Medical Biochemistry Commons^™

Plasmonic Sensor Based Detection Of Dopamine, Sang Lee

Electronic Theses and Dissertations, 2020-2023

With a rapidly ageing population, neurological diseases are becoming increasingly relevant in the design of public health policies and strategies in western societies. In the last decades, biochemical research has consistently shown the critical role that neurotransmitters and their associated metabolites play as biomarkers in tracking and diagnosis of different brain disorders and cancers. In particular, dopamine, an organic electrochemical neurotransmitter, has been shown to be paramount for the proper functioning of the neural system. Dopamine's dysfunction, has been shown to underlie the pathogenesis in several neurological disorders such as Parkinson's disease, depression, chronic schizophrenia and psychosis. Unfortunately, currently available …

Liquid Biopsies To Occult Brain Metastasis, Asad Ur Rehman, Parvez Khan, Shailendra K. Maurya, Jawed A. Siddiqui, Juan A. Santamaria-Barria, Surinder K. Batra, Mohd W. Nasser

Journal Articles: Biochemistry & Molecular Biology

Brain metastasis (BrM) is a major problem associated with cancer-related mortality, and currently, no specific biomarkers are available in clinical settings for early detection. Liquid biopsy is widely accepted as a non-invasive method for diagnosing cancer and other diseases. We have reviewed the evidence that shows how the molecular alterations are involved in BrM, majorly from breast cancer (BC), lung cancer (LC), and melanoma, with an inception in how they can be employed for biomarker development. We discussed genetic and epigenetic changes that influence cancer cells to breach the blood-brain barrier (BBB) and help to establish metastatic lesions in the …

Depletion Of Transmembrane Mucin 4 (Muc4) Alters Intestinal Homeostasis In A Genetically Engineered Mouse Model Of Colorectal Cancer, Ramesh Pothuraju, Priya Pai, Sanjib Chaudhary, Jawed A. Siddiqui, Jesse L. Cox, Sukhwinder Kaur, Satyanarayana Rachagani, Hemant K. Roy, Michael Bouvet, Surinder K. Batra

Journal Articles: Biochemistry & Molecular Biology

Mucins are components of the mucus layer overlying the intestinal epithelial cells, which maintains physiological homeostasis. Altered mucin expression is associated with disease progression. Expression of MUC4 decreases in colorectal cancer (CRC); however, its functional role and implications in the intestinal pathology in CRC are not studied well. Therefore, we generated a genetically engineered Muc4 knockout (Muc4^-/-) CRC mouse model by crossing with Muc4^-/- and Apc^flox/flox mice in the presence of colon-specific inducible Cre. We observed that deficiency of Muc4 results in an increased number of macroscopic tumors in the colon and rectal region and leads …

Effects Of Chitosan Oligosaccharide And Probiotics On Chronic Kidney Disease Rats, Weerapat Anegkamol

Chulalongkorn University Theses and Dissertations (Chula ETD)

Chronic kidney disease (CKD) patients suffer from the accumulation of toxic substances in their blood due to the loss of kidney function, which results in hyperphosphatemia. This condition contributes to hyperparathyroidism, leading to the development of chronic kidney disease-related mineral bone disorder (CKD-MBD). Additionally, CKD patients experience changes in their gut microbiota, disrupting epithelial tight junctions and allowing excessive absorption of dietary phosphate. In this study, we aimed to investigate the effects of various oligosaccharides and probiotics on the gut microbiota, intestinal barrier, hyperphosphatemia, and hyperparathyroidism in CKD rats. We isolated Lactobacillus and Bifidobacterium strains from healthy participants and tested …

Roles Of Mtor Complex 2 In Canonical Wnt Signaling In Glioblastoma., Tankun Banlue

Chulalongkorn University Theses and Dissertations (Chula ETD)

Glioblastoma (GBM) is the most common type of primary brain tumor in adults, comprising 75% of cases. The failure of GBM treatments is closely related to a subset of cells known as glioblastoma stem cells (GSCs), which possess stemness characteristics. While the Wnt signaling pathway plays a crucial role in regulating stem cell homeostasis, the interplay between this pathway and the mTORC2 signaling pathway in GBM remains unclear. Thus, this research aimed to investigate the collaborative regulation of stemness-related mechanisms by mTORC2 and canonical Wnt signaling pathways in glioblastoma using 3D spheroid culture. The study found that inhibiting mTORC2 resulted …

Treatment Of Hypothyroidism: Desiccated Thyroid Extract, Aimee Fong

Capstone Showcase

The treatment of hypothyroidism with Levothyroxine (T4) has been well studied and FDA approved. However, many patients continue to have signs and symptoms of hypothyroidism while on Levothyroxine treatment despite reaching appropriate thyroid levels. An additional thyroid treatment known as desiccated thyroid extract (DTE) is made from dried pig thyroid glands and is advertised as a “natural” alternative to Levothyroxine. Despite lack of FDA approval and studies surrounding DTE, clinicians have prescribed DTE to patients, many of whom reported relief of their symptoms. The following poster highlights the approach to the treatment of hypothyroidism with Levothyroxine and DTE and outlines …

Defining Patient Cohorts For Guiding Clinical Trials And Treatment In Lafora Disease: A Model For The Rare Disease Community, Katherine Janae Donohue

Theses and Dissertations--Molecular and Cellular Biochemistry

In the US, approximately 8000 rare diseases have been identified. Combined, rare diseases impact more than 30 million people in the U.S. alone, with 75% of those being children. However, research, funding, and therapeutic development for the rare disease community remains challenging because of the incredible diversity – not only between diseases, but often even within a single disease.

LD is an ultra-rare childhood dementia and epilepsy caused by mutations in one of two driver genes: EPM2A, which encodes for the glycogen phosphatase laforin, and EPM2B/NHLRC1, which encodes the E3 ubiquitin ligase malin. Children with LD …

Ubiquitous Aberration In Cholesterol Metabolism Across Pancreatic Ductal Adenocarcinoma, Venugopal Gunda, Thiago C. Genaro-Mattos, Jyoti B. Kaushal, Ramakanth C. Venkata, Gopalakrishnan Natarajan, Kavita Mallya, Paul M. Grandgenett, Karoly Mirnics, Surinder K. Batra, Zeljka Korade, Satyanarayana Rachagani

Journal Articles: Biochemistry & Molecular Biology

Pancreatic cancer (PC) is characterized by metabolic deregulations that often manifest as deviations in metabolite levels and aberrations in their corresponding metabolic genes across the clinical specimens and preclinical PC models. Cholesterol is one of the critical metabolites supporting PC, synthesized or acquired by PC cells. Nevertheless, the significance of the de novo cholesterol synthesis pathway has been controversial in PC, indicating the need to reassess this pathway in PC. We utilized preclinical models and clinical specimens of PC patients and cell lines and utilized mass spectrometry-based sterol analysis. Further, we also performed in silico analysis to corroborate the significance …

The Gsk3 Kinase And Lztr1 Protein Regulate The Stability Of Ras Family Proteins And The Proliferation Of Pancreatic Cancer Cells, Chitra Palanivel, Neha Chaudhary, Parthasarathy Seshacharyulu, Jesse L. Cox, Ying Yan, Surinder K. Batra, Michel M. Ouellette

Journal Articles: Biochemistry & Molecular Biology

Ras family proteins are membrane-bound GTPases that control proliferation, survival, and motility. Many forms of cancers are driven by the acquisition of somatic mutations in a RAS gene. In pancreatic cancer (PC), more than 90% of tumors carry an activating mutation in KRAS. Mutations in components of the Ras signaling pathway can also be the cause of RASopathies, a group of developmental disorders. In a subset of RASopathies, the causal mutations are in the LZTR1 protein, a substrate adaptor for E3 ubiquitin ligases that promote the degradation of Ras proteins. Here, we show that the function of LZTR1 is regulated …

Tumor Microenvironment Enriches The Stemness Features: The Architectural Event Of Therapy Resistance And Metastasis, Palanisamy Nallasamy, Rama Krishna Nimmakayala, Seema Parte, Abhirup C. Are, Surinder K. Batra, Moorthy P. Ponnusamy

Journal Articles: Biochemistry & Molecular Biology

Cancer divergence has many facets other than being considered a genetic term. It is a tremendous challenge to understand the metastasis and therapy response in cancer biology; however, it postulates the opportunity to explore the possible mechanism in the surrounding tumor environment. Most deadly solid malignancies are distinctly characterized by their tumor microenvironment (TME). TME consists of stromal components such as immune, inflammatory, endothelial, adipocytes, and fibroblast cells. Cancer stem cells (CSCs) or cancer stem-like cells are a small sub-set of the population within cancer cells believed to be a responsible player in the self-renewal, metastasis, and therapy response of …

Exploring Roles Of Mir-372-3p In Proliferation Of Hepatocellular Carcinoma Cells, Pannathon Thamjamrassri

Chulalongkorn University Theses and Dissertations (Chula ETD)

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. HCC has a replicative immortality and sustained proliferation rate. In addition, cell cycle-related protein regulating proliferation in cancer are often found dysregulated, allowing cancer cells to proceed their proliferation uncontrollably. Recently, a small non-coding RNA, microRNA (miRNA), was found to play an important role in numerous biological functions. Specific miRNA may ameliorate or promote cancer progression through different target mRNA. MiR-372-3p has been explored in various cancers such as colon cancer, colorectal cancer, and glioma. However, its functions have been rarely studied in HCC, especially in the aspect …

Role Of Mtorc2 In The Regulation Of Glycolytic Metabolism In Glioblastoma Through Pkcδ Phosphorylation, Chatchapon Chuenjit

Chulalongkorn University Theses and Dissertations (Chula ETD)

Glioblastoma (GBM) is the most common and highly aggressive primary cancer within the central nervous system (CNS). The mTORC2 is a primary regulator of glycolytic reprogramming in highly malignant cells through both Akt-dependent and AKT-independent pathways. However, the mechanism that cancer glycolysis through AKT-independent pathways remains largely unexplored. This study aimed to investigate the mechanism of mTORC2/ PKCδ signaling-regulated glycolysis of GBM cells by AKT-independent mechanisms. We examined the impact of various pharmacological inhibitors on the suppression of mTORC1, mTORC2, AKT, and PKCδ signaling. Our results revealed that the phosphorylation of PKCδ at residue serine 664 was diminished by AZD8055, …

Exploring Roles Of Mir-885-5p In Hepatocellular Carcinoma, Archittapon Nokkeaw

Chulalongkorn University Theses and Dissertations (Chula ETD)

Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, exerts a significant burden on Southeast Asian countries and stands as the third leading cause of cancer-related mortality worldwide. Despite this alarming impact, effective treatments for HCC are lacking, resulting in low survival rates and high recurrence rates. Therefore, a comprehensive understanding of the disease's underlying mechanisms is crucial for the development of novel and potent therapies. Recently, it has been recognized that microRNAs (miRNAs) play a vital role in tumorigenesis, including HCC. Our bioinformatic analysis has highlighted hsa-miR-885-5p as a potential candidate miRNA due to its downregulation in HCC …

Classification Of Bacteria And Fungi In Peritoneal Dialysis Fluids Of Patients With Chronic Kidney Disease Based On Metagenomic Analysis, Suthida Visedthorn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Chronic kidney disease (CKD) is a long-term condition where sustained damage of the renal parenchyma leads to the chronic deterioration of renal function that may gradually progress to end-stage kidney disease (ESKD). Peritoneal dialysis (PD) is a type of ESKD treatment that is beneficial to improve a patient's quality of life. However, PD-associated peritonitis is a major complication that contributes cause of death, and the detection of the pathogen provided a high culture-negative rate. This study aims to apply metagenomic approaches for identifying the bacteria and fungi in peritoneal dialysis effluent (PDE) of CKD patients based on the full-length 16S …

Detection Of Egfr Mutations In Lung Cancer Based On Oxford Nanopore Sequencing Technology, Patinya Akkhasutthikun

Chulalongkorn University Theses and Dissertations (Chula ETD)

Epidermal growth factor receptor (EGFR) mutation is an important and highly prevalent oncogene driver in patients with non-small cell lung cancer (NSCLC) in East Asia. The detection of EGFR mutations is a standard biomarker testing that routinely performed in patients with advanced lung cancer for the selection of targeted therapy. Here, we aimed to develop a portable and cost-effective new technique for detecting EGFR 19Del, T790M and L858R mutations based on blocker displacement amplification (BDA) combined with Oxford Nanopore Technologies (ONT). The method optimization was performed using wild-type and mutant EGFR allele generated from lung cancer cell lines. The assay …

ผลของการบริโภคฟักข้าวต่อระดับไตรเมทิลามีนเอ็นออกไซด์ในเลือดและการเกิดโรคหัวใจในหนูไตวายเรื้อรัง, ภานุมาศ เข้มแข็ง

Chulalongkorn University Theses and Dissertations (Chula ETD)

บทนํา: ไตรเมทิลามีน (Trimethylamine) เป็นสารที่สร้างจากแบคทีเรียในลําไส้และเป็นสารตั้งต้นในการสร้าง Trimethylamine N-oxide (TMAO) ซึ่งทําให้เกิดโรคหัวใจและหลอดเลือดโดยเฉพาะในวิธีการทดลอง: หนูแรทเพศผู้สายพันธุ์วิสตาร์จํานวนกลุ่มละ 9 ตัว แบ่งออกเป็น 6 กลุ่ม ได้แก่ กลุ่มควบคุม (Control) กลุ่มไตเรื้อรัง (chronic kidney disease) กลุ่มสารทดสอบฟักข้าว (Gac) กลุ่มสารทดสอบไลโคปีนและเบต้าแคโรทีน (STD) กลุ่มสารทดสอบฟักข้าวร่วมกับแบคทีเรีย B. longum และ L. salivarius (Synbiotic) และกลุ่มสารโปรไบโอติกควบคุม L. Casei (Lactobacillus Casei) โดยหนูกลุ่มทดสอบจะถูกเหนี่ยวนําให้เป็นไตวาเรื้อรังโดย Cisplatinและทุกกลุ่มได้รับอาหารเสริม choline เป็นระยะเวลา 15 สัปดาห์ ผลการทดลอง: พบว่าหนูกลุ่ม Synbiotic มีระดับ serum TMAO ลดลงอย่างมีนัยสําคัญทางสถิติ (P<0.05)เมื่อเปรียบเทียบกับกลุ่ม CKD รวมถึงยังพบการลดลงของเชื้อในกลุ่ม Proteobacteria ในลําไส้และลดการแสดงออกของเอนไซม์ Trimethylamine-(TMA) lyase ซึ่งจําเป็นต่อการสร้าง TMA อย่างมีนัยสําคัญทางสถิติ(P<0.05) นอกจากนี้ยังพบว่าการเสริม Synbiotics ยังกระตุ้นการแสดงออกของ Zonula occludens type 1 (ZO-1) ซึ่งเป็น tight junction gene ที่บริเวณลําไส้ใหญ่ (Colon) อย่างมีนัยสําคัญ ในขณะที่การให้สารสกัดฟักข้าวเพียงอย่างเดียว หรือการให้โปรไบโอติกควบคุมไม่พบความเปลี่ยนแปลงเมื่อเปรียบเทียบกับกลุ่ม CKD สรุปผล: การเสริม Synbiotic ซึ่งประกอบด้วยสารสกัดฟักข้าว และโปรไบโอติกชนิด B. longum และ L.salivarius ที่มีประสิทธิภาพในการลดการรั่วที่ผนังลําไส้ ช่วยลดเชื้อ Proteobacteria ในลําไส้หนู CKD ลดการแสดงออกของ TMA lyase enzyme เพิ่มการแสดงออกของ tight junction gene ZO-1 และสามารถลดระดับ serum TMAO ได้อย่างมีนัยสําคัญ หรือ การเสริม Synbiotic ซึ่งประกอบด้วยสารสกัดฟักข้าว และโปรไบโอติกชนิด B. longum และ L. salivarius สารถลดระดับ serum TMAO ในหนูโรคไตเรื้อรังได้อย่างมีนัยสําคัญมีความเป็นไปได้ในการพัฒนาเป็นผลิตภัณฑ์ช่วยลดความเสี่ยงต่อการเกิดภาวะแทรกซ้อนทางหัวใจและหลอดเลือดในผู้ป่วยโรคไตเรื้อรังต่อไต

ผลกระทบของการปลูกถ่ายจุลินทรีย์ในลำไส้ของผู้ป่วยโรคนิ่วไตต่อการเกิดโรคนิ่วแคลเซียมออกซาเลตในทางเดินปัสสาวะของหนู, สิทธิพงษ์ หุ่นไทย

Chulalongkorn University Theses and Dissertations (Chula ETD)

โรคนิ่วไตพบมากในคนไทยโดยเฉพาะผู้ที่อาศัยในเขตภาคตะวันออกเฉียงเหนือและภาคเหนือ มีปัจจัยเสี่ยงคือ ภาวะซิเตรทในปัสสาวะต่ำ แคลเซียมและออกซาเลตในปัสสาวะสูง โดยพบมากในผู้ที่มีอายุ 40 ปีขึ้นไป จากการศึกษาก่อนหน้าพบความแตกต่างของประชากรจุลินทรีย์ในลำไส้ของผู้ป่วยโรคนิ่วไตจากคนสุขภาพดี จึงเชื่อว่าความแตกต่างของจุลินทรีย์ลำไส้ส่งผลให้เกิดความเสี่ยงของการเกิดโรคนิ่วไต เพื่อศึกษาความผิดปกตินี้ ผู้วิจัยจึงศึกษาความแตกต่างของจุลินทรีย์ในลำไส้เปรียบเทียบระหว่างอาสาสมัครคนปกติและผู้ป่วยโรคนิ่วไต พบว่าจุลินทรีย์ phylum Bacteroidata ในอุจจาระของผู้ป่วยโรคนิ่วไตสูงกว่าคนสุขภาพดี และพบ genus Bifidobacterium ต่ำกว่าคนสุขภาพดี จากนั้นนำจุลินทรีย์จากอุจจาระของอาสาสมัครทั้งสองกลุ่ม ปลูกถ่ายลงในหนู Wistar เป็นเวลา 4 สัปดาห์ พบว่า หนูกลุ่มที่ได้รับจุลินทรีย์จากกลุ่มผู้ป่วยโรคนิ่วไตมีปริมาณออกซาเลตในปัสสาวะมีแนวโน้มสูงขึ้น ปริมาณแมกนีเซียมในปัสสาวะลดลง รวมทั้ง pH ในปัสสาวะเป็นด่างมากขึ้น และพบดัชนีความเสี่ยงต่อการเกิดนิ่ว (Tiselius’s supersaturation index) เพิ่มสูงขึ้น นอกจากนี้ ยังพบ จุลินทรีย์ genus Muribaculaceae สูงขึ้นในหนูที่ได้รับการปลูกถ่ายเชื้อจุลินทรีย์จากผู้ป่วยโรคนิ่วไต และ genus Roseburia มีจำนวนลดลง รวมถึงการแสดงออกของ tight junction (Zonula occluden-1 หรือ ZO-1) ที่ลดลง และพบการแสดงออกของ oxalate transporter มีแนวโน้มสูงขึ้น สรุปได้ว่าหนูที่ได้รับเชื้อจุลินทรีย์ในอุจจาระจากผู้ป่วยโรคนิ่วไตมีความเสี่ยงต่อการเกิดโรคนิ่วสูงขึ้น โดยมีกลไกจากการแสดงออกของโปรตีน ZO-1 ลดลง และเพิ่ม oxalate transporter ที่ลำไส้ ทำให้ร่างกายได้รับออกซาเลตจากอาหารในลำไส้เพิ่มขึ้น และขับออกทางปัสสาวะเพิ่มขึ้น เป็นหลักฐานยืนยันว่าความผิดปกติของสมดุลเชื้อจุลินทรีย์ในลำไส้เพิ่มความเสี่ยงต่อการเกิดโรคนิ่วไต

Characterization Of A New Whim Syndrome Mutant Reveals Mechanistic Differences In Regulation Of The Chemokine Receptor Cxcr4, Jiansong Luo, Francesco De Pascali, G Wendell Richmond, Amer M Khojah, Jeffrey L Benovic

Department of Biochemistry and Molecular Biology Faculty Papers

WHIM syndrome is a rare immunodeficiency disorder that is characterized by warts, hypogammaglobulinemia, infections, and myelokathexis. While several gain-of-function mutations that lead to C-terminal truncations, frame shifts and point mutations in the chemokine receptor CXCR4 have been identified in WHIM syndrome patients, the functional effect of these mutations are not fully understood. Here, we report on a new WHIM syndrome mutation that results in a frame shift within the codon for Ser339 (S339fs5) and compare the properties of S339fs5 with wild-type CXCR4 and a previously identified WHIM syndrome mutant, R334X. The S339fs5 and R334X mutants exhibited significantly increased signaling compared …

Time-Resolved Cryo-Em Visualizes Ribosomal Translocation With Ef-G And Gtp, Christine E Carbone, Anna B Loveland, Howard Gamper, Ya-Ming Hou, Gabriel Demo, Andrei A Korostelev

Department of Biochemistry and Molecular Biology Faculty Papers

During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and …

Targeting Oncogenic Gαq/11 In Uveal Melanoma, Dominic Lapadula, Jeffrey L Benovic

Department of Biochemistry and Molecular Biology Faculty Papers

Uveal melanoma is the most common intraocular cancer in adults and arises from the transformation of melanocytes in the uveal tract. While treatment of the primary tumor is often effective, 36–50% of patients develop metastatic disease primarily to the liver. While various strategies have been used to treat the metastatic disease, there remain no effective treatments that improve survival. Significant insight has been gained into the pathways that are altered in uveal melanoma, with mutually exclusive activating mutations in the GNAQ and GNA11 genes being found in over 90% of patients. These genes encode the alpha subunits of the hetetrotrimeric …

The Physiological Benefits Of A Plant-Based Diet On Cardiovascular Health, Jenevieve Petray

Nursing | Senior Theses

Cardiovascular disease (CVD) is increasingly more prevalent in today’s society and is attributed to an alarming percentage of American hospitalizations and deaths. Americans are unhealthier than ever before, and the main contributor is the Western diet. Diet is a double-edged sword that can offer benefits or detriments to one’s health. CVD encompasses numerous diagnoses originating from various underlying physiological alterations. These alterations are downstream effects of increased body weight and BMI, increased cholesterol levels, decreased insulin sensitivity and increased arterial plaque buildup. Research shows that a plant-based diet has the potential to manage and reverse all fundamental physiological alterations that …

Effects Of Localized Oxygen Production By Electrolysis On The First-Generation Glucose Sensor Response, Nandita Halder

Graduate Theses and Dissertations

Glucose sensors are very important for detecting blood glucose both in vitro and in vivo. First-generation glucose biosensors were based on the glucose oxidase (GOx) enzyme using molecular oxygen as the electron acceptor and therefore oxygen dependent. Unfortunately for in-vivo work, oxygen in the body is variable and limited. Alternative approaches to overcome the oxygen dependency came with their own limitations. The widely used and commercially available ex-vivo glucose test strip uses a mediator in place of oxygen to free it from oxygen dependency. The mediator-based technology, in most cases cannot be transferred to in vivo applications due to the …

Alterations In Excitatory And Inhibitory Synaptic Development Within The Mesolimbic Dopamine Pathway In A Mouse Model Of Prenatal Drug Exposure, Taylor Boggess, James C. Williamson, Ethan B. Niebergall, Hannah Sexton, Richard D. Egleton, Larry Grover, Chris Risher

Biomedical Sciences

The rise in rates of opioid abuse in recent years in the United States has led to a dramatic increase in the incidence of neonatal abstinence syndrome (NAS). Despite improved understanding of NAS and its acute symptoms, there remains a paucity of information regarding the long-term effects of prenatal exposure to drugs of abuse on neurological development. The primary goal of this study was to investigate the effects of prenatal drug exposure on synaptic connectivity within brain regions associated with the mesolimbic dopamine pathway, the primary reward pathway associated with drug abuse and addiction, in a mouse model. Our secondary …

Characterizing And Overcoming Resistance To Aminomethylspectinomycins In Gram-Negative Bacteria, Nisha Das

Theses and Dissertations (ETD)

Spectinomycin (SPC) is a broad-spectrum aminocyclitol antibiotic. Its use in agriculture has led to widespread resistance in enteric bacteria, necessitating the development of more effective analogs. Aminomethyl spectinomycins (amSPC) are modified spectinomycins with increased potency against many bacterial species. These species include Legionella pneumophila, which harbors a chromosomally encoded aminoglycoside modifying enzyme (AME). In this study, we follow up on this observation and examine the extent to which the amSPCs are substrates for AMEs through adenylation (ANTs) and phosphorylation (APH). APH(9)-Ia and ANT(3")(9) were expressed in E. coli BL21(DE3) and purified using the Ni-affinity chromatography. The ability of AMEs to …

Understanding Blue Light Retinal Damages And The Methods Of Prevention, Amelia Lee

Senior Honors Theses

Light emitting diode (LED) lights that comprise television screens, phone displays, laptops, and tablets have been studied by scientists in order to understand the implications of blue light radiation and the effects that it has on the human body—especially the retina of the eye. The retina is comprised of highly metabolic cells, and when those cells are placed under oxidative stress, death occurs causing ocular disease. Additionally, excess blue light exposure causes shifts in biological rhythms that govern patterns of alertness and sleep. Recently scientists began studying the methods of blue light prevention. Some studies show that blue light radiation …

Association Of Serum Magnesium With Blood Pressure In Patients With Hypertensive Crises: A Retrospective Cross-Sectional Study, Ifeanyichukwu O. Onor, Lashira M. Hill, Modupe M. Famodimu, Mallory R. Coleman, Carolkim H. Huynh, Robbie A. Beyl, Casey J. Payne, Emily K. Johnston, John I. Okogbaa, Christopher J. Gillard, Daniel F. Sarpong, Amne Borghol, Samuel C. Okpechi, Ifeyinwa Norbert, Shane E. Sanne, Shane G. Guillory

School of Graduate Studies Faculty Publications

The role of magnesium in blood pressure has been studied among hypertensive patients; however, there is a dearth of studies exploring the role of magnesium in hypertensive crises. The primary objective of this study was to evaluate the relationship between serum magnesium and blood pressure in patients with hypertensive crises. This was a singlecenter, retrospective, chart review, cross-sectional study of patients with hypertensive crises. Patients were included if they were eighteen years of age or older, with an international classification disease ninth revision (ICD-9) code of 401.9 (hypertensive crises: emergency or urgency) and a documented magnesium level on their electronic …

Tera-Seq: True End-To-End Sequencing Of Native Rna Molecules For Transcriptome Characterization, Fadia Ibrahim, Jan Oppelt, Manolis Maragkakis, Zissimos Mourelatos

Department of Biochemistry and Molecular Biology Faculty Papers

Direct sequencing of single, native RNA molecules through nanopores has a strong potential to transform research in all aspects of RNA biology and clinical diagnostics. The existing platform from Oxford Nanopore Technologies is unable to sequence the very 5′ ends of RNAs and is limited to polyadenylated molecules. Here, we develop True End-to-end RNA Sequencing (TERA-Seq), a platform that addresses these limitations, permitting more thorough transcriptome characterization. TERA-Seq describes both poly-and non-polyadenylated RNA molecules and accurately identifies their native 5′ and 3′ ends by ligating uniquely designed adapters that are sequenced along with the transcript. We find that capped, full-length …

Expression And Purification Of Phage T7 Ejection Proteins For Cryo-Em Analysis, Nicholas A. Swanson, Ravi K Lokareddy, Fenglin Li, Chun-Feng Hou, Mikhail Pavlenok, Michael Niederweis, Gino Cingolani

Department of Biochemistry and Molecular Biology Faculty Papers

Bacteriophages of the Podoviridae family densely package their genomes into precursor capsids alongside internal virion proteins called ejection proteins. In phage T7 these proteins (gp14, gp15, and gp16) are ejected into the host envelope forming a DNA-ejectosome for genome delivery. Here, we describe the purification and characterization of recombinant gp14, gp15, and gp16. This protocol was used for high-resolution cryo-EM structure analysis of the T7 periplasmic tunnel and can be adapted to study ejection proteins from other phages. For complete details on the use and execution of this protocol, please refer to Swanson et al.

Inability To Switch From Arid1a-Baf To Arid1b-Baf Impairs Exit From Pluripotency And Commitment Towards Neural Crest Formation In Arid1b-Related Neurodevelopmental Disorders, Luca Pagliaroli, Patrizia Porazzi, Alyxandra T Curtis, Chiara Scopa, Harald M M Mikkers, Christian Freund, Lucia Daxinger, Sandra Deliard, Sarah A Welsh, Sarah Offley, Connor A Ott, Bruno Calabretta, Samantha A Brugmann, Gijs W E Santen, Marco Trizzino

Department of Biochemistry and Molecular Biology Faculty Papers

Subunit switches in the BAF chromatin remodeler are essential during development. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause neurodevelopmental disorders, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we leveraged ARID1B+/- Coffin-Siris patient-derived iPSCs and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF). ARID1B-BAF regulates exit from pluripotency and lineage commitment by attenuating thousands of enhancers and genes of …

Multifunctionality Of Prostatic Acid Phosphatase In Prostate Cancer Pathogenesis, Evgenia Alpert, Armin Akhavan, Arie Gruzman, William J. Hansen, Joshua Lehrer-Graiwer, Steven C. Hall, Eric Johansen, Sean Mcallister, Mittul Gulati, Ming-Fong Lin, Vishwanath R Lingappa

Journal Articles: Biochemistry & Molecular Biology

The role of human prostatic acid phosphatase (PAcP, P15309|PPAP_HUMAN) in prostate cancer was investigated using a new proteomics tool termed signal sequence swapping (replacement of domains from the native cleaved amino terminal signal sequence of secretory/membrane proteins with corresponding regions of functionally distinct signal sequence subtypes). This manipulation preferentially redirects proteins to different pathways of biogenesis at the endoplasmic reticulum (ER), magnifying normally difficult to detect subsets of the protein of interest. For PAcP, this technique reveals three forms identical in amino acid sequence but profoundly different in physiological functions, subcellular location, and biochemical properties. These three forms of PAcP …