Critical‐sized defects in bone, whether induced by primary tumor resection, trauma, or selective surgery have in many cases presented insurmountable challenges to the current gold standard treatment for bone repair. The primary purpose of a tissue‐engineered scaffold is to use engineering principles to incite and promote the natural healing process of bone which does not occur in critical‐sized defects. A synthetic bone scaffold must be biocompatible, biodegradable to allow native tissue integration, and mimic the multidimensional hierarchical structure of native bone. In addition to being physically and chemically biomimetic, an ideal scaffold is capable of eluting bioactive molecules (e.g., BMPs, TGF‐βs, etc., to accelerate extracellular matrix production and tissue integration) or drugs (e.g., antibiotics, cisplatin, etc., to prevent undesired biological response such as sepsis or cancer recurrence) in a temporally and spatially controlled manner. Various biomaterials including ceramics, metals, polymers, and composites have been investigated for their potential as bone scaffold materials. However, due to their tunable physiochemical properties, biocompatibility, and controllable biodegradability, polymers have emerged as the principal material in bone tissue engineering. This article briefly reviews the physiological and anatomical characteristics of native bone, describes key technologies in mimicking the physical and chemical environment of bone using synthetic materials, and provides an overview of local drug delivery as it pertains to bone tissue engineering is included. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009

Summary The transcription factor p53 responds to DNA double strand breaks by increasing in concentration in a series of pulses of fixed amplitude, duration, and period. How p53 pulses influence the dynamics of p53 target gene expression is not understood. Here we show that in bulk cell populations, patterns of p53 target gene expression cluster into groups with stereotyped temporal behaviors, including pulsing and rising dynamics. These behaviors correlate statistically with the mRNA decay rates of target genes: short mRNA half-lives produce pulses of gene expression. This relationship can be recapitulated by mathematical models of p53-dependent gene expression in single cells and cell populations. Single-cell transcriptional profiling demonstrates that expression of a subset of p53 target genes is coordinated across time within single cells; p53 pulsing attenuates this coordination. These results help delineate how p53 orchestrates the complex DNA damage response and give insight into the function of pulsatile signaling pathways.

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Summary In response to stresses, cells often halt normal cellular processes; yet stress-specific pathways must bypass such inhibition to generate effective responses. We investigated how cells redistribute global transcriptional activity in response to DNA damage. We show that oscillatory increase of p53 levels in response to double-strand breaks drives counter-oscillatory decrease of MYC levels. Using RNA-seq of newly synthesized transcripts, we found that p53-mediated reduction of MYC suppressed general transcription, with the most highly expressed transcripts reduced to a greater extent. In contrast, upregulation of p53 targets was relatively unaffected by MYC suppression. Reducing MYC during the DNA damage response was important for cell fate regulation, as counteracting MYC repression reduced cell cycle arrest and elevated apoptosis. Our study shows that “global inhibition with specific activation” of transcriptional pathways is important for the proper response to DNA damage, and this mechanism may be a general principle used in many stress responses.

In fission yeast, the endoplasmic reticulum membranebound proteins Sre1 and Scp1, orthologs of mammalian sterol regulatory element binding protein (SREBP) and Scap, monitor sterol synthesis as an indirect measure of oxygen supply. When cellular oxygen levels are low, sterol synthesis is inhibited, and the Sre1-Scp1 complex responds by increasing transcription of genes required for adaptation to hypoxia. Sre1 and Scp1 are believed to detect a blockage in sterol synthesis by monitoring levels of particular sterols, but the evidence concerning which sterol signals this condition is unclear. Here, we demonstrate that Sre1-Scp1 senses ergosterol. Processing experimental data with a mathematical model of Sre1 and Scp1 function reveals a clear quantitative relationship between ergosterol concentration in the endoplasmic reticulum and Sre1 activation. Based on this relationship, we predict that the Sre1-Scp1 complex exists under "active" and "inactive" states and that the transition between these states is cooperatively mediated by ergosterol.Mammalian cholesterol synthesis is a tightly controlled process regulated by negative feedback inhibition (1). The central components of this process are two endoplasmic reticulum (ER) 4 -resident integral membrane proteins, SREBP and its binding partner Scap. SREBP is a membrane-bound transcription factor that, when proteolytically activated, enters the nucleus and induces transcription of genes required to increase intracellular cholesterol levels (2). Regulated SREBP activation requires both Scap and a third ER membrane protein, Insig.Scap senses ER cholesterol concentration by directly binding cholesterol in the membrane (3), and cholesterol binding induces a conformational change in Scap that promotes binding to Insig, retaining the SREBP-Scap complex in the ER (4, 5). When cholesterol is depleted, SREBP-Scap dissociates from Insig and can then be transported to the Golgi apparatus (4, 6). The N-terminal transcription factor domain of SREBP is liberated from the membrane by two Golgi-resident proteases, allowing SREBP to enter the nucleus and activate transcription of its target genes (2). Activation of SREBP target genes ultimately restores ER cholesterol, which in turn promotes Scap-Insig binding, thus blocking further ER-to-Golgi transport of SREBP-Scap and completing a negative feedback loop.Studies of SREBP in the genetically tractable fission yeast Schizosaccharomyces pombe revealed that this mammalian sterol-sensing mechanism is conserved and that SREBP functions as a principal hypoxic transcription factor in fungi (7). Importantly, in the pathogenic fungi Cryptococcus neoformans and Aspergillus fumigatus, SREBP is required for virulence in fungal disease models (8 -10). Fission yeast has homologs of SREBP and Scap called Sre1 and Scp1, respectively (11). The Sre1-Scp1 complex monitors synthesis of ergosterol, the fungal equivalent of cholesterol, as an indirect measure of oxygen supply. When cellular oxygen levels are low, oxygen-dependent sterol synthesis is inhibited...

In response to DNA damage, the transcription factor p53 accumulates in a series of pulses. While p53 dynamics play a critical role in regulating stress responses, how p53 pulsing affects target protein expression is not well understood. Recently, we showed that p53 pulses generate diversity in target mRNA expression dynamics; however, given that mRNA and protein expression are not necessarily well correlated, it remains to be determined how p53 pulses impact target protein expression. Using computational and experimental approaches, we show that target protein decay rates filter p53 pulses: Distinct target protein expression dynamics are generated depending on the relationship between p53 pulse frequency and target mRNA and protein stability. Furthermore, by mutating the targets MDM2 and PUMA to alter their stabilities, we show that downstream pathways are sensitive to target protein decay rates. This study delineates the mechanisms by which p53 dynamics play a crucial role in orchestrating the timing of events in the DNA damage response network.

The goal of current dental and orthopedic biomaterials research is to design implants that induce controlled and guided tissue growth, and rapid healing. In addition to acceleration of normal wound healing phenomena, these implants should result in the formation of a characteristic interfacial layer with adequate biomechanical properties. To achieve these goals, however, a better understanding of events at the bone-material interface is needed, as well as the development of new materials and approaches that promote osseointegration. Here we present novel nanostructured nanoarrays from tantala that can promote cell adhesion and differentiation. Our results suggest that tantala nanotube arrays enhance osteoblast cell adhesion, proliferation and differentiation. The routes of fabrication of tantala nanotube arrays are flexible and cost-effective, enabling realization of desired platform topologies on existing non-planar orthopedic implants.

The prolyl hydroxylase Ofd1 enables yeast cells to adapt to hypoxia by regulating the DNA binding and degradation of the hypoxic transcription factor Sre1N. These two regulatory functions are inseparable in vivo. A mathematical model of the Ofd1 system is used to show that both functions are necessary for Ofd1 to work as observed.