Biotechnology Commons^™

Vision-Based Size Estimation And Centroid Positioning Of Partially Occluded Fruits, Kyu Mya Thin Kyu, Aung Nay Zar

ASEAN Journal on Science and Technology for Development

The objective of this study was to propose a simple and efficient image processing algorithm for estimating the size and centroid of partially occluded round fruits. In the proposed method, the size and centroid of partially occluded fruit were estimated based on the mathematical properties of the arc-radius. The experimental tests were conducted in a laboratory with orange, Sunkist, apple, and tomato fruits by setting different occlusion conditions. The occlusion percentage was varied between 0% and 90%. The accuracy and processing time of the proposed method were compared with that of the widely-used conic-section circle fitting method. The results showed …

Exploration Of Local Microorganisms From Rumen And Their Potential To Make Silage From Agricultural Waste, Purnamasari Listya, Purnomo Hari, Setyawan Hidayat Bambang

ASEAN Journal on Science and Technology for Development

Agricultural wastes are very diverse in type and have low nutrient values, especially in lignin and cellulose, which are difficult to digest. One way of overcoming this problem is by biological treatment using microorganisms, also known as silage. The availability of bio-activators that are both cost-efficient and easy to make further suggests that using local microorganisms may be an effective possible solution. This study focused on processing food crop waste (corn leaves) into silage using local microorganisms as the bio-activators. Research took place in the Agrotechnology Laboratory, University of Jember. The experimental design was completely randomized with four treatments: Treatment …

Two Approaches To Measure Trace Metals Fluxes At The Sediment–Water Interface: Sediment Porewater Profile And Benthic Incubation, Harmesa, Wahyudi Johan

ASEAN Journal on Science and Technology for Development

The biogeochemical cycle of trace metals is very likely affected by the global change in the ocean, especially due to the increasing of sea surface temperature and acidity. Thus, assessing biogeochemical cycle of trace metals will beneficial in elucidating the potential impact of climate change as well as ocean acidification. The assessment of the biogeochemical cycle of trace metals can be performed by measuring trace metals fluxes crossing the sediment–water interface. The main challenge in this measurement is the difficulty of measuring metal concentrations at trace levels due to either physical factors or biological factors that can affect the total …

Spatio-Temporal Variations In Bacterial Abundance With An Emphasis On Fecal Indicator Bacteria And Vibrio Spp. In And Around Visakhapatnam Port, East Coast Of India, Khandeparker Lidita, Desai Dattesh V., Sawant Subhash Shivram, Krishnamurthy Venkat, Chandrashekar Anil Arga

ASEAN Journal on Science and Technology for Development

The ecological health of port environments, which are dynamic and hotspots of anthropogenic activities, can be analyzed using specific pathogenic bacteria as they provide definite evidence and source of pollution. The influence of seasons and environmental settings on total bacterial count (TBC), distribution of fecal indicators, and Vibrio spp. was explored in Visakhapatnam port, located along the east coast of India. South-west monsoon had a significant influence on TBC, fecal indicators, and Vibrio spp., and the abundance was influenced by the eutrophic environment in the inner harbour. Fecal indicators were one order higher in sub-surface water when compared with sediment, …

Sea Level Rise In Indonesia: The Drivers And The Combined Impacts From Land Subsidence, Triana Karlina, Wahyudi A'An Johan

ASEAN Journal on Science and Technology for Development

Sea level changes play an important role as an indicator of climate change. However, without climate change, the sea level itself shows strong regional patterns, both in space and time, that could deviate significantly from global averages. The spatial variability of sea level changes in Indonesia can be divided based on its drivers, i.e., climatic and seasonal weather-driven and non-climatic and geological-driven. Seasonally, the sea level in Indonesia is generally high in northwest monsoon and low in southeast monsoon. Nevertheless, there is a possibility of extreme natural phenomenon influences that generate anomalies and a thermosteric process that also affects the …

Establishing An Ocean Acidification Monitoring System For The Tropical Waters Of Indonesia Facing Regional Climate Variability, Prayitno Hanif Budi, Puspitasari Rachma, Jandang Suppakarn, Triana Karlina, Taufiqurrahman Edwards, Lestari, Afdal, Wulandari, Harmesa, Meirinawati Hanny, Lastrini Suci, Kaisupy Muhamad Taufik, Wahyudi A'An Johan

ASEAN Journal on Science and Technology for Development

The emission of greenhouse gases, including high CO2 and other materials, initiates global warming and climate change. Atmospheric CO2 that affects the carbonate system of seawater causes ocean acidification (OA). OA affects marine organisms directly, as well as humans economically and ecologically. Considering the high impact of OA and following the United Nations' Sustainable Development Goals, systematic research and monitoring of OA is necessary in Indonesia, whose seas play an important role in this emerging phenomenon. This review discusses the urgency of OA monitoring systems and suggests carbonate system monitoring, as well as carbon biogeochemistry. OA significantly affects marine production …

Modeling Residence Time Distribution Of Chromatographic Perfusion Resin For Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study, Kevin Vehar

KGI Theses and Dissertations

The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation's physical resource demand. Specifically, …

Bioscience: How One Industry Won The Pandemic And Will Change Us All, Sonya Swink

Capstones

A video and print capstone about the next great generation of biological sciences as a private industry since 2020. It encompasses the pandemic as the boost the industry needed, discussion of science’s bad reputation and the potential benefits, especially for new workspaces and real estate investors. Colorado is a focus as a burgeoning market. The news value of this story as a primer is how this will be both a beneficial industry and one that must be held to account if it becomes too monopolistic. Comparisons are from the viewpoint that bioscience is like the next Silicon Valley, but statements …

Single-Fluorophore Sensors For Mechanical Force In Living Cells, Sarah Kricheff

Honors Scholar Theses

Mechanotransduction is the process by which a mechanical stimulus is converted to a cellular signal. This process is heavily influential of cell morphology, differentiation, and behavior. However, altered levels of mechanical stimuli are also found in many pathological contexts. For example, cancerous cells have stiffer surrounding tissue than healthy cells, and research suggests that this alters cell behavior and promotes metastasis. Despite these findings, the cellular processes behind these signaling alterations remain widely unknown. Understanding these cascades is critical, as involved proteins can give us a deeper understanding of the role of mechanotransduction, and certain proteins can potentially be targeted …

Molecular Identification, Antioxidant Efficacy Of Phenolic Compounds, And Antimicrobial Activity Of Beta-Carotene Isolated From Fruiting Bodies Of Suillus Sp, Shimal Yonuis Abdulhadi, Raghad Nawaf Gergees, Ghazwan Qasim Hasan

Karbala International Journal of Modern Science

Suillus species, in general, are edible mushrooms, and environmentally important that are associated mostly with pine trees in the tropics regions. These fungi considered a remarkable source of phenolic compounds that play a crucial role as antioxidants which may reduce the risk of most human chronic diseases such as cancer, diabetes, asthma, atherosclerosis, Alzheimer, and others. On the other hand, carotenoids (β carotene) are the most popular natural pigments which play an important role to protect the plants from photo-oxidative reactions. In human, these compounds prevent oxidative stress and expects to have antimicrobial activity. Here, the phenolic compounds were …

Peningkatan Pertumbuhan Tunas Kunyit Putih Pada Perbanyakan In Vitro Melalui Aplikasi Berbagai Jenis Dan Konsentrasi Sitokinin, Murgayanti, Fatilla Nur Ramadhanti, Sumadi

Jurnal Kultivasi

Kunyit putih (Kaempferia rotunda L.) merupakan tanaman obat yang bermanfaat dan perlu dibudidayakan lebih luas, namun terkendala oleh penyediaan bibit bermutu yang terbatas sehingga menjadi langka. Perbanyakan tanaman dengan cara konvensional memerlukan bibit bermutu dalam jumlah dan waktu yang lama, sedangkan ketersediaan benih masih terbatas. Perbanyakan secara in vitro dapat mengatasi kelangkaan bibit kunyit putih yang bermutu tinggi dalam jumlah besar dan bebas patogen. Ketersediaan bibit unggul yang dihasilkan secara in vitro bergantung pada jenis dan konsentrasi sitokinin yang ditambahkan pada media kultur. Tujuan penelitian adalah untuk menentukan jenis dan konsentrasi sitokinin yang paling baik pengaruhnya terhadap pertumbuhan tunas kunyit …

Multiplikasi Cepat Tunas Tiga Aksesi Stevia Secara In Vitro, Suseno Amien, Dion Nugraha Aji, Tuti Mamluatul

Jurnal Kultivasi

Stevia (Stevia rebaudiana (Bertoni)) telah menjadi pelengkap untuk memenuhi kebutuhan bahan pemanis yang terus meningkat di Indonesia. Jumlah varietas unggul Stevia di Indonesia masih terbatas. Keterbatasan ini perlu diimbangi dengan metode perbanyakan yang cepat. Multiplikasi tunas merupakan salah satu metode dalam kultur jaringan yang dapat dimanfaatkan untuk perbanyakan cepat bibit Stevia. Penelitian ini bertujuan untuk memperoleh respon aksesi-aksesi stevia terhadap multiplikasi tunas stevia pada komposisi media berbeda. Penelitian telah dilaksanakan dalam dua tahap percobaan. Penelitian menggunakan Rancangan Acak Lengkap (RAL) faktorial yang masing-masing terdiri atas dua faktor. Percobaan pertama terdiri dari dua faktor. Faktor pertama adalah tiga aksesi stevia yakni …

Multiplikasi In Vitro Stroberi Kultivar Tochiotome Dengan Penambahan Jenis Dan Konsentrasi Sitokinin Untuk Perbanyakan Bibit, Ega Raisya, Denny Sobardini Sobarna, Anne Nuraini, Syariful Mubarok, Erni Suminar, Masako Akutsu

Jurnal Kultivasi

Perbanyakan tanaman stroberi secara konvensional dilakukan dengan menggunakan stolon, tetapi kurang efektif serta kualitas bibit yang dihasilkan kurang baik akibat adanya akumulasi penyakit. Budidaya stroberi memerlukan adanya perbanyakan bibit secara massal, tetapi tidak mengubah kualitasnya. Multiplikasi in vitro menjadi solusi untuk penyediaan bibit berkualitas dalam jumlah besar. Upaya untuk mendapatkan tunas in vitro dalam jumlah banyak yakni perlu adanya penambahan zat pengatur tumbuh golongan sitokinin seperti Benzylaminopurine (BAP) atau Thidiazuron (TDZ). Tujuan penelitian ini adalah mengetahui dan menetapkan jenis serta konsentrasi sitokinin dengan hasil terbaik dalam multiplikasi stroberi kultivar Tochiotome. Percobaan dilaksanakan di Laboratorium Kultur Jaringan Tanaman, Teknologi Benih, Fakultas …

Sestrins: Emerging Dynamic Stress-Sensors In Metabolic And Environmental Health, Seung Hyun Ro, Julianne Fay, Cesar I. Cyuzuzo, Yura Jang, Naeun Lee, Hyun Seob Song, Edward N. Harris

Department of Biochemistry: Faculty Publications

Proper timely management of various external and internal stresses is critical for metabolic and redox homeostasis in mammals. In particular, dysregulation of mechanistic target of rapamycin complex (mTORC) triggered from metabolic stress and accumulation of reactive oxygen species (ROS) generated from environmental and genotoxic stress are well-known culprits leading to chronic metabolic disease conditions in humans. Sestrins are one of the metabolic and environmental stress-responsive groups of proteins, which solely have the ability to regulate both mTORC activity and ROS levels in cells, tissues and organs. While Sestrins are originally reported as one of several p53 target genes, recent studies …

Carbon Dots As Artificial Peroxidases For Analytical Applications, Shih-Chun Wei, Yang-Wei Lin, Huan-Tsung Chang

Journal of Food and Drug Analysis

Nanozymes have become attractive in analytical and biomedical fields, mainly because of their low cost, long shelf life, and less environmental sensitivity. Particularly, nanozymes formed from nanomaterials having high surface area and rich active sites are interesting since their activities can be tuned through carefully controlling their size, morphology, and surface properties. This review article focuses on preparation of carbon dots (C dots) possessing peroxidase-like activity and their analytical applications. We highlight the important roles of the oxidation states and surface residues of C dots and their nanocomposites with metal, metal oxides, or metal sulfides playing on determining their specificity …

Environmental Hygiene For Covid-19: It's All About The Mask, Daniel B. Oerther, Mona Shattell

Civil, Architectural and Environmental Engineering Faculty Research & Creative Works

No abstract provided.

Does The Presence Of Multiple Β-Lactamases In Gram-Negative Bacilli Impact The Results Of Antimicrobial Susceptibility Tests And Extended-Spectrum Β-Lactamase And Carbapenemase Confirmation Methods?, Fred C. Tenover, Caitlin M. Dela Cruz, Scott Dewell, Victoria M. Le, Isabella A. Tickler

Biology Faculty Publications

Objectives: Many multidrug-resistant Gram-negative bacilli (MDR-GNB) harbour multiple β-lactamases. The aim of this study was to assess the impact of multiple β-lactamase carriage on the accuracy of susceptibility tests and extended-spectrum β-lactamase (ESBL) and carbapenemase confirmation methods.

Methods: A total of 50 MDR-GNB, of which 29 carried multiple β-lactamases, underwent broth microdilution (BMD) and disk diffusion (DD) testing as well as confirmation tests for ESBLs and carbapenemases. Whole-genome sequencing (WGS) was used for β-lactamase gene identification.

Results: Categorical agreement of BMD and DD testing results ranged from 86.5 to 97.7% for 10 β-lactam agents. BMD and DD algorithms for ESBL …

Assessment Of The Potential Anti-Tumour Effect Of Salvia Triloba And The Combination Of Salvia Triloba And Paclitaxel On Ovarian Cancer: Skov3 Cell Line, Naela Adel Mohammed

Archived Theses and Dissertations

No abstract provided.

Ionic Mechanism Of Lysosomal Function And Cell Metabolism, Jian Xiong

Dissertations and Theses (Open Access)

Two Pore Channels (TPCs) are endolysosomal ion channels that are permeable to sodium and calcium. Defects in TPCs have been implicated to impair vesicle trafficking, autophagy and cell metabolism control; however, the detailed mechanism remains largely unknown. In this study, I show that TPCs are critical for appropriate cargo delivery to the lysosomes and deletion of either TPC1 or TPC2 leads to delayed clearance of autophagosomes, resulting in enlarged lysosomes and accumulated contents inside the lysosomes. Cells with both TPC deleted also exhibit 50% reduction in lysosomal amino acids under normal culture conditions, leading to reduced homeostatic mTORC1 activation.

Glutamine …

Editorial: Structure And Function Of Chloroplasts - Volume Ii, Yan Lu, Lu Ning Liu, Rebecca L. Roston, Jurgen Soll, Hongbo Gao

Department of Biochemistry: Faculty Publications

No abstract provided.

Evaluation Of The Xpert Carba-R Nxg Assay For Detection Of Carbapenemase Genes In A Global Challenge Set Of Pseudomonas Aeruginosa Isolates, Fred C. Tenover, Christian M. Gill, Tomefa E. Asempa, Isabella A. Tickler, Caitlin M. Dela Cruz, David P. Nicolau

Biology Faculty Publications

The growing prevalence and diversity of carbapenemase producers among carbapenem-resistant Pseudomonas aeruginosa (CRPA) isolates warrants an expansion of detection capabilities. The purpose of this study was to evaluate the performance of the commercially available Xpert Carba-R (Carba-R) and the research-use-only Xpert Carba-R NxG (Carba-R NxG) in a global collection of P. aeruginosa. The challenge set included 123 P. aeruginosa clinical isolates from 12 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP)-harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and …

A Co-Opted Steroid Synthesis Gene, Maintained In Sorghum But Not Maize, Is Associated With A Divergence In Leaf Wax Chemistry, Lucas Busta, Elizabeth Schmitz, Dylan K. Kosma, James C. Schnable, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Virtually all land plants are coated in a cuticle, a waxy polyester that prevents nonstomatal water loss and is important for heat and drought tolerance. Here, we describe a likely genetic basis for a divergence in cuticular wax chemistry between Sorghum bicolor, a drought tolerant crop widely cultivated in hot climates, and its close relative Zea mays (maize). Combining chemical analyses, heterologous expression, and comparative genomics, we reveal that: 1) sorghum and maize leaf waxes are similar at the juvenile stage but, after the juvenile-to-adult transition, sorghum leaf waxes are rich in triterpenoids that are absent from maize; 2) biosynthesis …

Antibacterial Activity Of Selected Plant Extracts On Methicillin Resistant Staphylococcus Aureus, Lubna Abdallah

Journal of the Arab American University مجلة الجامعة العربية الامريكية للبحوث

Based on the importance of herbal plants in medicine, this study was conducted to evaluate the antibacterial efficacy of aqueous, ethanol and methanol extracts of Thymbra spicata, Nepeta curviflora, and Verbascum fruticulosum against two clinical isolates (I and II) of the gram positive methicillin resistant Staphylococcus aureus (MRSA). Agar well diffusion method was performed to examine the antibacterial activity of all studied plant extracts. Micro-broth dilution method was used to measure the minimum inhibitory concentration (MIC) then the minimum bacteriocidal concentration (MBC) for all active extracts. The examined isolates were susceptible to the prepared plant extracts. Ethanol and methanol extracts …

Prevalence Of Brca1 And Brca2 Mutations Among Breast And Ovarian Cancer Patients In Northern Emirates, Zahra Ahmed Mohammed Saeed

Theses

Breast Cancer (BC) is the most common cancer and the second most cause of death among women. Mutations in BRCA1 and BRCA2 genes confer high susceptibility to both breast and ovarian cancer. However, data on the prevalence of the BRCA1/2 mutations among breast and ovarian cancer patients is limited. The genetic component of breast cancer in the UAE is largely unknown and no study has evaluated the BRCA mutations status in breast and ovarian cancer patients in the UAE population. This retrospective study aimed to establish mutation frequencies of the BRCA genes in breast and ovarian cancer patients from the …

In Vitro Invistigation Of The Heterodimerization Between Angiotensin Ii And Thrombin Receptors, Isra Mansur Al Zamel

Biology Theses

The renin angiotensin system (RAS) through its hormone angiotensin (AngII) and the protease thrombin are two major physiological regulators of vascular and renal functions. RAS is involved in the regulation of blood pressure and water-electrolytes hemostasis, while thrombin has a crucial role in platelets activation and thrombosis. The interplay between these two systems at the physiological and the pathophysiological levels has been documented in many studies. However, such an interplay at the pharmacological level between the AngII and thrombin receptors still has not been explored. Our study aimed to explore the interplay between the AngII type 1 receptor (AT1R) and …

Molecular And Physiological Assessment Of Salinity Stress Tolerance In Transgenic Arabidopsis Lines Expressing A Solanum Tuberosum Ribosome-Binding Protein, Onoud Rashed Saeed Ali Alyammahi

Biology Theses

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily associated with translation of mRNA leading to protein synthesis. Additionally, some of these proteins are known to play critical role in plants RNA metabolism during stress responses, growth, and development. In this study, transgenic Arabidopsis plants expressing a ribosomal protein S27 (hereafter D26) isolated from Solanum tuberosum was subjected to NaCl-induced salinity stress conditions, to evaluate their putative stress resistance. Transgenic plants were exposed to high salinity stress, induced by 200 mM NaCl and physiological and biochemical assays were performed. The D26 transgenic plants demonstrated improved plant height and …

Identification Of Inherited And De Novo Exomic Variations In An Emirati Family With Neurodevelopmental Disorders, Asmaa Samir Muhammed Abdelaziz Refaey

Biology Theses

Neurodevelopmental disorders (NDDs) are a heterogenous group of disorders that affect children at any point of development and lead to mental and motor function deficits. Often, the underlying cause could be genetic and inherited. This study investigated possible genetic variations that could have led to these neurological abnormalities and other genetic disorders in an Emirati family. Whole exome sequencing (WES) was used to sequence the protein-coding regions of the genome to identify potential de novo and inherited variants that are associated with disorders in this family.

WES of DNA from the parents and ten children were performed. Several variants were …

Antibacterial Action Of Graphene Oxide Towards Bacteria And Its Toxicological Effects On Human Epidermal Keratinocytes, Thiruchelvi Pulingam

Student Works (2020-2029)

The antibacterial nature of graphene oxide (GO) has stimulated wide interest in the medical field. Although the antibacterial activity of GO towards bacteria has been well studied, a deeper understanding of the mechanism of action of GO is still lacking. The objectives of the study were to characterize the physicochemical properties of GO, to determine the antibacterial and antibiofilm activity and the mechanistic action of GO against Gram-positive Staphylococcus aureus and Enterococcus faecalis and Gram-negative Escherichia coli and Pseudomonas aeruginosa, to determine the synergistic behaviour of GO with selected antibiotics against bacterial cells in suspension and biofilm and to determine …

Curie Temperature Engineering In A Novel 2d Analog Of Iron Ore (Hematene) Via Strain, Renu Singla, Timothy A. Hackett, Sarvesh Kumar, Jyotsna Sharma, Manish K. Kashyap

Department of Biochemistry: Faculty Publications

As a newly exfoliated magnetic 2D material from hematite, hematene is the most far-reaching ultrathin magnetic indirect bandgap semiconductor. We have carried out a detailed structural analysis of hematene via prefacing strain by means of first-principles calculations based on density functional theory (DFT). Hematene in the pristine form emerges out to be a magnetic semiconductor with a bandgap of 1.0/2.0 eV for the majority/minority spin channel. The dependence of magnetic anisotropy energy (MAE), T_C, and the bandgap on compressive and tensile strains has been scanned exclusively. It is examined that T_C depends firmly on the compressive strain …

A Review Of Integrative Imputation For Multi-Omics Datasets, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Hui Shen, Ping Gong, Chaoyang Zhang, Hong Wen Deng

Michigan Tech Publications, Part 1

Multi-omics studies, which explore the interactions between multiple types of biological factors, have significant advantages over single-omics analysis for their ability to provide a more holistic view of biological processes, uncover the causal and functional mechanisms for complex diseases, and facilitate new discoveries in precision medicine. However, omics datasets often contain missing values, and in multi-omics study designs it is common for individuals to be represented for some omics layers but not all. Since most statistical analyses cannot be applied directly to the incomplete datasets, imputation is typically performed to infer the missing values. Integrative imputation techniques which make use …