The primordial metabolism: an ancestral interconnection between leucine,arginine, and lysine biosynthesis

Background

It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution.

Results

The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted.

Conclusion

The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.

     

Quantification and identification of lightning damage in tropical forests

Accurate estimates of tree mortality are essential for the development of mechanistic forest dynamics models, and for estimating carbon storage and cycling. However, identifying agents of tree mortality is difficult and imprecise. Although lightning kills thousands of trees each year and is an important agent of mortality in some forests, the frequency and distribution of lightning‐caused tree death remain unknown for most forests. Moreover, because all evidence regarding the effects of lightning on trees is necessarily anecdotal and post hoc, rigorous tests of hypotheses regarding the ecological effects of lightning are impossible. We developed a combined electronic sensor/camera‐based system for the location and characterization of lightning strikes to the forest canopy in near real time and tested the system in the forest of Barro Colorado Island, Panama. Cameras mounted on towers provided continuous video recordings of the forest canopy that were analyzed to determine the locations of lightning strikes. We used a preliminary version of this system to record and locate 18 lightning strikes to the forest over a 3‐year period. Data from field surveys of known lightning strike locations (obtained from the camera system) enabled us to develop a protocol for reliable, ground‐based identification of suspected lightning damage to tropical trees. In all cases, lightning damage was relatively inconspicuous; it would have been overlooked by ground‐based observers having no knowledge of the event. We identified three types of evidence that can be used to consistently identify lightning strike damage in tropical forests: (1) localized and directionally biased branch mortality associated with flashover among tree and sapling crowns, (2) mortality of lianas or saplings near lianas, and (3) scorched or wilting epiphytic and hemiepiphytic plants. The longitudinal trunk scars that are typical of lightning‐damaged temperate trees were never observed in this study. Given the prevalence of communications towers worldwide, the lightning detection system described here could be implemented in diverse forest types. Data from multiple systems would provide an outstanding opportunity for comparative research on the ecological effects of lightning. Such comparative data are increasingly important given expected increases in lightning frequency with climatic change.     

Uptake and recycling of pro-BDNF for transmitter-induced secretion by cortical astrocytes

Activity-dependent secretion of brain-derived neurotrophic factor (BDNF) is thought to enhance synaptic plasticity, but the mechanisms controlling extracellular availability and clearance of secreted BDNF are poorly understood. We show that BDNF is secreted in its precursor form (pro-BDNF) and is then cleared from the extracellular space through rapid uptake by nearby astrocytes after θ-burst stimulation in layer II/III of cortical slices, a paradigm resulting in long-term potentiation of synaptic transmission. Internalization of pro-BDNF occurs via the formation of a complex with the pan-neurotrophin receptor p75 and subsequent clathrin-dependent endocytosis. Fluorescence-tagged pro-BDNF and real-time total internal reflection fluorescence microscopy in cultured astrocytes is used to monitor single endocytic vesicles in response to the neurotransmitter glutamate. We find that endocytosed pro-BDNF is routed into a fast recycling pathway for subsequent soluble NSF attachment protein receptor–dependent secretion. Thus, astrocytes contain an endocytic compartment competent for pro-BDNF recycling, suggesting a specialized form of bidirectional communication between neurons and glia.     

AFLP analysis to assess genomic stability in Solanum regenerants derived from wild and cultivated species

The cultivated potato as well as its tuber-bearing relatives are considered model plants for cell and tissue culture, and therefore for exploiting the genetic variation induced by in vitro culture. The association between molecular stability and tissue culture in different genetic backgrounds and ploidy levels has already been explored. However, it still remains to be ascertained whether somaclonal variation differs between callus-derived chromosome-doubled and undoubled regenerants. Our research aimed at investigating, through amplified fragment length polymorphism (AFLP) markers, the genetic changes in marker-banding patterns of diploid and tetraploid regenerants obtained from one clone each of Solanum bulbocastanum Dunal and S. cardiophyllum Lindl (both 2n = 2x = 24) and tetraploids from cultivated S. tuberosum L. (2n = 4x = 48). Pairwise comparisons between the banding patterns of regenerants and parents allowed detecting considerable changes associated to in vitro culture both at diploid and tetraploid level. The percentages of polymorphic bands between diploid and tetraploid regenerants were, respectively, 57 and 69% in S. bulbocastanum and 58 and 63% in S. cardiophyllum. On average, the frequencies of lost parental fragments in regenerants were significantly higher than novel bands both in S. bulbocastanum (48 vs. 22%) and S. tuberosum (36 vs. 18%) regenerants. By contrast, in S. cardiophyllum, a similar incidence of the two events was detected (32 vs. 29%). Our results revealed that structural changes after tissue culture process strongly affected the genome of the species studied, but diploid and tetraploids regenerated plants responded equally.     

Higher biodiversity is required to sustain multiple ecosystem processes across temperature regimes

Biodiversity loss is occurring rapidly worldwide, yet it is uncertain whether few or many species are required to sustain ecosystem functioning in the face of environmental change. The importance of biodiversity might be enhanced when multiple ecosystem processes (termed multifunctionality) and environmental contexts are considered, yet no studies have quantified this explicitly to date. We measured five key processes and their combined multifunctionality at three temperatures (5, 10 and 15 °C) in freshwater aquaria containing different animal assemblages (1–4 benthic macroinvertebrate species). For single processes, biodiversity effects were weak and were best predicted by additive‐based models, i.e. polyculture performances represented the sum of their monoculture parts. There were, however, significant effects of biodiversity on multifunctionality at the low and the high (but not the intermediate) temperature. Variation in the contribution of species to processes across temperatures meant that greater biodiversity was required to sustain multifunctionality across different temperatures than was the case for single processes. This suggests that previous studies might have underestimated the importance of biodiversity in sustaining ecosystem functioning in a changing environment.     

In Vivo Evidence for Serine Biosynthesis-Defined Sensitivity of Lung Metastasis,but Not of Primary Breast Tumors,to mTORC1 Inhibition

1. Download : Download high-res image (198KB)
2. Download : Download full-size image

     

Using LiDAR Data to Measure the 3D Green Biomass of Beijing Urban Forest in China

The purpose of the paper is to find a new approach to measure 3D green biomass of urban forest and to testify its precision. In this study, the 3D green biomass could be acquired on basis of a remote sensing inversion model in which each standing wood was first scanned by Terrestrial Laser Scanner to catch its point cloud data, then the point cloud picture was opened in a digital mapping data acquisition system to get the elevation in an independent coordinate, and at last the individual volume captured was associated with the remote sensing image in SPOT5(System Probatoired''Observation dela Tarre)by means of such tools as SPSS (Statistical Product and Service Solutions), GIS (Geographic Information System), RS (Remote Sensing) and spatial analysis software (FARO SCENE and Geomagic studio11). The results showed that the 3D green biomass of Beijing urban forest was 399.1295 million m³, of which coniferous was 28.7871 million m³ and broad-leaf was 370.3424 million m³. The accuracy of 3D green biomass was over 85%, comparison with the values from 235 field sample data in a typical sampling way. This suggested that the precision done by the 3D forest green biomass based on the image in SPOT5 could meet requirements. This represents an improvement over the conventional method because it not only provides a basis to evalue indices of Beijing urban greenings, but also introduces a new technique to assess 3D green biomass in other cities.     

Infectivity of DWV Associated to Flower Pollen: Experimental Evidence of a Horizontal Transmission Route

Deformed wing virus (DWV) is a honeybee pathogen whose presence is generally associated with infestation of the colony by the mite Varroa destructor, leading to the onset of infections responsible for the collapse of the bee colony. DWV contaminates bee products such as royal jelly, bee-bread and honey stored within the infected hive. Outside the hive, DWV has been found in pollen loads collected directly from infected as well as uninfected forager bees. It has been shown that the introduction of virus-contaminated pollen into a DWV-free hive results in the production of virus-contaminated food, whose role in the development of infected bees from virus-free eggs has been experimentally demonstrated. The aim of this study was twofold: (i) to ascertain the presence of DWV on pollen collected directly from flowers visited by honeybees and then quantify the viral load and (ii) determine whether the virus associated with pollen is infective. The results of our investigation provide evidence that DWV is present on pollen sampled directly from visited flowers and that, following injection in individuals belonging to the pollinator species Apis mellifera, it is able to establish an active infection, as indicated by the presence of replicating virus in the head of the injected bees. We also provide the first indication that the pollinator species Osmia cornuta is susceptible to DWV infection.