Greenhouse gas emissions from laboratory-scale fires in wildland fuels depend on fire spread mode and phase of combustion

© Author(s) 2015. Free-burning experimental fires were conducted in a wind tunnel to explore the role of ignition type and thus fire spread mode on the resulting emissions profile from combustion of fine (2, CH4 and N2O) and CO were quantified using off-axis integrated-cavity-output spectroscopy. Emissions factors calculated using a carbon mass balance technique (along with statistical testing) showed that most of the carbon was emitted as CO2, with heading fires emitting 17% more CO2 than flanking and 9.5% more CO2 than backing fires, and about twice as much CO as flanking and backing fires. Heading fires had less than half as much carbon remaining in combustion residues. Statistically significant differences in CH4 and N2O emissions factors were not found with respect to fire spread mode. Emissions factors calculated per unit of dry fuel consumed showed that combustion phase (i.e. flaming or smouldering) had a statistically significant impact, with CO and N2O emissions increasing during smouldering combustion and CO2 emissions decreasing. Findings on the equivalence of different emissions factor reporting methods are discussed along with the impact of our results for emissions accounting and potential sampling biases associated with our work. The primary implication of this study is that prescribed fire practices could be modified to mitigate greenhouse gas emissions from forests by judicial use of ignition methods to induce flanking and backing fires over heading fires

Incorrect interpretation of carbon mass balance biases global vegetation fire emission estimates

© 2016, Nature Publishing Group. All rights reserved. Vegetation fires are a complex phenomenon in the Earth system with many global impacts, including influences on global climate. Estimating carbon emissions from vegetation fires relies on a carbon mass balance technique that has evolved with two different interpretations. Databases of global vegetation fire emissions use an approach based on 'consumed biomass', which is an approximation to the biogeochemically correct 'burnt carbon' approach. Here we show that applying the 'consumed biomass' approach to global emissions from vegetation fires leads to annual overestimates of carbon emitted to the atmosphere by 4.0% or 100 Tg compared with the 'burnt carbon' approach. The required correction is significant and represents ∼9% of the net global forest carbon sink estimated annually. Vegetation fire emission studies should use the 'burnt carbon' approach to quantify and understand the role of this burnt carbon, which is not emitted to the atmosphere, as a sink enriched in carbon

Comparison of nekton utilization of smooth cordgrass (Spartina alterniflora) marsh based on marsh size and degree of isolation from like habitat : do size and site location matter?

Influence of salt marsh size and proximity to like habitat on nekton use was examined. Comparisons were made among six naturally occurring isolated island marshes, three each of small (~400-1,000 m ) and large 2 (~3,000-10,000 m2) island size classes and six paired mainland marshes (at least 76,000 m2 in size). Two species representing opposites for dispersal ability and life history strategies, mummichog (Fundulus heteroclitus) and pinfish (Lagodon rhomboides), were used as representative species to examine population patterns. Fundulus heteroclitus exclusively utilized marsh habitats and not adjacent shallow flats during high tide while L. rhomboides utilized both. At high tide island marshes acted as a refuge for F. heteroclitus among shallow water flat habitats. Densities of marsh dependent species, including F. heteroclitus, were an order of magnitude lower within the large island compared to the mainland marshes, and nonexistent within small island marshes. Similarities among mainland and large island marshes for larvae and disparity in juvenile F. heteroclitus abundances suggested a bottleneck constrained adult and juvenile F. heteroclitus populations at large island marshes. Differential predation rates among marsh types significantly contributed to disparities in young of year abundance. Patterns of abundance suggest two crucial time periods for F. heteroclitus population maintenance, one during late spring/early summer spawn-recruitment and the second during the dispersal/emigration during the late fall/winter time period when water temperatures are colder and predator levels are significantly reduced. In contrast, L. rhomboides recruitment and dispersal occurs simultaneously during the late fall/winter when low predator levels create an optimal time for recruitment to estuaries

Master regulators of FGFR2 signalling and breast cancer risk.

The fibroblast growth factor receptor 2 (FGFR2) locus has been consistently identified as a breast cancer risk locus in independent genome-wide association studies. However, the molecular mechanisms underlying FGFR2-mediated risk are still unknown. Using model systems we show that FGFR2-regulated genes are preferentially linked to breast cancer risk loci in expression quantitative trait loci analysis, supporting the concept that risk genes cluster in pathways. Using a network derived from 2,000 transcriptional profiles we identify SPDEF, ERα, FOXA1, GATA3 and PTTG1 as master regulators of fibroblast growth factor receptor 2 signalling, and show that ERα occupancy responds to fibroblast growth factor receptor 2 signalling. Our results indicate that ERα, FOXA1 and GATA3 contribute to the regulation of breast cancer susceptibility genes, which is consistent with the effects of anti-oestrogen treatment in breast cancer prevention, and suggest that fibroblast growth factor receptor 2 signalling has an important role in mediating breast cancer risk.This is the final version of the article. It was originally published in Nature Communications here: http://www.nature.com/ncomms/2013/130917/ncomms3464/full/ncomms3464.html

A synthesis of the effects of cheatgrass invasion on the US Great Basin carbon storage

Non‐native, invasive Bromus tectorum (cheatgrass) is pervasive in sagebrush ecosystems in the Great Basin ecoregion of the western United States, competing with native plants and promoting more frequent fires. As a result, cheatgrass invasion likely alters carbon (C) storage in the region. Many studies have measured C pools in one or more common vegetation types: native sagebrush, invaded sagebrush and cheatgrass‐dominated (often burned) sites, but these results have yet to be synthesized. We performed a literature review to identify studies assessing the consequences of invasion on C storage in above‐ground biomass (AGB), below‐ground biomass (BGB), litter, organic soil and total soil. We identified 41 articles containing 386 unique studies and estimated C storage across pools and vegetation types. We used linear mixed models to identify the main predictors of C storage. We found consistent declines in biomass C with invasion: AGB C was 55% lower in cheatgrass (40 ± 4 g C/m2) than native sagebrush (89 ± 27 g C/m2) and BGB C was 62% lower in cheatgrass (90 ± 17 g C/m2) than native sagebrush (238 ± 60 g C/m2). In contrast, litter C was \u3e4× higher in cheatgrass (154 ± 12 g C/m2) than native sagebrush (32 ± 12 g C/m2). Soil organic C (SOC) in the top 10 cm was significantly higher in cheatgrass than in native or invaded sagebrush. SOC below 20 cm was significantly related to the time since most recent fire and losses were observed in deep SOC in cheatgrass \u3e5 years after a fire. There were no significant changes in total soil C across vegetation types. Synthesis and applications. Cheatgrass invasion decreases biodiversity and rangeland productivity and alters fire regimes. Our findings indicate cheatgrass invasion also results in persistent biomass carbon (C) losses that occur with sagebrush replacement. We estimate that conversion from native sagebrush to cheatgrass leads to a net reduction of C storage in biomass and litter of 76 g C/m2, or 16 Tg C across the Great Basin without management practices like native sagebrush restoration or cheatgrass removal

Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247(T), BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6%) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S-23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, gin/I, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EKO5(T) (=LMG 24129(T)) to. be the most closely related type strain (95.7% sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C-16:0 and summed feature 8 (18:1 omega 6c/18:1 omega 7c)] DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium. Results of DNA-DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nil/-I) placed the novel species in a new branch within the genus Bradyrhizobium. Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247(T) (=HAMBI 3599(T))

Ostriches Sleep like Platypuses

Mammals and birds engage in two distinct states of sleep, slow wave sleep (SWS) and rapid eye movement (REM) sleep. SWS is characterized by slow, high amplitude brain waves, while REM sleep is characterized by fast, low amplitude waves, known as activation, occurring with rapid eye movements and reduced muscle tone. However, monotremes (platypuses and echidnas), the most basal (or ‘ancient’) group of living mammals, show only a single sleep state that combines elements of SWS and REM sleep, suggesting that these states became temporally segregated in the common ancestor to marsupial and eutherian mammals. Whether sleep in basal birds resembles that of monotremes or other mammals and birds is unknown. Here, we provide the first description of brain activity during sleep in ostriches (Struthio camelus), a member of the most basal group of living birds. We found that the brain activity of sleeping ostriches is unique. Episodes of REM sleep were delineated by rapid eye movements, reduced muscle tone, and head movements, similar to those observed in other birds and mammals engaged in REM sleep; however, during REM sleep in ostriches, forebrain activity would flip between REM sleep-like activation and SWS-like slow waves, the latter reminiscent of sleep in the platypus. Moreover, the amount of REM sleep in ostriches is greater than in any other bird, just as in platypuses, which have more REM sleep than other mammals. These findings reveal a recurring sequence of steps in the evolution of sleep in which SWS and REM sleep arose from a single heterogeneous state that became temporally segregated into two distinct states. This common trajectory suggests that forebrain activation during REM sleep is an evolutionarily new feature, presumably involved in performing new sleep functions not found in more basal animals

Lessons Learned Developing a Diagnostic Tool for HIV-Associated Dementia Feasible to Implement in Resource-Limited Settings: Pilot Testing in Kenya

Objective: To conduct a preliminary evaluation of the utility and reliability of a diagnostic tool for HIV-associated dementia (HAD) for use by primary health care workers (HCW) which would be feasible to implement in resource-limited settings. Background: In resource-limited settings, HAD is an indication for anti-retroviral therapy regardless of CD4 T-cell count. Anti-retroviral therapy, the treatment for HAD, is now increasingly available in resource-limited settings. Nonetheless, HAD remains under-diagnosed likely because of limited clinical expertise and availability of diagnostic tests. Thus, a simple diagnostic tool which is practical to implement in resource-limited settings is an urgent need. Methods: A convenience sample of 30 HIV-infected outpatients was enrolled in Western Kenya. We assessed the sensitivity and specificity of a diagnostic tool for HAD as administered by a primary HCW. This was compared to an expert clinical assessment which included examination by a physician, neuropsychological testing, and in selected cases, brain imaging. Agreement between HCW and an expert examiner on certain tool components was measured using Kappa statistic. Results: The sample was 57 % male, mean age was 38.6 years, mean CD4 T-cell count was 323 cells/mL, and 54 % had less than a secondary school education. Six (20%) of the subjects were diagnosed with HAD by expert clinical assessment. The diagnostic tool was 63 % sensitive and 67 % specific for HAD. Agreement between HCW and expert examiners was poor for many individual items of the diagnostic tool (K =.03–.65). This diagnostic tool had moderate sensitivity and specificity fo

IKZF1 Deletions with COBL Breakpoints Are Not Driven by RAG-Mediated Recombination Events in Acute Lymphoblastic Leukemia

IKZF1 deletion (ΔIKZF1) is an important predictor of relapse in both childhood and adult B-cell precursor acute lymphoblastic leukemia (B-ALL). Previously, we revealed that COBL is a hotspot for breakpoints in leukemia and could promote IKZF1 deletions. Through an international collaboration, we provide a detailed genetic and clinical picture of B-ALL with COBL rearrangements (COBL-r). Patients with B-ALL and IKZF1 deletion (n = 133) were included. IKZF1 ∆1-8 were associated with large alterations within chromosome 7: monosomy 7 (18%), isochromosome 7q (10%), 7p loss (19%), and interstitial deletions (53%). The latter included COBL-r, which were found in 12% of the IKZF1 ∆1-8 cohort. Patients with COBL-r are mostly classified as intermediate cytogenetic risk and frequently harbor ETV6, PAX5, CDKN2A/B deletions. Overall, 56% of breakpoints were located within COBL intron 5. Cryptic recombination signal sequence motifs were broadly distributed within the sequence of COBL, and no enrichment for the breakpoint cluster region was found. In summary, a diverse spectrum of alterations characterizes ΔIKZF1 and they also include deletion breakpoints within COBL. We confirmed that COBL is a hotspot associated with ΔIKZF1, but these rearrangements are not driven by RAG-mediated recombination

A mechanism for the inhibition of DNA-PK-mediated DNA sensing by a virus

The innate immune system is critical in the response to infection by pathogens and it is activated by pattern recognition receptors (PRRs) binding to pathogen associated molecular patterns (PAMPs). During viral infection, the direct recognition of the viral nucleic acids, such as the genomes of DNA viruses, is very important for activation of innate immunity. Recently, DNA-dependent protein kinase (DNA-PK), a heterotrimeric complex consisting of the Ku70/Ku80 heterodimer and the catalytic subunit DNA-PKcs was identified as a cytoplasmic PRR for DNA that is important for the innate immune response to intracellular DNA and DNA virus infection. Here we show that vaccinia virus (VACV) has evolved to inhibit this function of DNA-PK by expression of a highly conserved protein called C16, which was known to contribute to virulence but by an unknown mechanism. Data presented show that C16 binds directly to the Ku heterodimer and thereby inhibits the innate immune response to DNA in fibroblasts, characterised by the decreased production of cytokines and chemokines. Mechanistically, C16 acts by blocking DNA-PK binding to DNA, which correlates with reduced DNA-PK-dependent DNA sensing. The C-terminal region of C16 is sufficient for binding Ku and this activity is conserved in the variola virus (VARV) orthologue of C16. In contrast, deletion of 5 amino acids in this domain is enough to knockout this function from the attenuated vaccine strain modified vaccinia virus Ankara (MVA). In vivo a VACV mutant lacking C16 induced higher levels of cytokines and chemokines early after infection compared to control viruses, confirming the role of this virulence factor in attenuating the innate immune response. Overall this study describes the inhibition of DNA-PK-dependent DNA sensing by a poxvirus protein, adding to the evidence that DNA-PK is a critical component of innate immunity to DNA viruses