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1. VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

   https://doi.org/10.1186/s12859-022-04973-8  

   Espinoza, Josh L. ; Dupont, Chris L. ( October 2022 , BMC Bioinformatics)

   With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth’s natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ,however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

   In this study, we introduce theViral Eukaryotic Bacterial Archaeal(VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge,VEBAis the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes.VEBAimplements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone.VEBAincludes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification.VEBAalso provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally,VEBAis the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments.VEBA’s capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

   TheVEBAsoftware suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways.VEBAfully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions ofVEBAto the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks.VEBAallows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.

    

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2. Viruses in astrobiology

   https://doi.org/10.3389/fmicb.2022.1032918  

   de la Higuera, Ignacio ; Lázaro, Ester ( October 2022 , Frontiers in Microbiology)

   Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.

    

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3. Duty to Respond: The Challenges Social Service Providers Face When Charged with Keeping Youth Safe Online

   https://doi.org/10.1145/3567556  

   Caddle, Xavier V. ; Naher, Nurun ; Miller, Zachary P. ; Badillo-Urquiola, Karla ; Wisniewski, Pamela J. ( January 2023 , Proceedings of the ACM on Human-Computer Interaction)

   Social service providers play a vital role in the developmental outcomes of underprivileged youth as they transition into adulthood. Educators, mental health professionals, juvenile justice officers, and child welfare caseworkers often have first-hand knowledge of the trials uniquely faced by these vulnerable youth and are charged with mitigating harmful risks, such as mental health challenges, child abuse, drug use, and sex trafficking. Yet, less is known about whether or how social service providers assess and mitigate the online risk experiences of youth under their care. Therefore, as part of the National Science Foundation (NSF) I-Corps program, we conducted interviews with 37 social service providers (SSPs) who work with underprivileged youth to determine what (if any) online risks are most concerning to them given their role in youth protection, how they assess or become aware of these online risk experiences, and whether they see value in the possibility of using artificial intelligence (AI) as a potential solution for online risk detection. Overall, online sexual risks (e.g., sexual grooming and abuse) and cyberbullying were the most salient concern across all social service domains, especially when these experiences crossed the boundary between the digital and the physical worlds. Yet, SSPs had to rely heavily on youth self-reports to know whether and when online risks occurred, which required building a trusting relationship with youth; otherwise, SSPs became aware only after a formal investigation had been launched. Therefore, most SSPs found value in the potential for using AI as an early detection system and to monitor youth, but they were concerned that such a solution would not be feasible due to a lack of resources to adequately respond to online incidences, access to the necessary digital trace data (e.g., social media), context, and concerns about violating the trust relationships they built with youth. Thus, such automated risk detection systems should be designed and deployed with caution, as their implementation could cause youth to mistrust adults, thereby limiting the receipt of necessary guidance and support. We add to the bodies of research on adolescent online safety and the benefits and challenges of leveraging algorithmic systems in the public sector. 

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4. Brachypodium distachyon Seedlings Display Accession-Specific Morphological and Transcriptomic Responses to the Microgravity Environment of the International Space Station

   https://doi.org/10.3390/life13030626  

   Su, Shih-Heng ; Levine, Howard G. ; Masson, Patrick H. ( March 2023 , Life)

   Plants have been recognized as key components of bioregenerative life support systems for space exploration, and many experiments have been carried out to evaluate their adaptability to spaceflight. Unfortunately, few of these experiments have involved monocot plants, which constitute most of the crops used on Earth as sources of food, feed, and fiber. To better understand the ability of monocot plants to adapt to spaceflight, we germinated and grew Brachypodium distachyon seedlings of the Bd21, Bd21-3, and Gaz8 accessions in a customized growth unit on the International Space Station, along with 1-g ground controls. At the end of a 4-day growth period, seedling organ’s growth and morphologies were quantified, and root and shoot transcriptomic profiles were investigated using RNA-seq. The roots of all three accessions grew more slowly and displayed longer root hairs under microgravity conditions relative to ground control. On the other hand, the shoots of Bd21-3 and Gaz-8 grew at similar rates between conditions, whereas those of Bd21 grew more slowly under microgravity. The three Brachypodium accessions displayed dramatically different transcriptomic responses to microgravity relative to ground controls, with the largest numbers of differentially expressed genes (DEGs) found in Gaz8 (4527), followed by Bd21 (1353) and Bd21-3 (570). Only 47 and six DEGs were shared between accessions for shoots and roots, respectively, including DEGs encoding wall-associated proteins and photosynthesis-related DEGs. Furthermore, DEGs associated with the “Oxidative Stress Response” GO group were up-regulated in the shoots and down-regulated in the roots of Bd21 and Gaz8, indicating that Brachypodium roots and shoots deploy distinct biological strategies to adapt to the microgravity environment. A comparative analysis of the Brachypodium oxidative-stress response DEGs with the Arabidopsis ROS wheel suggests a connection between retrograde signaling, light response, and decreased expression of photosynthesis-related genes in microgravity-exposed shoots. In Gaz8, DEGs were also found to preferentially associate with the “Plant Hormonal Signaling” and “MAP Kinase Signaling” KEGG pathways. Overall, these data indicate that Brachypodium distachyon seedlings exposed to the microgravity environment of ISS display accession- and organ-specific responses that involve oxidative stress response, wall remodeling, photosynthesis inhibition, expression regulation, ribosome biogenesis, and post-translational modifications. The general characteristics of these responses are similar to those displayed by microgravity-exposed Arabidopsis thaliana seedlings. However, organ- and accession-specific components of the response dramatically differ both within and between species. These results suggest a need to directly evaluate candidate-crop responses to microgravity to better understand their specific adaptability to this novel environment and develop cultivation strategies allowing them to strive during spaceflight. 

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5. Emerging threats and persistent conservation challenges for freshwater biodiversity

   https://doi.org/10.1111/brv.12480  

   Reid, Andrea J. ; Carlson, Andrew K. ; Creed, Irena F. ; Eliason, Erika J. ; Gell, Peter A. ; Johnson, Pieter T. J. ; Kidd, Karen A. ; MacCormack, Tyson J. ; Olden, Julian D. ; Ormerod, Steve J. ; et al ( November 2018 , Biological Reviews)

   In the 12 years since Dudgeonet al. (2006) reviewed major pressures on freshwater ecosystems, the biodiversity crisis in the world's lakes, reservoirs, rivers, streams and wetlands has deepened. While lakes, reservoirs and rivers cover only 2.3% of the Earth's surface, these ecosystems host at least 9.5% of the Earth's described animal species. Furthermore, using the World Wide Fund for Nature's Living Planet Index, freshwater population declines (83% between 1970 and 2014) continue to outpace contemporaneous declines in marine or terrestrial systems. The Anthropocene has brought multiple new and varied threats that disproportionately impact freshwater systems. We document 12 emerging threats to freshwater biodiversity that are either entirely new since 2006 or have since intensified: (i) changing climates; (ii) e‐commerce and invasions; (iii) infectious diseases; (iv) harmful algal blooms; (v) expanding hydropower; (vi) emerging contaminants; (vii) engineered nanomaterials; (viii) microplastic pollution; (ix) light and noise; (x) freshwater salinisation; (xi) declining calcium; and (xii) cumulative stressors. Effects are evidenced for amphibians, fishes, invertebrates, microbes, plants, turtles and waterbirds, with potential for ecosystem‐level changes through bottom‐up and top‐down processes. In our highly uncertain future, the net effects of these threats raise serious concerns for freshwater ecosystems. However, we also highlight opportunities for conservation gains as a result of novel management tools (e.g. environmental flows, environmental DNA) and specific conservation‐oriented actions (e.g. dam removal, habitat protection policies, managed relocation of species) that have been met with varying levels of success. Moving forward, we advocate hybrid approaches that manage fresh waters as crucial ecosystems for human life support as well as essential hotspots of biodiversity and ecological function. Efforts to reverse global trends in freshwater degradation now depend on bridging an immense gap between the aspirations of conservation biologists and the accelerating rate of species endangerment.

    

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