BIOL6193 - Colloquium in Molecular and Cell Biology

Dr. Campbell   rna

RNA Specificity




RNA Control Permeates Pain


Human proteome

Does the Poly A Binding Protein(PABP) play a role?


Dr. Lin Jia   inflammation alcohol obesity

Obesity-associated Low-grade Inflammation

Insulin Resistance and glucose control

Insulin sensitive

Insulin resistant

Toll-like Receptor 4 (TLR4)

Tested mice for glucose tolerance

Alcohol and Liver inflammation

Endotoxemia and AALD


Instagastric infusion

Alcohol in the drinking water



Increase in fats in liver

Increase in cytokines

Future Projects

#1 Role of hepatoctye TLR4 in alcohol and insulin resistance

#2 Risk Factors in AALD

#3 Tissue-specific Lipogenesis in AALD

#4 Adipose Tissue Lipolysis in AALD

#6 Exercise and AALD

Running mice with alcohol had significantly less lipid content

Please list four risk factors that will affect the development of alcohol-associated liver disease.   question

Gender, Genetics, drinking pattern, obesity.

Dr. Jyoti R. Misra

Organisms grow to a predictable size

Hippo pathway

Hippo pathway is a conserved regulator of growth

Mis-regulated in most cancers

Dachsous-Fat signaling regulates growth through the Hippo pathway

Disruption of planar cell polarity affects organ shape

Gal4-UAS systme for transgene expression

Started cutting out around 30 min

Treatment with Choloroquine increases stability of Fat and Fat4. This means these proteins are degraded by _?   question


Dr. Nikki Delk :cancer:inflammation:breast-cancer:prostate-cancer:

Androgen Receptor drives PCa

BCa & PCa Develop Resistance to Hormone & HR-Targeted Therapy

Tumor Microenvironment

Interleukin-1(IL-1) Signaling

Expose cancer cell lines to IL-1 acutely

Creates a subline from Chronic IL-1


Inflammation drives breast and prostate cancer progression & Treatment Resistance

Differential Gene Expression

Epigenetics & Proteomics

How can both loss and restoration of the accumulation of androgen receptor lead to treatment resistance?   question

The over express the HR to the point to where the drug is not functional, a gain of function mutations .

Hormone independent activation can also occur where the cancer cells can adapt and survive without the hormone.

Dr. Michael Q. Zhang

Functional relevance of enhancers

Pervasive Enhancer RNA (eRNA) transcription at active enhancers

PAF1 Complex

PAF1 is a pausing factor

ChIP-seq profiling

PAF1 binds primarily to enhancers

Analysis of 4C-seq with SERPINE2 promoter

Heat Shock Genes are inducible

Enhancer activity correlates with genes in heat shock response

Enhancer transcription affects Pol II pause release

Inducible enhancer and promoter pairs

The unexpected finding

The fate of an enhancer can be different from the promoter it regulates

Briefly describe what's genomic enhancer and Enhancer RNA (eRNA), and what their functions are.   question

An enhancer is a distal regulatory DNA segment that enhances the transcription of a target gene by interacting with the target gene promoter.

Enhancer RNA (eRNA) is a type of Non-coding RNA (ncRNA) transcribed from the enhancer that are tissue specific. Their function is thought to be in aiding in pulling Transcription Factor (TF) like beads on a string.

Dr. Duane Winkler

What role(s) can biochemists, who mostly work in vitro and at the molecular level, have in the mission to promote human health?   question

By creating a better understanding of molecules that play an important role in various diseases, such as Sod1 and ALS. A better understanding of all of the disease causing variants allows for better a better understanding of how to solve the issues with the protein

Dr. Faurck Morcos

Evolutionary Information Lab

Protein/RNA Structure

Molecular Interactions


Specificity & Design

Mutations throughout history provide examples on structure conservation

Conpensatory Mutation

Can you take a sequence and get the folded protein

Direct Coupling Analysis predicts 3D contacts in proteins

Recent Research Efforts

Protein-RNA specificity can be determined with Global probability models

DCA-MOL a visualization and analysis tool for evolutionary couplings


Modular swapping strategy

Evironmental sensing module(ESM)

DNA regognition module(DRM)

Inducibility of hybrid repressors

The compatibility score C(s) is a good predictor of repressor induction

Why is coevolutionary information a promising tool for protein design?   question

The proteins that evolved in parallel may have different sequences, but they can be used to better understand the relationship between changes and structure.

Dr. Tae Hoon Kim

Searching for meaning in the noncoding genome


A continuous time course genomic data can yield dynamic activity map to identify correct enhancer-promoter sets


How many enhancers in the human genome associated with all 20000 genes?   question

> 2 Million

Nicole J. De Nisco

Joined 2 years ago

Is health urine sterile?   question


Oct. 21st Dr. Lawrence Reitzer

Bacteria grow very quickly in urine

Motitlity and virulence

Swimming Motility most studied

Many forms of surface motility

Is motility required for UTIs?

Pathogenic bacteria are fast

RNA-seq Analysis: Search for other metabolic differences

arcA mutant has aerobic growth defect

FsaB-mediated glycolysis



UPEC metabolism is different

Why does UTI occur and recur?   question

Motility, metabolism of UPEC strains(bacterial factor), Urine composition(host factor) is why they occur.The infection becomes increasingly antibiotic resistant is why they recur.

2020-10-28 - Zhenyu Xuan

Computational Study of Genomic and Transcriptomic Changes Associated with Complex Diseases

Genomic variants

Association study

Two Examples

Fisher-exact test


Typical GWAS results

The Central Dogma

How could genomic variants cause disease?

Variants, Expression and Disease

Nuclear lncRNA

Some projects in my lab

Idenfity differential expressed genes expecially lncRNA

Study enhancer functions associated with gene expression and cell differentiation

Understand the non-coding regulators in embryo development

How could we connect genomic variants with potentially affected gene's function through computational methods?   question

Use GWAS to understand how the variants relate to the genes. Then we need to find the differential gene expression that relates to the disease using eQTLs, which helps to build up the GWAS edge.

Li Zhang

Heme and Common Diseases

Heme and Lung Cancer

Heme-targeting agents effectively supress lung tumors

Heme-targeting agents effectively increase vascular oxygen saturation, normalize vascular function, and alleviate tumor hypoxia

Futher studies

Mentored Prof. Xuan

Lung Cancer and Alzheimer's disease

Dr. Kelli Palmer


Entreococcus faecalis

Briefly describe the native function of CRISPR-Cas systems in bacteria.   question

It's function is to provide an immune system against viral infections. It functions by taking small snippets from the viral genome and storing them in the bacteria genome as a new spacer. These spacers are then used to created crRNA which are used in CAS as guide RNAs, and they then match up with foreign genetic material and cleave it to inactivate the foreign genetic material.

Dr. Spiro

He's from Manchester

Interests are mainly in Microbiology

Alfred Noble

Nitro Glycerin


Write a one sentence description for each of three different roles that nitric oxide plays in biology.   question

NO dilates blood vessels which are smooth muscles in a process called vasodilation. NO is generated by WBC and plays a role in the innate immune system and it's response. NO can also be used to for bacterial respiration when they are deprived of oxygen in an anaerobic process