A novel series of positive modulators of the AMPA receptor: Structure-based lead optimization

Starting from lead compound 1, we demonstrate how X-ray structural data can be used to understand SAR and expediently optimize bioavailability in a novel series of AMPA receptor modulators, furnishing 5 with improved bioavailability and robust in vivo activity.     

Acute dyspnoea and single tracheal localisation of mantle cell lymphoma

We report a case of a 48-year-old Chinese female with end-stage renal disease and chronic anemia on hemodialysis. Clonazepam was prescribed for myoclonus disorder two weeks prior to her hospitalization. Subsequently, she was hospitalized for neutropenic fever with thrombocytopenia and worsening anemia. Bone marrow examination demonstrated a markedly hypocellular marrow (10-20% total cellularity). Clonazepam was discontinued, with gradual improvement of thrombocytopenia, and neutropenia in 1-2 weeks. To our knowledge, this is the first reported case of pancytopenia associated with clonazepam. We recommend patients taking clonazepam to be monitored with regular complete blood count to check for clinically significant pancytopenia or thrombocytopenia.     

Efficient Bayesian Sample Size Calculation for Designing a Clinical Trial with Multi‐Cluster Outcome Data

Health care utilization and outcome studies call for hierarchical approaches. The objectives were to predict major complications following percutaneous coronary interventions by health providers, and to compare Bayesian and non‐Bayesian sample size calculation methods. The hierarchical data structure consisted of: (1) Strata: PGY4, PGY7, and physician assistant as providers with varied experiences; (2) Clusters: k_s providers per stratum; (3) Individuals: n_s patients reviewed by each provider. The main outcome event illustrated was mortality modeled by a Bayesian beta‐binomial model. Pilot information and assumptions were utilized to elicit beta prior distributions. Sample size calculations were based on the approximated average length, fixed at 1%, of 95% posterior intervals of the mean event rate parameter. Necessary sample sizes by both non‐Bayesian and Bayesian methods were compared. We demonstrated that the developed Bayesian methods can be efficient and may require fewer subjects to satisfy the same length criterion.     

Bcl-2 and Bcl-XL regulate proinflammatory caspase-1 activation by interaction with NALP1

Caspases are intracellular proteases that cleave substrates involved in apoptosis or inflammation. In C. elegans, a paradigm for caspase regulation exists in which caspase CED-3 is activated by nucleotide-binding protein CED-4, which is suppressed by Bcl-2-family protein CED-9. We have identified a mammalian analog of this caspase-regulatory system in the NLR-family protein NALP1, a nucleotide-dependent activator of cytokine-processing protease caspase-1, which responds to bacterial ligand muramyl-dipeptide (MDP). Antiapoptotic proteins Bcl-2 and Bcl-X(L) bind and suppress NALP1, reducing caspase-1 activation and interleukin-1beta (IL-1beta) production. When exposed to MDP, Bcl-2-deficient macrophages exhibit more caspase-1 processing and IL-1beta production, whereas Bcl-2-overexpressing macrophages demonstrate less caspase-1 processing and IL-1beta production. The findings reveal an interaction of host defense and apoptosis machinery.     

Unique mutational patterns in the envelope alpha 2 amphipathic helix and acquisition of length in gp120 hypervariable domains are associated with resistance to autologous neutralization of subtype C human immunodeficiency virus type 1

Autologous neutralizing antibodies (NAb) against human immunodeficiency virus type 1 generate viral escape variants; however, the mechanisms of escape are not clearly defined. In a previous study, we determined the susceptibilities of 48 donor and 25 recipient envelope (Env) glycoproteins from five subtype C heterosexual transmission pairs to NAb in donor plasma by using a virus pseudotyping assay, thereby providing an ideal setting to probe the determinants of susceptibility to neutralization. In the present study, acquisition of length in the Env gp120 hypervariable domains was shown to correlate with resistance to NAb in donor plasma (P = 0.01; Kendall's tau test) but not in heterologous plasma. Sequence divergence in the gp120 V1-to-V4 region also correlated with resistance to donor (P = 0.0002) and heterologous (P = 0.001) NAb. A mutual information analysis suggested possible associations of nine amino acid positions in V1 to V4 with NAb resistance to the donor's antibodies, and five of these were located within an 18-residue amphipathic helix (alpha2) located on the gp120 outer domain. High nonsynonymous-to-synonymous substitution (dN/dS) ratios, indicative of positive selection, were also found at these five positions in subtype C sequences in the database. Nevertheless, exchange of the entire alpha2 helix between resistant donor Envs and sensitive recipient Envs did not alter the NAb phenotype. The combined mutual information and dN/dS analyses suggest that unique mutational patterns in alpha2 and insertions in the V1-to-V4 region are associated with NAb resistance during subtype C infection but that the selected positions within the alpha2 helix must be linked to still other changes in Env to confer antibody escape. These findings suggest that subtype C viruses utilize mutations in the alpha2 helix for efficient viral replication and immune avoidance.     

DNA branch nuclease activity of vaccinia A22 resolvase

DNA replication, recombination, and repair can result in formation of diverse branched DNA structures. Many large DNA viruses are known to encode DNA branch nucleases, but several of the expected activities have not previously been found among poxvirus enzymes. Vaccinia encodes an enzyme, A22 resolvase, which is known to be active on four-stranded DNA junctions (Holliday junctions) or Holliday junction-like structures containing three of the four strands. Here we report that A22 resolvase in fact has a much wider substrate specificity than previously appreciated. A22 resolvase cleaves Y-junctions, single-stranded DNA flaps, transitions from double strands to unpaired single strands ("splayed duplexes"), and DNA bulges in vitro. We also report site-directed mutagenesis studies of candidate active site residues. The results identify the likely active site and support a model in which a single active site is responsible for cleavage on Holliday junctions and splayed duplexes. Lastly, we describe possible roles for the A22 resolvase DNA-branch nuclease activity in DNA replication and repair.     

A search for phylogenetically informative wood characters within Lecythidaceae s.l

The wood structure of 71 species representing 24 genera of the pantropical Lecythidaceae s.l., including the edible Brazil nuts (Bertholletia excelsa) and the spectacular cannon-ball tree (Couroupita guianensis), was investigated using light and scanning electron microscopy. This study focused on finding phylogenetically informative characters to help elucidate any obscure evolutionary patterns within the family. The earliest diverging subfamily Napoleonaeoideae has mixed simple/scalariform vessel perforations, scalariform vessel-ray pitting, and high multiseriate rays, all features that are also present in Scytopetaloideae. The wood structure of Napoleonaea is distinct, but its supposed close relative Crateranthus strongly resembles Scytopetaloideae. The isolated position of Foetidia (Foetidioideae) can be supported by a unique type of vessel-ray pitting that is similar in shape and size to intervessel pitting (distinctly bordered, <5 μm). The more derived Planchonioideae and Lecythidoideae share exclusively simple perforations and two types of vessel-ray pitting, but they can easily be distinguished from each other by the size of intervessel pitting, shape of body ray cells in multiseriate rays, and the type of crystalliferous axial parenchyma cells. The anatomical diversity observed is clearly correlated with differences in plant size (shrubs vs. tall trees): the percentage of scalariform perforations, as well as vessel density, and the length of vessel elements, fibers, and multiseriate rays are negatively correlated with increasing plant size, while the reverse is true for vessel diameter.