LTR-retrotransposons from Bdelloid rotifers capture additional ORFs shared between highly diverse retroelement types

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Viruses 9 (2017): 78, doi:10.3390/v9040078.Rotifers of the class Bdelloidea, microscopic freshwater invertebrates, possess a highlydiversified repertoire of transposon families, which, however, occupy less than 4% of genomic DNA in the sequenced representative Adineta vaga. We performed a comprehensive analysis of A. vaga retroelements, and found that bdelloid long terminal repeat (LTR)retrotransposons, in addition to conserved open reading frame (ORF) 1 and ORF2 corresponding to gag and pol genes, code for an unusually high variety of ORF3 sequences. Retrovirus-like LTR families in A. vaga belong to four major lineages, three of which are rotiferspecific and encode a dUTPase domain. However only one lineage contains a canonical envlike fusion glycoprotein acquired from paramyxoviruses (non-segmented negative-strand RNA viruses), although smaller ORFs with transmembrane domains may perform similar roles. A different ORF3 type encodes a GDSL esterase/lipase, which was previously identified as ORF1 in several clades of non-LTR retrotransposons, and implicated in membrane targeting. Yet another ORF3 type appears in unrelated LTR-retrotransposon lineages, and displays strong homology to DEDDy-type exonucleases involved in 3′-end processing of RNA and single-stranded DNA. Unexpectedly, each of the enzymatic ORF3s is also associated with different subsets of Penelope-like Athena retroelement families. The unusual association of the same ORF types with retroelements from different classes reflects their modular structure with a high degree of flexibility, and points to gene sharing between different groups of retroelements.This work was supported by the National Institutes of Health grant GM111917 to I.A.; A.K. was supported by the Research Experiences for Undergraduates supplement to the National Science Foundation grant MCB-1121334 to I.A

Cal Poly Engineering PhotoBot: Final Design Review

The purpose of this project was to create a remotely controlled camera device; the PhotoBot captures images and videos of various plants and perhaps animals for biological analysis. The features for such a device allows a user to capture images and videos from various angles and heights with minimal outside assistance. Furthermore, the device is designed for users that do not wish to spend an extensive amount of time and effort taking pictures and videos in the rainforest. The key constraints of the device includes safety, versatility, ease of use, and durability. Ultimately, this project was completed for Dr. Cris Cristoffer as a senior project through the Mechanical Engineering Department at Cal Poly

A Pilot Trial of Universal School-Based Mental Health Screening in El Salvador: Traumatic Stress in an Underresourced School Environment

Salvadoran youth have an elevated risk of trauma exposure and related mental health problems. However, investigations of childhood trauma exposure and mental health sequelae in El Salvador are limited. The present study aimed to (a) explore the prevalence of exposure to potentially traumatic events and symptoms of posttraumatic stress, anxiety, and depression and (b) evaluate the associations between specific trauma types and emotional functioning among Salvadoran youth. A total of 1,296 youth aged 8–21 years from seven public schools completed self-report measures of trauma exposure, posttraumatic stress symptoms (PTSS), anxiety, and depression. Participants reported high levels of trauma exposure, endorsing an average of 3.62 (SD = 2.32) trauma types. In total, 34.5% of participants reported clinically elevated PTSS; fewer youths reported elevated depressive (8.7%) and anxiety symptoms (8.6%). Although boys reported exposure to more trauma types than girls, d = 0.22, girls were more likely to endorse elevated PTSS, V = .11; anxiety, V = .06; and depression, V = .10. Adolescents reported exposure to more trauma types than younger children, d = 0.23, and were more likely to endorse elevated PTSS, V = .07; anxiety, V = .13; and depression, V = .16. Undergoing a frightening medical procedure, OR = 2.30; female sex, OR = 1.92; witnessing domestic violence, OR = 1.70; and experiencing war between gangs, OR = 1.61, were strong predictors of elevated PTSS. This broad, school-based screening was a critical step toward better understanding the rate of trauma exposure and trauma-related symptoms among Salvadoran youth

Listen, Don’t Tell: Partnership and Adaptation to Implement Trauma-Focused Cognitive Behavioral Therapy in Low-Resourced Settings

Clinical psychological science has developed many efficacious treatments for diverse emotional and behavioral difficulties encountered by children and adolescents, although randomized trials investigating these treatments have disproportionally been conducted by American, university-based research labs. The subsection of the world population involved in these studies, however, represents very few people among those in need of psychological services whose voices, perspectives, and orientations to therapy have not generally been reflected in well-funded research trials. Dissemination and implementation of evidence-based services designed to meet the needs of this broader global population, therefore, may require cultural and contextual adaptation to be successful. The current article describes the implementation of Trauma-Focused Cognitive Behavioral Therapy (TF-CBT) in 3 separate low-resourced settings (rural South Carolina, Puerto Rico, and El Salvador) utilizing the Exploration, Preparation, Implementation, and Sustainment (EPIS) framework and guided by a community-based participatory research framework. Emphasis is placed on description of program development, building collaborative and responsive partnerships, and the use of implementation strategies to guide continuous quality improvement. Program evaluation data comparing baseline to posttreatment trauma symptoms and treatment completion rates for all sites are also presented, which suggests that treatment was associated with a large reduction in symptoms, exceeding that noted in many TF-CBT randomized trials. The implications of attention to context, adaptation, and methods of building partnerships with global communities are discussed, with a particular focus on propelling more refined models and controlled studies in the future

Xylem and soil CO2 fluxes in a Quercus pyrenaica Willd. coppice: Root respiration increases with clonal size

Xylem and soil CO2 fluxes in coppiced oak forests increase with clonal size suggesting larger expenditures of energy for root respiration. An imbalance between root demand and shoot production of carbohydrates may contribute to the degradation of abandoned coppices

Feasibility and acceptability of self-collection of Human Papillomavirus samples for primary cervical cancer screening on the Caribbean Coast of Nicaragua: A mixed-methods study

BackgroundCervical cancer is the primary cause of cancer death for women in Nicaragua, despite being highly preventable through vaccination against high-risk genotypes of the Human Papillomavirus (hrHPV), screening for hrHPV, and early detection of lesions. Despite technological advances designed to increase access to screening in low resource settings, barriers to increasing population-level screening coverage persist. On the Caribbean Coast of Nicaragua, only 59% of women have received one lifetime screen, compared to 78.6% of eligible women living on the Pacific and in the Interior. In concordance with the WHO’s call for best practices to eliminate cervical cancer, we explored the feasibility and acceptability of self-collection of samples for hrHPV testing on the Caribbean Coast of Nicaragua through a multi-year, bi-national, community-based mixed methods study.MethodsBetween 2016 and 2019, focus groups (n=25), key informant interviews (n=12) [phase I] and an environmental scan [phase II] were conducted on the Caribbean Coast of Nicaragua in partnership and collaboration with long-term research partners at the University of Virginia and community-based organizations. In spring 2020, underscreened women on the Caribbean Coast of Nicaragua were recruited and screened for hrHPV, with the choice of clinician collection or self-collection of samples.ResultsOver the course of the study, providers and potential patients expressed significant acceptability of self-collection of samples as a strategy to reduce barriers currently contributing to the low rates of screening (phases I and II). Ultimately 99.16% (n=1,767) of women chose to self-collect samples, demonstrating a high level of acceptability of self-collection in this pilot sample (phase III). Similarly, focus groups, key informant interviews, and the environmental scan (phases I and II) of resources indicated critical considerations for feasibility of implementation of both HPV primary screening and subsequently, self-collection of samples. Through phase III, we piloted hrHPV screening (n=1,782), with a 19.25% hrHPV positivity rate.ConclusionSelf-collection of samples for hrHPV testing demonstrated high acceptability and feasibility. Through concerted effort at the local, regional, and national levels, this project supported capacity building in reporting, monitoring, and surveilling cervical cancer screening across the continuum of cervical cancer control

Mapping child growth failure across low- and middle-income countries

Child growth failure (CGF), manifested as stunting, wasting, and underweight, is associated with high 5 mortality and increased risks of cognitive, physical, and metabolic impairments. Children in low- and middle-income countries (LMICs) face the highest levels of CGF globally. Here we illustrate national and subnational variation of under-5 CGF indicators across LMICs, providing 2000–2017 annual estimates mapped at a high spatial resolution and aggregated to policy-relevant administrative units and national levels. Despite remarkable declines over the study period, many LMICs remain far from the World Health 10 Organization’s ambitious Global Nutrition Targets to reduce stunting by 40% and wasting to less than 5% by 2025. Large disparities in prevalence and rates of progress exist across regions, countries, and within countries; our maps identify areas where high prevalence persists even within nations otherwise succeeding in reducing overall CGF prevalence. By highlighting where subnational disparities exist and the highest-need populations reside, these geospatial estimates can support policy-makers in planning locally 15 tailored interventions and efficient directing of resources to accelerate progress in reducing CGF and its health implications

The potential science and engineering value of samples delivered to Earth by Mars sample return

© The Meteoritical Society, 2019. Executive Summary: Return of samples from the surface of Mars has been a goal of the international Mars science community for many years. Affirmation by NASA and ESA of the importance of Mars exploration led the agencies to establish the international MSR Objectives and Samples Team (iMOST). The purpose of the team is to re-evaluate and update the sample-related science and engineering objectives of a Mars Sample Return (MSR) campaign. The iMOST team has also undertaken to define the measurements and the types of samples that can best address the objectives. Seven objectives have been defined for MSR, traceable through two decades of previously published international priorities. The first two objectives are further divided into sub-objectives. Within the main part of the report, the importance to science and/or engineering of each objective is described, critical measurements that would address the objectives are specified, and the kinds of samples that would be most likely to carry key information are identified. These seven objectives provide a framework for demonstrating how the first set of returned Martian samples would impact future Martian science and exploration. They also have implications for how analogous investigations might be conducted for samples returned by future missions from other solar system bodies, especially those that may harbor biologically relevant or sensitive material, such as Ocean Worlds (Europa, Enceladus, Titan) and others. Summary of Objectives and Sub-Objectives for MSR Identified by iMOST: Objective 1 Interpret the primary geologic processes and history that formed the Martian geologic record, with an emphasis on the role of water. Intent To investigate the geologic environment(s) represented at the Mars 2020 landing site, provide definitive geologic context for collected samples, and detail any characteristics that might relate to past biologic processesThis objective is divided into five sub-objectives that would apply at different landing sites. 1.1 Characterize the essential stratigraphic, sedimentologic, and facies variations of a sequence of Martian sedimentary rocks. Intent To understand the preserved Martian sedimentary record. Samples A suite of sedimentary rocks that span the range of variation. Importance Basic inputs into the history of water, climate change, and the possibility of life 1.2 Understand an ancient Martian hydrothermal system through study of its mineralization products and morphological expression. Intent To evaluate at least one potentially life-bearing “habitable” environment Samples A suite of rocks formed and/or altered by hydrothermal fluids. Importance Identification of a potentially habitable geochemical environment with high preservation potential. 1.3 Understand the rocks and minerals representative of a deep subsurface groundwater environment. Intent To evaluate definitively the role of water in the subsurface. Samples Suites of rocks/veins representing water/rock interaction in the subsurface. Importance May constitute the longest-lived habitable environments and a key to the hydrologic cycle. 1.4 Understand water/rock/atmosphere interactions at the Martian surface and how they have changed with time. Intent To constrain time-variable factors necessary to preserve records of microbial life. Samples Regolith, paleosols, and evaporites. Importance Subaerial near-surface processes could support and preserve microbial life. 1.5 Determine the petrogenesis of Martian igneous rocks in time and space. Intent To provide definitive characterization of igneous rocks on Mars. Samples Diverse suites of ancient igneous rocks. Importance Thermochemical record of the planet and nature of the interior. Objective 2 Assess and interpret the potential biological history of Mars, including assaying returned samples for the evidence of life. Intent To investigate the nature and extent of Martian habitability, the conditions and processes that supported or challenged life, how different environments might have influenced the preservation of biosignatures and created nonbiological “mimics,” and to look for biosignatures of past or present life.This objective has three sub-objectives: 2.1 Assess and characterize carbon, including possible organic and pre-biotic chemistry. Samples All samples collected as part of Objective 1. Importance Any biologic molecular scaffolding on Mars would likely be carbon-based. 2.2 Assay for the presence of biosignatures of past life at sites that hosted habitable environments and could have preserved any biosignatures. Samples All samples collected as part of Objective 1. Importance Provides the means of discovering ancient life. 2.3 Assess the possibility that any life forms detected are alive, or were recently alive. Samples All samples collected as part of Objective 1. Importance Planetary protection, and arguably the most important scientific discovery possible. Objective 3 Quantitatively determine the evolutionary timeline of Mars. Intent To provide a radioisotope-based time scale for major events, including magmatic, tectonic, fluvial, and impact events, and the formation of major sedimentary deposits and geomorphological features. Samples Ancient igneous rocks that bound critical stratigraphic intervals or correlate with crater-dated surfaces. Importance Quantification of Martian geologic history. Objective 4 Constrain the inventory of Martian volatiles as a function of geologic time and determine the ways in which these volatiles have interacted with Mars as a geologic system. Intent To recognize and quantify the major roles that volatiles (in the atmosphere and in the hydrosphere) play in Martian geologic and possibly biologic evolution. Samples Current atmospheric gas, ancient atmospheric gas trapped in older rocks, and minerals that equilibrated with the ancient atmosphere. Importance Key to understanding climate and environmental evolution. Objective 5 Reconstruct the processes that have affected the origin and modification of the interior, including the crust, mantle, core and the evolution of the Martian dynamo. Intent To quantify processes that have shaped the planet's crust and underlying structure, including planetary differentiation, core segregation and state of the magnetic dynamo, and cratering. Samples Igneous, potentially magnetized rocks (both igneous and sedimentary) and impact-generated samples. Importance Elucidate fundamental processes for comparative planetology. Objective 6 Understand and quantify the potential Martian environmental hazards to future human exploration and the terrestrial biosphere. Intent To define and mitigate an array of health risks related to the Martian environment associated with the potential future human exploration of Mars. Samples Fine-grained dust and regolith samples. Importance Key input to planetary protection planning and astronaut health. Objective 7 Evaluate the type and distribution of in-situ resources to support potential future Mars exploration. Intent To quantify the potential for obtaining Martian resources, including use of Martian materials as a source of water for human consumption, fuel production, building fabrication, and agriculture. Samples Regolith. Importance Production of simulants that will facilitate long-term human presence on Mars. Summary of iMOST Findings: Several specific findings were identified during the iMOST study. While they are not explicit recommendations, we suggest that they should serve as guidelines for future decision making regarding planning of potential future MSR missions. The samples to be collected by the Mars 2020 (M-2020) rover will be of sufficient size and quality to address and solve a wide variety of scientific questions. Samples, by definition, are a statistical representation of a larger entity. Our ability to interpret the source geologic units and processes by studying sample sub sets is highly dependent on the quality of the sample context. In the case of the M-2020 samples, the context is expected to be excellent, and at multiple scales. (A) Regional and planetary context will be established by the on-going work of the multi-agency fleet of Mars orbiters. (B) Local context will be established at field area- to outcrop- to hand sample- to hand lens scale using the instruments carried by M-2020. A significant fraction of the value of the MSR sample collection would come from its organization into sample suites, which are small groupings of samples designed to represent key aspects of geologic or geochemical variation. If the Mars 2020 rover acquires a scientifically well-chosen set of samples, with sufficient geological diversity, and if those samples were returned to Earth, then major progress can be expected on all seven of the objectives proposed in this study, regardless of the final choice of landing site. The specifics of which parts of Objective 1 could be achieved would be different at each of the final three candidate landing sites, but some combination of critically important progress could be made at any of them. An aspect of the search for evidence of life is that we do not know in advance how evidence for Martian life would be preserved in the geologic record. In order for the returned samples to be most useful for both understanding geologic processes (Objective 1) and the search for life (Objective 2), the sample collection should contain BOTH typical and unusual samples from the rock units explored. This consideration should be incorporated into sample selection and the design of the suites. The retrieval missions of a MSR campaign should (1) minimize stray magnetic fields to which the samples would be exposed and carry a magnetic witness plate to record exposure, (2) collect and return atmospheric gas sample(s), and (3) collect additional dust and/or regolith sample mass if possible

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data