ICAM-1 and CD11b inhibition worsen outcome in rats with E. coli pneumonia.

We investigated whether inhibiting an endothelial adhesion molecule [intracellular adhesion molecule 1 (ICAM-1)] would alter outcome and lung injury in a similar fashion to inhibition of a leukocyte adhesion molecule (integrin CD11b) in a rat model of gram-negative pneumonia. Inhibition of ICAM-1 with monoclonal antibody (MAb) 1A29 (1 mg/kg sc or 0.2 or 2 mg/kg iv, q 12 h x 3) or of CD11b with MAb 1B6 (1 mg/kg sc, q 12 h x 3) were compared against similarly administered placebo proteins in rats challenged with intrabronchial Escherichia coli. After challenge, all animals were treated with antibiotics. ICAM-1 MAb (6 mg/kg, iv, total dose) increased mortality vs. control (P = 0.03). CD11b MAb (3 mg/kg, sc, total dose) did not significantly (P = 0.16) increase mortality rates, but this was not in a range of probability to exclude a harmful effect. All other doses of MAb had no significant effect on survival rates. ICAM-1 and CD11b MAbs had significantly different effects on the time course of lung injury, circulating white cells and lymphocytes, and lung lavage white cells and neutrophils (P = 0.04-0.003). CD11b MAb decreased, whereas ICAM-1 MAb increased these measures compared with control from 6 to 12 h after E. coli. However, from 144 to 168 h after E. coli both MAbs increased these measures compared with control rats but to a greater level with CD11b MAb. Thus both ICAM-1 and CD11b appear to be necessary for survival during E. coli pneumonia. Although these adhesion molecules may participate differently in early lung injury, with CD11b increasing and ICAM-1 decreasing inflammation and injury, both are important for the resolution of later injury. During gram-negative pneumonia the protective roles of ICAM-1 and CD11b may make their therapeutic inhibition difficult.     

A defect in beta-oxidation causes abnormal inflorescence development in Arabidopsis.

The abnormal inflorescence meristem1 (aim1) mutation affects inflorescence and floral development in Arabidopsis. After the transition to reproductive growth, the aim1 inflorescence meristem becomes disorganized, producing abnormal floral meristems and resulting in plants with severely reduced fertility. The derived amino acid sequence of AIM1 shows extensive similarity to the cucumber multifunctional protein involved in beta-oxidation of fatty acids, which possesses l-3-hydroxyacyl-CoA hydrolyase, l-3-hydroxyacyl-dehydrogenase, d-3-hydroxyacyl-CoA epimerase, and Delta(3), Delta(2)-enoyl-CoA isomerase activities. A defect in beta-oxidation has been confirmed by demonstrating the resistance of the aim1 mutant to 2,4-diphenoxybutyric acid, which is converted to the herbicide 2,4-D by the beta-oxidation pathway. In addition, the loss of AIM1 alters the fatty acid composition of the mature adult plant.     

Persistence of historical population structure in an endangered species despite near‐complete biome conversion in California's San Joaquin Desert

Genomic responses to habitat conversion can be rapid, providing wildlife managers with time‐limited opportunities to enact recovery efforts that use population connectivity information that reflects predisturbance landscapes. Despite near‐complete biome conversion, such opportunities may still exist for the endemic fauna and flora of California's San Joaquin Desert, but comprehensive genetic data sets are lacking for nearly all species in the region. To fill this knowledge gap, we studied the rangewide population structure of the endangered blunt‐nosed leopard lizard Gambelia sila, a San Joaquin Desert endemic, using restriction site‐associated DNA (RAD), microsatellite and mtDNA data to test whether admixture patterns and estimates of effective migration surfaces (EEMS) can identify land areas with high population connectivity prior to the conversion of native xeric habitats. Clustering and phylogenetic analyses indicate a recent shared history between numerous isolated populations and EEMS reveals latent signals of corridors and barriers to gene flow over areas now replaced by agriculture and urbanization. Conflicting histories between the mtDNA and nuclear genomes are consistent with hybridization with the sister species G. wislizenii, raising important questions about where legal protection should end at the southern range limit of G. sila. Comparative analysis of different data sets also adds to a growing list of advantages in using RAD loci for genetic studies of rare species. We demonstrate how the results of this work can serve as an evolutionary guidance tool for managing endemic, arid‐adapted taxa in one of the world's most compromised landscapes.     

Terrigenous sediment-dominated reef platform infilling: an unexpected precursor to reef island formation and a test of the reef platform size–island age model in the Pacific

Low-lying coral reef islands are considered highly vulnerable to climate change, necessitating an improved understanding of when and why they form, and how the timing of formation varies within and among regions. Several testable models have been proposed that explain inter-regional variability as a function of sea-level history and, more recently, a reef platform size model has been proposed from the Maldives (central Indian Ocean) to explain intra-regional (intra-atoll) variability. Here we present chronostratigraphic data from Pipon Island, northern Great Barrier Reef (GBR), enabling us to test the applicability of existing regional island evolution models, and the platform size control hypothesis in a Pacific context. We show that reef platform infilling occurred rapidly (~4–5 mm yr⁻¹) under a “bucket-fill” type scenario. Unusually, this infilling was dominated by terrigenous sedimentation, with platform filling and subsequent reef flat formation complete by ~5000 calibrated years BP (cal BP). Reef flat exposure as sea levels slowly fell post highstand facilitated a shift towards intertidal and subaerial-dominated sedimentation. Our data suggest, however, a lag of ~1500 yr before island initiation (at ~3200 cal BP), i.e. later than that reported from smaller and more evolutionarily mature reef platforms in the region. Our data thus support: (1) the hypothesis that platform size acts to influence the timing of platform filling and subsequent island development at intra-regional scales; and (2) the hypothesis that the low wooded islands of the northern GBR conform to a model of island formation above an elevated reef flat under falling sea levels.

     

An analytical pipeline for genomic representations used for cytosine methylation studies

Motivation: Representations of the genome can be generated bythe selection of a subpopulation of restriction fragments usingligation-mediated PCR. Such representations form the basis fora number of high-throughput assays, including the HELP assayto study cytosine methylation. We find that HELP data analysisis complicated not only by PCR amplification heterogeneity butalso by a complex and variable distribution of cytosine methylation.To address this, we created an analytical pipeline and novelnormalization approach that improves concordance between microarray-deriveddata and single locus validation results, demonstrating thevalue of the analytical approach. A major influence on the PCRamplification is the size of the restriction fragment, requiringa quantile normalization approach that reduces the influenceof fragment length on signal intensity. Here we describe allof the components of the pipeline, which can also be appliedto data derived from other assays based on genomic representations. Contact: jgreally{at}aecom.yu.edu Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Joaquin Dopazo     

Competition between Lolium perenne and Digitaria sanguinalis: Ecological consequences for harbouring an endosymbiotic fungus

Abstract. This study examined the influence of the fungal endophyte Neotyphodium lolii on the competitive interactions between its perennial, cool season host, Lolium perenne (perennial ryegrass), and a warm season, annual grass, Digitaria sanguinalis (large crabgrass), in densely planted stands (>1000 plant.m^?2) in the glasshouse. Endophyte infection had little or no effect on L. perenne tiller production, above‐ or below‐ground biomass or root: shoot ratio in monoculture. However, endophyte infection significantly reduced L. perenne tiller production and above‐ground biomass in mixtures with D. sanguinalis. Conversely, D. sanguinalis had significantly higher above‐ground biomass and yielded more seed (g) when competing with endophyte infected L. perenne. An apparent trade‐off between allocation of resources to reproductive vs root tissues was observed in D. sanguinalis– root: shoot ratio was significantly lower when competing with endophyte infected L. perenne. Results indicate negative ecological consequences for harbouring the fungal endophyte when competing with the fast growing annual grass in newly established stands. These findings underscore the existence of a physiological cost of harbouring the fungal endophyte which is often overlooked.