RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems

Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.     

Presence of two types of flowers with respect to nectar sugar in two gregariously flowering species

Many species of animal-pollinated flowers are known to vary widely in the nectar content of flowers. Some proportion of flowers in many species is apparently nectarless, and such flowers are believed to be ‘cheaters’. Cheating may explain a part of the variability in nectar content. If cheating exists as a qualitatively different strategy then we expect bimodality in the distribution of nectar content of flowers. It has been shown in a multispecies study that gregarious species have a higher proportion of cheater flowers. We studied the frequency distribution of total nectar sugar in two gregariously flowering species Lantana camara and Utricularia purpurascens, which differed in other floral and ecological characters. At the population level, both the species showed significant bimodality in the total sugar content of flowers. The obvious sources of heterogeneity in the data did not explain bimodality. In Lantana camara, bimodality was observed within flowers of some of the individual plants sampled. In Utricularia purpurascens the proportion of nectarless flowers was more in high-density patches, suggesting that the gregariousness hypothesis may work within a species as well. The results support the hypothesis of cheating as a distinct strategy since two distinct types of flowers were observed in both the species. The effect of density in Utricularia purpurascens also supports the gregariousness hypothesis.     

Quantitative comparison of two types of planar lipid bilayers--folded and painted--with respect to fusion with vesicles

Two major types of planar lipid bilayers, painted and folded, were compared with respect to vesicle fusion using one chamber for the preparation of both bilayers. Liposomes containing ion channels composed of nystatin and ergosterol were used as the vesicle sample. Fusion of the liposome to either bilayer elicited a spike-like current change, which corresponds to a fusion event. The lag time between the first fusion event and the addition of the vesicles is an index of the ease with which the vesicles fuse with the bilayers. The lag time in the painted bilayer at a KCl concentration (cis) of 450 mM was 1.58+/-1.18 min, similar to that in the folded bilayer (1.65+/-0.64 min). The lag time decreased with increase of the osmotic difference across the painted bilayer, whereas this change was small in the folded bilayer. The fusion of the liposomes to the painted bilayer was markedly reduced by stopping the stirring in the cis compartment, whereas the fusion to the folded bilayer was not affected significantly. These results imply that no practical difference exists in the ability of vesicles to fuse with the painted and folded bilayers. For the study of single channel behavior, the painted bilayer could have an advantage because simply stopping the stirring prevents excess fusion.     

Intrinsic organization of snake lateral cortex

Lateral cortex is the most laterally placed of the four cortical areas in snakes. Earlier studies suggest that it is composed of several subdivisions but provide no information on their organization. This paper first investigates the structure of lateral cortex in boa constrictors (Constrictor constrictor), garter snakes (Thamnophis sirtalis), and banded water snakes (Natrix sipedon) using Nissl and Golgi preparations; and secondly examines the relation of main olfactory bulb projections to the subdivisions of lateral cortex using Fink-Heimer and electron microscopic preparations. Lateral cortex is divided on cytoarchitectonic grounds into two major parts called rostral and caudal lateral cortex. Each part is further divided into dorsal and ventral subdivisions so that lateral cortex has a total of four subdivisions: dorsal rostral lateral cortex (drL), ventral rostral lateral cortex (vrL), dorsal caudal lateral cortex (dcL) and ventral caudal lateral cortex (vcL). Systematic analyses of Golgi preparations indicate that the rostral and caudal parts each contain distinct populations of neurons. Rostral lateral cortex contains bowl cells whose dendrites arborize widely in the outer cortical layer (layer 1). The axons of some bowl cells can be traced medially into dorsal cortex, dorsomedial cortex and medial cortex. Caudal lateral cortex contains pyramidal cells whose somata occur in layers 2 and 3 and whose dendrites extend radially up to the pial surface. In addition, three populations of neurons occur in both rostral and caudal lateral cortex. Stellate cells occur in all three layers and have dendrites which arborize in all directions. Double pyramidal cells occur primarily in layer 2 and have dendrites which form two conical fields whose long axes are oriented radially. Horizontal cells occur in layer 3 and have dendrites oriented concentric with the ependyma. Fink-Heimer preparations of snakes which underwent lesions of the main olfactory bulb show that the primary olfactory projections to cortex are bilateral and restricted precisely to rostral lateral cortex. Electron microscopic degeneration experiments indicate that the olfactory bulb fibers end as terminals which have clear, spherical vesicles and asymmetric active zones. The majority are presynaptic to dendritic spines in outer layer 1. These studies establish that lateral cortex in snakes is heterogeneous and contains two major parts, each containing two subdivisions. The rostral and caudal parts have characteristic neuronal populations. Primary olfactory input is restricted to rostral lateral cortex and seems to terminate heavily on the distal dendrites of bowl cells. Axons of some of these cells leave lateral cortex, so that the rostral lateral cortex forms a direct route by which olfactory information reaches other cortical areas. The functional role of caudal lateral cortex is not clear.     

Discriminative ability with respect to amino acid types: assessing the performance of knowledge-based potentials without threading

We present a novel method designed to analyze the discriminative ability of knowledge-based potentials with respect to the 20 residue types. The method is based on the preference of amino acids for specific types of protein environment, and uses a virtual mutagenesis experiment to estimate how much information a given potential can provide about environments of each amino acid type. This allows one to test and optimize the performance of real potentials at the level of individual amino acids, using actual data on residue environments from a dataset of known protein structures. We have applied our method to long-range and medium-range pairwise distance-dependent potentials. The results of our study indicate that these potentials are only able to discriminate between a very limited number of residue types, and that discriminative ability is extremely sensitive to the choice of parameters used to construct the potentials, and even to the size of the training dataset. We also show that different types of pairwise distance potentials are dominated by different types of interactions. These dominant interactions strongly depend on the type of approximation used to define residue position. For each potential, our methodology is able to identify a potential-specific amino acid distance matrix and a reduced amino acid alphabet of any specified size, which may have implications for sequence alignment and multibody models.     

Creative teaching assistant organization to maintain an Integrative Physiology course with 440 students

We were recently challenged with trying to maintain the integrity and learning experience of our Physiology course, which included the use of long-answer, essay-style test questions, with a class size that increased over 2 yr by approximately 200 students. We reorganized the teaching assistant (TA) support structure in an attempt to keep the testing style and mark (or grade) the exams accurately, in a timely fashion, and provide feedback to the students that want it. Each of four TAs became experts in two sections of the course. To assess our success, TA time allocation for specific duties was recorded. Marking (or grading) accuracy was assessed by recording test data including the number of tests returned for remarking and how much marks changed by when a grade was reassessed. Student feedback was solicited to determine whether this structure provided adequate feedback and support to the students. TAs spent an average of 115 h and 35 min +/- 7 h 21 min of a total of 140 h contracted. On average, 13.2 +/- 0.5% of the tests were identified as being inaccurately graded by 4.2 +/- 0.7%. When asked to score whether the statement of assessment of students was fair, it scored 4.5 out of 5, where 5 equals strongly agree. When asked whether the course provided a worthwhile learning experience, the question scored 4.84 out of 5. Thus, we were successful at marking the exams accurately, in a timely fashion, and providing the necessary feedback, and we were successful at maintaining the objectives of the Physiology course with a class size of 440 students.     

Distribution of serotonin and FMRF-amide in the brain of Lymnaea stagnalis with respect to the visual system

Despite serotonin’s and FMRF-amide’s wide distribution in the nervous system of invertebrates and their importance as neurotransmitters,the exact roles they play in neuronal networks leaves many questions.We mapped the presence of serotonin and FMRF-amide-immunoreactivity in the central nervous system and eyes of the pond snail Lymnaea stagnalis and interpreted the results in connection with our earlier findings on the central projections of different peripheral nerves.Since the chemical nature of the intercellular connections in the retina of L.stagnalis is still largely unknown,we paid special attention to clarifying the role of serotonin and FMRF-amide in the visual system of this snail and compared our findings with those reported from other species.At least one serotonin-and one FMRF-amidergic fibre were labeled in each optic nerve,and since no cell bodies in the eye showed immunoreactivity to these neurotransmitters,we believe that efferent fibres with somata located in the central ganglia branch at the base of the eye and probably release 5HT and FMRF-amide as neuro-hormones.Double labelling revealed retrograde transport of neurobiotin through the optic nerve,allowing us to conclude that the central pathways and serotonin-and FMRF-amideimmunoreactive cells and fibres have different locations in the CNS in L.stagnalis.The chemical nature of the fibres,which connect the two eyes in L.stagnalis,is neither serotoninergic nor FMRF-amidergic.     

Plant centromere organization: a dynamic structure with conserved functions

Although the structural features of centromeres from most multicellular eukaryotes remain to be characterized, recent analyses of the complete sequences of two centromeric regions of rice, together with data from Arabidopsis thaliana and maize, have illuminated the considerable size variation and sequence divergence of plant centromeres. Despite the severe suppression of meiotic chromosomal exchange in centromeric and pericentromeric regions of rice, the centromere core shows high rates of unequal homologous recombination in the absence of chromosomal exchange, resulting in frequent and extensive DNA rearrangement. Not only is the sequence of centromeric tandem and non-tandem repeats highly variable but also the copy number, spacing, order and orientation, providing ample natural variation as the basis for selection of superior centromere performance. This review article focuses on the structural and evolutionary dynamics of plant centromere organization and the potential molecular mechanisms responsible for the rapid changes of centromeric components.     

Binding of adriamycin to liposomes as a probe for membrane lateral organization.

A stopped-flow spectrofluorometer equipped with a rapid scanning emission monochromator was utilized to monitor the binding of adriamycin to phospholipid liposomes. The latter process is evident as a decrease in fluorescence emission from a trace amount of a pyrene-labeled phospholipid analog (PPDPG, 1-palmitoyl-2-[(6-pyren-1-yl)]decanoyl-sn-glycero-3-phospho-rac-++ +glyce rol) used as a donor for resonance energy transfer to adriamycin. For zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) liposomes, fluorescence decay was slow, with a half-time t1/2 of approximately 2 s. When the mole fraction of the acidic phospholipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-rac-glycerol (POPG), was increased to XPG >/= 0.04, the decay of fluorescence became double exponential, and an additional, significantly faster process with t1/2 in the range between 2 and 4 ms was observed. Subsequently, as XPG was increased further, the amplitude of the fast process increased, whereas the slower process was attenuated, its t1/2 increasing to 20 s. Increasing [NaCl] above 50 mM or [CaCl2] above 150 microM abolished the fast component, thus confirming this interaction to be electrostatic. The critical dependence of the fast component on XPG allows the use of this process to probe the organization of acidic phospholipids in liposomes. This was demonstrated with 1, 2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes incorporating PPDPG (XPPDPG = 0.03), i.e., conditions where XPG in fluid bilayers is below the required threshold yielding the fast component. In keeping with the presence of clusters of PPDPG, the fast component was observed for gel-state liposomes. At approximately 34 degreesC (i.e., 6 degrees below Tm), the slower fluorescence decay also appeared, and it was seen throughout the main phase transition region as well as in the liquid-crystalline state. The fluorescence decay behavior at temperatures below, above, and at the main phase transition temperature is interpreted in terms of thermal density fluctuations and an intermediate state between gel and liquid-crystalline states being involved in the phospholipid main phase transition. This is the first observation of a cluster constituted by acidic phospholipids controlling the membrane association of a drug.     

Visuomotor functions of the lateral pre-motor cortex

Recent studies have provided new insights into the visuomotor functions of the dorsal and ventral regions of the lateral pre-motor cortex. Anatomical and physiological investigations in non-human primates have demonstrated that these regions have differing patterns of cortical connectivity and distinctive neuronal responses. Brain-imaging techniques and lesion studies have begun to probe the functions of homologous regions in humans.     

Imaging lipid lateral organization in membranes with C-laurdan in a confocal microscope

Lateral organization of biological membranes is frequently studied using fluorescence microscopy. One of the most widely used probes for these studies is 2-dimethylamino-6-lauroylnaphthalene (laurdan). The fluorescence of this probe is sensitive to the environment polarity, and thus laurdan reports the local penetration of water when inserted in membranes. Unfortunately, this probe can only be used under two-photon excitation due to its low photostability. This is a very important limitation, because there are not too many laboratories with capability for two-photon microscopy. In this work, we explored the performance of 6-dodecanoyl-2-[N-methyl-N-(carboxymethyl)amino]naphthalene (C-laurdan), a carboxyl-modified version of laurdan, for imaging biological membranes using a conventional confocal microscopy setup. We acquired generalized polarization (GP) images of C-laurdan inserted in giant unillamelar vesicles composed of binary mixtures of lipids and verified that the probe allows observing the coexistence of different phases. We also tested the performance of the probe for measurement with living cells and registered GP images of melanophore cells labeled with C-laurdan in which we could observe highly ordered regions such as filopodia. These findings show that C-laurdan can be successfully employed for studies of membrane lateral organization using a conventional confocal microscope and can open the possibility of studying a wide variety of membrane-related processes.     

Partly functional temporal process regression with semiparametric profile estimating functions

Summary .  Marginal mean models of temporal processes in event time data analysis are gaining more attention for their milder assumptions than the traditional intensity models. Recent work on fully functional temporal process regression (TPR) offers great flexibility by allowing all the regression coefficients to be nonparametrically time varying. The existing estimation procedure, however, prevents successive goodness-of-fit test for covariate coefficients in comparing a sequence of nested models. This article proposes a partly functional TPR model in the line of marginal mean models. Some covariate effects are time independent while others are completely unspecified in time. This class of models is very rich, including the fully functional model and the semiparametric model as special cases. To estimate the parameters, we propose semiparametric profile estimating equations, which are solved via an iterative algorithm, starting at a consistent estimate from a fully functional model in the existing work. No smoothing is needed, in contrast to other varying-coefficient methods. The weak convergence of the resultant estimators are developed using the empirical process theory. Successive tests of time-varying effects and backward model selection procedure can then be carried out. The practical usefulness of the methodology is demonstrated through a simulation study and a real example of recurrent exacerbation among cystic fibrosis patients.