GABAA receptor transmembrane amino acids are critical for alcohol action: disulfide cross‐linking and alkyl methanethiosulfonate labeling reveal relative location of binding sites

Alcohols and inhaled anesthetics modulate GABA_A receptor (GABA_AR) function via putative binding sites within the transmembrane regions. The relative position of the amino acids lining these sites could be either inter‐ or intra‐subunit. We introduced cysteines in relevant TM locations and tested the proximity of cysteine pairs using oxidizing and reducing agents to induce or break disulfide bridges between cysteines, and thus change GABA‐mediated currents in wild‐type and mutant α1β2γ2 GABA_ARs expressed in Xenopus laevis oocytes. We tested for: (i) inter‐subunit cross‐linking: a cysteine located in α1TM1 [either α1(Q229C) or α1(L232C)] was paired with a cysteine in different positions of β2TM2 and TM3; (ii) intra‐subunit cross‐linking: a cysteine located either in β2TM1 [β2(T225C)] or in TM2 [β2(N265C)] was paired with a cysteine in different locations along β2TM3. Three inter‐subunit cysteine pairs and four intra‐subunits cross‐linked. In three intra‐subunit cysteine combinations, the alcohol effect was reduced by oxidizing agents, suggesting intra‐subunit alcohol binding. We conclude that the structure of the alcohol binding site changes during activation and that potentiation or inhibition by binding at inter‐ or intra‐subunit sites is determined by the specific receptor and ligand.

     

Identification of genes responsive to low-intensity pulsed ultrasound stimulations

This study was designed to compare the temporal changes of gene expression profile in osteoblastic cell lines (SaOS-2) treated with low-intensity pulsed ultrasound stimulation (LIPUS) using complementary DNA (cDNA) microarrays. SaOS-2 cells were treated with LIPUS for 20 min. Thereafter, cells were harvested and RNA was extracted twice at 4 and 24 h, respectively. Using cDNA microarrays, 7488 genes with changes in expression in SaOS-2 cells were identified for comparison. Microarray analysis revealed a total of 165 genes in SaOS-2 cells were regulated at 4 and 24 h after LIPUS treatment. Except for 30 known LIPUS-regulated genes, our study demonstrated for the first time that over 100 genes were related to the underlying molecular mechanism of LIPUS and suggested that LIPUS might regulate a transient expression of numerous critical genes in osteoblastic cells. These results provide further understanding of the role of LIPUS in the regulation of osteoblastic gene expression potentially involved in the molecular mechanism of osteogenesis in fracture repair.     

Survival Chances of Mutants Starting With One Individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N individuals of the mutant after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N _p individuals of the primary mutant and N _m individuals of the new form after the multiplication phase M of the n-th generation (probability ɛ of an error in the replication of the primary mutant giving the new form) and after the following selection phase S (probabilities β _p and β _m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained. The online version of the original article can be found at .     

Anxiolytic and antidepressant-like activity of a standardized extract from Galphimia glauca

An infusion prepared with aerial parts from Galphimia glauca has been widely used in Mexican traditional medicine as a remedy for nervous excitement. The sedative activity of a methanolic extract from this plant has been demonstrated by neuropharmacological tests. This effect was attributed to the nor-secotriterpene named galphimine B (GB). In the present work, the anxiolytic and antidepressant-like effects of G. glauca methanolic extract (standardized on GB content, 8.3mg/g) were assayed by using the elevated plus-maze, light-dark test and the forced swimming paradigm, on ICR albino mice. This extract, administered orally, three times (24, 18 and 1h before the test), and in different doses (125, 250, 500, 1,000 and 2,000 mg/kg) was able to increase significantly (p<0.05) the number of entries, as well as the time spent in the open arms of the elevated plus-maze, indicating an anxiolytic-like effect. A similar effect was observed in the light-dark paradigm test, the time spent in the light box was increased in treated mice. Nevertheless, this treatment was unable to change any parameter in the forced swimming test. Altogether, these results suggest an anxiolytic-like effect to the methanolic standardized extract of G. glauca on ICR inbred mice.     

The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA)

A model has been proposed suggesting that the tRNA molecule must have originated by direct duplication of an RNA hairpin structure [Di Giulio, M., 1992. On the origin of the transfer RNA molecule. J. Theor. Biol. 159, 199-214]. A non-monophyletic origin of this molecule has also been theorized [Di Giulio, M., 1999. The non-monophyletic origin of tRNA molecule. J. Theor. Biol. 197, 403-414]. In other words, the tRNA genes evolved only after the evolutionary stage of the last universal common ancestor (LUCA) through the assembly of two minigenes codifying for different RNA hairpin structures, which is what the exon theory of genes suggests when it is applied to the model of tRNA origin. Recent observations strongly corroborate this theorization because it has been found that some tRNA genes are completely separate in two minigenes codifying for the 5' and 3' halves of this molecule [Randau, L., et al., 2005a. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature 433, 537-541]. In this paper it is shown that these tRNA genes codifying for the 5' and 3' halves of this molecule are the ancestral form from which the tRNA genes continuously codifying for the complete tRNA molecule are thought to have evolved. This, together with the very existence of completely separate tRNA genes codifying for their 5' and 3' halves, proves a non-monophyletic origin for tRNA genes, as a monophyletic origin would exclude the existence of these genes which have, on the contrary, been observed. Here the polyphyletic origin of genes codifying for proteins is also suggested and discussed. Moreover, a hypothesis is advanced to suggest that the LUCA might have had a fragmented genome made up of RNA and the possibility that 'Paleokaryotes' may exist is outlined. Finally, the characteristic of the indivisibility of homology that these polyphyletic origins seem to remove at the sequence level is discussed.     

Energy flow and subsidies associated with the complex life cycle of ambystomatid salamanders in ponds and adjacent forest in southern Illinois

Breeding adults and metamorphosing larval amphibians transfer energy between freshwater and terrestrial ecosystems during seasonal migrations and emergences, although rarely has this been quantified. We intensively sampled ambystomatid salamander assemblages (Ambystoma opacum,A. maculatum, and A. tigrinum) in five forested ponds in southern Illinois to quantify energy flow associated with egg deposition, larval production, and emergence of metamorphosed larvae. Oviposition by female salamanders added 7.0–761.4 g ash-free dry mass (AFDM) year⁻¹ to ponds (up to 5.5 g AFDM m⁻² year⁻¹). Larval production ranged from 0.4 to 7.4 g AFDM m⁻² year⁻¹ among populations in three ponds that did not dry during larval development, with as much as 7.9 g AFDM m⁻² year⁻¹ produced by an entire assemblage. Mean larval biomass during cohort production intervals in these three ponds ranged from 0.1 to 2.3 g AFDM m⁻² and annual P/B (production/biomass) ranged from 4 to 21 for individual taxa. Emergent biomass averaged 10% (range=2–35%) of larval production; larval mortality within ponds accounted for the difference. Hydroperiod and intraguild predation limited larval production in some ponds, but emerging metamorphs exported an average of 70.0±33.9 g AFDM year⁻¹ (range=21.0–135.2 g AFDM year⁻¹) from ponds to surrounding forest. For the three ponds where larvae survived to metamorphosis, salamander assemblages provided an average net flux of 349.5±140.8 g AFDM year⁻¹ into pond habitats. Among all ponds, net flux into ponds was highest for the largest pond and decreased for smaller ponds with higher perimeter to surface area ratios (r ² =0.94, P<0.05, n=5). These results are important in understanding the multiple functional roles of salamanders and the impact of amphibian population declines on ecosystems. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Proteomic strategy for probing complementary lethality of kinase inhibitors against pancreatic cancer

In the present study, proteomic analysis was performed to discover combinational molecular targets for therapy and chemoresistance by comparing differential protein expression from Panc‐1 cells treated with FDA‐approved drugs such as sunitinib, imatinib mesylate, dasatinib, and PD184352. A total of 4041 proteins were identified in the combined data from all of the treatment groups by nano‐electrospray ultra‐performance LC and MS/MS analysis. Most of the proteins with significant changes are involved in apoptosis, cytoskeletal remodeling, and epithelial‐to‐mesenchymal transition. These processes are associated with increased chemoresistance and progression of pancreatic cancer. Among the differentially expressed proteins, heme oxygenase‐1 (HO‐1) was found in the sunitinib and imatinib mesylate treatment groups, which possibly acts as a specific target for synthetic lethality in combinational treatment. HO‐1 was found to play a key role in sensitizing the chemoresistant Panc‐1 cell line to drug therapy. Viability was significantly decreased in Panc‐1 cells cotreated with sunitinib and imatinib mesylate at low doses, compared to those treated with sunitinib or imatinib mesylate alone. The results suggest that induction of chemosensitization by manipulating specific molecular targets can potentiate synergistic chemotherapeutic effects at lower, better tolerated doses, and in turn reduce the toxicity of multidrug treatment of pancreatic cancer.     

Does metazooplankton regulate the ciliate community in a shallow eutrophic lake?

1. As grazers on picoplankton and nanoplankton, planktonic ciliates form an important link in pelagic food webs. Ciliate communities may be controlled by predation by metazooplankton. In eutrophic systems, however, where the number of large crustaceans is often low, the mechanisms that regulate ciliate dynamics have rarely been described. 2. We conducted an enclosure experiment with natural and screened (145 μm) summer plankton communities to investigate the effect of the small‐sized crustacean zooplankton on ciliate community structure and the microbial loop in a shallow eutrophic lake. 3. The removal of the larger fraction of crustaceans initiated a decrease in total ciliate abundance. At the community level, we observed a substantial increase in large‐sized predacious ciliates (>100 μm) and a simultaneous decrease in the abundance of smaller ciliates (<20–40 μm) that were mostly bacterivores and bacterio‐herbivores. The compositional shift in the ciliate community, however, did not cascade down to the level of bacteria and edible phytoplankton.     

Novel mutations in SAR1B and MTTP genes in Tunisian children with chylomicron retention disease and abetalipoproteinemia

Monogenic hypobetalipoproteinemias include three disorders: abetalipoproteinemia (ABL) and chylomicron retention disease (CMRD) with recessive transmission and familial hypobetalipoproteinemia (FHBL) with dominant transmission. We investigated three unrelated Tunisian children born from consanguineous marriages, presenting hypobetalipoproteinemia associated with chronic diarrhea and retarded growth. Proband HBL-108 had a moderate hypobetalipoproteinemia, apparently transmitted as dominant trait, suggesting the diagnosis of FHBL. However, she had no mutations in FHBL candidate genes (APOB, PCSK9 and ANGPTL3). The analysis of MTTP gene was also negative, whereas SAR1B gene resequencing showed that the patient was homozygous for a novel mutation (c.184G>A), resulting in an amino acid substitution (p.Glu62Lys), located in a conserved region of Sar1b protein. In the HBL-103 and HBL-148 probands, the severity of hypobetalipoproteinemia and its recessive transmission suggested the diagnosis of ABL. The MTTP gene resequencing showed that probands HBL-103 and HBL-148 were homozygous for a nucleotide substitution in the donor splice site of intron 9 (c.1236+2T>G) and intron 16 (c.2342+1G>A) respectively. Both mutations were predicted in silico to abolish the function of the splice site. In vitro functional assay with splicing mutation reporter MTTP minigenes showed that the intron 9 mutation caused the skipping of exon 9, while the intron 16 mutation caused a partial retention of this intron in the mature mRNA. The predicted translation products of these mRNAs are non-functional truncated proteins.