Toward Patient-Specific,Biologically Optimized Radiation Therapy Plans for the Treatment of Glioblastoma

Purpose

To demonstrate a method of generating patient-specific, biologically-guided radiotherapy dose plans and compare them to the standard-of-care protocol.

Methods and Materials

We integrated a patient-specific biomathematical model of glioma proliferation, invasion and radiotherapy with a multiobjective evolutionary algorithm for intensity-modulated radiation therapy optimization to construct individualized, biologically-guided plans for 11 glioblastoma patients. Patient-individualized, spherically-symmetric simulations of the standard-of-care and optimized plans were compared in terms of several biological metrics.

Results

The integrated model generated spatially non-uniform doses that, when compared to the standard-of-care protocol, resulted in a 67% to 93% decrease in equivalent uniform dose to normal tissue, while the therapeutic ratio, the ratio of tumor equivalent uniform dose to that of normal tissue, increased between 50% to 265%. Applying a novel metric of treatment response (Days Gained) to the patient-individualized simulation results predicted that the optimized plans would have a significant impact on delaying tumor progression, with increases from 21% to 105% for 9 of 11 patients.

Conclusions

Patient-individualized simulations using the combination of a biomathematical model with an optimization algorithm for radiation therapy generated biologically-guided doses that decreased normal tissue EUD and increased therapeutic ratio with the potential to improve survival outcomes for treatment of glioblastoma.     

Lateral thinking: CaMKII uncouples kainate receptors from mossy fibre synapses

EMBO J (2013) 32: 496–510 doi:10.1038/emboj.2012.334; published online January042013Alteration of the efficacy of excitatory synaptic transmission between neurons is a critical element in the processes of learning, memory, and behaviour. Despite decades of research aimed at elucidating basic cellular mechanisms underlying synaptic plasticity, new pathways and permutations continue to be discovered. Carta et al (2013) now show that activation of the calcium/calmodulin dependent kinase II (CaMKII) induces an unusual postsynaptic form of long-term depression (LTD) at the hippocampal mossy fibre synapse by promoting lateral diffusion of kainate receptors (KARs), a family of ionotropic glutamate receptors (iGluRs) that influence pyramidal neuron excitability. This report therefore reveals a new and mechanistically unique way of fine-tuning synaptic plasticity at this central synapse in the hippocampus.Information transfer within the nervous system is regulated at the synaptic level by diverse cellular mechanisms. Synaptic efficacy is not static (i.e., it is ‘plastic''), and the capacity to adjust the strength of communication between neurons in a network has been shown to be a critical component of diverse aspects of brain function that include many forms of behavioural learning (Martin et al, 2000). The complex means by which neurons adjust their synaptic properties in response to changes in local and global activity in the central nervous system has been the subject of intensive investigation spanning multiple decades (Malenka and Bear, 2004; Feldman, 2009). Nonetheless, new mechanisms underlying plasticity of excitatory and inhibitory synaptic transmission continue to be elucidated; these can vary depending on the experimental parameters for induction of plasticity, the particular type of synapse under investigation, and even the prior history of activation at the synapse. Long-term potentiation (LTP) and LTD of excitatory synaptic transmission are two well-known phenomena in which efficacy is increased or decreased, respectively, and at many synapses in the CNS occur through concomitant alterations in the number of postsynaptic iGluRs. The movement of excitatory receptors in and out of synapses, and more generally to and from the neuronal plasma membrane, is dictated by their association with a wide variety of scaffolding and chaperone proteins, whose interactions are often controlled by various protein kinases (Anggono and Huganir, 2012).It is generally appreciated now that long-term synaptic plasticity can be elicited by a variety of mechanisms even within a single type of synaptic connection. In addition to postsynaptic alterations in receptor content, for example, synaptic efficacy can also be tuned by regulated alterations in the probability of vesicular release of the neurotransmitter. Until recently, this presynaptic form of plasticity was thought to be the exclusive mechanism for altering excitatory synaptic strength at a morphologically unusual synapse in the hippocampus formed between large bouton-like presynaptic terminals arising from granule cell axons, or mossy fibres, and proximal dendrites on CA3 pyramidal neurons (Nicoll and Schmitz, 2005). These synaptic connections allow for single dentate granule cells to profoundly influence the likelihood of action potential firing in CA3 pyramidal neurons in a frequency-dependent manner, and for that reason have been referred to as ‘conditional detonator'' synapses (Henze et al, 2002). The precise mechanisms that lead to increased vesicular release probability following LTP-inducing stimulation of mossy fibre axons, including a potential role for retrograde signalling, remain the subject of debate, although there is general consensus that activation of presynaptic protein kinase A (PKA) is a key step in this form of synaptic plasticity (Figure 1A). Enhancing release probability impacts signalling through all three types of iGluRs present at mossy fibre synapses—AMPA, NMDA, and KARs. Recently, however, novel postsynaptic forms of mossy fibre plasticity were discovered in which induction protocols specifically increased the number of NMDA receptors (Kwon and Castillo, 2008; Rebola et al, 2008) or decreased the number of KARs (Selak et al, 2009), expanding the mechanistic repertoire at this historical site of focus of research on presynaptic LTP. Alterations in the synaptic content of particular iGluRs could serve as an additional means to fine-tune synaptic integration at the mossy fibre—CA3 synapse and therefore have important consequences for hippocampal network excitability.Open in a separate windowFigure 1Kainate receptor-dependent plasticity mechanisms at the hippocampal mossy fibre–CA3 synapse. (A) Activation of presynaptic receptors enhances glutamate release from the mossy fibre terminals. (B) A spike-timing-dependent plasticity protocol known to activate postsynaptic CaMKII results in long-term synaptic depression. CaMKII phosphorylates the GluK5 kainate receptor subunit, which uncouples the receptor from PSD-95 in the postsynaptic density. This leads to an increase in receptor mobility and diffusion away from the synapse. (C) Low-frequency stimulation of mossy fibres and activation of postsynaptic group 1 mGluRs leads to activation of PKC, which promotes the association of SNAP-25 to the GluK5 kainate receptor subunit and the subsequent endocytosis of synaptic receptors.In this issue, Carta et al (2013) identify a new postsynaptic mechanism for shaping mossy fibre plasticity that is specific to synaptic KARs, which serve to influence temporal integration of synaptic input as well as pyramidal neuron excitability through modulation of intrinsic ion channels. The authors paired postsynaptic depolarization of CA3 pyramidal neurons with a precisely timed presynaptic release of glutamate in a pattern that is known to produce LTP at many central synapses (Feldman, 2012). At mossy fibre synapses, however, this form of spike-timing-dependent plasticity (STDP) instead caused LTD of KAR-mediated excitatory synaptic potentials (KAR-LTD) while leaving AMPA receptor function unaltered (Figure 1B) (Carta et al, 2013). Using a series of genetic and pharmacological manipulations, Carta et al (2013) found that KAR-LTD was dependent upon the activation of postsynaptic KARs themselves, a rise in postsynaptic Ca²⁺, and CaMKII phosphorylation of a specific protein component of synaptic KARs, the GluK5 subunit. Unlike other mechanisms of postsynaptic mossy fibre plasticity, KAR-LTD was independent of NMDA or metabotropic glutamate receptor activation. Most surprisingly, KAR-LTD did not require receptor endocytosis from the plasma membrane, as is the case with most other forms of postsynaptic depression of excitatory transmission, including a distinct form of KAR-LTD reported previously (Selak et al, 2009) (Figure 1C). Instead, CaMKII-mediated phosphorylation of GluK5 subunits likely uncoupled receptors from the postsynaptic scaffolding protein PSD-95, which then led to enhanced lateral diffusion of KARs out of mossy fibre synapses. As KAR endocytosis was not altered in mossy fibre STDP, the activity-dependent reduction in KAR signalling was effectively limited to those receptors in the synapse. A molecular replacement strategy was employed using biolistic-based expression of mutant KARs in cultured hippocampal slices prepared from KAR knockout mice, which allowed Carta et al (2013) to corroborate their detailed biochemical studies by showing that reconstituted KAR currents in CA3 neurons expressing recombinant GluK5 phosphorylation site substitutions were unable to express KAR-LTD. In summary, KAR-mediated activation of CaMKII leads to phosphorylation of the GluK5 subunit and subsequent KAR-LTD through enhanced lateral mobility of synaptic receptors (Figure 1B).These findings are intriguing for several reasons. Most notably, they stand in stark contrast to studies in which CaMKII activation primarily triggers potentiation, rather than depression, of excitatory synaptic transmission at other synapses (Lisman et al, 2012). CaMKII recently was shown to cause diffusional trapping of AMPA receptor complexes within the postsynaptic density following phosphorylation of a closely associated auxiliary subunit, stargazin (Opazo et al, 2010), which is precisely the opposite of the effects of activation of the enzyme on KAR mobility at mossy fibre synapses. Further, these divergent consequences are both dependent upon carboxy-terminal PDZ interactions with scaffolding proteins, although in each case further research is needed to dissect out the relevant binding partners that control lateral mobility. It is of interest that KAR-LTD required synaptic activation of KARs to initiate signalling via CaMKII, which implies a tight coupling exists between KARs and the holoenzyme in the mossy fibre postsynaptic density. This observation also raises the possibility that activated CaMKII could phosphorylate other targets to effect other, yet-to-be-discovered, changes in synaptic function. Finally, the report by Carta et al expands our understanding of how excitatory synaptic transmission is fine-tuned at an important central synapse and underscores the fact that even well-trod ground (or synapses) continue to yield surprises that inform our understanding of the remarkable mechanistic diversity underlying synaptic plasticity in the CNS.     

Kainate Receptor Post-translational Modifications Differentially Regulate Association with 4.1N to Control Activity-dependent Receptor Endocytosis

Kainate receptors exhibit a highly compartmentalized distribution within the brain; however, the molecular and cellular mechanisms that coordinate their expression at neuronal sites of action are poorly characterized. Here we report that the GluK1 and GluK2 kainate receptor subunits interact with the spectrin-actin binding scaffolding protein 4.1N through a membrane-proximal domain in the C-terminal tail. We found that this interaction is important for the forward trafficking of GluK2a receptors, their distribution in the neuronal plasma membrane, and regulation of receptor endocytosis. The association between GluK2a receptors and 4.1N was regulated by both palmitoylation and protein kinase C (PKC) phosphorylation of the receptor subunit. Palmitoylation of the GluK2a subunit promoted 4.1N association, and palmitoylation-deficient receptors exhibited reduced neuronal surface expression and compromised endocytosis. Conversely, PKC activation decreased 4.1N interaction with GluK2/3-containing kainate receptors in acute brain slices, an effect that was reversed after inhibition of PKC. Our data and previous studies therefore demonstrate that these two post-translational modifications have opposing effects on 4.1N association with GluK2 kainate and GluA1 AMPA receptors. The convergence of the signaling pathways regulating 4.1N protein association could thus result in the selective removal of AMPA receptors from the plasma membrane while simultaneously promoting the insertion and stabilization of kainate receptors, which may be important for tuning neuronal excitability and synaptic plasticity.     

One-dimensional TRFLP-SSCP is an effective DNA fingerprinting strategy for soil Archaea that is able to simultaneously differentiate broad taxonomic clades based on terminal fragment length polymorphisms and closely related sequences based on single stranded conformation polymorphisms

DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples.     

Effects of Supplemental Fructooligosaccharides Plus Mannanoligosaccharides on Immune Function and Ileal and Fecal Microbial Populations in Adult Dogs

The goal of this study was to examine whether supplemental fructooligosaccharides (FOS) plus mannanoligosaccharides (MOS) influenced immune function and ileal and fecal microbial populations of adult dogs. Eight adult dogs surgically fitted with ileal cannulas were used in a crossover design. Dogs were fed 200g of a dry, extruded, kibble diet twice daily. At each feeding, dogs were dosed with either 1g sucrose (placebo) or 2g FOS plus 1g MOS orally via gelatin capsule. Fecal, ileal, and blood samples were collected at the end of each 14-d period to measure microbial populations and immune characteristics. Treatment least squares means were compared using the GLM procedure of SAS. Supplementation of FOS plus MOS increased fecal bifidobacteria and fecal and ileal lactobacilli concentrations. Dogs fed FOS plus MOS also tended to have lower blood neutrophils and greater blood lymphocytes vs placebo. Serum, fecal, and ileal immunoglobulin concentrations were unchanged by treatment. Supplementation of FOS plus MOS beneficially altered indices of gut health by improving ileal and fecal microbial ecology. Supplementation of FOS plus MOS also altered immune function by causing a shift in blood immune cells.     

N-Way FRET Microscopy of Multiple Protein-Protein Interactions in Live Cells

Fluorescence Resonance Energy Transfer (FRET) microscopy has emerged as a powerful tool to visualize nanoscale protein-protein interactions while capturing their microscale organization and millisecond dynamics. Recently, FRET microscopy was extended to imaging of multiple donor-acceptor pairs, thereby enabling visualization of multiple biochemical events within a single living cell. These methods require numerous equations that must be defined on a case-by-case basis. Here, we present a universal multispectral microscopy method (N-Way FRET) to enable quantitative imaging for any number of interacting and non-interacting FRET pairs. This approach redefines linear unmixing to incorporate the excitation and emission couplings created by FRET, which cannot be accounted for in conventional linear unmixing. Experiments on a three-fluorophore system using blue, yellow and red fluorescent proteins validate the method in living cells. In addition, we propose a simple linear algebra scheme for error propagation from input data to estimate the uncertainty in the computed FRET images. We demonstrate the strength of this approach by monitoring the oligomerization of three FP-tagged HIV Gag proteins whose tight association in the viral capsid is readily observed. Replacement of one FP-Gag molecule with a lipid raft-targeted FP allowed direct observation of Gag oligomerization with no association between FP-Gag and raft-targeted FP. The N-Way FRET method provides a new toolbox for capturing multiple molecular processes with high spatial and temporal resolution in living cells.     

Economic evaluation of water loss saving due to the biological control of water hyacinth at New Year’s Dam,Eastern Cape province,South Africa

Water hyacinth Eichhornia crassipes is considered the most damaging aquatic weed in the world. However, few studies have quantified the impact of this weed economically and ecologically, and even fewer studies have quantified the benefits of its control. This paper focuses on water loss saving as the benefit derived from biological control of this plant between 1990 and 2013 at New Year’s Dam, Alicedale, Eastern Cape, South Africa. Estimates of water loss due to evapotranspiration from water hyacinth vary significantly; therefore, the study used three different rates, high, medium and low. A conservative raw agriculture value of R 0.26 per m³ was used to calculate the benefits derived by the water saved. The present benefit and cost values were determined using 10% and 5% discount rates. The benefit/cost ratio at the low evapotranspiration rate was less than one, implying that biological control was not economically viable but, at the higher evapotranspiration rates, the return justified the costs of biological control. However, at the marginal value product of water, the inclusion of the costs of damage to infrastructure, or the adverse effects of water hyacinth on biodiversity, would justify the use of biological control, even at the low transpiration rate.     

GPS Tracking of Free-Ranging Pigs to Evaluate Ring Strategies for the Control of Cysticercosis/Taeniasis in Peru

Background

Taenia solium, a parasitic cestode that affects humans and pigs, is the leading cause of preventable epilepsy in the developing world. T. solium eggs are released into the environment through the stool of humans infected with an adult intestinal tapeworm (a condition called taeniasis), and cause cysticercosis when ingested by pigs or other humans. A control strategy to intervene within high-risk foci in endemic communities has been proposed as an alternative to mass antihelminthic treatment. In this ring strategy, antihelminthic treatment is targeted to humans and pigs residing within a 100 meter radius of a pig heavily-infected with cysticercosis. Our aim was to describe the roaming ranges of pigs in this region, and to evaluate whether the 100 meter radius rings encompass areas where risk factors for T. solium transmission, such as open human defecation and dense pig activity, are concentrated.

Methodology/Principal Findings

In this study, we used Global Positioning System (GPS) devices to track pig roaming ranges in two rural villages of northern Peru. We selected 41 pigs from two villages to participate in a 48-hour tracking period. Additionally, we surveyed all households to record the locations of open human defecation areas. We found that pigs spent a median of 82.8% (IQR: 73.5, 94.4) of their time roaming within 100 meters of their homes. The size of home ranges varied significantly by pig age, and 93% of the total time spent interacting with open human defecation areas occurred within 100 meters of pig residences.

Conclusions/Significance

These results indicate that 100 meter radius rings around heavily-infected pigs adequately capture the average pig’s roaming area (i.e., home range) and represent an area where the great majority of exposure to human feces occurs.     

Accounting for host cell protein behavior in anion‐exchange chromatography

Host cell proteins (HCP) are a problematic set of impurities in downstream processing (DSP) as they behave most similarly to the target protein during separation. Approaching DSP with the knowledge of HCP separation behavior would be beneficial for the production of high purity recombinant biologics. Therefore, this work was aimed at characterizing the separation behavior of complex mixtures of HCP during a commonly used method: anion‐exchange chromatography (AEX). An additional goal was to evaluate the performance of a statistical methodology, based on the characterization data, as a tool for predicting protein separation behavior. Aqueous two‐phase partitioning followed by two‐dimensional electrophoresis provided data on the three physicochemical properties most commonly exploited during DSP for each HCP: pI (isoelectric point), molecular weight, and surface hydrophobicity. The protein separation behaviors of two alternative expression host extracts (corn germ and E. coli) were characterized. A multivariate random forest (MVRF) statistical methodology was then applied to the database of characterized proteins creating a tool for predicting the AEX behavior of a mixture of proteins. The accuracy of the MVRF method was determined by calculating a root mean squared error value for each database. This measure never exceeded a value of 0.045 (fraction of protein populating each of the multiple separation fractions) for AEX. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1453–1463, 2016