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Methane production by phosphate-starved SAR11 chemoheterotrophic marine bacteria
The oxygenated surface waters of the world’s oceans are supersaturated with methane relative to the atmosphere, a phenomenon termed the ‘marine methane paradox’. The production of methylphosphonic acid (MPn) by marine archaea related to
Nitrosopumilus maritimus
and subsequent decomposition of MPn by phosphate-starved bacterioplankton may partially explain the excess methane in surface waters. Here we show that
Pelagibacterales sp.
strain HTCC7211, an isolate of the SAR11 clade of marine α-proteobacteria, produces methane from MPn, stoichiometric to phosphorus consumption, when starved for phosphate. Gene transcripts encoding phosphonate transport and hydrolysis proteins are upregulated under phosphate limitation, suggesting a genetic basis for the methanogenic phenotype. Strain HTCC7211 can also use 2-aminoethylphosphonate and assorted phosphate esters for phosphorus nutrition. Despite strain-specific differences in phosphorus utilization, these findings identify
Pelagibacterales
bacteria as a source of biogenic methane and further implicate phosphate starvation of chemoheterotrophic bacteria in the long-observed methane supersaturation in oxygenated waters.
Methane levels in the oceans’ surface waters are higher than those in the atmosphere, which is puzzling. Here the authors show that marine bacteria of the ubiquitous SAR11 group can release significant amounts of methane when feeding on phosphorus-containing compounds such as methylphosphonic acid.
Journal Article
Cultivating Trust in the Face of Crisis: Science as Moderator in Collaborative Forest Management
Conflict over resources and often-ensuing political gridlock present a profound threat to local communities and to the broader sustainability of ecologies within which they are embedded. The American west has experienced drastic shifts in its approach to forests since the timber industry and environmental movement’s protracted clash dubbed the ‘timber wars.’ In the shadow of conflict and in the face of increasingly devastating fire seasons, collaborative forest management (CFM) offers an arduous but viable path forward. This paper examines a successful case of CFM in Oregon, USA—a partnership of once-feuding enemies that has navigated ecological and political crisis. The case study draws on data collected through rapid-ethnography and in-depth interviews with partnership members and other stakeholders. The study unpacks the science-led governance model and collaborative culture that has resulted in the restoration of thousands of acres of forest, advanced scientific understanding, and supported job growth in rural communities. The paper argues the importance of meso-level governance systems that build civic and scientific capacity to address shifting conditions, and crises, into the future.
Journal Article
Do mindfulness interventions cause harm? Findings from the Learning to Apply Mindfulness to Pain (LAMP) Pragmatic Clinical Trial
Background
Although mindfulness-based interventions (MBIs) are widely used in clinical and nonclinical settings, there has been little systematic study of their potential risks. To address this gap, we examined differences in psychological and physical worsening among participants in the usual care and intervention conditions of a 3-group, randomized pragmatic trial (Learning to Apply Mindfulness to Pain [LAMP]) that tested the effectiveness of 2 approaches to delivering MBIs to patients with chronic pain.
Methods
The sample consisted of 374 male and 334 female patients with chronic pain enrolled in the LAMP trial who completed a 10-week follow-up survey, 61% of whom had a mental health diagnosis. Psychological and physical worsening was assessed by a checklist asking whether participants experienced specific symptoms since beginning the study. We used multivariable logistic regression models with imputed data to determine whether predicted probabilities of increased symptoms differed between usual care and the 2 MBIs.
Results
Participants in usual care were more likely to report experiencing increased psychological and physical worsening than were those in the MBIs, including an increase in disturbing memories; sadness, anxiousness, and fatigue; isolation and loneliness; and feeling more upset than usual when something reminded them of the past.
Conclusions
MBIs do not appear to cause harm, in terms of increased symptoms, for this population of patients with chronic pain and high levels of mental health comorbidities.
Clinical trial registration
Preregistration with an analysis plan at www.ClinicalTrials.gov: NCT04526158. Patient enrollment began December 4, 2020.
Journal Article
An all-atom model of the human cardiac sodium channel in a lipid bilayer
Voltage-gated sodium channels (Na
V
) are complex macromolecular proteins that are responsible for the initial upstroke of an action potential in excitable cells. Appropriate function is necessary for many physiological processes such as heartbeat, voluntary muscle contraction, nerve conduction, and neurological function. Dysfunction can have life-threatening consequences. During the past decade, there have been significant advancements with ion channel structural characterization by CryoEM, yet descriptions of cytosolic components are often lacking. Many investigations have biophysically characterized reconstituted cytosolic components and their interactions. However, extrapolating the structural alterations and allosteric communication within an intact ion channel can be challenging. To address this, we have developed an all-atom model of the human cardiac sodium channel (Na
V
1.5) in a lipid bilayer with explicit salt and water. Our simulations contain descriptions of cytosolic components that are poorly predicted by AlphaFold and lacking in many CryoEM structures. Leveraging the latest advancements of the Amber force fields (ff19sb and Lipid21) and water model (OPC), our simulations improved protein backbone torsion angles and generated structural information across time (four independent one-microsecond simulations). Our analysis provided descriptions of lipid and solvent contacts and insight into the C-Terminal Domain - inactivation gate and inactivation gate - latch receptor interactions.
Journal Article
Potential C-terminal domain interactions of the cardiac voltage gated sodium channel
CryoEM structural characterization of the cardiac sodium channel (Na
V
1.5) captured the cytosolic C-terminal domain (CTD) interacting with the cytosolic loop that connects domains III and IV (inactivation gate). Our previous modeling efforts focused on improving descriptions of the cytosolic components and unexpectedly captured dissociation of this complex. Other reports have provided evidence of CTD interaction with a different cytosolic Na
V
1.5 component. Specifically, NMR spectroscopy demonstrated that a reconstituted CTD (93 amino acids construct, helices I–IV) could engage a peptide corresponding to an IQ motif (helix VI) that is also contained on the C-terminus of the Na
V
1.5 channel. Here, we leverage recent MD simulation advancements to expand upon this work and investigate the potential of the CTD–IQ motif interaction within the context of a full-length sodium channel imbedded within a lipid bilayer. Four independent one microsecond simulations (with explicit lipids, salts, and water) depicted a stable CTD–IQ motif complex for the duration of each simulation. An additional four independent one microsecond simulations of the CTD molecule dissociated from both the inactivation gate and IQ motif failed to capture an association event, suggesting the existence of at least three CTD energetic minima within the context of the full-length alpha subunit.
Journal Article
SAR11 lipid renovation in response to phosphate starvation
Significance Nonphosphorus lipids produced by heterotrophic bacteria have been measured in marine ecosystems without an understanding of their origins or role. This work shows SAR11 chemoheterotrophic bacteria synthesize multiple nonphosphorus lipids in response to phosphate depletion. Because this process results in a reduced cellular P:C ratio, it impacts our understanding of ocean processes related to cellular elemental stoichiometry by showing how different environmental parameters alter P:C ratios in heterotrophs. Also, SAR11 grown with excess organophosphonate synthesized phosphorus-free lipids. This finding contrasts the contemporary view of organophosphorus utilization because organophosphate-derived phosphorus did not equally substitute for inorganic phosphate in lipids. Considering lipid phosphorus content was lower in cells using organophosphonate, phosphorus-based productivity estimates may vary as a function of phosphorus source.
Phytoplankton inhabiting oligotrophic ocean gyres actively reduce their phosphorus demand by replacing polar membrane phospholipids with those lacking phosphorus. Although the synthesis of nonphosphorus lipids is well documented in some heterotrophic bacterial lineages, phosphorus-free lipid synthesis in oligotrophic marine chemoheterotrophs has not been directly demonstrated, implying they are disadvantaged in phosphate-deplete ecosystems, relative to phytoplankton. Here, we show the SAR11 clade chemoheterotroph Pelagibacter sp. str. HTCC7211 renovates membrane lipids when phosphate starved by replacing a portion of its phospholipids with monoglucosyl- and glucuronosyl-diacylglycerols and by synthesizing new ornithine lipids. Lipid profiles of cells grown with excess phosphate consisted entirely of phospholipids. Conversely, up to 40% of the total lipids were converted to nonphosphorus lipids when cells were starved for phosphate, or when growing on methylphosphonate. Cells sequentially limited by phosphate and methylphosphonate transformed >75% of their lipids to phosphorus-free analogs. During phosphate starvation, a four-gene cluster was significantly up-regulated that likely encodes the enzymes responsible for lipid renovation. These genes were found in Pelagibacterales strains isolated from a phosphate-deficient ocean gyre, but not in other strains from coastal environments, suggesting alternate lipid synthesis is a specific adaptation to phosphate scarcity. Similar gene clusters are found in the genomes of other marine α-proteobacteria, implying lipid renovation is a common strategy used by heterotrophic cells to reduce their requirement for phosphorus in oligotrophic habitats.
Journal Article
the war on drugs turns 50
A discussion of major developments since the war on drugs launched in 1971 including mass incarceration, the overdose crisis, and the Mexican drug war. Challenges are described and solutions considered.
Journal Article