Can splenocytes enhance pancreatic β-cell function and mass in 90% pancreatectomized rats fed a high fat diet?

AimsRecent studies have shown that splenocytes may act as a possible neogenic source with regard to β-cells in rodent diabetic models. Accordingly, we sought to determine whether splenocytes played an important role in promoting β-cell function and mass among type 2 diabetic rats with and without spleen.Main methodsWe randomly divided female 90% pancreatectomized (Px) Sprague Dawley rats into three groups: splenectomy (SPX), splenectomy plus the injection of male splenocytes (SPI), and no splenectomy (NSP). They were administered with 40 energy percent fat diets over the course of five weeks. At the end of the experimental period, insulin secretion capacity was measured by hyperglycemic clamp. At 6 h after BrdU⁺ injection, the pancreas was prepared with 4% paraformaldehyde in order to perform immunohistochemistry.Key findingsSPX increased and sustained serum glucose levels more than NSP and SPI during oral glucose tolerance testing. During hyperglycemic clamp, first and second phase insulin secretion decreased in the SPX rats while splenocyte injections counteracted this. Beta-cell mass in the SPX group was reduced more than among NSP and SPI. This was the result of a decrease in the number of small β-cell clusters in SPX, which is indicative of a decrease in β-cell neogenesis.SignificanceSplenocytes play an important role with regard to the neogenesis of β-cells in insulin deficient type 2 diabetic rats, although they are not critical for β-cell regeneration.     

Secondary structure prediction for aligned RNA sequences

Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation. Comparison with phylogenetic structures of rRNAs shows that a reliability of prediction of more than 80% is achieved for only five related sequences. As an application we show that the Early Noduline mRNA contains significant secondary structure that is supported by sequence covariation.     

Design of multistable RNA molecules

We show that the problem of designing RNA sequences that can fold into multiple stable secondary structures can be transformed into a combinatorial optimization problem that can be solved by means of simple heuristics. Hence it is feasible to design RNA switches with prescribed structural alternatives. We discuss the theoretical background and present an efficient tool that allows the design of various types of switches. We argue that both the general properties of the sequence structure map of RNA secondary structures and the ease with which our design tool finds bistable RNAs strongly indicates that RNA switches are easily accessible in evolution. Thus conformational switches are yet another function for which RNA can be employed.     

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

Facing the ever-growing list of newly discovered classes of functional RNAs, it can be expected that further types of functional RNAs are still hidden in recently completed genomes. The computational identification of such RNA genes is, therefore, of major importance. While most known functional RNAs have characteristic secondary structures, their free energies are generally not statistically significant enough to distinguish RNA genes from the genomic background. Additional information is required. Considering the wide availability of new genomic data of closely related species, comparative studies seem to be the most promising approach. Here, we show that prediction of consensus structures of aligned sequences can be a significant measure to detect functional RNAs. We report a new method to test multiple sequence alignments for the existence of an unusually structured and conserved fold. We show for alignments of six types of well-known functional RNA that an energy score consisting of free energy and a covariation term significantly improves sensitivity compared to single sequence predictions. We further test our method on a number of non-coding RNAs from Caenorhabditis elegans/Caenorhabditis briggsae and seven Saccharomyces species. Most RNAs can be detected with high significance. We provide a Perl implementation that can be used readily to score single alignments and discuss how the methods described here can be extended to allow for efficient genome-wide screens.     

Oxygen and proton pathways in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump, which couples the reduction of oxygen to water to the translocation of protons across the membrane. The recently solved x-ray structures of cytochrome c oxidase permit molecular dynamics simulations of the underlying transport processes. To eventually establish the proton pump mechanism, we investigate the transport of the substrates, oxygen and protons, through the enzyme. Molecular dynamics simulations of oxygen diffusion through the protein reveal a well-defined pathway to the oxygen-binding site starting at a hydrophobic cavity near the membrane-exposed surface of subunit I, close to the interface to subunit III. A large number of water sites are predicted within the protein, which could play an essential role for the transfer of protons in cytochrome c oxidase. The water molecules form two channels along which protons can enter from the cytoplasmic (matrix) side of the protein and reach the binuclear center. A possible pumping mechanism is proposed that involves a shuttling motion of a glutamic acid side chain, which could then transfer a proton to a propionate group of heme α₃. Proteins 30:100–107, 1998. © 1998 Wiley-Liss, Inc.     

Genbank accession #: AJ131961

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