Primate DNA suggests long‐term stability of an African rainforest

Red colobus monkeys, due to their sensitivity to environmental change, are indicator species of the overall health of their tropical rainforest habitats. As a result of habitat loss and overhunting, they are among the most endangered primates in the world, with very few viable populations remaining. Traditionally, extant indicator species have been used to signify the conditions of their current habitats, but they have also been employed to track past environmental conditions by detecting previous population fluctuations. Kibale National Park (KNP) in Uganda harbors the only remaining unthreatened large population of red colobus. We used microsatellite DNA to evaluate the historical demography of these red colobus and, therefore, the long‐term stability of their habitat. We find that the red colobus population throughout KNP has been stable for at least ~40,000 years. We interpret this result as evidence of long‐term forest stability because a change in the available habitat or population movement would have elicited a corresponding change in population size. We conclude that the forest of what is now Kibale National Park may have served as a Late Pleistocene refuge for many East African species.     

Global Analysis of the Role of Autophagy in Cellular Metabolism and Energy Homeostasis in Arabidopsis Seedlings under Carbon Starvation

Germination and early seedling establishment are developmental stages in which plants face limited nutrient supply as their photosynthesis mechanism is not yet active. For this reason, the plant must mobilize the nutrient reserves provided by the mother plant in order to facilitate growth. Autophagy is a catabolic process enabling the bulk degradation of cellular constituents in the vacuole. The autophagy mechanism is conserved among eukaryotes, and homologs of many autophagy-related (ATG) genes have been found in Arabidopsis thaliana. T-DNA insertion mutants (atg mutants) of these genes display higher sensitivity to various stresses, particularly nutrient starvation. However, the direct impact of autophagy on cellular metabolism has not been well studied. In this work, we used etiolated Arabidopsis seedlings as a model system for carbon starvation. atg mutant seedlings display delayed growth in response to carbon starvation compared with wild-type seedlings. High-throughput metabolomic, lipidomic, and proteomic analyses were performed, as well as extensive flux analyses, in order to decipher the underlying causes of the phenotype. Significant differences between atg mutants and wild-type plants have been demonstrated, suggesting global effects of autophagy on central metabolism during carbon starvation as well as severe energy deprivation, resulting in a morphological phenotype.     

Zooplankton contribution to the particulate N and P in Lake Kinneret,Israel, under changing water levels

The association of water level changes and the relative (%) contributions of crustacean zooplankton to particulate N (PNz) and particulate P (PPz) in Lake Kinneret, Israel were studied. The PNz and PPz were assessed for a period of 10 years (1999–2008) in relation to water level (WL) changes which occurred during that period. We estimated PNz and PPz, based on crustacean N and P content measured seasonally over 2 years, and a 10-year record of zooplankton densities. Mean cladoceran N and P contents were 8.7 and 1.2% of dry weight, respectively, while for copepods they were 9.5 and 1.5% of dry weight, respectively. Zooplankton density, and hence PNz and PPz, changed dramatically during the 10 years, concurrent with extreme variations in the lake’s WL. The lowest mean values of PNz and PPz occurred during high WL years and the highest PNz and PPz were during low WL years. PNz and PPz were negatively correlated with the total PN and PP concentrations, respectively, in the lake. The reduction in zooplankton contribution to the particulate N and P during high WL is probably due to higher loading of particulate matter in wet years, causing an increase of PN and PP concentration in the lake, as well as lower densities of zooplankton, caused by higher fish predation pressure, both are a by-product of the large water influx during extreme wet winters.     

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

Mass spectrometry (MS)-based proteomics is increasingly applied in a quantitative format, often based on labeling of samples with stable isotopes that are introduced chemically or metabolically. In the stable isotope labeling by amino acids in cell culture (SILAC) method, two cell populations are cultured in the presence of heavy or light amino acids (typically lysine and/or arginine), one of them is subjected to a perturbation, and then both are combined and processed together. In this study, we describe a different approach--the use of SILAC as an internal or 'spike-in' standard--wherein SILAC is only used to produce heavy labeled reference proteins or proteomes. These are added to the proteomes under investigation after cell lysis and before protein digestion. The actual experiment is therefore completely decoupled from the labeling procedure. Spike-in SILAC is very economical, robust and in principle applicable to all cell- or tissue-based proteomic analyses. Applications range from absolute quantification of single proteins to the quantification of whole proteomes. Spike-in SILAC is especially advantageous when analyzing the proteomes of whole tissues or organisms. The protocol describes the quantitative analysis of a tissue sample relative to super-SILAC spike-in, a mixture of five SILAC-labeled cell lines that accurately represents the tissue. It includes the selection and preparation of the spike-in SILAC standard, the sample preparation procedure, and analysis and evaluation of the results.