Topography of nucleic acid helices in solutions. 28. Evidence for a dynamic structure of DNA in solution

Proton magnetic resonance (pmr), ultraviolet absorption, induced circular dichroism (CD), and viscometric evidence is presented which show that reporter molecules $\text{1}$ and $\text{2}$ bind to DNA via an intercalation process. Preliminary kinetic studies show that the DNA·$\text{1}$ complex forms rapidly (i.e., <1 msec), whereas the DNA·$\text{2}$ complex forms at a considerably slower rate ($\text{t}{}_{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}\text{> 100 msec}$). The kinetic results, and the steric requirements for intercalation of $\text{2}$ can be explained on the basis of a dynamic structure of DNA.     

L16, a bifunctional ribosomal protein and the enhancing effect of L6 and L11

L16 exhibits both peptide bond and transesterification activities when reconstituted into 2 M LiCl core particles. L6 and L11, when reconstituted in a similar manner in the absence of L16, manifest significant transesterification activity. Both L6 and L11 enhance the transesterification activity of L16; L11 being more active than L6 in this respect. However, both L6 and L11 have minimal effect on peptide bond formation when reconstituted with L16 at concentrations more than 2.5 M equivalents. Both L6 and L11 exhibit a differential effect on transesterification. The affinity-labelling agents, like PhCH2SO2F, diisopropylfluorophosphate and ethoxyformic anhydride, have been used to explore the role of residues in peptide bond formation and transesterification. It is proposed that the Ser-Phe combination present in L16, L11 and L6 is involved in transesterification in addition to the single histidine in L16. The single histidine in L16 appears to be important in the catalysis of peptide bond formation and transesterification.     

The fluorescent protein iLOV as a reporter for screening of high-yield production of antimicrobial peptides in Pichia pastoris

The methylotrophic yeast Pichia pastoris is commonly used for the production of recombinant proteins at scale. The identification of an optimally overexpressing strain following transformation can be time and reagent consuming. Fluorescent reporters like GFP have been used to assist identification of superior producers, but their relatively big size, maturation requirements and narrow temperature range restrict their applications. Here, we introduce the use of iLOV, a flavin-based fluorescent protein, as a fluorescent marker to identify P. pastoris high-yielding strains easily and rapidly. The use of this fluorescent protein as a fusion partner is exemplified by the production of the antimicrobial peptide NI01, a difficult target to overexpress in its native form. iLOV fluorescence correlated well with protein expression level and copy number of the chromosomally integrated gene. An easy and simple medium-throughput plate-based screen directly following transformation is demonstrated for low complexity screening, while a high-throughput method using fluorescence-activated cell sorting (FACS) allowed for comprehensive library screening. Both codon optimization of the iLOV_NI01 fusion cassettes and different integration strategies into the P. pastoris genome were tested to produce and isolate a high-yielding strain. Checking the genetic stability, process reproducibility and following the purification of the active native peptide are eased by visualization of and efficient cleavage from the iLOV reporter. We show that this system can be used for expression and screening of several different antimicrobial peptides recombinantly produced in P. pastoris.     

Abdominal Distension and Escherichia coli Peritonitis in Mice Lacking Myeloid Differentiation Factor 88

Here we describe the gross and microscopic findings of naturally occurring, β-hemolytic Escherichia coli peritonitis in B6.129-Myd88^tm1Aki male and female mice. Over approximately 5 mo, 10 homozygous mutant mice deficient in myeloid differentiation factor 88 (C57BL/6 strain; male and female) that had not been used in research protocols developed rapid-onset abdominal swelling associated with copious viscous ascites. Each mouse developed an anterior peritonitis, primarily involving the parietal peritoneum and the visceral surface of the spleen, liver, diaphragm, and stomach. Inflammation was confined to the organ surfaces, with no indication of septicemia or grossly apparent gastrointestinal perforation or other tissue compromise that would initiate peritonitis. Peritonitis was likely attributable to compromised antibacterial innate immunity; cohoused, similarly immunodeficient littermates did not develop similar clinical signs. An unusual finding in all cases was mesothelial cell hyperplasia and hypertrophy. Although the underlying innate immune deficiency accounts for much of the observed pathology, the remarkable mesothelial cell morphology and the episodic nature of the peritonitis in some littermates and not others remain unexplained.Abbreviations: MyD88, myeloid differentiation response 88; TLR, Toll-like receptorMice deficient in myeloid differentiation factor 88 (myD88) are commonly studied in immunologic research as models of various diseases, including inflammatory bowel disease and diabetes.^2,3 MyD88 is a key signal transduction molecule for most of the Toll-like receptors (TLR) and IL1 family receptors, initiating cytokine release essential for effective innate immunity.¹⁸ The loss of this adapter protein impairs production of IL1, IL6, IL18, macrophage inhibitory proteins 1 and 2, and various chemokines.^1,12,14 Knockout mutant mice are especially susceptible to gram-negative bacteria, because TLR4, which triggers signaling through MyD88, mediates responses to LPS.^7,17 These immunologic mutants are common in research animal colonies, but their development of clinical signs and lesions consistent with Escherichia coli peritonitis, which arose at different times and affected only some of the immunodeficient mice, was previously unknown.     

T-cell Receptor-optimized Peptide Skewing of the T-cell Repertoire Can Enhance Antigen Targeting

Altered peptide antigens that enhance T-cell immunogenicity have been used to improve peptide-based vaccination for a range of diseases. Although this strategy can prime T-cell responses of greater magnitude, the efficacy of constituent T-cell clonotypes within the primed population can be poor. To overcome this limitation, we isolated a CD8⁺ T-cell clone (MEL5) with an enhanced ability to recognize the HLA A*0201-Melan A_27–35 (HLA A*0201-AAGIGILTV) antigen expressed on the surface of malignant melanoma cells. We used combinatorial peptide library screening to design an optimal peptide sequence that enhanced functional activation of the MEL5 clone, but not other CD8⁺ T-cell clones that recognized HLA A*0201-AAGIGILTV poorly. Structural analysis revealed the potential for new contacts between the MEL5 T-cell receptor and the optimized peptide. Furthermore, the optimized peptide was able to prime CD8⁺ T-cell populations in peripheral blood mononuclear cell isolates from multiple HLA A*0201⁺ individuals that were capable of efficient HLA A*0201⁺ melanoma cell destruction. This proof-of-concept study demonstrates that it is possible to design altered peptide antigens for the selection of superior T-cell clonotypes with enhanced antigen recognition properties.     

GQ-16, a Novel Peroxisome Proliferator-activated Receptor γ (PPARγ) Ligand, Promotes Insulin Sensitization without Weight Gain

The recent discovery that peroxisome proliferator-activated receptor γ (PPARγ) targeted anti-diabetic drugs function by inhibiting Cdk5-mediated phosphorylation of the receptor has provided a new viewpoint to evaluate and perhaps develop improved insulin-sensitizing agents. Herein we report the development of a novel thiazolidinedione that retains similar anti-diabetic efficacy as rosiglitazone in mice yet does not elicit weight gain or edema, common side effects associated with full PPARγ activation. Further characterization of this compound shows GQ-16 to be an effective inhibitor of Cdk5-mediated phosphorylation of PPARγ. The structure of GQ-16 bound to PPARγ demonstrates that the compound utilizes a binding mode distinct from other reported PPARγ ligands, although it does share some structural features with other partial agonists, such as MRL-24 and PA-082, that have similarly been reported to dissociate insulin sensitization from weight gain. Hydrogen/deuterium exchange studies reveal that GQ-16 strongly stabilizes the β-sheet region of the receptor, presumably explaining the compound's efficacy in inhibiting Cdk5-mediated phosphorylation of Ser-273. Molecular dynamics simulations suggest that the partial agonist activity of GQ-16 results from the compound's weak ability to stabilize helix 12 in its active conformation. Our results suggest that the emerging model, whereby "ideal" PPARγ-based therapeutics stabilize the β-sheet/Ser-273 region and inhibit Cdk5-mediated phosphorylation while minimally invoking adipogenesis and classical agonism, is indeed a valid framework to develop improved PPARγ modulators that retain antidiabetic actions while minimizing untoward effects.     

It's all coming back to me now: perception and memory in amnesia

Medial temporal lobe (MTL) structures may constitute a representational hierarchy, rather than a dedicated system for memory. Barense et al. (2012) show that intact memory for object features can interfere with perception of complex objects in individuals with MTL amnesia.     

Role of A-type K+ channels in spike broadening observed in soma and axon of Hermissenda type-B photoreceptors: A simulation study

In Hermissenda type-B photoreceptors, the spike is generated in the axon and back-propagated to the soma, resulting in smaller somatic spikes. Experimentally, blocking the A-type K⁺ current (I_K,A) results in broadening of somatic spikes. Similarly, in a compartmental model of the photoreceptor, reducing the maximum A-type K⁺ conductance (g_K,Amax) results in broadening of somatic spikes. However, simulations predict that little or no broadening of axonal spikes occurs when g_K,Amax is reduced. The results can be explained by the voltage-dependent properties of I_K,A and the different potential ranges that the somatic and axonal spike traverse. Because of the steeper I-V curve and faster activation of the K⁺ channels at higher potentials, the recruitment of additional K⁺ channels in the axon is able to compensate for the decrease in K⁺ conductance, yielding less spike broadening. These results also support the idea that spike duration in the axon may not be reliably inferred based upon recordings collected from the soma. Action Editor: Jonathan D. Victor