http://hdl.handle.net/2144/971 2012-10-15T04:53:37Z 2012-10-15T04:53:37Z Lam, Raymond H. W. Kim, Min-Cheol Thorsen, Todd http://hdl.handle.net/2144/3455 2012-01-13T07:01:01Z 2009-06-11T00:00:00Z

Culturing Aerobic and Anaerobic Bacteria and Mammalian Cells with a Microfluidic Differential Oxygenator Lam, Raymond H. W.; Kim, Min-Cheol; Thorsen, Todd In this manuscript, we report on the culture of anaerobic and aerobic species within a disposable multilayer polydimethylsiloxane (PDMS) microfluidic device with an integrated differential oxygenator. A gas-filled microchannel network functioning as an oxygen−nitrogen mixer generates differential oxygen concentration. By controlling the relative flow rate of the oxygen and nitrogen input gases, the dissolved oxygen (DO) concentration in proximal microchannels filled with culture media are precisely regulated by molecular diffusion. Sensors consisting of an oxygen-sensitive dye embedded in the fluid channels permit dynamic fluorescence-based monitoring of the DO concentration using low-cost light-emitting diodes. To demonstrate the general utility of the platform for both aerobic and anaerobic culture, three bacteria with differential oxygen requirements (E. coli, A. viscosus, and F. nucleatum), as well as a model mammalian cell line (murine embryonic fibroblast cells (3T3)), were cultured. Growth characteristics of the selected species were analyzed as a function of eight discrete DO concentrations, ranging from 0 ppm (anaerobic) to 42 ppm (fully saturated).

2009-06-11T00:00:00Z Oddsson, Lars IE Karlsson, Robin Konrad, Janusz Ince, Serdar Williams, Steve R Zemkova, Erika http://hdl.handle.net/2144/3347 2012-01-12T07:01:00Z 2007-07-10T00:00:00Z

A Rehabilitation Tool for Functional Balance using Altered Gravity and Virtual Reality Oddsson, Lars IE; Karlsson, Robin; Konrad, Janusz; Ince, Serdar; Williams, Steve R; Zemkova, Erika BACKGROUND There is a need for effective and early functional rehabilitation of patients with gait and balance problems including those with spinal cord injury, neurological diseases and recovering from hip fractures, a common consequence of falls especially in the elderly population. Gait training in these patients using partial body weight support (BWS) on a treadmill, a technique that involves unloading the subject through a harness, improves walking better than training with full weight bearing. One problem with this technique not commonly acknowledged is that the harness provides external support that essentially eliminates associated postural adjustments (APAs) required for independent gait. We have developed a device to address this issue and conducted a training study for proof of concept of efficacy. METHODS We present a tool that can enhance the concept of BWS training by allowing natural APAs to occur mediolaterally. While in a supine position in a 90 deg tilted environment built around a modified hospital bed, subjects wear a backpack frame that is freely moving on air-bearings (cf. puck on an air hockey table) and attached through a cable to a pneumatic cylinder that provides a load that can be set to emulate various G-like loads. Veridical visual input is provided through two 3-D automultiscopic displays that allow glasses free 3-D vision representing a virtual surrounding environment that may be acquired from sites chosen by the patient. Two groups of 12 healthy subjects were exposed to either strength training alone or a combination of strength and balance training in such a tilted environment over a period of four weeks. RESULTS Isokinetic strength measured during upright squat extension improved similarly in both groups. Measures of balance assessed in upright showed statistically significant improvements only when balance was part of the training in the tilted environment. Postural measures indicated less reliance on visual and/or increased use of somatosensory cues after training. CONCLUSION Upright balance function can be improved following balance specific training performed in a supine position in an environment providing the perception of an upright position with respect to gravity. Future studies will implement this concept in patients.

2007-07-10T00:00:00Z Hazony, Yehonathan Lu, Jun St. Hilaire, Cynthia Ravid, Katya http://hdl.handle.net/2144/3225 2012-01-12T07:01:17Z 2006-08-26T00:00:00Z

Hematopoietic Gene Promoters Subjected to a Group-Combinatorial Study of DNA Samples: Identification of a Megakaryocytic Selective DNA Signature Hazony, Yehonathan; Lu, Jun; St. Hilaire, Cynthia; Ravid, Katya Identification of common sub-sequences for a group of functionally related DNA sequences can shed light on the role of such elements in cell-specific gene expression. In the megakaryocytic lineage, no one single unique transcription factor was described as linage specific, raising the possibility that a cluster of gene promoter sequences presents a unique signature. Here, the megakaryocytic gene promoter group, which consists of both human and mouse 5′ non-coding regions, served as a case study. A methodology for group-combinatorial search has been implemented as a customized software platform. It extracts the longest common sequences for a group of related DNA sequences and allows for single gaps of varying length, as well as double- and multiple-gap sequences. The results point to common DNA sequences in a group of genes that is selectively expressed in megakaryocytes, and which does not appear in a large group of control, random and specific sequences. This suggests a role for a combination of these sequences in cell-specific gene expression in the megakaryocytic lineage. The data also point to an intrinsic cross-species difference in the organization of 5′ non-coding sequences within the mammalian genomes. This methodology may be used for the identification of regulatory sequences in other lineages.

2006-08-26T00:00:00Z Shakhnovich, Boris E http://hdl.handle.net/2144/3211 2012-01-12T07:00:54Z 2005-06-24T00:00:00Z

Improving the Precision of the Structure–Function Relationship by Considering Phylogenetic Context Shakhnovich, Boris E Understanding the relationship between protein structure and function is one of the foremost challenges in post-genomic biology. Higher conservation of structure could, in principle, allow researchers to extend current limitations of annotation. However, despite significant research in the area, a precise and quantitative relationship between biochemical function and protein structure has been elusive. Attempts to draw an unambiguous link have often been complicated by pleiotropy, variable transcriptional control, and adaptations to genomic context, all of which adversely affect simple definitions of function. In this paper, I report that integrating genomic information can be used to clarify the link between protein structure and function. First, I present a novel measure of functional proximity between protein structures (F-score). Then, using F-score and other entirely automatic methods measuring structure and phylogenetic similarity, I present a three-dimensional landscape describing their inter-relationship. The result is a "well-shaped" landscape that demonstrates the added value of considering genomic context in inferring function from structural homology. A generalization of methodology presented in this paper can be used to improve the precision of annotation of genes in current and newly sequenced genomes. Synopsis. The author provides a novel perspective on a key problem of structural biology: the structure–function relationship in proteins. While relatedness in protein structure correlates with general description of function, attempts to use this relationship predictively are often complicated by its ambiguous nature. A structure encoded by a family of sequences may be implicated in a set of diverse functions across a variety of organisms. The author outlines an innovative approach that underlines the importance of considering genomic context when using structure-comparison methods for functional prediction. First, the author defines two distance measures: in genomic space and in function space. Then, the author describes a landscape of functional distance based on both structural and phylogenetic relatedness. It turns out that this landscape forms a "functional well" where proximity occurs when the structures are similar and occur in the same set of genomes. This result may have implications in future research into functional prediction. With the increasing pace of sequence deposition into databanks, this result suggests a simple way to improve functional prediction via structure homology by complementing existing methods with emerging techniques from comparative genomics.

2005-06-24T00:00:00Z