Latitudinal patterns of range size and species richness of New World woody plants

Aim  Relationships between range size and species richness are contentious, yet they are key to testing the various hypotheses that attempt to explain latitudinal diversity gradients. Our goal is to utilize the largest data set yet compiled for New World woody plant biogeography to describe and assess these relationships between species richness and range size.
Location  North and South America.
Methods  We estimated the latitudinal extent of 12,980 species of woody plants (trees, shrubs, lianas). From these estimates we quantified latitudinal patterns of species richness and range size. We compared our observations with expectations derived from two null models.
Results   Peak richness and the smallest- and largest-ranged species are generally found close to the equator. In contrast to prominent diversity hypotheses: (1) mean latitudinal extent of tropical species is greater than expected; (2) latitudinal extent appears to be decoupled from species richness across New World latitudes, with abrupt transitions across subtropical latitudes; and (3) mean latitudinal extents show equatorial and north temperate peaks and subtropical minima. Our results suggest that patterns of range size and richness appear to be influenced by three broadly overlapping biotic domains (biotic provinces) for New World woody plants.
Main conclusions  Hypotheses that assume a direct relationship between range size and species richness may explain richness patterns within these domains, but cannot explain gradients in richness across the New World.     

Organic matter and nitrogen accumulation and nitrogen fixation during early ecosystem development in Hawaii

We used a chronosequence comprised of 10 y, 52 y and 142 yold `a'a lava flows on Mauna Loa, Hawaii, to determine theaccumulation of organic matter and nitrogen and rates of nitrogenfixation through time. The mass of organic matter (live and deadbiomass and soil organic matter) on the 1984, 1942 and 1852 lavaflows was 0.6, 2.2 and 7.6 kg m^{– 2}, respectively, while total N was 4.8, 10.9 and 85.7 g m^{– 2}.We estimated the total rates of nitrogen fixation for thethree different aged ecosystems using an acetylene reduction assaycalibrated with ¹⁵N incubations. While mean rates of total N fixation remained largely constant across the three sites – between2.0 and 3.1 kg ha^{– 1} y^{– 1} – the most important sources of N fixation changed. On the 10 y flow, the most important fixer was the pioneering cyanolichen, Stereocaulon vulcani. After 52 years ofecosystem development, the most important N fixer was a cyanoalga,while after 142 years, the predominant N fixers were heterotrophicbacteria associated with leaf litter, twigs and detritus. The totalamount of N accumulated after 52 years of ecosystem development wasequivalent to cumulative inputs through biological N fixation. After 142 years, however, cumulative inputs from N fixation couldonly account for between 27–59% of the total nitrogen accrued.We used fertilizer additions of all essential nutrients otherthan N to test whether the availability of lithophilic nutrientsregulated rates of N fixation in early ecosystem development. Ratesof nitrogen fixation by the lichen, S. vulcani, approximately doubled when fertilized on the 1984 and 1942 flows. Rates of N-fixation by heterotrophic nitrogen fixing bacteria on leaf litter ofMetrosideros polymorpha also increased significantly when fertilized with lithophilic nutrients. These findings suggest that weathering rates of lava in part regulate rates of nitrogen fixation in these young ecosystems.     

Recent developments in membrane-protein structural genomics

Recent work has identified the topology of almost all the inner membrane proteins in Escherichia coli, and advances in nuclear magnetic resonance spectroscopy now allow the determination of α-helical membrane protein structures at high resolution. Together these developments will help overcome the current limitations of high-throughput determination of membrane protein structures.     

Comparative molecular field analysis and QSAR on substrates binding to cytochrome p450 2D6

In this study, we utilized comparative molecular field analysis (CoMFA) to gain a better understanding of the steric and electrostatic features of the cytochrome P450 2D6 (CYP2D6) active site. The training set consists of 24 substrates with reported K_M values from liver microsomal CYP2D6 spanning an activity range of almost three log units. The low energy conformers were fit by root mean square (RMS) to minaprine at the site of metabolism and to the protonated nitrogen. In this manner, we constructed two CoMFA models, one model with a distance constraint and another without. The model with the distance parameter (non-crossvalidated R²=0.99) was approximately equal to the CoMFA without a distance parameter (non-cross-validated R²=0.98). Validation of our CoMFA was accomplished by predicting the K_M values of 15 diverse CYP2D6 substrates not in the original training set resulting in a predictive R²=0.62. Finally, we also pursued correlations of pK_a and log P with CYP2D6 substrate K_M in an effort to investigate other physicochemical properties.     

Reconciling empirical interactions and species coexistence

Coexistence in ecological communities is governed largely by the nature and intensity of species interactions. Countless studies have proposed methods to infer these interactions from empirical data, yet models parameterised using such data often fail to recover observed coexistence patterns. Here, we propose a method to reconcile empirical parameterisations of community dynamics with species‐abundance data, ensuring that the predicted equilibrium is consistent with the observed abundance distribution. To illustrate the approach, we explore two case studies: an experimental freshwater algal community and a long‐term time series of displacement in an intertidal community. We demonstrate how our method helps recover observed coexistence patterns, capture the core dynamics of the system, and, in the latter case, predict the impacts of experimental extinctions. Collectively, these results demonstrate an intuitive approach for reconciling observed and empirical data, improving our ability to explore the links between species interactions and coexistence in natural systems.     

Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria

The microarray approach has been proposed for high throughput analysis of the microbial community by providing snapshots of the microbial diversity under different environmental conditions. For this purpose, a prototype of a 16S rRNA-based taxonomic microarray was developed and evaluated for assessing bacterial community diversity. The prototype microarray is composed of 122 probes that target bacteria at various taxonomic levels from phyla to species (mostly Alphaproteobacteria). The prototype microarray was first validated using bacteria in pure culture. Differences in the sequences of probes and potential target DNAs were quantified as weighted mismatches (WMM) in order to evaluate hybridization reliability. As a general feature, probes having a WMM > 2 with target DNA displayed only 2.8% false positives. The prototype microarray was subsequently tested with an environmental sample, which consisted of an Agrobacterium-related polymerase chain reaction amplicon from a maize rhizosphere bacterial community. Microarray results were compared to results obtained by cloning-sequencing with the same DNA. Microarray analysis enabled the detection of all 16S rRNA gene sequences found by cloning-sequencing. Sequences representing only 1.7% of the clone library were detected. In conclusion, this prototype 16S rRNA-based taxonomic microarray appears to be a promising tool for the analysis of Alphaproteobacteria in complex ecosystems.     

Historic emergence, impact and current status of shrimp pathogens in Asia

It is estimated that approximately 60% of disease losses in shrimp aquaculture have been caused by viral pathogens and 20% by bacterial pathogens. By comparison, losses to fungi and parasites have been relatively small. For bacterial pathogens, Vibrio species are the most important while for viral pathogens importance has changed since 2003 when domesticated and genetically selected stocks of the American whiteleg shrimp Penaeus (Litopenaeus) vannamei (Boone 1931) replaced the formerly dominant giant tiger or black tiger shrimp Penaeus (Penaeus) monodon (Fabricius 1798) as the dominant cultivated species. For both species, white spot syndrome virus (WSSV) and yellow head virus (YHV) are the most lethal. Next most important for P. vannamei is infectious myonecrosis virus (IMNV), originally reported from Brazil, but since 2006 from Indonesia where it was probably introduced by careless importation of shrimp aquaculture stocks. So far, IMNV has not been reported from other countries in Asia. Former impacts of Taura syndrome virus (TSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) on this species have dramatically declined due to the introduction of tolerant stocks and to implementation of good biosecurity practices. Another problem recently reported for P. vannamei in Asia is abdominal segment deformity disease (ASDD), possibly caused by a previously unknown retrovirus-like agent. Next most important after WSSV and YHV for P. monodon is monodon slow growth syndrome (MSGS) for which component causes appear to be Laem Singh virus (LSNV) and a cryptic integrase containing element (ICE). Hepatopancreatic parvovirus (HPV) and monodon baculovirus (MBV) may be problematic when captured P. monodon are used to produce larvae, but only in the absence of proper preventative measures. Since 2009 increasing losses with P. vannamei in China, Vietnam and now Thailand are associated with acute hepatopancreatic necrosis syndrome (AHPNS) of presently unknown cause. Despite these problems, total production of cultivated penaeid shrimp from Asia will probably continue to rise as transient disease problems are solved and use of post larvae originating from domesticated SPF shrimp stocks in more biosecure settings expands.     

Expression, purification, and characterization of a structurally disordered and functional C-terminal autoinhibitory domain (AID) of the 70 kDa 40S ribosomal protein S6 kinase-1 (S6K1)

S6K1 is a member of the AGC subfamily of serine-threonine protein kinases, whereby catalytic activation requires dual phosphorylation of critical residues in the conserved T-loop (T229) and hydrophobic motif (HM; T389) peptide regions of its catalytic kinase domain (residues 1-398). In addition to its kinase domain, S6K1 contains a C-terminal autoinhibitory domain (AID; residues 399-502), which prevents T-loop and HM phosphorylation; and autoinhibition is relieved on multi-site Ser-Thr phosphorylation of the AID (S411, S418, T421, and S424). Interestingly, 66 of the 104 C-terminal AID amino acid residues were computer predicted to exist in structurally disordered peptide regions, begetting interest as to how such dynamics could be coupled to autoregulation. To begin addressing this issue, we developed and optimized protocols for efficient AID expression and purification. Consistent with computer predictions, aberrant mobilities in both SDS-PAGE and size-exclusion chromatography, as well as low chemical shift dispersion in (1)H-(15)N HSQC NMR spectra, indicated purified recombinant AID to be largely unfolded. Yet, trans-addition of purified AID effectively inhibited PDK1-catalyzed T-loop phosphorylation of a catalytic kinase domain construct of S6K1. Using an identical purification protocol, similar protein yields of a tetraphospho-mimic mutant AID(D(2)ED) construct were obtained; and this construct displayed only weak inhibition of PDK1-catalyzed T229 phosphorylation. Purification of the structurally 'disordered' and functional C-terminal AID and AID(D(2)ED) constructs will facilitate studies aimed to understand the role of conformational plasticity and protein phosphorylation in modulating autoregulatory domain-domain interactions.     

Characterization of human aggrecanase 2 (ADAM-TS5): substrate specificity studies and comparison with aggrecanase 1 (ADAM-TS4).

ADAM-TS5 (aggrecanase 2), one of two cartilage aggrecanases is a member of the ADAM protein family. Like ADAM-TS4 (aggrecanase 1) the enzyme cleaves cartilage aggrecan at the Glu(373)-Ala(374) bond, a marker of aggrecanase activity. In this study we have characterized the substrate specificity of ADAM-TS5 and compared it with that of ADAM-TS4. The recombinant human ADAM-TS5, like ADAM-TS4 cleaves aggrecan at Glu(1480)-Gly(1481), Glu(1667)-Gly(1668), Glu(1771)-Ala(1772) and Glu(1871)-Leu(1872) bonds more readily than at the Glu(373)-Ala(374) bond. In addition, ADAM-TS5 exhibited an additional site of cleavage in the region spanning residues Gly(1481) and Glu(1667), representing a unique cleavage of ADAM-TS5. ADAM-TS5 cleaved aggrecan approximately 2-fold slower than ADAM-TS4. Neither ADAM-TS5 nor ADAM-TS4 was able to cleave the extracellular matrix proteins fibronectin, thrombospondin, type I collagen, type II collagen, gelatin or general protein substrates such as casein and transferrin. Finally, the zymogen of stromelysin (MMP-3) was not activated by either ADAM-TS4 or ADAM-TS5.