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Sickle cell disease (SCD) is a collection of genetic lesions that manifest in the diminished effectiveness of hemoglobin. We collected and reviewed the recent and extant literature on SARS-CoV-2 (COVID-19) and SCD. We posit an answer to the question associated with any adaptive responses to COVID-19 in individuals with SCD. We collected papers from MEDLINE and all available published papers on COVID-19 and SCD. Unlike a formal meta-analysis, given the early phase of this review in the pandemic, we did not seek unpublished papers. We found an emerging literature where case studies dominated, and traditional large N epidemiological studies were absent. Patients with SCD share many comorbid illnesses with an increased risk of mortality associated with contracting COVID-19. There is sufficient empirical justification to accelerate research on the impact of a viral pathogen like COVID-19 on individuals with SCD. *************************************************************** List of all authors: Michaela Boggan,1,2,3 Christopher L. Edwards,1,2,3 Jordan Meek,1,2,3 Mary Wood,4 W. Jeff Bryson,5 John J. Sollers,1,2,3 Debra O. Parker,1,2,3 Camela S. Barker,2,5 Jessica Miller,2,6 Brianna Downey,2,5 Asha Lockett,2,5 Jazmin Rosales,1,2,3 Courtney Munroe, Jr.,2 Noa Wax,2,5 Sharena Scott,1,2,3 Bridget Pittman,1,2,3 Merell Turner,1,2,3 Hillary T. Dietahin,1,2,3 Eric Smith,1,2,3 Alexandria McDougald,1,2,3 Samantha Beavers,1,2,3 Lakaiya Meadows,1,2,3 Maya Walker,1,2,3 Andrea Richardson,1,2,3 John J. Sollers, IV,2,8 Grace D. Donahue,2,8 Goldie Byrd,7 Malik Muhammad,1,2 Alvin Kidd,9 Walter Charles,1,2 Jonathan Livingston,1,2,3 Shiv Sudhakar10 1North Carolina Central University; 2NCCU Psychoneuroendocrine and Rare Diseases Laboratory; 3NCCU Debra O. Parker Research Incubator; 4Duke University Medical Center; 5Fielding Graduate University; 6Bridges Point Sickle Cell Foundation; 7Wake Forest Medical Center; 8Thomas Moore University; 9Livingston College; 10California Northstate University, United States

ABSTRACT Zinc cluster transcription factors (ZCFs) are a family of transcription regulators that are almost exclusively found in the fungal kingdom. Activating mutations in the ZCFs Mrr1, Tac1, and Upc2 frequently cause acquired resistance to the widely used antifungal drug fluconazole in the pathogenic yeast Candida albicans. Similar to a hyperactive Tac1, a constitutively active form of the ZCF Znc1 causes increased fluconazole resistance by upregulating the multidrug efflux pump-encoding gene CDR1. Hyperactive forms of both Tac1 and Znc1 also cause overexpression of RTA3, which encodes a seven-transmembrane receptor protein involved in the regulation of asymmetric lipid distribution in the plasma membrane. RTA3 expression is also upregulated by miltefosine, an antiparasitic drug that is active against fungal pathogens and considered for treatment of invasive candidiasis, and rta3Δ mutants are hypersensitive to miltefosine. We found that activated forms of both Tac1 and Znc1 confer increased miltefosine resistance, which was dependent on RTA3 whereas CDR1 was dispensable. Intriguingly, the induction of RTA3 expression by miltefosine depended on Znc1, but not Tac1, in contrast to the known Tac1-dependent RTA3 upregulation by fluphenazine. In line with this observation, znc1Δ mutants were hypersensitive to miltefosine, whereas tac1Δ mutants showed wild-type tolerance. Forced expression of RTA3 reverted the hypersensitivity of znc1Δ mutants, demonstrating that the hypersensitivity was caused by the inability of the mutants to upregulate RTA3 in response to the drug. These findings establish Znc1 as a key regulator of miltefosine-induced RTA3 expression that is important for wild-type miltefosine tolerance.IMPORTANCETranscription factors are central regulators of gene expression, and knowledge about which transcription factor regulates specific genes in response to a certain signal is important to understand the behavior of organisms. In the pathogenic yeast Candida albicans, the RTA3 gene is required for wild-type tolerance of miltefosine, an antiparasitic drug that is considered for treatment of invasive candidiasis. Activated forms of the transcription factors Tac1 and Znc1 cause constitutive overexpression of RTA3 and thereby increased miltefosine resistance, but only Tac1 mediates upregulation of RTA3 in response to the known inducer fluphenazine. RTA3 expression is also induced by miltefosine, and we found that this response depends on Znc1, whereas Tac1 is dispensable. Consequently, znc1Δ mutants were hypersensitive to miltefosine, whereas tac1Δ mutants showed wild-type tolerance. These findings demonstrate that Znc1 is the key regulator of RTA3 expression in response to miltefosine that is important for wild-type miltefosine tolerance.

ABSTRACT The adaptation of gene deletion methods based on the CRISPR-Cas9 system has facilitated the genetic manipulation of the pathogenic yeast Candida albicans, because homozygous mutants of this diploid fungus can now be generated in a single step, allowing the rapid screening of candidate genes for their involvement in a phenotype of interest. However, the Cas9-mediated double-strand breaks at the target site may result in an undesired loss of heterozygosity (LOH) on the affected chromosome and cause phenotypic alterations that are not related to the function of the investigated gene. In our present study, we harnessed Cas9-facilitated gene deletion to probe a set of genes that are constitutively overexpressed in strains containing hyperactive forms of the transcription factor Mrr1 for a possible contribution to the fluconazole resistance of such strains. To this aim, we used gene deletion cassettes containing two different dominant selection markers, caSAT1 and HygB, which confer resistance to nourseothricin and hygromycin, respectively, for simultaneous genomic integration in a single step, hypothesizing that this would minimize undesired LOH events at the target locus. We found that selection for resistance to both nourseothricin and hygromycin strongly increased the proportion of homozygous deletion mutants among the transformants compared with selection on media containing only one of the antibiotics, but it did not avoid undesired LOH events. Our results demonstrate that LOH on the target chromosome is a significant problem when using Cas9 for the generation of C. albicans gene deletion mutants, which demands a thorough examination of recombination events at the target site.IMPORTANCECandida albicans is one of the medically most important fungi and a model organism to study fungal pathogenicity. Investigating gene function in this diploid yeast has been facilitated by the adaptation of gene deletion methods based on the bacterial CRISPR-Cas9 system, because they enable the generation of homozygous mutants in a single step. We found that, in addition to increasing the efficiency of gene replacement by selection markers, the Cas9-mediated double-strand breaks also result in frequent loss of heterozygosity on the same chromosome, even when two different selection markers were independently integrated into the two alleles of the target gene. Since loss of heterozygosity for other genes can result in phenotypic alterations that are not caused by the absence of the target gene, these findings show that it is important to thoroughly analyze recombination events at the target locus when using Cas9 to generate gene deletion mutants in C. albicans.

Abstract The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant–herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.

Climate tipping elements are large-scale subsystems of the Earth that may transgress critical thresholds (tipping points) under ongoing global warming, with substantial impacts on the biosphere and human societies. Frequently studied examples of such tipping elements include the Greenland Ice Sheet, the Atlantic Meridional Overturning Circulation (AMOC), permafrost, monsoon systems, and the Amazon rainforest. While recent scientific efforts have improved our knowledge about individual tipping elements, the interactions between them are less well understood. Also, the potential of individual tipping events to induce additional tipping elsewhere or stabilize other tipping elements is largely unknown. Here, we map out the current state of the literature on the interactions between climate tipping elements and review the influences between them. To do so, we gathered evidence from model simulations, observations, and conceptual understanding, as well as examples of paleoclimate reconstructions where multi-component or spatially propagating transitions were potentially at play. While uncertainties are large, we find indications that many of the interactions between tipping elements are destabilizing. Therefore, we conclude that tipping elements should not only be studied in isolation, but also more emphasis has to be put on potential interactions. This means that tipping cascades cannot be ruled out on centennial to millennial timescales at global warming levels between 1.5 and 2.0 ∘C or on shorter timescales if global warming surpassed 2.0 ∘C. At these higher levels of global warming, tipping cascades may then include fast tipping elements such as the AMOC or the Amazon rainforest. To address crucial knowledge gaps in tipping element interactions, we propose four strategies combining observation-based approaches, Earth system modeling expertise, computational advances, and expert knowledge.

Prior research suggests COVID-19 has amplified stress on Academic Clinician Frontline-Workers (ACFW). The aim of this paper is: (1) to better understand the experiences of ACFW during the COVID-19 pandemic including their mental-emotional wellbeing, academic productivity, clinical experiences, and (2) to examine any gender differences. A cross-sectional survey was administered to University of Minnesota/M Health Fairview systems’ faculty February-June 2021. Of the 291 respondents, 156 were clinicians, with 91 (58 %) identifying as Frontline-Workers (ACFW). Faculty wellbeing was assessed using validated measures in addition to measures of productivity and sociodemographics. For example, ACFW reported a higher Work-Family Conflict (WFC) scores compared to non-ACFW (26.5 vs. 24.1, p = 0.057) but did not report higher Family-Work Conflict (FWC) scores (17.7 vs. 16.3, p = 0.302). Gender sub-analyses, revealed that women ACFW compared to men ACFW reported higher WFC scores (27.7 vs. 24.1, p = 0.021) and FWC (19.3 vs. 14.3, p = 0.004). Academically, ACFW reported submitting fewer grants and anticipated delays in promotion and tenure due to the COVID-19 (p = 0.035). Results suggest COVID-19 has exacerbated ACFW stress and gender inequities. Reports of anticipated delay in promotion for ACFW may pose a challenge for the long-term academic success of ACFW, especially women ACFW. In addition, women may experience higher FWC and WFC as compared to men. Schools of academic medicine should consider re-evaluating promotion/tenure processes and creating resources to support women ACFW as well as ACFW caregivers.

Summary: Recent studies have revealed cellular heterogeneity of mesenchymal stromal cells and immune cells in adipose tissue and emphasized the need for quantitative analysis of small numbers of functionally distinct cells using state-of-the-art “omics” technologies. Here, we present an optimized protocol for precise protein quantification from minute amounts of samples. We describe steps for isolation of mouse adipose progenitor cells, proteomics sample preparation, mass spectrometry measurement, and computational analysis. This protocol can be adapted to other samples with limited amounts.For complete details on the use and execution of this protocol, please refer to Shan et al. (2022).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Abstract Premise The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in. For a set of genes, summarizing GO annotations using pre‐defined, higher‐order terms (GO slims) is often desirable in order to characterize the overall function of the data set, and it is impractical to do this manually. Methods and Results The GOgetter pipeline consists of bash and Python scripts. From an input FASTA file of nucleotide gene sequences, it outputs text and image files that list (1) the best hit for each input gene in a set of reference gene models, (2) all GO terms and annotations associated with those hits, and (3) a summary and visualization of GO slim categories for the data set. These output files can be queried further and analyzed statistically, depending on the downstream need(s). Conclusions GO annotations are a widely used “universal language” for describing gene functions and products. GOgetter is a fast and easy‐to‐implement pipeline for obtaining, summarizing, and visualizing GO slim categories associated with a set of genes.

Readily accessible and easily understood forecasts of the phenology of invasive insects have the potential to support and improve strategic and tactical decisions for insect surveillance and management. However, most phenological modeling tools developed to date are site-based, meaning that they use data from a weather station to produce forecasts for that single site. Spatial forecasts of phenology, or phenological maps, are more useful for decision-making at area-wide scales, such as counties, states, or entire nations. In this review, we provide a brief history on the development of phenological mapping technologies with a focus on degree-day models and their use as decision support tools for invasive insect species. We compare three different types of phenological maps and provide examples using outputs of web-based platforms that are presently available for real-time mapping of invasive insects for the contiguous United States. Next, we summarize sources of climate data available for real-time mapping, applications of phenological maps, strategies for balancing model complexity and simplicity, data sources and methods for validating spatial phenology models, and potential sources of model error and uncertainty. Lastly, we make suggestions for future research that may improve the quality and utility of phenological maps for invasive insects.

Despite extensive characterization of crassulacean acid metabolism (CAM) in terrestrial angiosperms, little attention has been given to aquatics and early diverging land plants. Here, the authors assemble the genome of Isoetes taiwanensis and investigate the genetic factors driving CAM in this aquatic lycophyte.

Abstract Cardiovacular disease (CVD) is the leading cause of death among older adults and is often accompanied by functional decline. It is unclear what is driving this co-occurrence, but it may be behavioral, environmental and/or genetic. We used a family-based study to estimate the phenotypic and shared genetic correlation between CVD risk factors and physical and cognitive functional measures. Participants (n = 1,881) were from the Long Life Family Study, which enrolled families based on their exceptional longevity (sample mean age = 69.4 years, 44% female). Cardiovascular disease risk factors included carotid vessel measures [intima-media thickness and inter-adventitial diameter], obesity [body mass index (BMI) and waist circumference], and hypertension [systolic and diastolic blood pressures]. Function was measured in the physical [gait speed, grip strength, chair stand] and cognitive [digital symbol substitution test, retained and working memory, semantic fluency, and trail making tests] domains. We used SOLAR to estimate the genetic, environmental, and phenotypic correlation between each pair adjusting for age, age2, sex, field center, smoking, height, and weight. There were significant phenotypic correlations (range |0.05–0.22|) between CVD risk factors and physical and cognitive function (all P

Coptis chinensis represents an early-diverging eudicot lineage with diverse medicinal applications. Here, the authors report its chromosome-scale genome assembly, infer a single ancient whole-genome duplication, and characterize the function of CYP719 in diversification of protoberberine-type alkaloids.

Abstract Background Dementia with Lewy bodies (DLB) and dementia in Parkinson’s disease (PDD) are recognised to be under-recognised in clinical practice in the UK, with only one third to a half of expected cases diagnosed. We aimed to assess whether clinical diagnostic rates could be increased by the introduction of a structured assessment toolkit for clinicians. Methods We established baseline diagnostic rates for DLB and PDD in four memory clinics and three movement disorder/Parkinson’s disease (PD) clinics in two separate geographical regions in the UK. An assessment toolkit specifically developed to assist with the recognition and diagnosis of DLB and PDD was then introduced to the same clinical teams and diagnostic rates for DLB and PDD were reassessed. For assessing DLB diagnosis, a total of 3820 case notes were reviewed before the introduction of the toolkit, and 2061 case notes reviewed after its introduction. For PDD diagnosis, a total of 1797 case notes were reviewed before the introduction of the toolkit and 3405 case notes after it. Mean values and proportions were analysed using Student’s t test for independent samples and χ 2 test, respectively. Results DLB was diagnosed in 4.6% of dementia cases prior to the introduction of the toolkit, and 6.2% of dementia cases afterwards, an absolute rise of 1.6%, equal to a 35% increase in the number of DLB cases diagnosed when using the toolkit (χ 2 = 4.2, P = 0.041). The number of PD patients diagnosed with PDD was not found overall to be significantly different when using the toolkit: 9.6% of PD cases before and 8.2% of cases after its introduction (χ 2 = 1.8, P = 0.18), though the ages of PD patients assessed after the toolkit’s introduction were lower (73.9 years vs 80.0 years, t = 19.2, p

ObjectiveSubjective cognitive decline (SCD) has emerged as one of the first manifestations of Alzheimer’s disease (AD). However, discrepancies in its relationship with tests of memory and other cognitive abilities have hindered SCD’s diagnostic utility. Inter-individual heterogeneity in metamemory, or memory awareness, and the use of clinical measures of cognition lacking sensitivity to early cognitive dysfunction, may contribute to these discrepancies. We aimed to assess if the relationship between SCD and markers of early cognitive dysfunction is moderated by metamemory abilities.MethodsThe sample included 79 cognitively healthy older adults (77% female, 68% White, and 32% Black participants) with a mean age of 74.4 (SD = 6.1) and 15.9 (SD = 2.7) years of education. Metamemory was assessed using an episodic Feeling of Knowing test with four 5-item trials. Outcome measures included a resolution metric defined as a gamma correlation reflecting the accuracy of item-level predictions (“Will you know the correct answer?”). Early cognitive dysfunction was measured through the Loewenstein-Acevedo Scale for Semantic Interference and Learning (LASSI-L) and the Short-Term Memory Binding Test (STMB), measures sensitive to preclinical AD. SCD was assessed with a 20-item questionnaire that asked participants to compare themselves to others their age on a 7-point Likert scale. Regression analyses examined whether a potential relation between SCD and early cognitive dysfunction was moderated by metamemory.ResultsSubjective cognitive decline was associated with susceptibility to semantic proactive interference such that greater complaints were associated with increased susceptibility to semantic proactive interference (b = −0.30, p = 0.003) only. Metamemory moderated the association between SCD and susceptibility to and recovery of semantic proactive interference such that those with more accurate metamemory showed a stronger association between increased complaints and susceptibility to semantic proactive interference (b = −0.71, p = 0.005; b = −0.62, p = 0.034). Metamemory, however, did not moderate the association of SCD with retroactive semantic interference nor short term memory binding.DiscussionThe accuracy of an individual’s metamemory, specifically their ability to adjust moment to moment predictions in line with their performance, can influence the extent to which SCD maps onto objective cognition. Such self-referential assessment should be considered when interpreting SCD.

Pharmacokinetics are highly variable in critical illness, and suboptimal antibiotic exposure is associated with treatment failure. Benzylpenicillin is a commonly used beta-lactam antibiotic, and pharmacokinetic data of its use in critically ill adults are lacking. We performed a pharmacokinetic study of critically unwell patients receiving benzylpenicillin, using data from the ABDose study. Population pharmacokinetic modelling was undertaken using NONMEM version 7.5, and simulations using the final model were undertaken to optimize the pharmacokinetic profile. We included 77 samples from 12 participants. A two-compartment structural model provided the best fit, with allometric weight scaling for all parameters and a creatinine covariate effect on clearance. Simulations (n = 10,000) demonstrated that 25% of simulated patients receiving 2.4 g 4-hourly failed to achieve a conservative target of 50% of the dosing interval with free drug above the clinical breakpoint MIC (2 mg/L). Simulations demonstrated that target attainment was improved with continuous or extended dosing. To our knowledge, this study represents the first full population PK analysis of benzylpenicillin in critically ill adults.

ABSTRACT Resistance to fluconazole is one of clinical characteristics most frequently challenging the treatment of invasive Candida auris infections, and is observed among >90% of all characterized clinical isolates. In this work, the native C. auris ERG11 allele in a previously characterized fluconazole-susceptible clinical isolate was replaced with the ERG11 alleles from three highly fluconazole-resistant clinical isolates (MIC ≥256 mg/L), encoding the amino acid substitutions VF125AL, Y132F, and K143R, using Cas9-ribonucleoprotein (RNP) mediated transformation system. Reciprocally, the ERG11WT allele from the same fluconazole-susceptible clinical isolate, lacking any resistance-associated mutation, was introduced into a previously characterized fluconazole-resistant clinical isolate, replacing the native ERG11K143R allele, using the same methods. The resulting collection of strains was subjected to comprehensive triazole susceptibility testing, and the direct impact each of these clinically-derived ERG11 mutations on triazole MIC was determined. Introduction of each of the three mutant ERG11 alleles was observed to increase fluconazole and voriconazole MIC by 8- to 16-fold. The MIC for the other clinically available triazoles were not significantly impacted by any ERG11 mutation. In the fluconazole-resistant clinical isolate background, correction of the K143R encoding mutation led to a similar 16-fold decrease in fluconazole MIC, and 8-fold decrease in voriconazole MIC, while the MIC of other triazoles were minimally changed. Taken together, these findings demonstrate that mutations in C. auris ERG11 significantly contribute to fluconazole and voriconazole resistance, but alone cannot explain the substantially elevated MIC observed among clinical isolates of C. auris. IMPORTANCE Candida auris is an emerging multidrug-resistant and health care-associated pathogen of urgent clinical concern. The triazoles are the most widely prescribed antifungal agents worldwide and are commonly utilized for the treatment of invasive Candida infections. Greater than 90% of all C. auris clinical isolates are observed to be resistant to fluconazole, and nearly all fluconazole-resistant isolates of C. auris are found to have one of three mutations (encoding VF125AL, Y132F, or K143R) in the gene encoding the target of the triazoles, ERG11. However, the direct contribution of these mutations in ERG11 to fluconazole resistance and the impact these mutations may have the susceptibility of the other triazoles remains unknown. The present study seeks to address this knowledge gap and potentially inform the future application the triazole antifungals for the treatment of infections caused by C. auris.

We study the forces and optical pumping within grating magneto-optical traps (MOTs) operating on transitions with non-trivial level structure. In contrast to the standard six-beam MOT configuration, rate equation modeling predicts that the asymmetric laser geometry of a grating MOT will produce spin-polarized atomic samples. Furthermore, the Landé g -factors and total angular momenta of the trapping transition strongly influence both the confinement and equilibrium position of the trap. Using the intuition gained from the rate equation model, we realize a grating MOT of fermionic ^87 Sr and observe that it forms closer to the center of the trap’s quadrupole magnetic field than its bosonic counterpart. We also explore the application of grating MOTs to molecule laser cooling, where the rate equations suggest that dual-frequency operation is necessary, but not sufficient, for stable confinement for type-II level structures. To test our molecule laser cooling models, we create grating MOTs using the D _1 line of ^7 Li and see that only two of the four possible six-beam polarization configurations operate in the grating geometry. Our results will aid the development of portable atom and molecule traps for time keeping, inertial navigation, and precision measurement.

Vulvovaginal candidiasis (VVC), caused primarily by the human fungal pathogen Candida albicans, results in significant quality-of-life issues for women worldwide. Candidalysin, a toxin derived from a polypeptide (Ece1p) encoded by the ECE1 gene, plays a crucial role in driving immunopathology at the vaginal mucosa. This study aimed to determine if expression and/or processing of Ece1p differs across C. albicans isolates and whether this partly underlies differential pathogenicity observed clinically. Using a targeted sequencing approach, we determined that isolate 529L harbors a similarly expressed, yet distinct Ece1p isoform variant that encodes for a predicted functional candidalysin; this isoform was conserved amongst a collection of clinical isolates. Expression of the ECE1 open reading frame (ORF) from 529L in an SC5314-derived ece1Δ/Δ strain resulted in significantly reduced vaginopathogenicity as compared to an isogenic control expressing a wild-type (WT) ECE1 allele. However, in vitro challenge of vaginal epithelial cells with synthetic candidalysin demonstrated similar toxigenic activity amongst SC5314 and 529L isoforms. Creation of an isogenic panel of chimeric strains harboring swapped Ece1p peptides or HiBiT tags revealed reduced secretion with the ORF from 529L that was associated with reduced virulence. A genetic survey of 78 clinical isolates demonstrated a conserved pattern between Ece1p P2 and P3 sequences, suggesting that substrate specificity around Kex2p-mediated KR cleavage sites involved in protein processing may contribute to differential pathogenicity amongst clinical isolates. Therefore, we present a new mechanism for attenuation of C. albicans virulence at the ECE1 locus.

New ice cores retrieved from the Taylor Glacier (Antarctica) blue ice area contain ice and air spanning the Marine Isotope Stage (MIS) 5–4 transition, a period of global cooling and ice sheet expansion. We determine chronologies for the ice and air bubbles in the new ice cores by visually matching variations in gas- and ice-phase tracers to preexisting ice core records. The chronologies reveal an ice age–gas age difference (Δage) approaching 10 ka during MIS 4, implying very low snow accumulation in the Taylor Glacier accumulation zone. A revised chronology for the analogous section of the Taylor Dome ice core (84 to 55 ka), located to the south of the Taylor Glacier accumulation zone, shows that Δage did not exceed 3 ka. The difference in Δage between the two records during MIS 4 is similar in magnitude but opposite in direction to what is observed at the Last Glacial Maximum. This relationship implies that a spatial gradient in snow accumulation existed across the Taylor Dome region during MIS 4 that was oriented in the opposite direction of the accumulation gradient during the Last Glacial Maximum.

The concentration of CO2 in the atmosphere is sensitive to changes in the depth at which sinking particulate organic matter is remineralized: often described as a change in the exponent “b” of the Martin curve. Sediment trap observations from deep and intermediate depths suggest there is a spatially heterogeneous pattern of b, particularly varying with latitude, but disagree over the exact spatial patterns. Here we use a biogeochemical model of the phosphorus cycle coupled with a steady-state representation of ocean circulation to explore the sensitivity of preformed phosphate and atmospheric CO2 to spatial variability in remineralization depths. A Latin hypercube sampling method is used to simultaneously vary the Martin curve independently within 15 different regions, as a basis for a regression-based analysis used to derive a quantitative measure of sensitivity. Approximately 30 % of the sensitivity of atmospheric CO2 to changes in remineralization depths is driven by changes in the subantarctic region (36 to 60∘ S) similar in magnitude to the Pacific basin despite the much smaller area and lower export production. Overall, the absolute magnitude of sensitivity is controlled by export production, but the relative spatial patterns in sensitivity are predominantly constrained by ocean circulation pathways. The high sensitivity in the subantarctic regions is driven by a combination of high export production and the high connectivity of these regions to regions important for the export of preformed nutrients such as the Southern Ocean and North Atlantic. Overall, regionally varying remineralization depths contribute to variability in CO2 of between around 5 and 15 ppm, relative to a global mean change in remineralization depth. Future changes in the environmental and ecological drivers of remineralization, such as temperature and ocean acidification, are expected to be most significant in the high latitudes where CO2 sensitivity to remineralization is also highest. The importance of ocean circulation pathways to the high sensitivity in subantarctic regions also has significance for past climates given the importance of circulation changes in the Southern Ocean.

Despite the economic importance of the allotetraploid crop Brassica napus, our knowledge of its phylogenomic relationships, genetic structure, and diversification is limited. Here, the authors show its complex origin and diversification by analyzing transcriptome and organellar sequencing data.

Premise Large‐scale projects such as the National Ecological Observatory Network (NEON) collect ecological data on entire biomes to track climate change. NEON provides an opportunity to launch community transcriptomic projects that ask integrative questions in ecology and evolution. We conducted a pilot study to investigate the challenges of collecting RNA‐seq data from diverse plant communities. Methods We generated >650 Gbp of RNA‐seq for 24 vascular plant species representing 12 genera and nine families at the Harvard Forest NEON site. Each species was sampled twice in 2016 (July and August). We assessed transcriptome quality and content with TransRate, BUSCO, and Gene Ontology annotations. Results Only modest differences in assembly quality were observed across multiple k‐mers. On average, transcriptomes contained hits to >70% of loci in the BUSCO database. We found no significant difference in the number of assembled and annotated transcripts between diploid and polyploid transcriptomes. Discussion We provide new RNA‐seq data sets for 24 species of vascular plants in Harvard Forest. Challenges associated with this type of study included recovery of high‐quality RNA from diverse species and access to NEON sites for genomic sampling. Overcoming these challenges offers opportunities for large‐scale studies at the intersection of ecology and genomics.

Boxwood blight caused by Cps is an emerging disease that has had devastating impacts on Buxus spp. in the horticultural sector, landscapes, and native ecosystems. In this study, we produced a process-based climatic suitability model in the CLIMEX program and combined outputs of four different correlative modeling algorithms to generate an ensemble correlative model. All models were fit and validated using a presence record dataset comprised of Cps detections across its entire known invaded range. Evaluations of model performance provided validation of good model fit for all models. A consensus map of CLIMEX and ensemble correlative model predictions indicated that not-yet-invaded areas in eastern and southern Europe and in the southeastern, midwestern, and Pacific coast regions of North America are climatically suitable for Cps establishment. Most regions of the world where Buxus and its congeners are native are also at risk of establishment. These findings provide the first insights into Cps global invasion threat, suggesting that this invasive pathogen has the potential to significantly expand its range.

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. Based on an abstract mathematical model able to capture the parameters and behaviors of a population of single-celled organisms whose survival is correlated to information retrieval from the environment, this paper explores the aforementioned disconnect between classical information theory and biology. In this paper, we present a model, specified as a computational state machine, which is then utilized in a simulation framework constructed specifically to reveal emergence of a “subjective information”, i.e., trade-off between a living system’s capability to maximize the acquisition of information from the environment, and the maximization of its growth and survival over time. Simulations clearly show that a strategy that maximizes information efficiency results in a lower growth rate with respect to the strategy that gains less information but contains a higher meaning for survival.

Initiation and inhibition are executive functions whose disruption in Parkinson's disease impacts substantially on everyday activities. Management of Parkinson's disease with subthalamic deep brain stimulation (DBS) modifies initiation and inhibition, with prior work suggesting that these effects may be mediated via the connectivity of the subthalamic nucleus (STN) with the frontal cortex. Here, we employed high-resolution structural neuroimaging to investigate the variability in initiation, inhibition and strategy use in a cohort of twenty-five (ten females, mean age 62.5, mean Hoehn and Yahr stage 2.5) participants undertaking subthalamic DBS for Parkinson's disease. Neuropsychological assessment of initiation and inhibition was performed preoperatively and at six months postoperatively. We first reconstructed the preoperative connectivity of the STN with a frontal network of anterior and superior medial cortical regions. We then modelled the postoperative site of subthalamic stimulation and reconstructed the connectivity of the stimulation field within this same network. We found that, at both pre- and postoperative intervals, inter-individual variability in inhibition and initiation were strongly associated with structural network connectivity. Measures of subcortical atrophy and local stimulation effects did not play a significant role. Preoperatively, we replicated prior work, including a role for the right inferior frontal gyrus in inhibition and strategy use, as well as the left inferior frontal gyrus in tasks requiring selection under conditions of maintained inhibition. Postoperatively, greater connectivity of the stimulation field with right anterior cortical regions was associated with greater rule violations and suppression errors, supporting prior work implicating right-hemispheric STN stimulation in disinhibition. Our findings suggest that, in Parkinson's disease, connectivity of the frontal cortex with the STN is an important mediator of individual variability in initiation and inhibition,. Personalised information on brain network architecture could guide individualised brain circuit manipulation to minimise neuropsychological disruption after STN-DBS.

ABSTRACT Candida auris has emerged as a multidrug-resistant pathogen of great clinical concern. Approximately 90% of clinical C. auris isolates are resistant to fluconazole, the most commonly prescribed antifungal agent, and yet it remains unknown what mechanisms underpin this fluconazole resistance. To identify novel mechanisms contributing to fluconazole resistance in C. auris, fluconazole-susceptible C. auris clinical isolate AR0387 was passaged in media supplemented with fluconazole to generate derivative strains which had acquired increased fluconazole resistance in vitro. Comparative analyses of comprehensive sterol profiles, [3H]fluconazole uptake, sequencing of C. auris genes homologous to genes known to contribute to fluconazole resistance in other species of Candida, and relative expression levels of C. auris ERG11, CDR1, and MDR1 were performed. All fluconazole-evolved derivative strains were found to have acquired mutations in the zinc-cluster transcription factor-encoding gene TAC1B and to show a corresponding increase in CDR1 expression relative to the parental clinical isolate, AR0387. Mutations in TAC1B were also identified in a set of 304 globally distributed C. auris clinical isolates representing each of the four major clades. Introduction of the most common mutation found among fluconazole-resistant clinical isolates of C. auris into fluconazole-susceptible isolate AR0387 was confirmed to increase fluconazole resistance by 8-fold, and the correction of the same mutation in a fluconazole-resistant isolate, AR0390, decreased fluconazole MIC by 16-fold. Taken together, these data demonstrate that C. auris can rapidly acquire resistance to fluconazole in vitro and that mutations in TAC1B significantly contribute to clinical fluconazole resistance. IMPORTANCE Candida auris is an emerging multidrug-resistant pathogen of global concern, known to be responsible for outbreaks on six continents and to be commonly resistant to antifungals. While the vast majority of clinical C. auris isolates are highly resistant to fluconazole, an essential part of the available antifungal arsenal, very little is known about the mechanisms contributing to resistance. In this work, we show that mutations in the transcription factor TAC1B significantly contribute to clinical fluconazole resistance. These studies demonstrated that mutations in TAC1B can arise rapidly in vitro upon exposure to fluconazole and that a multitude of resistance-associated TAC1B mutations are present among the majority of fluconazole-resistant C. auris isolates from a global collection and appear specific to a subset of lineages or clades. Thus, identification of this novel genetic determinant of resistance significantly adds to the understanding of clinical antifungal resistance in C. auris.

Summary:. The reversed glove sleeve technique is a simple, available, reproducible, and cost-effective method of achieving “no touch” breast implant insertion. It allows a new glove to be used for each side, thus reducing the risk of contamination by reusing a sleeve/funnel for the subsequent implant insertion. The link between bacterial contamination of breast implants and capsular contracture is established. Further prospective evaluation of this technique is underway to show if there is benefit in reducing the risk of capsular contracture.

ABSTRACT This research analyzed six Aspergillus fumigatus genes encoding putative efflux proteins for their roles as transporters. The A. fumigatus genes abcA, abcC, abcF, abcG, abcH, and abcI were cloned into plasmids and overexpressed in a Saccharomyces cerevisiae strain in which the highly active endogenous ABC transporter gene PDR5 was deleted. The activity of each transporter was measured by efflux of rhodamine 6G and accumulation of alanine β-naphthylamide. The transporters AbcA, AbcC, and AbcF had the strongest efflux activities of these compounds. All of the strains with plasmid-expressed transporters had more efflux activity than did the PDR5-deleted background strain. We performed broth microdilution drug susceptibility testing and agar spot assays using an array of compounds and antifungal drugs to determine the transporter specificity and drug susceptibility of the strains. The transporters AbcC and AbcF showed the broadest range of substrate specificity, while AbcG and AbcH had the narrowest range of substrates. Strains expressing the AbcA, AbcC, AbcF, or AbcI transporter were more resistant to fluconazole than was the PDR5-deleted background strain. Strains expressing AbcC and AbcF were additionally more resistant to clotrimazole, itraconazole, ketoconazole, and posaconazole than was the background strain. Finally, we analyzed the expression levels of the genes by reverse transcription-quantitative PCR (RT-qPCR) in triazole-susceptible and -resistant A. fumigatus clinical isolates. All of these transporters are expressed at a measurable level, and transporter expression varied significantly between strains, demonstrating the high degree of phenotypic variation, plasticity, and divergence of which this species is capable. IMPORTANCE One mechanism behind drug resistance is altered export out of the cell. This work is a multifaceted analysis of membrane efflux transporters in the human fungal pathogen A. fumigatus. Bioinformatics evidence infers that there is a relatively large number of genes in A. fumigatus that encode ABC efflux transporters. However, very few of these transporters have been directly characterized and analyzed for their potential role in drug resistance. Our objective was to determine if these undercharacterized proteins function as efflux transporters and then to better define whether their efflux substrates include antifungal drugs used to treat fungal infections. We chose six A. fumigatus potential plasma membrane ABC transporter genes for analysis and found that all six genes produced functional transporter proteins. We used two fungal systems to look for correlations between transporter function and drug resistance. These transporters have the potential to produce drug-resistant phenotypes in A. fumigatus. Continued characterization of these and other transporters may assist in the development of efflux inhibitor drugs.

Accurately predicting the mortality of trees that initially survive a fire event is important for management, such as planning post-fire salvage, planting, and prescribed fires. Although crown scorch has been successfully used to predict post-fire mortality (greater than one-year post-fire), it remains unclear whether other first-order fire effect metrics (e.g., stem char) and information on growing conditions can improve such predictions. Droughts can also elevate mortality and may interact, synergistically, with fire effects to influence post-fire tree survival. We used logistic regression to test whether drought exposure, as indicated by summarized monthly Palmer Drought Severity Index (PDSI) over ten-years could improve predictions of delayed mortality (4–9 years post-fire) at the individual tree level in fire-affected forest inventory and analysis (FIA) plots in California (USA). We included crown scorch, bark thickness, stem char, soil char, slope, and aspect in the model as predictors. We selected the six most prevalent species to include in the model: canyon live oak, Douglas-fir, Jeffrey pine, incense-cedar, ponderosa pine, and white fir. Mean delayed mortality, based on tree count, across all FIA plots across all tree species and plots was 17%, and overall accuracy was good (AUC = 79%). Our model performed well, correctly predicting survivor trees (sensitivity of 0.98) but had difficulty correctly predicting the smaller number of mortality trees (specificity of 0.27) at the standard probability=0.5 mortality threshold. Crown scorch was the most influential predictor of tree mortality. Increasing crown scorch was associated with greater risk of delayed mortality for all six species, with trees exhibiting over 75% crown scorch having a probability of dying that exceeded 0.5. Increasing levels of stem char and soil char (first order indicators) were associated with increasing mortality risk but to less effect than crown scorch. We expected that greater drought exposure would increase delayed post-fire mortality, but we found that increasing drought exposure (median and minimum PDSI) was associated with a modest decrease in post-fire mortality. However, we did find that trees with high levels of crown scorch were less likely to survive with increasing drought exposure (median PDSI). Delayed mortality risk decreased as terrain slope increased. Taken together, our results suggest that trees with substantial crown damage may be more vulnerable to delayed mortality if exposed to drought and that crown scorch is an effective post-fire mortality predictor up to 10 years post-fire.

Temporal lobe epilepsy (TLE) is a common form of adult epilepsy involving the limbic structures of the temporal lobe. Subiculum neurons act to provide a major output from the hippocampus and consist of a large population of endogenously bursting excitatory neurons. In TLE, subiculum neurons are largely spared, become hyperexcitable and show spontaneous epileptiform activity. The basis for this hyperexcitability is unclear, but is likely to involve alterations in the expression levels and function of various ion channels. In this study, we sought to determine the importance of sodium channel currents in facilitating neuronal hyperexcitability of subiculum neurons in the continuous hippocampal stimulation (CHS) rat model of TLE. Subiculum neurons from TLE rats were hyperexcitable, firing a higher frequency of action potentials after somatic current injection and action potential (AP) bursts after synaptic stimulation. Voltage clamp recordings revealed increases in resurgent (INaR) and persistent (INaP) sodium channel currents and pro-excitatory shifts in sodium channel activation and inactivation parameters that would facilitate increases in AP generation. Attenuation of INaR and INaP currents with 4,9-anhydro-tetrodotoxin (4,9-ah TTX; 100nM), a toxin with increased potency against Nav1.6 channels, suppressed neuronal firing frequency and inhibited AP bursting induced by synaptic stimulation in TLE neurons. These findings support an important role of sodium channels, particularly Nav1.6, in facilitating subiculum neuron hyperexcitability in TLE and provide further support for the importance of INaR and INaP currents in establishing epileptiform activity of subiculum neurons.

Abstract Background In a macro-molecular complex, any minor change may prove detrimental. For a supra-molecular nano-machine like the bacterial flagellum, which consists of several distinct parts with specific characteristics, stability is important. During the rotation of the bacterial flagellar motor, which is located in the membrane, the flagella rotate at speeds between 200 and 2000 rpm, depending on the bacterial species. The hook substructure of the bacterial flagellum acts as a universal joint connecting the motor to the flagellar filament. We investigated the formation of the bacterial flagellar hook and its overall stability between the FlgE subunits that make up the hook and attempted to understand how this stability differs between bacteria. Results An intrinsically disordered segment plays an important role for overall hook stability and for its structural cohesion during motor rotation. The length of this linker segment depends on the species of bacteria; for Salmonella enterica and Campylobacter jejuni it is approximately 37 and 54 residues, respectively. Few residues of the linker are conserved and mutating the conserved residues of the linker yields non-flagellated cells. In the case of Campylobacter, which rotates its flagella at a speed much higher than that of Salmonella, shortening the linker leads to a rupture of the hook at its base, decreasing cell motility. Our experiments show that this segment is required for polymerization and stability of the hook, demonstrating a surprising role for a disordered region in one of the most finely tuned and closely studied macromolecular machines. Conclusions This study reveals a detailed functional characteristic of an intrinsically disordered segment in the hook protein. This segment evolved to fulfill a specific role in the formation of the hook, and it is at the core of the stability and flexibility of the hook. Its length is important in the case of bacteria with high-speed rotating flagella. Finding a way of disrupting this linker in Campylobacter might help in preventing infections.

The growing burden of stroke in Russia, along with the increasingcost of healthcare calls for new, more effective strategies forstroke prevention. These strategies should include increasingawareness of stroke symptoms, awareness of risk factors, andprovision of easily available information on means of modifyingrisk factors. The Stroke Riskometer App is exactly such a tool,available in Russian, for adult individuals to calculate their riskof stroke over the next 5 and 10 years and identify their individualstroke risk factors and linking them to possible means of modifyingthese risk factors. The use of this App could reduce the risk ofstroke for individuals in the Russian population and contribute tosignificant reduction in stroke burden in Russia

Rapidly detecting and responding to new invasive species and the spread of those that are already established is essential for reducing their potential threat to food production, the economy, and the environment. We describe a new spatial modeling platform that integrates mapping of phenology and climatic suitability in real-time to provide timely and comprehensive guidance for stakeholders needing to know both where and when invasive insect species could potentially invade the conterminous United States. The Degree-Days, Risk, and Phenological event mapping (DDRP) platform serves as an open-source and relatively easy-to-parameterize decision support tool to help detect new invasive threats, schedule monitoring and management actions, optimize biological control, and predict potential impacts on agricultural production. DDRP uses a process-based modeling approach in which degree-days and temperature stress are calculated daily and accumulate over time to model phenology and climatic suitability, respectively. Outputs include predictions of the number of completed generations, life stages present, dates of phenological events, and climatically suitable areas based on two levels of climate stress. Species parameter values can be derived from laboratory and field studies or estimated through an additional modeling step. DDRP is written entirely in R, making it flexible and extensible, and capitalizes on multiple R packages to generate gridded and graphical outputs. We illustrate the DDRP modeling platform and the process of model parameterization using two invasive insect species as example threats to United States agriculture: the light brown apple moth, Epiphyas postvittana, and the small tomato borer, Neoleucinodes elegantalis. We then discuss example applications of DDRP as a decision support tool, review its potential limitations and sources of model error, and outline some ideas for future improvements to the platform.

ObjectiveDecades of research have established how to measure metacognition (i.e., awareness of one's cognitive abilities), whereas relatively little is known about how to assess the integrity of financial awareness (FA; awareness of one's financial abilities), a related construct with practical implications for vulnerable older adults. The current study's goal was to apply established metacognitive frameworks to identify an objective measure of FA.MethodsMetacognitive ratings were integrated into two financial decision making (FDM) assessments in order to derive two types of FA metrics: absolute accuracy (calibration) and relative accuracy (resolution) in each FDM task. Associations between each FA metric, demographic variables, FDM performances, and metamemory were examined.Design & settingCross-sectional, community-based, prospective study.Participants93 individuals with mean age = 59 years (SD = 15.12); mean education = 15.70 (SD = 2.39); 60% females.MeasuresFA was calculated using the Financial Competency Assessment Inventory (FCAI) and Decision Making Competence Assessment Tool, Finance Module (DMC-F), and memory awareness was calculated using an objective metamemory test.ResultsNone of the FA metrics was associated with age, education or gender. FCAI calibration was inversely associated with FDM, and positively correlated with DMC-F calibration and metamemory calibration. None of the FA metrics for DMC-F was associated with metamemory.ConclusionsMirroring findings from metamemory studies, overconfidence in FDM was associated with lower FDM accuracy in healthy adults. Moreover, calibration scores on the FCAI and metamemory were related, suggesting that FA taps into metacognitive abilities. Our findings provide preliminary evidence for how to measure FA in both clinical and research contexts.

Whether language information influences recognition of emotion from facial expressions remains the subject of debate. The current studies investigate how variations in emotion labels that are paired with expressions influences participants' judgments of the emotion displayed. Static (Study 1) and dynamic (Study 2) facial expressions depicting eight emotion categories were paired with emotion labels that systematically varied in arousal (low and high). Participants rated the arousal, valence, and dominance of expressions paired with labels. Isolated faces and isolated labels were also rated. As predicted, the label presented influenced participants' judgments of the expressions. Across both studies, higher arousal labels were associated with: 1) higher ratings of arousal for sad, angry, and scared expressions, and 2) higher ratings of dominance for angry, proud, and disgust expressions. These results indicate that emotion labels influence judgments of facial expressions.

Abstract Understanding the factors that influence vegetation responses to disturbance is important because vegetation is the foundation of food resources, wildlife habitat, and ecosystem properties and processes. We integrated vegetation cover data derived from field plots and remotely sensed Landsat images in two focal areas over a 37‐yr period (1979–2016) to investigate how historical changes to community composition influence contemporary responses of vegetation to fire in sagebrush ecosystems in the Great Basin. Our objectives were (1) to quantify the magnitude and direction of change in the cover of native and exotic plant functional groups in relation to their exposure to fire; (2) to relate plant community changes to their historical composition, exposure to fire, and environmental conditions; and (3) to test for consistency of trends revealed by vegetation cover data derived from field plots and Landsat images. Historical (1979–1981) field data originated from 298 locations, Landsat‐derived data and contemporary (2011–2016) field data originated from 448 locations, and an expanded set of locations were included in some analyses of Landsat‐derived data. We found that areas burned by fire since the 1980s had higher annual herbaceous cover than unburned areas both historically and contemporarily. Models revealed a significant interaction between historical community composition and exposure to fire, which suggests that plots with historically high herbaceous cover were more susceptible to burning. Trends revealed by field and Landsat‐derived cover data were only partially consistent, potentially due in part to methods used to predict cover values from Landsat images, and the time period over which each data set was collected. Our results suggest that burned areas historically occupied by sagebrush‐dominated plant communities may have been invaded by exotic annuals prior to burning, possibly because of prior land uses, and after burning, have now transitioned to a persistent herbaceous‐dominated state. This type of state transition has important consequences for forage quality, wildlife habitat, soil nutrients, and future disturbances, such as drought and wildfire.

The bacterial flagellar hook is made up of many copies of the protein FlgE. Here, the authors report the full structure of the hook from Campylobacter jejuni and show that its overall structure is different from that of the previously published filament.

Laser-cooled atoms are a key technology for many calibration-free measurement platforms—including clocks, gyroscopes, and gravimeters—and are a promising system for quantum networking and quantum computing. The optics and vacuum hardware required to prepare these gases are often bulky and not amenable to large-volume manufacturing, limiting the practical realization of devices benefiting from the properties of cold atoms. Planar, lithographically produced optics including photonic integrated circuits, optical metasurfaces (MSs), and gratings offer a pathway to develop chip-scale, manufacturable devices utilizing cold atoms. As a demonstration of this technology, we have realized laser cooling of atomic Rb in a grating-type magneto-optical trap (MOT) using planar optics for beam launching, beam shaping, and polarization control. Efficient use of available light is accomplished using MS-enabled beam shaping, and the performance of the planar optics MOT is competitive with Gaussian-beam illuminated grating MOTs.