Differential profile of CRF receptor distribution in the rat stomach and duodenum assessed by newly developed CRF receptor antibodies

Peripheral corticotropin-releasing factor (CRF) receptor ligands inhibit gastric acid secretion and emptying while stimulating gastric mucosal blood flow in rats. Endogenous CRF ligands are expressed in the upper gastrointestinal (GI) tissues pointing to local expression of CRF receptors. We mapped the distribution of CRF receptor type 1 (CRF1) and 2 (CRF2) in the rat upper GI. Polyclonal antisera directed against the C-terminus of the CRF receptor protein were generated in rabbits and characterized by western blotting and immunofluorescence using CRF1- and CRF2-transfected cell lines and in primary cultured neurons from rat brain cortex. A selective anti-CRF1 antiserum (4467a-CRF1) was identified and used in parallel with another antiserum recognizing both CRF1 and CRF2 (4392a-CRF1&2) to immunostain gastric tissue sections. Antiserum 4467a-CRF1 demonstrated specific immunostaining in a narrow zone in the upper oxyntic gland within the stomach corpus. Conversely, 4392a-CRF1&2 labeled cells throughout the oxyntic gland and submucosal blood vessels. Pre-absorption with the specific antigen peptide blocked immunostaining in all experiments. Doublestaining showed co-localization of 4392a-CRF1&2 but not 4467a-CRF1 immunoreactivity with H/K-ATPase and somatostatin immunostaining in parietal and endocrine cells of the oxyntic gland. No specific staining was observed in the antrum with either antisera, whereas only antiserum 4392a-CRF1&2 showed modest immunoreactivity in the duodenal mucosa. Finally, co-localization of CRF2 and urocortin immunoreactivity was found in the gastric glands. These results indicate that both CRF receptor subtypes are expressed in the rat upper GI tissues with a distinct pattern and regional differences suggesting differential function.     

Specific interaction of ERp57 and calnexin determined by NMR spectroscopy and an ER two-hybrid system

Calnexin and ERp57 act cooperatively to ensure a proper folding of proteins in the endoplasmic reticulum (ER). Calnexin contains two domains: a lectin domain and an extended arm termed the P-domain. ERp57 is a protein disulfide isomerase composed of four thioredoxin-like repeats and a short basic C-terminal tail. Here we show direct interactions between the tip of the calnexin P-domain and the ERp57 basic C-terminus by using NMR and a novel membrane yeast two-hybrid system (MYTHS) for mapping protein interactions of ER proteins. Our results prove that a small peptide derived from the P-domain is active in binding ERp57, and we determine the structure of the bound conformation of the P-domain peptide. The experimental strategy of using the MYTHS two-hybrid system to map interaction sites between ER proteins, together with NMR, provides a powerful new strategy for establishing the function of ER complexes.     

The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications

The mitochondrial genome (mtDNA) of the entomopathogenic fungus Lecanicillium muscarium (synonym Verticillium lecanii) with a total size of 24,499-bp has been analyzed. So far, it is the smallest known mitochondrial genome among Pezizomycotina, with an extremely compact gene organization and only one group-I intron in its large ribosomal RNA (rnl) gene. It contains the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, one intronic ORF coding for a possible ribosomal protein (rps), and a set of 25 tRNA genes which recognize codons for all amino acids, except alanine and cysteine. All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed some characteristic common features like uninterrupted gene pairs, overlapping genes, and extremely variable intergenic regions, that can all be exploited for the study of fungal mitochondrial genomes. Moreover, a minimum common mtDNA gene order could be detected, in two units, for all known Sordariomycetes namely nad1-nad4-atp8-atp6 and rns-cox3-rnl, which can be extended in Hypocreales, to nad4L-nad5-cob-cox1-nad1-nad4-atp8-atp6 and rns-cox3-rnl nad2-nad3, respectively. Phylogenetic analysis of all fungal mtDNA essential protein-coding genes as one unit, clearly demonstrated the superiority of small genome (mtDNA) over single gene comparisons.     

Optimality of the genetic code with respect to protein stability and amino-acid frequencies

Background

The genetic code is known to be efficient in limiting the effect of mistranslation errors. A misread codon often codes for the same amino acid or one with similar biochemical properties, so the structure and function of the coded protein remain relatively unaltered. Previous studies have attempted to address this question quantitatively, by estimating the fraction of randomly generated codes that do better than the genetic code in respect of overall robustness. We extended these results by investigating the role of amino-acid frequencies in the optimality of the genetic code.

Results

We found that taking the amino-acid frequency into account decreases the fraction of random codes that beat the natural code. This effect is particularly pronounced when more refined measures of the amino-acid substitution cost are used than hydrophobicity. To show this, we devised a new cost function by evaluating in silico the change in folding free energy caused by all possible point mutations in a set of protein structures. With this function, which measures protein stability while being unrelated to the code's structure, we estimated that around two random codes in a billion (10⁹) are fitter than the natural code. When alternative codes are restricted to those that interchange biosynthetically related amino acids, the genetic code appears even more optimal.

Conclusions

These results lead us to discuss the role of amino-acid frequencies and other parameters in the genetic code's evolution, in an attempt to propose a tentative picture of primitive life.     

Impacts of granivorous and frugivorous arthropods on pre-dispersal seed production of western juniper (<Emphasis Type="Italic">Juniperus occidentalis</Emphasis>)

Arthropods impact seed production in various juniper species, but effects of pre-dispersal seed predation are generally unknown for arthropods that feed on western juniper (Juniperus occidentalis). From 2009 to 2013, we quantified impacts of three arthropod granivores and a frugivorous insect on western juniper seed production at two N. California field sites—Madeline and Shinn Peak. Insect larvae were genetically identified using the COI barcode region. Seed damage by all arthropod taxa varied both spatially and temporally. Juniper berry mites (Trisetacus quadricetus) had the greatest effect on reducing seed production at Madeline, and granivorous moths (Periploca spp. and Argyresthia spp.) had the greatest effect at Shinn Peak. Three findings supported the predator satiation hypothesis, which suggests that unpredictable masting events overwhelm responses of seed predators. First, estimated berry production had significant negative effects on the proportion of seeds damaged across sites by a chalcidoid wasp (Eurytoma juniperina) and by granivorous moths at Shinn Peak. Second, seed damage by granivorous moths was significantly reduced in a mast year of juniper berry production. Third, number of seeds per berry positively affected seed damage across sites by granivorous moths in all years except the mast year as well as damage by a frugivorous tortricid moth (Henricus infernalis) at Madeline. Distance to neighboring trees had positive, site-specific effects on damage by granivorous moths and Henricus, perhaps due to limited movement of parasitoids that attack these insects. Our results suggest that arthropod damage can significantly impact seed production of western juniper.     

From lamprey to salamander: an exploratory modeling study on the architecture of the spinal locomotor networks in the salamander

The evolutionary transition from water to land required new locomotor modes and corresponding adjustments of the spinal “central pattern generators” for locomotion. Salamanders resemble the first terrestrial tetrapods and represent a key animal for the study of these changes. Based on recent physiological data from salamanders, and previous work on the swimming, limbless lamprey, we present a model of the basic oscillatory network in the salamander spinal cord, the spinal segment. Model neurons are of the Hodgkin–Huxley type. Spinal hemisegments contain sparsely connected excitatory and inhibitory neuron populations, and are coupled to a contralateral hemisegment. The model yields a large range of experimental findings, especially the NMDA-induced oscillations observed in isolated axial hemisegments and segments of the salamander Pleurodeles waltlii. The model reproduces most of the effects of the blockade of AMPA synapses, glycinergic synapses, calcium-activated potassium current, persistent sodium current, and $h$ -current. Driving segments with a population of brainstem neurons yields fast oscillations in the in vivo swimming frequency range. A minimal modification to the conductances involved in burst-termination yields the slower stepping frequency range. Slow oscillators can impose their frequency on fast oscillators, as is likely the case during gait transitions from swimming to stepping. Our study shows that a lamprey-like network can potentially serve as a building block of axial and limb oscillators for swimming and stepping in salamanders.     

Spelling Protein Structure

Abstract

We would be tempted to state that there has never been a Levinthal paradox. Indeed, Levinthal raised an interesting problem about protein folding, as he realized that proteins have no time to explore exhaustively their conformational space on the way to their native structure. He did not seem to find this paradoxical and immediately proposed a straightforward solution, which has essentially never been refuted. In other words, Levinthal solved his own paradox.     

Pattern of some Silurian bioevents

The best‐known Silurian bioevent occurred at the end of the Wenlock: the lundgreni event, together with the nassa‐ludensis crisis, was established among planktic graptolites. The East Baltic data show several peaks of high diversity (especially triangulatus, turriculatus, scanicus zones) and three levels of low diversity of graptolites (antennularius, radians, ludensis zones). These are more or less coincident with sea‐level changes. Energetic innovation of the shallow shelf corals started in the early Silurian. The late Wenlock regression seems not to affect them seriously but the late Silurian decline coincides with the aridization of the climate and a regression of the shelf seas. The Agnatha had strong radiations in the Wenlock (ludensis Zone) and Ludlow (leintwardinensis Zone), the fishes in the Pridoli. Many Silurian vertebrates were long‐ranging and extinction rate was relatively low; only at the late leintwardinensis level and in the latest Ludlow did considerable extinctions occur.