Structure and thermal stability of pyruvated carrageenans from the red alga Coccotylus truncatus

The composition, structure, and thermal stability of carrageenans from unattached Coccotylus truncatus (the Baltic Sea, Estonia) were investigated. The complex polysaccharide was characterized by ¹³C NMR and FTIR spectroscopy, ICP-OES and gel permeation chromatography methods. The main components of C. truncatus galactan are 3,6-anhydro-α-d-galactose-2-sulfate (30 ± 1.5%) and β-d-galactose-4-sulfate (45.3%), indicating a ι-carrageenan backbone. As the minor components, α-d-galactose-2,6-disulfate (12 ± 2%) from ν-carrageenan and 4′,6′-pyruvated β-d-galactopyranosyl residues (1.4%) from pyruvated α-carrageenan are found to be present, latter being responsible for the undersulfated nature of the galactan. The native polysaccharide with the average molecular weight of about 1500 kDa is highly susceptible to thermal degradation. The high-temperature treatment of this galactan gives products with 3,6-anhydro-α-d-galactose units predominantly at the reducing end. The carrageenan extraction from C. truncatus gives characteristically low yields (12-17%); weak gelling ability of the polysaccharides from this seaweed species (gel strength 30-40 g/cm²) does not depend significantly on extraction conditions.     

Heterochronic parabiosis for the study of the effects of aging on stem cells and their niches

Aging is unmistakable and undeniable in mammals. Interestingly, mice develop cataracts, muscle atrophy, osteoporosis, obesity, diabetes and cognitive deficits after just 2–3 postnatal years, while it takes seven or more decades for the same age-specific phenotypes to develop in humans. Thus, chronological age corresponds differently with biological age in metazoan species and although many theories exist, we do not understand what controls the rate of mammalian aging. One interesting idea is that species-specific rate of aging represents a ratio of tissue attrition to tissue regeneration. Furthermore, current findings suggest that the age-imposed biochemical changes in the niches of tissue stem cells inhibit performance of this regenerative pool, which leads to the decline of tissue maintenance and repair. If true, slowing down stem cell and niche aging, thereby promoting tissue regeneration, could slow down the process of tissue and organismal aging. In this regard, recent studies of heterochronic parabiosis provide important clues as to the mechanisms of stem cell aging and suggest novel strategies for enhancing tissue repair in the old. Here we review current literature on the relationship between the vigor of tissue stem cells and the process of aging, with an emphasis on the rejuvenation of old tissues by the extrinsic modifications of stem cell niches.     

Genome-wide identification and characterization of replication origins by deep sequencing

Background

DNA replication initiates at distinct origins in eukaryotic genomes, but the genomic features that define these sites are not well understood.

Results

We have taken a combined experimental and bioinformatic approach to identify and characterize origins of replication in three distantly related fission yeasts: Schizosaccharomyces pombe, Schizosaccharomyces octosporus and Schizosaccharomyces japonicus. Using single-molecule deep sequencing to construct amplification-free high-resolution replication profiles, we located origins and identified sequence motifs that predict origin function. We then mapped nucleosome occupancy by deep sequencing of mononucleosomal DNA from the corresponding species, finding that origins tend to occupy nucleosome-depleted regions.

Conclusions

The sequences that specify origins are evolutionarily plastic, with low complexity nucleosome-excluding sequences functioning in S. pombe and S. octosporus, and binding sites for trans-acting nucleosome-excluding proteins functioning in S. japonicus. Furthermore, chromosome-scale variation in replication timing is conserved independently of origin location and via a mechanism distinct from known heterochromatic effects on origin function. These results are consistent with a model in which origins are simply the nucleosome-depleted regions of the genome with the highest affinity for the origin recognition complex. This approach provides a general strategy for understanding the mechanisms that define DNA replication origins in eukaryotes.     

Molecular modeling approach to predict a binding mode for the complex methotrexate-carboxypeptidase G<Subscript>2</Subscript>

Carboxypeptidase G₂ (CPG₂) is a zinc-metalloenzyme employed in a range of cancer chemotherapy strategies by activating selectively nontoxic prodrugs into cytotoxic drugs in tumor as well as in the treatment of intoxication caused by high-doses of the anticancer drug methotrexate (MTX). CPG₂ catalyzes the hydrolytic cleavage of C-terminal of glutamate moiety from folic acid and analogues. Regardless of its extensive application, its mechanism of catalysis has not yet been determined and, so far, no co-crystallized complex has been published. So, in this study, molecular docking and a short molecular dynamics (MD) simulation sampling scheme, as a function of temperature, were performed to investigate a possible binding mode for MTX, a recognized substrate of CPG₂. The findings suggested that MTX interacts possibly in quite specific points of the CPG₂ active site, which are probably responsible for the molecular recognition and cleavage procedures. The MTX substrate fits well in the catalytic site by accommodating the pteridine moiety in an adjacent pocket to the active site whereas a glutamate moiety is pointed toward the protein surface. Additionally, a glutamate residue can interact with a crystallization water molecule in the active site, supporting its activation as a nucleophilic group.     

Aminoglycoside binding to human and bacterial A-Site rRNA decoding region constructs

The 16S bacterial ribosomal A-site decoding rRNA region is thought to be the pharmacological target for the aminoglycoside antibiotics. The clinical utility of aminoglycosides could possibly depend on the preferential binding of these drugs to the prokaryotic A-site versus the corresponding A-site from eukaryotes. However, quantitative aminoglycoside binding experiments reported here on prokaryotic and eukaryotic A-site RNA constructs show that there is little in the way of differential binding affinities of aminoglycosides for the two targets. The largest difference in affinity is 4-fold in the case of neomycin, with the prokaryotic A-site construct exhibiting the higher binding affinity. Mutational studies revealed that decoding region constructs retaining elements of non-Watson-Crick (WC) base pairing, specifically bound aminoglycosides with affinities in the muM range. These studies are consistent with the idea that aminoglycoside antibiotics can specifically bind to RNA molecules as long as the latter have non-A form structural elements allowing access of aminoglycosides to the narrow major groove.     

Molecular logic of 11-cis-retinoid biosynthesis in a cone-dominated species

The biochemical pathway to visual chromophore biosynthesis in rod-dominated animals involves minimally a two component system in which all-trans-retinyl esters, generated by the action of lecithin retinol acyltransferase (LRAT) on vitamin A, are processed into 11-cis-retinol by isomerohydrolase. Possible differences in retinoid metabolism in cone-dominated animals have been noted in the literature, so it was of interest to explore whether these differences are tangential or fundamental. Central to this issue is whether cone-dominated animals use an isomerohydrolase (IMH)-based mechanism in the predominant pathway to 11-cis-retinoids. Here, it is shown that all-trans-retinyl esters (tREs) are the direct precursors of 11-cis-retinol formation in chicken retinyl pigment epithelium/retina preparations. This conclusion is based on at least three avenues of evidence. First, reagents that block tRE synthesis from vitamin A also block 11-cis-retinol synthesis. Second, pulse-chase experiments also establish that tREs are the precursors to 11-cis-retinol. Finally, 11-cis-retinyl-bromoacetate, a known affinity-labeling agent of isomerohydrolase, also blocks chromophore biosynthesis in the cone system.     

Remarkable preservation of undigested muscle tissue within a Late Cretaceous tyrannosaurid coprolite from Alberta,Canada

Exceptionally detailed soft tissues have been identified within the fossilized feces of a large Cretaceous tyrannosaurid. Microscopic cord-like structures in the coprolitic ground mass are visible in thin section and with scanning electron microscopy. The morphology, organization, and context of these structures indicate that they are the fossilized remains of undigested muscle tissue. This unusual discovery indicates specific digestive and taphonomic conditions, including a relatively short gut-residence time, rapid lithification, and minimal diagenetic recrystallization. Rapid burial of the feces probably was facilitated by a flood event on the ancient coastal lowland plain on which the fecal mass was deposited.