All new graduate students need to attend UMBC and Departmental Orientation Sessions. UMBC Orientation Sessions are the week of Aug 13, and Departmental Orientation will take place the week of Aug 20, 2012.

For a schedule of both UMBC (page 1) and Departmental (page 2) Orientation activity see this link...
CBEE Department Orientation Calendar.

Bhargavi Kondragunta successfully defended her PhD today. Bhargavi preformed her research in the Moreira Lab. The title of her dissertation was "Bioprocess Convergence Using Sentinel Genes for Process Parameter Tuning."

Jose Vallejos Membreno successfully defended his PhD today. Jose preformed his research in the Rao Lab. The title of his dissertation was "Improving Upstream Bioprocessing by Enabling Process Scouting Devices with Low Cost, Disposable Oxygen and pH Sensors."

Andreia Ribeiro successfully defended her PhD today. Andreia preformed her research in the Leach Lab. The title of her dissertation was "Translating Neuronal Responses From 2D to 3D Microenvironments to Improve the Design of Biomaterials."

Miguel Acosta successfully defended his PhD today. Miguel preformed his research in the Leach Lab. The title of his dissertation was "Miniaturized probes for cell microenvironment: development, characterization, and application of fluorescent oxygen-sensing microparticles."

Goncalo Maia successfully defended his PhD today. Goncalo preformed his research in the Castellanos Lab. The title of his dissertation was "Design of Large Scale Kinetic Metabolic Models: Applications in Mammalian and Algae Metabolism."

Ben Keshet successfully defended his PhD today. Ben preformed his research in the Good Lab. The title of his dissertation was "Towards understanding the molecular details of beta amyloid neurotoxicity in Alzheimer's disease."

Jessica Schwartz successfully defended her MS today. Jessica preformed her research in the Ross lab. The title of her dissertation was "The Influence of Human Serum on Staphylococcus aureus Growth, Collagen and Fibrinogen Receptor Expression and Adhesion to Immobilized Collagen and Fibrinogen under Dynamic Shear."

Silviya Petrova Zustiak successfully defended her PhD today. Silviya preformed her research in the Leach Lab. The title of her dissertation was "Star poly(ethylene glycol) as a tunable scaffold for neural tissue engineering."

Patrick Ymele-Leki successfully defended his PhD today. Patrick preformed his research in the Ross Lab. The title of his dissertation was "Quantitative analysis of the accumulation, architectural organization, detachment and reseeding of Staphylococcus aureus biofilms under physiological fluid shear conditions."

Irina Ramos successfully defended her PhD today. Irina preformed her research in the Good Lab. The title of her dissertation was "Role of β-Amyloid Structure and residue accessibility in cell interactions associated with Alzheimer’s disease."

Dr. David Klinke, West Virginia University

DATE/TIME/LOCATION:
Monday, April 6 12:00PM, TRC, Rm 206

TITLE:
A Bayesian Perspective on Understanding Cell Signaling Pathways using Mathematical Models

ABSTRACT:
Cellular response to extracellular stimuli is governed by biochemical reactions that allow the transfer of information from the cell membrane to the nucleus and back. The integrity of this mechanism for information processing is attributed to a series of dynamic protein-protein interactions. Decades of scientific scrutiny have revealed the molecular players in many cellular signaling networks. Yet how these molecular players create a dynamic flow of information – by interacting in space, in time, and in specific systems – remains relatively unknown. Our lab focuses on combining aspects of chemical kinetics, Bayesian inference, and proteomics to quantify the functional consequences of genetic variation. The functional consequences of interest give rise to differences in the flow of information within cellular signaling pathways. Our approach will be illustrated using two examples. To provide a context for these examples, I will provide a semi-biased review the current state-of-the-art in analyzing cell signaling pathways using mathematical models. The first example focuses on understanding differences in signaling pathways among cellular models of breast cancer. The second example focuses on understanding the regulation of Interleukin-12 signaling within naïve CD4+ T cells.

Joe Piekarski successfully defended his MS today. Joe preformed his research in the Castellanos lab. The title of his dissertation was "Construction of a Dual Infection Mechanism for HIV."

Hui Guo successfully defended her MS today. Hui preformed her research in the Frey lab. The title of her dissertation was "Dispersion phenomena in micropellicular HPLC columns."

Prof. George Georgiou, PhD
Cockrell Family Regent’s Chair in Engineering #9
Department of Biomedical Engineering
Institute for Cellular and Molecular Biology
The University of Texas at Austin

Every year our department remembers our beloved former colleague, Janice Lumpkin, by sponsoring the Lumpkin Memorial Lecture, which as been presented by some of the most prominent names in biochemical engineering.

DATE/TIME/LOCATION:
UMBC's Look Ahead Conference
Wednesday, November 12, 2008
3:30 – 6:30 pm

TITLE:
Engineering the Next Generation of Protein Therapeutics

ABSTRACT:
A major long-term interest of our group is the engineering of proteins for pharmaceutical and biotechnology applications. To this end, we have developed a set of high throughput screening techniques relying on bacterial expression and flow cytometry that enable the isolation of novel proteins with desired functions from ensembles (“libraries”) of hundreds of millions of protein variants. These studies have led to the engineering of antibodies exhibiting ultra-high antigen affinity, serum and/or novel effector functions, and of therapeutic enzymes that exhibit exquisite catalytic activity and optimal pharmacological properties. Examples that will be discussed as part of this talk include:
(a) The isolation, expression and therapeutic optimization (Fc engineering) of IgG in E.coli
(b) “Humanized” non-immunogenic enzymes for amino acid depletion in cancer.
(c) Proteases that exhibit exceptional activity and selectivity towards the cleavage of desired peptide targets.

You are cordially invited to the dissertation defense of Yonghyun (John) Kim.

Date: October 10, 2008
Time: 2:00pm
Location: BIOL 004

Some refreshments will be provided.

TITLE: Proteomic Identification of Novel Regulators and Effectors of Osmoadaptaion and Autophagy of Model Filamentous Fungi Aspergillus nidulans

ABSTRACT:
The genus Aspergillus is an important grouping of filamentous fungi for study, as it contains a number of species which are either extremely helpful (e.g., in the bioprocess industry) or harmful (e.g., human/animal/crop pathogens). Here, we focus on a representative, model species, Aspergillus nidulans, and study a key cellular process called autophagy. Autophagy (more specifically, macroautophagy) is an important cellular mechanism by which cells first degrade and subsequently recycle portions of the cytosol when there is limited nutrient supply. Autophagy proteins (and regulation of their expression) are highly conserved from yeast to man, and thus our study has potentially broad implications for all eukaryotes. Currently, only a few studies exist which have characterized autophagy in fungi. To further this understanding, we employed proteomic analysis, a systems biology tool which provides a panoptic, large-scale profiling of protein expression level changes. Our broad goal here was to utilize proteomic analysis to develop a better fundamental understanding of protein expression associated with autophagy in filamentous fungi. When fully developed, this understanding may allow us to intelligently manipulate fungi at the molecular level to harness increased benefit from fungi used in the bioprocess industry and diminish detriment from pathogenic fungi.

We began by establishing one of the first, published A. nidulans proteome maps. We did this while studying osmoadaptation, which has been tied to autophagy and is a relatively well understood stress response. This study also served to validate our proteomic experimental approach. Our analysis identified a number of novel proteins that were, for the first time, linked with osmoadaptation. Next, we studied differences in protein expression patterns when A. nidulans is grown in the presence of two known inducers of autophagy, carbon starvation and rapamycin treatment. Our data suggest that some downstream effectors are shared between the rapamycin-regulated pathways and carbon-starvation regulated pathways (e.g. polar growth, cell wall degradation), that the mechanism by which they are regulated are seemingly different (e.g. 14-3-3 ArtA involved in regulating polar growth during carbon-starvation but not during rapamycin treatment), and that there are other effectors which are distinct between the two inducers (e.g. reduced amino acid biosynthesis only observed in carbon-starvation). Our final study builds on this theme by reporting the time-dependent response of an autophagy-impaired mutant (ΔAtg8) exposed to rapamycin. Our proteomic data suggest that A. nidulans, when challenged with rapamycin, upregulates gluconeogenesis, the pentose phosphate pathway, amino acid biosynthesis, secretory pathway, polarized growth, and ribosome turnover even without a fully functioning autophagy pathway. Taken together, these data imply that rapamycin-mediated effectors are distinct from those of autophagy.

James Pallikal successfully defended his MS today. James preformed his research in the Good lab. The title of his dissertation was "Investigation of MUC1 in Alzheimer's Applications."

You are all invited to attend Jessica Drew's MS thesis defense.

Date: Tuesday, July 8th
Time: 10 am
Location: ITE 227

Some refreshments will be provided, however no food is allowed in the
actual room.

Title: Application of High Throughput Bioreactors in
Subclone Selection

Abstract: The demand for monoclonal antibodies in pharmaceutical drug production
requires the highest technology be invested in obtaining a stable, high
producing cell line. Currently the most common method of selection is by
limiting dilution cloning, done in well plates. The highest producing
cell is chosen after samples from the stationary plates have been
analyzed for antibody production. The selection is based on stationary
culture, even though after scale-up cells will grow in a stirred
environment. This research investigates a way to test multiple clones in
a stirred environment by using high throughput bioreactors (HTBRs) in the
early stages of clone selection. It has been found that simply selecting
subclones based on results from stationary culture could result in the
chance of missing even higher producing clones. Instead, choosing a
clone after analyzing its performance in a stirred environment is an
improved method to select a cell line for further scale-up.

The UMBC College of Engineering and Information Technology (COEIT) invites those interested to a Pre-Commencement Breakfast and Awards Reception

Thursday May 22, 2008
8:30 to 10:30am
Engineering Building Atrium and LH5

The CBE departmental reception for our M.S. and Ph.D. graduating students, which
will be held at noon in ITE 456. The reception consists of a catered lunch, a champagne toast, and an assortment of additional entertaining activities. This event is to celebrate the accomplishments of our graduates. For pictures click here.

Ivan R. Kennedy, PhD DSc(Agric)
Director, SUNFix Centre for Nitrogen Fixation
Associate Dean (Research)
Faculty of Agriculture, Food and Natural Resources,
University of Sydney, NSW Australia

DATE/TIME/LOCATION:
Monday, May 12 12:00PM, ITE Building, Rm 227

TITLE:
Biothermodynamics for sustainability: Revisiting entropy in the form of biological action directed by DNA

ABSTRACT:
The doctrine of increasing disorder usually said to be predicted by the 2nd Law has given entropy a needlessly bad press. A more positive view of entropy relates it to the physical property of action; entropy then acts as a capacity factor indicating the distribution of energy needed to sustain the current action at a level greater than Planck’s quantum of action characteristic of zero Kelvin. We can consider life as a set of purposive action processes, dependent for its maintenance on access to specific forms of stored action potential or free energy. In this overview (which will consider entropy in all three of its thermal, statistical and action aspects) the thesis that the DNA code-script provides highly selected information needed by living organisms to ensure their survival, by directing available energy towards specific actions, will be discussed.

Anton J. Geisz, Jr. successfully defended his MS today. Anton preformed his research in the Good lab. The title of his dissertation was "Multivalent Sialtic Acid Polymers: A Novel Chemistry."

Jacob A. MGill successfully defended his MS today. Jacob preformed his research in the Castellanos lab. The title of his dissertation was "Development of an Intracellular Infection Model and Integration of Diffusional Virus Effects into a Cellular Automata Simulation."

Christopher B. Cowan successfully defended his PhD today. Christopher preformed his research in the Good lab. The title of his dissertation was "Developing Novel Materials that Capture the Alzheimer's Diseaase Associated Protein Beta Amyloid for Therapeutic & Detection Applications."

Bradford Gates successfully defended his MS today. Brad performed his research in the Castellanos lab. The title of his dissertation was "Beta Amyloid-Neuron Interactions Explored via Computational Modeling.

Derek Smith successfully defended his PhD today. Derek preformed his research in the Center for Advanced Sensing Technologies (CAST). The title of his dissertation was "Plasmonic Enhancement for the Development of High Sensitivity, Low-Cost Fluorescence Sensing With Ultrafast Detection."

Judith Kadarusman Pollack successfully defended her PhD today. Judith preformed her research in the Marten lab. The title of her dissertation was "Study of the morphology and physiology of filamentous fungi during nutrient starvation using the parallel plate flow chamber."

Michael A. Johnson successfully defended his PhD today. Michael performed his research in the Ross lab. The title of his dissertation was "Platelet-S. aureus Interactions: A Study of Thrombus Formation in Whole Blood in the Presence of Bacteria Under Physiological Shear Conditions."

Two CBE graduate students were awarded the Ph.D. in December 2007. Mike Hanson, successfully defended his dissertation, "High Throughput Bioreactor Validation and Use in Mammalian Cell Culture Process Change Studies Utilizing Gene Expression Data," (Co-Advisors Moreira and Rao). Also successfully defending was Wendy Lea, whose research topic was, "Development, Validation and Application of a Biological Antioxidant Capacity Assay using sodA::gfp as a Living Sensor" (Co-Advisors Tolosa and Rao).