Life Sciences Commons^™

Comparative Lipid Profiles Of Milk Bank Breast Milk And Infant Formulas, Anya Oleynik, Tatiana Eliseeva, Jack Y. Vanderhoek

Biochemistry and Molecular Medicine Faculty Publications

Lipid profiles of seven human breast milk samples obtained from milk banks and four infant formulas were compared in view of the potential food hypersensitivities of certain infants to human milk.The cholesterol (0.15-0.26 mM) content of the human samples was about 50% lower than that found in the infant formulas whereas the triglyceride (TG, 173-386 mM) contents of these products were found to be comparable.The major saturated fatty acid (SFA) and mono-unsaturated fatty acid (MUFA) were 16:0 and 18:1 respectively. The major poly-unsaturated fatty acid (PUFA) was 18:2 with otherPUFA members of the C18, C20 and C22 families identified and …

Draft Genome Sequences Of Burkholderia Cenocepacia Et12 Lineage Strains K56-2 And Bc7, John J. Varga, Liliana Losada, Adrian M. Zelazny, Maria Kim, Jamison Mccorrison, Lauren Brinkac, Elizabeth P. Sampaio, David E. Greenberg, Indresh Singh, Cheryl Heiner, Meredith Ashby, William C. Nierman, Steven M. Holland, Joanna B. Goldberg

Biochemistry and Molecular Medicine Faculty Publications

The Burkholderia cepacia complex (BCC) is a group of closely related bacteria that are responsible for respiratory infections in immunocompromised humans, most notably those with cystic fibrosis (CF). We report the genome sequences forBurkholderia cenocepacia ET12 lineage CF isolates K56-2 and BC7.

Differential Recruitment Of Coregulators To The Rora Promoter Adds Another Layer Of Complexity To Gene (Dys)Regulation By Sex Hormones In Autism, Tewarit Sarachana, Valerie Wailin Hu

Biochemistry and Molecular Medicine Faculty Publications

Background

Our independent cohort studies have consistently shown the reduction of the nuclear receptor RORA (retinoic acid-related orphan receptor-alpha) in lymphoblasts as well as in brain tissues from individuals with autism spectrum disorder (ASD). Moreover, we have found that RORA regulates the gene for aromatase, which converts androgen to estrogen, and that male and female hormones regulate RORA in opposite directions, with androgen suppressing RORA, suggesting that the sexually dimorphic regulation of RORA may contribute to the male bias in ASD. However, the molecular mechanisms through which androgen and estrogen differentially regulate RORA are still unknown.

Methods

Here we use …

Pathoscope: Species Identification And Strain Attribution With Unassembled Sequencing Data., Owen E Francis, Matthew Bendall, Solaiappan Manimaran, Changjin Hong, Nathan L Clement, Eduardo Castro-Nallar, Quinn Snell, G Bruce Schaalje, Mark J Clement, Keith A Crandall, W Evan Johnson

Computational Biology Institute

Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner. We present a statistical framework to analyze raw next-generation sequence reads from purified or mixed environmental or targeted infected tissue samples for rapid species identification and strain attribution against a robust database of known biological agents. Our method, Pathoscope, capitalizes on a Bayesian statistical framework that accommodates information on sequence …

Identification Of Novel Gene Targets And Functions Of P21-Activated Kinase 1 During Dna Damage By Gene Expression Profiling, Mona Motwani, Da-Qiang Li, Anelia Horvath, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

P21-activated kinase 1 (PAK1), a serine/threonine protein kinase, modulates many cellular processes by phosphorylating its downstream substrates. In addition to its role in the cytoplasm, PAK1 also affects gene transcription due to its nuclear localization and association with chromatin. It is now recognized that PAK1 kinase activity and its nuclear translocation are rapidly stimulated by ionizing radiation (IR), and that PAK1 activation is a component of the DNA damage response. Owing to the role of PAK1 in the cell survival, its association with the chromatin, and now, stimulation by ionizing radiation, we hypothesize that PAK1 may be contributing to modulation …

Evidence For A Novel Mechanism Of The Pak1 Interaction With The Rho-Gtpases Cdc42 And Rac, Yong Jae Shin, Eun Hye Kim, Adhiraj Roy, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

P21-activated kinase 1 (PAK1) is activated by binding to GTP-bound Rho GTPases Cdc42 and Rac via its CRIB domain. Here, we provide evidence that S79 in the CRIB domain of PAK1 is not directly involved in this binding but is crucial for PAK1 activation. S79A mutation reduces the binding affinity of PAK1 for the GTPases and inhibits autophosphorylation and kinase activity of PAK1. Thus, this mutation abrogates the ability of PAK1 to induce changes in cell morphology and motility and to promote malignant transformation of prostate epithelial cells. We also show that growth of the prostate cancer cell line PC3 …

Dna Homologous Recombination Factor Sfr1 Physically And Functionally Interacts With Estrogen Receptor Alpha, Yuxin Feng, David Singleton, Chun Guo, Amanda Gardner, Suresh Pakala, Rakesh Kumar, Elwood Jensen, Jinsong Zhang, Sohaib Khan

Biochemistry and Molecular Medicine Faculty Publications

Estrogen receptor alpha (ERα), a ligand-dependent transcription factor, mediates the expression of its target genes by interacting with corepressors and coactivators. Since the first cloning of SRC1, more than 280 nuclear receptor cofactors have been identified, which orchestrate target gene transcription. Aberrant activity of ER or its accessory proteins results in a number of diseases including breast cancer. Here we identified SFR1, a protein involved in DNA homologous recombination, as a novel binding partner of ERα. Initially isolated in a yeast two-hybrid screen, the interaction of SFR1 and ERα was confirmed in vivo by immunoprecipitation and mammalian one-hybrid assays. SFR1 …

A Novel Stratification Method In Linkage Studies To Address Inter- And Intra-Family Heterogeneity In Autism, Zohreh Talebizadeh, Dan E. Arking, Valerie Wailin Hu

Biochemistry and Molecular Medicine Faculty Publications

Most genome linkage scans for autism spectrum disorders (ASDs) have failed to be replicated. Recently, a new ASD phenotypic sub-classification method was developed which employed cluster analyses of severity scores from the Autism Diagnostic Interview-Revised (ADI-R). Here, we performed linkage analysis for each of the four identified ADI-R stratified subgroups. Additional stratification was also applied to reduce intra-family heterogeneity and to investigate the impact of gender. For the purpose of replication, two independent sets of single nucleotide polymorphism markers for 392 families were used in our study. This deep subject stratification protocol resulted in 16 distinct group-specific datasets for linkage …

Phage Cluster Relationships Identified Through Single Gene Analysis., Kyle C Smith, Eduardo Castro-Nallar, Joshua Nb Fisher, Donald P Breakwell, Julianne H Grose, Sandra H Burnett

Computational Biology Institute

BACKGROUND: Phylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it …

Novel Regulatory Small Rnas In Streptococcus Pyogenes, Rafael A. Tesorero, Ning Yu, Jordan O. Wright, Juan P. Svencionis, Qiang Cheng, Jeong-Ho Kim, Kyu Hong Cho

Biochemistry and Molecular Medicine Faculty Publications

Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in …

Clinical And Technical Factors Associated With Skin Intrinsic Fluorescence In Subjects With Type 1 Diabetes From The Diabetes Control And Complications Trial/Epidemiology Of Diabetes Interventions And Complications Study, Patricia A. Cleary, Barbara H. Braffett, Trevor J. Orchard, Timothy J. Lyons, John D. Maynard, Catherine C. Cowie, Rose A. Gubitosi-Klug, Jeff F. Way, Karen L. Anderson, Annette Barnie, Stephan Villavicencio

Biochemistry and Molecular Medicine Faculty Publications

Background: The Diabetes Control and Complications Trial (DCCT)/Epidemiology of Diabetes Interventions and Complications (EDIC) studies have established multiyear mean hemoglobin A1c (HbA1c) as predictive of microvascular complications in persons with type 1 diabetes. However, multiyear mean HbA1c is not always available in the clinical setting. Skin advanced glycation end products (AGEs) are thought to partially reflect effects of hyperglycemia over time, and measurement of skin AGEs might be a surrogate for multiyear mean HbA1c. As certain AGEs fluoresce and skin fluorescence has been demonstrated to correlate with the concentration of skin AGEs, noninvasive measurement by skin intrinsic fluorescence (SIF) facilitates …

Ckap2 Ensures Chromosomal Stability By Maintaining The Integrity Of Microtubule Nucleation Sites, Chanelle M. Case, Dan L. Sackett, Danny Wangsa, Tatiana S. Karpova, James G. Mcnally, Thomas Ried, Jordi Camps

Biochemistry and Molecular Medicine Faculty Publications

Integrity of the microtubule spindle apparatus and intact cell division checkpoints are essential to ensure the fidelity of distributing chromosomes into daughter cells. Cytoskeleton-associated protein 2, CKAP2, is a microtubule-associated protein that localizes to spindle poles and aids in microtubule stabilization, but the exact function and mechanism of action are poorly understood. In the present study, we utilized RNA interference to determine the extent to which the expression of CKAP2 plays a role in chromosome segregation. CKAP2-depleted cells showed a significant increase of multipolar mitoses and other spindle pole defects. Notably, when interrogated for microtubule nucleation capacity, CKAP2-depleted cells showed …

Genome-Wide Identification Of Transcriptional Targets Of Rora Reveals Direct Regulation Of Multiple Genes Associated With Autism Spectrum Disorder, Tewarit Sarachana, Valerie Wailin Hu

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.

Mth1 Regulates The Interaction Between The Rgt1 Repressor And The Ssn6-Tup1 Corepressor Complex By Modulating Pka-Dependent Phosphorylation Of Rgt1, Adhiraj Roy, Yong Jae Shin, Kyu Hong Cho, Jeong-Ho Kim

Biochemistry and Molecular Medicine Faculty Publications

Glucose uptake, the first, rate-limiting step of its utilization, is facilitated by glucose transporters. Expression of several glucose transporter (HXT) genes in yeast is repressed by the Rgt1 repressor, which recruits the glucose-responsive transcription factor Mth1 and the general corepressor complex Ssn6-Tup1 in the absence of glucose; however, it is derepressed when Mth1 is inactivated by glucose. Here we show that Ssn6-Tup1 interferes with the DNA-binding ability of Rgt1 in the absence of Mth1 and that the Rgt1 function abrogated by Ssn6 overexpression is restored by co-overexpression of Mth1. Thus Mth1 likely regulates Rgt1 function not by modulating …

Rna Sequencing Of Cancer Reveals Novel Splicing Alterations, Jeyanthy Eswaran, Anelia Horvath, Sucheta Godbole, Sirigiri Divijendra Natha Reddy, Prakriti Mudvari, Kazufumi Ohshiro, Dinesh Cyanam, Sujit S. Nair, Suzanne A.W. Fuqua, Kornelia Polyak, Liliana D. Florea, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

Breast cancer transcriptome acquires a myriad of regulation changes, and splicing is critical for the cell to “tailor-make” specific functional transcripts. We systematically revealed splicing signatures of the three most common types of breast tumors using RNA sequencing: TNBC, non-TNBC and HER2-positive breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We …

A Positive Feedback Loop Regulates The Expression Of Polycomb Group Protein Bmi1 Via Wnt Signaling Pathway, Joon-Ho Cho, Manjari Dimri, Goberdhan P. Dimri

Biochemistry and Molecular Medicine Faculty Publications

Polycomb group protein BMI1 plays an important role in cellular homeostasis by maintaining a balance between proliferation and senescence. It is often overexpressed in cancer cells and is required for self-renewal of stem cells. At present, very little is known about the signaling pathways that regulate the expression of BMI1. Here, we report that BMI1 autoactivates its own promoter via an E-box present in its promoter. We show that BMI1 acts as an activator of the WNT pathway by repressing Dickkopf (DKK) family of WNT inhibitors. BMI1 mediated repression of DKK proteins; in particular, DKK1 led to up-regulation of WNT …

Acidic Nucleoplasmic Dna-Binding Protein (And-1) Controls Chromosome Congression By Regulating The Assembly Of Centromere Protein A (Cenp-A) At Centromeres, Aimee Jaramillo-Lambert, Jing Hao, Haijie Xiao, Yongming Li, Zhiyong Han, Wenge Zhu

Biochemistry and Molecular Medicine Faculty Publications

Background: The incorporation of CENP-A at centromeres is important for chromosome segregation during mitosis.

Results: And-1 together with HJURP regulates the assembly of new CENP-A onto centromeres.

Conclusion: And-1 facilitates the recruitment of CENP-A to centromeres.

Significance: These studies reveal a novel role of And-1 in the regulation of chromosome congression during mitosis.

Community Annotation And The Evolution Of Cooperation: How Patience Matters, Atin Basuchoudhary, Vahan Simoyan, Raja Mazumder

Biochemistry and Molecular Medicine Faculty Publications

We investigate why biologists fail to contribute to biological databases although almost all of them use these databases for research. We find, using evolutionary game theory and computer simulations, that (a) the initial distribution of contributors who are patient determines whether a culture of contribution will prevail or not (b) institutions (where institution means “a significant practice, relationship, or organization in a society or culture”) that incentivize patience and therefore limit free riding make contribution more likely and, (c) a stable institution, whether it incentivizes patience or not, will increase contribution. As a result we suggest there is a trade-off …

A Comprehensive, Multi-Scale Dynamical Model Of Erbb Receptor Signal Transduction In Human Mammary Epithelial Cells, Tomas Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumy Naramura, Srikumar M. Raja, Vimla Band, Hamid Band, Jim A. Rogers

Biochemistry and Molecular Medicine Faculty Publications

The non-receptor tyrosine kinase Src and receptor tyrosine kinase epidermal growth factor receptor (EGFR/ErbB1) have been established as collaborators in cellular signaling and their combined dysregulation plays key roles in human cancers, including breast cancer. In part due to the complexity of the biochemical network associated with the regulation of these proteins as well as their cellular functions, the role of Src in EGFR regulation remains unclear. Herein we present a new comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells. This model, constructed manually from published biochemical literature, consists of 245 nodes representing proteins …

Extraction Of Molecular Features Through Exome To Transcriptome Alignment, Prakriti Mudvari, Kamran Kowsari, Charles Cole, Raja Mazumder, Anelia Horvath

Biochemistry and Molecular Medicine Faculty Publications

Integrative Next Generation Sequencing (NGS) DNA and RNA analyses have very recently become feasible, and the published to date studies have discovered critical disease implicated pathways, and diagnostic and therapeutic targets. A growing number of exomes, genomes and transcriptomes from the same individual are quickly accumulating, providing unique venues for mechanistic and regulatory features analysis, and, at the same time, requiring new exploration strategies. In this study, we have integrated variation and expression information of four NGS datasets from the same individual: normal and tumor breast exomes and transcriptomes. Focusing on SNP-centered variant allelic prevalence, we illustrate analytical algorithms that …

Novel Insights Into Breast Cancer Genetic Variance Through Rna Sequencing, Anelia Horvath, Suresh B. Pakala, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Kazufumi Ohshiro, Sandra Casimiro, Ricardo Pires, Suzanne A.W. Fuqua, Masakazu Toi, Luis Costa, Sujit S. Nair, Saraswati Sukumar, Rakesh Kumar

Biochemistry and Molecular Medicine Faculty Publications

Using RNA sequencing of triple-negative breast cancer (TNBC), non-TBNC and HER2-positive breast cancer sub-types, here we report novel expressed variants, allelic prevalence and abundance, and coexpression with other variation, and splicing signatures. To reveal the most prevalent variant alleles, we overlaid our findings with cancer- and population-based datasets and validated a subset of novel variants of cancer-related genes: ESRP2, GBP1, TPP1, MAD2L1BP, GLUD2 and SLC30A8. As a proof-of-principle, we demonstrated that a rare substitution in the splicing coordinator ESRP2(R353Q) impairs its ability to bind to its substrate FGFR2 pre-mRNA. In addition, we describe novel SNPs and INDELs in …