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molecular cellar biology primary infection of B-cells, transcription, EBV, molecules, dna, etc.
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Viral encephalitis Viral encephalitis is an inflammation of the brain caused by viral infection, leading to swelling, neuronal damage, and potentially life-threatening complications (1). In neonates, it is particularly dangerous because their immune systems are immature, making them less able to control viral spread (1). Additionally, their blood-brain barrier is more permeable, allowing viruses easier access to the central nervous system, which can result in seizures, developmental delays, or death if not promptly treated. In pediatric cases, infectious viral agents are recognized contributors not only to viral encephalitis but also to a range of clinical symptoms that can mimic signs of child neglect, such as failure-to-thrive (FTT), involuntary convulsions, and seizures (1). These viruses include several herpesviruses, notably herpes simplex virus-1 (HSV-1) and HSV- 2, varicella-zoster virus (VZV or chickenpox), human herpesvirus 4 ( HHV- 4 or Epstein-Barr virus or EBV ), human herpesvirus 5 (HHV-5 or cytomegalovirus or CMV), and human herpesvirus 6 (HHV-6 or roseolovirus) (1). Human oncoviruses Human oncoviruses are viruses known to contribute to the development of cancer through chronic infection, immune evasion, and disruption of normal cellular control mechanisms ( Figure 10- 1 ) (2,3). For instance, Epstein-Barr virus ( EBV ) is a herpesvirus linked to several lymphomas, including Burkitt lymphoma and Hodgkin lymphoma, as well as nasopharyngeal carcinoma (4–11). Hepatitis B virus (HBV) and Hepatitis C virus (HCV) both cause chronic liver infections that can progress to cirrhosis and hepatocellular carcinoma (2,3). Human herpesvirus 8 (HHV-8) is associated with Kaposi’s sarcoma, particularly in immunocompromised individuals (2,3). Human papillomavirus (HPV), especially high-risk types like HPV-16 and HPV-18, is a major cause of cervical, anal, and oropharyngeal cancers through the action of viral oncogenes that inactivate tumor suppressor proteins (2,3). Human T-lymphotropic virus type 1 (HTLV-1) causes adult T-cell leukemia/lymphoma by integrating into host DNA and promoting uncontrolled T-cell proliferation (2,3). Lastly, Merkel cell polyomavirus (MCPyV) has been implicated in the development of Merkel cell carcinoma, a rare but aggressive skin cancer, particularly in the elderly and immunosuppressed (2,3). Oncoviruses leverage multi-hit models of oncogenic transformation in target cells (Figure 10-2) (2,3,12). Figure 10- 1. The human oncovirus landscape.
Figure 10- 2. The human oncovirus role in the multi-hit model of oncogenic transformation. While HTLV-1 must fully integrate into the host genome, some oncoviruses like EBV (HHV-4) and KSHV (HHV-8) form an episome which is a circular viral genome that associates with the host genome using viral proteins like ENBA or LANA, respectively. Viruses that utilize episomes during latency are not fully integrated but rather associate with the host genome. EBV Lifecycle Overview The Epstein-Barr virus (EBV) lifecycle is characterized by distinct phases: primary infection , latency , and lytic reactivation (13–17). EBV persists in the host via dynamic shifts in viral tropism and a gene expression pattern to support its complex viral lifecycle (13–17). Viral tropism refers to the preferred host cell target for a virus at a specified point across its viral lifecycle (13–17).
25). Lytic reactivation of EBV includes the full complement of lytic gene expression, leading to viral DNA replication, production of new virions, and cell lysis ( Figure 10- 3 ) (23–25). This facilitates viral shedding in saliva, promoting transmission to new hosts. Reactivation is particularly significant in immunocompromised individuals, where uncontrolled lytic replication can lead to tissue damage and increase the risk of EBV-associated cancers (23–25). The goal of today’s lab is to examine the extent by which primary infection stages of EBV upon host resting B-cells might misregulate the expression of genetic loci that have critical roles in normal mitochondrial function (26–31). This is especially important since pediatric cases of viral encephalitis exhibit seizures and epilepsy which is a shared clinical manifestation for of mitochondrial disease patients afflicted by POLG lesions, especially for alleles that disrupt the POLG CTD that contains the polymerase’s active site (1,18,19,32–38). In such cases, EBV-induced haploinsufficiency at the POLG locus of a pediatric POLG heterozygote may result in an amplification of clinical manifestations and pose very serious risk to the patient (1,18,19,32–38). Today, we will re-analyze a public-domain RNA-seq dataset involving EBV infection of primary resting B cells:
All activities in Lab 10 can be done in any browser inside or outside of the IHACK high-performance cluster (HPC), Gannon University’s supercomputer. I have tested everything in a Windows environment running Google Chrome browsers. Please keep in mind that the Microsoft Edge and the MacOS Safari browsers do not always work for all tasks. For a more hands-on, guided tutorial of how to use iDEP, please refer to the Lab 09 exercise.
c. Make sure to use short, simple names. d. When pruning the Wang et al., 2019 GSE125974 dataset, keep only the 0 days and 2 days treatments. e. You should end with only 6 final columns where each column represents a treatment group replicate.