Dream Bizarreness and Inner Thought

The paper offers a critique of bizarreness studies that compare dreams to real world probability ratios and directed thought processes as a basis for determining the degree of bizarreness in dreams. It examines two cases from the literature and suggests that dreams are better compared to non-directed, or imaginative waking thought processes, specifically Inner Thought and Speech (or speech for oneself, in Lev Vygotsky's definition), in which associative mechanisms operate freely hand in hand with (primarily) visual imagery before logical thought mechanisms come into play. The article suggests that dreams create a world order, or umwelt, with its own distinct cognitive domain in which waking considerations of efficiency, logic, and common sense are only thematically relevant. Dreams follow their own logic and can only be approached as thought-in-progress, or a search for coherence leading up many blind alleys. Finally, the relevance to dreams of the Inner Thought principle of predication, or abbreviation is examined.     

Vector redesign and in-droplet cell-growth improves enrichment and recovery in live Escherichia coli

Directed evolution (DE) is a widely used method for improving the function of biomolecules via multiple rounds of mutation and selection. Microfluidic droplets have emerged as an important means to screen the large libraries needed for DE, but this approach was so far partially limited by the need to lyse cells, recover DNA, and retransform into cells for the next round, necessitating the use of a high-copy number plasmid or oversampling. The recently developed live cell recovery avoids some of these limitations by directly regrowing selected cells after sorting. However, repeated sorting cycles used to further enrich the most active variants ultimately resulted in unfavourable recovery of empty plasmid vector-containing cells over those expressing the protein of interest. In this study, we found that engineering of the original expression vector solved the problem of false positives (i.e. plasmids lacking an insert) cells containing empty vectors. Five approaches to measure activity of cell-displayed enzymes in microdroplets were compared. By comparing various cell treatment methods prior to droplet sorting two things were found. Substrate encapsulation from the start, that is prior to expression of enzyme, showed no disadvantage to post-induction substrate addition by pico-injection with respect to recovery of true positive variants. Furthermore in-droplet cell growth prior to induction of enzyme production improves the total amount of cells retrieved (recovery) and proportion of true positive variants (enrichment) after droplet sorting.     

Spore coat architecture of Clostridium novyi NT spores

Spores of the anaerobic bacterium Clostridium novyi NT are able to germinate in and destroy hypoxic regions of tumors in experimental animals. Future progress in this area will benefit from a better understanding of the germination and outgrowth processes that are essential for the tumorilytic properties of these spores. Toward this end, we have used both transmission electron microscopy and atomic force microscopy to determine the structure of both dormant and germinating spores. We found that the spores are surrounded by an amorphous layer intertwined with honeycomb parasporal layers. Moreover, the spore coat layers had apparently self-assembled, and this assembly was likely to be governed by crystal growth principles. During germination and outgrowth, the honeycomb layers, as well as the underlying spore coat and undercoat layers, sequentially dissolved until the vegetative cell was released. In addition to their implications for understanding the biology of C. novyi NT, these studies document the presence of proteinaceous growth spirals in a biological organism.     

Structure of compstatin in complex with complement component C3c reveals a new mechanism of complement inhibition

Undesired complement activation is a major cause of tissue injury in various pathological conditions and contributes to several immune complex diseases. Compstatin, a 13-residue peptide, is an effective inhibitor of the activation of complement component C3 and thus blocks a central and crucial step in the complement cascade. The precise binding site on C3, the structure in the bound form, and the exact mode of action of compstatin are unknown. Here we present the crystal structure of compstatin in complex with C3c, a major proteolytic fragment of C3. The structure reveals that the compstatin-binding site is formed by the macroglobulin (MG) domains 4 and 5. This binding site is part of the structurally stable MG-ring formed by domains MG 1-6 and is far away from any other known binding site on C3. Compstatin does not alter the conformation of C3c, whereas compstatin itself undergoes a large conformational change upon binding. We propose a model in which compstatin sterically hinders the access of the substrate C3 to the convertase complexes, thus blocking complement activation and amplification. These insights are instrumental for further development of compstatin as a potential therapeutic.     

Chlorpyrifos immersion to eliminate third instars of Japanese beetle (Coleoptera: Scarabaeidae) in balled and burlapped trees and subsequent treatment effects on red maple

This study examined chlorpyrifos immersion of balled and burlapped (B&B) nursery trees for elimination of third instars of Japanese beetle, Popillia japonica Newman (Coleoptera: Scarabaeidae), and for phytotoxicity on red maple, Acer rubrum L. Trees were harvested as 45- and 60-cm-diameter B&B and immersed in chlorpyrifos at U.S. Domestic Japanese Beetle Harmonization Plan rate (0.24 kg active ingredient [AI/100 liters) or lower rates of 0.015, 0.03, 0.06, and 0.12 kg (AI)/100 liters. The 0.03, 0.06, and 0.24 kg (AI) rates provided 100% control of Japanese beetle grubs in both 45- and 60-cm B&B. The 0.015 and 0.12 kg (AI) chlorpyrifos rates were 100% effective in three tests. However, in another test, 0.015 and 0.12 kg (AI) chlorpyrifos treatments had four (93% control) and one (98% control) grubs recovered, respectively. Root ball soils consisted of loam, silt loam, or clay loam texture classifications. Trunk diameter and internode growth of red maple harvested as 45-cm B&B decreased linearly with increasing chlorpyrifos dip rate during the first year, but effects were unapparent in the second year. Chlorpyrifos rates had no measurable impact on growth of red maples harvested as 60-cm B&B. No visual phytotoxicity symptoms were detected for chlorpyrifos rate or root ball size treatments. In conclusion, results support lowering the U.S. Domestic Japanese Beetle Harmonization Plan chlorpyrifos dip rate for category 2 states to at least 0.03 kg (AI) for B&B diameters < or =60 cm. Chlorpyrifos rates < 0.24 kg (AI) will lower cost, reduce worker exposure, and lessen potential environmental contamination.     

Development and validation of a liquid chromatography/tandem mass spectrometry method for the determination of DMXAA in human and mouse plasma

A rapid, sensitive, and specific LC/MS/MS-based method was developed for determining the concentration of DMXAA in human and mouse plasma. Sample preparation involved a single protein precipitation step using acetonitrile. Separation of DMXAA and 6-isopropoxy-9-oxoxanthene-2-carboxylic acid, the internal standard, was achieved on a Waters X-Terra C(18) (50 mm x 2.1mm i.d., 3.5 microm) analytical column using a mobile phase consisting of acetonitrile/10 mM ammonium acetate (55:45, v/v) containing 0.1% formic acid and isocratic flow at 0.2 mL/min for 3 min. The analytes were monitored by tandem mass spectrometry with electrospray positive ionization. Linear calibration curves were generated over the range of 5-3000 ng/mL. The values for precision and accuracy were <9.6%, except at the LLOQ (5 ng/mL) level, which was within 16.8%. Recovery of DMXAA in mouse plasma was >65%. DMXAA was stable through 2 freeze/thaw cycles, to 2h in mouse plasma or 50% acetonitrile, and on the autosampler to 5.1h. This method was subsequently used to measure concentrations of DMXAA in mice following intraperitoneal administration.     

Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.     

Scleractinian corals (Fungiidae,Agariciidae and Euphylliidae) of Pulau Layang-Layang,Spratly Islands,with a note on Pavona maldivensis (Gardiner, 1905)

Layang-Layang is a small island part of an oceanic atoll in the Spratly Islands off Sabah, Malaysia. As the reef coral fauna in this part of the South China Sea is poorly known, a survey was carried out in 2013 to study the species composition of the scleractinian coral families Fungiidae, Agariciidae and Euphylliidae. A total of 56 species was recorded. The addition of three previously reported coral species brings the total to 59, consisting of 32 Fungiidae, 22 Agariciidae, and five Euphylliidae. Of these, 32 species are new records for Layang-Layang, which include five rarely reported species, i.e., the fungiids Lithophyllon ranjithi, Podabacia sinai, Sandalolitha boucheti, and the agariciids Leptoseris kalayaanensis and Leptoseris troglodyta. The coral fauna of Layang-Layang is poor compared to other areas in Sabah, which may be related to its recovery from a crown-of-thorns seastar outbreak in 2010, and its low habitat diversity, which is dominated by reef slopes consisting of steep outer walls. Based on integrative molecular and morphological analyses, a Pavona variety with small and extremely thin coralla was revealed as Pavona maldivensis. Since specimens from Sabah previously identified as Pavona maldivensis were found to belong to Pavona explanulata, the affinities and distinctions of Pavona maldivensis and Pavona explanulata are discussed.     

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.