Photoconversion and nuclear trafficking cycles determine phytochrome A's response profile to far-red light

Phytochrome A (phyA) is the only photoreceptor in plants, initiating responses in far-red light and, as such, essential for survival in canopy shade. Although the absorption and the ratio of active versus total phyA are maximal in red light, far-red light is the most efficient trigger of phyA-dependent responses. Using a joint experimental-theoretical approach, we unravel the mechanism underlying this shift of the phyA action peak from red to far-red light and show that it relies on specific molecular interactions rather than on intrinsic changes to phyA's spectral properties. According to our model, the dissociation rate of the phyA-FHY1/FHL nuclear import complex is a principle determinant of the phyA action peak. The findings suggest how higher plants acquired the ability to sense far-red light from an ancestral photoreceptor tuned to respond to red light.     

A novel DNA nuclease is stimulated by association with the GINS complex

Chromosomal DNA replication requires the spatial and temporal coordination of the activities of several complexes that constitute the replisome. A previously uncharacterized protein, encoded by TK1252 in the archaeon Thermococcus kodakaraensis, was shown to stably interact with the archaeal GINS complex in vivo, a central component of the archaeal replisome. Here, we document that this protein (TK1252p) is a processive, single-strand DNA-specific exonuclease that degrades DNA in the 5' → 3' direction. TK1252p binds specifically to the GINS15 subunit of T. kodakaraensis GINS complex and this interaction stimulates the exonuclease activity in vitro. This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed.     

Temporal expression profiles indicate a primary function for microRNA during the peak of DNA replication after rat partial hepatectomy

The liver has the unique capacity to regenerate after surgical resection. However, the regulation of liver regeneration is not completely understood. Recent reports indicate an essential role for small noncoding microRNAs (miRNAs) in the regulation of hepatic development, carcinogenesis, and early regeneration. We hypothesized that miRNAs are critically involved in all phases of liver regeneration after partial hepatectomy. We performed miRNA microarray analyses after 70% partial hepatectomy in rats under isoflurane anesthesia at different time points (0 h to 5 days) and after sham laparotomy. Putative targets of differentially expressed miRNAs were determined using a bioinformatic approach. Two-dimensional (2D)-PAGE proteomic analyses and protein identification were performed on specimens at 0 and 24 h after resection. The temporal dynamics of liver regeneration were characterized by 5-bromo- 2-deoxyuridine, proliferating cell nuclear antigen, IL-6, and hepatocyte growth factor. We demonstrate that miRNA expression patterns changed during liver regeneration and that these changes were most evident during the peak of DNA replication at 24 h after resection. Expression of 13 miRNAs was significantly reduced 12-48 h after resection (>25% change), out of which downreguation was confirmed in isolated hepatocytes for 6 miRNAs at 24 h, whereas three miRNAs were significantly upregulated. Proteomic analysis revealed 65 upregulated proteins; among them, 23 represent putative targets of the differentially expressed miRNAs. We provide a temporal miRNA expression and proteomic dataset of the regenerating rat liver, which indicates a primary function for miRNA during the peak of DNA replication. These data will assist further functional studies on the role of miRNAs during liver regeneration.     

Human�Cenvironment interactions in mountain rainforests: archaeobotanical evidence from central Sulawesi, Indonesia

Palaeoecology may contribute to the debate on nature conservation and the preservation of cultural heritage. Here we present two palaeo-records from the Lore Lindu Biosphere Reserve and National Park in central Sulawesi, Indonesia. The park comprises one of the largest remaining and most biodiverse mountain forests of Sulawesi. Outstanding megalithic sites reveal long-term human impact on the area. Thus, modern vegetation composition within the park has been determined by complex site histories, natural and anthropogenic. Palaeo-records from sites between 1,000 and 1,400 m a.s.l. demonstrate that human activity as well as climate variations have to be considered as the main drivers of vegetation changes in the region for the last 2,000 years. Human impact is reflected by large amounts of charred fragments in the pollen records plus low values of arboreal pollen resulting from forest clearance. The stratigraphy of one of the pollen records shows effects of a general cooling trend during the Little Ice Age (LIA). Biomass loss due to the conversion of lower montane rainforest to grassland has reduced the carbon storage potential in the area of the Lore Lindu Park. Recommendations for conservation policy that may be made from the environmental history within the biosphere reserve thus include the consideration of human influence in easily accessible areas, particularly in face of recent settlement intensification.     

Biodiversity Increases the Productivity and Stability of Phytoplankton Communities

Global biodiversity losses provide an immediate impetus to elucidate the relationships between biodiversity, productivity and stability. In this study, we quantified the effects of species richness and species combination on the productivity and stability of phytoplankton communities subject to predation by a single rotifer species. We also tested one mechanism of the insurance hypothesis: whether large, slow-growing, potentially-defended cells would compensate for the loss of small, fast-growing, poorly-defended cells after predation. There were significant effects of species richness and species combination on the productivity, relative yield, and stability of phytoplankton cultures, but the relative importance of species richness and combination varied with the response variables. Species combination drove patterns of productivity, whereas species richness was more important for stability. Polycultures containing the most productive single species, Dunaliella, were consistently the most productive. Yet, the most species rich cultures were the most stable, having low temporal variability in measures of biomass. Polycultures recovered from short-term negative grazing effects, but this recovery was not due to the compensation of large, slow-growing cells for the loss of small, fast-growing cells. Instead, polyculture recovery was the result of reduced rotifer grazing rates and persisting small species within the polycultures. Therefore, although an insurance effect in polycultures was found, this effect was indirect and unrelated to grazing tolerance. We hypothesize that diverse phytoplankton assemblages interfered with efficient rotifer grazing and that this “interference effect” facilitated the recovery of the most productive species, Dunaliella. In summary, we demonstrate that both species composition and species richness are important in driving patterns of productivity and stability, respectively, and that stability in biodiverse communities can result from an alteration in consumer functioning. Our findings underscore the importance of predator-prey dynamics in determining the relationships between biodiversity, productivity and stability in producer communities.     

Crop growing and gathering in the northern German Neolithic: a review supplemented by new results

New archaeobotanical results from 15 Neolithic sites in northern Germany are presented in a review of the Neolithic plant economy in northern and north-western Europe. Available archaeobotanical data from north-western Europe are evaluated and compared with our new results. In the whole region, barley and emmer were the main crops. Regional and diachronic differences are observed in the cultivation of einkorn, spelt and naked wheat. For oil plants and pulses only rare information from macro remains is available, as we mainly deal with charred material. It is noticeable that gathered plants played an important role in the Funnel Beaker economy. Plant choice, especially the relevance of cultivated versus gathered plants is discussed, based on new and existing data. Based on a structural comparison of charred plant assemblages from domestic sites and tombs, we develop a research hypothesis that settlement finds provide insight into production and consumption of food from crops, while tombs mainly yield evidence of plants gathered in the wild or in semi-wild areas in the vicinity of former settlements. Therefore, we suggest a model of different purposes and meanings of plants, depending on whether primarily an economic or a social/ritual sphere is regarded. But, for all evaluations and interpretations, it is essential to consider the taphonomic processes and conditions. Therefore, further research is necessary to verify our hypothesis, which derives from first insights into new material.     

Holocene history of environment and human impact on two islands in the Ostholstein lakeland area, Northern Germany

Holocene sediment cores from contemporary terrestrialised kettle holes on two islands in the Ostholstein lakeland area, Northern Germany, were investigated by palaeoenvironmental methods. Records from such isolated locations, such as these island mires, are an important source of information on small-scale vegetation changes. Pollen, non-pollen palynomorphs and macrofossils were used to reveal anthropogenic impact as well as lake level fluctuations. Changes in the peat decomposition and the ratio of organic to minerogenic content in the sediment facilitated correlation with past ground water table levels and accordingly with former lake levels. The palynological surveys indicate that human impact on the islands expanded in prehistoric times during phases of low lake levels or periods of stable hydrological conditions. The first distinct low level is recorded between ca. 8210 and 7740?cal.?yr b.p. Another major low level period was detected for the time span from approximately 5290 to 4600?cal.?yr b.p. After a subsequent period with a wetter climate, indicated by rising and fluctuating lake levels culminating at ca. 2420 to 2180?cal.?yr b.p., a third lowering occurred until about 660?cal.?yr b.p. This period was interrupted by minor fluctuations in lake levels from ca. 1770 to 1630?cal.?yr b.p. and from ca. 1370 to 1010?cal.?yr b.p.     

Drosophila auditory organ genes and genetic hearing defects

The Drosophila auditory organ shares equivalent transduction mechanisms with vertebrate hair cells, and both are specified by atonal family genes. Using a whole-organ knockout strategy based on atonal, we have identified 274 Drosophila auditory organ genes. Only four of these genes had previously been associated with fly hearing, yet one in five of the genes that we identified has a human cognate that is implicated in hearing disorders. Mutant analysis of 42 genes shows that more than half of them contribute to auditory organ function, with phenotypes including hearing loss, auditory hypersusceptibility, and ringing ears. We not only discover ion channels and motors important for hearing, but also show that auditory stimulus processing involves chemoreceptor proteins as well as phototransducer components. Our findings demonstrate mechanosensory roles for ionotropic receptors and visual rhodopsins and indicate that different sensory modalities utilize common signaling cascades.