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Monarch Science Observer, Volume 18, College Of Sciences, Old Dominion University Apr 2024

Monarch Science Observer, Volume 18, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2024, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Monarch Science Observer, Volume 17, College Of Sciences, Old Dominion University Sep 2023

Monarch Science Observer, Volume 17, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2023, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Monarch Science Observer, Volume 16, College Of Sciences, Old Dominion University Mar 2023

Monarch Science Observer, Volume 16, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2023, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He Jan 2023

Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He

College of Sciences Posters

Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary …

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Monarch Science Observer, Volume 15, College Of Sciences, Old Dominion University Sep 2022

Monarch Science Observer, Volume 15, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2022, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Monarch Science Observer, Volume 13, College Of Sciences, Old Dominion University Mar 2022

Monarch Science Observer, Volume 13, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2022, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Monarch Science Observer, Volume 12, College Of Sciences, Old Dominion University Dec 2021

Monarch Science Observer, Volume 12, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Winter 2021 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Monarch Science Observer, Volume 11, College Of Sciences, Old Dominion University Oct 2021

Monarch Science Observer, Volume 11, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2021 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Monarch Science Observer, Volume 10, College Of Sciences, Old Dominion University Jul 2021

Monarch Science Observer, Volume 10, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Summer 2021 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Alexandrium In The Arctic: Are Harmful Algae Spreading As The Arctic Warms?, Sveinn Einarsson, Kate Lowry, Robert Pickart, Karin Ashjian, P. Dreux Chappell Apr 2021

Alexandrium In The Arctic: Are Harmful Algae Spreading As The Arctic Warms?, Sveinn Einarsson, Kate Lowry, Robert Pickart, Karin Ashjian, P. Dreux Chappell

College of Sciences Posters

Alexandrium tamerense is a well-studied dinoflagellate known for its ability to produce the neurotoxin that causes paralytic shellfish poisoning. Until 1970 Alexandrium tamerense was only found in Europe, North America, and Japan but has been increasingly found all over the globe. Alexandrium is characteristically found in temperate and subtropical regions and as the Arctic warms, there is considerable concern that it may be expanding into the Arctic. We found Alexandrium tamerense during a research expedition to the Alaskan Beaufort Sea shelf to study upwelling. Upwelling events are known to support seasonal blooms of phytoplankton, which are important primary producers at …

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Seasonal Variability In Diazotroph Abundance And Gene Expression At A Coastal N2 Fixation Hotspot (Outer Banks, Nc), Katherine Crider, Corday Selden, Kimberly Powell, P. Dreux Chappell Apr 2021

Seasonal Variability In Diazotroph Abundance And Gene Expression At A Coastal N2 Fixation Hotspot (Outer Banks, Nc), Katherine Crider, Corday Selden, Kimberly Powell, P. Dreux Chappell

College of Sciences Posters

Marine microbial dinitrogen (N2) fixation, the conversion of gaseous N2 to bioavailable species, is the primary source of new oceanic nitrogen (N). N is present in nucleic acids, amino acids, and proteins, and is essential to all life. Long considered to be a primarily oligotrophic ocean process, significant N2 fixation rates have recently been observed in coastal environments, including along the Cape Hatteras front. To see if elevated N2 fixation was a persistent feature in this region, N2 fixation rates and N2 fixer (diazotroph) abundance and gene expression were investigated through roughly monthly …

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Monarch Science Observer, Volume 9, College Of Sciences, Old Dominion University Apr 2021

Monarch Science Observer, Volume 9, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Spring 2021 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Influence Of Monovalent And Divalent Ions In The Conformational Change Of Caspase-Cleaved Par-4 (Cl-Par-4) Tumor Suppressor Protein, Krishna K. Raut, Komala Ponniah, Steven M. Pascal Apr 2021

Influence Of Monovalent And Divalent Ions In The Conformational Change Of Caspase-Cleaved Par-4 (Cl-Par-4) Tumor Suppressor Protein, Krishna K. Raut, Komala Ponniah, Steven M. Pascal

College of Sciences Posters

Prostate apoptosis response-4 (Par-4) is a pro-apoptotic tumor suppressor protein. We have shown that this 38 kDa full-length Par-4 (Fl-Par-4) protein is predominantly intrinsically disordered in vitro. In vivo, Par-4 is cleaved by caspase-3 at Asp-131 to generate a 24 kDa functionally active cleaved Par-4 (cl-Par-4) fragment. The cl-Par-4 protein inhibits the NF-κB-mediated cell survival pathway and causes selective apoptosis in various tumor cells. Our laboratory is interested in how the disorder-order balance within Fl-Par-4 and cl-Par-4 may be related to the balance between cell survival and cell death. Currently, we are using biophysical techniques such as circular …

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Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman Apr 2021

Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are the “caps” of the chromosomes and their vital role is to protect them. Possible telomere dysfunction caused by telomere rearrangements can be fatal for the cell and result in age-related diseases, including cancer. The telomeres and subtelomeres are regions that are hard to investigate. The current technology cannot provide their complete sequence, instead the DNA is given in multiple pieces. Current methods of assembling the pieces of these regions are not accurate enough due to the region’s high variability and complex repeated patterns. We propose a hybrid assembly method, the NPGREAT, which utilizes two of the latest …

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Monarch Science Observer, Volume 7, College Of Sciences, Old Dominion University Dec 2020

Monarch Science Observer, Volume 7, College Of Sciences, Old Dominion University

College of Sciences Newsletter

December-Fall 2020 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Monarch Science Observer, Volume 6, College Of Sciences, Old Dominion University Oct 2020

Monarch Science Observer, Volume 6, College Of Sciences, Old Dominion University

College of Sciences Newsletter

October-Fall 2020 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Monarch Science Observer, Volume 5, College Of Sciences, Old Dominion University Aug 2020

Monarch Science Observer, Volume 5, College Of Sciences, Old Dominion University

College of Sciences Newsletter

August-Summer 2020 issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Monarch Science Observer, Volume 4, College Of Sciences, Old Dominion University May 2020

Monarch Science Observer, Volume 4, College Of Sciences, Old Dominion University

College of Sciences Newsletter

May-Spring 2020 Issue of Monarch Science Observer, ODU College of Sciences Newsletter.

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Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman Apr 2020

Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore …

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Monarch Science Observer, Volume 3, College Of Sciences, Old Dominion University Apr 2020

Monarch Science Observer, Volume 3, College Of Sciences, Old Dominion University

College of Sciences Newsletter

April-Spring 2020, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He Apr 2020

Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He

College of Sciences Posters

Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a …

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Monarch Science Observer, Volume 2, College Of Sciences, Old Dominion University Jan 2020

Monarch Science Observer, Volume 2, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Winter 2020, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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Monarch Science Observer, Volume 1, College Of Sciences, Old Dominion University Oct 2019

Monarch Science Observer, Volume 1, College Of Sciences, Old Dominion University

College of Sciences Newsletter

Fall 2019, issue of Monarch Science Observer, ODU Colleges of Sciences Newsletter.

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