Biotechnology Commons^™

Black Soldier Fly (Hermetia Illucens) As A Potential Agent Of Organic Waste Bioconversion, Purnamasari Listya, Khasanah Himmatul

ASEAN Journal on Science and Technology for Development

The use of black soldier fly (BSF) as a bioconversion agent has become an emerging breakthrough in waste processing. Organic wastes, such as household waste and livestock manure, can be used as a growth medium for BSF larvae and converted into favorable products. The average composting time of BSF larvae is around 12– 15 days, which is faster than that of microbes or earthworms (4–5 weeks). BSF shows potential as a feed and food ingredient because it has a high nutritional content, such as enzyme, chitin, medium-chain fatty acid, and antimicrobial peptides, and can be used as a functional food …

Defect And Distortion In Powder Bed Fusion Of Metal Additive Manufacturing Parts, Maurya Ajay Kumar, Kumar Amit

ASEAN Journal on Science and Technology for Development

One of the state-of-the-art technologies for metal fabrication is laser powder bed fusion, which includes the following printing techniques: selective laser melting, selective laser sintering, direct metal laser sintering, and electron beam melting. This work examines defect formation in laser powder bed fusion, predominately focusing on selective laser melting. It also explores recent research findings on defect formation and classification and analyzes various internal defects, such as porosity, lack of fusion, balling, and solidification cracking. The influence of process parameters on defect formation and the effect of defects on mechanical properties are analyzed. This review also discusses defect inspection technologies …

Ncoa4 Regulates Iron Recycling And Responds To Hepcidin Activity And Lipopolysaccharide In Macrophages, Cole A. Guggisberg, Juyoung Kim, Jaekwon Lee, Xiaoli Chen, Moon-Suhn Ryu

Department of Biochemistry: Faculty Publications

Macrophages, via erythrophagocytosis, recycle iron from effete erythrocytes to newly developing red blood cells. Conversion of potentially cytotoxic levels of iron from its heme into nonheme form during iron recycling is safely accomplished via coordinated regulations of cellular iron transport and homeostasis. Herein, we demonstrate the roles and regulation of NCOA4 (nuclear receptor coactivator 4)-mediated ferritinophagy in macrophages after erythrophagocytosis using the mouse macrophage cell line J774 cells. Ferritin in J774 cells increased with the rise of nonheme iron by erythrocyte ingestion and declined when total cellular iron contents subsequently decreased. NCOA4, a selective autophagic cargo receptor for ferritin, was …

Mechanisms Of Carbapenemase-Mediated Resistance Among High-Risk Pseudomonas Aeruginosa Lineages In Peru, Isabella A. Tickler, Juan Carlos Gomez De La Torre, Luis Alvarado, Anne E. Obradovich, Fred C. Tenover

Biology Faculty Publications

Objectives: Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru.

Methods: A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes.

Results: wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed …

Editorial: Mitochondria, Metabolism And Cardiovascular Diseases, Jun-Ichiro Koga, Xinghui Sun, Masuko Ushio-Fukai

Department of Biochemistry: Faculty Publications

No abstract provided.

Analysis Effect Of Shade Level On The Physiological And Anatomical Characteristics Of Hybrid Phalaenopsis Orchid At The Acclimatization Stage, Ade Arisma Fauziah, Nintya Setiari, Endang Saptiningsih

Jurnal Kultivasi

Production of hybrid Phalaenopsis seedlings is generally applied by in vitro culture techniques. The final stage of in vitro culture is acclimatization. The acclimatization stage is crucial because the plantlets must adapt to the ex-vitro environment. Shade supports plantlet growth during the early stages of acclimatization. This study aims to determine the effect of shade level on the physiological and anatomical characteristics of the Phalaenopsis hybrid orchid at the acclimatization stage. The research used Phalaenopsis plantlet hybrid and shading level. Plantlets were shaded at 40%, 55%, and 70%. Parameters measured included: photosynthetic pigment content, number and area of leaves, number …

Effect Of Paclobutrazol On Growth And Root Morphology Of 12 Crossed Stevia In Vitro, Suseno Amien, Qurrota Aini, Noladhi Wicaksana

Jurnal Kultivasi

Stevia (Stevia rebaudiana Bertoni) is a low-calorie alternative sweetener. The superior varieties of Stevia in Indonesia are limited. Availability of seeds plays an important role in the Stevia plant breeding program for both the selection stage and the production of high-yielding varieties. Tissue culture is the best method of Stevia propagation, but the low adaptability of plantlets causes death in the acclimatization phase. The growth and root morphology of 12 crossbreed Stevia were evaluated. A Completely Randomized Design was used with factorial consisting of two factors were Stevia genotypes (STG1,7,8,10, SBG3,4,5,7,10, SGB2,3, and SBT11) and the plant growth regulator (PGR) …

Deep Learning Prediction Of Chemical-Induced Dose-Dependent And Context-Specific Multiplex Phenotype Responses And Its Application To Personalized Alzheimer’S Disease Drug Repurposing, You Wu, Qiao Liu, Yue Qiu, Lei Xie

Publications and Research

Predictive modeling of drug-induced gene expressions is a powerful tool for phenotype-based compound screening and drug repurposing. State-of-the-art machine learning methods use a small number of fixed cell lines as a surrogate for predicting actual expressions in a new cell type or tissue, although it is well known that drug responses depend on a cellular context. Thus, the existing approach has limitations when applied to personalized medicine, especially for many understudied diseases whose molecular profiles are dramatically different from those characterized in the training data. Besides the gene expression, dose-depen- dent cell viability is another important phenotype readout and is …

Pengaruh Konsentrasi Benzylaminopurine Terhadap Pertumbuhan Eksplan Tunas Aksilar Rami Klon Lokal Wonosobo Secara In Vitro, Anne Nuraini, Eva Aprilia, Murgayanti, Asri Peni Wulandari

Jurnal Kultivasi

Saat ini, perbanyakan rami menggunakan rizoma sebagai bahan tanamnya, tetapi dalam produksinya membutuhkan waktu yang lama dan sebagai bahan tanam umur simpannya singkat. Kultur jaringan merupakan salah satu teknologi untuk mendapatkan bahan tanam yang seragam dan sehat dalam waktu yang singkat. Tujuan dilakukannya penelitian ini adalah untuk mengetahui pengaruh konsentrasi BAP terhadap pertumbuhan tunas aksilar pada rami klon lokal Wonosobo dan konsentrasi mana yang memberikan pengaruh terbaik. Percobaan dilakukan di Laboratorium Kultur Jaringan, Teknologi Benih, Fakultas Pertanian, Universitas Padjadjaran. Nodus batang dari rami klon lokal Wonosobo diklturkan pada media MS dengan penambahan berbagai konsentrasi BAP selama 8 minggu dan diamati …

Efektifitas Perbedaan Konsentrasi Bap Terhadap Pertumbuhan Planlet Pisang Cavendish Dengan Teknik Thin Cells Layer, Hidayati Karamina, Edyson Indawan, Fila Isti Kumala Agustina

Jurnal Kultivasi

Pisang murupakan komoditi dengan produksi paling tinggi di antara buah-buahan lainnya. Salah satu pisang yang diminati ialah Pisang Cavendish (Musa acuminata L.), namun pembibitan secara konvensional kurang memenuhi permintaan pasar. Salah satu alternatif untuk meningkatkan jumlah bibit pisang Cavendish adalah dengan perbanyakan tanaman secara in vitro. Teknik thin cell layer (TCL) merupakan teknik dalam kultur jaringan dengan mengiris tipis bagian tanaman yang dapat memperbanyak jumlah tunas planlet pisang Cavendish. Penelitian ini bertujuan untuk mengetahui konsentrasi BAP yang cocok untuk pertumbuhan planlet pisang Cavendish dengan menggunakan teknik TCL. Penelitian ini menggunakan rancangan acak lengkap (RAL) dengan 5 perlakuan dan 5 ulangan. …

Perturbation Modeling For Molecular Design Of Protein Tyrosine Kinase Inhibitors Using Unsupervised Machine Learning, Keerthi Krishnan

Computational and Data Sciences (MS) Theses

The field of computational drug discovery and development has grown, with the aid of new computational tools for novel molecule discovery. In specific, generative deep learning models have excelled as tools to aid in navigating the large space of known molecules and in the creation of new molecules. These models are fed various representations of molecules as inputs and learn to perform a variety of things, such as the optimization of these molecules towards a targeted property. Ultimately, these generative learning models allow us to build bridges between chemical and continuous spaces to understand the compromise between invoking small incremental …

Metabolite Damage And Damage Control In A Minimal Genome, Drago Haas, Antje M. Thamm, Jiayi Sun, Lili Huang, Lijie Sun, Guillaume A.W. Beaudoin, Kim S. Wise, Claudia Lerma-Ortiz, Steven D. Bruner, Marian Breuer, Zaida Luthey-Schulten, Jiusheng Lin, Mark A. Wilson, Greg Brown, Alexander F. Yakunin, Inna Kurilyak, Jacob Folz, Oliver Fiehn, John I. Glass, Andrew D. Hanson, Christopher S. Henry, Valérie De Crécy-Lagard

Department of Biochemistry: Faculty Publications

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and …

Tau-Dependent Neurodegeneration And Alleviation By Etas®50, Clifford Tyree Castleberry

Theses (2016-Present)

Brain growth factors are a broad group of molecules that enable the brain to adapt to stress. In a study on Alzheimer’s mice (APP), we tested the role of an asparagus supplement, ETAS®50, to mitigate the stress caused by the Alzheimer’s condition in this mouse model. Gene expression data revealed regulation of genes related to neuronal growth and function, such as tau, which were severely stressed in the APP mice to be alleviated.

Radioluminescence Based Biochemical Sensing And Imaging Strategies To Measure Local Drug Release And Ph, Gretchen B. Schober

All Dissertations

In this dissertation we describe methods for measuring infection relevant biochemical analytes using radioluminescent and ultrasound luminescent materials. Films and nanoparticles fabricated with europium doped gadolinium oxysulfide (Gd₂O₂S:Eu³⁺) are used to quantitatively measure radiolabeled pharmaceutical concentration, specifically tritium labeled vancomycin (³H-vancomycin). Europium and dysprosium doped strontium aluminate is used to fabricate an ultrasound modulated, pH sensing film. These methods are indicated for theranostic evaluation of implant associated infection. Bacterial biofilms are inherently resistant to traditional antibiotic treatment and can coat biomedical implants. These biofilm related infections are difficult or impossible to eradicate …

Identifying A Glucocorticoid-Activated Gpcr That Rapidly And Non-Genomically Increases Camp Levels In Mammalian Cells, Francisco Nunez

Pharmaceutical Sciences (PhD) Dissertations

Glucocorticoids (GCs) are steroid hormones that regulate diverse physiological processes. Synthetic versions of GCs are commonly used to treat inflammatory diseases such as asthma by modulating gene expression to suppressing several inflammatory activities. However, it is estimated that 5-10% of asthmatics are unresponsive to GCs, which may be explained by receptor desensitization and/or the presence of a neutrophilic endotype. One understudied phenomenon of GCs is their ability to induce rapid, non-genomic actions. For example, GCs can acutely modulate calcium concentrations levels, induce smooth muscle relaxation and modulate nitric oxide synthase activity, within minutes and sometimes seconds, which is too rapid …

Spatial Charting Of Single-Cell Transcriptomes In Tissues, Runmin Wei, Siyuan He, Shanshan Bai, Emi Sei, Min Hu, Ken Chen, Nicholas E Navin

Faculty, Staff and Student Publications

Single-cell RNA sequencing methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile spatial regions in tissue sections, but do not have single-cell resolution. Here, we developed a computational method called CellTrek that combines these two datasets to achieve single-cell spatial mapping through coembedding and metric learning approaches. We benchmarked CellTrek using simulation and in situ hybridization datasets, which demonstrated its accuracy and robustness. We then applied CellTrek to existing mouse brain and kidney datasets and showed that CellTrek can detect topological patterns of different cell types and cell states. We …

Application In Medicine: Has Artificial Intelligence Stood The Test Of Time, Mir Ibrahim Sajid, Shaheer Ahmed, Usama Waqar, Javeria Tariq, Mohsin Chundrigar, Samira Shabbir Balouch, Sajid Abaidullah

Medical College Documents

Artificial intelligence (AI) has proven time and time again to be a game-changer innovation in every walk of life, including medicine. Introduced by Dr. Gunn in 1976 to accurately diagnose acute abdominal pain and list potential differentials, AI has since come a long way. In particular, AI has been aiding in radiological diagnoses with good sensitivity and specificity by using machine learning algorithms. With the coronavirus disease 2019 pandemic, AI has proven to be more than just a tool to facilitate healthcare workers in decision making and limiting physician-patient contact during the pandemic. It has guided governments and key policymakers …

Performance Of Machine Learning Classifiers In Classifying Stunting Among Under-Five Children In Zambia, Obvious Nchimunya Chilyabanyama, Roma Chilengi, Roma Chilengi, Michelo Simuyandi, Caroline C. Chisenga, Masuzyo Chirwa, Kalongo Hamusonde, Rakesh Kumar Saroj, Najeeha Talat Iqbal, Innocent Ngaruye

Department of Paediatrics and Child Health

Stunting is a global public health issue. We sought to train and evaluate machine learning (ML) classification algorithms on the Zambia Demographic Health Survey (ZDHS) dataset to predict stunting among children under the age of five in Zambia. We applied Logistic regression (LR), Random Forest (RF), SV classification (SVC), XG Boost (XgB) and Naïve Bayes (NB) algorithms to predict the probability of stunting among children under five years of age, on the 2018 ZDHS dataset. We calibrated predicted probabilities and plotted the calibration curves to compare model performance. We computed accuracy, recall, precision and F1 for each machine learning algorithm. …

Cellular Mechanisms Underlying State-Dependent Neural Inhibition With Magnetic Stimulation, Hui Ye, Vincent Chiun-Fan Chen, Jenna Hendee

Engineering Science Faculty Publications

Novel stimulation protocols for neuromodulation with magnetic fields are explored in clinical and laboratory settings. Recent evidence suggests that the activation state of the nervous system plays a significant role in the outcome of magnetic stimulation, but the underlying cellular and molecular mechanisms of state-dependency have not been completely investigated. We recently reported that high frequency magnetic stimulation could inhibit neural activity when the neuron was in a low active state. In this paper, we investigate state-dependent neural modulation by applying a magnetic field to single neurons, using the novel micro-coil technology. High frequency magnetic stimulation suppressed single neuron activity …

Methanogen Metabolic Flexibility, Sean R. Carr

School of Biological Sciences: Dissertations, Theses, and Student Research

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest are …