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BackgroundMitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing. We amplified the mitochondrial genome of 677 specimens in two partially overlapping amplicons and implemented an asymmetric PCR-based indexing approach to multiplex 1,159 long amplicons together on a single PacBio SMRT Sequel II cell. We also tested this method on Oxford Nanopore Technologies (ONT) MinION R9.4 to assess if this method could be applied to other long-read technologies. We implemented several optimizations that make this method significantly more efficient than alternative mitochondrial genome sequencing methods.ResultsWith the PacBio sequencing data we recovered at least one of the two fragments for 96% of samples (~ 80-90%) with mean coverage ~ 1,500x. The ONT data recovered less than 50% of input fragments likely due to low throughput and the design of the Barcoded Universal Primers which were optimized for PacBio sequencing. We compared a single mitochondrial gene alignment to half and full mitochondrial genomes and found, as expected, increased tree support with longer alignments, though whole mitochondrial genomes were not significantly better than half mitochondrial genomes.ConclusionsThis method can effectively capture thousands of long amplicons in a single run and be used to build more robust phylogenies quickly and effectively. We provide several recommendations for future users depending on the evolutionary scale of their system. A natural extension of this method is to collect multi-locus datasets consisting of mitochondrial genomes and several long nuclear loci at once.

The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (547 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.

Arctic soils contain a large pool of terrestrial C and are of interest due to their potential for releasing significant carbon dioxide (CO2) and methane (CH4) to the atmosphere. Due to substantial landscape heterogeneity, predicting ecosystem-scale CH4 and CO2 production is challenging. This study assessed dissolved inorganic carbon (DIC = Σ (total) dissolved CO2) and CH4 in watershed drainages in Barrow, Alaska as critical convergent zones of regional geochemistry, substrates, and nutrients. In July and September of 2013, surface waters and saturated subsurface pore waters were collected from 17 drainages. Based on simultaneous DIC and CH4 cycling, we synthesized isotopic and geochemical methods to develop a subsurface CH4 and DIC balance by estimating mechanisms of CH4 and DIC production and transport pathways and oxidation of subsurface CH4. We observed a shift from acetoclastic (July) toward hydrogenotropic (September) methanogenesis at sites located toward the end of major freshwater drainages, adjacent to salty estuarine waters, suggesting an interesting landscape-scale effect on CH4 production mechanism. The majority of subsurface CH4 was transported upward by plant-mediated transport and ebullition, predominantly bypassing the potential for CH4 oxidation. Thus, surprisingly, CH4 oxidation only consumed approximately 2.51 ± 0.82% (July) and 0.79 ± 0.79% (September) of CH4 produced at the frost table, contributing to

Terrestrial Radiocarbon Database Workshop; Berkeley, California, 20–22 July 2011 Soils play a large role in the global carbon (C) cycle, but soil C stocks and dynamics remain highly uncertain. Radiocarbon (14C) observations provide critical information on the rates of exchange of soil C with the atmosphere and hydrosphere and how those rates vary with edaphic (soil-related) factors and over a range of time scales. For example, the degree to which radio decay has affected 14C demonstrates the importance of short-range-order minerals for stabilizing organic C on millennial time scales in some soils. Time series that track the infiltration of “bomb” 14C help identify the components of soil C that cycle on decadal to centennial time scales.

Objective: To determine the effects of mindfulness training for primary care (MTPC), an integrated warmmindfulness training program, on emotion regulation and its relationship with health behavior change. Interventions that improve self-regulation, particularly emotion regulation, are needed for the self-management of comorbid chronic physical and mental illnesses. Mindfulness-based interventions (MBIs) may impact self-regulation and facilitate health behavior change. Method: A randomized controlled comparative effectiveness trial was conducted in a population of adult primary care patients to evaluate the impact of MTPC versus a low-dose mindfulness comparator (LDC) on self-reported difficulties in emotion regulation (DERS) total score and other assays of self-regulation at baseline, Weeks 8 and 24. Self-reported action plan initiationwas reported betweenWeeks 8 and 10. Participants had diagnoses of anxiety, depression, or stress-related disorders.MTPC is an 8-week insurance-reimbursable warm MBI designed to cultivate mindfulness and self-compassion and to catalyze chronic illness self-management related health behavior change. Results: Compared to LDC, MTPC participants had statistically significant reductions in DERS total score at 8 weeks (d=-0.59, ß=-12.98, 95% CI [-23.3 to -2.6]; p= .01) and 24 weeks (d=-0.61, ß=-13.35, [-24.3, -2.4]; p=.02). Compared to 38% for LDC, 63% of MTPC participants successfully initiated their action plan within 3 weeks (OR=2.87, [1.1, 7.9]; p= .04). Conclusions: This randomized controlled trial demonstrated MTPCenhanced emotion regulation and facilitated initiation of chronic illness self-management and health behavior change among primary care patients with anxiety, depression, and stress-related disorders, replicating previous reports. [ABSTRACT FROM AUTHOR]

Background: A mindfulness‐based intervention that reduces comorbid pain, anxiety, and substance use during office‐based opioid treatment (OBOT) could enhance retention and prevent overdose. We conducted a pilot study of the Mindful Recovery OUD Care Continuum (M‐ROCC), a 24‐week trauma‐informed program with a motivationally‐sensitive curriculum. Methods: Patients prescribed buprenorphine (N = 18) enrolled in M‐ROCC. We collected urine toxicology biweekly. At 0, 4, and 24 weeks, participants completed PROMIS‐Pain, PROMIS‐Anxiety, Mindfulness (FFMQ), Experiential Avoidance (BEAQ), Interoceptive Awareness (MAIA), and Self‐Compassion (SCS‐SF) scales. We estimated changes over time using mixed models. Participants completed qualitative interviews at 4 and 24 weeks. Results: Positive urine toxicology decreased over time for cocaine (β = −.266, p =.008) and benzodiazepines (β = −.208, p =.028). M‐ROCC reduced PROMIS‐Pain (Z = −2.29; p =.022), BEAQ (Z = −2.83; p =.0005), and increased FFMQ (Z = 3.51; p <.001), MAIA (Z = 3.40; p =.001), and SCS‐SF (Z = 2.29; p =.022). Participants with co‐morbid anxiety had decreased PROMIS‐Anxiety (Z = −2.53; p =.012). Interviewed participants commonly used mindfulness practices for stress and anxiety (12/12, 100%), and to reduce pain catastrophizing and rumination (7/12, 58%). Conclusion and Scientific Significance: This is the first study to report the effects of a 24‐week mindfulness program during buprenorphine treatment on common comorbidities, including pain interference, anxiety, cocaine, and benzodiazepine use. The findings that M‐ROCC is associated with reduced experiential avoidance, as well as increased interoceptive awareness and self‐compassion, align with proposed mechanisms that are now extended to OUD treatment. Future larger randomized controlled trials are needed before effectiveness can be established and the role of these mechanisms can be confirmed. [ABSTRACT FROM AUTHOR]