Preliminary x-ray studies of the interaction of salmon sperm DNA with spermine

The interaction of spermine with salmon sperm DNA was studied by X-ray diffraction methods. In the fibers of the complex, DNA was in the B-configuration with ten nucleotide pairs per turn (34 Å) of the helix at 92% or higher relative humidity, while, at 75% and lower relative humidity, it was at least partly in the A-configuration, which was not observed in a similar experiment by Suwalsky et al. (1969) with calf thymus DNA. The A to B transition of the complex fibers was reversible.     

The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.     

Transport genes and chemotaxis in Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is a Gram-negative, sea gull-shaped rod associated with community-acquired gastroenteritis. The bacterium has been found in diverse freshwater environments including fish, frogs and drinking water reservoirs. Using the complete genome sequence data of L. hongkongensis, we performed a comprehensive analysis of putative transport-related genes and genes related to chemotaxis, motility and quorum sensing, which may help the bacterium adapt to the changing environments and combat harmful substances.

Results

A genome-wide analysis using Transport Classification Database TCDB, similarity and keyword searches revealed the presence of a large diversity of transporters (n = 457) and genes related to chemotaxis (n = 52) and flagellar biosynthesis (n = 40) in the L. hongkongensis genome. The transporters included those from all seven major transporter categories, which may allow the uptake of essential nutrients or ions, and extrusion of metabolic end products and hazardous substances. L. hongkongensis is unique among closely related members of Neisseriaceae family in possessing higher number of proteins related to transport of ammonium, urea and dicarboxylate, which may reflect the importance of nitrogen and dicarboxylate metabolism in this assacharolytic bacterium. Structural modeling of two C⁴-dicarboxylate transporters showed that they possessed similar structures to the determined structures of other DctP-TRAP transporters, with one having an unusual disulfide bond. Diverse mechanisms for iron transport, including hemin transporters for iron acquisition from host proteins, were also identified. In addition to the chemotaxis and flagella-related genes, the L. hongkongensis genome also contained two copies of qseB/qseC homologues of the AI-3 quorum sensing system.

Conclusions

The large number of diverse transporters and genes involved in chemotaxis, motility and quorum sensing suggested that the bacterium may utilize a complex system to adapt to different environments. Structural modeling will provide useful insights on the transporters in L. hongkongensis.     

Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest

The effects of global glaciations on the distribution of organisms is an essential element of many diversification models. However, the empirical evidence supporting this idea is mixed, in particular with respect to explaining tropical forest evolution. In the present study, we evaluated the impacts of range shifts associated with Pleistocene global glacial cycles on the evolution of tropical forests. In particular, we tested the predictions: (1) that population genetic structure increases with fragmentation variation between the present and the Last Glacial Maximum (LGM) and also (2) with geographical range instability; and (3) that genetic diversity increases with range stability and (4) decreases with fragmentation variation between periods. To address our predictions, we studied population genetic structures and modelled present and past distributions of 15 Atlantic Forest (AF) endemic birds. Afterwards, we evaluated the relationship of population genetic parameters with metrics of species range shifts between the present and the LGM. We found that geographical ranges of AF birds changed in concert with Pleistocene glacial cycles but, unexpectedly, our findings suggest the novel idea that ranges during glacial maxima were slightly larger on average, as well as equally fragmented and displaced from the interglacial ranges. Our findings suggest that range shifts over the late Pleistocene impacted on the diversification of forest organisms, although they did not show that those range shifts had a strong effect. We found that a combination of fragmentation variation across time, small current range size, and range stability increased population genetic structure. However, neither fragmentation, nor range stability affected genetic diversity. Our study showed that evolutionary responses to range shifts across AF birds have a high variance, which could explain the mixed support given by single‐species studies to the action of Pleistocene range shifts on population evolution.     

The assembly of montane biotas: linking Andean tectonics and climatic oscillations to independent regimes of diversification in Pionus parrots

The mechanisms underlying the taxonomic assembly of montane biotas are still poorly understood. Most hypotheses have assumed that the diversification of montane biotas is loosely coupled to Earth history and have emphasized instead the importance of multiple long-distance dispersal events and biotic interactions, particularly competition, for structuring the taxonomic composition and distribution of montane biotic elements. Here we use phylogenetic and biogeographic analyses of species in the parrot genus Pionus to demonstrate that standing diversity within montane lineages is directly attributable to events of Earth history. Phylogenetic relationships confirm three independent biogeographic disjunctions between montane lineages, on one hand, and lowland dry-forest/wet-forest lineages on the other. Temporal estimates of lineage diversification are consistent with the interpretation that the three lineages were transported passively to high elevations by mountain building, and that subsequent diversification within the Andes was driven primarily by Pleistocene climatic oscillations and their large-scale effects on habitat change. These results support a mechanistic link between diversification and Earth history and have general implications for explaining high altitudinal disjuncts and the origin of montane biotas.     

Intrahepatic territory of the accessory hepatic artery in the human

The accessory hepatic artery was found in 12 human livers and its intrahepatic territory was investigated. The artery supplies an entire lobe or more without joining the usual hepatic artery in 93% of the cases. The accessory hepatic artery has an important significance for the arterial supply of the liver.     

Seed dispersal of the Korean pine,Pinus koraiensis,by the red squirrel,Sciurus vulgaris

Seed hoarding behavior of the red squirrel,Sciurus vulgaris, was studied in relation to the amount of dispersed seeds of the Korean pine,Pinus koraiensis, and the distribution of its seedlings. After removing a cone from a tree, squirrels sat on the ground and ripped off its cone scales before transporting it. A mean of 3.2 seeds were scatter-hoarded per hole. Of 7.7×10⁴ mature seeds produced in a 0.21 ha planted Korean pine forest, 22% were estimated to be directly eaten by four squirrels, 9% were hoarded by them in the pine forest and 65% were cached outside the forest. Squirrels rediscovered hoarded seeds frequently, until the ground was covered with snow, during the period from snow fall until seed germination the next spring, few hoarded seeds were utilized. Korean pine seedlings were found up to 600 m from their mother trees. Scatter-hoarding by squirrels extensively contributes to seed dispersal to places suitable for the regeneration of the Korean pine. The large size of the cone, the absciss-layer at the cone penduncle, the infrequent dehiscence of cone scales, the large and wingless seeds, and the thick seed-coats have probably all been specialized to facilitate utilization by GenusSciurus.     

Misincorporation in DNA synthesis after modification of template or polymerase by MNNG, MMS and UV radiation

The synthetic DNA polymers, poly(dG-dC), poly(dC), poly(dA-dT), poly(dA) and poly(dT), were treated with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), methyl methanesulfonate (MMS) and UV irradiation. The modified polymers were used as templates to examine the incorporation of non-complementary nucleotides by E. coli DNA polymerase I. Methylation of poly(dG-dC) by MNNG predominantly induced the misincorporation of dTMP, whereas methylation by MMS induced that of dAMP. Treatment of poly(dT) with MNNG caused the misincorporation of dGMP to a considerable extent, but MMS did not enhance the error on poly(dT). The misincorporation of dAMP on poly(dC) and that of dGMP on poly(dA) were also increased by these chemicals. UV irradiation of poly(dT) and poly(dC) induced the error of dGMP and dAMP, respectively. These data on MNNG and MMS in vitro were in fair agreement with the directions of mutation in vivo. But the predominant induction of transitions by UV in vitro did not agree with the UV-induced transversions in E. coli. This inconsistency suggested the participation of other factors than direct mispairing in UV-induced transversion. Modification of DNA polymerase I by MNNG changed the ratio of polymerase to 3' leads to 5' exonuclease activity altering the fidelity of this enzyme, whereas MMS and UV-irradiation did not alter the fidelity of the enzyme.     

Production of Ochratoxin A by Aspergillus ochraceus Isolated in Japan from Moldy Rice

A simple thin-layer chromatography-fluorodensitometric method for quantitative analysis of ochratoxin A was developed. This method proved to be of use in investigating the production of the toxin and the nutritional factors affecting the toxin production by two strains of Aspergillus ochraceus isolated from moldy rice in Japan. These fungi produced large amounts of ochratoxin A in a nutrient solution containing 1% l-phenylalanine and 2% yeast extract.