A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.     

Influence of carbon availability on the production of NO, N2O, N2 and CO2 by soil cores during anaerobic incubation

Net productions of permanent soil atmosphere gases (N₂, CO₂, O₂) and temporary gases (N₂O, NO) were monitored in soil cores using a non-interfering, fully automated measuring technique allowing highly time resolved measurements over prolonged periods. The influence of changes in available organic carbon on CO₂, N₂O, NO and N₂ production was studied by changing the soil carbon content through aerobic preincubations of different length, up to 21 days.The aerobic preincubation caused an increase in NO₃ ^- concentration and a decrease in available carbon content. Available carbon content dominated both CO₂ and total N gas (N₂+N₂O+NO) production during anaerobiosis. Both CO₂ and total N gas production rates decreased with increasing length of the previous aerobic preincubation, this in spite of the higher initial NO₃ ^- concentration.Total denitrification rates were closely related to the anaerobic CO₂ production rates. No relation was found between water soluble carbon content and total denitrification. The N₂O/N₂ ratio could be explained by an interaction of carbon availability, NO₃ ^- concentration and enzyme status. Net N₂O consumption was monitored. The balance between cumulative total N gas production and NO₃ ^- consumption varied according to the different treatments. Cumulative N₂O production exceeded cumulative N₂ production for 0 up to 5 days.     

Growth and growth substrate levels in spinach under non-steady state conditions of nitrogen nutrition and light

Spinach plants ( Spinacia oleracea L. cv. Subito) were grown in a complete nutrient solution under ample light intensity (14 h day⁻¹ at 660 μmol m⁻² s⁻¹) before being transferred either to a minus-N solution (experiment 1), or to limiting light conditions (6 h day⁻¹ at 220 μmol m⁻² s⁻¹; experiment 2). Shoot growth in experiment 1 decreased significantly from 0.24 day⁻¹ to 0.07 day⁻¹ after the fourth day of transfer. Root relative growth rate increased after 1 day from 0.25 to 0.31 day⁻¹, but decreased on the fifth day after transfer to 0.11 day⁻¹. Shoot growth in experiment 2 decreased significantly from 0.25 to 0.17 day⁻¹ after the fourth day of transfer, while root growth decreased to half of its original level (0.25 day⁻¹) already on the second day. Growth substrate levels in the plants (free sugars, free amino acids) and starch levels depended on the plant age, the moment in the diurnal cycle, and the imposed treatment. Fluctuations in shoot growth or root growth resulting from the light or N limitation could not be explained by a correspondent increase or decrease in the levels of growth substrates. The hypotheses underlying the functional equilibrium theory, assuming shoot and root growth to be controlled by N- and C-containing substrates respectively, and several other growth and partitioning models are therefore questioned. A neglect of the osmotic role of the free sugars in these models might be the explanation for this.     

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927 . Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the ‘odd man out’ pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER , here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.     

Impact of elevated CO2 on soil organic matter dynamics as related to changes in aggregate turnover and residue quality

Increasing global atmospheric CO₂ concentration can potentially affect C cycling in terrestrial ecosystems. This study was conducted to assess the impact of elevated CO₂ concentration on soil organic matter and aggregate dynamics in Lolium perenne and Trifolium repens pastures. Soil samples from a 6 year old `free air CO₂ enrichment' (FACE) experiment were separated in four aggregate size classes (<53, 53–250, 250–2000, and > 2000 m). Free light fraction (i.e. particulate organic matter (POM) outside of aggregates; free LF) and intra-aggregate-POM (i.e. POM occluded within the aggregate structure; iPOM) were isolated. The distinct ¹³C-signature of the CO₂ used to raise the ambient CO₂ concentration in FACE allowed us to calculate proportions of recently incorporated C (< 6 yr) in the physically defined soil fractions. The proportion of new C increased with increasing aggregate size class, except the two largest aggregate size classes had a similar proportion of new C; this indicates a faster turnover of macroaggregates compared to microaggregates. In addition, higher proportions of new C in macroaggregates under T. repens compared to L. perenne indicate a faster macroaggregate turnover under T. repens. This faster macroaggregate turnover is hypothesized to be a result of the higher residue quality (C:N ratio) of T. repens compared to L. perenne and reduces the potential of sequestering C under elevated CO₂. In the L. perenne soil, elevated CO₂ did not significantly increase total C, but led to: (1) a 54% increase in aggregation and (2) a 40% increase in total iPOM-C. It is hypothesized that the sequestration of iPOM-C induced by elevated CO₂ in the low residue quality, L. perenne treatment, resulted from an increase in the proportion of large macroaggregates with a slow turnover.     

Continuous-time modeling of cell fate determination in Arabidopsis flowers

Background  

The genetic control of floral organ specification is currently being investigated by various approaches, both experimentally and through modeling. Models and simulations have mostly involved boolean or related methods, and so far a quantitative, continuous-time approach has not been explored.     

Loss of HAUSP-mediated deubiquitination contributes to DNA damage-induced destabilization of Hdmx and Hdm2

The p53 tumor suppressor protein has a major role in protecting the integrity of the genome. In unstressed cells, p53 is maintained at low levels by the ubiquitin-proteasome pathway. A balance between ubiquitin ligase activity (Hdm2, COP1, and Pirh2) and the ubiquitin protease activity of the Herpes virus-associated ubiquitin-specific protease (HAUSP) determines the half-life of p53. HAUSP also modulates p53 stability indirectly by deubiquitination and stabilization of Hdm2. The Hdmx protein affects p53 stability as well through its interaction with and regulation of Hdm2. Vice versa, Hdmx is a target for Hdm2-mediated ubiquitination and degradation. Here, we show that HAUSP also interacts with Hdmx, resulting in its direct deubiquitination and stabilization. HAUSP activity is required to maintain normal Hdmx protein levels. Therefore, the balance between HAUSP and Hdm2 activity determines Hdmx protein stability. Importantly, impaired deubiquitination of Hdmx/Hdm2 by HAUSP contributes to the DNA damage-induced degradation of Hdmx and transient instability of Hdm2.