Last FSSHH of this year: Jacob Koskimaki

Last FSSHH of this year!!!!

Come enjoy Jacob's presentation, free food + drinks and awesome company of fellow BMEers!

Dec 11th (Friday) 5pm at Clark 110.

Title & abstract: Peptide optimization strategies: merging experimental data with bioinformatics tools to develop potent inhibitors of angiogenesis in breast cancer

The emergence of genomics, proteomics and new peptidomics has provided several advances in the data available to develop endogenous regulators of angiogenesis. Angiogeneis, or neovascularization, is the process where new vessels form from a preexisting microvasculature, and involves interactions among several cell types. Tumors require a blood supply to grow; similarly, abrogating this blood supply is an emerging paradigm to treat diseases such as breast cancer. Our laboratory recently developed a systematic bioinformatics-based methodology to identify several endogenous regulators of angiogenesis, and experimentally verified their activity in vitro and in vivo breast xenograft models. We now have begun to optimize these sequences to enhance activity, and show different experimental techniques combined with bioinformatics tools to increase activity of endogenous therapeutics.

FSSHH Friday Nov 6

This Friday Nov 6, 5pm - 6pm, Med school (Traylor 709)

Mohsen Mollazadeh is presenting! Title and abstract coming soon

title: Monitoring of neuronal activity during dexterous hand movements.
abstract: In the first part of the talk, I will present the VLSI circuit we have developed for monitoring neuronal activity in awake behaving studies. In the second part, I will present the study of population neuronal activity in primate's motor cortex during dexterous hand movements. I will present how LFP signals are modulated with various grasp patterns and their relationship to single unit activity.

FSSHH this Friday!!!

This Friday Sept 25th 5pm - 6pm, Med school (Traylor 709)

Kartik is presenting on 'optical techniques and VLSI systems for structural and functional brain imaging'.

See you all there!

Abstract: optical techniques for investigating the brain offer several key strengths - non-contact, minimally invasive, multi-scale (single cells to populations), functional/structural observation. currently, most small animal imaging is restricted to restrained &/or anesthetized animals. electrophysiology in awake, behaving rodents has led to many interesting behavioral results, but imaging in a similar scenario has not been explored well. i've been working on designing miniaturized optical imaging systems that incorporate illumination, optics and image sensing electronics in a small volume device that can be mounted on a rodent for chronic imaging in awake and behaving animals. i'll talk about the design and characterization of the imaging system and the image sensor and some preliminary experiments in rats.

Next FSSHH Friday Sept 11 2009: Sabyasachi Roy

FSSHH Returns this fall on Friday Setp 11, 2009. Sabyasachi Roy will be presenting at Talbot Library (Traylor 709)

Abstract:
Application of multi-channel telemetry in auditory neurophysiology & behavior

The neural basis of vocal control and auditory feedback has long interested neuroscientist and biomedical engineers alike. Our lab has focused on studying the cortical neural activity in the common marmoset in understanding this basic sensory-motor system. The marmoset monkeys (Callithrix Jacchus) is an ideal animal model given the fact that they remain highly vocal in captivity. This essential vocal behavior is primarily elicited when the subject is in a natural behavior state i.e. free roaming condition. Typically, neurophysiological experiments on vocal production and feedback have involved either restrained subjects or tethered setups that severely restrict the behavior of the subject. This is where multi-channel neural telemetry can play a vital role of enabling the vocal behavior of primates during auditory experiments and providing the same quality of neural data as tethered setups. We are developing the essential wireless radio link as well as the backend processing capability to make this technology practical and effective. These small, lightweight wireless devices can continuously transmit multiple channels of neural data from the relevant cortical area of the marmoset while it is engaged in an experimental task. I will briefly highlight our progress in developing custom telemetry system and integrating existing devices as well as the experimental opportunities that this technology opens up.

Need volunteers for Fall 2009!

please email luke ( lukejohnson07 AT gmail.com) and/or Yoonju (cho.yoonju AT jhmi.edu) to volunteer!


What is the Friday Student Seminar and Happy Hour?

FSSHH is a regularly scheduled seminar series for Johns Hopkins BME grad students and other interested students that includes a seminar talk, happy hour refreshments (beer, soda appetizers), and fun social interactions.

Why have it?

It has gives students opportunities to present their work and learn about their peers research in a relaxed environment. It also is a great opportunity for students to socialize and meet students from other labs and years.

When is it?

One or two Fridays a month @ 5pm

Where is it?

Either Homewood Clark 110, or 7th floor Library in Traylor (Talbot) at the Med Campus

What will go on?

Generally, the first 15 - 30 minutes will be spent drinking, eating snacks, etc, and the last 20-30 minutes there will be a talk by a fellow grad student. The nature of the talk is completely up to the presenter, but the hope is that they wont be overly technical, so that anybody from our very diverse department could listen and be interested and at least somewhat understand.

Questions/Comments? email lukejohnson07 AT gmail.com or cho.yoonju AT jhmi.edu

June 19th, Homewood Clark 110

-- Yi Zhang

We performed on-chip DNA methylation analysis using methylation-specific PCR (MSP) within an arrayed micro droplet-in-oil platform that is designed for more practical application of microfluidic droplet technologies in clinical applications. Unique features of this ready-to-use device include arrayed primers that are pre-deposited into micro-reaction chambers and use of the oil phase as a companion fluid for both sample actuation and compartmentalization. These technical advantages allow for infusion of minute amounts of sample for arrayed MSP analysis, without the added complexities inherent in microfluidic droplet-based studies. Ease of use of this micro device is exemplified by analysis of two tumor suppressor promoters, p15 and TMS1 using an on-chip methylation assay. These results were consistent with standard MSP protocols, yet the simplicity of the droplet-in-oil microfluidic PCR platform provides and easy and efficient tool for DNA methylation analysis in a large-scale arrayed manner.

May 15, 2009; Homewood, Clark 110
-- Chris Puleo

Title: "Accessible Single Molecule Detection Technologies: Microfluidic Interfaces
for Diagnostic and Single Cell Applications"

Abstract: The long term goal of this proposal is to develop microfluidic technologies that enable the widespread use of confocal fluorescence spectroscopy (CFS) for single molecule detection (SMD) in vital applications including, single molecule diagnostics and single cell analysis. Currently amplification techniques have been used to determine the presence of rare biomolecules in such applications; however, the cost, complexity, and time requirements associated with these tests limit clinical value and general utility. Direct molecule-by-molecule assessment using SMD remains an intriguing replacement for amplification technologies due to high sensitivity, assay simplicity, and low costs; however, technical challenges continue to limit the utility of these single molecule techniques. We use microfluidic interfaces for SMD platforms to expand applicability in the analysis of rare molecules from complex biological fluids. The overall goal of this work is apply microfluidics to SMD assays in order to obtain the lowest possible detection limits from the smallest possible sample volume. Direct implications are clear, high-throughput biomolecular analysis from the most precious and rare biological samples. In theory, single molecule sensitivity confers infinite detection limits in CFS platforms; however, in practice SMD platforms rely on continuous flow formats and bulk probe-target reactions. These design flaws yield significant fundamental pitfalls and result in practical limitations: 1) Analyte delivery to the microscale sensing elements is wasteful, leading to extremely low measurement efficiencies and the need for excessive sample volumes. 2) Passive probe-target interactions result in slow reaction kinetics and prohibitive assay run times. 3) Unoptimized and manual processing of target molecules results in low molecular throughput and incompatibility with arrayed formats. Experiments will be performed using two microfluidic platforms, multilayer soft lithography and water-in-oil droplets. Coupling these discrete volume control technologies with SMD provides direct control over probe hybridization, efficient transfer of target molecules to optical detection volumes, and automated processing of large numbers of sample in relatively short assay times. These improvements serve to open the door to practical use of single molecule assays in areas of vital need, such as, non-invasive diagnostic screening and investigation of cell-to-cell heterogeneity. Our lab stands in a unique position to take advantage of this potential due to practical experience in all three aspects of this challenge, including single molecule probe design, microfluidic device design and fabrication, and optical CFS platform engineering.

FSSHH still in water!

Need a pregame(?) before the cruise?

This Friday 4/17 Hannah will be presenting at Homewood Clark 110 from 5:00 though 6:00pm (5:00 for food and 5:30 for the talk). We still need a volunteer for food and drinks, so if you are interested in it, please contact me (cho.yoonju@jhmi.edu) or Luke (luke.johnson@jhu.edu).

This is going to be AWESOME so just come and enjoy some 1st light dinner for the day before your 2nd light dinner at the cruise :)

See you all there!

April 17, 2009; Homewood, Clark 110
-- Hannah Carter

In cancer, normal cells are transformed through accumulated genetic alterations that confer a selective advantage. Somatic missense mutations are one form of genetic aberration that contribute to tumor initiation and progression. Each tumor harbors a set of these mutations, but it is unclear which are drivers, causally associated with the tumor's progression, and which are passengers, neutral in the context of selective advantage for the cancer cell. We have applied modern machine learning techniques to develop a high-throughput method for discriminating between driver and passenger somatic missense mutations identified in large scale tumor sequencing studies.

April 3, 2009; Homewood, Clark 110
-- Raymond Cheong

Title: "How to use bioinformatics and other methods to win sports pools without knowing anything (much) about sports"

Abstract: In sports pools, such as those related to the ongoing men's college basketball tournament, it is often observed that those who know the least about sports end up making more accurate predictions than those who are more "knowledgeable" about sports. As a hobby project over the past ~10 years, I have been putting this idea to the test by investigating the performance of unsupervised algorithms to predict the winner of team sports. In this informal talk, I will highlight a variety of creative algorithms and discuss associated methodology and strategy. These algorithms include simple coin-flipping and Google-based methods, as well as bioinformatics-inspired linear models, network-oriented ratings, and clustering.

First FSSHH of 2009!!!!

FSSHH is back for 2009!!

The honorable speaker of this year's first FSSHH is Deok-Ho and it will be held on Jan 23rd Friday - of course ;) - at Homewood Clark 110 from 5:00pm through 6:00pm. As usual, the food and drinks at 5pm and the talk will begin at 5:30.

Hope to see you all there!

Jan 23, 2009; Homewood Clark 110
-- Deok-Ho Kim

Title: Analysis and Engineering of Cell Function with Nanoscale Cues

Abstract: In this talk, I will present multidisciplinary efforts directed towards better understanding of how diverse cell functions are controlled by the nano-scale features of cell micro-environment through active mechanosensing. I will particularly focus on three different settings in normal and pathophysiological contexts, in which cellular sensing of local force and geometry can have dramatic consequences: guided cell migration by well organized extracellular matrix, controlled stem cell differentiation via matrix topology, and development of tissue-engineered cardiac grafts. As novel tools to address these questions, I will introduce a series of biomimetic micro-devices combining the advantages of precise definition of both nano-topographic features and chemical ligands on chips, and then discuss how these tools help to gain better understanding of the fundamental aspects of establishment of cell polarity and guidance, and allow us to establish general principles for development of more precise and defined scaffolds for tissues engineering.