Diurnal and seasonal changes in the mate-locating behavior of the satyrine butterfly <Emphasis Type="Italic">Lethe diana</Emphasis>

The time schedule of mate-locating behavior in the male satyrine butterfly Lethe diana was studied. Males displayed territorial behavior only in the afternoon, but it was not known whether they attempted to locate mates in the morning. In order for males of most butterfly species to mate with a virgin female, it would be most effective to initiate mate-locating behavior in the morning, when synchronous eclosions occur. Males of L.diana flew patrols in the morning and displayed territorial behavior in the afternoon. The cost of territorial behavior is probably less than that of patrolling, as territorial flights are shorter than those when patrolling. The temporal switching of mate-locating behavior is theoretically favored, since the reproductive value of females decreases later in the day, when males perform the less costly mate-locating behavior. Thus, the diurnal switching of male mate-locating behavior may be an adaptive strategy in response to the rapid decline in the reproductive value of females over the course of a day.     

Ion permeation of pores in model membranes: selectivity,fluctuations and the role of surface charge

Fluctuation of surface charge on pore walls provides a realistic, additional mechanism for generating fluctuation of ionic current and ionic selectivity in narrow pores.     

Synthesis of poly(hydroxyalkanoates) by Escherichia coli expressing mutated and chimeric PHA synthase genes

Pseudomonas resinovorans phaC1 _Pre and phaC2 _Pre genes coding for poly(hydroxyalkanoate) (PHA) synthases were cloned by PCR and expressed in E. coli LS1298 (fadB). Repeat-unit composition analysis showed that -hydroxydecanoate (67–75 mol%) and -hydroxyoctanoate (25–33 mol%) are the major monomers of the PHA produced in cells grown on decanoate. Sequence analysis showed that the gene products of phaC1 _Pre and phaC2 _Pre had 61% identical (75% positive) amino-acid sequence matches, and both sequences contained a conserved /-hydrolase fold in the carboxy-terminal portion of the proteins. Switching the /-hydrolase folds of phaC1 _Pre and phaC2 _Pre yielded chimeric pha7 and pha8 genes that afforded PHA synthesis in E. coli LS1298. The repeat-unit compositions of PHA in cells containing pha7 and pha8 were similar to those found in transformants containing the parental genes. Deletion mutants of phaC1 _Pre and phaC2 _Pre that resulted in potential translational fusions also supported PHA synthesis with similar repeat-unit compositions. Chimeric genes obtained from the switching of fragments containing the /-hydrolase folds of phaC1 _Pre and Ralstonia eutropha phbC did not direct the synthesis of PHA in transformed cells.     

Phenylalanine-Binding RNAs and Genetic Code Evolution

We isolated RNAs by selection–amplification, selecting for affinity to Phe–Sepharose and elution with free l-phenylalanine. Constant sequences did not contain Phe condons or anticodons, to avoid any possible confounding influence on initially randomized sequences. We examined the eight most frequent Phe-binding RNAs for inclusion of coding triplets. Binding sites were defined by nucleotide conservation, protection, and interference data. Together these RNAs comprise 70% of the 105 sequenced RNAs. The K _D for the strongest sites is ≈50 μM free amino acid, with strong stereoselectivity. One site strongly distinguishes free Phe from Trp and Tyr, a specificity not observed previously. In these eight Phe-binding RNAs, Phe codons are not significantly associated with Phe binding sites. However, among 21 characterized RNAs binding Phe, Tyr, Arg, and Ile, containing 1342 total nucleotides, codons are 2.7-fold more frequent within binding sites than in surrounding sequences in the same molecules. If triplets were not specifically related to binding sites, the probability of this distribution would be 4.8 × 10⁻¹¹. Therefore, triplet concentration within amino acid binding sites taken together is highly likely. In binding sites for Arg, Tyr, and Ile cognate codons are overrepresented. Thus Arg, Tyr, and Ile may be amino acids whose codons were assigned during an era of direct RNA–amino acid affinity. In contrast, Phe codons arguably were assigned by another criterion, perhaps during later code evolution.     

Direct analysis of drugs in plasma by column-switching liquid chromatography-mass spectrometry using a methylcellulose-immobilized reversed-phase pretreatment column

A novel methylcellulose-immobilized reversed-phase pretreatment column (MC-ODS) for column switching liquid chromatography-mass spectrometry (LC-MS) was investigated to improve recovery and durability. Pretreatment and analytical conditions were optimized so that high throughput and high selectivity was ensured during mass spectrometric analysis. Analytical runs, including deproteinization and gradient LC analysis, were conducted in a 6-min cycle. As a consequence, recoveries for test drugs (metoprolol, propranolol, lidocaine, dibucaine, bupivacaine) were greater than 90% and more than 300 plasma samples spiked with target compounds were directly injected and measured without compromising MS detection or system performance.     

Analysis of zinc binding sites in protein crystal structures

The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations.     

Predictable fold switching by the SARS‐CoV‐2 protein ORF9b

Extant fold‐switching proteins remodel their secondary structures and change their functions in response to environmental stimuli. These shapeshifting proteins regulate biological processes and are associated with a number of diseases, including tuberculosis, cancer, Alzheimer''s, and autoimmune disorders. Thus, predictive methods are needed to identify more fold‐switching proteins, especially since all naturally occurring instances have been discovered by chance. In response to this need, two high‐throughput predictive methods have recently been developed. Here we test them on ORF9b, a newly discovered fold switcher and potential therapeutic target from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2). Promisingly, both methods correctly indicate that ORF9b switches folds. We then tested the same two methods on ORF9b1, the ORF9b homolog from SARS‐CoV‐1. Again, both methods predict that ORF9b1 switches folds, a finding consistent with experimental binding studies. Together, these results (a) demonstrate that protein fold switching can be predicted using high‐throughput computational approaches and (b) suggest that fold switching might be a general characteristic of ORF9b homologs.     

“Sensory Switching” in Elbow Reconstruction

In the treatment of the soft tissue defect of the elbow, flap reconstruction is necessitated in many cases because of thinness of soft tissue at this region. In addition, reacquirement of tactile sensation is desirable because of the anatomical and specific functions of the elbow. Of three cases treated for elbow defects, one was reconstructed with a pedicled island forearm flap containing the lateral cutaneous nerve of the forearm, another was reconstructed with a venoneuro-accompanying artery fasciocutaneous flap (VNAF flap) containing the basilic vein, and the third with the VNAF flap containing the cephalic vein. The three cases demonstrated a sudden change of sensory territory 4 to 6 months after surgery, which was confirmed by touching the reconstructed region with patients'' eye-closed: from its original territory to the elbow in a “switching”-like action. Here we describe and discuss the concept of “sensory switching.”