Microhabitat preferences and spatial distribution of the vesper rat (Nyctomys sumichrasti) in Colima,Mexico

The vesper rat (Nyctomys sumichrasti), a little-known arboreal rodent, was encountered during mark-recapture studies in Colima, Mexico, in January 2003-2007. We trapped on the Pacific coast at Playa de Oro (2003-2005) and in northern Colima (2006-2007). Each year five trap grids were established in heavily vegetated areas and typically run for 8 nights (100 trap stations per grid, each station with a ground trap and an arboreal trap elevated 1-2 m, 10×10 configuration with adjacent stations 10 m apart; 1,600 trap-nights per grid; 40,000 trap-nights total). Nyctomys sumichrasti occurs throughout most of Colima. On grids we captured 29 individuals a total of 41 times, with 90.2% of captures in arboreal traps and 69.0% of animals being adults. The sex ratio of adults was 1.22:1 (males:females), not statistically different from 1:1. Most adult females (77.8%) were pregnant or lactating. Mean mass was 41.3 and 38.6 g for males and females, respectively (P>0.05). Mean greatest distances traveled were longer for males (60.6 m) than females (20.2 m), with an overall mean of 40.4 m. One to six individuals were captured on 9 of 25 grids, with density estimates of 0.87-4.09/ha. We contrasted 14 environmental measures (most involving vegetation structure) for stations where N. sumichrasti was caught and not caught using logistic regression and nonparametric multiplicative regression, finding the species frequented sites flat to moderate in slope with considerable ground litter and relatively sparse high vegetation. In northern Colima, N. sumichrasti used areas with close trees, an open understory, and little grass. Other studies indicate the species sometimes occupies similar areas but with a relatively dense understory.     

Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve

Bicuspid Aortic Valve (BAV) is a highly heritable congenital heart defect. The low frequency of BAV (1% of general population) limits our ability to perform genome-wide association studies. We present the application of four a priori SNP selection techniques, reducing the multiple-testing penalty by restricting analysis to SNPs relevant to BAV in a genome-wide SNP dataset from a cohort of 68 BAV probands and 830 control subjects. Two knowledge-based approaches, CANDID and STRING, were used to systematically identify BAV genes, and their SNPs, from the published literature, microarray expression studies and a genome scan. We additionally tested Functionally Interpolating SNPs (fitSNPs) present on the array; the fourth consisted of SNPs selected by Random Forests, a machine learning approach. These approaches reduced the multiple testing penalty by lowering the fraction of the genome probed to 0.19% of the total, while increasing the likelihood of studying SNPs within relevant BAV genes and pathways. Three loci were identified by CANDID, STRING, and fitSNPS. A haplotype within the AXIN1-PDIA2 locus (p-value of 2.926×10⁻⁰⁶) and a haplotype within the Endoglin gene (p-value of 5.881×10⁻⁰⁴) were found to be strongly associated with BAV. The Random Forests approach identified a SNP on chromosome 3 in association with BAV (p-value 5.061×10⁻⁰⁶). The results presented here support an important role for genetic variants in BAV and provide support for additional studies in well-powered cohorts. Further, these studies demonstrate that leveraging existing expression and genomic data in the context of GWAS studies can identify biologically relevant genes and pathways associated with a congenital heart defect.     

Posttranslational modifications and receptor-associated proteins in AMPA receptor trafficking and synaptic plasticity

AMPA-type glutamate receptors (AMPARs) mediate most fast excitatory synaptic transmission in the mammalian brain. It is widely believed that the long-lasting, activity-dependent changes in synaptic strength, including long-term potentiation and long-term depression, could be the molecular and cellular basis of experience-dependent plasticities, such as learning and memory. Those changes of synaptic strength are directly related to AMPAR trafficking to and away from the synapse. There are many forms of synaptic plasticity in the mammalian brain, while the prototypic form, hippocampal CA1 long-term potentiation, has received the most intense investigation. After synthesis, AMPAR subunits undergo posttranslational modifications such as glycosylation, palmitoylation, phosphorylation and potential ubiquitination. In addition, AMPAR subunits spatiotemporally associate with specific neuronal proteins in the cell. Those posttranslational modifications and receptor-associated proteins play critical roles in AMPAR trafficking and regulation of AMPAR-dependent synaptic plasticity. Here, we summarize recent studies on posttranslational modifications and associated proteins of AMPAR subunits, and their roles in receptor trafficking and synaptic plasticity.     

Novel translocation responses of cytosolic phospholipase A2alpha fluorescent proteins

Cytosolic phospholipase A2 (cPLA2)alpha responds to the rise in cytosolic Ca2+ ([Ca2+]i) attending cell stimulation by moving to intracellular membranes, releasing arachidonic acid (AA) from these membranes, and thereby initiating the synthesis of various lipid mediators. Under some conditions, however, cPLA2alpha translocation occurs without any corresponding changes in [Ca2+]i. The signal for such responses has not been identified. Using confocal microscopy to track fluorescent proteins fused to cPLA2alpha or cPLA2alpha's C2 domain, we find that AA mimics Ca2+ ionophores in stimulating cPLA(2)alpha translocations to the perinuclear ER and to a novel site, the lipid body. Unlike the ionophores, AA acted independently of [Ca2+](i) rises and did not translocate the proteins to the Golgi. AA's action did not involve its metabolism to eicosanoids or acylation into cellular lipids. Receptor agonists also stimulated translocations targeting lipid bodies. We propose that AA is a signal for Ca2+-independent cPLA2alpha translocation and that lipid bodies are common targets of cPLA2alpha and contributors to stimulus-induced lipid mediator synthesis.     

Uncertainties in structural determinations of oligosaccharide conformation, using measurements of nuclear Overhauser effects

A fundamental problem in the determination of molecular structure by n.m.r. spectroscopy is insufficient experimental constraints. This problem is particularly marked for oligosaccharides, where few constraints are available across glycosidic linkages. By calculating distances as a function of dihedral angle, it is shown that, in general, two n.O.e. constraints result in two possible conformations for each glycosidic linkage, one of which can usually be discarded on the basis of model building or energy calculations. Using these calculations, an estimate of the uncertainty in the structure can be obtained.     

Color-Vision Mechanisms in the Peripheral Retinas of Normal and Dichromatic Observers

It is possible that so-called normal trichromatic vision occurs only between the central blue-blind fixation area and about 30° peripherally. Beyond about 30° vision has been alleged to become dichromatic (red-green blind), and beyond about 60°, monochromatic. Hence every form of color blindness may characterize various zones of the normal retina. We have studied mechanisms of peripheral color vision, mainly by measuring the spectral sensitivities of the blue-, green-, and red-sensitive systems, isolated by differential color adaptation. In normal observers the sensitivity of the blue-mechanism falls off about 2 log units by 80° out. The green- and red-sensitive systems decline only about 0.7 log unit over the same range. Protanopes, deuteranopes, and tritanopes exhibit comparable changes. We have not found any color mechanism present centrally to be wholly lost peripherally. Nor, for dichromats, have we found any mechanism missing centrally to be present peripherally. Whatever evidences of peripheral color blindness have been observed appear to involve other mechanisms than failure of receptors, probably including some fusion of neural pathways from receptors to centers.     

Characterisation of the asparagine-linked oligosaccharides from Trypanosoma brucei type-I variant surface glycoproteins

The complete primary structures of the Asn-linked oligosaccharides from the conserved glycosylation site of the type-I variant surface glycoproteins of Trypanosoma brucei MITat 1.4 and MITat 1.6 were determined using a combination of exoglycosidase digestions, permethylation analysis, acetolysis and 1H NMR. Both variants contained almost exclusively oligomannose-type oligosaccharides, identical in structure to those of mammalian glycoproteins. The oligosaccharides ranged in size from (Man)9(GlcNAc)2 to (Man)5(GlcNAc)2. The relative abundance of each component was similar in both variants. The major components were (Man)8(GlcNAc)2 and (Man)7(GlcNAc)2 with slightly less (Man)9(GlcNAc)2 and (Man)6(GlcNAc)2 and much less (Man)5(GlcNAc)2. Both variants also contained the same structural isomers. The close similarity of the oligomannose series indicates identical processing at the conserved site in both variants.