Decisions in Force Field Development: An Alternative to Those Described by Roterman et al.

Abstract

We attempt to give an alternate point of view of the analysis by Roterman et al. (J. Biolmol. Struct. Dyn. 7, 415 (1989)). In particular, we argue for the use of flexible geometry and explicit inclusion of solvent effects in analyzing φ psi; maps of peptides.     

Long non‐coding RNAs in melanoma

Melanoma is the most lethal cutaneous cancer with a highly aggressive and metastatic phenotype. While recent genetic and epigenetic studies have shed new insights into the mechanism of melanoma development, the involvement of regulatory non‐coding RNAs remain unclear. Long non‐coding RNAs (lncRNAs) are a group of endogenous non‐protein‐coding RNAs with the capacity to regulate gene expression at multiple levels. Recent evidences have shown that lncRNAs can regulate many cellular processes, such as cell proliferation, differentiation, migration and invasion. In the melanoma, deregulation of a number of lncRNAs, such as HOTAIR, MALAT1, BANCR, ANRIL, SPRY‐IT1 and SAMMSON, have been reported. Our review summarizes the functional role of lncRNAs in melanoma and their potential clinical application for diagnosis, prognostication and treatment.     

The worm re-turns: hiding behavior of a tube-dwelling marine polychaete, Serpula vermicularis

The polychaete worm Serpula vermicularis (Serpulidae) filterfeeds at the mouth of its calcareous tube, but retreats intothe tube when startled by mechanical stimuli likely to be associatedwith predators. While in its tube, a worm is safe but cannotfeed. Thus, hiding has a lost-opportunity cost. We show thatthis cost can be substantial, given that food in the naturalhabitat appears in pulses, and good feeding conditions may notlast long or recur frequently. We expect that a worm's hidingtime will be sensitive to the lost-opportunity cost, and wepresent data from a series of experiments that support thisprediction. The worms seem able to track relatively short-termchanges in food availability, and some evidence suggests thatthey assess food availability on a relative basis, comparingcurrent feeding conditions to those recently experienced. Hidingand other types of cryptic behavior are common antipredatortactics, and animals may commonly adjust the durations of suchbehaviors to current benefits and costs (including lost opportunity),as they perceive them     

A 13C-methylation study of glycophorin A in intact erythrocytes by 13C-NMR spectroscopy

N-terminal $\text{N}{}^{\mathrm{\alpha }}\text{-[}{}^{13}\text{C]monomethylamino}$ derivatives for the N-terminal serine and leucine residues of glycophorins A^M and A^N, respectively, were obtained by reductively ¹³C-methylating homozygous human erythrocytes (MM, NN). The ¹³C-labeled glycophorins, A^M and A^N, were then isolated. A unique structural state was observed in solution reductively ¹³C-methylated glycophorin A^M that was not observed in glycophorin A^M derived from ¹³C-methylated erythrocytes. We attribute this state to the fact that some of the glycophorin A^M forms a head-to-head dimer when subjected to reductive ¹³C-methylation in aqueous solution. The ¹³C chemical shift data and pH titration data for the N-terminal [¹³C]dimethylamino and [¹³C]monomethylamino groups of glycophorin A^M and A^N derived from reductively ¹³C-methylated erythrocytes were in agreement with the chemical shift and titration data previously obtained for the N-terminal [¹³C]dimethylamino groups of solution reductively ¹³C-methylated glycophorins and related glycopeptides and peptides and N-terminal [¹³C]monomethylamino groups of related glycopeptides and peptides.     

Determination of the mode of interaction of Mn2+ and Cu2+ with cis-inositol by 13C NMR spectroscopy

Natural abundance ¹³C nuclear magnetic resonance spectroscopy (¹³C NMR) was used to study the mode of binding of Mn²⁺ and Cu²⁺ to the cyclitol, cis-inositol. Resonance linewidths and the electron nuclear relaxation rates [(T₁^e)^?1 values] were used to establish that a unique binding site exists for these metal-ions on this cyclitol involving only the three axial hydroxyl groups. This work may aid in the development of new organometallic complexes used as paramagnetic relaxation agents in magnetic resonance imaging research.     

Effects of water dilution, housing, and food on rat urine collected from the metabolism cage

The objective of the study reported here was to investigate three factors that may affect the amounts of water consumed and urine excreted by a rat in the metabolism cage: water dilution, housing, and food. Young F344/N rats (eight per group) were used for all experiments. Food was withheld from rats before each 16-h urine collection, then rats were transferred into a metabolism cage. For trial A (water dilution), urine was collected from rats supplied with dyed water (0.05%, vol/vol). This was repeated three times over a 2-week period. Dye in water or urine was quantified, using a spectrophotometer. For trial B (housing), rats were individually housed in wire cages for 3 weeks before the first urine collection. Then they were group housed in the solid-bottom cage (four per cage). After 2 weeks of acclimation, urine collection was repeated. For trial C (food), one group of rats was provided with food, the other was not, during urine collection. About 8% of urine samples of small volume (< or = 3 ml) from trial A were contaminated with drinking water up to 13% of volume. The average urine volume associated with individual housing was approximately twice as large as that associated with group housing. When food was provided during urine collection, rats consumed similar amounts of water but excreted significantly smaller amounts of urine than did rats without food. It was concluded that water dilution of a urine sample from a sipper bottle is relatively small; rats individually housed in wire caging before urine collection can consume and excrete a larger quantity of water, compared with rats group housed in solid-bottom cages; and highly variable urine volumes are, in part, associated with lack of access to food during urine collection.     

Changes in odor quality discrimination following recovery from olfactory nerve transection

Following recovery from olfactory nerve transection, animals regain their ability to discriminate between odors. Odor discrimination is restored after new neurons establish connections with the olfactory bulb. However, it is not known if the new connections alter odor quality perception. To address this question, 20 adult hamsters were first trained to discriminate between cinnamon and strawberry odors. After reaching criterion (> or = 90% correct response), half of the animals received a bilateral nerve transection (BTX) and half a surgical sham procedure. Animals were not tested again until day 40, a point in recovery when connections are re-established with the bulb. When BTX animals were tested without food reinforcement, they could not perform the odor discrimination task. Sham animals, however, could discriminate, demonstrating that the behavioral response had not been extinguished during the 40 day period. When reinforcement was resumed, BTX animals were able to discriminate between cinnamon and strawberry after four test sessions. In addition, their ability to discriminate between these two familiar odors was no different than that of BTX and sham animals tested with two novel odors, baby powder and coffee. These findings suggest that, after recovery from nerve transection, there are alterations in sensory perception and that restoration of odor quality discrimination requires that the animal must again learn to associate individual odor sensations with a behavioral response.      

Amino acid immobilization of fungal motile cells

Summary A 0.2 M mixture of L-leucine and L-lysine, a pair of amino acids which Machlis (1969) had shown could attract the zoospores of Allomyces in much lower concentrations, was found to immobilize zoospores by stopping flagellar motion. While the age of the spores does not affect the response to the amino acid mixture, the time for 100% immobilization does increase with increasing numbers of spores. Viability of the spores is not altered by treatment with the mixture of L-leucine and L-lysine and subsequent germling development is highly synchronized.Several other amino acid mixtures had a similar effect upon the Allomyces' flagellum. Indeed, L-lysine by itself seems to be the most effective compound tested. Immobilization of flagella in other fungi, algae, and one protozoan was also caused by treatment with L-leucine and L-lysine. Nothing is known of the mechanism of action of this amino acid treatment.     

Male mating strategies under predation risk: do females call the shots?

Many authors have reported that, under elevated risk of predation,male guppies (Poecilia reticulata) alter their behavior fromcourtship to forced copulation (gonopodial thrusts not precededby sigmoid displays). This shift is presumed to benefit thebrightly colored male, whose intense courting activity mightotherwise increase his risk of detection and attack by predators.However, there is some evidence that females engaged in reproductiveactivity with males may be even more vulnerable to predatorsthan the males themselves, which suggests an alternative hypothesis:females in high-risk situations are less receptive to male courtship,and this leads males to change their behavior. We tested thishypothesis by providing either males and females separately,or both sexes concurrently, with information about elevatedpredation risk from a cichlid (Crenicichla sp.). We found thatwhen only females were provided with information about increased risk,males performed fewer courtship displays and fewer thrusts.They did not perform more forced copulations in any treatmentgroup. Nonetheless, our results suggest that the female's perceptionof predation risk can be at least as important as the male'sin changing male mating behavior.