelter, which the Indonesian government provides in the transition phase of emergency responses. Several innovations in the provision of temporary shelter have arisen in terms of packaging and fast unloading. This research aimed to examine the effective value of OTTV energy (overall thermal transfer value), differences in room temperature, and thermal comfort in existing temporary shelters. OTTV values and thermal …

Theranostics For Antiretroviral Biodistribution And Pharmacokinetics, Brendan M. Ottemann

Theses & Dissertations

RATIONALE: Our laboratories birthed the field of human immunodeficiency virus (HIV) theranostics. The new field allows simultaneous detection (diagnostics) and treatment (therapeutic) for the identification, treatment and inevitable elimination of virus in cell and tissue compartments. By employing theranostics, antiretroviral drugs (ARVs) can be tracked in lymph nodes, gut, spleen and liver. Cellular viral reservoirs including CD4+ T cell populations and mononuclear phagocytes (MP; monocytes, macrophages, microglia and dendritic cells) along with subcellular endosomal structures can now be targeted for drug delivery bringing therapeutics to areas where virus replicates. The overarching idea rests in improving precision targeted ARV delivery. …

Feeding The Future Meat Doesn’T Come Cheap, Lukas C. Southard

Capstones

Cultured – or as it is referred to by companies innovating the technology clean – meat is expected to be the next innovation to change the way the world gets its animal protein. Meat from animal cells grown in a lab seems like science fiction but it is around the corner from hitting your supermarket shelves. The technology has been developed but how these companies intend on scaling up their production to meet retail demands remains a mystery. So far companies have relied on seed and early stage investment from venture capital companies and private sources to fund research. Predictions …

Total Phenolic And Flavonoid Contents Of Anacyclus Pyrethrum Link Plant Extracts And Their Antioxidant Activity, Hanane Elazzouzi, Nadia Zekri, Touriya Zair, Mohamed Alaoui El Belghiti

Karbala International Journal of Modern Science

In this study, Anacyclus pyrethrm Link (roots) is a medicinal plant from the Asteraceae family, endemic to Morocco and is widely used in traditional medicine; was investigated for their total phenolics, flavonoids contents and antioxidant activities. The quantitative estimation of total flavonoids and phenols by the colorimetric method showed that the extracts were prepared by fractionation of the crude hydromethanolic extract (ethyl acetate and n-butanol). The phenol content of various extracts, estimated by the Folin-Ciocalteu method, was between 1,44 and 12,82 mg EAG / g extract of A. pyrethrum. Moreover, it is clear that ethyl acetate was the …

Interaction Between Fusarium Head Blight And Crown Rot Disease Incidence And Environmental Factors And Soil Physiochemical Analysis On Wheat In The South Of Iraq, Basra Province, Mohammed Hussein Minati Dr., Mohanad Khalaf Mohammed-Ameen Dr.

Karbala International Journal of Modern Science

This study was conducted to evaluate the interaction between disease incidence of both Fusarium head blight (FHB) and crown rot (FCR) and physiochemical parameters for soil samples and environmental factors in 14 selected wheat fields in the North of Basra province. The results showed that both diseases were occurred in all surveyed fields. The level of FCR incidence was higher than FHB. The incidence of both diseases was increased with favourable weather conditions (high humidity and temperature ˃15 °C), reaching the highest levels in crucial periods before and during the ripening stage. The percentage of disease incidence ranged between 6 …

Structural Basis Of Non-Canonical Transcriptional Regulation By The A-Bound Iron-Sulfur Protein Whib1 In M. Tuberculosis, Tao Wan, Shanren Li, Daisy Guiza Beltran, Andrew Schacht, Lu Zhang, Donald F. Becker, Limei Zhang

Department of Biochemistry: Faculty Publications

WhiB1 is amonomeric iron–sulfur cluster-containing transcription factor in the WhiB-like family that is widely distributed in actinobacteria including the notoriously persistent pathogen Mycobacterium tuberculosis (M. tuberculosis). WhiB1 plays multiple roles in regulating cell growth and responding to nitric oxide stress inM. tuberculosis, but its underlying mechanism is unclear. Here we report a 1.85 A° -resolution crystal structure of the [4Fe–4S] cluster-bound (holo- )WhiB1 in complex with the C-terminal domain of the 70-family primary sigma factor A of M. tuberculosis containing the conserved region 4 (A 4). Region 4 of the 70-family primary sigma factors is commonly used by transcription factors …

High-Throughput Nano-Scale Characterization Of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography, Alex J. Vecchio, Robert M. Stroud

Department of Biochemistry: Faculty Publications

Structural biology has revealed predicting heterologous expression levels, homogeneity, and stability of a protein from its primary structure are exceedingly difficult. Membrane proteins, in particular, present numerous challenges that make obtaining milligram quantities of quality samples problematic. For structural and functional investigation of these molecules, however, this is what is required. Fluorescence size-exclusion chromatography (F-SEC), a technique where a protein of biological interest is fused to green fluorescent protein (GFP) and monitored, circumvents many bottlenecks inherent to membrane protein structural biology. In vivo expression yields, as well as in vitro homogeneity and stability, can be rapidly evaluated utilizing nanogram quantities …

Inhibition Of Serine, Glycine, One-Carbon Metabolism Reduces Proinflammatory Response, Ashlynn Mccall

Honor’s College Freeman Research Journal

Acute lung injury affects around 200,000 critically ill patients annually, with a mortality rate near 33%. With a lack of targeted therapies, it is vital to discover and understand the fundamental cellular processes that drive macrophage inflammation. In the field of macrophage immunometabolism, it is accepted that macrophages upregulating glycolysis indicates a role in proinflammatory processes, however, there is a lack of knowledge surrounding the intermediate pathways in glycolysis. This study examined the effects of serine, glycine, one-carbon metabolism inhibition on LPS-induced inflammation in bone marrow-derived macrophages. We show that the enzymatic expression of PHGDH and PSATl is unaffected when …

The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi

Dissertations

Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …

Deepep: A Deep Learning Framework For Identifying Essential Proteins, Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li, Yi Pan

Computer Science Faculty Publications

Background: Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have been proposed to handle this problem. However, traditional centrality methods cannot fully represent the topological features of biological networks. In addition, identifying essential proteins is an imbalanced learning problem; but few current shallow machine learning-based methods are designed to handle the imbalanced characteristics. Results: We develop DeepEP based on a deep learning framework that uses the node2vec technique, multi-scale convolutional neural networks and a sampling technique to identify essential proteins. …

Biotech: Not Just For Geeks, Fred D. Ledley

Science and Industry

Business students get high marks for scientific literacy

Molecular Survey Of Helminths Infecting Ground Dwelling Birds In The Grouse Subfamily Tetraoninae, Briana M. Sesmundo

Honors College Theses

Alaskan grouse and ptarmigan (Galliformes) are important avian game species in Alaska. Interestingly, gallids harbor a fairly diverse helminth fauna, particularly cestodes, which may make birds with high parasite loads more susceptible to predation. Unfortunately, there is limited information available on the helminth fauna of Alaskan gallids, and no molecular surveys. The present study aims to develop baseline data on diversity of intestinal and subcutaneous (filariid) helminth infections in galliforms using morphological and molecular (DNA) approaches. These data can then be used to better understand changes in helminth community structure given current environmental volatility. The intestines, cloaca, liver and kidneys …

Cgste11 Mediates Cross Tolerance To Multiple Environmental Stressors In Candida Glabrata, Mian Huang, Jibran Khan, Manpreet Kaur, Julian Daniel Torres Vanega, Orlando Andres Aguilar Patiño, Anand Ramasubramanian, Katy Kao

Faculty Publications

Candida glabrata is a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeast Saccharomyces cerevisiae than other Candida spp. Compared with S. cerevisiae, C. glabrata exhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms of C. glabrata adaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome …

Structural Basis For Chloroperoxidase Catalyzed Enantioselective Epoxidations And Mechanisms Of Selected Anticancer Drug Induced Apoptosis, Yongjian Guo

FIU Electronic Theses and Dissertations

Chloroperoxidase (CPO), a member of the heme peroxidase family, has diverse catalytic activities toward a broad range of substrates. In addition to catalyzing halogenation reactions involved in the biosynthesis of halogen-containing compounds, CPO also catalyzes reactions typical of traditional heme peroxidases, catalases, and cytochrome P450 enzymes. Despite the powerful and versatile catalytic activity of CPO, its applications have been thwarted by the difficulty in regenerating the active enzyme and substrate (peroxide) induced protein inactivation. To overcome these shorting comings of the protein, we investigate the fabrication and characterization of chloroperoxidase (CPO) and glucose oxidase (GOx) on the surface of MGO. …

Comparison Of Montage With Conventional Stereoscopic Seven‑Field Photographs For Assessment Of Etdrs Diabetic Retinopathy Severity, Nam V. Nguyen, Erin M. Vigil, Muhammad Hassan, Muhammad S. Halim, Sean C. Baluyot, Hugo A. Guzman, Rubbia Afridi, Diana V. Do, Yasir J. Sepah

Department of Biochemistry: Faculty Publications

Background: The ETDRS stereoscopic seven-field (7F) has been a standard imaging and grading protocol for assessment of diabetic retinopathy (DR) severity score in many clinical trials. To the best of our knowledge, the comparison between montage and stereoscopic 7F has not been reported in the literature. Therefore, the main purpose of this study is to compare agreement between montage and stereoscopic seven-field (7F) photographs in the assessment of DR severity.

Methods: Stereoscopic 7F photographs were captured from subjects with DR. Montages of monoscopic 7F images were created using Adobe Photoshop CS6 Extended©. The best quality image of each stereo pair …

Updating Molecular Diagnostics For Detecting Methicillin- Susceptible And Methicillin-Resistant Staphylococcus Aureus Isolates In Blood Culture Bottles, Fred C. Tenover, Isabella A. Tickler, Victoria M. Le, Scott Dewell, Rodrigo E. Mendes, Richard V. Goering, Mrsa Consortium

Biology Faculty Publications

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotypephenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette …

Remodeling Of Chlamydomonas Metabolism Using Synthetic Inducers Results In Lipid Storage During Growth, Nishikant Wase, Boqiang Tu, Girish Kumar Rasineni, Ronald Cerny, Ryan Grove, Jiri Adamec, Paul N. Black, Concetta Dirusso

Department of Biochemistry: Faculty Publications

Microalgae accumulate lipids during stress such as that of nutrient deprivation, concomitant with cessation of growth and depletion of chloroplasts. By contrast, certain small chemical compounds selected by high-throughput screening in Chlamydomonas reinhardtii can induce lipid accumulation during growth, maintaining biomass. Comprehensive pathway analyses using proteomics, transcriptomics, and metabolomics data were acquired from Chlamydomonas cells grown in the presence of one of two structurally distinct lipid activators. WD10784 stimulates both starch and lipid accumulation, whereas WD30030-treated cells accumulate only lipids. The differences in starch accumulation are largely due to differential effects of the two compounds on substrate levels that feed …

In Vitro Investigation Of The Effect Of Camel Milkproteins And Its Fractions On Insulin Receptor Function, Arshida Ashraf

Biology Theses

Camel milk (CM) has been reported to have anti-diabetic properties in many in vitro and in vivo studies but the molecular basis of such beneficial properties are still elusive. Recently, camel milk whey proteins (CWPs) have been shown to positively affect the activity of the human insulin receptor (hIR) in cell lines. In this study, we profiled crude CWPs and their hydrolysates as well as camel milk lactoferrin (CMLF) for their pharmacological and functional effects on hIR activity and its downstream signaling in both human embryonic kidney (HEK293) and hepatocarcinoma (HepG2) cell lines. For this, bioluminescence resonance energy transfer (BRET) …

Forensic Evaluation Of 6-Dye Chemistry Kit Composed Of 23 Loi With Casework Samples, Naeema Saleh Al Janaahi

Biology Theses

Short Tandem Repeats (STRs) are short nucleotide sequence repeats consisting of 2-8 base pairs (bp), representing approximately 3% of human DNA. Markers of STRs have been widely used as genetic markers in forensic DNA analysis and have proven to be an extremely discriminating method for human identification in forensics. The main objective of this research was to evaluate a six-dye STR multiplex assay (Virifiler™ Plus) composed of 23 autosomal STR loci, one insertion/deletion polymorphic marker on the Y chromosome, Amelogenin and two internal quality control markers (IQCS and IQCL) using biological stains found in different crime scenes. The study investigated …

Label-Free Microrna Optical Biosensors, Meimei Lai, Gymama Slaughter

Bioelectrics Publications

MicroRNAs (miRNAs) play crucial roles in regulating gene expression. Many studies show that miRNAs have been linked to almost all kinds of disease. In addition, miRNAs are well preserved in a variety of specimens, thereby making them ideal biomarkers for biosensing applications when compared to traditional protein biomarkers. Conventional biosensors for miRNA require fluorescent labeling, which is complicated, time-consuming, laborious, costly, and exhibits low sensitivity. The detection of miRNA remains a big challenge due to their intrinsic properties such as small sizes, low abundance, and high sequence similarity. A label-free biosensor can simplify the assay and enable the direct detection …

The Association Of Dna And Histone Methyltransferase Genes With Different Methylation Levels In Fragile X Syndrome Individuals, Sara Humaid Sembaij

Theses

Fragile X Mental Retardation 1 (FMR1) gene produces an FMR protein (FMRP) which is known to regulate the translation process in various organs. It has a significant role in neurons function, maturation, and synaptic plasticity. FMR1 gene encompasses 5 - 30 CGG repeats and the greater number of repeats has the potential to expand during gametogenesis. The expansion depending on the number of CGG repeat undergoes hyper-methylation and is considered as a dynamic mutation in which the expansion increases through generation. Methylation of expanded CGG repeats results in inhibiting the transcription and silencing the gene. There are two types of …

The Democratization And Development Of Cell-Free Protein Synthesis, Max Z. Levine

Master's Theses

Cell-free protein synthesis (CFPS) using crude lysates has developed into a robust platform technology over the last 60 years to express numerous types of recombinant proteins. The open-nature, elimination of reliance on cell viability, and focus of all energy towards production of the protein of interest represent substantial advantages of CFPS over in vivo protein expression methods. CFPS has provided new opportunities across a series of research fields that include metabolic engineering, therapeutic and vaccine development, education, biosensors, and many more. In recent years, optimizations of CFPS have even allowed the platform to reach the industrial level of protein production. …

The Catalytic Urease Subunit Urec Is Critical For Bifidobacterium Longum Urea Utilization, Yang Lyu

Doctoral Dissertations

In the first study, we investigated the utilization of a human milk nitrogen source, urea, by Bifidobacterium. Urea accounts for ~15% in human milk, which is an abundant non-protein nitrogen (NPN). Some bifidobacteria are found to harbor urease gene clusters that potentially enable their hydrolysis of the human milk urea. However, the underlying mechanisms are still unclear. To incisively link the urease gene cluster with bifidobacterial urea utilization, chemical mutagenesis (i.e. ethyl methanesulfonate) was performed on the urease-positive Bifidobacterium longum subsp. suis UMA399. Mutants were selected on differential media and genetic lesions were identified using whole genome sequencing. …

Engineering Of An Antibody-Conjugated Nanogel Platform For Targeted Drug Delivery To T Lymphocytes, Mine Canakci

Doctoral Dissertations

In an ideal chemotherapy, cytotoxic drugs travel through the bloodstream, reach cells all over the body and preferentially kill abnormal cells. Yet, the hydrophilic or lipophilic property of the small-molecule drugs affects their ability to reach cells from the bloodstream. So, only a small portion of the drug reaches to the diseased tissue. A selective cell killing approach for cancer therapy gained momentum after the realization that cancer cells carry unique set of molecular markers on their cell surface. The development of antibody drug conjugates (ADC) revolutionized the targeted approach for drug delivery. ADCs are composed of cytotoxic agents covalently …

Investigating The Role Of Lbh During Early Embryonic Development In Xenopus Laevis, Emma Weir

Masters Theses

LBH is a highly conserved protein whose role during vertebrate development is relatively under-studied. In collaboration with the Albertson lab, our lab has previously shown that it is necessary for cranial neural crest cell migration in the zebrafish and in Xenopus laevis. The molecular mechanisms through which it acts are not well understood.

In Xenopus, LBH is a maternally deposited protein. As such, studying its role in early development has not been feasible through the morpholino-mediated knockdown techniques that prevent translation of target genes. Recently, a technique for degrading endogenous proteins was developed, called Trim-Away. This was developed in mammalian …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Yevgeniy (Eugene) Shakirov

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

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

Yevgeniy (Eugene) Shakirov

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 …