Eddy correlation measurements of oxygen fluxes in permeable sediments exposed to varying current flow and light

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 1329–1343, doi:10.4319/lo.2013.58.4.1329.Based on noninvasive eddy correlation measurements at a marine and a freshwater site, this study documents the control that current flow and light have on sediment–water oxygen fluxes in permeable sediments. The marine sediment was exposed to tidal-driven current and light, and the oxygen flux varied from night to day between −29 and 78 mmol m−2 d−1. A fitting model, assuming a linear increase in oxygen respiration with current flow, and a photosynthesis–irradiance curve for light-controlled production reproduced measured fluxes well (R2 = 0.992) and revealed a 4-fold increase in oxygen uptake when current velocity increased from ∼ 0 to 20 cm s−1. Application of the model to a week-long measured record of current velocity and light showed that net ecosystem metabolism varied substantially among days, between −27 and 31 mmol m−2 d−1, due to variations in light and current flow. This variation is likely typical of many shallow-water systems and highlights the need for long-term flux integrations to determine system metabolism accurately. At the freshwater river site, the sediment–water oxygen flux ranged from −360 to 137 mmol m−2 d−1. A direct comparison during nighttime with concurrent benthic chamber incubations revealed a 4.1 times larger eddy flux than that obtained with chambers. The current velocity during this comparison was 31 cm s−1, and the large discrepancy was likely caused by poor imitation by the chambers of the natural pore-water flushing at this high current velocity. These results emphasize the need for more noninvasive oxygen flux measurements in permeable sediments to accurately assess their role in local and global carbon budgets.Support for this study was provided by the following National Science Foundation grants: OCE-0420575, OCE- 0536431, and OCE-1061364

Reversible linkage of two distinct small molecule inhibitors of myc generates a dimeric inhibitor with improved potency that is active in myc over-expressing cancer cell lines

We describe the successful application of a novel approach for generating dimeric Myc inhibitors by modifying and reversibly linking two previously described small molecules.We synthesized two directed libraries of monomers, each comprised of a ligand, a connector, and a bioorthogonal linker element, to identify the optimal dimer configuration required to inhibit Myc. We identified combinations of monomers, termed self-assembling dimeric inhibitors, which displayed synergistic inhibition of Myc-dependent cell growth. We confirmed that these dimeric inhibitors directly bind to Myc blocking its interaction with Max and affect transcription of MYC dependent genes. Control combinations that are unable to form a dimer do not show any synergistic effects in these assays. Collectively, these data validate our new approach to generate more potent and selective inhibitors of Myc by self-assembly from smaller, lower affinity components. This approach provides an opportunity for developing novel therapeutics against Myc and other challenging protein:protein interaction (PPI) target classes. © 2015 Wanner et al

The current consensus on the clinical management of intracranial ependymoma and its distinct molecular variants

Multiple independent genomic profiling efforts have recently identified clinically and molecularly distinct subgroups of ependymoma arising from all three anatomic compartments of the central nervous system (supratentorial brain, posterior fossa, and spinal cord). These advances motivated a consensus meeting to discuss: (1) the utility of current histologic grading criteria, (2) the integration of molecular-based stratification schemes in future clinical trials for patients with ependymoma and (3) current therapy in the context of molecular subgroups. Discussion at the meeting generated a series of consensus statements and recommendations from the attendees, which comment on the prognostic evaluation and treatment decisions of patients with intracranial ependymoma (WHO Grade II/III) based on the knowledge of its molecular subgroups. The major consensus among attendees was reached that treatment decisions for ependymoma (outside of clinical trials) should not be based on grading (II vs III). Supratentorial and posterior fossa ependymomas are distinct diseases, although the impact on therapy is still evolving. Molecular subgrouping should be part of all clinical trials henceforth

Structural and Functional Profiling of the Human Histone Methyltransferase SMYD3

The SET and MYND Domain (SMYD) proteins comprise a unique family of multi-domain SET histone methyltransferases that are implicated in human cancer progression. Here we report an analysis of the crystal structure of the full length human SMYD3 in a complex with an analog of the S-adenosyl methionine (SAM) methyl donor cofactor. The structure revealed an overall compact architecture in which the “split-SET” domain adopts a canonical SET domain fold and closely assembles with a Zn-binding MYND domain and a C-terminal superhelical 9 α-helical bundle similar to that observed for the mouse SMYD1 structure. Together, these structurally interlocked domains impose a highly confined binding pocket for histone substrates, suggesting a regulated mechanism for its enzymatic activity. Our mutational and biochemical analyses confirm regulatory roles of the unique structural elements both inside and outside the core SET domain and establish a previously undetected preference for trimethylation of H4K20

A general model for predicting the binding affinity of reversibly and irreversibly dimerized ligands.

Empirical data has shown that bivalent inhibitors can bind a given target protein significantly better than their monomeric counterparts. However, predicting the corresponding theoretical fold improvements has been challenging. The current work builds off the reacted-site probability approach to provide a straightforward baseline reference model for predicting fold-improvements in effective affinity of dimerized ligands over their monomeric counterparts. For the more familiar irreversibly linked bivalents, the model predicts a weak dependence on tether length and a scaling of the effective affinity with the 3/2 power of the monomer's affinity. For the previously untreated case of the emerging technology of reversibly linking dimers, the effective affinity is also significantly improved over the affinity of the non-dimerizing monomers. The model is related back to experimental quantities, such as EC50s, and the approaches to fully characterize the system given the assumptions of the model. Because of the predicted significant potency gains, both irreversibly and reversibly linked bivalent ligands offer the potential to be a disruptive technology in pharmaceutical research

Schematic representation of the possible interactions between a single two site target and bivalent molecules.

<p>The target (brown) may have no ligand (pink) bound (a), only one ligand bound [only one of the two possible arrangements is depicted] (b), or two ligands bound. For the later scenario, the two bound ligands could be from the same bivalent molecule (c) or from two separate bivalent molecules (d). Whenever a ligand is depicted as unbound, it is done so as a convenience, since its binding state is irrelevant to determining the probability of site occupancy on an individual target molecule.</p

Significant increases in potency are possible for reversibly connected monomers over a wide range of tether lengths and monomer affinities.

<p>A) Fraction of monomer in solution at a starting concentration equal to the EC₅₀, as a function of dimerization constant K_Dim and tether length <i>ρ</i>_<i>p</i>, when the K_D of the monomer is 1 mM. In the remaining insets, fold improvement in the EC₅₀ relative to that for a single site target, single ligand system is plotted as a function of the dimerization constant and tether length with K_D = 1 mM B), K_D = 1 μM C), or K_D = 1 nM D).</p

Schematic representation of the possible interactions between two site targets and dimerizing monomers.

<p>The green bar represents the linker (i.e., the dimerization moiety) attached to a ligand (pink). For calculating target occupancy probabilities, a single target (brown) may have no monomer bound (a), only one monomer bound (b), or two monomers bound. For the latter scenario, the two monomers could dimerize (c) or lack any association with each other (d) on a single target. Whenever a ligand is depicted as undimerized in (b)-(d), it is done so as a convenience, since its dimerization state is irrelevant to determining the probability of site occupancy on a single target molecule. For calculating ligand occupancy probabilities, occupancies for both the monomeric and dimeric states must be included. A single monomer may have its ligand bound (f) or not (e). A single dimer can have no ligands bound (g), one ligand bound (h), or two ligands bound. When two ligands are bound, they could share the same target (c) or be bound to separate target molecules (i). Whenever a target is depicted as having an unbound site in (f)-(i), it is done so as a convenience, since the occupancy of its other site is irrelevant to determining the probability of site occupancy on a single ligand.</p

Preclinical Studies on LY237733, a Potent and Selective Serotonergic Antagonist

is an ergoline with potent and highly selective 5-hydroxytryptamine (5-HI) antagonist activity