Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction

We have determined the crystal structure of the enzyme-product complex of the hammerhead ribozyme by using a reinforced crystal lattice to trap the complex prior to dissociation and by employing X-ray holographic image reconstruction, a real-space electron density imaging and refinement procedure. Subsequent to catalysis, the cleavage site residue (C-17), together with its 2',3'-cyclic phosphate, adopts a conformation close to and approximately perpendicular to the Watson-Crick base-pairing faces of two highly conserved purines in the ribozyme's catalytic pocket (G-5 and A-6). We observe several interactions with functional groups on these residues that have been identified as critical for ribozyme activity by biochemical analyses but whose role has defied explanation in terms of previous structural analyses. These interactions may therefore be relevant to the hammerhead ribozyme reaction mechanism.     

Large Hawk‐Cuckoo Hierococcyx sparverioides parasitism on the Chinese Babax Babax lanceolatus may be an evolutionarily recent host–parasite system

We documented brood parasitism by the poorly studied Large Hawk‐Cuckoo on a previously unknown host species, the Chinese Babax. Furthermore, we describe a new egg colour for the Large Hawk‐Cuckoo. The parasitism rate of Chinese Babax nests over 4 years was 6.9% (11 of 159 nests), with significant temporal variation. The Large Hawk‐Cuckoo laid immaculate white eggs that appeared non‐mimetic to the blue Babax eggs, an impression that was confirmed by avian visual modelling. Nevertheless, most Cuckoo eggs were accepted by the host, suggesting that this host–parasite system may be evolutionarily recent.     

Where on earth can animals use a geomagnetic bi‐coordinate map for navigation?

Many animal taxa have been shown to possess the ability of true navigation. In this study we investigated the possibilities for geomagnetic bi‐coordinate map navigation in different regions of the earth by analysing angular differences between isolines of geomagnetic total intensity and inclination. In ‘no‐grid’ zones where isolines were running almost parallel, efficient geomagnetic bi‐coordinate navigation would probably not be feasible. These zones formed four distinct areas with a north‐south extension in the northern hemisphere, whereas the pattern in the southern hemisphere was more diffuse. On each side of these zones there was often a mirror effect where identical combinations of the geomagnetic parameters appeared. This may potentially cause problems for species migrating long distances east‐west across longitudes, since they may pass areas with identical geomagnetic coordinates. Migration routes assumed for four populations of migratory passerine birds were used to illustrate the possibilities of geomagnetic bi‐coordinate map navigation along different routes. We conclude that it is unlikely that animal navigation is universally based on a geomagnetic bi‐coordinate map mechanism only, and we predict that the relative importance of geomagnetic coordinate information differs between animals, areas and routes, depending on the different conditions for bi‐coordinate geomagnetic navigation in different regions of the earth.     

Effects of aging and reproduction on protein quality control in soma and gametes of Drosophila melanogaster

In organisms with a soma-germ demarcation, the germline must be 'preserved' such that harmful damage is not transmitted to the offspring. Keeping the progeny free of damage may be achieved by gametes enjoying elevated, and/or more functional, homeostatic maintenance systems. This possibility was approached here by testing whether the soma and maturating oocytes (eggs) dissected from female Drosophila melanogaster in reproductive ages display differential capacities for protein quality control and whether these capacities change during aging and mating. Eggs exhibited a high capacity to prevent protein aggregation, strong capacity for 26S proteasome-dependent degradation and reduced levels of oxidatively damaged (carbonylated) proteins compared to the soma. The capacity to prevent protein aggregation was not affected in either soma or eggs by age and/or mating, while the 26S proteasome capacity declined in the soma but was maintained in the eggs of aged females. However, the levels of carbonylated proteins increased with age in both soma and eggs, and this increase was more pronounced in females allowed to mate continuously. Furthermore, the levels of carbonylated proteins in the eggs of mated flies correlated negatively with the propensity of the eggs to develop into an adult fly. In young flies, mating caused a decrease in 26S proteasome capacity and an increase in protein carbonylation in the soma, but not in the eggs. These results are in line with trade-off theories of aging where aging is considered a consequence of investment in reproduction over somatic maintenance.     

Trace Element Concentrations in Soil,Sediments, and Waters in the Vicinity of Geita Gold Mines and North Mara Gold Mines in Northwest Tanzania

The “Geita Gold Mine” (GGM) and “North Mara Gold Mines” (NMGM) have developed large quarries in the middle of fertile agricultural lands. Possible hazardous impact on the natural recourse has warranted a study on the trace element concentrations in soils, sediments, and natural waters. Generally, the study shows a great variation in type of elements and intensity of their spill to soils, sediments, and waters. We found indications of acid mine drainage (AMD) of trace metals near the GGM waste rock tailings, but the data are inconclusive. The environmental impact at NMGM was, on the other hand, more extensive. Severe trace element contamination of sediments and waters near one of the mining facilities managed by NMGM is connected to an accidental acid spill in 2009. However, we found strong indication that, in addition to the accident, leakage of alkaline wastewater into surface soils and free water took place from a large wastewater reservoir. We found very high concentrations, especially of As in sediments and water samples downside this reservoir. Water from several sites contained As concentration in the free water at more than one order of magnitude higher than the WHO drinking water recommendations. The chemical speciation of water samples indicated high fraction of Free Ion Activity (FIA) in several samples and the change in pH had a significant impact on the FIA. Due to extensive alkaline and acidic runoff from these sites, more information about hydrological transport routes and the chemical speciation of the free water is of great importance for assessing potential risk of these mines.     

Identification of distant Agouti-like sequences and re-evaluation of the evolutionary history of the Agouti-related peptide (AgRP)

The Agouti-like peptides including AgRP, ASIP and the teleost-specific A2 (ASIP2 and AgRP2) peptides have potent and diverse functional roles in feeding, pigmentation and background adaptation mechanisms. There are contradictory theories about the evolution of the Agouti-like peptide family as well the nomenclature. Here we performed comprehensive mining and annotation of vertebrate Agouti-like sequences. We identified A2 sequences from salmon, trout, seabass, cod, cichlid, tilapia, gilt-headed sea bream, Antarctic toothfish, rainbow smelt, common carp, channel catfish and interestingly also in lobe-finned fish. Moreover, we surprisingly found eight novel homologues from the kingdom of arthropods and three from fungi, some sharing the characteristic C-x(6)-C-C motif which are present in the Agouti-like sequences, as well as approximate sequence length (130 amino acids), positioning of the motif sequence and sharing of exon-intron structures that are similar to the other Agouti-like peptides providing further support for the common origin of these sequences. Phylogenetic analysis shows that the AgRP sequences cluster basally in the tree, suggesting that these sequences split from a cluster containing both the ASIP and the A2 sequences. We also used a novel approach to determine the statistical evidence for synteny, a sinusoidal Hough transform pattern recognition technique. Our analysis shows that the teleost AgRP2 resides in a chromosomal region that has synteny with Hsa 8, but we found no convincing synteny between the regions that A2, AgRP and ASIP reside in, which would support that the Agouti-like peptides were formed by whole genome tetraplodization events. Here we suggest that the Agouti-like peptide genes were formed through classical subsequent gene duplications where the AgRP is the most distantly related to the three other members of that group, first splitting from a common ancestor to ASIP and A2, and then later the A2 split from ASIP followed by a split resulting in ASIP2 and AgRP2.