Bioinformatics Commons^™

Attack Of The Clones: Elucidating The Role Of Clonality In The Invasion Success Of Carpobrotus Edulis, Eduardo Luis Cruz

Electronic Theses, Projects, and Dissertations

Transcriptomics is a modern technique in genomics that utilizes RNA sequences to get a snapshot of genetic expression. This is a powerful tool in non-model species lacking a reference genome. Thus, the application of comparative transcriptomics has the potential to help us elucidate the evolutionary mechanisms that facilitate species invasion. Carpobrotus edulis is a prolific and widespread invasive succulent plant belonging to the Aizoaceae family. A native to South Africa, this species has become a dominant invader of many Mediterranean coastal areas. In this study, we leveraged the use of RNAseq to investigate evolutionary changes among invasive populations. RNA-seq data …

Selection Pressure On Surface Exposed Virus Proteins, Sareh Bagherichimeh

Electronic Thesis and Dissertation Repository

Viral infection requires the interaction between virus surface-exposed (SE) proteins and host cell receptors. This can result in an “arms race” that is assumed to drive accelerated rates of evolution, and some well known examples of diversifying selection involve surface pro- teins (HIV-1 env, influenza hemagglutinin). We conducted a systematic analysis to determine whether this is truly a distinctive feature of SE virus proteins, in comparison to non-SE proteins encoded by the same genomes.

We obtained reference and all neighbour genomes of 52 human viruses from the NCBI Viral Genomes database. The coding sequences (CDS) of each genome extracted by …

Detecting Bacterial Species From Ancient Human Skeletal Samples, Ariel Owens, Daisy Mcgrath, Tsai-Tien Tseng

Symposium of Student Scholars

Diagnosis of tuberculosis (TB) via morphological analysis is difficult and often inconsistent. With next-generation sequencing (NGS), ancient host microbiomes can be subjected to metagenomic analyses for the detection of TB in silico. Suitable bioinformatic workflows are needed for reliable ancient DNA (aDNA) analysis of causative agents. This study aims to enhance available bioinformatic screening methods to create more suitable bioinformatic processes and generate insights in relation to TB.

This research utilizes publicly available NGS data accessed through the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Initial quality control steps included adapter trimming with Trim …

Designing And Synthesizing A Warhead-Fragment Inhibitory Ligand For Ivyp1 Through Fragment-Based Drug Discovery, Samuel Moore

Symposium of Student Scholars

Fragment-based drug discovery (FBDD) is a powerful tool for developing anticancer and antimicrobial agents. Within this, magnetic resonance spectroscopy (NMR) provides a comprehensive qualitative and quantitative approach to screening and validating weak and robust binders with targeted proteins, making NMR among the most attractive strategies in FBDD. Inhibitor of vertebrate lysozyme (Ivyp1) of P. aeruginosa serves as an excellent target because of its active cellular location and implications in clinical prognosis for cystic fibrosis and immunocompromised patients. This study uses current NMR and biophysical techniques to develop a covalent, fragment-linked warhead inhibitor for Ivyp1 through synthetic methods, warhead linking, and …

A Machine Learning Approach For Predicting Patient Mortality With Heart Rate Variability Statistics, Matthew Thiele, Dario Ghersi

Theses/Capstones/Creative Projects

The prediction of patient mortality in the healthcare system provides a metric by which hospitals can better manage patient care and assess the needs of each individual patient. As such, the development of better predictive methods is vital for improving patient outcomes and overall quality of care. Heart rate variability (HRV) is a measure of the heart’s complex beating patterns, giving medical professionals additional insight into patient health. Previous research has demonstrated the potential use of heart rate variability as a metric for patient mortality prediction for various conditions, however more work is necessary to validate HRV as a metric …

Identification Of The Type Eleven Secretion System (T11ss) And Characterization Of T11ss-Dependent Effector Proteins, Alex S. Grossman

Doctoral Dissertations

Host-associated microbes live in dangerous environments as a result of host immune killing, nutrient provisioning, and physiological conditions. Bacteria have evolved a host of surface and secreted proteins to help interact with this host environment and overcome nutrient limitation. The studies included within this dissertation describe the identification of a novel bacterial secretion system which has evolved to transport these symbiosis mediating proteins. This system, termed the type eleven secretion system (T11SS), is present throughout the Gram negative phylum Proteobacteria, including many human pathogens such as Neisseria meningitidis, Acinetobacter baumanii, Haemophilus haemolyticus, and Proteus vulgaris. Furthermore, …

Model-Free Identification Of Relevant Variables From Response Data, Alan Veliz-Cuba, David Murrugarra

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Characterization Of The Poly (Adp-Ribose) Polymerase Family In The Fusarium Oxysporum Species Complex, Daniel Norment

Masters Theses

Fusarium oxysporum is a filamentous fungus that is known to invade over a hundred different hosts and poses a major threat to the economy and food supply world-wide. Poly (Adenosine diphosphate-Ribose) Polymerase (PARP) is a family of regulatory proteins that affect change in the cell through transfer of ADP-Ribose moieties onto target molecules. The most well-studied PARP protein is the human PARP1, a PARylating nuclear protein that serves as our model PARP protein. F. oxysporum was found to contain a large expansion of PARP catalytic-domain-containing proteins compared to other filamentous fungi. We utilized in silico multiple sequence alignments and domain …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

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 …

Radiation Exposure Determination In A Secure, Cloud-Based Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …

Ngly1 Deficiency Affects Glycosaminoglycan Biosynthesis And Wnt Signaling Pathway In Mice, Amy Batten

PANDION: The Osprey Journal of Research and Ideas

Individuals affected by NGLY1 Deficiency cannot properly deglycosylate and recycle certain proteins. Even though less than 100 people worldwide have been diagnosed with this rare autosomal recessive condition, thousands are affected by similar glycosylation disorders. Common phenotypic manifestations of NGLY1 Deficiency include severe neural and intellectual delay, impaired muscle and liver function, and seizures that may become intractable. Very little is currently known about the various mechanisms through which NGLY1 deficiency affects the body and this has led to a lack of viable treatment options for those afflicted. This experiment uses a loss-of-function (LOF) mouse model of NGLY1 Deficiency homologous …

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 …

In Silico Evaluation Of The Antimalarial Potential Of The Phytoconstituents Of The Azadirachta Indica Plant, Areh E.T., Atolani O., Kambizi L

Al-Bahir Journal for Engineering and Pure Sciences

Background and Objectives: Malaria, a parasitic protozoan disease caused primarily by Plasmodium falciparum, has killed millions of people in Africa, particularly those with meager or no access to orthodox medical facilities and therapies. Extracts from the Azadirachta indica (neem) plant is believed to possess antimalaria properties among the locals that rely on herbs. Numerous in - vivo studies have suggested the antimalarial properties of neem extract and phytochemicals. This study employs an in - silico method through molecular docking techniques to provide insight while adding credence to the antimalarial potential of phytochemicals of neem plants as claimed …

Preliminary Study Of Structural Changes Of Glucose-6-Phosphate Dehydrogenase Deficiency Variants, Naveen Eugene Louis, Muaawia Ahmed Hamza, Puteri Nur Sarah Diana Engku Baharuddin, Shamini Chandran, Nurriza Ab Latif, Mona Awad Alonazi, Khairul Bariyyah Abd Halim, Arjumand Warsy, Syazwani Itri Amran

BioMedicine

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency disorder affecting over 400 million individuals worldwide. G6PD protects red blood cells (RBC) from the harmful effects of oxidative substances. There are more than 400 G6PD mutations, of which 186 variants have shown to be linked to G6PD deficiency by decreasing the activity or stability of the enzyme. Different variants manifest different clinical phenotypes which complicate comprehending the mechanism of the disease. In order to carry out computational approaches to elucidate the structural changes of different G6PD variants that are common to the Asian population, a complete G6PD monomer-ligand complex …

Pharmacophore-Based Virtual Screening From Indonesian Herbal Database To Find Putative Selective Estrogen Receptor Degraders, Aisyah F. Prawiningrum, Rafika Indah Paramita, Linda Erlina

Indonesian Journal of Medical Chemistry and Bioinformatics

Most breast cancer cases are luminal subtypes which are estrogen receptor-sensitive or progesterone receptor-sensitive. Common treatments include surgery and adjuvant endocrine therapy by prescribing selective estrogen receptor degraders (SERD). SERD is a type of medication that inhibits estrogen receptor (ER) activity by degrading it, and as a result, downregulating it. The current FDA-approved SERD can only be administered through intramuscular injection. The aim of this study is to find orally non-toxic and bioavailable herbal alternatives of SERDs in Indonesian Herbal Database by doing virtual screening using LigandScout. The hit compounds were further analyzed using a molecular docking tool, AutoDock. Three …

Analysis And Visualization Of Molecular Docking 2hi4 Protein, Innas Widiasti

Indonesian Journal of Medical Chemistry and Bioinformatics

The crystal structure of the human microsomal complex P450 1A2 with alpha-naphthoflavone, a cytochrome P450 (CYP) enzyme is particularly important, as it is abundant in the human liver and alters a more diverse xenobiotic array than any other group of metabolic enzymes. CYP1A2 is abundantly found in the liver and involved in the metabolism of about 10% of clinically used drugs metabolized by CYP enzymes. The current drug discovery and development mostly uses high-throughput screening (HTS). However, this regular method is time-consuming and costly. To address the issue, an advanced drug discovery and development method namely chemical compound database screening …

Molecular Docking Of Vitamin D3 Receptor (Vdr) With Potential Herbal Substance As Ligand To Prevent Excessive Hair Loss In Menopausal Women, Aditya Parawangsa, Syailendra Karuna Sugito, Ariestiana Ayu Ananda Latifa, Nadya Dinda Safira, Shafa Ayuthaya, Raissa Rahmalia Az Zahra

Indonesian Journal of Medical Chemistry and Bioinformatics

Hair loss is commonly found in menopausal women. Hair loss is one of the consequences of hormonal dynamics when a woman stops having menstrual cycle, which affect calcium and vitamin D level in the body. Although it is clear enough that hormonal adjustment is required, older people and another sociodemographic factor prefer herbal-based therapeutic rather than synthetic-based due to tradition and positive experience factors. This study is an in-silico study which aims to point out the possible ligand candidates that can work as Vitamin D Receptor (VDR) agonists. We perform molecular docking using Autodock version 4.2 with the criteria of …

Capturing Within Host Hiv-1 Evolution Dynamics Using Simulation Methods, Emmanuel Wong

Electronic Thesis and Dissertation Repository

The persistent latent reservoir of long-lived cells carrying integrated HIV DNA is the source of reinfection upon treatment interruption, and a primary focus for cure research. The reservoir is difficult to study because these cells are relatively rare or located in tissues that are difficult to sample. Sequencing proviral DNA in the latent reservoir is an important source of information about reservoir establishment and persistence, especially from the presence of identical (clonal) sequences. I evaluated the relationship between select measures of these clonal sequences and drivers of reservoir persistence, e.g., clonal expansion, by implementing a simulation model of within-host HIV …

Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris

Electronic Thesis and Dissertation Repository

Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.

Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …