Molecular Biology Commons^™

Evaluation Of Mdm2 Mrna Expression According To Clinicopathological Characteristics In Oral Squamous Cell Carcinoma (Oscc) Patients, Tirta Wardana

Chulalongkorn Medical Journal

Background: The murine double minute 2 (MDM2) gene encodes an E3 ubiquitin ligase that targets p53 for degradation, thereby influencing the pathogenesis of oral squamous cell carcinoma (OSCC).

Objective. The present study investigates MDM2 mRNA expression and its association with clinical and pathological characteristics in OSCC patients.

Methods: We conducted an observational-analytical study using a cross-sectional design. The study involved 39 OSCC patients. RNA extraction, cDNA synthesis, and quantitative PCR (qPCR) were performed. We quantified relative MDM2 mRNA expression using the Livak method (2-ΔΔCT) and GenEX MultiD software version 6.0. Statistical significance was assessed using independent t-tests.

Results: Although no …

Comparative Screening Of Cytotoxic Potential Of Berberis Aristata And Senna Alexandrina Extracts, Rida Noor Akhtar, Javaria Zahoor, Rizwan Ullah Khan, Aziz Ullah, Naila Malkani

Journal of Bioresource Management

Medicinal plants provide a safe and efficient source of drugs for cancer treatment. Berberis aristata and Senna alexandrina are traditionally used to treat several ailments because they contain compounds with antimicrobial, antitoxic, anti-inflammatory, and other properties. The objective of the study was to prepare crude ethanolic extracts of B. aristata and S. alexandrina and to determine their cytotoxic potential against cancer cells. Ethanolic extracts were prepared for both plants. Hepatocellular carcinoma cells (HepG2) were used for all assays. The cytotoxicity of extracts was determined by 3‑(4,5‑Dimethylthiazol‑2‑yl)‑2,5‑diphenyltetrazolium bromide (MTT) assay using various concentrations of extracts. The obtained sub-lethal concentrations were used …

Influence Of Smoking On Mlh1 Gene Polymorphism: Insights Into Colorectal Cancer Incidence, Ali Mohammed Al-Abedi, Rand Muhammed Abdul-Hussein Al-Husseini

Al-Bahir

Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. The MutL Homolog 1 (MLH1) gene plays a critical role in DNA mismatch repair (MMR). Evidence suggests cigarette smoking increases CRC risk, potentially interacting with genetic factors.

Materials and Methods: This case-control study involved 50 Iraqi CRC patients and 50 age- and gender-matched healthy controls. The PCR-RFLP technique was employed for genotyping the -93G/A (rs1800734) polymorphism. Statistical analysis included Chi-square, Fisher's Exact Test, and logistic regression adjusted for confounders. Hardy-Weinberg Equilibrium (HWE) was assessed in controls.

Results: The frequency of the rs1800734 variant was significantly higher in CRC …

The Universe Under A Microscope, Claire Chabot

Caravel Undergraduate Research Journal

No abstract provided.

Disrupted Nuclear Function And Nucleocytoplasmic Transport In Parkinson’S Disease, Ichiro M. Matoba

The Cardinal Edge

No abstract provided.

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Why Acromegaly Dies: A Systematic Review, Isam Noori Salman, Safaa Ehssan Atta, Baydaa Ahmed Abed, Noor Ulhuda G. Mohammed

Maaen Journal for Medical Sciences

Acromegaly is a rare endocrine clinical syndrome characterized by long-term elevated production of growth hormone (GH) due to a pituitary adenoma tumor. The main problem of acromegaly patients (AC-PTs) is prolonged elevated GH concentration, which leads to increased insulin-like growth factor 1 (IGF-1) production, causing the characteristic tissue and bone overgrowth. The appearance of diabetes in AC-PTs was linked with the high risks of cardiovascular morbidity, indicating that individuals with both conditions face heightened health challenges. Acromegaly typically has a higher cancer incidence rather than the general population. Without early diagnosis and effective treatment, excess GH can have widespread systemic …

Missense Mutation Of Msh6 Leucine 696 Has No Apparent Effect On The Dna Mismatch Repair Process, Razan H. Hammad, Rafia Rashid, Essence Tarrence, Christopher Bolden, Joanna E. Haye-Bertolozzi

XULAneXUS

Lynch Syndrome and Constitutional Mismatch Repair Deficiency are human diseases implicated in mutations of DNA mismatch repair (MMR) genes. This experiment tested a mutation of an MMR gene, MSH6, and evaluated how the mutation affected overall MMR effectiveness. Using the yeast Saccharomyces cerevisiae, we performed the CAN1 forward mutation assay to study msh6-L696F and its implications in the MMR process. We hypothesized that there would be a significant change in molecular function in the Msh6 protein in the presence of this mutation. Bioinformatic tools predicted that this amino acid change would have deleterious effects on MMR function. However, …

Crispr-Induced Mutagenesis Of Arabidopsis Thaliana Gene Apetala3, Hazel Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

This project aims to create CRISPR-CAS9 mutations in the APETELA3 (AP3) gene of the model plant Arabidopsis thaliana. AP3 is a class B gene critical to the petal and stamen development of Arabidopsis flowers. AP3 is defined in a MADS domain, which binds directly to DNA and may be responsible for the expression of the CaRG-box genes. AP3 works in conjunction with PISTILLATA (PI), AGAMOUS (AG), APETALA1 (AP1), and SEPALLATA (SEP) genes to specify the development in the second and third whorls of the flower. While several alleles of AP3 already exist, these alleles are strong alleles that knockout gene …

Inter-Simple Sequence Repeats Application On The Identification Of Genetic Variation Of A New Indonesian Melon Cultivar “Melona”, Tantri Ajeng Salma Salsabila, Adib Fakhruddin Yusuf, Wiko Arif Wibowo, Prima Sekti Kusnanda, Budi Setiadi Daryono

Makara Journal of Science

The field of identification of molecular markers has seen significant advancements, with the Inter-Simple Sequence Repeat (ISSR) emerging as a prominent tool for characterizing genetic variation within species. This study focuses on the new Indonesian melon cultivar “Melona,” developed through selective breeding of commercial melons. This study aimed to assess the utility of ISSR markers in evaluating the genetic variation and stability of the “Melona” cultivar. Comparisons were made with established cultivars—‘Inthanon,” “Rich Sweetness,” “Chamoe,” and “Hikapel”—using five ISSR primers: UBC 807, UBC 808, UBC 810, UBC 812, and UBC 826. A total of 70 DNA fragments with a high …

Ivy Proteins As Guardians Of Bacterial Cell Wall Integrity: Regulation Of Lytic Transglycosylases Explored, Aamna Aijaz, Trinity E. Alamutu, Vy T. Dao, Nathaniel R. Davis, Michael D. Landers, Nykolas K. Mackevicius, Liliana Ortiz, Irina F. Padilla-Montoya, Kacy J. Smith, Maria L. Snyder, Anthony J. Stefanie, Blaise M. Williams, Thomas C. Leeper

The Kennesaw Journal of Undergraduate Research

Lytic transglycosylases (LTs) are bacterial enzymes involved in biosynthesis and maintenance of the peptidoglycan cell wall. LTs are reported to be regulated by two paralogs of Inhibitor of Vertebrate Lysozymes: Ivyp1 and Ivyp2. This study investigated the regulatory dynamics between the soluble LT (SltB1), and Ivy paralogs as putative regulators in Pseudomonas aeruginosa (PA). The secondary objective was to delineate the critical roles played by a glutamic acid at position 135 in SltB1 and a histidine at position 62 in Ivyp1 in governing their molecular interaction through site directed mutagenesis. Isolated SltB1 shows no lytic activity in our assay, in …

Retracted: Conserved Domains In Promoters Of Differentially Expressed Genes: How To Find Them And What Can They Tell Us?, Emalynn E. Tobias

Mako: NSU Undergraduate Student Journal

THIS ARTICLE HAS BEEN RETRACTED DUE TO THE FOLLOWING REASON: inadvertent errors in several citations.

The complex process of regulating gene expression involves a large number of cis- and trans-acting components. The cis elements also referred to as cis regulatory elements (CREs) are highly conserved across species, and are often referred to as conserved domains mainly located in the promoters of genes. The trans acting sequences such as enhancers, moderators and insulators are also crucial in the regulation of gene expression. With an increased influx of genomic and transcriptomic data, study of differentially expressed genes (DEGs) is highly effective in …

Assessing The Bioactivity Of Salvia Phytochemicals Against Breast Cancers, Allison C. Portaro, Jared L. Scott, David J. Schultz

The Cardinal Edge

Breast cancer is one of the most common cancers diagnosed in adults, with 2.3 million new cases worldwide in 2020. Plants have been used in traditional medicine and are a potential source of pharmaceuticals. One example is the large Lamiaceae (mint) family. The Salvia genus, commonly known as the sages, is the largest genus in Lamiaceae with almost 900 known species. Different species of salvia are found in parts of the US, and some have a history in traditional medicine to treat cancers and other ailments. Preliminary research on three salvia species (S. lyrata, S. lyrata var. Purple …

Hepatic Targets To Control Blood Glucose And Potentially Aid In The Treatment Of Diabetes, Rena A. Velissarios

PANDION: The Osprey Journal of Research and Ideas

Maintaining glucose homeostasis is extremely important to remain in good health and prevent disease. This homeostasis is achieved via the regulation of hepatic metabolic pathways like gluconeogenesis and glycogenesis by insulin, which is expressed during high blood glucose. Insulin is responsible for facilitating the uptake of glucose into other tissues from the blood, as well as signaling whether to stimulate or slow glucose metabolism in the liver. Hyperglycemia is one of the main effects of diabetes, a disease characterized by the body’s inability to produce or respond to insulin. Without insulin, hepatic glucose output continues and blood glucose accumulates, causing …

Serum Proteomic Profile Of Subclinical Babesia Bovis Infection In Pcr-Positive Eld's Deer Using Serum Protein Electrophoresis Coupled With Lc-Ms/Ms, Vichayanee Pumpitakkul, Sittiruk Roytrakul, Narumon Phaonakrop, Gunnaporn Suriyaphol Assoc. Prof.

The Thai Journal of Veterinary Medicine

Subclinical babesiosis observed in captive Eld’s deer, which act as reservoirs for ticks, poses a risk to healthy herds. However, the knowledge of biomarkers for subclinically infected Eld’s deer and host-parasite interactions is limited. This study aimed to investigate the serum proteomic profiles and protein interactions of Babesia bovis and subclinically infected Eld’s deer, PCR-positive for B. bovis, using automated serum protein electrophoresis and liquid chromatography-tandem mass spectrometry (LC-MS/MS). The findings revealed albumin and four globulin fractions: alpha-1, alpha-2, beta, and gamma globulin. Albumin protein (ALB) was consistently detected across all fractions, highlighting its role in maintaining osmotic balance …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

Du Undergraduate Showcase Abstracts: Research, Scholarship, And Creative Works, August Alexander, Kevin Summers, E. Paige Lloyd, Alyssa Aragon, Lauren Wols, Erica Larson, Colton Arciniaga, Lily Baeza, Ellie Barnett-Cashman, Sidney Barbier, Maverick Bartholomew, Ryan Bell, Trevor Briggs, Amanda Brown, Cory Marchi, Maddy Pontius, Jennifer Gallagher, Claire Kwok, Channing Bullock, Alex Mccollister, Kim Gorgens, Daniela Chavez, Yamilet Espinoza Nuñez, Giovanni Valladares Giron, William Christensen, Olivia Kachulis, Daniel Cierasynski, Brandon Cohen, Spenser Dobbs, Lindsay Goolsby, Noah Craver, Nyah Cubbison, Liam Doherty, Nicole Doris, Yan Qin, Alexander Nguyen, Lily Harmon, Shubh Todi, Naichen Zhao, Noah Fagello, Stacia Fritz, Paola Gascot-Chinea, Alex Volkova, Janelyn Geronimo, Elsie Harrington, Shane Simmons, Clarice Hise, Laura Moreno Palmer, Henry Xu, Yesu Leela Pasupula, Emily Fisher, Zachary Hogan, Colin Kleckner, Alyssa Knaus, Erin Kubat, Sam Werkema, Katie Lamberton, Lilliya Larson, Allie Leary, Vanessa Leon-Gamez, James H. Gallagher, E. Dale Broder, Robin M. Tinghitella, Emma Loeber, Alina Mali, Ixchel Marquez, Lauren Mcgrath, Ella Matthews, Grace Naegelen, Audrey Ng, Megan Lucyshyn, Rachel Brough, Alexandra Norman, Joe Ontiveros Rodriguez, Ben Dossett, Ori Miller, Janamejay Sharma, Christopher Reardon, Vincent Pandey, Regan Parish, Ren Pratt, Alisha Pravasi, Sanchari Das, Cari Reichel, Emma Robson, Victoria Rockwell, Jayce Rumsey, Steven Said, Norah Schroder, Alaina Smith, Shannon Murphy, Shujan A. Sharafeldeen, Stanley M. Kanai, James T. Nichols, David E. Clouthier, Macalia R. Augustus, Daniel Silva Rios, Scott Simpson, Anna Sparling, Chase Spurbeck, Kimberly Chiew, Christine Stadnik-Poteroba, Jacqueline Stephenson, Evelyn Stovin, Mia Supan, Lauren Tapper, Will Thrush, Anna Vogt, Michaela Walheim, Jon Weber, Hunter Whitehouse, Kansas Wood, Hayley Sayre, Lydia Mccann, Maread Mclaughlin, Kelly Krumrie, Olivia Wuttke

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Research Showcase.

The Impact Of Mutations In The Arabidopsis Apetela (Ap3) Gene, Hazel R. Frans, Tara Phelps-Durr

SACAD: Scholarly Activities

The purpose of this research is to understand the molecular functioning of the Arabidopsis thaliana Apetela (Ap3) gene. We created mutations in two sites of the gene, AP3-3 and AP3-5. These are predicted to change AP3 protein structure, which may result in a mutated flower. Analyzing the effects of new mutations allows an understanding of protein formation both in plants and humans.

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …

Identification Of Regulatory Elements In The Untranslated Regions Of Streptolysin S Associated Gene A Messenger Rna From Group A Streptococcus, Cameron R. Carroll, Sara G. Nibar, Alexis S. Brown, Lauren R. Angello, Gabriela C. Pérez-Alvarado, Brian M. Lee

Journal of the South Carolina Academy of Science

Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a human pathogen associated with a variety of diseases such as strep throat, scarlet fever, toxic shock syndrome, and necrotizing fasciitis. One of the virulence factors released by GAS during an invasive infection is a cytotoxic peptide, streptolysin S (SLS), which inhibits the immune response to necrotizing fasciitis. The streptolysin S associated gene A product, SagA, is modified to produce SLS. Thesag operon includes sagA and the genes required for enzyme-mediated post-translational modifications of SagA and the export of SLS. The sagA gene is contained within the pleiotropic …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Using In Silico Tools To Analyze The 5ʹ Untranslated Regions Of The Alcohol Dehydrogenase Gene From Arabidopsis Thaliana And Omega Sequence, Reza Mohammadhassan, Tina Asadishad

Makara Journal of Science

The 5ʹ ends of protein-encoding genes contain 5ʹ untranslated regions (5ʹUTRs), which can effectively participate in regulating gene expression. The 5ʹUTRs of Arabidospis thaliana–derived alcohol dehydrogenase gene (AtADH) and omega (Ω) sequence from tobacco mosaic virus (TMV) are the most effective enhancers in biotechnology. In this study, bioinformatics techniques were employed to analyze the characteristics of the above sequences. After 5ʹUTR sequence collection, the inner ribosome entrance sites; small RNA (sRNA) target sequences; nucleotide contents; and upstream start and stop codons, ORFs, and coding DNA sequences of the Ω sequence and AtADH 5ʹUTR were identified. Moreover, the …

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …

Sars-Cov-2: Tale Of A Microscopic Murderer, Josiah P. Garner

Quest

Independent Study

Research in progress for BIOL1406: Biology for Science Majors I

Faculty Mentor: Amina Tassa, Ph.D.

I am delighted to introduce Josiah Garner’s “SARS-CoV-2: Tale of a Microscopic Murderer.” This independent study assignment explores the impact of a novel, deadly, and worldwide virus. The assignment also examines the fast development of vaccines to control the spread and reduce the symptoms of the virus.

Josiah’s paper focuses on the early history of the emergence of COVID-19, the world response, and vaccine development. He demonstrates critical thinking skills and effectively utilizes various research methods to obtain and communicate his information. Josiah …

Identification Of A Small Regulatory Rna Usps Associated With The Universal Stress Protein In Lactobacillus Species, Zarah M. Fowler, Sasha S. Bronovitskiy, Finn K. Rose, Brian M. Lee

Journal of the South Carolina Academy of Science

The gut microbiome is a complex habitat with many bacterial species, each playing crucial roles in regulating various physiological processes in the body. As the use of probiotics to combat human disease continues to increase, it is important to understand the mechanisms by which probiotic bacteria regulate their interactions with other bacteria and their host. Our exploration of the physiological functions of probiotic bacteria hopes to elucidate the role of small regulatory RNA (sRNA) in regulating gene expression within the microbiome. The goal of this project was to characterize the structure and function of the sRNA, UspS, which is found …

Potential Use Of The Gel Extract Of Butterfly Pea Flower As Topical Therapy To Prevent Photodamage By Downregulating Tnf-Α And Caspase-3 Expression Levels In Uvb-Exposed Rats, Elvana Cahyani, Agung Putra, Prasetyowati Subchan

Makara Journal of Health Research

Background: Prolonged exposure to UVB radiation causes DNA damage in skin cells by raising the levels of reactive oxygen species, resulting in the production of inflammatory factors and skin issues. Plant extracts are frequently used to counteract photodamage due to their antioxidant properties. One example is the floral extract of the butterfly pea plant, which contains flavonoid antioxidants. However, the effect of the extract on inflammatory factors is unknown. This study investigated how tumor necrosis factor-alpha (TNF-α) and caspase-3 expression changed when a butterfly pea flower extract gel was applied topically to UVB-exposed animals.

Methods: Experimental and control …

Serving Justice Case By Case, Michael Becker

WRIT: Journal of First-Year Writing

Forensic Science is an integral part of serving justice in today's society, and majority of the world has little understanding of what forensics is. Read this article on forensic science and how it relates to writing in today's world.

Apoptotic Effect Of Bortezomib On Pancreatic Islet Cells In Stz-Induced Diabetic Rats, Çiğdem Ekin, Neslihan Tekin Karacaer, Mehtap Tarhan Karaoğlan, Ibrahim Örün, Kamile Öztürk

Makara Journal of Health Research

Background: This study aimed to investigate the possible apoptotic role of bortezomib (BMZ) on pancreatic islets of streptozotocin (STZ)-induced diabetic rats.

Methods: Sprague-Dawley rats were divided into groups that were administered BMZ alone or in combination with STZ. To evaluate the effect of BMZ on the development of diabetes, blood glucose levels were measured regularly in the animals. Islet cell viability was determined by staining the islets with fluorescein diacetate and propidium iodide. Expression of the Bcl-2 and bax genes was determined in islet cells by quantitative real-time polymerase chain reaction.

Results: Administering STZ-induced hyperglycemia in the …

Therapies For Mitochondrial Disorders, Kayli Sousa Smyth, Anne Mulvihill

SURE Journal: Science Undergraduate Research Experience Journal

Mitochondria are cytoplasmic, double-membrane organelles that synthesise adenosine triphosphate (ATP). Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is maternally inherited from the oocyte. Mitochondrial proteins are encoded by either nuclear DNA (nDNA) or mtDNA, and both code for proteins forming the mitochondrial oxidative phosphorylation (OXPHOS) complexes of the respiratory chain. These complexes form a chain that allows the passage of electrons down the electron transport chain (ETC) through a proton motive force, creating ATP from adenosine diphosphate (ADP). This study aims to explore current and prospective therapies for mitochondrial disorders (MTDS). MTDS are clinical syndromes coupled with abnormalities …

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 …