Collagen-mimetic peptide-modifiable hydrogels for articular cartilage regeneration

Regenerative medicine strategies for restoring articular cartilage face significant challenges to recreate the complex and dynamic biochemical and biomechanical functions of native tissues. As an approach to recapitulate the complexity of the extracellular matrix, collagen-mimetic proteins offer a modular template to incorporate bioactive and biodegradable moieties into a single construct. We modified a Streptococcal collagen-like 2 protein with hyaluronic acid (HA) or chondroitin sulfate (CS)-binding peptides and then cross-linked with a matrix metalloproteinase 7 (MMP7)-sensitive peptide to form biodegradable hydrogels. Human mesenchymal stem cells (hMSCs) encapsulated in these hydrogels exhibited improved viability and significantly enhanced chondrogenic differentiation compared to controls that were not functionalized with glycosaminoglycan-binding peptides. Hydrogels functionalized with CS-binding peptides also led to significantly higher MMP7 gene expression and activity while the HA-binding peptides significantly increased chondrogenic differentiation of the hMSCs. Our results highlight the potential of this novel biomaterial to modulate cell-mediated processes and create functional tissue engineered constructs for regenerative medicine applications

Suppression of mitochondrial respiration through recruitment of p160 myb binding protein to PGC-1α : modulation by p38 MAPK

The transcriptional coactivator PPAR gamma coactivator 1 α (PGC-1α) is a key regulator of metabolic processes such as mitochondrial biogenesis and respiration in muscle and gluconeogenesis in liver. Reduced levels of PGC-1α in humans have been associated with type II diabetes. PGC-1α contains a negative regulatory domain that attenuates its transcriptional activity. This negative regulation is removed by phosphorylation of PGC-1α by p38 MAPK, an important kinase downstream of cytokine signaling in muscle and β-adrenergic signaling in brown fat. We describe here the identification of p160 myb binding protein (p160MBP) as a repressor of PGC-1α. The binding and repression of PGC-1α by p160MBP is disrupted by p38 MAPK phosphorylation of PGC-1α. Adenoviral expression of p160MBP in myoblasts strongly reduces PGC-1α's ability to stimulate mitochondrial respiration and the expression of the genes of the electron transport system. This repression does not require removal of PGC-1α from chromatin, suggesting that p160MBP is or recruits a direct transcriptional suppressor. Overall, these data indicate that p160MBP is a powerful negative regulator of PGC-1α function and provide a molecular mechanism for the activation of PGC-1α by p38 MAPK. The discovery of p160MBP as a PGC-1α regulator has important implications for the understanding of energy balance and diabetes

Control of Drosophila imaginal disc development by rotund and roughened eye: differentially expressed transcripts of the same gene encoding functionally distinct zinc finger proteins

The Drosophila rotund gene is required in the wings, antenna, haltere, proboscis and legs. A member of the Rac family of GTPases, denoted the rotund racGAP gene, was previously identified in the rotund region. However, previous studies indicated that rotund racGAP was not responsible for the rotund phenotypes and that the rotund gene had yet to be identified. We have isolated the rotund gene and show that it is a member of the Kruppel family of zinc finger genes. The adjacent roughened eye locus specifically affects the eye and is genetically separable from rotund. However, roughened eye and rotund are tightly linked, and we have therefore also isolated the roughened eye transcript. Intriguingly, we show that roughened eye is part of the rotund gene but is represented by a different transcript. The rotund and roughened eye transcripts result from the utilization of two different promoters that direct expression in non-overlapping domains in the larval imaginal discs. The predicted Rotund and Roughened Eye proteins share the same C-terminal region, including the zinc finger domain, but differ in their N-terminal regions. Each cDNA can rescue only the corresponding mutation and show negative effects when expressed in each others domain of expression. These results indicate that in addition to the differential expression of rotund and roughened eye, their proteins have distinct activities. rotund and roughened eye act downstream of early patterning genes such as dachshund and appear to be involved in Notch signaling by regulating Delta, scabrous and Serrate

The Alestle - Vol. 58 No. 66 - 07/26/2006

Vol. 58 No. 6

Estimating Shifts in Phenology and Habitat Use of Cobia in Chesapeake Bay Under Climate Change

Cobia (Rachycentron canadum) is a large coastal pelagic fish species that represents an important fishery in many coastal Atlantic states of the U.S. They are heavily fished in Virginia when they migrate into Chesapeake Bay during the summer to spawn and feed. These coastal habitats have been subjected to warming and increased hypoxia which in turn could impact the timing of migration and the habitat suitability of Chesapeake Bay. With conditions expected to worsen, we project current and future habitat suitability of Chesapeake Bay for cobia and predict changes in their arrival and departure times as conditions shift. To do this we developed a depth integrated habitat model from archival tagging and physiology data from cobia that used Chesapeake Bay, and applied the model to contemporary and future temperature and oxygen output from a coupled hydrodynamic-biogeochemical model of Chesapeake Bay. We found that estimated arrival occurs earlier and estimated departure time occurs later when temperatures are warmer and that by mid- and end-of-century cobia may spend on average up to 30 and 65 more days, respectively, in Chesapeake Bay. By mid-century we do not expect habitat suitability to change substantially for cobia, but by end-of-century we project it will significantly decline and shift closer to the mouth of Chesapeake Bay. Our study provides evidence that cobia will have the capacity to withstand near term impacts of climate change, but that their migration phenology varies from year to year with changing temperatures. These findings emphasize the need to incorporate the relationship between fishes and their environment into how fisheries are managed. This information can also help guide managers when deciding the timing and allocation of a fishery

High-throughput molecular imaging via deep-learning-enabled Raman spectroscopy.

Raman spectroscopy enables nondestructive, label-free imaging with unprecedented molecular contrast, but is limited by slow data acquisition, largely preventing high-throughput imaging applications. Here, we present a comprehensive framework for higher-throughput molecular imaging via deep-learning-enabled Raman spectroscopy, termed DeepeR, trained on a large data set of hyperspectral Raman images, with over 1.5 million spectra (400 h of acquisition) in total. We first perform denoising and reconstruction of low signal-to-noise ratio Raman molecular signatures via deep learning, with a 10× improvement in the mean-squared error over common Raman filtering methods. Next, we develop a neural network for robust 2-4× spatial super-resolution of hyperspectral Raman images that preserve molecular cellular information. Combining these approaches, we achieve Raman imaging speed-ups of up to 40-90×, enabling good-quality cellular imaging with a high-resolution, high signal-to-noise ratio in under 1 min. We further demonstrate Raman imaging speed-up of 160×, useful for lower resolution imaging applications such as the rapid screening of large areas or for spectral pathology. Finally, transfer learning is applied to extend DeepeR from cell to tissue-scale imaging. DeepeR provides a foundation that will enable a host of higher-throughput Raman spectroscopy and molecular imaging applications across biomedicine

FlyBase 101 – the basics of navigating FlyBase

FlyBase (http://flybase.org) is the leading database and web portal for genetic and genomic information on the fruit fly Drosophila melanogaster and related fly species. Whether you use the fruit fly as an experimental system or want to apply Drosophila biological knowledge to another field of study, FlyBase can help you successfully navigate the wealth of available Drosophila data. Here, we review the FlyBase web site with novice and less-experienced users of FlyBase in mind and point out recent developments stemming from the availability of genome-wide data from the modENCODE project. The first section of this paper explains the organization of the web site and describes the report pages available on FlyBase, focusing on the most popular, the Gene Report. The next section introduces some of the search tools available on FlyBase, in particular, our heavily used and recently redesigned search tool QuickSearch, found on the FlyBase homepage. The final section concerns genomic data, including recent modENCODE (http://www.modencode.org) data, available through our Genome Browser, GBrowse