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Molecular Biosciences Theses and Dissertations

Theses/dissertations from 2024 2024.

Androgen Drives Melanoma Invasiveness and Metastatic Spread by Inducing Tumorigenic Fucosylation , Qian Liu

Theses/Dissertations from 2023 2023

Exploring strain variation and bacteriophage predation in the gut microbiome of Ciona robusta , Celine Grace F. Atkinson

Distinct Nrf2 Signaling Thresholds Mediate Lung Tumor Initiation and Progression , Janine M. DeBlasi

Thermodynamic frustration of TAD2 and PRR contribute to autoinhibition of p53 , Emily Gregory

Utilization of Detonation Nanodiamonds: Nanocarrier for Gene Therapy in Non-Small Cell Lung Cancer , Allan E. Gutierrez

Role of HLA-DRB1 Fucosylation in Anti-Melanoma Immunity , Daniel K. Lester

Targeting BET Proteins Downregulates miR-33a To Promote Synergy with PIM Inhibitors in CMML , Christopher T. Letson

Regulated Intramembrane Proteolysis by M82 Peptidases: The Role of PrsS in the Staphylococcus aureus Stress Response , Baylie M. Schott

Histone Deacetylase 8 is a Novel Therapeutic Target for Mantle Cell Lymphoma and Preserves Natural Killer Cell Cytotoxic Function , January M. Watters

Theses/Dissertations from 2022 2022

Regulation of the Heat Shock Response via Lysine Acetyltransferase CBP-1 and in Neurodegenerative Disease in Caenorhabditis elegans , Lindsey N. Barrett

Determining the Role of Dendritic Cells During Response to Treatment with Paclitaxel/Anti-TIM-3 , Alycia Gardner

Cell-free DNA Methylation Signatures in Cancer Detection and Classification , Jinyong Huang

The Role Of Eicosanoid Metabolism in Mammalian Wound Healing and Inflammation , Kenneth D. Maus

A Holistic Investigation of Acidosis in Breast Cancer , Bryce Ordway

Characterizing the Impact of Postharvest Temperature Stress on Polyphenol Profiles of Red and White-Fruited Strawberry Cultivars , Alyssa N. Smith

Theses/Dissertations from 2021 2021

Multifaceted Approach to Understanding Acinetobacter baumannii Biofilm Formation and Drug Resistance , Jessie L. Allen

Cellular And Molecular Alterations Associated with Ovarian and Renal Cancer Pathophysiology , Ravneet Kaur Chhabra

Ecology and diversity of boletes of the southeastern United States , Arian Farid

CircREV1 Expression in Triple-Negative Breast Cancer , Meagan P. Horton

Microbial Dark Matter: Culturing the Uncultured in Search of Novel Chemotaxonomy , Sarah J. Kennedy

The Multifaceted Role of CCAR-1 in the Alternative Splicing and Germline Regulation in Caenorhabditis elegans , Doreen Ikhuva Lugano

Unraveling the Role of Novel G5 Peptidase Family Proteins in Virulence and Cell Envelope Biogenesis of Staphylococcus aureus , Stephanie M. Marroquin

Cytoplasmic Polyadenylation Element Binding Protein 2 Alternative Splicing Regulates HIF1α During Chronic Hypoxia , Emily M. Mayo

Transcriptomic and Functional Investigation of Bacterial Biofilm Formation , Brooke R. Nemec

A Functional Characterization of the Omega (ω) subunit of RNA Polymerase in Staphylococcus aureus , Shrushti B. Patil

The Role Of Cpeb2 Alternative Splicing In TNBC Metastasis , Shaun C. Stevens

Screening Next-generation Fluorine-19 Probe and Preparation of Yeast-derived G Proteins for GPCR Conformation and Dynamics Study , Wenjie Zhao

Theses/Dissertations from 2020 2020

Understanding the Role of Cereblon in Hematopoiesis Through Structural and Functional Analyses , Afua Adutwumwa Akuffo

To Mid-cell and Beyond: Characterizing the Roles of GpsB and YpsA in Cell Division Regulation in Gram-positive Bacteria , Robert S. Brzozowski

Spatiotemporal Changes of Microbial Community Assemblages and Functions in the Subsurface , Madison C. Davis

New Mechanisms That Regulate DNA Double-Strand Break-Induced Gene Silencing and Genome Integrity , Dante Francis DeAscanis

Regulation of the Heat Shock Response and HSF-1 Nuclear Stress Bodies in C. elegans , Andrew Deonarine

New Mechanisms that Control FACT Histone Chaperone and Transcription-mediated Genome Stability , Angelo Vincenzo de Vivo Diaz

Targeting the ESKAPE Pathogens by Botanical and Microbial Approaches , Emily Dilandro

Succession in native groundwater microbial communities in response to effluent wastewater , Chelsea M. Dinon

Role of ceramide-1 phosphate in regulation of sphingolipid and eicosanoid metabolism in lung epithelial cells , Brittany A. Dudley

Allosteric Control of Proteins: New Methods and Mechanisms , Nalvi Duro

Microbial Community Structures in Three Bahamian Blue Holes , Meghan J. Gordon

A Novel Intramolecular Interaction in P53 , Fan He

The Impact of Myeloid-Mediated Co-Stimulation and Immunosuppression on the Anti-Tumor Efficacy of Adoptive T cell Therapy , Pasquale Patrick Innamarato

Investigating Mechanisms of Immune Suppression Secondary to an Inflammatory Microenvironment , Wendy Michelle Kandell

Posttranslational Modification and Protein Disorder Regulate Protein-Protein Interactions and DNA Binding Specificity of p53 , Robin Levy

Mechanistic and Translational Studies on Skeletal Malignancies , Jeremy McGuire

Novel Long Non-Coding RNA CDLINC Promotes NSCLC Progression , Christina J. Moss

Genome Maintenance Roles of Polycomb Transcriptional Repressors BMI1 and RNF2 , Anthony Richard Sanchez IV

The Ecology and Conservation of an Urban Karst Subterranean Estuary , Robert J. Scharping

Biological and Proteomic Characterization of Cornus officinalis on Human 1.1B4 Pancreatic β Cells: Exploring Use for T1D Interventional Application , Arielle E. Tawfik

Evaluation of Aging and Genetic Mutation Variants on Tauopathy , Amber M. Tetlow

Theses/Dissertations from 2019 2019

Investigating the Proteinaceous Regulome of the Acinetobacter baumannii , Leila G. Casella

Functional Characterization of the Ovarian Tumor Domain Deubiquitinating Enzyme 6B , Jasmin M. D'Andrea

Integrated Molecular Characterization of Lung Adenocarcinoma with Implications for Immunotherapy , Nicholas T. Gimbrone

The Role of Secreted Proteases in Regulating Disease Progression in Staphylococcus aureus , Brittney D. Gimza

Advanced Proteomic and Epigenetic Characterization of Ethanol-Induced Microglial Activation , Jennifer Guergues Guergues

Understanding immunometabolic and suppressive factors that impact cancer development , Rebecca Swearingen Hesterberg

Biochemical and Proteomic Approaches to Determine the Impact Level of Each Step of the Supply Chain on Tomato Fruit Quality , Robert T. Madden

Enhancing Immunotherapeutic Interventions for Treatment of Chronic Lymphocytic Leukemia , Kamira K. Maharaj

Characterization of the Autophagic-Iron Axis in the Pathophysiology of Endometriosis and Epithelial Ovarian Cancers , Stephanie Rockfield

Understanding the Influence of the Cancer Microenvironment on Metabolism and Metastasis , Shonagh Russell

Modeling of Interaction of Ions with Ether- and Ester-linked Phospholipids , Matthew W. Saunders

Novel Insights into the Multifaceted Roles of BLM in the Maintenance of Genome Stability , Vivek M. Shastri

Conserved glycine residues control transient helicity and disorder in the cold regulated protein, Cor15a , Oluwakemi Sowemimo

A Novel Cytokine Response Modulatory Function of MEK Inhibitors Mediates Therapeutic Efficacy , Mengyu Xie

Novel Strategies on Characterizing Biologically Specific Protein-protein Interaction Networks , Bi Zhao

Theses/Dissertations from 2018 2018

Characterization of the Transcriptional Elongation Factor ELL3 in B cells and Its Role in B-cell Lymphoma Proliferation and Survival , Lou-Ella M.m. Alexander

Identification of Regulatory miRNAs Associated with Ethanol-Induced Microglial Activation Using Integrated Proteomic and Transcriptomic Approaches , Brandi Jo Cook

Molecular Phylogenetics of Floridian Boletes , Arian Farid

MYC Distant Enhancers Underlie Ovarian Cancer Susceptibility at the 8q24.21 Locus , Anxhela Gjyshi Gustafson

Quantitative Proteomics to Support Translational Cancer Research , Melissa Hoffman

A Systems Chemical Biology Approach for Dissecting Differential Molecular Mechanisms of Action of Clinical Kinase Inhibitors in Lung Cancer , Natalia Junqueira Sumi

Investigating the Roles of Fucosylation and Calcium Signaling in Melanoma Invasion , Tyler S. Keeley

Synthesis, Oxidation, and Distribution of Polyphenols in Strawberry Fruit During Cold Storage , Katrina E. Kelly

Investigation of Alcohol-Induced Changes in Hepatic Histone Modifications Using Mass Spectrometry Based Proteomics , Crystina Leah Kriss

Off-Target Based Drug Repurposing Using Systems Pharmacology , Brent M. Kuenzi

Investigation of Anemarrhena asphodeloides and its Constituent Timosaponin-AIII as Novel, Naturally Derived Adjunctive Therapeutics for the Treatment of Advanced Pancreatic Cancer , Catherine B. MarElia

The Role of Phosphohistidine Phosphatase 1 in Ethanol-induced Liver Injury , Daniel Richard Martin

Theses/Dissertations from 2017 2017

Changing the Pathobiological Paradigm in Myelodysplastic Syndromes: The NLRP3 Inflammasome Drives the MDS Phenotype , Ashley Basiorka

Modeling of Dynamic Allostery in Proteins Enabled by Machine Learning , Mohsen Botlani-Esfahani

Uncovering Transcriptional Activators and Targets of HSF-1 in Caenorhabditis elegans , Jessica Brunquell

The Role of Sgs1 and Exo1 in the Maintenance of Genome Stability. , Lillian Campos-Doerfler

Mechanisms of IKBKE Activation in Cancer , Sridevi Challa

Discovering Antibacterial and Anti-Resistance Agents Targeting Multi-Drug Resistant ESKAPE Pathogens , Renee Fleeman

Functional Roles of Matrix Metalloproteinases in Bone Metastatic Prostate Cancer , Jeremy S. Frieling

Disorder Levels of c-Myb Transactivation Domain Regulate its Binding Affinity to the KIX Domain of CREB Binding Protein , Anusha Poosapati

Role of Heat Shock Transcription Factor 1 in Ovarian Cancer Epithelial-Mesenchymal Transition and Drug Sensitivity , Chase David Powell

Cell Division Regulation in Staphylococcus aureus , Catherine M. Spanoudis

A Novel Approach to the Discovery of Natural Products From Actinobacteria , Rahmy Tawfik

Non-classical regulators in Staphylococcus aureus , Andy Weiss

Theses/Dissertations from 2016 2016

In Vitro and In Vivo Antioxidant Capacity of Synthetic and Natural Polyphenolic Compounds Identified from Strawberry and Fruit Juices , Marvin Abountiolas

Quantitative Proteomic Investigation of Disease Models of Type 2 Diabetes , Mark Gabriel Athanason

CMG Helicase Assembly and Activation: Regulation by c-Myc through Chromatin Decondensation and Novel Therapeutic Avenues for Cancer Treatment , Victoria Bryant

Computational Modeling of Allosteric Stimulation of Nipah Virus Host Binding Protein , Priyanka Dutta

Cell Cycle Arrest by TGFß1 is Dependent on the Inhibition of CMG Helicase Assembly and Activation , Brook Samuel Nepon-Sixt

Gene Expression Profiling and the Role of HSF1 in Ovarian Cancer in 3D Spheroid Models , Trillitye Paullin

VDR-RIPK1 Interaction and its Implications in Cell Death and Cancer Intervention , Waise Quarni

Regulation of nAChRs and Stemness by Nicotine and E-cigarettes in NSCLC , Courtney Schaal

Targeting Histone Deacetylases in Melanoma and T-cells to Improve Cancer Immunotherapy , Andressa Sodre De Castro Laino

Nonreplicative DNA Helicases Involved in Maintaining Genome Stability , Salahuddin Syed

Theses/Dissertations from 2015 2015

Functional Analysis of the Ovarian Cancer Susceptibility Locus at 9p22.2 Reveals a Transcription Regulatory Network Mediated by BNC2 in Ovarian Cells , Melissa Buckley

Exploring the Pathogenic and Drug Resistance Mechanisms of Staphylococcus aureus , Whittney Burda

Regulation and Targeting of the FANCD2 Activation in DNA Repair , Valentina Celeste Caceres

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Page 1 of 17

PSMD1 and PSMD2 regulate HepG2 cell proliferation and apoptosis via modulating cellular lipid droplet metabolism

Obesity and nonalcoholic steatohepatitis (NASH) are well-known risk factors of hepatocellular carcinoma (HCC). The lipid-rich environment enhances the proliferation and metastasis abilities of tumor cells. Pre...

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The effect of BACE1-AS on β-amyloid generation by regulating BACE1 mRNA expression

The BACE1 antisense transcript (BACE1-AS) is a conserved long noncoding RNA (lncRNA). The level of BACE1-AS is significantly increased and the level of the BACE1 mRNA is slightly increased in subjects with AD....

Overlapping transcriptional expression response of wheat zinc-induced facilitator-like transporters emphasize important role during Fe and Zn stress

Hexaploid wheat is an important cereal crop that has been targeted to enhance grain micronutrient content including zinc (Zn) and iron (Fe). In this direction, modulating the expression of plant transporters i...

MiR-32-5p influences high glucose-induced cardiac fibroblast proliferation and phenotypic alteration by inhibiting DUSP1

The current study aimed to investigate the effects of miR-32-5p on cardiac fibroblasts (CFs) that were induced with high levels of glucose; we also aimed to identify the potential mechanisms involved in the re...

Correction to: A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone

The original article [1] contains three erroneous mentions of usage of a restriction enzyme— Bst Z17I—in the Methods section as displayed in the following sentences.

The original article was published in BMC Molecular Biology 2018 19 :3

Comparison of miRNA - 101a - 3p and miRNA - 144a - 3p regulation with the key genes of alpaca melanocyte pigmentation

Many miRNA functions have been revealed to date. Single miRNAs can participate in life processes by regulating more than one target gene, and more than one miRNA can also simultaneously act on one target mRNA....

Correction to: MicroRNA-325-3p protects the heart after myocardial infarction by inhibiting RIPK3 and programmed necrosis in mice

The original article [1] contains an error whereby Fig. 7 displays incorrect results; the correct version of Fig. 7 can be viewed ahead in this Correction article and should be considered in place of the origi...

The original article was published in BMC Molecular Biology 2019 20 :17

MicroRNA-325-3p protects the heart after myocardial infarction by inhibiting RIPK3 and programmed necrosis in mice

Receptor-interacting serine-threonine kinase 3 (RIPK3)-mediated necroptosis has been implicated in the progression of myocardial infarction (MI), but the underlying mechanisms, particularly whether microRNAs (...

The Correction to this article has been published in BMC Molecular Biology 2019 20 :18

Giant group I intron in a mitochondrial genome is removed by RNA back-splicing

The mitochondrial genomes of mushroom corals (Corallimorpharia) are remarkable for harboring two complex group I introns; ND5-717 and COI-884. How these autocatalytic RNA elements interfere with mitochondrial ...

Exploration of carbohydrate binding behavior and anti-proliferative activities of Arisaema tortuosum lectin

Lectins have come a long way from being identified as proteins that agglutinate cells to promising therapeutic agents in modern medicine. Through their specific binding property, they have proven to be anti-ca...

Characterization of cadmium-responsive MicroRNAs and their target genes in maize ( Zea mays ) roots

Current research has shown that microRNAs (miRNAs) play vital roles in plant response to stress caused by heavy metals such as aluminum, arsenic, cadmium (Cd), and mercury. Cd has become one of the most hazard...

Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute

With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene e...

Small nucleolar RNA Sf-15 regulates proliferation and apoptosis of Spodoptera frugiperda Sf9 cells

Small nucleolar RNAs (snoRNAs) function in guiding 2′- O -methylation and pseudouridylation of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In recent years, more and more snoRNAs have been found to play ...

Key genes differential expressions and pathway involved in salt and water-deprivation stresses for renal cortex in camel

Camels possess the characteristics of salt- and drought-resistances, due to the long-time adaption to the living environment in desert. The camel resistance research on transcriptome is rare and deficient, esp...

Development of a novel selection/counter-selection system for chromosomal gene integrations and deletions in lactic acid bacteria

The underlying mechanisms by which probiotic lactic acid bacteria (LAB) enhance the health of the consumer have not been fully elucidated. Verification of probiotic modes of action can be achieved by using sin...

Selection of reference genes for the quantitative real-time PCR normalization of gene expression in Isatis indigotica fortune

Isatis indigotica , a traditional Chinese medicine, produces a variety of active ingredients. However, little is known about the key genes and corresponding expression profiling involved in the biosynthesis pathwa...

MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells

Myocyte enhancer factor 2A (MEF2A) plays an important role in cell proliferation, differentiation and survival. Functional deletion or mutation in MEF2A predisposes individuals to cardiovascular disease mainly...

Transcriptomic responses to grazing reveal the metabolic pathway leading to the biosynthesis of domoic acid and highlight different defense strategies in diatoms

A major cause of phytoplankton mortality is predation by zooplankton. Strategies to avoid grazers have probably played a major role in the evolution of phytoplankton and impacted bloom dynamics and trophic ene...

RNA sequencing, selection of reference genes and demonstration of feeding RNAi in Thrips tabaci (Lind.) (Thysanoptera: Thripidae)

Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this ins...

A fragment activity assay reveals the key residues of TBC1D15 GTPase-activating protein (GAP) in Chiloscyllium plagiosum

GTPase-activating proteins (GAPs) with a TBC (Tre-2/Bub2/Cdc16) domain architecture serve as negative regulators of Rab GTPases. The related crystal structure has been studied and reported by other members of ...

HexA is required for growth, aflatoxin biosynthesis and virulence in Aspergillus flavus

Woronin bodies are fungal-specific organelles whose formation is derived from peroxisomes. The former are believed to be involved in the regulation of mycotoxins biosynthesis, but not in their damage repair fu...

Genome-wide identification of brain miRNAs in response to high-intensity intermittent swimming training in Rattus norvegicus by deep sequencing

Physical exercise can improve brain function by altering brain gene expression. The expression mechanisms underlying the brain’s response to exercise still remain unknown. miRNAs as vital regulators of gene ex...

Graphene oxide down-regulates genes of the oxidative phosphorylation complexes in a glioblastoma

Recently different forms of nanographene were proposed as the material with high anticancer potential. However, the mechanism of the suppressive activity of the graphene on cancer development remains unclear. ...

MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness

MicroRNAs (miRNAs) are small noncoding RNAs of approximately 22 nucleotides, highly conserved among species, which modulate gene expression by cleaving messenger RNA target or inhibiting translation. MiRNAs ar...

The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication

DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to a...

Matrix association region/scaffold attachment region (MAR/SAR) sequence: its vital role in mediating chromosome breakages in nasopharyngeal epithelial cells via oxidative stress-induced apoptosis

Oxidative stress is known to be involved in most of the aetiological factors of nasopharyngeal carcinoma (NPC). Cells that are under oxidative stress may undergo apoptosis. We have previously demonstrated that...

Molecular analysis of NPAS3 functional domains and variants

NPAS3 encodes a transcription factor which has been associated with multiple human psychiatric and neurodevelopmental disorders. In mice, deletion of Npas3 was found to cause alterations in neurodevelopment, as w...

Integration of transcriptome and proteome profiles in glioblastoma: looking for the missing link

Glioblastoma (GB) is the most common and aggressive tumor of the brain. Genotype-based approaches and independent analyses of the transcriptome or the proteome have led to progress in understanding the underly...

Analyses of changes in myocardial long non-coding RNA and mRNA profiles after severe hemorrhagic shock and resuscitation via RNA sequencing in a rat model

Ischemia–reperfusion injury has been proven to induce organ dysfunction and death, although the mechanism is not fully understood. Long non-coding RNAs (lncRNAs) have drawn wide attention with their important ...

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis

Brucella melitensis bacteria cause persistent, intracellular infections in small ruminants as well as in humans, leading to significant morbidity and economic loss worldwide. The majority of experiments on the tr...

Positive cofactor 4 (PC4) contributes to the regulation of replication-dependent canonical histone gene expression

Core canonical histones are required in the S phase of the cell cycle to pack newly synthetized DNA, therefore the expression of their genes is highly activated during DNA replication. In mammalian cells, this...

Evaluation of suitable reference genes for qRT-PCR normalization in strawberry ( Fragaria  ×  ananassa ) under different experimental conditions

Strawberry has received much attention due to its nutritional value, unique flavor, and attractive appearance. The availability of the whole genome sequence and multiple transcriptome databases allows the grea...

Laser capture microdissection for transcriptomic profiles in human skin biopsies

The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-...

Targeting miR-9 in gastric cancer cells using locked nucleic acid oligonucleotides

Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recently, it has been demonstrated that gastric cancer cells display a specific miRNA expression profile, with increasing eviden...

Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

BATF family transcription factors (BATF, BATF2 and BATF3) form hetero-trimers with JUNB and either IRF4 or IRF8 to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the heter...

pH-mediated upregulation of AQP1 gene expression through the Spi-B transcription factor

Bicarbonate-based peritoneal dialysis (PD) fluids enhance the migratory capacity and damage-repair ability of human peritoneal mesothelial cells by upregulating AQP1. However, little is known about the underly...

A protocol for custom CRISPR Cas9 donor vector construction to truncate genes in mammalian cells using pcDNA3 backbone

Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided adaptive immune systems are found in prokaryotes to defend cells from foreign DNA. CRISPR Cas9 systems have been modified and employ...

The Correction to this article has been published in BMC Molecular Biology 2019 20 :20

Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples

Glomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve r...

Nutrient depletion and TOR inhibition induce 18S and 25S ribosomal RNAs resistant to a 5′-phosphate-dependent exonuclease in Candida albicans and other yeasts

Messenger RNA (mRNA) represents a small percentage of RNAs in a cell, with ribosomal RNA (rRNA) making up the bulk of it. To isolate mRNA from eukaryotes, typically poly-A selection is carried out. Recently, a...

An optimized rapid bisulfite conversion method with high recovery of cell-free DNA

Methylation analysis of cell-free DNA is a encouraging tool for tumor diagnosis, monitoring and prognosis. Sensitivity of methylation analysis is a very important matter due to the tiny amounts of cell-free DN...

Sumoylation in p27kip1 via RanBP2 promotes cancer cell growth in cholangiocarcinoma cell line QBC939

Cholangiocarcinoma is one of the deadly disease with poor 5-year survival and poor response to conventional therapies. Previously, we found that p27kip1 nuclear-cytoplasmic translocation confers proliferation ...

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing

Formalin-fixed paraffin embedded (FFPE) tissue constitutes a vast treasury of samples for biomedical research. Thus far however, extraction of RNA from FFPE tissue has proved challenging due to chemical RNA–pr...

Physical shearing imparts biological activity to DNA and ability to transmit itself horizontally across species and kingdom boundaries

We have recently reported that cell-free DNA (cfDNA) fragments derived from dying cells that circulate in blood are biologically active molecules and can readily enter into healthy cells to activate DNA damage...

Interaction between NFATc2 and the transcription factor Sp1 in pancreatic carcinoma cells PaTu 8988t

Nuclear factors of activated T-cells (NFATs) have been mainly characterized in the context of immune response regulation because, as transcription factors, they have the ability to induce gene transcription. N...

Splicing arrays reveal novel RBM10 targets, including SMN2 pre-mRNA

RBM10 is an RNA binding protein involved in message stabilization and alternative splicing regulation. The objective of the research described herein was to identify novel targets of RBM10-regulated splicing. ...

Growth arrest specific gene 2 in tilapia ( Oreochromis niloticus ): molecular characterization and functional analysis under low-temperature stress

Growth arrest specific 2 ( gas2 ) gene is a component of the microfilament system that plays a major role in the cell cycle, regulation of microfilaments, and cell morphology during apoptotic processes. However, li...

Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands

G-quadruplex is a DNA secondary structure that has been shown to play an important role in biological systems. In a previous study, we identified 1998 G-quadruplex-forming sequences using a mouse CpG islands D...

Mitochondrial RNA processing in absence of tRNA punctuations in octocorals

Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interes...

Microarray expression profiling in the denervated hippocampus identifies long noncoding RNAs functionally involved in neurogenesis

The denervated hippocampus provides a proper microenvironment for the survival and neuronal differentiation of neural progenitors. While thousands of lncRNAs were identified, only a few lncRNAs that regulate n...

Early growth response protein 1 regulates promoter activity of α -plasma membrane calcium ATPase 2, a major calcium pump in the brain and auditory system

Along with sodium/calcium (Ca 2+ ) exchangers, plasma membrane Ca 2+ ATPases (ATP2Bs) are main regulators of intracellular Ca 2+ levels. There are four ATP2B paralogs encoded by four different genes. Atp2b2 encodes t...

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Page 1 of 24

Circulating microRNAs as potential biomarkers of physical activity in geriatric patients with HCV

Circulating microRNAs have been implicated in a diverse array of biological and pathological phenomena. Their potential utility as noninvasive biomarkers for screening and diagnosing various diseases has been ...

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Correction: The primary cilium dampens proliferative signaling and represses a G2/M transcriptional network in quiescent myoblasts

The original article was published in BMC Molecular and Cell Biology 2020 21 :25

Upregulated dual oxidase 1-induced oxidative stress and caspase-1-dependent pyroptosis reflect the etiologies of heart failure

Oxidative stress is implicated in the pathogenesis of heart failure. Dual oxidase 1 (DUOX1) might be important in heart failure development through its mediating role in oxidative stress. This study was design...

Comparing chemical transfection, electroporation, and lentiviral vector transduction to achieve optimal transfection conditions in the Vero cell line

Transfection is an important analytical method for studying gene expression in the cellular environment. There are some barriers to efficient DNA transfection in host cells, including circumventing the plasma ...

High-fat diet enhances cell proliferation and compromises intestinal permeability in a translational canine intestinal organoid model

Emerging evidence underscores the responsiveness of the mammalian intestine to dietary cues, notably through the involvement of LGR5 + intestinal stem cells in orchestrating responses to diet-driven signals. H...

mTOR signaling pathway regulation HIF-1 α effects on LPS induced intestinal mucosal epithelial model damage

Sepsis-induced small-intestinal injury is associated with increased morbidity and mortality. Our previous study and other papers have shown that HIF-1α has a protective effect on intestinal mucosal injury in s...

Long non-coding RNA SOX2OT in tamoxifen-resistant breast cancer

Hormone receptor (HR)-positive breast cancer can become aggressive after developing hormone-treatment resistance. This study elucidated the role of long non-coding RNA (lncRNA) SOX2OT in tamoxifen-resistant (T...

Mice lacking DIO3 exhibit sex-specific alterations in circadian patterns of corticosterone and gene expression in metabolic tissues

Disruption of circadian rhythms is associated with neurological, endocrine and metabolic pathologies. We have recently shown that mice lacking functional type 3 deiodinase (DIO3), the enzyme that clears thyroi...

Optimization of seeding density of OP9 cells to improve hematopoietic differentiation efficiency

OP9 mouse stromal cell line has been widely used to induce differentiation of human embryonic stem cells (hESCs) into hematopoietic stem/progenitor cells (HSPCs). However, the whole co-culture procedure usuall...

Development of an in vitro human alveolar epithelial air-liquid interface model using a small molecule inhibitor cocktail

The alveolar epithelium is exposed to numerous stimuli, such as chemicals, viruses, and bacteria that cause a variety of pulmonary diseases through inhalation. Alveolar epithelial cells (AECs) cultured in vitr...

Mechanical stretch leads to increased caveolin-1 content and mineralization potential in extracellular vesicles from vascular smooth muscle cells

Hypertension-induced mechanical stress on vascular smooth muscle cells (VSMCs) is a known risk factor for vascular remodeling, including vascular calcification. Caveolin-1 (Cav-1), an integral structural compo...

Melatonin reduces lung injury in type 1 diabetic mice by the modulation of autophagy

In recent years, the role of autophagy has been highlighted in the pathogenesis of diabetes and inflammatory lung diseases. In this study, using a diabetic model of mice, we investigated the expression of auto...

TonEBP/NFAT5 expression is associated with cisplatin resistance and migration in macrophage-induced A549 cells

Macrophages promote angiogenesis, metastasis, and drug resistance in several cancers. Similarly, TonEBP/NFAT5 induces metastasis in renal carcinoma and colon cancer cells. However, the role of this transcripti...

Optimizing combination therapy in prostate cancer: mechanistic insights into the synergistic effects of Paclitaxel and Sulforaphane-induced apoptosis

Combination therapies in cancer treatment have demonstrated synergistic or additive outcomes while also reducing the development of drug resistance compared to monotherapy. This study explores the potential of...

CTC together with Shh and Nrf2 are prospective diagnostic markers for HNSCC

The lack of appropriate prognostic biomarkers remains a significant obstacle in the early detection of Head and Neck Squamous Cell Carcinoma (HNSCC), a cancer type with a high mortality rate. Despite considera...

Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis

Trypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug resistance. While identifying novel drug targets is vital, the process is dela...

Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function

Fas-associated factor 1 (FAF1) is a multidomain protein that interacts with diverse partners to affect numerous cellular processes. Previously, we discovered two Small Ubiquitin-like Modifier (SUMO)-interactin...

Loss of Dec1 inhibits alcohol-induced hepatic lipid accumulation and circadian rhythm disorder

Chronic alcohol exposure increases liver damage such as lipid accumulation and hepatitis, resulting in hepatic cirrhosis. Chronic alcohol intake is known to disturb circadian rhythms in humans and animals. DEC...

Association between plasma L-carnitine levels and mitochondrial DNA copy number

Mitochondria are key cytoplasmic organelles in eukaryotic cells that generate adenosine triphosphate (ATP) through the electron transport chain and oxidative phosphorylation. Mitochondrial DNA (mtDNA) copy num...

Effect of Emi1 gene silencing on the proliferation and invasion of human breast cancer cells

Breast cancer is the most common malignant tumour in women. The early silk-splitting inhibitor protein 1 Emi1 is responsible for mediating ubiquitin protein degradation. The present study investigated the effe...

TNFα induces Caspase-3 activity in hematopoietic progenitor cells CD34+, CD33+, and CD41 + of myelodysplastic syndromes

Cytopenia is the primary feature of Myelodysplastic Syndrome, even in the presence of hypercellular bone marrow. TNFα is recognized as both a proinflammatory, and proapoptotic cytokine with a well established ...

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Basic Concepts in Molecular Biology

Cite this chapter.

• Paul J. R. Barton Ph.D. 2 ,
• Kenneth R. Boheler Ph.D. 2 ,
• Nigel J. Brand Ph.D. 2 &
• Penny S. Thomas D.Phil. 2  

Part of the book series: Medical Intelligence Unit ((MIU.LANDES))

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1 Citations

T he term molecular biology is generally used to refer to basic and clinical research which involves the techniques of molecular cloning and genetic engineering. Within this rather broad range of interests three overlapping and complementary themes can be identified. Firstly, molecular biology can be thought of as a basic science in its own right. In this respect it refers to research into the molecular mechanisms which are involved in gene expression and its regulation. This area of research is of fundamental importance to the understanding of embryonic and fetal development which is characterized by precise temporal and spatial patterns of gene expression leading, ultimately, to the formation of specialized tissue types. 1 Secondly, molecular biology has provided the technological basis for rapid advances in the field of medical genetics. 2 The ability to identify and isolate individual genes has led to the characterization of gene defects involved in inherited disorders including cystic fibrosis, 3 Duchenne muscular dystrophy, 4 Marfan syndrome 5 and familial cases of hypertrophic cardiomyopathy 6,7 (see chapter 6). Thirdly, molecular biology provides powerful and versatile tools for examining and manipulating biological processes at the molecular level. DNA can be manipulated in vitro and reintroduced into cells in culture or into whole animals (using for example transgenic techniques), allowing the functional role of cellular components to be examined in vivo.

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Barton, P.J.R., Boheler, K.R., Brand, N.J., Thomas, P.S. (1995). Basic Concepts in Molecular Biology. In: Molecular Biology of Cardiac Development and Growth. Medical Intelligence Unit. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-22192-1_1

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Induction of differentiation of intrahepatic cholangiocarcinoma cells to functional hepatocytes using an organoid culture system

• Yoshimasa Saito
• Toshiaki Nakaoka
• Hidetsugu Saito

Whole-Mount Adult Ear Skin Imaging Reveals Defective Neuro-Vascular Branching Morphogenesis in Obese and Type 2 Diabetic Mouse Models

• Tomoko Yamazaki
• Yoh-suke Mukouyama

Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages

• Abu Hena M. Kamal
• Jayanta K. Chakrabarty
• Saiful M. Chowdhury

A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis

• Felix J. Hartmann
• Erin F. Simonds
• Sean C. Bendall

A selective high affinity MYC-binding compound inhibits MYC:MAX interaction and MYC-dependent tumor cell proliferation

• Alina Castell
• Lars-Gunnar Larsson

Mitochondrial imaging in live or fixed tissues using a luminescent iridium complex

• Alexandra Sorvina
• Christie A. Bader
• Douglas A. Brooks

The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation

• Andrew J. McKenzie
• Stephanie R. Hicks
• Alan K. Howe

Dysregulation in Actin Cytoskeletal Organization Drives Increased Stiffness and Migratory Persistence in Polyploidal Giant Cancer Cells

• Deepraj Ghosh
• Michelle R. Dawson

Targeted Delivery of Cell Penetrating Peptide Virus-like Nanoparticles to Skin Cancer Cells

• Bee Koon Gan
• Chean Yeah Yong
• Wen Siang Tan

Stage-specific Effects of Bioactive Lipids on Human iPSC Cardiac Differentiation and Cardiomyocyte Proliferation

• Arun Sharma

Pathways of cellular internalisation of liposomes delivered siRNA and effects on siRNA engagement with target mRNA and silencing in cancer cells

• Abdullah Alshehri
• Anna Grabowska
• Snow Stolnik

Contrasting epigenetic states of heterochromatin in the different types of mouse pluripotent stem cells

• Matteo Tosolini
• Vincent Brochard
• Alice Jouneau

Remodeling of the Actin/Spectrin Membrane-associated Periodic Skeleton, Growth Cone Collapse and F-Actin Decrease during Axonal Degeneration

• Nicolas Unsain
• Martin D. Bordenave
• Alfredo O. Cáceres

A cell surface display fluorescent biosensor for measuring MMP14 activity in real-time

• Alexander Braun
• Matthew J. Farber
• Kenneth A. Myers

Informative three-dimensional survey of cell/tissue architectures in thick paraffin sections by simple low-vacuum scanning electron microscopy

• Akira Sawaguchi
• Takeshi Kamimura
• Yujiro Asada

A novel method for expansion and differentiation of mouse tracheal epithelial cells in culture

• Evelien Eenjes
• Tinne C. J. Mertens
• Pieter S. Hiemstra

Secretome analysis of in vitro aged human mesenchymal stem cells reveals IGFBP7 as a putative factor for promoting osteogenesis

• Arantza Infante
• Clara I. Rodríguez

Exercise prevents impaired autophagy and proteostasis in a model of neurogenic myopathy

• Juliane C. Campos
• Leslie M. Baehr
• Julio C. B. Ferreira

Affimer proteins for F-actin: novel affinity reagents that label F-actin in live and fixed cells

• Anna Lopata
• Ruth Hughes
• Michelle Peckham

TRPV4-mediates oscillatory fluid shear mechanotransduction in mesenchymal stem cells in part via the primary cilium

• Michele A. Corrigan
• Gillian P. Johnson
• David A. Hoey

Formation of Multi-Component Extracellular Matrix Protein Fibers

• Seungkuk Ahn
• Keel Yong Lee
• Kwanwoo Shin

Reduced Autophagy by a microRNA-mediated Signaling Cascade in Diabetes-induced Renal Glomerular Hypertrophy

• Supriya Deshpande
• Maryam Abdollahi
• Rama Natarajan

Identification of microRNAs differentially expressed in glioblastoma stem-like cells and their association with patient survival

• Ondrej Slaby

β-catenin-independent regulation of Wnt target genes by RoR2 and ATF2/ATF4 in colon cancer cells

• Oksana Voloshanenko
• Uwe Schwartz
• Michael Boutros

In vivo monitoring of hair cycle stages via bioluminescence imaging of hair follicle NG2 cells

• Yasuhisa Tamura
• Kumi Takata
• Yosky Kataoka

Down-regulation of guanylate binding protein 1 causes mitochondrial dysfunction and cellular senescence in macrophages

• Xiaoxue Qiu
• Xiaoli Chen

Dual role of E-cadherin in the regulation of invasive collective migration of mammary carcinoma cells

• Yair Elisha
• Vyacheslav Kalchenko
• Benjamin Geiger

Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA and membrane proteins

• Alberto Benito-Martin
• Stephen Redenti

A cleavage product of Polycystin-1 is a mitochondrial matrix protein that affects mitochondria morphology and function when heterologously expressed

• Cheng-Chao Lin
• Mahiro Kurashige
• Gregory G. Germino

The live cell DNA stain SiR-Hoechst induces DNA damage responses and impairs cell cycle progression

• Adrian T. Saurin
• Jonathan M. G. Higgins

Metastatic Brain Tumors Disrupt the Blood-Brain Barrier and Alter Lipid Metabolism by Inhibiting Expression of the Endothelial Cell Fatty Acid Transporter Mfsd2a

• Shweta Tiwary
• John E. Morales
• Joseph H. McCarty

Beta-catenin cleavage enhances transcriptional activation

• Tatiana Goretsky
• Emily M. Bradford
• Terrence A. Barrett

Glucose starvation induces LKB1-AMPK-mediated MMP-9 expression in cancer cells

• Hitoshi Endo
• Satoshi Owada
• Masayuki Tatemichi

Endocrine cell type sorting and mature architecture in the islets of Langerhans require expression of Roundabout receptors in β cells

• Melissa T. Adams
• Jennifer M. Gilbert

Prediction of sarcopenia using a combination of multiple serum biomarkers

• Ju Yeon Kwak
• Hyeoncheol Hwang
• Ki-Sun Kwon

Vertical Transmission of the Zika Virus Causes Neurological Disorders in Mouse Offspring

• Yingchao Shi
• Xiaoqun Wang

Quantifying extracellular matrix turnover in human lung scaffold cultures

• Oskar Rosmark
• Emma Åhrman
• Johan Malmström

Embryonic germ cell extracts erase imprinted genes and improve the efficiency of induced pluripotent stem cells

• Qiaoshi Zhao

From individual to collective 3D cancer dissemination: roles of collagen concentration and TGF-β

• Y. Juste-Lanas
• J. M. García-Aznar

Intracellular calcium signal at the leading edge regulates mesodermal sheet migration during Xenopus gastrulation

• Kentaro Hayashi
• Takamasa S. Yamamoto

Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis

• Megan E. Forrest
• Alina Saiakhova
• Ahmad M. Khalil

Dynamic modelling of the mTOR signalling network reveals complex emergent behaviours conferred by DEPTOR

• Thawfeek M. Varusai
• Lan K. Nguyen

Magnesium enhances the chondrogenic differentiation of mesenchymal stem cells by inhibiting activated macrophage-induced inflammation

Development of new method to enrich human iPSC-derived renal progenitors using cell surface markers

• Azusa Hoshina
• Tatsuya Kawamoto
• Kenji Osafune

VPS4 is a dynamic component of the centrosome that regulates centrosome localization of γ-tubulin, centriolar satellite stability and ciliogenesis

• Carolyn Ott
• Dikla Nachmias
• Natalie Elia

Multipotent Adult Progenitor Cells Support Lymphatic Regeneration at Multiple Anatomical Levels during Wound Healing and Lymphedema

• Manu Beerens
• Xabier L. Aranguren
• Aernout Luttun

MALAT1: An Epigenetic Regulator of Inflammation in Diabetic Retinopathy

• Saumik Biswas
• Anu Alice Thomas
• Subrata Chakrabarti

Molecular mechanism of ER stress-induced pre-emptive quality control involving association of the translocon, Derlin-1, and HRD1

• Hisae Kadowaki
• Pasjan Satrimafitrah
• Hideki Nishitoh

Monitoring voltage fluctuations of intracellular membranes

• Masoud Sepehri Rad
• Lawrence B. Cohen
• Bradley J. Baker

Premyogenic progenitors derived from human pluripotent stem cells expand in floating culture and differentiate into transplantable myogenic progenitors

• Fusako Sakai-Takemura
• Asako Narita
• Yuko Miyagoe-Suzuki

Multicilin and activated E2f4 induce multiciliated cell differentiation in primary fibroblasts

• Seongjae Kim
• Chris Kintner

Using intracellular markers to identify a novel set of surface markers for live cell purification from a heterogeneous hIPSC culture

• Elizabeth J. Paik
• Alison L. O’Neil
• Lee L. Rubin

Ultrastructural and Immunohistochemical Features of Telocytes in Placental Villi in Preeclampsia

• Natalia V. Nizyaeva
• Tatiana V. Sukhacheva
• Gennadiy T. Sukhikh

Diverse patterns of molecular changes in the mechano-responsiveness of focal adhesions

• Rahuman S. Malik-Sheriff
• Sarah Imtiaz

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

• Atsushi Matsuda
• Lothar Schermelleh
• Yasushi Hiraoka

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