Fire‐induced tree mortality in a neotropical forest: the roles of bark traits,tree size,wood density and fire behavior

Large‐scale wildfires are expected to accelerate forest dieback in Amazônia, but the fire vulnerability of tree species remains uncertain, in part due to the lack of studies relating fire‐induced mortality to both fire behavior and plant traits. To address this gap, we established two sets of experiments in southern Amazonia. First, we tested which bark traits best predict heat transfer rates (R) through bark during experimental bole heating. Second, using data from a large‐scale fire experiment, we tested the effects of tree wood density (WD), size, and estimated R (inverse of cambium insulation) on tree mortality after one to five fires. In the first experiment, bark thickness explained 82% of the variance in R, while the presence of water in the bark reduced the difference in temperature between the heat source and the vascular cambium, perhaps because of high latent heat of vaporization. This novel finding provides an important insight for improving mechanistic models of fire‐induced cambium damage from tropical to temperate regions. In the second experiment, tree mortality increased with increasing fire intensity (i.e. as indicated by bark char height on tree boles), which was higher along the forest edge, during the 2007 drought, and when the fire return interval was 3 years instead of one. Contrary to other tropical studies, the relationship between mortality and fire intensity was strongest in the year following the fires, but continued for 3 years afterwards. Tree mortality was low (≤20%) for thick‐barked individuals (≥18 mm) subjected to medium‐intensity fires, and significantly decreased as a function of increasing tree diameter, height and wood density. Hence, fire‐induced tree mortality was influenced not only by cambium insulation but also by other traits that reduce the indirect effects of fire. These results can be used to improve assessments of fire vulnerability of tropical forests.     

Map kinase phosphatase 5 protects against sepsis-induced acute lung injury

Mitogen-activated protein kinases (MAPKs) play a critical role in inflammation. Although activation of MAPK in inflammatory cells has been studied extensively, much less is known about the inactivation of these kinases. MAPK phosphatase 5 (MKP5) is a member of the dual-specificity phosphatase family that dephosphorylates activated MAPKs. Here we report that MKP5 protects sepsis-induced acute lung injury. Mice lacking MKP5 displayed severe lung tissue damage following LPS challenge, characterized with increased neutrophil infiltration and edema compared with wild-type (WT) controls. In response to LPS, MKP5-deficient macrophages produced significantly more inflammatory factors including inflammatory cytokines, nitric oxide, and superoxide. Phosphorylation of p38 MAPK, JNK, and ERK were enhanced in MKP5-deficient macrophages upon LPS stimulation. Adoptive transfer of MKP5-deficient macrophages led to more severe lung inflammation than transfer of WT macrophages, suggesting that MKP5-deficient macrophages directly contribute to acute lung injury. Taken together, these results suggest that MKP5 is crucial to homeostatic regulation of MAPK activation in inflammatory responses.     

The effects of interspecific competition and prey odor on foraging behavior in the rock crab, Cancer irroratus (Say)

The effects of competitor pressure and prey odor on foraging behavior of the rock crab, Cancer irroratus (Say), were investigated. The Jonah crab, Cancer borealis (Stimpson), was chosen as the interspecific competitor because it shares resources with C. irroratus. Four treatments were tested for their effect on foraging: the presence or absence of a competitor and two types of prey odor; body odor (living mussel) and tissue extract (dead mussel tissue). The presence of Jonah crabs did not influence location time, search time, prey size selected, or handling time of the rock crabs. However, rock crabs responded differently to the presence of body odor and tissue extract cues. The presence of extract odor decreased the time to locate prey while increasing the number of prey manipulated and prey size selected. When prey body odor was present, rock crabs displayed less investigative behaviors than in the presence of extract odor, illustrated by reduced location time. Extract odor provided a stronger and more attractive cue than body odor, but increased prey manipulation and search time. Extract odor induced increases in manipulation and searching for prey but canceled out the benefits of decreased location time, resulting in crabs from both treatments displaying similar search times. These elevated behaviors may be associated with foraging for injured and cracked prey or may indicate an area of conspecific feeding.     

Patterns of endemism of the eastern North American cave fauna

Aim Over 250 species of obligate terrestrial cave‐dwelling animals (troglobionts) are known from single caves in the eastern United States. We investigate their geographical distribution, especially in relation to other troglobionts. We relate these patterns to taxonomic group, opportunities for dispersal and geographical location. Location Caves of the United States east of the Mississippi River. Methods We associated over 3000 records of more than 450 troglobiotic species and subspecies with hexagons of 1000, 5000 and 10,000 km² in size. We calculated Moran's I, black–white joins and cubic regression of endemics on non‐endemics at all three spatial scales. For 5000 km² hexagons, we modelled the spatial autocorrelation of the residuals of the cubic regression of endemics on non‐endemics. Results Differences among orders in percentage single‐cave endemism were not significant, except for Pseudoscorpionida, which was higher (69%) than any other order. At all three scales, Moran's I and black–white joins were significant, indicating a clumped distribution of both single‐cave endemics and other troglobionts. Spatial patterns were similar at all three scales and Moran's I was highest at 5000 km². The cubic fit of endemics to non‐endemics was consistently better, with less systematic error or residuals, than were linear or quadratic models. Residuals showed a significant geographical pattern with excess endemics in more southerly locations. Main conclusions There was both a non‐spatial and spatial component to the pattern of single‐cave endemism. The non‐spatial component was the association of high levels of single‐cave endemism with areas of high diversity of non‐endemics. It may be that both are high because of high secondary productivity. Spatially, single‐cave endemism is high in central rather than peripheral areas and in the southern part of the range. It is not higher in areas of more dissected limestone, which would reduce migration rates; if anything endemism is lower. Regional spatial effects are important, indicating that cave communities cannot be understood (or protected) in isolation.     

Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains

Background  

Homologous recombination mediated by the λ-Red genes is a common method for making chromosomal modifications in Escherichia coli. Several protocols have been developed that differ in the mechanisms by which DNA, carrying regions homologous to the chromosome, are delivered into the cell. A common technique is to electroporate linear DNA fragments into cells. Alternatively, DNA fragments are generated in vivo by digestion of a donor plasmid with a nuclease that does not cleave the host genome. In both cases the λ-Red gene products recombine homologous regions carried on the linear DNA fragments with the chromosome. We have successfully used both techniques to generate chromosomal mutations in E. coli K-12 strains. However, we have had limited success with these λ-Red based recombination techniques in pathogenic E. coli strains, which has led us to develop an enhanced protocol for recombineering in such strains.     

A Genome-Wide Association Study of Hypertension and Blood Pressure in African Americans

The evidence for the existence of genetic susceptibility variants for the common form of hypertension (“essential hypertension”) remains weak and inconsistent. We sought genetic variants underlying blood pressure (BP) by conducting a genome-wide association study (GWAS) among African Americans, a population group in the United States that is disproportionately affected by hypertension and associated complications, including stroke and kidney diseases. Using a dense panel of over 800,000 SNPs in a discovery sample of 1,017 African Americans from the Washington, D.C., metropolitan region, we identified multiple SNPs reaching genome-wide significance for systolic BP in or near the genes: PMS1, SLC24A4, YWHA7, IPO7, and CACANA1H. Two of these genes, SLC24A4 (a sodium/potassium/calcium exchanger) and CACNA1H (a voltage-dependent calcium channel), are potential candidate genes for BP regulation and the latter is a drug target for a class of calcium channel blockers. No variant reached genome wide significance for association with diastolic BP (top scoring SNP rs1867226, p = 5.8×10⁻⁷) or with hypertension as a binary trait (top scoring SNP rs9791170, p = 5.1×10⁻⁷). We replicated some of the significant SNPs in a sample of West Africans. Pathway analysis revealed that genes harboring top-scoring variants cluster in pathways and networks of biologic relevance to hypertension and BP regulation. This is the first GWAS for hypertension and BP in an African American population. The findings suggests that, in addition to or in lieu of relying solely on replicated variants of moderate-to-large effect reaching genome-wide significance, pathway and network approaches may be useful in identifying and prioritizing candidate genes/loci for further experiments.     

NIK is involved in nucleosomal regulation by enhancing histone H3 phosphorylation by IKKalpha

The exact physiological role of NF-kappaB-inducing kinase (NIK) in the NF-kappaB activation pathway has not been defined, although it is an upstream kinase of IKKalpha. Recent studies have indicated that IKKalpha is a nucleosomal modifier of NF-kappaB signaling. We hypothesized that NIK generates a proximal signal that contributes to IKKalpha modification of nucleosomal structure through phosphorylation of histone H3 and enhancement of target gene expression. By using a chromatin immunoprecipitation assay, our data show that endogenous IKKalpha is recruited to the promoter site of several NF-kappaB-dependent genes in macrophages. Our data show that immunoreactive NIK is rapidly recruited to nuclear compartment in macrophages in response to treatment with endotoxin where it augments phosphorylation of histone H3 by inducing phosphorylation and kinase activity of IKKalpha. A small interfering RNA knockdown of NIK markedly reduces phosphorylation of histone H3 in endotoxin treated macrophages. These data, together, demonstrate a novel role for NIK as a histone H3 modifier, through an accessory pathway from NIK to IKKalpha, that could play an important role in the endotoxin response through modification of nucleosomal structure.     

Abundance, diversity, and activity of ammonia-oxidizing prokaryotes in the coastal Arctic ocean in summer and winter

Ammonia oxidation, the first step in nitrification, is performed by certain Beta- and Gammaproteobacteria and Crenarchaea to generate metabolic energy. Ammonia monooxygenase (amoA) genes from both Bacteria and Crenarchaea have been found in a variety of marine ecosystems, but the relative importance of Bacteria versus Crenarchaea in ammonia oxidation is unresolved, and seasonal comparisons are rare. In this study, we compared the abundance of betaproteobacterial and crenarchaeal amoA genes in the coastal Arctic Ocean during summer and winter over 2 years. Summer and winter betaproteobacterial amoA clone libraries were significantly different, although the gene sequences were similar to those found in temperate and polar environments. Betaproteobacterial and crenarchaeal amoA genes were 30- to 115-fold more abundant during the winter than during the summer in both years of the study. Archaeal amoA genes were more abundant than betaproteobacterial amoA genes in the first year, but betaproteobacterial amoA was more abundant than archaeal amoA the following year. The ratio of archaeal amoA gene copies to marine group I crenarchaeal 16S rRNA genes averaged 2.9 over both seasons and years, suggesting that ammonia oxidation was common in Crenarchaea at this location. Potential nitrification rates, as well as the total amoA gene abundance, were highest in the winter when competition with phytoplankton was minimal and ammonium concentrations were the highest. These results suggest that ammonium concentrations were important in determining the rates of ammonia oxidation and the abundance of ammonia-oxidizing Betaproteobacteria and Crenarchaea.