Bioinformatics Commons^™

From Formulas To Futures: Mathematical Insights Into Endosomal Escape, Fnu Nisha

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

An Insight Into The Physicochemical, Drug-Likeness, Pharmacokinetics And Toxicity Profile Of Kigelia Africana (Lam) Bioactive Compounds, Sulyman Olalekan Ibrahim, Halimat Yusuf Lukman, Marili Funmilayo Zubair, Oluwagbemiga Tayo Amusan, Fatimah Ronke Abdulkadri, Bashir Lawal, Lateefat Bello Abdulfatah, Olubunmi Atolani

Al-Bahir Journal for Engineering and Pure Sciences

Kigelia africana plant is multipurpose plant whose therapeutic potential has been thoroughly investigated. The physicochemical, solubilities, ADMET, pharmacological, and drug-like properties of this plant have not been reported in details. This study makes use of the information that is currently known on the chemical make-up of the plant to forecast its overall toxicity as well as the potential for the phytochemicals it contains to be employed in medication discovery. The study also employed free web servers for the lipophilicity, water solubility, drug-likness, bioavailability score, medicinal chemistry and toxicological profiling of the compounds of K. africana. Artemether, a known antimalaria …

Urobiome Screening For Antimicrobial Peptides Against Uropathogenic Escherichia Coli, Jennifer Jones

ORBioM (Open Research BioSciences Meeting)

BACKGROUND: Urinary tract infections (UTIs) are one of the most common bacterial infections worldwide. As global incidences of UTIs caused by multidrug resistant bacteria continue to increase, so too does the demand for novel antimicrobial therapies.

Due to its relatively understudied nature, the urinary microbiome represents a niche with an untapped source of potentially novel antimicrobials (e.g., bacteriocins). Improvements to bacterial culturing and sequencing techniques have highlighted these potential alternative treatments and control strategies to target antibiotic resistant uropathogenic E. coli (UPEC).

METHODS: Expanded quantitative urine culture (EQUC) was used to culture bacterial isolates from mid-stream urine samples. Urinary isolates …

Microbiome And Virome Analysis In Early Life, Lakshmi Priyadarshini

ORBioM (Open Research BioSciences Meeting)

A wide variety of microorganisms, including bifidobacteria, are known to colonise the human gastrointestinal tract. Bifidobacteria are beneficial bacteria known to be particularly prevalent and abundant in the gut of healthy and breast-fed infants. Together with bacteria, bacteriophages can be vertically transmitted from mother to newborn during vaginal delivery and they are believed to play a role in influencing bacterial levels and microbiota composition in early in life. While there is a significant amount of information on early bacterial colonisers in the infant gut, there is currently very limited knowledge of diversity and prevalence of gut bacteriophages and their impact …

Investigating The Effect Of Agronomic Factors On Microbiome Of Horticulture Produce, Maryada Bohra

ORBioM (Open Research BioSciences Meeting)

The ranged microbiome in fruits and vegetables contributes substantially to the health of vegetation which, in effect, benefits human health. These microorganisms undertake an extensive variety of responsibilities including flavour creation, ripening and health preservation via the production of second-generation metabolites. There is limited information however on the influence of agronomic practices such as crop ripening stage at harvest, storage, packing material and how they impact the microbiome of the crop itself. The overall role of the crop microbiome in gut health is also not fully clear.

The Meta-Hort project will examine the effects of premature harvesting along with tray …

The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley

ORBioM (Open Research BioSciences Meeting)

In livestock populations, recessive lethal alleles are a known contributor to poor reproductive performance due to embryonic death in homozygous individuals. Despite their lethal effect in the recessive form, these alleles may be maintained at high frequencies among carrier animals because of their positive pleiotropic effects on economically important traits. Although several such recessive alleles have been identified in cattle and pig populations, limited studies have been completed in sheep, and none within Irish sheep populations. Genotype data for 69,034 animals from five major Irish sheep breeds genotyped on a variety of panels was available for this study. Only animals …

Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay

Dartmouth College Ph.D Dissertations

The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …

In Silico Prediction Of Sodium-Glucose Co-Transporter-2 (Sglt2) Inhibition Activity By Allium Fistulosum Compound Based On Skelspheres Molecular Descriptor, Rudy Heryanto, Aryo Tedjo, Dimas Noor

Indonesian Journal of Medical Chemistry and Bioinformatics

The Sodium-Glucose co-transporter-2 (SGLT2) inhibitor represents a novel agent for the treatment of type 2 diabetes. Drugs of this class function by inhibiting glucose reabsorption in the kidneys, thereby controlling blood glucose levels. It is known that SGLT2 inhibitors activate the AMPK signaling pathway by increasing the expression and activity of AMP-activated protein kinase (AMPK). In vivo tests have demonstrated that ethanolic and aqueous extracts of Welsh onion leaves (Allium fistulosum L) can reduce body weight, liver weight, adipocyte size, and enhance AMP-activated protein kinase (AMPK) expression. In this study, the inhibitory activity (IC50) of compounds within Allium fistulosum against …

Fortifying Iot Against Crimpling Cyber-Attacks: A Systematic Review, Usman Tariq, Irfan Ahmed, Muhammad Attique Khan, Ali Kashif Bashir

Karbala International Journal of Modern Science

The rapid growth and increasing demand for Internet of Things (IoT) devices in our everyday lives create exciting opportunities for human involvement, data integration, and seamless automation. This fully interconnected ecosystem considerably impacts crucial aspects of our lives, such as transportation, healthcare, energy management, and urban infrastructure. However, alongside the immense benefits, the widespread adoption of IoT also brings a complex web of security threats that can influence society, policy, and infrastructure conditions. IoT devices are particularly vulnerable to security violations, and industrial routines face potentially damaging vulnerabilities. To ensure a trustworthy and robust security framework, it is crucial to …

Metabolomic Insights Into Tuberculosis: Machine Learning Approaches For Biomarker Identification, Miftahul Khair Akbar, Arief Aulia Rahman

Indonesian Journal of Medical Chemistry and Bioinformatics

The lung parenchyma is largely impacted by the infectious condition known as pulmonary tuberculosis (pulmonary TB) when the immune system creates a wall around the germs in the lungs, a tiny, hard bulge known as a tubercle develops, earning the disease the name tuberculosis. Although the majority of TB germs target the lungs, they can also harm other bodily organs. The identification of TB biomarkers, which are crucial for diagnosis, treatment monitoring, risk analysis, and prognosis, has been the subject of extensive research. Differences in metabolites between normal cells and tuberculosis are considered to be able to support the diagnosis …

Precise Method To Identify Kinase Drug Targets In Complex Diseases: The First Step Towards Sustainable And Effective Treatment, Hasbanny Irisson, Marzieh Ayati

Research Symposium

Background: Kinases are enzymes that have proven to be important drug targets due to their role in critical biological mechanisms such as phosphorylation. Phosphorylation happens when a kinase catalyzes the transfer of a phosphate group to a protein in a phosphorylated site, which then becomes known as the substrate of the kinase. Any dysregulation of protein phosphorylation causes a wide range of complex diseases including cancer. Thus, discovering the links between kinases and their substrates (i.e. predicting kinase-substrate associations (KSAs)) is crucial in developing effective and sustainable treatments. Presently, less than 5% of phosphorylated sites have an associated kinase, and …

Exploration Of Potential Natural Inhibitors Against Kras-G12d In Pancan: Protein Centered Pharmacophore Htvs Approach., Anupam Dhasmana, Swati Dhasmana, Sudhir Kotnala, Vivek Kumar Kashyap, Sheema Khan, Murali M. Yallapu, Meena Jaggi, Subhash C. Chuahan

Research Symposium

Background: As per key statistics of American Cancer Society 2021, Pancreatic Cancer (PanCan) affects around 60,430 persons a year in the U.S. and is tricky to diagnose & treat. Studies revealed that African Americans have a 50–90% higher incidence of PanCan compared to other ethnic groups. Oncogenic KRAS mutation is the signature genetic incident in the progression and development of PDAC. KRAS is the most common protein which is 95% times mutated in PDAC condition. By considering this alarming situation our group is now focused on to develop therapeutic portfolio against KRAS-G12D mutation associated PanCan by using high through-put virtual …

Cell-Based Experimental Evidence To The Anti-Covid-19 Potential Of Ashwagandha And Honeybee Propolis Ingredients, Renu Wadhwa, Durai Sundar, Yoshiyuki Ishida, Keiji Terao, Sunil C. Kaul

Research Symposium

Background: The COVID-19 pandemic emerged in December 2019 by a novel strain of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has led to new endeavours in repurposing of existing drugs, anti-COVID-19 vaccine and drug development. Natural products, due to their general safety and wider availability, have attracted research and public attention. In this study, we report anti-COVID potential of compounds from honeybee propolis and Ayurvedic herb, Ashwagandha. Effect of active ingredients was studied on human cell surface receptors (ACE-2:Angiotensin Converting Enzyme-2/Spike protein and TMPRSS2:Transmembrane Protease Serine 2), critical for virus infection and virus main protease (Mpro, essential for virus replication), …

Pro-Apoptosis Activity Of Pogostemon Cablin Benth. Against Nasopharyngeal Carcinoma Through The Bcl-2 Inhibition Signaling Pathway: A Computational Investigation, Aigia Syahraini, Essy Harnelly, Feri Eko Hermanto

Makara Journal of Science

Resistance to chemotherapy and radiotherapy frequently emerges in the later stage of nasopharyngeal carcinoma (NPC) tumorigenesis. The decreased response of NPC to radiotherapy and chemotherapy occurs owing to the inhibition of cancer cell apoptosis by the B-cell lymphoma-2 (BCL-2) protein. Thus, inhibiting BCL-2 protein may become a powerful approach to eliminate NPC through apoptosis regulation. Meanwhile, Pogostemon cablin is reported to exhibit anticancer properties, but there are limited studies on its use for NPC treatment. The objective of this study is to investigate the potential bioactive compounds in P. cablin as anti-apoptosis BCL-2 protein inhibitors using in-silico approach. Natural compounds …

The Use Of Prognostic Markers To Predict Disease Progression And Clinical Outcome In Monoclonal Gammopathy Of Undetermined Significance, Smouldering Multiple Myeloma And Multiple Myeloma., Róisín C. Mcmonagle

International Undergraduate Journal of Health Sciences

Multiple Myeloma (MM) is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smouldering Multiple Myeloma (SMM) precede MM, with variable risks and rates of disease progression. The continuing high relapse and death rate in MM cases has prompted research into more accurate prognostic markers to predict progression from MGUS and SMM to MM, as well as identify MM cases with aggressive disease, in order to begin early, targeted and effective therapeutic intervention. Many studies have focused on utilising current markers more effectively, including M-protein, serum-free light chain ratio, …

Drug Repurposing Using Gene Expression Data Mining, Yue Qiu

Dissertations, Theses, and Capstone Projects

The conventional drug discovery process that employs the "one disease, one target, one drug'' paradigm is expensive, time-consuming, and has a high rate of failure for multi-genic complex diseases. An alternative approach to drug discovery is to repurpose an existing drug that has been used to treat some medical conditions. Drug repurposing is considered a promising method due to its accelerated the process of drug discovery and lower overall cost and risk.

Drug-perturbed gene expression profiles are powerful phenotype readouts of biological systems, and they have been widely used in drug repurposing studies. However, the existing drug-perturbed gene expression datasets …

State-Of-The-Art Approaches For Sequencing, Assembling And Annotating Naphthenic Acid Degrading Bacterial Metagenomes, Henry H. Say

Electronic Thesis and Dissertation Repository

Naphthenic acids (NAs) are the main toxic component of oil refinery wastewater and require special processes to be removed. Harnessing bacterial biodegradation for NA removal has the potential to be effective, yet NA-degrading bacteria and pathways are poorly understood and uncharacterized. To improve our understanding of NA degradation, I characterize the metagenomes of novel NA-degrading bacterial communities seeded in NA-enriched granulated activated carbon (GAC) filters. I demonstrate methods that maximize the throughput of extraction, sequencing, and annotation of novel metagenomes - producing 72 MAGs and other 5432 circular contigs - 226 of which were putative phages. I also include state-of-the-art …

Generative Ai-Assisted Pathway Analysis And Interpretation Of Rna-Seq Experiment Data, Junguk Hur

AI Assignment Library

No abstract provided.

Predicting Marine Teleost Responses To Ocean Warming And Pollution, Akila Harishchandra

Electronic Theses and Dissertations

Ocean warming and pollution are two detrimental anthropogenic factors causing rapid marine ecosystem degradation recorded in the past decades. These factors alter the marine environment intolerable for many marine species, forcing them to either adapt or shift their contemporary habitat ranges to reduce the extinction risk embedded with environmental degradation. Estimating marine species’ habitat range shifts, and their potential for developing adaptive mechanisms are critical for ecosystem conservation and management, human health risk assessment, and climate change vulnerability assessments. Given that, for the first chapter of this thesis, we focused on developing a species distribution model (SDM) integrating marine species …

Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena

Electronic Thesis and Dissertation Repository

Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.

To characterize …