The reproductive biology of the soft shell clam Mya arenaria in Ireland and the possible impacts of climate variability

Little is known about the biology of the softshell clam in Europe, despite it being identified as a potential species to culture for food in the future. Monthly samples of the softshell clam, Mya arenaria, were collected intertidally from Co. Wexford, Ireland, over a period of sixteen months. The mean weight of sampled individuals was 7 4 ± 4 . 9  g and mean length was 8 . 2 ± 0 . 2  cm. Histological examination revealed a female-to-male ratio of 1 : 1.15. In 2010, M. arenaria at this site matured over the summer months, with both sexes either ripe or spawning by August. A single spawning event was recorded in 2010, completed by November. Two unusually cold winters, followed by a warmer-than-average spring, appear to have affected M. arenaria gametogenesis in this area, potentially affecting the time of spawning, fertilisation success, and recruitment of this species. No hermaphrodites were observed in the samples collected, nor were any pathogens observed. Timing of development and spawning is compared with the coasts of eastern North America and with other European coasts.

Redox biology of myeloid leukaemias

Internal tandem duplication of FMS-like receptor tyrosine kinase (FLT3-ITD) has been associated with an aggressive AML phenotype. FLT3-ITD expressing cell lines have been shown to generate increased levels of reactive oxygen species (ROS) and DNA double strand breaks (dsbs). However, the molecular basis of how FLT3-ITD-driven ROS leads to the aggressive form of AML is not clearly understood. Herein, we observe that the majority of H2O2 in FLT3-ITD-expressing MV4-11 cells colocalises to the endoplasmic reticulum (ER). Furthermore, ER localisation of ROS in MV4-11 cells corresponds to the localisation of p22phox, a small membrane-bound subunit of NOX complex. Furthermore, we show that 32D cells, a myeloblast-like cell line transfected with FLT3-ITD, possess higher steady protein levels of p22phox than their wild type FLT3 (FLT3-WT)-expressing counterparts. Moreover, the inhibition of FLT3-ITD, using various FLT3 tyrosine kinase inhibitors, uniformly results in a posttranslational downregulation of p22phox. We also show that depletion of NOX2 and NOX4 and p22phox, but not NOX1 proteins causes a reduction in endogenous H2O2 levels. We show that genomic instability induced by FLT3-ITD leads to an increase in nuclear levels of H2O2. The presence of H2O2 in the nucleus is largely reduced by inhibition of FLT3-ITD or NOX. Furthermore, similar results are also observed following siRNA knockdowns of p22phox or NOX4. We demonstrate that 32D cells transfected with FLT3-ITD have a higher level of DNA damage than 32D cells transfected with FLT3-WT. Additionally, inhibition of FLT3-ITD, p22phox and NOX knockdowns decrease the number of DNA dsbs. In summary, this study presents a novel mechanism of genomic instability generation in FLT3-ITD-expressing AML cells, whereby FLT3-ITD activates NOX complexes by stabilising p22phox. This in turn leads to elevated generation of ROS and DNA damage in these cells.

Organic nitrogen in PM2.5 aerosol at a forest site in the Southeast US

There is growing evidence that organo-nitrogen compounds may constitute a significant fraction of the aerosol nitrogen (N) budget. However, very little is known about the abundance and origin of this aerosol fraction. In this study, the concentration of organic nitrogen (ON) and major inorganic ions in PM2.5 aerosol were measured at the Duke Forest Research Facility near Chapel Hill, NC, during January and June of 2007. A novel on-line instrument was used, which is based on the Steam Jet Aerosol Collector (SJAC) coupled to an on-line total carbon/total nitrogen analyzer and two on-line ion chromatographs. The concentration of ON was determined by tracking the difference in concentrations of total nitrogen and of inorganic nitrogen (determined as the sum of N-ammonium and N-nitrate). The time resolution of the instrument was 30 min with a detection limit for major aerosol components of ∼0.1 mu;gm-3. Nitrogen in organic compounds contributed ∼33% on average to the total nitrogen concentration in PM2.5, illustrating the importance of this aerosol component. Absolute concentrations of ON, however, were relatively low (lt;1.0 mu;gm-3) with an average of 0.16 mu;gm-3. The absolute and relative contribution of ON to the total aerosol nitrogen budget was practically the same in January and June. In January, the concentration of ON tended to be higher during the night and early morning, while in June it tended to be higher during the late afternoon and evening. Back-trajectories and correlation with wind direction indicate that higher concentrations of ON occur in air masses originating over the continental US, while marine air masses are characterized by lower ON concentrations. The data presented in this study suggests that ON has a variety of sources, which are very difficult to quantify without information on chemical composition of this important aerosol fraction.

Global fire emissions and the contribution of deforestation, savanna, forest, agricultural, and peat fires (1997-2009)

New burned area datasets and top-down constraints from atmospheric concentration measurements of pyrogenic gases have decreased the large uncertainty in fire emissions estimates. However, significant gaps remain in our understanding of the contribution of deforestation, savanna, forest, agricultural waste, and peat fires to total global fire emissions. Here we used a revised version of the Carnegie-Ames-Stanford-Approach (CASA) biogeochemical model and improved satellite-derived estimates of area burned, fire activity, and plant productivity to calculate fire emissions for the 1997-2009 period on a 0.5° spatial resolution with a monthly time step. For November 2000 onwards, estimates were based on burned area, active fire detections, and plant productivity from the MODerate resolution Imaging Spectroradiometer (MODIS) sensor. For the partitioning we focused on the MODIS era. We used maps of burned area derived from the Tropical Rainfall Measuring Mission (TRMM) Visible and Infrared Scanner (VIRS) and Along-Track Scanning Radiometer (ATSR) active fire data prior to MODIS (1997-2000) and estimates of plant productivity derived from Advanced Very High Resolution Radiometer (AVHRR) observations during the same period. Average global fire carbon emissions according to this version 3 of the Global Fire Emissions Database (GFED3) were 2.0 PgC year-1 with significant interannual variability during 1997-2001 (2.8 Pg Cyear-1 in 1998 and 1.6 PgC year-1 in 2001). Globally, emissions during 2002-2007 were rela-tively constant (around 2.1 Pg C year-1) before declining in 2008 (1.7 Pg Cyear-1) and 2009 (1.5 PgC year-1) partly due to lower deforestation fire emissions in South America and tropical Asia. On a regional basis, emissions were highly variable during 2002-2007 (e.g., boreal Asia, South America, and Indonesia), but these regional differences canceled out at a global level. During the MODIS era (2001-2009), most carbon emissions were from fires in grasslands and savannas (44%) with smaller contributions from tropical deforestation and degradation fires (20%), woodland fires (mostly confined to the tropics, 16%), forest fires (mostly in the extratropics, 15%), agricultural waste burning (3%), and tropical peat fires (3%). The contribution from agricultural waste fires was likely a lower bound because our approach for measuring burned area could not detect all of these relatively small fires. Total carbon emissions were on average 13% lower than in our previous (GFED2) work. For reduced trace gases such as CO and CH4, deforestation, degradation, and peat fires were more important contributors because of higher emissions of reduced trace gases per unit carbon combusted compared to savanna fires. Carbon emissions from tropical deforestation, degradation, and peatland fires were on average 0.5 PgC year-1. The carbon emissions from these fires may not be balanced by regrowth following fire. Our results provide the first global assessment of the contribution of different sources to total global fire emissions for the past decade, and supply the community with an improved 13-year fire emissions time series. © 2010 Author(s).

Morphometrics and testicle size of rain forest lemur species from southeastern Madagascar

Six species of prosimians inhabiting the montane rain forest of the Ranomafana National Park located in southeastern Madagascar were captured, weighed, and measured during the months of May or June of 1987, 1988, and 1989. There were no significant differences in body weights and measurements between male and femaleEulemur rubriventer (red-bellied lemur) orEulemur fulvus rufus (red-fronted lemur). Adult femalePropithecus diadema edwardsi (Milne Edward's sifaka) were heavier than males but the difference was not significant. A fewAvahi laniger laniger (woolly lemur),Hapalemur aureus (golden bamboo lemur) andH. g. griseus (gentle bamboo lemur) also were captured and measured. Body weights of the same individual adultP. d. edwardsi changed over the three years, suggesting variation in food availability. Although there was no difference in body weight among adult males of two groups ofP. d. edwardsi, one male in each group had a testicular volume four times larger than that of other males, even though these measurements were taken five months after the breeding season. These data suggest that only one adult male mates in each group. Testicular size of the polygynousE. f. rufus males was significantly larger than that of the monogamousE. rubriventer. © 1992 Academic Press Limited.

Seeing the forest for the fuel

We demonstrate a new approach to understanding the role of fuelwood in the rural household economy by applying insights from travel cost modeling to author-compiled household survey data and meso-scale environmental statistics from Ruteng Park in Flores, Indonesia. We characterize Manggarai farming households' fuelwood collection trips as inputs into household production of the utility yielding service of cooking and heating. The number of trips taken by households depends on the shadow price of fuelwood collection or the travel cost, which is endogenous. Econometric analyses using truncated negative binomial regression models and correcting for endogeneity show that the Manggarai are 'economically rational' about fuelwood collection and access to the forests for fuelwood makes substantial contributions to household welfare. Increasing cost of forest access, wealth, use of alternative fuels, ownership of kerosene stoves, trees on farm, park staff activity, primary schools and roads, and overall development could all reduce dependence on collecting fuelwood from forests. © 2004 Cambridge University Press.

Four-decade responses of soil trace elements to an aggrading old-field forest: B, Mn, Zn, Cu, and Fe.

In the ancient and acidic Ultisol soils of the Southern Piedmont, USA, we studied changes in trace element biogeochemistry over four decades, a period during which formerly cultivated cotton fields were planted with pine seedlings that grew into mature forest stands. In 16 permanent plots, we estimated 40-year accumulations of trace elements in forest biomass and O horizons (between 1957 and 1997), and changes in bioavailable soil fractions indexed by extractions of 0.05 mol/L HCl and 0.2 mol/L acid ammonium oxalate (AAO). Element accumulations in 40-year tree biomass plus O horizons totaled 0.9, 2.9, 4.8, 49.6, and 501.3 kg/ha for Cu, B, Zn, Mn, and Fe, respectively. In response to this forest development, samples of the upper 0.6-m of mineral soil archived in 1962 and 1997 followed one of three patterns. (1) Extractable B and Mn were significantly depleted, by -4.1 and -57.7 kg/ha with AAO, depletions comparable to accumulations in biomass plus O horizons, 2.9 and 49.6 kg/ha, respectively. Tree uptake of B and Mn from mineral soil greatly outpaced resupplies from atmospheric deposition, mineral weathering, and deep-root uptake. (2) Extractable Zn and Cu changed little during forest growth, indicating that nutrient resupplies kept pace with accumulations by the aggrading forest. (3) Oxalate-extractable Fe increased substantially during forest growth, by 275.8 kg/ha, about 10-fold more than accumulations in tree biomass (28.7 kg/ha). The large increases in AAO-extractable Fe in surficial 0.35-m mineral soils were accompanied by substantial accretions of Fe in the forest's O horizon, by 473 kg/ha, amounts that dwarfed inputs via litterfall and canopy throughfall, indicating that forest Fe cycling is qualitatively different from that of other macro- and micronutrients. Bioturbation of surficial forest soil layers cannot account for these fractions and transformations of Fe, and we hypothesize that the secondary forest's large inputs of organic additions over four decades has fundamentally altered soil Fe oxides, potentially altering the bioavailability and retention of macro- and micronutrients, contaminants, and organic matter itself. The wide range of responses among the ecosystem's trace elements illustrates the great dynamics of the soil system over time scales of decades.

The Justice Gap in Global Forest Governance

Claims of injustice in global forest governance are prolific: assertions of colonization, marginalization and disenfranchisement of forest-dependent people, and privatization of common resources are some of the most severe allegations of injustice resulting from globally-driven forest conservation initiatives. At its core, the debate over the future of the world's forests is fraught with ethical concerns. Policy makers are not only deciding how forests should be governed, but also who will be winners, losers, and who should have a voice in the decision-making processes. For 30 years, policy makers have sought to redress the concerns of the world's 1.6 billion forest-dependent poor by introducing rights-based and participatory approaches to conservation. Despite these efforts, however, claims of injustice persist. This research examines possible explanations for continued claims of injustice by asking: What are the barriers to delivering justice to forest-dependent communities? Using data collected through surveys, interviews, and collaborative event ethnography in Laos and at the Tenth Conference of Parties to the Convention on Biological Diversity, this dissertation examines the pursuit of justice in global forest governance across multiple scales of governance. The findings reveal that particular conceptualizations of justice have become a central part of the metanormative fabric of global environmental governance, inhibiting institutional evolution and therewith perpetuating the justice gap in global forest governance.

The Effects of Geography, Environment and Phylogeny on Community Assembly and Gene Flow Dynamics

It is increasingly evident that evolutionary processes play a role in how ecological communities are assembled. However the extend to which evolution influences how plants respond to spatial and environmental gradients and interact with each other is less clear. In this dissertation I leverage evolutionary tools and thinking to understand how space and environment affect community composition and patterns of gene flow in a unique system of Atlantic rainforest and restinga (sandy coastal plains) habitats in Southeastern Brazil.

In chapter one I investigate how space and environment affect the population genetic structure and gene flow of Aechmea nudicaulis, a bromeliad species that co-occurs in forest and restinga habitats. I genotyped seven microsatellite loci and sequenced one chloroplast DNA region for individuals collected in 7 pairs of forest / restinga sites. Bayesian genetic clustering analyses show that populations of A. nudicaulis are geographically structured in northern and southern populations, a pattern consistent with broader scale phylogeographic dynamics of the Atlantic rainforest. On the other hand, explicit migration models based on the coalescent estimate that inter-habitat gene flow is less common than gene flow between populations in the same habitat type, despite their geographic discontinuity. I conclude that there is evidence for repeated colonization of the restingas from forest populations even though the steep environmental gradient between habitats is a stronger barrier to gene flow than geographic distance.

In chapter two I use data on 2800 individual plants finely mapped in a restinga plot and on first-year survival of 500 seedlings to understand the roles of phylogeny, functional traits and abiotic conditions in the spatial structuring of that community. I demonstrate that phylogeny is a poor predictor of functional traits in and that convergence in these traits is pervasive. In general, the community is not phylogenetically structured, with at best 14% of the plots deviating significantly from the null model. The functional traits SLA, leaf dry matter content (LDMC), and maximum height also showed no clear pattern of spatial structuring. On the other hand, leaf area is strongly overdispersed across all spatial scales. Although leaf area overdispersion would be generally taken as evidence of competition, I argue that interpretation is probably misleading. Finally, I show that seedling survival is dramatically increased when they grow shaded by an adult individual, suggesting that seedlings are being facilitated. Phylogenetic distance to their adult neighbor has no influence on rates of survival though. Taken together, these results indicate that phylogeny has very limited influence on the fine scale assembly of restinga communities.

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Climate change and forest sinks: Factors affecting the costs of carbon sequestration

The possibility of encouraging the growth of forests as a means of sequestering carbon dioxide has received considerable attention, partly because of evidence that this can be a relatively inexpensive means of combating climate change. But how sensitive are such estimates to specific conditions? We examine the sensitivity of carbon sequestration costs to changes in critical factors, including the nature of management and deforestation regimes, silvicultural species, relative prices, and discount rates. (C) 2000 Academic Press.

Conversion of natural forests to managed forest plantations decreases tree resistance to prolonged droughts

© 2015 Published by Elsevier B.V.Throughout the southern US, past forest management practices have replaced large areas of native forests with loblolly pine plantations and have resulted in changes in forest response to extreme weather conditions. However, uncertainty remains about the response of planted versus natural species to drought across the geographical range of these forests. Taking advantage of a cluster of unmanaged stands (85-130year-old hardwoods) and managed plantations (17-20year-old loblolly pine) in coastal and Piedmont areas of North Carolina, tree water use, cavitation resistance, whole-tree hydraulic (Ktree) and stomatal (Gs) conductances were measured in four sites covering representative forests growing in the region. We also used a hydraulic model to predict the resilience of those sites to extreme soil drying. Our objectives were to determine: (1) if Ktree and stomatal regulation in response to atmospheric and soil droughts differ between species and sites; (2) how ecosystem type, through tree water use, resistance to cavitation and rooting profiles, affects the water uptake limit that can be reached under drought; and (3) the influence of stand species composition on critical transpiration that sets a functional water uptake limit under drought conditions. The results show that across sites, water stress affected the coordination between Ktree and Gs. As soil water content dropped below 20% relative extractable water, Ktree declined faster and thus explained the decrease in Gs and in its sensitivity to vapor pressure deficit. Compared to branches, the capability of roots to resist high xylem tension has a great impact on tree-level water use and ultimately had important implications for pine plantations resistance to future summer droughts. Model simulations revealed that the decline in Ktree due to xylem cavitation aggravated the effects of soil drying on tree transpiration. The critical transpiration rate (Ecrit), which corresponds to the maximum rate at which transpiration begins to level off to prevent irreversible hydraulic failure, was higher in managed forest plantations than in their unmanaged counterparts. However, even with this higher Ecrit, the pine plantations operated very close to their critical leaf water potentials (i.e. to their permissible water potentials without total hydraulic failure), suggesting that intensively managed plantations are more drought-sensitive and can withstand less severe drought than natural forests.

Clinical Insights Into the Biology and Treatment of Pancreatic Cancer.

Pancreatic cancer is a devastating disease with a universally poor prognosis. In 2015, it is estimated that there will be 48,960 new cases of pancreatic cancer and that 40,560 people will die of the disease. The 5-year survival rate is 7.2% for all patients with pancreatic cancer; however, survival depends greatly on the stage at diagnosis. Unfortunately, 53% of patients already have metastatic disease at diagnosis, which corresponds to a 5-year survival rate of 2.4%. Even for the 9% of patients with localized disease confined to the pancreas, the 5-year survival is still modest at only 27.1%. These grim statistics highlight the need for ways to identify cohorts of individuals at highest risk, methods to screen those at highest risk to identify preinvasive pathologic precursors, and development of effective systemic therapies. Recent clinical and translational progress has emphasized the relationship with diabetes, the role of the stroma, and the interplay of each of these with inflammation in the pathobiology of pancreatic cancer. In this article, we will discuss these relationships and how they might translate into novel management strategies for the treatment of this disease.

Biological parameters and glomalin levels as quality indicators in a soil implanted with exotic forest species in Argentine Patagonia

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The forage supply service in the Chaco native forest : an approach to economic analysis

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