Detecting consistent common lines in cryo-EM by voting

The single-particle reconstruction problem of electron cryo-microscopy (cryo-EM) is to find the three-dimensional structure of a macromolecule given its two-dimensional noisy projection images at unknown random directions. Ab initio estimates of the 3D structure are often obtained by the “Angular Reconstitution” method, in which a coordinate system is established from three projections, and the orientation of the particle giving rise to each image is deduced from common lines among the images. However, a reliable detection of common lines is difficult due to the low signal-to-noise ratio of the images. In this paper we describe a global self-correcting voting procedure in which all projection images participate to decide the identity of the consistent common lines. The algorithm determines which common line pairs were detected correctly and which are spurious. We show that the voting procedure succeeds at relatively low detection rates and that its performance improves as the number of projection images increases. We demonstrate the algorithm for both simulative and experimental images of the 50S ribosomal subunit.     

Interactions between the immune and nervous systems in pain

Immune cells and glia interact with neurons to alter pain sensitivity and to mediate the transition from acute to chronic pain. In response to injury, resident immune cells are activated and blood-borne immune cells are recruited to the site of injury. Immune cells not only contribute to immune protection but also initiate the sensitization of peripheral nociceptors. Through the synthesis and release of inflammatory mediators and interactions with neurotransmitters and their receptors, the immune cells, glia and neurons form an integrated network that coordinates immune responses and modulates the excitability of pain pathways. The immune system also reduces sensitization by producing immune-derived analgesic and anti-inflammatory or proresolution agents. A greater understanding of the role of the immune system in pain processing and modulation reveals potential targets for analgesic drug development and new therapeutic opportunities for managing chronic pain.     

A conformationally constrained peptidomimetic binds to the extracellular region of HER2 protein

Human epidermal growth factor receptor 2 (HER2) is a member of the human epidermal growth factor receptor kinases (other members include EGFR or HER1, HER3, and HER4) that are involved in signaling cascades for cell growth and differentiation. It is well established that HER2-mediated heterodimerization has important implications in cancer. Deregulation of signaling pathways and overexpression of HER2 is known to occur in cancer cells, indicating a role of HER2 in tumorigenesis. Therefore, blocking HER2-mediated signaling has potential therapeutic value. We have designed several peptidomimetics to inhibit HER2-mediated signaling for cell growth. One of the compounds (HERP5, Arg-beta Naph-Phe) exhibited antiproliferative activity with IC(50) values in the micromolar-to-nanomolar range in breast cancer cell lines. Binding of fluorescently labeled HERP5 to HER2 protein was evaluated by fluorescence assay, microscopy, and circular dichroism spectroscopy. Results indicated that HERP5 binds to the extracellular region of the HER2 protein. Structure of the peptidomimetic HERP5 was studied by NMR and molecular dynamics simulations. Based on these results a model was proposed for HER2-EGFR dimerization and possible blocking by HERP5 peptidomimetic using a protein-protein docking method.     

Effects of salinity and light on biomass and growth of <Emphasis Type="Italic">Vallisneria americana</Emphasis> from Lower St. Johns River,FL, USA

A mesocosm study was conducted to determine the effects of variable salinity and light on Vallisneria americana Michx. (wild celery) and associated algal community components in the lower St. Johns River, Florida. Fifteen centimeter diameter intact plant plugs were collected from the LSJR in March 2001 and transported to mesocosm facilities in Lafayette, Louisiana. A factorial experimental design was used consisting of three salinity levels (1, 8, and 18 ppt), three light levels (0, 50, and 90% shading), and three replicate mesocosms of each for a total of 27 mesocosms. The experiment consisted of a 4-week acclimation period followed by a 5-month treatment period. V. americana responded negatively to increased salinity. Although V. americana survived 8 ppt salinity, growth was limited. At 18 ppt, almost all V. americana aboveground biomass had perished within 10 weeks, but when salinity was lowered back to 1 ppt, approximately 20% of the aboveground biomass recovered within the following 10 weeks. At midtreatment harvest, light did not affect V. americana biomass directly (P = 0.8240), but by final harvest (20 weeks) light affected belowground biomass (P < 0.0014). Both salinity and light affected algal growth. Macroalgae dominated 1 ppt salinity treatments in ambient light, but phytoplankton dominated 8 and 18 ppt salinity treatments in ambient light. Algal communities were greatly inhibited by 90% shading. While salinity directly impacted V. americana growth and survival, light effects were less direct and involved algal community associations.     

Methylene amine substituted arylindenopyrimidines as potent adenosine A2A/A1 antagonists

A novel series of arylindenopyrimidines were identified as A_2A and A₁ receptor antagonists. The series was optimized for in vitro activity by substituting the 8- and 9-positions with methylene amine substituents. The compounds show excellent activity in mouse models of Parkinson’s disease when dosed orally.     

3-(3-Aryloxyaryl)imidazo[1,2-a]pyridine sulfones as liver X receptor agonists

Replacement of a quinoline with an imidazo[1,2-a]pyridine in a series of liver X receptor (LXR) agonists incorporating a [3-(sulfonyl)aryloxyphenyl] side chain provided high affinity LXR ligands 7. In functional assays of LXR activity, good agonist potency and efficacy were found for several analogs.     

Comparing mortality in renal patients on hemodialysis versus peritoneal dialysis using a marginal structural model

When comparing the causal effect of peritoneal dialysis (PD) and hemodialysis (HD) treatment on lowering mortality in renal patients, using observational data, it is necessary to adjust for different forms of confounding and informative censoring. Both the type of dialysis treatment that is started with and mortality are affected by baseline covariates. Longitudinal and baseline variables can affect both the probability of switching from one type of dialysis to the other, and mortality. Longitudinal and baseline variables can also affect the probability of receiving a kidney transplant, possibly causing informative censoring. Adjusting for longitudinal variables by including them as covariates in a regression model potentially causes bias, for instance by losing a possible indirect effect of dialysis on mortality via these longitudinal variables. Instead, we fitted a marginal structural model (MSM) to estimate the causal effect of dialysis type, adjusted for confounding and informative censoring. We used the MSM to compare the hazard of death as well as cumulative survival between the potential treatment trajectories "always PD" and "always HD" over time, conditional on age and diabetes mellitus status. We used inverse probability weighting (IPW) to fit the MSM.