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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.Ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example ecosystems database.

Hexanucleotide GGGGCC repeat expansion in C9ORF72 is the most prevalent genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the aberrant accumulation of dipeptide repeat (DPR) proteins produced by the unconventional translation of expanded RNA repeats. Here, we performed genome-wide CRISPR-Cas9 screens for modifiers of DPR protein production in human cells. We found that DDX3X, an RNA helicase, suppresses the repeat-associated non-AUG translation of GGGGCC repeats. DDX3X directly binds to (GGGGCC)n RNAs but not antisense (CCCCGG)n RNAs. Its helicase activity is essential for the translation repression. Reduction of DDX3X increases DPR levels in C9ORF72-ALS/FTD patient cells and enhances (GGGGCC)n-mediated toxicity in Drosophila. Elevating DDX3X expression is sufficient to decrease DPR levels, rescue nucleocytoplasmic transport abnormalities, and improve survival of patient iPSC-differentiated neurons. This work identifies genetic modifiers of DPR protein production and provides potential therapeutic targets for C9ORF72-ALS/FTD.

Hsp104 is a hexameric AAA+ ATPase and protein disaggregase found in yeast, which couples ATP hydrolysis to the dissolution of diverse polypeptides trapped in toxic preamyloid oligomers, phase-transitioned gels, disordered aggregates, amyloids, and prions. Hsp104 shows plasticity in disaggregating diverse substrates, but how its hexameric architecture operates as a molecular machine has remained unclear. Here, we highlight structural advances made via cryoelectron microscopy (cryo-EM) that enhance our mechanistic understanding of Hsp104 and other related AAA+ translocases. Hsp104 hexamers are dynamic and adopt open "lock-washer" spiral states and closed ring structures that envelope polypeptide substrate inside the axial channel. ATP hydrolysis-driven conformational changes at the spiral seam ratchet substrate deeper into the channel. Remarkably, this mode of polypeptide translocation is reminiscent of models for how hexameric helicases unwind DNA and RNA duplexes. Thus, Hsp104 likely adapts elements of a deeply rooted, ring-translocase mechanism to the specialized task of protein disaggregation.

Hsp104 is an AAA+ protein disaggregase, which can be potentiated via diverse mutations in its autoregulatory middle domain (MD) to mitigate toxic misfolding of TDP-43, FUS, and α-synuclein implicated in fatal neurodegenerative disorders. Problematically, potentiated MD variants can exhibit off-target toxicity. Here, we mine disaggregase sequence space to safely enhance Hsp104 activity via single mutations in nucleotide-binding domain 1 (NBD1) or NBD2. Like MD variants, NBD variants counter TDP-43, FUS, and α-synuclein toxicity and exhibit elevated ATPase and disaggregase activity. Unlike MD variants, non-toxic NBD1 and NBD2 variants emerge that rescue TDP-43, FUS, and α-synuclein toxicity. Potentiating substitutions alter NBD1 residues that contact ATP, ATP-binding residues, or the MD. Mutating the NBD2 protomer interface can also safely ameliorate Hsp104. Thus, we disambiguate allosteric regulation of Hsp104 by several tunable structural contacts, which can be engineered to spawn enhanced therapeutic disaggregases with minimal off-target toxicity.

Bacterial ClpB and yeast Hsp104 are homologous Hsp100 protein disaggregases that serve critical functions in proteostasis by solubilizing protein aggregates. Two AAA+ nucleotide binding domains (NBDs) power polypeptide translocation through a central channel comprised of a hexameric spiral of protomers that contact substrate via conserved pore-loop interactions. Here we report cryo-EM structures of a hyperactive ClpB variant bound to the model substrate, casein in the presence of slowly hydrolysable ATPγS, which reveal the translocation mechanism. Distinct substrate-gripping interactions are identified for NBD1 and NBD2 pore loops. A trimer of N-terminal domains define a channel entrance that binds the polypeptide substrate adjacent to the topmost NBD1 contact. NBD conformations at the seam interface reveal how ATP hydrolysis-driven substrate disengagement and re-binding are precisely tuned to drive a directional, stepwise translocation cycle.

While cytoplasmic aggregation of TDP-43 is a pathological hallmark of amyotrophic lateral sclerosis and frontotemporal dementia, how aggregates form and what drives its nuclear clearance have not been determined. Here we show that TDP-43 at its endogenous level undergoes liquid-liquid phase separation (LLPS) within nuclei in multiple cell types. Increased concentration of TDP-43 in the cytoplasm or transient exposure to sonicated amyloid-like fibrils is shown to provoke long-lived liquid droplets of cytosolic TDP-43 whose assembly and maintenance are independent of conventional stress granules. Cytosolic liquid droplets of TDP-43 accumulate phosphorylated TDP-43 and rapidly convert into gels/solids in response to transient, arsenite-mediated stress. Cytoplasmic TDP-43 droplets slowly recruit importin-α and Nup62 and induce mislocalization of RanGap1, Ran, and Nup107, thereby provoking inhibition of nucleocytoplasmic transport, clearance of nuclear TDP-43, and cell death. These findings identify a neuronal cell death mechanism that can be initiated by transient-stress-induced cytosolic de-mixing of TDP-43.

This study investigated the inter-rater reliability and validity of the Fulltrack AI application, to measure ball speed under a range of cricket training conditions in comparison to a radar gun. Ball speed (km/hr) of 1081 deliveries (pace = 783; spin = 298) from a range of training sessions and conditions were recorded simultaneously using a radar gun (Stalker Pro IIs) and iOS device running Fulltrack AI (v1.13.1). Statistical analyses were conducted in R Statistical Software. Reliability was assessed with standard error of measurement (SEM), coefficient of variation (CV) and intraclass correlation coefficient (ICC). Agreement was assessed using Bland Altman's 95% limits of agreement (LOA). Validity was assessed using generalised additive models (GAMs). Pace deliveries were associated with good agreement (ICC: 0.87–0.90, CV: 2.56–3.13%), whilst spin deliveries demonstrated lower agreement (ICC: 0.72–0.76, CV: 3.08–4.33%). LOA established poor to fair levels of agreement, exceeding maximal allowable differences (>3%). GAMs identified Fulltrack AI overestimated ball speed (pace: estimate 0.72–0.77 m/s, SE = 0.34–0.34; spin: estimate 1.09–1.18 m/s, SE = 0.23–0.25) when compared to the radar gun. Fulltrack AI is an ecologically valid and reliable field-based method for measuring ball speed. However, caution is warranted given the significant overestimation of ball speed in contrast with a radar gun, even after controlling for different training conditions, suggesting software could benefit from refinement. [ABSTRACT FROM AUTHOR]

Suction cups are commonly used to attach biologging tags to cetaceans, and interact mechanically with compliant integument, an organ primarily composed of skin and blubber. However, the impact of compliance on suction cup performance is difficult to predict because knowledge about in vivo integument mechanics is lacking. Here, an experimental approach is used to investigate the mechanical properties of common bottlenose dolphin (Tursiops truncatus) integument using a custom instrument, the static suction cup (SSCup), to collect data from both trained dolphins and wild individuals (n = 17) during a static pose. Three loading profiles were applied at three sites to quantify nonlinear stiffness, hysteresis, and creep. The site at the dorsal fin insertion exhibited the highest stiffness, while sites posterior to the blowhole and above the pectoral fin showed greater energy dissipation during cyclic loading. Viscoelastic behavior was observed across all sites. Suction cup performance on a surrogate material with broadly similar compliance showed reduced performance compared to cups on rigid acrylic: the maximum applied force at detachment on acrylic (50 N) was twice as large as the compliant substrate (25 N). Site‐dependent compliance of integument may lead to varying performance of suction cups as an attachment method for tags. [ABSTRACT FROM AUTHOR]

Arginine-rich dipeptide repeat proteins (R-DPRs) are highly toxic proteins found in patients with C9orf72-linked amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). R-DPRs can cause toxicity by disrupting the natural phase behavior of RNA-binding proteins (RBPs). Mitigating this abnormal phase behavior is, therefore, crucial to reduce R-DPR-induced toxicity. Here, we use FUS as a model RBP to investigate the mechanism of R-DPR-induced aberrant RBP phase transition. We find that this phase transition can be mitigated by Kapβ2. However, as a nuclear import receptor and phase modifier for PY-NLS-containing RBPs, the function of WT Kapβ2 could lead to undesired interaction with its native substrates when used as therapeutics for C9-ALS/FTD. To address this issue, it is crucial to devise effective strategies that allow Kapβ2 to selectively target its binding to the R-DPRs, instead of the RBPs. We show that NLS-binding deficient Kapβ2W460A:W730A can indeed selectively interact with R-DPRs in FUS assembly without affecting normal FUS phase separation. Importantly, Kapβ2W460A:W730A prevents enrichment of poly(GR) in stress granules and mitigates R-DPR neurotoxicity. Thus, NLS-binding deficient Kapβ2 may be implemented as a potential therapeutic for C9-ALS/FTD. The NLS-binding deficient Kapβ2W460A:W730A was shown to be able to selectively target R-DPRs without disrupting normal FUS assembly, which offers a potential therapeutic avenue for C9 ALS/FTD. [ABSTRACT FROM AUTHOR]

Background: The ability to navigate obstacles and embrace iteration following failure is a hallmark of a scientific disposition and is hypothesized to increase students' persistence in science, technology, engineering, and mathematics (STEM). However, this ability is often not explicitly explored or addressed by STEM instructors. Recent collective interest brought together STEM instructors, psychologists, and education researchers through the National Science Foundation (NSF) research collaborative "Factors affecting Learning, Attitudes, and Mindsets in Education network" (FLAMEnet) to investigate intrapersonal elements (e.g., individual differences, affect, motivation) that may influence students' STEM persistence. One such element is "fear of failure" (FF), a complex interplay of emotion and cognition occurring when a student believes they may not be able to meet the needs of an achievement context. A validated measure for assessing FF, the Performance Failure Appraisal Inventory (PFAI) exists in the psychological literature. However, this measure was validated in community, athletic, and general undergraduate samples, which may not accurately reflect the motivations, experiences, and diversity of undergraduate STEM students. Given the potential role of FF in STEM student persistence and motivation, we felt it important to determine if this measure accurately assessed FF for STEM undergraduates, and if not, how we could improve upon or adapt it for this purpose. Results: Using exploratory and confirmatory factor analysis and cognitive interviews, we re-validated the PFAI with a sample of undergraduates enrolled in STEM courses, primarily introductory biology and chemistry. Results indicate that a modified 15-item four-factor structure is more appropriate for assessing levels of FF in STEM students, particularly among those from groups underrepresented in STEM. Conclusions: In addition to presenting an alternate factor structure, our data suggest that using the original form of the PFAI measure may significantly misrepresent levels of FF in the STEM context. This paper details our collaborative validation process and discusses implications of the results for choosing, using, and interpreting psychological assessment tools within STEM undergraduate populations.

Research quality is often based on the perceived quality of journals in which the research appears. Journal quality is subjectively based on a wide array of objective journal characteristics, including acceptance rates and citations. The authors expand on recently published research by examining the extent in which journal characteristics vary across national boundaries. It also expands upon the prior research by examining accounting journals, finance journals, and information systems journals. U.S. journals are compared with those from the United Kingdom, and other countries in general. Findings demonstrate that significant differences exist across disciplines and nations, thus making it necessary to consider these journal characteristics when gauging journal and research quality.

A dominant histopathological feature in neuromuscular diseases, including amyotrophic lateral sclerosis and inclusion body myopathy, is cytoplasmic aggregation of the RNA-binding protein TDP-43. Although rare mutations in TARDBP-the gene that encodes TDP-43-that lead to protein misfolding often cause protein aggregation, most patients do not have any mutations in TARDBP. Therefore, aggregates of wild-type TDP-43 arise in most patients by an unknown mechanism. Here we show that TDP-43 is an essential protein for normal skeletal muscle formation that unexpectedly forms cytoplasmic, amyloid-like oligomeric assemblies, which we call myo-granules, during regeneration of skeletal muscle in mice and humans. Myo-granules bind to mRNAs that encode sarcomeric proteins and are cleared as myofibres mature. Although myo-granules occur during normal skeletal-muscle regeneration, myo-granules can seed TDP-43 amyloid fibrils in vitro and are increased in a mouse model of inclusion body myopathy. Therefore, increased assembly or decreased clearance of functionally normal myo-granules could be the source of cytoplasmic TDP-43 aggregates that commonly occur in neuromuscular disease.

Environmental enrichment can be used to improve the welfare of dolphins in zoos and aquariums. Bottlenose dolphins under professional care are typically provided with a range of enrichment that has a variety of features and levels of complexity at various frequencies. In the present study, a subset of data from a larger study entitled “Towards understanding the welfare of cetaceans in zoos and aquariums” (colloquially called the Cetacean Welfare Study) was used to examine the relationship between activity level and enrichment buoyancy as well as enrichment provisioning schedules. Survey data were collected from accredited zoos and aquariums related to the types of enrichment provided to the dolphins and the frequency and duration they were supplied. Non-invasive bio-logging devices were used to record the dolphin kinematics one day per week over the course of two five-week data collection periods. Activity level related positively with the total duration of time non-stationary enrichment was provided. In addition, providing a larger number of enrichment types each between 26% and 50% of the days in a month (i.e., rotating many different types of enrichment across days on a moderate schedule) was positively related to activity level. Activity level was negatively related to the number of times sinking enrichment was provided. Understanding how the temporal schedule and features of various types of enrichment are related to activity levels will aid in developing progressively more effective enrichment programs.