The scaling of reproductive variability in trees

Seed output in perennial plant populations is temporally variable and often synchronous over large regions. The similarly complex spatiotemporal dynamics of animal populations have been characterized by the power‐law scaling of the variance in population numbers with mean abundance. Here we show that a large compilation of published reproductive time series exhibits largely invariant mean–variance scaling properties across both angiosperm and conifer tree species. A simple model of seed production in tree stands shows that observed values of the scaling exponent reflect very general aspects of plant ecology and life history as well as the temporal dynamics of seed production. Together, these results suggest that the continuum of reproductive variability and synchrony observed in trees may reflect the influence of a common set of ecological processes.     

Oligomeric Yeast Frataxin Drives Assembly of Core Machinery for Mitochondrial Iron-Sulfur Cluster Synthesis

Mitochondrial biosynthesis of iron-sulfur clusters (ISCs) is a vital process involving the delivery of elemental iron and sulfur to a scaffold protein via molecular interactions that are still poorly defined. Analysis of highly conserved components of the yeast ISC assembly machinery shows that the iron-chaperone, Yfh1, and the sulfur-donor complex, Nfs1-Isd11, directly bind to each other. This interaction is mediated by direct Yfh1-Isd11 contacts. Moreover, both Yfh1 and Nfs1-Isd11 can directly bind to the scaffold, Isu1. Binding of Yfh1 to Nfs1-Isd11 or Isu1 requires oligomerization of Yfh1 and can occur in an iron-independent manner. However, more stable contacts are formed when Yfh1 oligomerization is normally coupled with the binding and oxidation of Fe²⁺. Our observations challenge the view that iron delivery for ISC synthesis is mediated by Fe²⁺-loaded monomeric Yfh1. Rather, we find that the iron oxidation-driven oligomerization of Yfh1 promotes the assembly of stable multicomponent complexes in which the iron donor and the sulfur donor simultaneously interact with each other as well as with the scaffold. Moreover, the ability to store ferric iron enables oligomeric Yfh1 to adjust iron release depending on the presence of Isu1 and the availability of elemental sulfur and reducing equivalents. In contrast, the use of anaerobic conditions that prevent Yfh1 oligomerization results in inhibition of ISC assembly on Isu1. These findings suggest that iron-dependent oligomerization is a mechanism by which the iron donor promotes assembly of the core machinery for mitochondrial ISC synthesis.ISC³ biosynthesis is an essential function that eukaryotic cells initiate in mitochondria and probably other cellular compartments using three core components: a sulfur donor, an iron donor, and an ISC assembly scaffold (1, 2). In yeast mitochondria, the cysteine-desulfurase, Nfs1, and the iron-chaperone, Yfh1, are believed to provide sulfur and iron, respectively, for ISC assembly on the Isu1 scaffold (1), whereas the Nfs1-binding protein, Isd11, has been shown to stabilize Nfs1 (3). These components are highly conserved and the human orthologues of Yfh1 (frataxin), Isu1 (ISCU), and Isd11 (ISD11) are implicated in the etiology of severe disorders including Friedreich ataxia and mitochondrial myopathy (4).Previous studies have underscored the complexity of the interactions among eukaryotic ISC assembly components as well as their metal dependence. Supplementation of mitochondrial lysates with Fe²⁺ under aerobic conditions led to co-isolation of Yfh1 and Isu1 along with Nfs1 and Isd11 by pulldown or immunoprecipitation assays (5–7). Furthermore, aerobic preincubation of histidine-tagged Yfh1 monomer with Fe²⁺ enabled Isu1 to be pulled down by Yfh1 in the absence of other proteins (5). These studies have led to the current view that iron delivery for yeast ISC synthesis involves direct contacts between iron-loaded monomeric Yfh1 and Isu1 (5–7). Although Yfh1 oligomerization is normally coupled with iron binding, oxidation, and storage (5, 8), the possibility that Isu1 might also interact with oligomeric Yfh1 has remained largely unexplored.Similar to Yfh1, human frataxin was found to interact with multiple ISC assembly components in human cells; however, in this case immunoprecipitation data suggested that frataxin binds to ISCU indirectly, via nickel-dependent contacts with ISD11 (9). Whether direct interactions occur between Yfh1 and Isd11 has not yet been examined.While previous studies focused primarily on Yfh1-Isu1 and frataxin-ISD11 interactions, it is likely that the coordinate delivery of potentially toxic sulfur and iron to Isu1/ISCU involves multiple close interactions whereby the sulfur donor and the iron donor simultaneously interact with each other and with the ISC scaffold, as proposed for prokaryotic ISC assembly (10). However, it is currently unknown whether monomeric Yfh1/frataxin may form direct contacts with more than one partner, and the structure of the eukaryotic ISC assembly machinery is completely undefined. We show that iron oxidation-dependent oligomerization enables Yfh1 to have simultaneous direct interactions with Nfs1-Isd11 and Isu1. Our data provide insights about the sequence of events and the molecular architecture required for the initial step in mitochondrial ISC assembly.     

Isolation of highly enriched apical plasma membranes of the placental syncytiotrophoblast

The human placenta is a complex organ whose proper function is crucial for the development of the fetus. The placenta contains within its structure elements of the maternal and fetal circulatory systems. The interface with maternal blood is the lining of the placenta, that is a unique compartment known as the syncytiotrophoblast. This large syncytial structure is a single cell layer in thickness, and the apical plasma membrane of the syncytiotrophoblast interacts directly with maternal blood. Relatively little is known about the proteins that reside in this unique plasma membrane or how they may change in various placental diseases. Our goal was to develop methods for isolating highly enriched preparations of this apical plasma membrane compatible with high-quality proteomics analysis and herein describe the properties of these isolated membranes.     

Australian bird phenology: a search for climate signals

Temporal and climate‐related changes in avian phenology were assessed for seven species of south‐eastern Australia using data obtained from members of the public, naturalist groups and other organizations. Despite significantly warmer temperatures (～0.02–0.03°C per year) and reduced rainfall (～1.6–8.0 mm per year) over much of south‐eastern Australia in recent decades, most species showed no corresponding trends in their timing of migration or breeding, the notable exceptions being the grey fantail (Rhipidura fuliginosa) and the flame robin (Petroica phoenicea), which migrate through Melbourne, Victoria, during autumn and spring. In many species, however, migration or breeding timing appeared to be influenced to some extent by local, rather than regional, climate conditions, particularly local daily maximum and minimum temperatures. Whether these species will noticeably change their phenology to match projected changes in climate, perhaps when a currently unknown climate threshold is crossed, or whether these species are sufficiently flexible in their foraging strategies or food sources to be able to maintain their current timing, remains to be seen.     

Counteractive biomass allocation responses to drought and damage in the perennial herb Convolvulus demissus

Herbivory and water shortage are key ecological factors affecting plant performance. While plant compensatory responses to herbivory include reallocation of biomass from below‐ground to above‐ground structures, plant responses to reduced soil moisture involve increased biomass allocation to roots and a reduction in the number and size of leaves. In a greenhouse study we evaluated the effects of experimental drought and leaf damage on biomass allocation in Convolvulus demissus (Convolvulaceae), a perennial herb distributed in central Chile, where it experiences summer drought typical of Mediterranean ecosystems and defoliation by leaf beetles and livestock. The number of leaves and internode length were unaffected by the experimental treatments. The rest of plant traits showed interaction of effects. We detected that drought counteracted some plant responses to damage. Thus, only in the control watering environment was it observed that damaged plants produced more stems, even after correcting for main stem length (index of architecture). In the cases of shoot : root ratio, relative shoot biomass and relative root biomass we found that the damage treatment counteracted plant responses to drought. Thus, while undamaged plants under water shortage showed a significant increase in root relative biomass and a significant reduction in both shoot : root ratio and relative shoot biomass, none of these responses to drought was observed in damaged plants. Total plant biomass increased in response to simulated herbivory, apparently due to greater shoot size, and in response to drought, presumably due to greater root size. However, damaged plants under experimental drought had the same total biomass as control plants. Overall, our results showed counteractive biomass allocation responses to drought and damage in C. demissus. Further research must address the fitness consequences under field conditions of the patterns found. This would be of particular importance because both current and expected climatic trends for central Chile indicate increased aridity.     

Sauropod Trackway Reflecting an Unusual Walking Pattern from the Early Cretaceous of Shandong Province,China

The trackway of a quadrupedal dinosaur from the Early Cretaceous (Albian) Qingquan tracksite (Tancheng, Shandong Province) is redescribed, and the trackmaker is identified as a sauropod. The trackway makes a slight turn towards the northwest and is characterized by an extremely narrow gauge pattern and an unusual configuration, i.e., a conspicuous difference between the position of the left and right manus tracks with respect to the position of the preceding pes track. Left manus tracks are located on the inside of the trackway, very close (and sometimes even in connection) to the opposite right pes tracks. So far, the Qingquan trackway is possibly the only extremely narrow-gauge sauropod trackway known from China. However, it is not clear to what extent this extremely narrow gauge pattern is related to the turning or a special behavior, or even linked to an injury (“limping trackway”). We tentatively attribute the Qingquan trackway to cf. Parabrontopodus, even though it has a rather low heteropody that is significantly lower than in Parabrontopodus and not typical for narrow-gauge sauropod trackways, but occurs in the wide-gauge ichnotaxon Brontopodus. Because of this discrepancy, the Qingquan trackway cannot readily be attributed to a more basal sauropod, which is generally considered the producer of narrow-gauge trackways. Therefore, the identification of a distinct sauropod group is not possible presently. The only skeletal remains of sauropods from the Lower Cretaceous of Shandong Province belong to the large titanosauriform, Euhelopus zdanskyi.     

The E3 ubiquitin ligase NEDD4 is an LC3-interactive protein and regulates autophagy

The MAP1LC3/LC3 family plays an essential role in autophagosomal biogenesis and transport. In this report, we show that the HECT family E3 ubiquitin ligase NEDD4 interacts with LC3 and is involved in autophagosomal biogenesis. NEDD4 binds to LC3 through a conserved WXXL LC3-binding motif in a region between the C2 and the WW2 domains. Knockdown of NEDD4 impaired starvation- or rapamycin-induced activation of autophagy and autophagosomal biogenesis and caused aggregates of the LC3 puncta colocalized with endoplasmic reticulum membrane markers. Electron microscopy observed gigantic deformed mitochondria in NEDD4 knockdown cells, suggesting that NEDD4 might function in mitophagy. Furthermore, SQSTM1 is ubiquitinated by NEDD4 while LC3 functions as an activator of NEDD4 ligase activity. Taken together, our studies define an important role of NEDD4 in regulation of autophagy.     

Integrated metagenomic and metaproteomic analyses of marine biofilm communities

Metagenomic and metaproteomic analyses were utilized to determine the composition and function of complex air–water interface biofilms sampled from the hulls of two US Navy destroyers. Prokaryotic community analyses using PhyloChip-based 16S rDNA profiling revealed two significantly different and taxonomically rich biofilm communities (6,942 taxa) in which the majority of unique taxa were ascribed to members of the Gammaproteobacteria, Alphaproteobacteria and Clostridia. Although metagenomic sequencing indicated that both biofilms were dominated by prokaryotic sequence reads (> 91%) with the majority of the bacterial reads belonging to the Alphaproteobacteria, the Ship-1 metagenome harbored greater organismal and functional diversity and was comparatively enriched for sequences from Cyanobacteria, Bacteroidetes and macroscopic eukaryotes, whereas the Ship-2 metagenome was enriched for sequences from Proteobacteria and microscopic photosynthetic eukaryotes. Qualitative liquid chromatography-tandem mass spectrometry metaproteome analyses identified 678 unique proteins, revealed little overlap in species and protein composition between the ships and contrasted with the metagenomic data in that ~80% of classified and annotated proteins were of eukaryotic origin and dominated by members of the Bacillariophyta, Cnidaria, Chordata and Arthropoda (data deposited to the ProteomeXchange, identifier PXD000961). Within the shared metaproteome, quantitative ¹⁸O and iTRAQ analyses demonstrated a significantly greater abundance of structural proteins from macroscopic eukaryotes on Ship-1 and diatom photosynthesis proteins on Ship-2. Photosynthetic pigment composition and elemental analyses confirmed that both biofilms were dominated by phototrophic processes. These data begin to provide a better understanding of the complex organismal and biomolecular composition of marine biofilms while highlighting caveats in the interpretation of stand-alone environmental ‘-omics’ datasets.