An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material

Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo-environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo-investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub-optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non-ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best-practice ship-board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.Caitlin A. Selway, Linda Armbrecht, and David Thornalle

Behavioral mechanisms that mediate mental and physical health improvements in people with chronic pain who receive a digital health intervention: Prospective cohort pilot study

BACKGROUND: Preliminary evidence suggests that digital mental health intervention (Wysa for Chronic Pain) can improve mental and physical health in people with chronic musculoskeletal pain and coexisting symptoms of depression or anxiety. However, the behavioral mechanisms through which this intervention acts are not fully understood. OBJECTIVE: The purpose of this study was to identify behavioral mechanisms that may mediate changes in mental and physical health associated with use of Wysa for Chronic Pain during orthopedic management of chronic musculoskeletal pain. We hypothesized that improved behavioral activation, pain acceptance, and sleep quality mediate improvements in self-reported mental and physical health. METHODS: In this prospective cohort, pilot mediation analysis, adults with chronic (≥3 months) neck or back pain received the Wysa for Chronic Pain digital intervention, which uses a conversational agent and text-based access to human counselors to deliver cognitive behavioral therapy and related therapeutic content. Patient-reported outcomes and proposed mediators were collected at baseline and 1 month. The exposure of interest was participants\u27 engagement (ie, total interactions) with the digital intervention. Proposed mediators were assessed using the Behavioral Activation for Depression Scale-Short Form, Chronic Pain Acceptance Questionnaire, and Athens Insomnia Scale. Outcomes included Patient-Reported Outcomes Measurement Information System Anxiety, Depression, Pain Interference, and Physical Function scores. A mediation analysis was conducted using the Baron and Kenny method, adjusting for age, sex, and baseline mediators and outcome values. P\u3c.20 was considered significant for this pilot study. RESULTS: Among 30 patients (mean age 59, SD 14, years; 21 [70%] female), the mediation effect of behavioral activation on the relationship between increased intervention engagement and improved anxiety symptoms met predefined statistical significance thresholds (indirect effect -0.4, 80% CI -0.7 to -0.1; P=.13, 45% of the total effect). The direction of mediation effect was generally consistent with our hypothesis for all other proposed mediator or outcome relationships, as well. CONCLUSIONS: In a full-sized randomized controlled trial of patients with chronic musculoskeletal pain, behavioral activation, pain acceptance, and sleep quality may play an important role in mediating the relationship between use of a digital mental health intervention (Wysa for Chronic Pain) and improved mental and physical health. TRIAL REGISTRATION: ClinicalTrials.gov NCT05194722; https://clinicaltrials.gov/ct2/show/NCT05194722

Multi-stakeholder perspectives regarding preferred modalities for mental health intervention delivered in the orthopedic clinic: A qualitative analysis

BACKGROUND: Although depressive and anxious symptoms negatively impact musculoskeletal health and orthopedic outcomes, a gap remains in identifying modalities through which mental health intervention can realistically be delivered during orthopedic care. The purpose of this study was to understand orthopedic stakeholders\u27 perceptions regarding the feasibility, acceptability, and usability of digital, printed, and in-person intervention modalities to address mental health as part of orthopedic care. METHODS: This single-center, qualitative study was conducted within a tertiary care orthopedic department. Semi-structured interviews were conducted between January and May 2022. Two stakeholder groups were interviewed using a purposive sampling approach until thematic saturation was reached. The first group included adult orthopedic patients who presented for management of ≥ 3 months of neck or back pain. The second group included early, mid, and late career orthopedic clinicians and support staff members. Stakeholders\u27 interview responses were analyzed using deductive and inductive coding approaches followed by thematic analysis. Patients also performed usability testing of one digital and one printed mental health intervention. RESULTS: Patients included 30 adults out of 85 approached (mean (SD) age 59 [14] years, 21 (70%) women, 12 (40%) non-White). Clinical team stakeholders included 22 orthopedic clinicians and support staff members out of 25 approached (11 (50%) women, 6 (27%) non-White). Clinical team members perceived a digital mental health intervention to be feasible and scalable to implement, and many patients appreciated that the digital modality offered privacy, immediate access to resources, and the ability to engage during non-business hours. However, stakeholders also expressed that a printed mental health resource is still necessary to meet the needs of patients who prefer and/or can only engage with tangible, rather than digital, mental health resources. Many clinical team members expressed skepticism regarding the current feasibility of scalably incorporating in-person support from a mental health specialist into orthopedic care. CONCLUSIONS: Although digital intervention offers implementation-related advantages over printed and in-person mental health interventions, a subset of often underserved patients will not currently be reached using exclusively digital intervention. Future research should work to identify combinations of effective mental health interventions that provide equitable access for orthopedic patients. TRIAL REGISTRATION: Not applicable

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales

Latitudinal Variance in the Drivers and Pacing of Warmth During Mid-Pleistocene MIS 31 in the Antarctic Zone of the Southern Ocean

Early Pleistocene Marine Isotope Stage (MIS)-31 (1.081–1.062 Ma) is a unique interval of extreme global warming, including evidence of a West Antarctic Ice Sheet (WAIS) collapse. Here we present a new 1,000-year resolution, spanning 1.110–1.030 Ma, diatom-based reconstruction of primary productivity, relative sea surface temperature changes, sea-ice proximity/open ocean conditions and diatom species absolute abundances during MIS-31, from the Scotia Sea (59°S) using deep-sea sediments collected during International Ocean Discovery Program (IODP) Expedition 382. The lower Jaramillo magnetic reversal (base of C1r.1n, 1.071 Ma) provides a robust and independent time-stratigraphic marker to correlate records from other drill cores in the Antarctic Zone of the Southern Ocean (AZSO). An increase in open ocean species Fragilariopsis kerguelensis in early MIS-31 at 53°S (Ocean Drilling Program Site 1,094) correlates with increased obliquity forcing, whereas at 59°S (IODP Site U1537; this study) three progressively increasing, successive peaks in the relative abundance of F. kerguelensis correlate with Southern Hemisphere-phased precession pacing. These observations reveal a complex pattern of ocean temperature change and sustained sea surface temperature increase lasting longer than a precession cycle within the Atlantic sector of the AZSO. Timing of an inferred WAIS collapse is consistent with delayed warmth (possibly driven by sea-ice dynamics) in the southern AZSO, supporting models that indicate WAIS sensitivity to local sub-ice shelf melting. Anthropogenically enhanced impingement of relatively warm water beneath the ice shelves today highlights the importance of understanding dynamic responses of the WAIS during MIS-31, a warmer than Holocene interglacial.Postprin

The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems

AbstractWhether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem

Episodes of Early Pleistocene West Antarctic Ice Sheet Retreat Recorded by Iceberg Alley Sediments

Ice loss in the Southern Hemisphere has been greatest over the past 30 years in West Antarctica. The high sensitivity of this region to climate change has motivated geologists to examine marine sedimentary records for evidence of past episodes of West Antarctic Ice Sheet (WAIS) instability. Sediments accumulating in the Scotia Sea are useful to examine for this purpose because they receive iceberg-rafted debris (IBRD) sourced from the Pacific- and Atlantic-facing sectors of West Antarctica. Here we report on the sedimentology and provenance of the oldest of three cm-scale coarse-grained layers recovered from this sea at International Ocean Discovery Program Site U1538. These layers are preserved in opal-rich sediments deposited ∼1.2 Ma during a relatively warm regional climate. Our microCT-based analysis of the layer's in-situ fabric confirms its ice-rafted origin. We further infer that it is the product of an intense but short-lived episode of IBRD deposition. Based on the petrography of its sand fraction and the Phanerozoic 40Ar/39Ar ages of hornblende and mica it contains, we conclude that the IBRD it contains was likely sourced from the Weddell Sea and/or Amundsen Sea embayment(s) of West Antarctica. We attribute the high concentrations of IBRD in these layers to “dirty” icebergs calved from the WAIS following its retreat inland from its modern grounding line. These layers also sit at the top of a ∼366-m thick Pliocene and early Pleistocene sequence that is much more dropstone-rich than its overlying sediments. We speculate this fact may reflect that WAIS mass-balance was highly dynamic during the ∼41-kyr (inter)glacial world.Postprin

Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics

Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data