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Effector secretion is crucial for root endophytes to establish and protect their ecological niche. We used time-resolved transcriptomics to monitor effector gene expression dynamics in two closely related Sebacinales, Serendipita indica and Serendipita vermifera, during symbiosis with three plant species, competition with the phytopathogenic fungus Bipolaris sorokiniana, and cooperation with root-associated bacteria. We observed increased effector gene expression in response to biotic interactions, particularly with plants, indicating their importance in host colonization. Some effectors responded to both plants and microbes, suggesting dual roles in intermicrobial competition and plant-microbe interactions. A subset of putative antimicrobial effectors, including a GH18-CBM5 chitinase, was induced exclusively by microbes. Functional analyses of this chitinase revealed its antimicrobial and plant-protective properties. We conclude that dynamic effector gene expression underpins the ability of Sebacinales to thrive in diverse ecological niches with a single fungal chitinase contributing substantially to niche defense.

Horizontal genetic transfer (HGT) is a common phenomenon in eukaryotic genomes. However, the mechanisms by which HGT-derived genes persist and integrate into other pathways remain unclear. This topic is of significant interest because, over time, the stressors that initially favoured the fixation of HGT may diminish or disappear. Despite this, the foreign genes may continue to exist if they become part of a broader stress response or other pathways. The conventional model suggests that the acquisition of HGT equates to adaptation. However, this model may evolve into more complex interactions between gene products, a concept we refer to as the 'Integrated HGT Model' (IHM). To explore this concept further, we studied specialized HGT-derived genes that encode heavy metal detoxification functions. The recruitment of these genes into other pathways could provide clear examples of IHM. In our study, we exposed two anciently diverged species of polyextremophilic red algae from the Galdieria genus to arsenic and mercury stress in laboratory cultures. We then analysed the transcriptome data using differential and coexpression analysis. Our findings revealed that mercury detoxification follows a 'one gene-one function' model, resulting in an indivisible response. In contrast, the arsH gene in the arsenite response pathway demonstrated a complex pattern of duplication, divergence and potential neofunctionalization, consistent with the IHM. Our research sheds light on the fate and integration of ancient HGTs, providing a novel perspective on the ecology of extremophiles.

The term ‘tea polyphenols’ (TPs) comprises a broad range of polyphenol compounds present in tea, demonstrating positive health effects such as antioxidant activity, etc. in animals. This study investigated the effects of TPs supplementation in juvenile genetically improved farmed tilapia (GIFT); Oreochromis niloticus). Fifteen fish (weight: 13.46 ± 1.25 g) were distributed in six tanks and randomly assigned with diets containing graded levels of TPs (mg/kg): 0.00 (control), 100, 200, 300, 400 and 500 in quadruplicate for 8 weeks. After the trial, the fish fed 500 mg/kg TPs exhibited a significant reduction (p

Admixture estimation plays a crucial role in ancestry inference and genome-wide association studies (GWASs). Computer programs such as ADMIXTURE and STRUCTURE are commonly employed to estimate the admixture proportions of sample individuals. However, these programs can be overwhelmed by the computational burdens imposed by the 105 to 106 samples and millions of markers commonly found in modern biobanks. An attractive strategy is to run these programs on a set of ancestry-informative SNP markers (AIMs) that exhibit substantially different frequencies across populations. Unfortunately, existing methods for identifying AIMs require knowing ancestry labels for a subset of the sample. This supervised learning approach creates a chicken and the egg scenario. In this paper, we present an unsupervised, scalable framework that seamlessly carries out AIM selection and likelihood-based estimation of admixture proportions. Our simulated and real data examples show that this approach is scalable to modern biobank datasets. OpenADMIXTURE, our Julia implementation of the method, is open source and available for free.

Religious Pluralism in Indonesia: Threats and Opportunities for Democracy. Edited by Chiara Formichi. Ithaca: Cornell University Press, 2021. 276 pp. In post-Soeharto Indonesia, religion should be an uncomplicated matter. Since [...]

When selecting fillers to include in a police lineup, one must consider the level of similarity between the suspect and potential fillers. In order to reduce misidentifications, an innocent suspect should not stand out. Therefore, it is important that the fillers share some degree of similarity. Importantly, increasing suspect-filler similarity too much will render the task too difficult reducing correct identifications of a guilty suspect. Determining how much similarity yields optimal identification performance is the focus of the proposed study. Extant research on lineup construction has provided somewhat mixed results. In part, this is likely due to the subjective nature of similarity, which forces researchers to define similarity in relative terms. In the current study, we manipulate suspect-filler similarity via a multidimensional scaling model constructed using objective facial measurements. In doing so, we test the "propitious heterogeneity" and the diagnostic-feature-detection hypotheses which predict an advantage of lineups with low-similarity fillers in terms of discriminability. We found that filler similarity did not affect discriminability. We discuss limitations and future directions.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic and debilitating disease characterized by unexplained physical fatigue, cognitive and sensory dysfunction, sleeping disturbances, orthostatic intolerance, and gastrointestinal problems. People with ME/CFS often report a prodrome consistent with infections. Using regression, Bayesian and enrichment analyses, we conducted targeted and untargeted metabolomic analysis of plasma from 106 ME/CFS cases and 91 frequency-matched healthy controls. Subjects in the ME/CFS group had significantly decreased levels of plasmalogens and phospholipid ethers (p < 0.001), phosphatidylcholines (p < 0.001) and sphingomyelins (p < 0.001), and elevated levels of dicarboxylic acids (p = 0.013). Using machine learning algorithms, we were able to differentiate ME/CFS or subgroups of ME/CFS from controls with area under the receiver operating characteristic curve (AUC) values up to 0.873. Our findings provide the first metabolomic evidence of peroxisomal dysfunction, and are consistent with dysregulation of lipid remodeling and the tricarboxylic acid cycle. These findings, if validated in other cohorts, could provide new insights into the pathogenesis of ME/CFS and highlight the potential use of the plasma metabolome as a source of biomarkers for the disease.

When selecting fillers to include in a police lineup, one must consider the level of similarity between the suspect and potential fillers. In order to reduce misidentifications, an innocent suspect should not stand out. Therefore, it is important that the fillers share some degree of similarity. Importantly, increasing suspect-filler similarity too much will render the task too difficult reducing correct identifications of a guilty suspect. Determining how much similarity yields optimal identification performance is the focus of the proposed study. Extant research on lineup construction has provided somewhat mixed results. In part, this is likely because similarity is often defined in relative terms due to the subjective nature of similarity. In the current study, we propose an experiment in which we manipulate suspect-filler similarity via a multidimensional scaling model constructed using objective facial measurements. In doing so, we test the "propitious heterogeneity" and the diagnostic-feature-detection hypotheses which predict an advantage of lineups with low similarity fillers in terms of discriminability.

There is an increasing need in eyewitness identification research to identify factors that not only influence identification accuracy but may also impact the confidence--accuracy (CA) relationship. One such variable that has a notable impact on memory for faces is viewing distance, with faces encoded from a shorter distance remembered better than faces encoded at longer differences. In four pre-registered experiments, using both laboratory and online samples, we compared faces viewed at a simulated viewing distance at two different levels (medium and far) to faces that were viewed at a very near-simulated distance. Distance was simulated using a Gaussian blur function with higher levels of blur corresponding to greater simulated distance. We found that both medium and far simulated distances impaired memory performance overall relative to no simulated distance, with increased distance resulting in poorer memory. However, only far simulated distances impaired the CA relationship. In a fourth experiment, we found that a pre-test warning did not ameliorate this impairment of the CA relationship for faces viewed at a far simulated distance. These findings suggest that even high-confidence identifications made for faces viewed from long distances should be disregarded, and that estimator variables that impact memory may degrade the CA relationship when memory is reduced to critical levels.

Research suggests exposure to misinformation continues to impact belief and reasoning, even if that misinformation has been corrected (referred to as the Continued Influence Effect, CIE). The present experiment explores two potentially important factors that may impact the effect: (1) learner age; and (2) length of delay between retraction and final test. During initial learning, participants (both young and older adults) read six scenarios in which a critical piece of misinformation was either retracted or not retracted. Following no delay, a short (10 min) delay, or a long (2 days) delay, participants then answered inferential reasoning questions about the previously studied scenarios to evaluate how (if at all) the prior retraction impacts reliance on misinformation. Outcomes help us to understand the ways in which misinformation (even following retraction) impacts reasoning, an issue of exceeding importance as the proliferation of fake news shows no signs of slowing.

Presenting information in a perceptually disfluent format sometimes enhances memory. Recent work examining 1 type of perceptual disfluency manipulation, Sans Forgetica typeface, has yielded discrepant findings; some studies find support for the idea that the disfluent typeface improves memory whereas others do not. The current study examined a boundary condition that determines when disfluency is and is not beneficial to learning to explore this discrepancy. Specifically, we investigated whether knowledge about an upcoming test (high test expectancy) versus not (low test expectancy) helps clarify when mnemonic benefits arise for perceptually disfluent stimuli. In Experiment 1 (preregistered, N = 231), we found that Sans Forgetica is a memory-improving desirable difficulty, but only when there was no expectation of a final test. In Experiment 2 (preregistered, N = 232), we conceptually replicated the Sans Forgetica effect using a cued-recall test. In Experiment 3 (preregistered, N = 232), we ruled out a time-on-task explanation while replicating the results of Experiment 2. Though these data provide some evidence of San Forgetica's mnemonic benefits, caution should be taken in interpreting these results. Not only were the effect sizes moderate, but low test expectancy may not be realistically achievable in actual educational contexts. Though more research is warranted, we echo our prior arguments that students wanting to remember more and forget less should stick to other, more empirically supported desirable difficulties.

Research suggests exposure to misinformation continues to impact belief and reasoning, even if that misinformation has been corrected (referred to as the "Continued Influence Effect, CIE"). The proposed experiment explores two potentially important factors that may impact the effect: (a) learner age and (b) length of delay between retraction and final test. During initial learning, participants (both young and older adults) will read six scenarios in which a critical piece of misinformation is either retracted or not retracted. Following no delay, a short (10 min) delay, or a long (2 days) delay, participants will then answer inferential reasoning questions about the previously-studied scenarios to evaluate how (if at all) the prior retraction impacts reliance on misinformation. Outcomes will better help us to understand the ways in which misinformation (even following retraction) impacts reasoning, an issue of exceeding importance as the proliferation of fake news shows no signs of slowing.

Introduction: Patients with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) experience cognitive problems with attention, information processing speed, working memory, learning efficiency, and executive function. Commonly, patients report worsening of cognitive symptoms over time after physical and/or cognitive challenges. To determine, monitor, and manage longitudinal decrements in cognitive function after such exposures, it is important to be able to screen for cognitive dysfunction and changes over time in clinic and also remotely at home. The primary objectives of this paper were: (1) to determine whether a brief computerized cognitive screening battery will detect differences in cognitive function between ME/CFS and Healthy Controls (HC), (2) to monitor the impact of a full-day study visit on cognitive function over time, and (3) to evaluate the impact of exercise testing on cognitive dysfunction. Methods: This cognitive sub-study was conducted between 2013 and 2019 across seven U.S. ME/CFS clinics as part of the Multi-Site Clinical Assessment of ME/CFS (MCAM) study. The analysis included 426 participants (261 ME/CFS and 165 HC), who completed cognitive assessments including a computerized CogState Brief Screening Battery (CBSB) administered across five timepoints (T0-T4) at the start of and following a full day in-clinic visit that included exercise testing for a subset of participants (182 ME/CFS and 160 HC). Exercise testing consisted of ramped cycle ergometry to volitional exhaustion. The primary outcomes are performance accuracy and latency (performance speed) on the computerized CBSB administered online in clinic (T0 and T1) and at home (T2-T4). Results: No difference was found in performance accuracy between ME/CFS and HCs whereas information processing speed was significantly slower for ME/CFS at most timepoints with Cohen's d effect sizes ranging from 0.3–0.5 (p < 0.01). The cognitive decline over time on all CBSB tasks was similar for patients with ME/CFS independent of whether exercise testing was included in the clinic visit. Conclusion: The challenges of a clinic visit (including cognitive testing) can lead to further cognitive deficits. A single short session of intense exercise does not further reduce speed of performance on any CBSB tasks. [ABSTRACT FROM AUTHOR]

The pathogenesis of ME/CFS, a disease characterized by fatigue, cognitive dysfunction, sleep disturbances, orthostatic intolerance, fever, irritable bowel syndrome (IBS), and lymphadenopathy, is poorly understood. We report biomarker discovery and topological analysis of plasma metabolomic, fecal bacterial metagenomic, and clinical data from 50 ME/CFS patients and 50 healthy controls. We confirm reports of altered plasma levels of choline, carnitine and complex lipid metabolites and demonstrate that patients with ME/CFS and IBS have increased plasma levels of ceramide. Integration of fecal metagenomic and plasma metabolomic data resulted in a stronger predictive model of ME/CFS (cross-validated AUC = 0.836) than either metagenomic (cross-validated AUC = 0.745) or metabolomic (cross-validated AUC = 0.820) analysis alone. Our findings may provide insights into the pathogenesis of ME/CFS and its subtypes and suggest pathways for the development of diagnostic and therapeutic strategies.

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.