Biotechnology Commons^™

Digitally Predicting Protein Localization And Manipulating Protein Activity In Fluorescence Images Using 4d Reslicing Gan, Yang Jiao, Lingkun Gu, Yingtao Jiang, Mo Weng, Mei Yang

Electrical & Computer Engineering Faculty Research

While multi-channel fluorescence microscopy is a vital imaging method in biological studies, the number of channels that can be imaged simultaneously is limited by technical and hardware limitations such as emission spectra cross-talk. One solution is using deep neural networks to model the localization relationship between two proteins so that the localization of one protein can be digitally predicted. Furthermore, the input and predicted localization implicitly reflect the modeled relationship. Accordingly, observing the response of the prediction via manipulating input localization could provide an informative way to analyze the modeled relationships between the input and the predicted proteins.

A Pooling Strategy For Detecting Carbapenem Resistance Genes By The Xpert Carba-R Test In Rectal Swab Specimens, Fred C. Tenover, Peng Zhang, Qi Wang, Chaoe Zhou, Feifei Zhang, Xinghui Gao, Yi-Wei Tang, Hui Wang

Biology Faculty Publications

Rapid and accurate detection of carriers of carbapenemase-producing organisms (CPO) in hospitalized patients is critical for infection control and prevention. This study aimed to evaluate a pooling strategy for the detection of carbapenem resistance genes (CRG) in multiple specimens using the Xpert Carba-R test. Two rectal swabs each were collected from 415 unique patients. One swab was tested by Carba-R on the five specimen-pooled strategy. The other swab was tested individually by culture followed by DNA sequence analysis for CRG as the reference. At the first 5:1 pooling testing, 22 of 83 pools were positive, which yielded 34 positives from …

Piglet Cardiopulmonary Bypass Induces Intestinal Dysbiosis And Barrier Dysfunction Associated With Systemic Inflammation, Jeffrey D. Salomon, Haowen Qiu, Dan Feng, Jacob Owens, Ludmila Khailova, Suzanne Osorio Lujan, John Iguidbashian, Yashpal S. Chhonker, Daryl J. Murry, Jean-Jack Riethoven, Merry L. Lindsey, Amar B. Singh, Jesse A. Davidson

Nebraska Center for Biotechnology: Faculty and Staff Publications

The intestinal microbiome is essential to human health and homeostasis, and is implicated in the pathophysiology of disease, including congenital heart disease and cardiac surgery. Improving the microbiome and reducing inflammatory metabolites may reduce systemic inflammation following cardiac surgery with cardiopulmonary bypass (CPB) to expedite recovery postoperatively. Limited research exists in this area and identifying animal models that can replicate changes in the human intestinal microbiome after CPB is necessary. We used a piglet model of CPB with two groups, CPB (n=5) and a control group with mechanical ventilation (n=7), to evaluate changes to the microbiome, …

Characterization Of Algerian Apricots (Prunus Armeniaca) Using Morphological And Pomological Markers, Kaouther Boutiti, Ines Bellil, Douadi Khelifi

Karbala International Journal of Modern Science

The aim of this study was to evaluate the diversity of an Algerian apricot germplasm. This Algerian apricot was characterized by a green-yellow skin, a red ground color, and a light orange flesh color in general. Besides, highly positive and negative significant correlations were revealed between the studied characters. Whereby, the principal component analysis explained 81% of the variability. Fruit, stone and leaves dimensions were the main features that explained evidentially the majority of variability. Moreover, the cluster analysis divided the accessions into two major groups. Thus, Algerian accessions selected in this study may have the potential to be used …

A Review Of Radiation-Induced Alterations Of Multi-Omic Profiles, Radiation Injury Biomarkers, And Countermeasures, Sushil K. Shakyawar, Nitish K. Mishra, Neetha N. Vellichirammal, Lynnette Cary, Tomáš Helikar, Robert Powers, Rebecca E. Oberley-Deegan, David B. Berkowitz, Kenneth W. Bayles, Vijay K. Singh, Chittibabu Guda

Department of Biochemistry: Faculty Publications

Increasing utilization of nuclear power enhances the risks associated with industrial accidents, occupational hazards, and the threat of nuclear terrorism. Exposure to ionizing radiation interferes with genomic stability and gene expression resulting in the disruption of normal metabolic processes in cells and organs by inducing complex biological responses. Exposure to high-dose radiation causes acute radiation syndrome, which leads to hematopoietic, gastrointestinal, cerebrovascular, and many other organ-specific injuries. Altered genomic variations, gene expression, metabolite concentrations, and microbiota profiles in blood plasma or tissue samples reflect the whole-body radiation injuries. Hence, multi-omic profiles obtained from high-resolution omics platforms offer a holistic approach …

Synthesis And Characterization Of Nanocomposites For Environmental Remediation, Nethaji S

Technical Collection

My current work deals with the preparation and characterization of nanocomposites for effluent treatment applications. The expertise lies on the preparation of carbonaceous nanocomposites including graphitic materials. The prepared materials are characterized thoroughly by different methods like FE-SEM, TEM, FT-IR, XRD, VSM, surface area and porosity. The composite materials are used for the removal of conventional and emerging contaminants like antibiotics, pesticide residues, endocrine disruptors etc. In addition to the batch studies, fabrication of microcolumns to aid the scale-up of the process is also carried out. I have published 14 research publications with around 1000 citations and h-index of 11. …

Heterodimerization Between Chemokine Receptors Cxcr4 And Ccr7 And Its Role In Cancer, Maryam Naveed Muhammad Tariq

Theses

In physiology, the functional and physical interactions between cell surface receptors for signal molecules such as hormones, neurotransmitters, and cytokines, provides an important mechanism of diversity and regulation of signal transduction. Therefore, investigating the functional interactions between these receptors is of great importance for understanding their role in physiology and pathophysiology with potential application in drug discovery. In this context, numerous evidences support the implication of two chemokine receptors, CXCR4 and CCR7, in many cancer types. In this study, we hypothesized that the functional, and perhaps the physical interaction, occurring between CXCR4 and CCR7 may constitute one of the key …

Screening For Endophytic Actinobacteria To Enhance Growth And Salinity Tolerance Of Tomato Plants In The United Arab, Amira Hamdy Hassan

Theses

Salinity is one of the most decisive environmental factors limiting the productivity of crop plants, mainly in arid and semi-arid regions. An eco-friendly technology can be used to boost crop production in saline areas by using plant growth-bacteria. Endophytic actinobacteria that produce the enzyme 1-Aminocyclopropane-1-Carboxylic acid (ACC) Deaminase (ACCD) can modulate the levels of Ethylene (ET) in plants to reduce the effect of abiotic stresses including high salt stress. The main objectives of this study were to: (1) Evaluate endophytic actinobacterial isolates from healthy tomato plants cultivated in the UAE that are capable of producing ACCD in vitro; (2) …

Effect Of Carnosol On G Protein-Coupled Receptor Signaling In Cancer Cells, Laith Jehad Ahmad Abudawood

Theses

Carnosol is a plant polyphenol compound known for its beneficial properties against human diseases such as cancer and diabetes. However, the exact molecular and cellular mechanisms involved, and its molecular targets are not fully known. Carnosol was shown to bind and to modulate specific intracellular signaling proteins in cancer cell lines. In this study, we hypothesized that carnosol may pharmacologically target specific cell surface receptors including G Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinase (RTKs). Therefore, we tested the pharmacological effect of carnosol on the following receptors: Insulin Receptor (IR), Chemokine CXCL12 Receptor (CXCR4), Angiotensin II (AngII) Receptor (AT1R), Glucagon-Like …

Using The Embl-Ebi Clustal Omega Tool To Calculate Diversity Of Heavy Chain Phage-Display Libraries, Michael Bodri, Shane A. Webb

Georgia Journal of Science

Here we show that traditional Sanger sequencing combined with analysis tools available from the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), specifically EMBOSS Transeq and Clustal Omega, is extremely effective in the analysis of naïve phage display antibody libraries for the determination of library size and diversity. The free tools are easy to use and require little manipulation of reads by hand, allowing analysis to be performed on a standard personal computer. Utilization of this technique has applicability to researchers with limited access to deep sequencing. The primary drawback to this analysis methodology is that antibodies with particular molecular or …

An Active Biodegradable Layer-By-Layer Film Based On Chitosan-Alginate-Tio2 For The Enhanced Shelf Life Of Tomatoes, Kalpani Y. Perera, Shubham Sharma, Brendan Duffy, Shiviani Pathania, Amit K. Jaiswal, Swarma Jaiswal

Articles

This work aims at developing biodegradable active chitosan-alginate layer-by-layer bio-nanocomposite film with TiO₂NPs using the solvent casting method followed by CaCl₂ crosslinking for food packaging applications. The developed films enhanced the tensile strength and elongation at break by 14.76 and 2 folds (p < 0.05) respectively. The UV barrier properties of CH-SA-0.3%TiO₂ film increased by 88.6%, while the film transparency decreased by 87.23%. All films showed antimicrobial activity against foodborne pathogens E. coli, S. aureus, S. typhi, and L. monocytogene. The film with 0.1%TiO₂ showed the complete killing of gram-positive bacteria. The CH-SA-0.1%TiO₂ film was completely biodegraded during the …

Leaf Phenology And Freeze Tolerance Of The Invasive Tree Pyrus Calleryana (Roseaceae) And Potential Native Competitors, Margaret E. Maloney, Abby Hay, Eric B. Borth, Ryan W. Mcewan

Biology Faculty Publications

Pyrus calleryana is one of the most problematic invasive species in the eastern United States. The mechanisms that enable Py. calleryana to establish and outcompete native plants are not fully understood but likely include a profile of advantageous traits. Extended leaf phenology is a characteristic noted in many woody invasive plants. Leaf phenology of Py. calleryana and two native woody species, Populus deltoides and Platanus occidentalis, was observed in natural areas near Dayton, OH from December 2019 to November 2020. A frost event in May also gave us the serendipitous opportunity to assess frost tolerance of these species. We …

Reproducibility Of Protein X-Ray Diffuse Scattering And Potential Utility For Modeling Atomic Displacement Parameters, Zhen Su, Medhanjali Dasgupta, Frédéric Poitevin, Irimpan I. Mathews, Henry Van Den Bedem, Michael E. Wall, Chun Hong Yoon, Mark A. Wilson

Department of Biochemistry: Faculty Publications

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from …

Development And Optimization Of An Immunoassay For The Detection Of Antibodies Against Sars-Cov-2 With In-House Recombinant Rbd Protein, Safira Pinaka Pramestika Ratu, Silmi Mariya, Rachmitasari Noviana, Uus Saepuloh, Huda Salahudin Darusman

Makara Journal of Science

COVID-19 caused by SARS-CoV-2 poses a major threat to the global community, particularly in Indonesia. Countermeasures to prevent the spread of this disease have also been implemented, including the implementation of a vaccination program. An immunoassay technique that can be used to analyze antibodies that might develop following vaccination is the indirect enzyme-linked immunosorbent assay (ELISA). We produced the recombinant spike protein used in this study. The optimization comprised adjusted concentrations of spike recombinant protein (5 and 10 ng/mL), blocking agent (2.5% and 5%), and conjugate (1:1000 and 1:5000). The optimal conditions in this study included a spiked concentration of …

Mutation Of Aspergillus Sp. Using Ultraviolet Light And Nitrous Acid For Amylase Production From Banana Peels, Cyprian Erumiseli Oshoma, Johnson Oche Akor, Beckley Ikhajiagbe, Marcel James Ikenebomeh

Makara Journal of Science

Strain improvement through mutagenesis is important in the commercial development of microbial fermentation. This study aimed to produce amylase from banana (Musa sapientum) peels by using mutant Aspergillus sp. strains obtained via ultraviolet (UV) radiation and nitrous acid-based mutagenesis. Results revealed that banana peels pretreated with 0.8 N HCl had a biomass yield of 3.02 g/L and amylase activity of 2.81 U/L. Of the UV mutants, strain AUV1 had the highest biomass and amylase activity of 4.50 ± 0.21 g/L and 3.46 ± 0.14 U/L, respectively. Subsequently, HNO₂ mutants showed that strain ANA6 had 30.64% and …

Editorial: Function And Formation Of Mitochondrial Metalloproteome, Michał Wasilewski, Vishal M. Gohil, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

No abstract provided.

Loss Of Num1-Mediated Cortical Dynein Anchoring Negatively Impacts Respiratory Growth, Antoineen J. White, Clare S. Harper, Erica M. Rosario, Jonathan V. Dietz, Hannah G. Addis, Jennifer L. Fox, Oleh Khalimonchuk, Laura L. Lackner

Department of Biochemistry: Faculty Publications

Num1 is a multifunctional protein that both tethers mitochondria to the plasma membrane and anchors dynein to the cell cortex during nuclear inheritance. Previous work has examined the impact loss of Num1-based mitochondrial tethering has on dynein function in Saccharomyces cerevisiae; here, we elucidate its impact on mitochondrial function. We find that like mitochondria, Num1 is regulated by changes in metabolic state, with the protein levels and cortical distribution of Num1 differing between fermentative and respiratory growth conditions. In cells lacking Num1, we observe a reproducible respiratory growth defect, suggesting a role for Num1 in not only maintaining mitochondrial …

In Silico Screening Of Violacein As An Epidermal Growth Factor Receptor Inhibitor, Smitha S Bhat, Sindhu R, Shashanka K Prasad

International Journal of Health and Allied Sciences

EGFR is a key player in the signalling cascades of various kinds of cancers and tyrosine kinase inhibitors block EGFR signalling. Natural products have long been used as candidates for therapy in the management of cancer. Violacein, a bacterial pigment, has been known for its numerous biological applications such as antimicrobial, antileishmanial, antiviral, as well as antitumoral. Computational studies have concluded that it may have activity against cancers like pancreatic cancer, thyroid cancer, colorectal cancer, and endometrial cancer indicating its potential application as a broad range of anti-cancerous drug. This study aimed to perform the molecular docking of violacein with …

Visualizing Hormonal Effects On Cardiomyocyte Hypertrophic Growth Dynamics Using Digital Holographic Microscopy: Does Size Matter?, Jacquelyn Simmons

McNair Research Journal SJSU

Heart disease continues to be the leading cause of death in the United States. Humans are unable to regenerate their heart tissue following an injury. However, neonatal mice are able to regenerate their heart tissue when cardiomyocytes (CMs) proliferate. This regenerative ability is lost approximately one week after birth when proliferating mononucleated CMs become binucleated and can no longer complete the cell-cycle. Recent studies have shown the combined inhibition of thyroid hormone (T3) and norepinephrine (NE) increases CM proliferation, promotes heart regeneration, and reduces cell size in vivo. Using digital holographic microscopy, the aim of this study was to (1) …

Examination Of The Time Delayed Induction Between Prior Encapsulation Of Catalytic Enzymes In P22 Virus-Like Particles, Andrea Hernandez Irias

Chemistry Theses

Protein cages found in nature have the ability to protect and develop new nanomaterials in order to enhance catalytic reactions. This is due to the ability of these organelle structures to mimic protein-based organelles such as Virus-Like Particles (VLPs). VLPs have the ability to not only resemble virus protein structures but to encapsulate enzymes while retaining their activity. This research examines the in vitro encapsulation withing the bacteriophage P22 derived VLP, and show that some enzymes may require a delay in encapsulation to allowed proper folding

and maturation before they can be encapsulated inside P22 as fully active enzymes. Exploring …