NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes

The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression

Preparing the Next Generation of Sustainability Scientists

Graduate programs emerging in universities over recent decades support the advanced study of sustainability issues in complex socio-environmental systems. Constructing the problem-scope to address these issues requires graduate students to integrate across disciplines and synthesize the social and natural dimensions of sustainability. Graduate programs that are designed to foster inter- and transdisciplinary research acknowledge the importance of training students to use integrative research approaches. However, this training is not available in all graduate programs that support integrative research, often requiring students to seek external training opportunities. We present perspectives from a group of doctoral students with diverse disciplinary backgrounds conducting integrative research in universities across the United States who participated in a 10-day, National Science Foundation-funded integrative research training workshop to learn and develop socio-environmental research skills. Following the workshop, students conducted a collaborative autoethnographic study to share pre- and postworkshop research experiences and discuss ways to increase integrative research training opportunities. Results reveal that students, regardless of disciplinary background, face common barriers conducting integrative research that include: (1) lack of exposure to epistemological frameworks and team-science skills, (2) challenges to effectively include stakeholder perspectives in his/her research, and (3) variable levels of committee support to conduct integrative research. To overcome the identified barriers and advance integrative research, students recommend how training opportunities can be embedded within existing graduate programs. Students advocate that both internal and external training opportunities are necessary to support the next generation of sustainability scientists

Linking Symptom Inventories using Semantic Textual Similarity

An extensive library of symptom inventories has been developed over time to measure clinical symptoms, but this variety has led to several long standing issues. Most notably, results drawn from different settings and studies are not comparable, which limits reproducibility. Here, we present an artificial intelligence (AI) approach using semantic textual similarity (STS) to link symptoms and scores across previously incongruous symptom inventories. We tested the ability of four pre-trained STS models to screen thousands of symptom description pairs for related content - a challenging task typically requiring expert panels. Models were tasked to predict symptom severity across four different inventories for 6,607 participants drawn from 16 international data sources. The STS approach achieved 74.8% accuracy across five tasks, outperforming other models tested. This work suggests that incorporating contextual, semantic information can assist expert decision-making processes, yielding gains for both general and disease-specific clinical assessment

Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements

<p>Abstract</p> <p>Background</p> <p>Inteins and introns are genetic elements that are removed from proteins and RNA after translation or transcription, respectively. Previous studies have suggested that these genetic elements are found in conserved parts of the host protein. To our knowledge this type of analysis has not been done for group II introns residing within a gene. Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life.</p> <p>Results</p> <p>To determine whether or not inteins, group I, group II, and spliceosomal introns are found preferentially in conserved regions of their respective host protein, conservation profiles were generated and intein and intron positions were mapped to the profiles. Fisher's combined probability test was used to determine the significance of the distribution of insertion sites across the conservation profile for each protein. For a subset of studied proteins, the conservation profile and insertion positions were mapped to protein structures to determine if the insertion sites correlate to regions of functional activity. All inteins and most group I introns were found to be preferentially located within conserved regions; in contrast, a bacterial intein-like protein, group II and spliceosomal introns did not show a preference for conserved sites.</p> <p>Conclusions</p> <p>These findings demonstrate that inteins and group I introns are found preferentially in conserved regions of their respective host proteins. Homing endonucleases are often located within inteins and group I introns and these may facilitate mobility to conserved regions. Insertion at these conserved positions decreases the chance of elimination, and slows deletion of the elements, since removal of the elements has to be precise as not to disrupt the function of the protein. Furthermore, functional constrains on the targeted site make it more difficult for hosts to evolve immunity to the homing endonuclease. Therefore, these elements will better survive and propagate as molecular parasites in conserved sites. In contrast, spliceosomal introns and group II introns do not show significant preference for conserved sites and appear to have adopted a different strategy to evade loss.</p

Going beyond the Flood Insurance Rate Map: insights from flood hazard map co-production

Abstract. Flood hazard mapping in the United States (US) is deeply tied to the National Flood Insurance Program (NFIP). Consequently, publicly available flood maps provide essential information for insurance purposes, but do not necessarily provide relevant information for non-insurance aspects of flood risk management (FRM) such as public education and emergency planning. Recent calls for flood hazard maps that support a wider variety of FRM tasks highlight the need to deepen our understanding about the factors that make flood maps useful and understandable for local end-users. In this study, social scientists and engineers explore opportunities for improving the utility and relevance of flood hazard maps through the co-production of maps responsive to end-users' FRM needs. Specifically, two-dimensional flood modeling produced a set of baseline hazard maps for stakeholders of the Tijuana River Valley, US, and Los Laureles Canyon in Tijuana, Mexico. Focus groups with natural resource managers, city planners, emergency managers, academia, non-profit, and community leaders refined the baseline hazard maps by triggering additional modeling scenarios and map revisions. Several important end-user preferences emerged, such as (1) legends that frame flood intensity both qualitatively and quantitatively, and (2) flood scenario descriptions that report flood magnitude in terms of rainfall, streamflow, and its relation to an historic event. Regarding desired hazard map content, end-users' requests revealed general consistency with mapping needs reported in European studies and guidelines published in Australia. However, requested map content that is not commonly produced included: (1) standing water depths following the flood, (2) the erosive potential of flowing water, and (3) pluvial flood hazards, or flooding caused directly by rainfall. We conclude that the relevance and utility of commonly produced flood hazard maps can be most improved by illustrating pluvial flood hazards and by using concrete reference points to describe flooding scenarios rather than exceedance probabilities or frequencies

CRISPR required for host colonization

The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression

Addressing Pluvial Flash Flooding through Community-Based Collaborative Research in Tijuana, Mexico

Pluvial flash flooding (PFF) is a growing hazard facing cities around the world as a result of rapid urbanization and more intense precipitation from global warming, particularly for low-resourced settings in developing countries. We present collaborative modeling (CM) as an iterative process to meet diverse decision-making needs related to PFF through the co-production of flood hazard models and maps. CM resulted in a set of flood hazard maps accessible through an online viewer that end-users found useful and useable for understanding PFF threats, including debris blockages and barriers to mobility and evacuation. End-users of information included individuals concerned with general flood awareness and preparedness, and involved in infrastructure and emergency management, planning, and policy. CM also showed that rain-on-grid hydrodynamic modeling is needed to depict PFF threats in ways that are intuitive to end-users. These outcomes evidence the importance and transferability of public health rationale for community-based research and principles used here including recognizing community as a unit of identity, building on strengths of the community, and integrating knowledge for the benefit of all partners