Biotechnology Commons^™

Recent Advances In The Use Of Transglutaminase In Cheese Production, El Kiyat Warsono, Laurenthia Evlyn, Michaela Janice, Fariz Pari Rizfi

ASEAN Journal on Science and Technology for Development

Various enzymes are used in the food industry to improve product quality. The enzyme transglutaminase is used to modify proteins in various foods through the formation of inter- and intramolecular epsilon-(gamma-glutamyl) lysine bonds. Previous studies have revealed that using transglutaminase in cheese production can increase the yield and enhance the characteristics of various types of cheese. However, the enzyme concentration, temperature, and pH influence the quality of cheese. This review aimed to discuss the potential of transglutaminase in cheese production. Our analysis showed that transglutaminase catalyzes the formation of covalent bonds between milk proteins (crosslinking), which results in a greater …

Ethical Governance Of Gene Editing Technology, Huiyuan Wang, Pengfei Li, Lijuan Xu, Liwen Zhang, Caihong He, Yuelei Fan, Jianrong Yu, Zhihong Xu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Gene editing technology has been one of the breakthrough technologies for life science research. With the application in biomedical research, healthcare, food and agriculture field, related ethical issues are also concerned. This study summarized the research and application progress of gene editing technology involving ethical issues in recent years. Based on sorting out the international discussions, attitudes, and explorations about gene editing ethics issues, after analyzing the current status, discussions, and measures of applications of gene editing technology on human beings in China, we propose five suggestions about the ethical governance system construction of gene editing technology for China.

Stabilin Receptors Clear Lps And Control Systemic Inflammation, Fatima Cabral, Mustafa Al-Rahem, John Skaggs, Thushara A. Thomas, Naresh Kumar, Qian Wu, Paolo Fadda, Lianbo Yu, John M. Robinson, Jonghan Kim, Ekta Pandey, Xinghui Sun, Wael N. Jarjour, Murugesan V.S. Rajaram, Edward N. Harris, Latha P. Ganesan

Department of Biochemistry: Faculty Publications

Lipopolysaccharides (LPSs) cause lethal endotoxemia if not rapidly cleared from blood circulation. Liver sinusoidal endothelial cells (LSEC) systemically clear LPS by unknown mechanisms. We discovered that LPS clearance through LSEC involves endocytosis and lysosomal inactivation via Stabilin-1 and 2 (Stab1 and Stab2) but does not involve TLR4. Cytokine production was inversely related to clearance/endocytosis of LPS by LSEC. When exposed to LPS, Stabilin double knockout mice (Stab DK) and Stab1 KO, but not Stab2 KO, showed significantly enhanced systemic inflammatory cytokine production and early death compared with WT mice. Stab1 KO is not significantly different from Stab DK in circulatory …

Microbial And Chemical Profiles Of Sediments Isolated From Atlantis Ii And Discovery Deep Brine Pools In The Red Sea., Nardine G. Rasmy Marsis

Archived Theses and Dissertations

No abstract provided.

Role Of Autophagy In Acridocarpus Orientalis-Induced Anti-Breast Cancer Activity, Suhib Hisham Ahmed Saeed Altabbal

Theses

Breast cancer is the most frequently diagnosed cancer in women worldwide. Triple Negative Breast Cancer (TNBC), which lacks the expression of the hormonal Estrogen Receptor (ER) and Progesterone Receptor (PR), and the amplification of Human Epidermal Growth Factor Receptor 2 (HER2), is not responsive to the hormonal therapy. Therefore, chemotherapy and radiotherapy, which cause severe side effects, are the current available choices to treat TNBC. Hence, there is an urgent need to find new therapeutic choices for TNBC. It is estimated that 50% of all drugs in clinical use during the 21^st century are natural products and plants derived. …

Phenolic, Carotenoid And Saccharide Compositions Of Vietnamese Camellia Sinensis Teas And Herbal Teas, Danh C. Vu, Sophie Alvarez

Nebraska Center for Biotechnology: Faculty and Staff Publications

Tea (Camellia sinensis) and herbal tea have been recognized as rich sources of bioactive constituents with the ability to exert antioxidant actions. The aims of this study were to analyze phenolic, carotenoid and saccharide contents in a set of Vietnamese tea and herbal tea and compare the results with those of green and black teas marketed in the U.S. In total, 27 phenolics, six carotenoids and chlorophylls, and three saccharides were quantitatively identified. Catechins, quercetin glycosides and chlorogenic acid were the predominating phenolics in the teas, with the concentrations following the order: jasmine/green teas > oolong tea > black tea. …

Creating Reel Designs: Reflecting On Arthrogryposis Multiplex Congenita In The Community, Iris Layadi

Purdue Journal of Service-Learning and International Engagement

Because of its extreme rarity, the genetic disease arthrogryposis multiplex congenita (AMC) and the needs of individuals with the diagnosis are often overlooked. AMC refers to the development of nonprogressive contractures in disparate areas of the body and is characterized by decreased flexibility in joints, muscle atrophy, and developmental delays. Colton Darst, a seven-year-old boy from Indianapolis, Indiana, was born with the disorder, and since then, he has undergone numerous surgical interventions and continues to receive orthopedic therapy to reduce his physical limitations. His parents, Michael and Amber Darst, have hopes for him to regain his limbic motion and are …

Dynamic Evolution And Correlation Between Metabolites And Microorganisms During Manufacturing Process And Storage Of Fu Brick Tea, Jing Li, Ran Xu, Joseph Brake, Lizeng Cheng, Jie Wu, Xiaobin Wu

Department of Biochemistry: Faculty Publications

Fu brick tea (FBT) is one of the major brands of dark tea. Microbial fermentation is considered the key step in the development of the special characteristics of FBT. The systemic corelationship of the microbiome and metabolomics during manufacture of Fu brick tea is not fully understood. In this study, we comprehensively explored the microbiome and metabolite dynamic evolution during the FBT manufacturing processes, and revealed decisive factors for the quality and safety of FBT based on the grouped methods of metabolomics combined with biochemical measurements, microbiome sequencing combined with quantitative polymerase chain reaction (PCR), and multiplex analysis. Both the …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Mitochondrial Superoxide Dismutase Overexpression And Low Oxygen Conditioning Hormesis Improve The Performance Of Irradiated Sterile Males, Vanessa S. Dias, Carlos Cáceres, Andrew G. Parker, Rui Pereira, Güler Demirbas-Uzel, Adly M. M. Abd-Alla, Nicholas M. Teets, Marc F. Schetelig, Alfred M. Handler, Daniel A. Hahn

Entomology Faculty Publications

The Sterile Insect Technique (SIT) is a successful autocidal control method that uses ionizing radiation to sterilize insects. However, irradiation in normal atmospheric conditions can be damaging for males, because irradiation generates substantial biological oxidative stress that, combined with domestication and mass-rearing conditions, may reduce sterile male sexual competitiveness and quality. In this study, biological oxidative stress and antioxidant capacity were experimentally manipulated in Anastrepha suspensa using a combination of low-oxygen conditions and transgenic overexpression of mitochondrial superoxide dismutase (SOD2) to evaluate their role in the sexual behavior and quality of irradiated males. Our results showed that SOD2 overexpression enhances …

Recent Applications Of Quantitative Systems Pharmacology And Machine Learning Models Across Diseases, Sara Sadat Aghamiri1, Rada Amin, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Quantitative systems pharmacology (QSP) is a quantitative and mechanistic platform describing the phenotypic interaction between drugs, biological networks, and disease conditions to predict optimal therapeutic response. In this meta-analysis study, we review the utility of the QSP platform in drug development and therapeutic strategies based on recent publications (2019–2021). We gathered recent original QSP models and described the diversity of their applications based on therapeutic areas, methodologies, software platforms, and functionalities. The collection and investigation of these publications can assist in providing a repository of recent QSP studies to facilitate the discovery and further reusability of QSP models. Our review …

Purification And Initial Biochemical Characterization Of Atp:Cob(I)Alamin Adenosyltransferase (Eutt) Enzyme Of Salmonella Enterica, Nicole R. Buan, Jorge C. Escalante-Semerena

Department of Biochemistry: Faculty Publications

ATP:cob(I)alamin adenosyltransferase (EutT) of Salmonella enterica was overproduced and enriched to ~70% homogeneity, and its basic kinetic parameters were determined. Abundant amounts of EutT protein were produced, but all of it remained insoluble. Soluble active EutT protein (~70% homogeneous) was obtained after treatment with detergent. Under conditions in which cobalamin (Cbl) was saturating, K_m(ATP) = 10 μM, k_cat = 0.03 s^–1, and V_max = 54.5 nM min^–1. Similarly, under conditions in which MgATPwas saturating,K_m(Cbl)= 4.1μM, k_cat = 0.06 s^–1, andV_{max …}

The Simulation Experiment Description Markup Language (Sed-Ml): Language Specification For Level 1 Version 4, Lucian P. Smith,, Frank T. Bergmann, Alan Garny, Tomáš Helikar, Jonathan Karr, David Nickerson,, Herbert Sauro, Dagmar Waltemath, Matthias König

Department of Biochemistry: Faculty Publications

Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive collaboration among modelers, experimentalists, and engineers. The Minimum Information About a Simulation Experiment (MIASE) guidelines outline the information needed to share simulation experiments. SED-ML is a computer-readable format for the information outlined by MIASE, created as a community project and supported by many investigators and software tools. The first versions of SED-ML focused on deterministic and stochastic simulations of models. Level 1 Version 4 of SED-ML substantially expands these …

Liquid And Semisolid Lubricant Compositions , Methods Of Making , And Uses Thereof, Diana Berman, Kent Dean Chapman, Tervor Bradley Romsdahl, Edgar Benjamin Cahoon, Robert Earl Minto, Chunyu Zhang

Department of Biochemistry: Faculty Publications

Various liquid and semisolid lubricant compositions are provided, in particular lubricant compositions containing oil from the seeds of the Brassicaceae Orychophragmus violaceus, preferably those that have been esterified with one or more fatty acids such as palmitoleic acid, oleic acid, linoleic acid, lauric acid, palmitic acid, stearic acid, or a combination thereof. In various aspects, lubricant compositions are provided that include a petroleum or a synthetic base oil and about 40 % or less by weight of a liquid lubricant composition containing oil from the seeds of the Brassicaceae Orychophragmus violaceus preferably those that have been esterified with one …

Defining The Innate Immune Responses For Sars-Cov-2-Human Macrophage Interactions, Mai M. Abdelmoaty, Pravin Yeapuri, Jatin Machhi, Katherine E. Olson, Farah Shahjin, Vikas Kumar, You Zhou, Jingjing Liang, Kabita Pandey, Arpan Acharya, Siddappa N. Byrareddy, R. Lee Mosley, Howard E. Gendelman

Nebraska Center for Biotechnology: Faculty and Staff Publications

Host innate immune response follows severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and it is the driver of the acute respiratory distress syndrome (ARDS) amongst other inflammatory end-organ morbidities. Such life-threatening coronavirus disease 2019 (COVID-19) is heralded by virus-induced activation of mononuclear phagocytes (MPs; monocytes, macrophages, and dendritic cells). MPs play substantial roles in aberrant immune secretory activities affecting profound systemic inflammation and end-organ malfunctions. All follow the presence of persistent viral components and virions without evidence of viral replication. To elucidate SARS-CoV- 2-MP interactions we investigated transcriptomic and proteomic profiles of human monocyte-derived macrophages. While expression of the …

Mitochondrial Contact Site And Cristae Organizing System (Micos) Machinery Supports Heme Biosynthesis By Enabling Optimal Performance Of Ferrochelatase, Jonathan V. Dietz, Mathilda M. Willoughby, Robert B. Piel, Teresa A. Ross, Iryna Bohovych, Hannah G. Addis, Jennifer L. Fox, William N. Lanzilotta, Harry A. Dailey, James A. Wohlschlegel, Amit R. Reddi, Amy E. Medlock, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

Heme is an essential cofactor required for a plethora of cellular processes in eukaryotes. In metazoans the heme biosynthetic pathway is typically partitioned between the cytosol and mitochondria, with the first and final steps taking place in the mitochondrion. The pathway has been extensively studied and its biosynthetic enzymes structurally characterized to varying extents. Nevertheless, understanding of the regulation of heme synthesis and factors that influence this process in metazoans remains incomplete. Therefore, we investigated the molecular organization as well as the physical and genetic interactions of the terminal pathway enzyme, ferrochelatase (Hem15), in the yeast Saccharomyces cerevisiae. Biochemical and …

The Effect Of Low Dose Penicillin On Tumor Development In ApcMin/+ Mice, Kinsey Ann Sierra Meggett

Theses and Dissertations

Antibiotics have been our most effective weapon against bacterial infections since their discovery in the early 1900s. Their use has been critical in reducing mortality rate from infectious diseases. However, in the last few decades, the overuse of antibiotics, beginning at an early age and into adulthood, has become a growing concern globally. Penicillin is one of many extensively used antibiotics in early childhood that has been used to treat childhood infections. Recent studies showed that exposure to low dose penicillin can have adverse effects leading to chronic illness such as diabetes, allergies, inflammation, and susceptibility to obesity, with the …

The Classification Of Basket Neural Cells In The Mammalian Neocortex, Sreya Pudi

Senior Theses

Basket neuronal cells of the mammalian neocortex have been classically categorized into two or more groups. Originally, it was thought that the large and small types are the naturally occurring groups that emerge from reasons that relate to neurobiological function and anatomical position. Later, a study based on anatomical and physiological features of these neurons introduced a third type, the net basket cell which is intermediate in size as compared to the large and small types. In this study, multivariate analysis was used to test the hypothesis that the large and small types are morphologically distinct groups. The results of …

Using Molecular Diagnostics To Develop Therapeutic Strategies For Carbapenem-Resistant Gram-Negative Infections, Fred C. Tenover

Biology Faculty Publications

Infections caused by multidrug-resistant Gram-negative organisms have become a global threat. Such infections can be very difficult to treat, especially when they are caused by carbapenemase-producing organisms (CPO). Since infections caused by CPO tend to have worse outcomes than non-CPO infections, it is important to identify the type of carbapenemase present in the isolate or at least the Ambler Class (i.e., A, B, or D), to optimize therapy. Many of the newer beta-lactam/beta-lactamase inhibitor combinations are not active against organisms carrying Class B metallo-enzymes, so differentiating organisms with Class A or D carbapenemases from those with Class B enzymes rapidly …

Inner Ear Development And Advances In Inner Ear Organoid Formation, Paige Avery

The Cardinal Edge

The inner ear houses the cochlea which contains hair cells responsible for the transduction of sound waves. The process of forming these hair cells responsible for hearing is a complicated process consisting of many signaling factors that allow ectoderm to form into the otic placode, the otic vesicle, and finally prosensory cells such as hair cells (Schlosser, 2006). Loss of these hair cells contributes to deafness and hearing loss throughout life, and regeneration of these cells may serve as a therapeutic agent for those with irreversible damage. This review looks at the development of the otic placode and hair cells …

Novel Pilot Development Of A Closed-Loop Sustainable System Between Biogas Renewable Energy, Distilling, And Aquaculture By Vermiculture Of Stillage Wastes, Samuel C. Kessler

The Cardinal Edge

This study provides a mixed-methods approach in analyzing a potential closed-loop system between renewable biogas production from anaerobic digestion, vermiculture production, aquaculture production, and organic wastes with a particular focus on stillage wastes. Such system may hold significant promise for significantly reducing organic carbon and methane emissions from its components, and should be assessed for such. The 2021 IPCC report essentially identified methane reduction as the single fastest way to slow global warming (IPCC, 2021), making the study and implementation of methane-reducing systems and supportive policy for them critical. Knowledge gaps to implementing this system were qualitatively identified as disconnect …

Phenotypic/Genotypic Profile Of Oxa-10-Like-Harboring, Carbapenem-Resistant Pseudomonas Aeruginosa: Using Validated Pharmacokinetic/Pharmacodynamic In Vivo Models To Further Evaluate Enzyme Functionality And Clinical Implications, Fred C. Tenover, Christian M. Gill, Adrian Brink, Chun Yat Chu, Jennifer Coetzee, George Dimopoulos, Clinton Moodley, Christoffel Johannes Opperman, Spyros Pournaras, Isabella A. Tickler, Hafsah Deepa Tootla, Sophia Vourli, David P. Nicolau

Biology Faculty Publications

In vitro MICs and in vivo pharmacodynamics of ceftazidime and cefepime human-simulated regimens (HSR) against modified carbapenem inactivation method (mCIM)-positive Pseudomonas aeruginosa isolates harboring different OXA-10-like subtypes were described. The murine thigh model assessed ceftazidime (2 g every 8 h [q8h] HSR) and cefepime (2 g and 1 g q8h HSR). Phenotypes were similar despite possessing OXA-10-like subtypes with differing spectra. Ceftazidime produced ≥1-log10 killing in all isolates. Cefepime activity was dose dependent and MIC driven. This approach may be useful in assessing the implications of β-lactamase variants.

Assessment Of Trace Elements In Soils And Sediments In The Abandoned Mercury Mine Site In Puerto Princesa City, Philippines, Samaniego Jessie, Gibaga Cris Reven, Tanciongco Alexandria, Rastrullo Rasty

ASEAN Journal on Science and Technology for Development

An abandoned mercury mine area in Puerto Princesa City, which was previously operated by Palawan Quicksilver Mines, Inc. (PQMI) from 1953 to 1976, is known for its unrehabilitated open-pit of mercury-rich rocks and exposed mine waste calcine stockpiles in the vicinity. In order to establish an understanding on the geology of the abandoned mercury mine deposit and to obtain clues in determining the possible metal pollutants in the area, measurement of trace element concentrations of soil and sediments collected from the PQMI vicinity were conducted. Soil and sediment samples were analyzed for heavy metals, rare-earth elements and naturally occurring radioactive …

Phenotype Bias Determines How Natural Rna Structures Occupy The Morphospace Of All Possible Shapes, Fatme Ghaddar, Dr Kamaludin Dingle, Dr Petr Sulc, Prof Ard A. Louis

Undergraduate Research Symposium

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are firstly that only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately …

Seaweed Polysaccharide In Food Contact Materials (Active Packaging, Intelligent Packaging, Edible Films, And Coatings), Kalpani Y. Perera, Shubham Sharma, Amit K. Jaiswal, Swarna Jaiswal

Articles

Food contact materials (FCMs) are materials that come in contact with food products such as food packaging which play a significant role in the food quality and safety. Plastic, which is a major food packaging material, harms the eco-system, wildlife, and the environment. As a result, numerous researches have been in progress on alternative polymers, which has similar properties as plastic but is also environmentally friendly (biodegradable). In recent years, the utilization of seaweed polysaccharides has piqued interest due to its biodegradability, non-toxicity, antioxidant capabilities, and excellent film formation ability. However, it has a number of drawbacks such as low …

Anti-Angiogenic Effects Of Chemotherapeutic Agents And Their Enhancement With Ot-515 And S-Nach, Shimaa Adel Heikal

Theses and Dissertations

Chemotherapeutic agents have been used for the treatment of numerous types of tumors with great success. Cisplatin and Doxorubicin are among the well-known chemotherapeutic drugs that showed efficacy against various types of cancers. However, cell resistance and major side effects like chemotherapy-induced peripheral neuropathy (CIPN) are limiting factors in using these compounds. Using a combination or adjuvant compounds with anti-angiogenic effects is one of the strategies suggested to decrease resistance or ameliorate chemotherapeutic toxicity. The present study investigated the anti-angiogenic effects of Cisplatin and Doxorubicin alone and combined with Sulfated non-anticoagulant heparin (S-NACH), a low molecular weight heparin LMWH that …

Optimization Of Ethanol Production From Enzymatically Saccharified Biomass Of Acid-Pretreated Rice Straw, Muzammal Mateen Azhar, Qurban Ali, Arif Malik, Elham Khalili, Muhammad Arshad Javed, Shinawar Waseem Ali, Muhammad Saleem Haidar

The Philippine Agricultural Scientist

The substrate of rice (Oryza sativa) straw employed in this study was procured from local market and stored in polyethene bags until needed. The study was conducted to find out the effects of process optimization of ethanol production from enzymatically saccharified biomass of acid-pretreated rice straw. The results indicated that acid pretreatment has reduced lignin content about 50%. Resultantly, pretreatment raised cellulose contents up to 52% making it suitable for enzymatic saccharification. Optimization of saccharification illustrated that parameters such as biomass, enzyme concentration, temperature, incubation time and agitation indeed affected the action of cellulase on pretreated biomass releasing …

Spectral Lights Based Treatment Enhanced Biomass Accumulation And Secondary Metabolites Production In Callus Culture Of Citrus Reticulata, Faiza Anum, Naveed Iqbal Raja, Tahira Sultana, Abeer Kazmi, Amir Ali, Bushra Qayyum, Anza Afzal, Aneela Nijibat, Zia-Ur-Rehman Mashwani, Abeer Kazmi

The Philippine Agricultural Scientist

Citrus reticulata is a common fruit, belongs to the family Rutaceae. It contains terpenes, phenolics, flavonoids, and vitamin C in conjugation with sugars, amino acids, minerals, organic acids and other biologically important compounds. Application of light elicitation strategies in in vitro plant cultures is acquiring more interest for their potential in feasible biomass accumulation and therapeutically important secondary metabolites production. The present study was designed to investigate the effects of different monochromatic lights (white, red, blue, green, and yellow) on the proliferation and secondary metabolites accumulation in callus cultures of Citrus reticulata raised in response to treatment with AgNPs and …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Biocontrol Of Foodborne Pathogens Using Bacteriophages, Dzhuliya Ignatova, Erion Hogan, Simone Dakare, Jean Lu

Symposium of Student Scholars

Biocontrol of Foodborne Pathogens Using Bacteriophages

Dzhuliya Ignatova, Erion Hogan, Simone Dakare, and Jean Lu

Department of Molecular and Cellular Biology

Abstract

Salmonella and Shigella are two important groups of foodborne bacterial pathogens. Salmonella cause an illness called salmonellosis while Shigella cause shigellosis (bacillary dysentery). The most common symptoms of these illnesses are abdominal cramps, diarrhea, and fever. Shigella can also cause bloody diarrhea. It was estimated that each year Salmonella cause 93.8 million cases of gastroenteritis and 155,000 deaths globally. Shigella causes 164.7 million cases and 1.1 million deaths throughout the world yearly. People get these illnesses mainly by …