Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that...
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
Organic agriculture requires cultivars that can adapt to organic crop management systems without the use of synthetic
pesticides as well as genotypes with improved nutritional value. The aim of this study encompassing 16 experiments was to
compare 23 broccoli cultivars for the content of phytochemicals associated with health promotion grown...
Background: We present a model for reporting accelerometer paradata (process-related data produced from survey administration) collected in the International Study of Childhood Obesity Lifestyle and the Environment (ISCOLE), a multi-national investigation of >7000 children (averaging 10.5 years of age) sampled from 12 different developed and developing countries and five continents....
Fungal hyphae are among the most highly polarized cells. Hyphal polarized
growth is supported by tip-directed transport of secretory vesicles, which accumulate temporarily
in a stratified manner in an apical vesicle cluster, the Spitzenkörper. The exocyst complex
is required for tethering of secretory vesicles to the apical plasma membrane. We...
Anthropogenic and natural stressors often interact to affect organisms. Amphibian populations are undergoing unprecedented declines and extinctions with pesticides and emerging infectious diseases implicated as causal factors. Although these factors often co-occur, their effects on amphibians are usually examined in isolation. We hypothesized that exposure of larval and metamorphic amphibians...
Histone deacetylase (HDAC) inhibitors are undergoing clinical trials as anticancer agents, but some exhibit resistance mechanisms
linked to anti-apoptotic Bcl-2 functions, such as BH3-only protein silencing. HDAC inhibitors that reactivate BH3-only family
members might offer an improved therapeutic approach. We show here that a novel seleno-α-keto acid triggers global histone...
Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic...
Ligand activation of the aryl hydrocarbon (AHR) has profound effects upon the immunological status of the gastrointestinal tract, establishing and maintaining signaling networks, which facilitate host-microbe homeostasis at the mucosal interface. However, the identity of the ligand(s) responsible for such AHR-mediated activation within the gut remains to be firmly established....
As decomposers, fungi are key players in recycling plant material in global carbon cycles. We hypothesized that genomes of early diverging fungi may have inherited pectinases from an ancestral species that had been able to extract nutrients from pectin-containing land plants and their algal allies (Streptophytes). We aimed to infer,...
We investigated dissolved methane distributions along a 6 km transect crossing active seep sites at 40 m water depth in the central North Sea. These investigations were done under conditions of thermal stratification in summer (July 2013) and homogenous water column in winter (January 2014). Dissolved methane accumulated below the...
Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic...
To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in
mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus
striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive
behavior and retentive oceanographic conditions...
The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly
study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and
polyadenylated mRNA prepared from mycelium grown for 24 hr in the dark and then exposed to light for
0 (control) 15,...
Resolving the debate surrounding the nature and controls of seasonal variation in the structure and metabolism of Amazonian rainforests is critical to understanding their response to climate change. In situ studies have observed higher photosynthetic and evapotranspiration rates, increased litterfall and leaf flushing during the Sunlight-rich dry season. Satellite data...
Ligand activation of the aryl hydrocarbon (AHR) has profound effects upon the immunological status of the gastrointestinal tract, establishing and maintaining signaling networks, which facilitate host-microbe homeostasis at the mucosal interface. However, the identity of the ligand(s) responsible for such AHR-mediated activation within the gut remains to be firmly established....
Seascape ecology is an emerging discipline focused on understanding how features of the marine habitat influence the
spatial distribution of marine species. However, there is still a gap in the development of concepts and techniques for its
application in the marine pelagic realm, where there are no clear boundaries delimitating...
Using published dairy cattle liver transcriptomics dataset along with novel blood biomarkers of liver function, metabolism,
and inflammation we have attempted an integrative systems biology approach applying the classical functional enrichment
analysis using DAVID, a newly-developed Dynamic Impact Approach (DIA), and an upstream gene network analysis using
Ingenuity Pathway Analysis...
We investigated DNA methylomes of pediatric B-cell
acute lymphoblastic leukemias (B-ALLs) using
whole-genome bisulfite sequencing and high-definition
microarrays, along with RNA expression
profiles. Epigenetic alteration of B-ALLs occurred in
two tracks: de novo methylation of small functional
compartments and demethylation of large intercompartmental
backbones. The deviations were exaggerated
in lamina-associated...
Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species’ threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that...
Fungal hyphae are among the most highly polarized cells. Hyphal polarized
growth is supported by tip-directed transport of secretory vesicles, which accumulate temporarily
in a stratified manner in an apical vesicle cluster, the Spitzenkörper. The exocyst complex
is required for tethering of secretory vesicles to the apical plasma membrane. We...
Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure...
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily...
Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure...
BACKGROUND: After 2 decades of focused efforts to eradicate polio, the impact of eradication activities on health
systems continues to be controversial. This study evaluated the impact of polio eradication activities on routine immunization
(RI) and primary healthcare (PHC).
METHODS: Quantitative analysis assessed the effects of polio eradication campaigns on...
A feedback between decomposition and litter chemical composition occurs with decomposition altering composition that in turn influences the decomposition rate. Elucidating the temporal pattern of chemical composition is vital to understand this feedback, but the effects of plant species and climate on chemical changes remain poorly understood, especially over multiple...
Circadian clocks coordinate physiological, neurological, and behavioral functions into circa 24 hour rhythms, and the
molecular mechanisms underlying circadian clock oscillations are conserved from Drosophila to humans. Clock oscillations
and clock-controlled rhythms are known to dampen during aging; additionally, genetic or environmental clock disruption
leads to accelerated aging and increased...
Sodium-ion batteries are emerging as a highly promising technology for large-scale energy
storage applications. However, it remains a significant challenge to develop an anode with
superior long-term cycling stability and high-rate capability. Here we demonstrate that the
Na⁺ intercalation pseudocapacitance in TiO₂/graphene nanocomposites enables high-rate
capability and long cycle life...
Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure...
The 1994 Northwest Forest Plan (NWFP) shifted federal lands management from a focus on timber production to ecosystem management and biodiversity conservation. The plan established a network of conservation reserves and an ecosystem management strategy on ~10 million hectares from northern California to Washington State, USA, within the range of...
We investigated dissolved methane distributions along a 6 km transect crossing active seep sites at 40 m water depth in the central North Sea. These investigations were done under conditions of thermal stratification in summer (July 2013) and homogenous water column in winter (January 2014). Dissolved methane accumulated below the...
Circadian clocks coordinate physiological, neurological, and behavioral functions into circa 24 hour rhythms, and the
molecular mechanisms underlying circadian clock oscillations are conserved from Drosophila to humans. Clock oscillations
and clock-controlled rhythms are known to dampen during aging; additionally, genetic or environmental clock disruption
leads to accelerated aging and increased...
Widespread habitat degradation and uncharacteristic fire, insect, and disease outbreaks in forests across
the western United States have led to highly publicized calls to increase the pace and scale of forest restoration.
Despite these calls, we frequently lack a comprehensive understanding of forest restoration
needs. In this study we demonstrate...
A new functional gene database, FOAM (Functional
Ontology Assignments for Metagenomes), was developed
to screen environmental metagenomic sequence
datasets. FOAM provides a new functional
ontology dedicated to classify gene functions relevant
to environmental microorganisms based on Hidden
Markov Models (HMMs). Sets of aligned protein
sequences (i.e. ‘profiles’) were tailored to...
Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic...
We present high-resolution measurements of carbon
monoxide (CO) concentrations from a shallow ice core
of the North Greenland Eemian Ice Drilling project (NEEM-
2011-S1). An optical-feedback cavity-enhanced absorption
spectrometer (OF-CEAS) coupled to a continuous melter
system performed continuous, online analysis during a fourweek
measurement campaign. This analytical setup generated
stable...
Background: Like other transformative healthcare initiatives, patient-centered medical home (PCMH) implementation requires substantial investments of time and resources. Even though PCMH and PCMH-like models are being implemented by multiple provider practices and health systems, little is known about what facilitates their implementation. The purpose of this study was to assess...
The farnesoid X receptor (FXR) regulates bile acid, lipid and glucose metabolism. Here we show that treatment of mice with glycine-β-muricholic acid (Gly-MCA) inhibits FXR signalling exclusively in intestine, and improves metabolic parameters in mouse models of obesity. Gly-MCA is a selective high-affinity FXR inhibitor that can be administered orally...
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may
disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and
non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst
tethering complex, we...
Resazurin (Raz) and its reaction product resorufin
(Rru) have increasingly been used as reactive tracers to quantify
metabolic activity and hyporheic exchange in streams.
Previous work has indicated that these compounds undergo
sorption in stream sediments. We present laboratory experiments
on Raz and Rru transport, sorption, and transformation,
consisting of...
Large amount of organic carbon is stored in high latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and...
Background:
Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic...
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily...
The ongoing retreat of glaciers globally is one of the clearest manifestations of recent global warming associated with rising greenhouse gas concentrations. By comparison, the importance of greenhouse gases in driving glacier retreat during the most recent deglaciation, the last major interval of global warming, is unclear due to uncertainties...
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have
made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase
genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest...
The peptidyl nucleoside blasticidin S (BS) isolated from Streptomyces griseochromogenes was the first non-mercurial fungicide used on a large scale to prevent rice blast. In the biosynthesis of BS, leucylblasticidin S (LBS) was suggested as the penultimate metabolite with 20-fold less inhibitory activity than the final product BS. Incomplete conversion...
Resazurin (Raz) and its reaction product resorufin
(Rru) have increasingly been used as reactive tracers to quantify
metabolic activity and hyporheic exchange in streams.
Previous work has indicated that these compounds undergo
sorption in stream sediments. We present laboratory experiments
on Raz and Rru transport, sorption, and transformation,
consisting of...
Iron (Fe) and copper (Cu) are essential cofactors for microbial metalloenzymes, but little is known about the metalloenyzme inventory of anaerobic marine microbial communities despite their importance to the nitrogen cycle. We compared dissolved O₂ , NO₃⁻, NO₂⁻, Fe and Cu concentrations with nucleic acid sequences encoding Fe and Cu-binding...
A large amount of organic carbon is stored in high-latitude soils. A substantial proportion of this carbon stock is vulnerable and may decompose rapidly due to temperature increases that are already greater than the global average. It is therefore crucial to quantify and understand carbon exchange between the atmosphere and...
Using published dairy cattle liver transcriptomics dataset along with novel blood biomarkers of liver function, metabolism,
and inflammation we have attempted an integrative systems biology approach applying the classical functional enrichment
analysis using DAVID, a newly-developed Dynamic Impact Approach (DIA), and an upstream gene network analysis using
Ingenuity Pathway Analysis...