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Kinetoplastid parasites are responsible for both human and animal diseases across the globe where they have a great impact on health and economic well-being. Many species and life cycle stages are difficult to study due to limitations in isolation and culture, as well as to their existence as heterogeneous populations in hosts and vectors. Single-cell transcriptomics (scRNA-seq) has the capacity to overcome many of these difficulties, and can be leveraged to disentangle heterogeneous populations, highlight genes crucial for propagation through the life cycle, and enable detailed analysis of host–parasite interactions. Here, we provide a review of studies that have applied scRNA-seq to protozoan parasites so far. In addition, we provide an overview of sample preparation and technology choice considerations when planning scRNA-seq experiments, as well as challenges faced when analysing the large amounts of data generated. Finally, we highlight areas of kinetoplastid research that could benefit from scRNA-seq technologies.
The origin and stability of ground ice in the stable uplands of the McMurdo Dry Valleys remains poorly understood, with most studies focusing on the near-surface permafrost. The 2016 Friis Hills Drilling Project retrieved five cores reaching 50 m depth in mid-Miocene permafrost, a period when Antarctica transitioned to a hyper-arid environment. This study characterizes the cryostratigraphy of arguably the oldest permafrost on Earth and assesses 15 Myr of ground ice evolution using the REGO model. Four cryostratigraphic units were identified: 1) surficial dry permafrost (0–30 cm), 2) ice-rich to ice-poor permafrost (0.3–5.0 m) with high solute load and δ18O values (-16.2 ± 1.8‰) and low D-excess values (-65.6 ± 4.3‰), 3) near-dry permafrost (5–20 m) and 4) ice-poor to ice-rich permafrost (20–50 m) containing ice lenses with low solute load and δ18O values (-34.6 ± 1.2‰) and D-excess of 6.9 ± 2.6‰. The near-surface δ18O profile of ground ice is comparable to other sites in the stable uplands, suggesting that this ice is actively responding to changing surface environmental conditions and challenging the assumption that the surface has remained frozen for 13.8 Myr. The deep ice lenses probably originate from the freezing of meteoric water during the mid-Miocene, and their δ18O composition suggests mean annual air temperatures ~7–11°C warmer than today.
Cover crops are increasingly being used for weed management, and planting them as diverse mixtures has become an increasingly popular strategy for their implementation. While ecological theory suggests that cover crop mixtures should be more weed suppressive than cover crop monocultures, few experiments have explicitly tested this for more than a single temporal niche. We assessed the effects of cover crop mixtures (5- or 6-species and 14-species mixtures) and monocultures on weed abundance (weed biomass) and weed suppression at the time of cover crop termination. Separate experiments were conducted in Madbury, NH, from 2014 to 2017 for each of three temporal cover-cropping niches: summer (spring planting–summer termination), fall (summer planting–fall termination), and spring (fall planting–subsequent spring termination). Regardless of temporal niche, mixtures were never more weed suppressive than the most weed-suppressive cover crop grown as a monoculture, and the more diverse mixture (14 species) never outperformed the less diverse mixture. Mean weed-suppression levels of the best-performing monocultures in each temporal niche ranged from 97% to 98% for buckwheat (Fagopyrum esculentum Moench) in the summer niche and forage radish (Raphanus sativus L. var. niger J. Kern.) in the fall niche, and 83% to 100% for triticale (×Triticosecale Wittm. ex A. Camus [Secale × Triticum]) in the winter–spring niche. In comparison, weed-suppression levels for the mixtures ranged from 66% to 97%, 70% to 90%, and 67% to 99% in the summer, fall, and spring niches, respectively. Stability of weed suppression, measured as the coefficient of variation, was two to six times greater in the best-performing monoculture compared with the most stable mixture, depending on the temporal niche. Results of this study suggest that when weed suppression is the sole objective, farmers are more likely to achieve better results planting the most weed-suppressive cover crop as a monoculture than a mixture.
High-residue cover crops can facilitate organic no-till vegetable production when cover crop biomass production is sufficient to suppress weeds (>8000 kg ha−1), and cash crop growth is not limited by soil temperature, nutrient availability, or cover crop regrowth. In cool climates, however, both cover crop biomass production and soil temperature can be limiting for organic no-till. In addition, successful termination of cover crops can be a challenge, particularly when cover crops are grown as mixtures. We tested whether reusable plastic tarps, an increasingly popular tool for small-scale vegetable farmers, could be used to augment organic no-till cover crop termination and weed suppression. We no-till transplanted cabbage into a winter rye (Secale cereale L.)-hairy vetch (Vicia villosa Roth) cover crop mulch that was terminated with either a roller-crimper alone or a roller-crimper plus black or clear tarps. Tarps were applied for durations of 2, 4 and 5 weeks. Across tarp durations, black tarps increased the mean cabbage head weight by 58% compared with the no tarp treatment. This was likely due to a combination of improved weed suppression and nutrient availability. Although soil nutrients and biological activity were not directly measured, remaining cover crop mulch in the black tarp treatments was reduced by more than 1100 kg ha−1 when tarps were removed compared with clear and no tarp treatments. We interpret this as an indirect measurement of biological activity perhaps accelerated by lower daily soil temperature fluctuations and more constant volumetric water content under black tarps. The edges of both tarp types were held down, rather than buried, but moisture losses from the clear tarps were greater and this may have affected the efficacy of clear tarps. Plastic tarps effectively killed the vetch cover crop, whereas it readily regrew in the crimped but uncovered plots. However, emergence of large and smooth crabgrass (Digitaria spp.) appeared to be enhanced in the clear tarp treatment. Although this experiment was limited to a single site-year in New Hampshire, it shows that use of black tarps can overcome some of the obstacles to implementing cover crop-based no-till vegetable productions in northern climates.
Method of levels (MOL) is an innovative transdiagnostic cognitive therapy with potential advantages over existing psychological treatments for psychosis.
The Next Level study is a feasibility randomised controlled trial (RCT) of MOL for people experiencing first-episode psychosis. It aims to determine the suitability of MOL for further testing in a definitive trial (trial registration ISRCTN13359355).
The study uses a parallel group non-masked feasibilityRCT design with two conditions: (a) treatment as usual (TAU) and (b) TAU plus MOL. Participants (n = 36) were recruited from early intervention in psychosis services. Outcome measures are completed at baseline, 10 and 14 months. The primary outcomes are recruitment and retention.
Participants’ demographic and clinical characteristics are presented along with baseline data.
Next Level has recruited to target, providing evidence that it is feasible to recruit to a RCT of MOL for first-episode psychosis.
The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seedbanks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seedbank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seedbanks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific U.S. Department of Agriculture plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zones will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers.
Background: The value of clients’ reports of their experiences in therapy is widely recognized, yet quantitative methodology has rarely been used to measure clients’ self-reported perceptions of what is helpful over a single session. Aims: A video-rating method using was developed to gather data at brief intervals using process measures of client perceived experience and standardized measures of working alliance (Session Rating Scale; SRS). Data were collected over the course of a single video-recorded session of cognitive therapy (Method of Levels Therapy; Carey, 2006; Mansell et al., 2012). We examined the acceptability and feasibility of the methodology and tested the concurrent validity of the measure by utilizing theory-led constructs. Method: Eighteen therapy sessions were video-recorded and clients each rated a 20-minute session of therapy at two-minute intervals using repeated measures. A multi-level analysis was used to test for correlations between perceived levels of helpfulness and client process variables. Results: The design proved to be feasible. Concurrent validity was borne out through high correlations between constructs. A multi-level regression examined the independent contributions of client process variables to client perceived helpfulness. Client perceived control (b = 0.39, 95% CI .05 to 0.73), the ability to talk freely (b = 0.30, SE = 0.11, 95% CI .09 to 0.51) and therapist approach (b = 0.31, SE = 0.14, 95% CI .04 to 0.57) predicted client-rated helpfulness. Conclusions: We identify a feasible and acceptable method for studying continuous measures of helpfulness and their psychological correlates during a single therapy session.
We draw attention to studies indicating that phasic arousal increases interference effects in tasks necessitating the recruitment of cognitive control. We suggest that arousal-biased competition models such as GANE (glutamate amplifies noradrenergic effects) may be able to explain these findings by taking into account dynamic, within-trial changes in the relative salience of task-relevant and task-irrelevant features. However, testing this hypothesis requires a computational model.
Cover crops represent a potentially important biological filter during weed community assembly in agroecosystems. This filtering could be considered directional if different cover-crop species result in weed communities with predictably different species composition. We examined the following four questions related to the potential filtering effects of cover crops in a field experiment involving five cover crops grown in monoculture and mixture: (1) Do cover crops differ in their effect on weed community composition? (2) Is competition more intense between cover crops and weeds that are in the same family or functional group? (3) Is competition more intense across weed functional types in a cover-crop mixture compared with cover crops grown in monocultures? (4) Within a cover-crop mixture, is a higher seeding rate associated with more effective biotic filtering of the weed community? We found some evidence that cover crops differentially filtered weed communities and that at least some of these filtering effects were due to differential biomass production across cover-crop species. Monocultures of buckwheat and sorghum–sudangrass reduced the number of weed species relative to the no-cover-crop control by an average of 36 and 59% (buckwheat) and 25 and 40% (sorghum–sudangrass) in 2011 and 2012, respectively. We found little evidence that competition intensity was dependent upon the family or functional classification of the cover crop or weeds, or that cover-crop mixtures were stronger assembly filters than the most effective monocultures. Although our results do not suggest that annual cover crops exert strong directional filtering during weed community assembly, our methodological framework for detecting such effects could be applied to similar future studies that incorporate a greater number of cover-crop species and are conducted under a greater range of cover-cropping conditions.
To evaluate the potential of using surficial shell accumulations for paleoenvironmental studies, an extensive time series of individually dated specimens of the marine infaunal bivalve mollusk Semele casali was assembled using amino acid racemization (AAR) ratios (n = 270) calibrated against radiocarbon ages (n = 32). The shells were collected from surface sediments at multiple sites across a sediment-starved shelf in the shallow sub-tropical São Paulo Bight (São Paulo State, Brazil). The resulting 14C-calibrated AAR time series, one of the largest AAR datasets compiled to date, ranges from modern to 10,307 cal yr BP, is right skewed, and represents a remarkably complete time series: the completeness of the Holocene record is 66% at 250-yr binning resolution and 81% at 500-yr binning resolution. Extensive time-averaging is observed for all sites across the sampled bathymetric range indicating long water depth-invariant survival of carbonate shells at the sediment surface with low net sedimentation rates. Benthic organisms collected from active depositional surfaces can provide multi-millennial time series of biomineral records and serve as a source of geochemical proxy data for reconstructing environmental and climatic trends throughout the Holocene at centennial resolution. Surface sediments can contain time-rich shell accumulations that record the entire Holocene, not just the present.
Despite the high prevalence of postnatal depression (PND), few women seek help. Internet interventions may overcome many of the barriers to PND treatment use. We report a phase II evaluation of a 12-session, modular, guided Internet behavioural activation (BA) treatment modified to address postnatal-specific concerns [Netmums Helping With Depression (NetmumsHWD)].
To assess feasibility, we measured recruitment and attrition to the trial and examined telephone session support and treatment adherence. We investigated sociodemographic and psychological predictors of treatment adherence. Effectiveness outcomes were estimated with the Edinburgh Postnatal Depression Scale (EPDS), Generalized Anxiety Disorder-7, Work and Social Adjustment Scale, Postnatal Bonding Questionnaire, and Social Provisions Scale.
A total of 249 women were recruited via a UK parenting site, Netmums.com. A total of 83 women meeting DSM-IV criteria for major depressive disorder were randomized to NetmumsHWD (n = 41) or treatment-as-usual (TAU; n = 42). Of the 83 women, 71 (86%) completed the EPDS at post-treatment, and 71% (59/83) at the 6-month follow-up. Women completed an average of eight out of 12 telephone support sessions and five out of 12 modules. Working women and those with less support completed fewer modules. There was a large effect size favouring women who received NetmumsHWD on depression, work and social impairment, and anxiety scores at post-treatment compared with women in the TAU group, and a large effect size on depression at 6 months post-treatment. There were small effect sizes for postnatal bonding and perceived social support.
A supported, modular, Internet BA programme can be feasibly delivered to postpartum women, offering promise to improve depression, anxiety and functioning.
The IntCal09 and Marine09 radiocarbon calibration curves have been revised utilizing newly available and updated data sets from 14C measurements on tree rings, plant macrofossils, speleothems, corals, and foraminifera. The calibration curves were derived from the data using the random walk model (RWM) used to generate IntCal09 and Marine09, which has been revised to account for additional uncertainties and error structures. The new curves were ratified at the 21st International Radiocarbon conference in July 2012 and are available as Supplemental Material at www.radiocarbon.org. The database can be accessed at http://intcal.qub.ac.uk/intcal13/.
High-quality data from appropriate archives are needed for the continuing improvement of radiocarbon calibration curves. We discuss here the basic assumptions behind 14C dating that necessitate calibration and the relative strengths and weaknesses of archives from which calibration data are obtained. We also highlight the procedures, problems, and uncertainties involved in determining atmospheric and surface ocean 14C/12C in these archives, including a discussion of the various methods used to derive an independent absolute timescale and uncertainty. The types of data required for the current IntCal database and calibration curve model are tabulated with examples.
The coastline along the southern Arabian Gulf between Al Jubail, Kingdom of Saudi Arabia, and Dubai, UAE, appears to have risen at least 125 m in the last 18,000 years. Dating and topographic surveying of paleo-dunes (43–53 ka), paleo-marine terraces (17–30 ka), and paleo-marine shorelines (3.3–5.5 ka) document a rapid, > 1 mm/a subsidence, followed by a 6 mm/a uplift that is decreasing with time. The mechanism causing this movement remains elusive but may be related to the translation of the coastal area through the backbasin to forebulge hinge line movement of the Arabian plate or, alternatively, by movement of the underlying Infracambrian-age Hormuz salt in response to sea-level changes associated with continental glaciation. Independent of the mechanism, rapid and episodic uplift may impact the design of engineering projects such as nuclear power plants, airports, and artificial islands as well as the interpretation of sedimentation and archeology of the area.
Chemical genetics describes the use of molecules as “chemical probes” to investigate biological systems [1–3]. In contrast with traditional genetics, in which gene knockouts on the level of the DNA are used, chemical genetics uses biologically active small molecules to directly attenuate the corresponding biological macromolecular (usually protein) product. Thus, the ready availability of bioactive small molecules is of crucial importance in chemical genetics studies. Such small molecules can be identified by screening compound collections (libraries) in suitably designed assays. This chapter describes the use of diversity-oriented synthesis (DOS) to prepare structurally diverse small molecule libraries. Structurally diverse libraries show a greater variety in not only their physiochemical properties but also, and of most relevance here, in their biological activities. Herein we describe some of the most effective strategies that have been used in DOS library design and preparation.
Small molecules, chemical genetics, and chemical genomics
Chemical genetics experiments can be performed in either a forward or a reverse sense (Figure 4.1). The first step of both approaches requires the identification of a small molecule that either induces a desired phenotype (forward chemical genetics) or modulates the function of a specific protein of interest (reverse chemical genetics). Thus, in the former case, investigations proceed from phenotype to protein, whereas in the latter case, investigations progress from protein to phenotype.