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Pyrroloquinoline alkaloids are well known bioactive metabolites commonly found from latrunculiid sponges. Two new pyrroloquinoline alkaloids, 6-bromodamirone B (1) and makaluvamine W (2), were isolated from the Tongan sponge Strongylodesma tongaensis. Makaluvamine W (2) contains an oxazole moiety, which is rare in this large group of natural products, and is the first example of a pyrroloquinoline with nitrogen substitution at C-8. Both 1 and 2 lacked activity against a human promyelocytic leukemia cell line (HL-60), supporting the premise that an intact iminoquinone moiety plays a key role in the cytotoxicity of this compound class. The chemotaxonomic impact of these makaluvamine-type compounds is also discussed.

Visual Abstract, Highlights • The homozygous c.38T>G mutation in the LEMD2 gene causes arrhythmic cardiomyopathy with bilateral juvenile cataract in the Hutterite population. • The cardiac phenotype is characterized by localized inferior and inferolateral fibrosis of the left ventricle and mild impairment of left ventricular systolic function but severe ventricular arrhythmias leading to sudden cardiac death. • Affected heart tissue and fibroblasts exhibit abnormally shaped nuclei with condensed peripheral heterochromatin. • Functional assays on affected fibroblasts show decreased proliferation capacity, cellular senescence, and a prolonged G1 phase, suggesting premature aging and cellular senescence in proliferating cells., Summary Nuclear envelope proteins have been shown to play an important role in the pathogenesis of inherited dilated cardiomyopathy. Here, we present a remarkable cardiac phenotype caused by a homozygous LEMD2 mutation in patients of the Hutterite population with juvenile cataract. Mutation carriers develop arrhythmic cardiomyopathy with mild impairment of left ventricular systolic function but severe ventricular arrhythmias leading to sudden cardiac death. Affected cardiac tissue from a deceased patient and fibroblasts exhibit elongated nuclei with abnormal condensed heterochromatin at the periphery. The patient fibroblasts demonstrate cellular senescence and reduced proliferation capacity, which may suggest an involvement of LEM domain containing protein 2 in chromatin remodeling processes and premature aging.

We correct common assumptions about COVID burden and disease characteristics in high-income (HIC) versus low- and middle-income (LMIC) countries by augmenting widely-used surveillance data with auxiliary data sources. We constructed an empirically-based model of serological detection rates to quantify COVID reporting rates in national and sub-national locations. From those reporting rates, we estimated relative COVID burden, finding results that contrast with estimates based on case counts and modeling. To investigate COVID mortality by age in an LMIC context, we utilized a unique morgue study of COVID in Lusaka alongside the population attributable fraction method to account for HIV comorbidity. We calculated the comorbidity-corrected age-adjusted mortality curve in Lusaka and found it significantly skewed toward younger age groups as compared to HICs. This unexpected result recommends against the unexamined use of HIC-derived parameterizations of COVID characteristics in LMIC settings, and challenges the hypothesis of an age-structure protective factor for COVID burden in Africa. Indeed, we found overall COVID burden to be higher in Lusaka than in HICs. Concurrent with high COVID burden, many LMICs have high prevalence of other public health issues such as HIV, which compete for limited health investment resources. Given differences in age-structure, comorbidities, and healthcare delivery costs, we provide a case study comparing the cost efficacy of investment in COVID versus HIV and found that even in a high HIV prevalence setting, investment in COVID remains cost-effective. As a whole, these analyses have broad implications for interpretations of COVID burden, modeling applications, and policy decision-making.Significance StatementThe analyses presented here demonstrate the power of auxiliary COVID data sources to fill information gaps, particularly for LMICs. Our results reveal differences in COVID surveillance and disease dynamics between HICs and LMICs that challenge common perceptions and assumptions about COVID in these respective contexts. We show the divergence of COVID reporting rates between HICs and LMICs and the effects on relative estimated burden. Contradicting common modeling practices, our analysis demonstrates that the age-structure of COVID mortality cannot be accurately generalized from HICs to LMICs. We find higher COVID burden in LMIC contexts than HICs particularly in younger age groups and show that investment in COVID is cost-effective even in light of other public health concerns.

Recent studies suggest that context-specific eQTLs underlie genetic risk factors for complex diseases. However, methods for identifying them are still nascent, limiting their comprehensive characterization and downstream interpretation of disease-associated variants. Here, we introduce FastGxC, a method to efficiently and powerfully map context-specific eQTLs by leveraging the correlation structure of multi-context studies. We first show via simulations that FastGxC is orders of magnitude more powerful and computationally efficient than previous approaches, making previously year-long computations possible in minutes. We next apply FastGxC to bulk multi-tissue and single-cell RNA-seq data sets to produce the most comprehensive tissue- and cell-type-specific eQTL maps to date. We then validate these maps by establishing that context-specific eQTLs are enriched in corresponding functional genomic annotations. Finally, we examine the relationship between context-specific eQTLs and human disease and show that FastGxC context-specific eQTLs provide a three-fold increase in precision to identify relevant tissues and cell types for GWAS variants than standard eQTLs. In summary, FastGxC enables the construction of context-specific eQTL maps that can be used to understand the context-specific gene regulatory mechanisms underlying complex human diseases. For the related source code, see: Github For the preprint, see: biorxiv

The host's gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host's genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this using single-cell RNA-sequencing of 1.3M peripheral blood mononuclear cells from 120 individuals, longitudinally exposed to three different pathogens. These analyses indicate that cell-type-specificity is a more prominent factor than pathogen-specificity regarding contexts that affect how genetics influences gene expression (i.e., eQTL) and co-expression (i.e., co-expression QTL). In monocytes, the strongest responder to pathogen stimulations, 71.4% of the genetic variants whose effect on gene expression is influenced by pathogen exposure (i.e., response QTL) also affect the co-expression between genes. This indicates widespread, context-specific changes in gene expression level and its regulation that are driven by genetics. Pathway analysis on the CLEC12A gene that exemplifies cell-type-, exposure-time- and genetic-background-dependent co-expression interactions, shows enrichment of the interferon (IFN) pathway specifically at 3-h post-exposure in monocytes. Similar genetic background-dependent association between IFN activity and CLEC12A co-expression patterns is confirmed in systemic lupus erythematosus by in silico analysis, which implies that CLEC12A might be an IFN-regulated gene. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.

Purpose Deutetrabenazine is a deuterated form of tetrabenazine with a confirmed lower rate of CYP2D6 metabolism of the active metabolites, α- and β-HTBZ. In this study, we assessed the effect of paroxetine, a potent CYP2D6 inhibitor, on the pharmacokinetics and safety of deutetrabenazine and its metabolites. Methods In this open-label sequential drug-drug-interaction study, 24 healthy adults who were CYP2D6 extensive or intermediate metabolizers received a single deutetrabenazine 22.5-mg oral dose on days 1 and 11 and a single paroxetine 20-mg oral daily dose on days 4–12. Pharmacokinetics of deutetrabenazine and its metabolites were assessed on days 1–4 and 11–14. Paroxetine trough concentrations were obtained pre-dose on days 9–13. Safety examinations occurred throughout the study. Results Paroxetine administered under steady-state conditions, increased exposure of the deuterated active metabolites, α-HTBZ (1.2-fold Cmax and 1.8-fold AUC0–∞) and β-HTBZ (2.1-fold Cmax and 5.6-fold AUC0–∞), and correspondingly, 1.6-fold Cmax and threefold AUC0–∞ for total (α + β)-HTBZ. Sixteen subjects reported 45 adverse events and most were mild. Headache was the most common AE reported 8 times by 7 subjects (5 following paroxetine alone; 2 following deutetrabenazine + paroxetine). Conclusions Paroxetine-induced increases in exposure to the active deutetrabenazine metabolites were less than those previously reported for tetrabenazine, a finding expected to reduce the burden of drug interaction. In addition, single doses of 22.5 mg deutetrabenazine, when given alone or in the presence of steady-state paroxetine (20 mg daily), were safe.

Tomato is an important crop grown worldwide. Various plant diseases cause massive losses in tomato plants due to diverse biotic agents. Bacterial spot of tomato (BST) is a worldwide disease that results in high losses in processed and fresh tomato. Xanthomonas perforans, an aerobic, single-flagellated, rod-shaped, Gram-negative plant pathogenic bacterium, is one of the leading causes of BST. Over the past three decades, X. perforans has increasingly been reported from tomato-growing regions and became a major bacterial disease. X. perforans thrives under high humidity and high temperature, which is commonplace in tropical and subtropical climates. Distinguishing symptoms of BST are necrotic lesions that can coalesce and cause a shot-hole appearance. X. perforans can occasionally cause fruit symptoms depending on disease pressure during fruit development. Short-distance movement in the field is mainly dependent on wind-driven rain, whereas long distance movement occurs through contaminated seed or plant material. X. perforans harbors a suite of effectors that increase pathogen virulence, fitness, and dissemination. BST management mainly relies on copper-based compounds; however, resistance is widespread. Alternative compounds, such as nanomaterials, are currently being evaluated and show high potential for BST management. Resistance breeding remains difficult to attain due to limited resistant germplasm. While the increased genetic diversity and gain and loss of effectors in X. perforans limits the success of single-gene resistance, the adoption of effector-specific transgenes and quantitative resistance may lead to durable host resistance. However, further research that aims to more effectively implement novel management tools is required to curb disease spread. KEY POINTS: • Xanthomonas perforans causes bacterial spot on tomato epidemics through infected seedlings and movement of plant material. • Genetic diversity plays a major role in shaping populations which is evident in loss and gain of effectors. • Management relies on copper sprays, but nanoparticles are a promising alternative to reduce copper toxicity.

0.1BackgroundCOVID-19 case counts are the predominant measure used to track epidemiological dynamics and inform policy decision-making. Case counts, however, are influenced by testing rates and strategies, which have varied over time and space. A method to consistently interpret COVID-19 case counts in the context of other surveillance data is needed, especially for data-limited settings in low- and middle-income countries (LMICs).0.2MethodsWe leverage statistical analyses to detect changes in COVID-19 surveillance data. We apply the pruned exact linear time change detection method for COVID-19 case counts, number of tests, and test positivity rate over time. With this information, we categorize change points as likely driven by epidemiological dynamics or non-epidemiological influences such as noise.0.3FindingsHigher rates of epidemiological change detection are more associated with open testing policies than with higher testing rates. We quantify alignment of non-pharmaceutical interventions with epidemiological changes. LMICs have the testing capacity to measure prevalence with precision if they use randomized testing. Rwanda stands out as a country with an efficient COVID-19 surveillance system. Sub-national data reveal heterogeneity in epidemiological dynamics and surveillance.0.4InterpretationRelying solely on case counts to interpret pandemic dynamics has important limitations. Normalizing counts by testing rate mitigates some of these limitations, and open testing policy is key to efficient surveillance. Our findings can be leveraged by public health officials to strengthen COVID-19 surveillance and support programmatic decision-making.0.5FundingThis publication is based on models and data analysis performed by the Institute for Disease Modeling at the Bill & Melinda Gates Foundation.Research in ContextEvidence before this studyWe searched for articles on the current practices, challenges, and proposals for COVID-19 surveillance in LMICs. We used Google Scholar with search terms including “COVID surveillance.” Existing studies were found to be qualitative, anecdotal, or highly location-specific.Added value of this studyWe developed a quantitative method that makes use of limited information available from LMICs. Our approach improves interpretation of epidemiological data and enables evaluation of COVID-19 surveillance dynamics across countries.Implications of all the available evidenceOur results demonstrate the importance of open testing for strong surveillance systems, bolstering existing anecdotal evidence. We show strong alignment across LMICs between non-pharmaceutical interventions and epidemiological changes. We demonstrate the importance of considering sub-national heterogeneity of epidemiological dynamics and surveillance.

Pea microRNAs and their targets were identified, and their differential expression was analyzed during the development of symbiosis with rhizobia and mycorrhizal fungi, and under conditions of abiotic stress caused by cadmium.

The NLRP6 innate immune sensor is regulated by tissue-selective alternate promoters that facilitate translational gene silencing outside of the intestinal epithelium in both humans and mice., The pryin domain (PYD) domain is involved in protein interactions that lead to assembly of immune-sensing complexes such as inflammasomes. The repertoire of PYD-containing genes expressed by a cell type arms tissues with responses against a range of stimuli. The transcriptional regulation of the PYD gene family however is incompletely understood. Alternative promoter utilization was identified as a mechanism regulating the tissue distribution of human PYD gene family members, including NLRP6 that is translationally silenced outside of intestinal tissue. Results show that alternative transcriptional promoters mediate NLRP6 silencing in mice and humans, despite no upstream genomic synteny. Human NLRP6 contains an internal alternative promoter within exon 2 of the PYD, resulting in a truncated mRNA in nonintestinal tissue. In mice, a proximal promoter was used that expanded the 5′ leader sequence restricting nuclear export and abolishing translational efficiency. Nlrp6 was dispensable in disease models targeting the kidney, which expresses noncanonical isoforms. Thus, alternative promoter use is a critical mechanism not just for isoform modulation but for determining expression profile and function of PYD family members.

Before 1991

Author(s): Crawford, Emily D; Acosta, Irene; Ahyong, Vida; Anderson, Erika C; Arevalo, Shaun; Asarnow, Daniel; Axelrod, Shannon; Ayscue, Patrick; Azimi, Camillia S; Azumaya, Caleigh M; Bachl, Stefanie; Bachmutsky, Iris; Bhaduri, Aparna; Brown, Jeremy Bancroft; Batson, Joshua; Behnert, Astrid; Boileau, Ryan M; Bollam, Saumya R; Bonny, Alain R; Booth, David; Borja, Michael Jerico B; Brown, David; Buie, Bryan; Burnett, Cassandra E; Byrnes, Lauren E; Cabral, Katelyn A; Cabrera, Joana P; Caldera, Saharai; Canales, Gabriela; Castaneda, Gloria R; Chan, Agnes Protacio; Chang, Christopher R; Charles-Orszag, Arthur; Cheung, Carly; Chio, Unseng; Chow, Eric D; Citron, Y Rose; Cohen, Allison; Cohn, Lillian B; Chiu, Charles; Cole, Mitchel A; Conrad, Daniel N; Constantino, Angela; Cote, Andrew; Crayton-Hall, Tre'Jon; Darmanis, Spyros; Detweiler, Angela M; Dial, Rebekah L; Dong, Shen; Duarte, Elias M; Dynerman, David; Egger, Rebecca; Fanton, Alison; Frumm, Stacey M; Fu, Becky Xu Hua; Garcia, Valentina E; Garcia, Julie; Gladkova, Christina; Goldman, Miriam; Gomez-Sjoberg, Rafael; Gordon, M Grace; Grove, James CR; Gupta, Shweta; Haddjeri-Hopkins, Alexis; Hadley, Pierce; Haliburton, John; Hao, Samantha L; Hartoularos, George; Herrera, Nadia; Hilberg, Melissa; Ho, Kit Ying E; Hoppe, Nicholas; Hosseinzadeh, Shayan; Howard, Conor J; Hussmann, Jeffrey A; Hwang, Elizabeth; Ingebrigtsen, Danielle; Jackson, Julia R; Jowhar, Ziad M; Kain, Danielle; Kim, James YS; Kistler, Amy; Kreutzfeld, Oriana; Kulsuptrakul, Jessie; Kung, Andrew F

Highlights • Countries within the sub-Saharan Africa (SSA) region may experience high COVID-19 case fatality rates given limited healthcare capacity to manage critical cases and poor detection leading to delayed care-seeking. • Over the first months of the epidemic in SSA and consistent with findings from other countries globally, deceased cases tended to be majority male, over the age of 50, and have underlying comorbidities. • Delayed or no care-seeking was prevalent among deceased COVID-19 cases in Burkina Faso. • Analysis on a synthetic case population representative of demographic and health characteristics of Burkina Faso COVID-19 patients suggested that treatment with oxygen therapy or convalescent plasma reduced the odds of mortality, after adjusting for age, sex, and presence of underlying comorbid conditions. • Low-cost, scalable and sustainable strategies for COVID-19 case management in the SSA context warrant attention and investment to reduce disparity in case fatality., Background Absolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been significantly lower than those across the Americas, Asia, and Europe. As a result, there has been limited information about the demographic and clinical characteristics of deceased cases in the region, as well as the impacts of different case management strategies. Methods Data from deceased cases reported across SSA through May 10, 2020 and from hospitalized cases in Burkina Faso through April 15, 2020 were analyzed. Demographic, epidemiological, and clinical information on deceased cases in SSA was derived through a line-list of publicly available information and, for cases in Burkina Faso, from aggregate records at the Centre Hospitalier Universitaire de Tengandogo in Ouagadougou. A synthetic case population was derived probabilistically using distributions of age, sex, and underlying conditions from populations of West African countries to assess individual risk factors and treatment effect sizes. Logistic regression analysis was conducted to evaluate the adjusted odds of survival for patients receiving oxygen therapy or convalescent plasma, based on therapeutic effectiveness observed for other respiratory illnesses. Results Across SSA, deceased cases for which demographic data are available have been predominantly male (63/103, 61.2%) and over 50 years of age (59/75, 78.7%). In Burkina Faso, specifically, the majority of deceased cases either did not seek care at all or were hospitalized for a single day (59.4%, 19/32); hypertension and diabetes were often reported as underlying conditions. After adjustment for sex, age, and underlying conditions in the synthetic case population, the odds of mortality for cases not receiving oxygen therapy was significantly higher than those receiving oxygen, such as due to disruptions to standard care (OR: 2.07; 95% CI: 1.56 – 2.75). Cases receiving convalescent plasma had 50% reduced odds of mortality than those who did not (95% CI: 0.24 – 0.93). Conclusions Investment in sustainable production and maintenance of supplies for oxygen therapy, along with messaging around early and appropriate use for healthcare providers, caregivers, and patients could reduce COVID-19 deaths in SSA. Further investigation into convalescent plasma is warranted, as data on its effectiveness specifically in treating COVID-19 becomes available. The success of supportive or curative clinical interventions will depend on earlier treatment seeking, such that community engagement and risk communication will be critical components of the response.

Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.

Massively parallel reporter assays (MPRAs) can simultaneously measure the function of thousands of candidate regulatory sequences (CRSs) in a quantitative manner. In this method, CRSs are cloned upstream of a minimal promoter and reporter gene, alongside a unique barcode, and introduced into cells. If the CRS is a functional regulatory element, it will lead to the transcription of the barcode sequence, which is measured via RNA sequencing and normalized for cellular integration via DNA sequencing of the barcode. This technology has been used to test thousands of sequences and their variants for regulatory activity, to decipher the regulatory code and its evolution, and to develop genetic switches. Lentivirus-based MPRA (lentiMPRA) produces ‘in-genome’ readouts and enables the use of this technique in hard-to-transfect cells. Here, we provide a detailed protocol for lentiMPRA, along with a user-friendly Nextflow-based computational pipeline—MPRAflow—for quantifying CRS activity from different MPRA designs. The lentiMPRA protocol takes ~2 months, which includes sequencing turnaround time and data processing with MPRAflow.

BackgroundAbsolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been significantly lower than those across the Americas, Asia, and Europe. As a result, there has been limited information about the demographic and clinical characteristics of deceased cases in the region, as well as the impacts of different case management strategies.MethodsData from deceased cases reported across SSA through May 10, 2020 and from hospitalized cases in Burkina Faso through April 15, 2020 were analyzed. Demographic, epidemiological, and clinical information on deceased cases in SSA was derived through a line-list of publicly available information and, for cases in Burkina Faso, from aggregate records at the Center Hospitalier Universitaire de Tengandogo in Ouagadougou. A synthetic case population was derived probabilistically using distributions of age, sex, and underlying conditions from populations of West African countries to assess individual risk factors and treatment effect sizes. Logistic regression analysis was conducted to evaluate the adjusted odds of survival for patients receiving oxygen therapy or convalescent plasma, based on therapeutic effectiveness observed for other respiratory illnesses.ResultsAcross SSA, deceased cases for which demographic data are available have been predominantly male (63/103, 61.2%) and over 50 years of age (59/75, 78.7%). In Burkina Faso, specifically, the majority of deceased cases either did not seek care at all or were hospitalized for a single day (59.4%, 19/32); hypertension and diabetes were often reported as underlying conditions. After adjustment for sex, age, and underlying conditions in the synthetic case population, the odds of mortality for cases not receiving oxygen therapy was significantly higher than those receiving oxygen, such as due to disruptions to standard care (OR: 2.07; 95% CI: 1.56 – 2.75). Cases receiving convalescent plasma had 50% reduced odds of mortality than those who did not (95% CI: 0.24 – 0.93).ConclusionInvestment in sustainable production and maintenance of supplies for oxygen therapy, along with messaging around early and appropriate use for healthcare providers, caregivers, and patients could reduce COVID-19 deaths in SSA. Further investigation into convalescent plasma is warranted, as data on its effectiveness specifically in treating COVID-19 becomes available. The success of supportive or curative clinical interventions will depend on earlier treatment seeking, such that community engagement and risk communication will be critical components of the response.

Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein structures in living cells. Here, we use deep mutational scanning to investigate how a toxic conformation of α-synuclein, a dynamic protein linked to Parkinson’s disease, responds to perturbations of cellular proteostasis. In the context of a course for graduate students in the UCSF Integrative Program in Quantitative Biology, we screened a comprehensive library of α-synuclein missense mutants in yeast cells treated with a variety of small molecules that perturb cellular processes linked to α-synuclein biology and pathobiology. We found that the conformation of α-synuclein previously shown to drive yeast toxicity—an extended, membrane-bound helix—is largely unaffected by these chemical perturbations, underscoring the importance of this conformational state as a driver of cellular toxicity. On the other hand, the chemical perturbations have a significant effect on the ability of mutations to suppress α-synuclein toxicity. Moreover, we find that sequence determinants of α-synuclein toxicity are well described by a simple structural model of the membrane-bound helix. This model predicts that α-synuclein penetrates the membrane to constant depth across its length but that membrane affinity decreases toward the C terminus, which is consistent with orthogonal biophysical measurements. Finally, we discuss how parallelized chemical genetics experiments can provide a robust framework for inquiry-based graduate coursework.

Develop an automated exome analysis workflow that can produce a very small number of candidate variants yet still detect different numbers of deleterious variants between probands and unaffected siblings. Ninety-seven outbred nuclear families from the Undiagnosed Diseases Program/Network included single probands and the corresponding unaffected sibling(s). Single-nucleotide polymorphism (SNP) chip and exome analyses were performed on all, with proband and unaffected sibling considered independently as the target. The total burden of candidate genetic variants was summed for probands and siblings over all considered disease models. Exome analysis workflow include automated programs for ethnicity-matched genotype calling, salvage pathway for Mendelian inconsistency, compound heterozygous recessive detection, BAM file regional curation, population frequency filtering, pedigree-aware BAM file noise evaluation, and exon deletion filtration. This workflow relied heavily on BAM file analysis. A greater average pathogenic variant number was found compared with unaffected siblings. This was significant (p

A detailed examination of the red alga Callophycus serratus collected in Tonga led to the isolation of six new halogenated meroditerpenoids: callophycol C (1), callophycoic acid I (2), iodocallophycols E (3) and F (4), iodocallophycoic acid B (5), and callophycoic acid J (6). Of these, compounds 3–5 are new iodinated additions to the growing family of Callophycus meroditerpenoids. The relative configurations of compounds 1–6 were deduced by analyses of 1D NOE data and 1H–1H scalar coupling constants, and 3–6 are proposed to differ from the closely related compounds reported in the literature, iodocallophycoic acid A and iodocallophycols A–D. Iodocallophycol E (3) exhibited moderate cytotoxicity against the promyelocytic leukemia cell line HL-60 with an IC50 value of 6.0 μM.

Background: Maternal nutrient restriction (MNR) is a widespread cause of fetal growth restriction (FGR), an independent predictor of heart disease and cardiovascular mortality. Our objective was to examine the developmental and long-term impact of MNR-induced FGR on cardiac structure in a model that closely mimics human development. Methods: A reduction in total caloric intake spanning pregestation through to lactation in guinea pig sows was used to induce FGR. Proliferation, differentiation, and apoptosis of cardiomyocytes were assessed in late-gestation fetal, neonatal, and adult guinea pig hearts. Proteomic analysis and pathway enrichment were performed on fetal hearts. Results: Cardiomyocyte proliferation and the number of mononucleated cells were enhanced in the MNR–FGR fetal and neonatal heart, suggesting a delay in cardiomyocyte differentiation. In fetal hearts of MNR–FGR animals, apoptosis was markedly elevated and the total number of cardiomyocytes reduced, the latter remaining so throughout neonatal and into adult life. A reduction in total cardiomyocyte number in adult MNR–FGR hearts was accompanied by exaggerated hypertrophy and a disorganized architecture. Pathway analysis identified genes related to cell proliferation, differentiation, and survival. Conclusions: FGR influences cardiomyocyte development during critical windows of development, leading to a permanent deficiency in cardiomyocyte number and compensatory hypertrophy in a rodent model that recapitulates human development.

Power estimations are important for optimizing genotype-phenotype association study designs. However, existing frameworks are designed for common disorders, and thus ill-suited for the inherent challenges of studies for low-prevalence conditions such as rare diseases and infrequent adverse drug reactions. These challenges include small sample sizes and the need to leverage genetic annotation resources in association analyses for the purpose of ranking potential causal genes. We present SimPEL, a simulation-based program providing power estimations for the design of low-prevalence condition studies. SimPEL integrates the usage of gene annotation resources for association analyses. Customizable parameters, including the penetrance of the putative causal allele and the employed pathogenic scoring system, allow SimPEL to realistically model a large range of study designs. To demonstrate the effects of various parameters on power, we estimated the power of several simulated designs using SimPEL and captured power trends in agreement with observations from current literature on low-frequency condition studies. SimPEL, as a tool, provides researchers studying low-frequency conditions with an intuitive and highly flexible avenue for statistical power estimation. The platform-independent "batteries included" executable and default input files are available at https://github.com/precisionomics/SimPEL.

The purpose of this multiple case study was to describe the experiences of graduate education faculty of varying racial/ethnic backgrounds, learning to navigate difficult discourses on race effectively over time. The study employed positionality as a theoretical framework. Findings indicate that faculty balance what we refer to as strategies of self in a bid to work through difficult race talk. In turn, their practice may hold strong potential for influencing a fresh and more holistic approach to engaging in classroom race talk.

This study aimed to describe the efficacy of fulvestrant 500 mg in postmenopausal women with estrogen receptor (ER)-positive advanced/metastatic breast cancer who had disease progression after receiving anti-estrogen therapy in clinical practice, getting real-world data. Multicenter, retrospective, observational study conducted in Spain. Postmenopausal women with locally advanced/metastatic ER-positive breast cancer who received treatment with fulvestrant 500 mg after progression with a previous anti-estrogen therapy were eligible. The primary endpoint was progression-free survival (PFS); secondary endpoints were overall survival (OS), clinical benefit rate (CBR), duration of clinical benefit (DoCB), and safety profile. A total of 263 women were evaluated (median age, 65.8 years). At a median follow-up of 21.5 months, median PFS and OS were 10.6 and 43.2 months, respectively. PFS according to 1st, 2nd, 3rd, and ae 4th lines were 11.5, 10.6, 9.9, and 8.5 months, respectively (p = 0.0245). PFS in patients with visceral involvement was 10 months vs 10.6 months in patients without visceral involvement (p = 0.6604), 9.6 months in patients with high Ki67 vs 10 months in patients with low Ki67 (p = 0.7224), and 10.2 months in HER2+ patients vs 10.3 months in HER2- patients (p = 0.6809). The CBR was 56.5% and the DoCB was 18.4 months. The most frequently adverse events were injection site pain (10.3%) and musculoskeletal disorders (7.6%). Fulvestrant 500 mg administered in clinical practice was shown to be effective (PFS, 10.6 months; CBR, 56.5%) and well tolerated, in accordance with previous trials.

Two groups of unfit Standardbred mares (adult: 9-14 years, 540 kg, n=7) and old (20-25 years, 530 kg, n=5) were used to test two hypotheses, first, that aging and training would alter plasma and muscle glutamine [Gln] and glutamate [Glu] and second, that aging and training would alter Glut-4 expression in skeletal muscle. All animals were housed on pasture with free access to grass and all received hay and supplementation with a commercially prepared supplement (15% crude protein and 3.00 Mcal/kg dry matter) in individual stalls. Mares were fed to meet or exceed NRC (2007) nutrient recommendations for moderate to heavy exercise. The mares were exercise trained in a free-stall motorised circular exercise machine for 30 min/d, 5 d/week, for 8 weeks. Work intensity during training was set at a relative intensity of ~60% of the maximum heart rate, previously determined during an incremental exercise test (GXT). Blood samples and muscle biopsies (gluteus) obtained before and after 8 weeks of training were used for measurement of [Gln], [Glu] and Glut-4 abundance. Samples were collected before the initiation of training and at 24 h after cessation of last bout of exercise in the training period. All samples were immediately frozen in liquid nitrogen and stored at -80 °C until enzymatic analysis for [Gln], [Glu] and Western Blot analysis for Glut-4 protein abundance. Data were analysed by one-way or two-way ANOVA for repeated measures and the Pearson correlation method. Post-hoc differences were identified with the Tukey test. Significance was set at P0.05) in muscle [Glu] due to aging. Training decreased (P0.05) due to training. Glut-4 abundance analysis did not differ (P>0.05) between the young adult and old horses; however, there was a trend (P=0.063) towards an effect of training when samples from both groups were pooled. It was concluded that training and aging produce changes in plasma and muscle [Gln], which may affect immune function in athletic horses, but not in Glut-4.

Transcription-export complex 2 (TREX-2, or THSC) facilitates localization of actively transcribing genes such as GAL1 to the nuclear periphery, contributes to the generation of export-competent mRNPs and influences gene expression through interactions with Mediator. TREX-2 is based on a Sac3 scaffold to which Thp1, Sem1, Cdc31 and Sus1 bind and consists of three modules: the N-region (Sac3∼1-100), which binds mRNA export factor Mex67:Mtr2; the M-region, in which Thp1 and Sem1 bind to Sac3∼100-550; and the CID region in which Cdc31 and two Sus1 chains bind to Sac3∼720-805. Although the M-region of Sac3 was originally thought to encompass residues ∼250-550, we report here the 2.3Å resolution crystal structure of a complex containing Sac3 residues 60–550 that indicates that the TPR-like repeats of the M-region extend to residue 137 and that residues 90–125 form a novel loop that links Sac3 to Thp1. These new structural elements are important for growth and mRNA export in vivo. Although deleting Sac3 residues 1–90 produced a wild-type phenotype, deletion of the loop as well generated growth defects at 37°C, whereas the deletion of residues 1–250 impaired mRNA export and also generated longer lag times when glucose or raffinose was replaced by galactose as the carbon source.

This RNA Sequence Picking After Cutting Enzymatically (RNA SPACE) protocol is intended to enrich for a specific polyadenylated RNA, to be performed before the Oxford Nanopore Technologies (ONT) direct RNA sequencing protocol. This could be used to promote sequencing of a low abundance polyadenylated transcript in a mixture (e.g. polyadenylated viral RNA in a human clinical sample), or to elucidate the unknown 5' of a transcript (i.e. replacement for 5' RACE sequencing). This methods should become increasingly valuable as lower throughput nanopore devices such as the Flongle, Plongle and SmidgION get official support for direct RNA sequencing. The RNA SPACE protocol takes advantage of the unusual property of six DNA restriction enzymes (AvaII, AvrII, BanI, HaeIII, HinfI and Taq1) to cut the RNA strand in RNA:DNA duplexes. This introduces a 3' end that is uniquely targetable using the Oxford Nanopore Technologies protocol's sequence-specific "RTA Oligo B" probe option, rather than the standard poly(dT) overhang version of "RTA Oligo B" which pulls down all polyadenylated transcripts. The RNA SPACE software designs two oligonucleotide (oligo) probes for this protocol, for any given gene: the "RE" oligo to generate a RNA:DNA duplex in the known transcripts of interest the sequence-specific RTA Oligo B

Picoamperage signals are generated as each nucleotide of a DNA or RNA molecule is ratcheted through a nanosequencer's nanopores by motor proteins. These are segmented into step-current level signals, "squiggles", representing the nucleotide sequence. It has been suggested that applying dynamic time warp Barycentre Averaging (DBA) to multiple noisy squiggles can generate a lower noise, less-distorted, consensus signal that retains the key squiggle characteristics that would be distorted by other averaging approaches. We discuss experimental results obtained when developing DBA consensus signals from squiggles produced by an Oxford MinION nanosequencer squiggle convertor during an Enolase study. Metrics are proposed to identify differences between the known gold standard and consensus signals, and the level of self-consistency between consensus signals developed from noisy squiggles with different length distortions. A number of location-specific differences between the gold and consensus squiggles were identified.

In Saccharomyces cerevisiae generation of export-competent mRNPs terminates the nuclear phase of the gene expression pathway and facilitates transport to the cytoplasm for translation. Nab2 functions in this process to control both mRNP compaction that facilitates movement through nuclear pore complexes and the length of transcript poly(A) tails. Nab2 has a modular structure that includes seven CCCH Zn fingers that bind to A-rich RNAs and fingers 5–7 are critical for these functions. Here, we demonstrate, using both biophysical and structural methods, that binding A11G RNA induces dimerization of Zn fingers 5–7 mediated by the novel spatial arrangement of the fingers promoting each RNA chain binding two protein chains. The dimerization of Nab2 induced by RNA binding provides a basis for understanding its function in both poly(A) tail length regulation and in the compaction of mature transcripts to facilitate nuclear export.

A tip-enhanced near-field optical microscope, based on a shear-force atomic force microscope with plasmonic tip coupled to an inverted, confocal optical microscope, has been constructed for nanoscale chemical (Raman) imaging of surfaces. The design and validation of the instrument, along with its application to near-field Raman mapping of patterned organic thin films (coumarin-6 and Cu(II) phthalocyanine), are described. Lateral resolution of the instrument is estimated at 50 nm (better than λ/10), which is roughly dictated by the size of the plasmonic tip apex. Additional observations, such as the distance scaling of Raman enhancement and the inelastic scattering background generated by the plasmonic tip, are presented. Copyright © 2016 John Wiley & Sons, Ltd.

The article describes the technology for synthesis of full functional check programs for train traffic management systems. Algorithms for synthesis of a full set of safety functions and synthesis of minimized set of safety functions are also presented.

A novel tape termination method for tapering the ply end and removing the fibre discontinuity owing to a dropped ply in a tapered composite was demonstrated. The forces required for this process – referred to as tape scarfing – were experimentally investigated with respect to blade speed, scarfing ratio, tape thickness and width. Tensile tests were conducted on unidirectional laminate specimens with a scarfed ply at two different aspect ratios to examine the effect of scarfing ratio on the delamination behaviour of the specimens. The results showed that the ply scarfing ratio is a critical parameter controlling the cutting force and delamination behaviour in a tapered specimen, and upon reaching a certain threshold delamination can be completely suppressed. The method demonstrated has potential for implementation in commercial AFP machines, theoretically realising a more compact cutting mechanism, with the capability of preventing delamination in the ply drop regions.

Author(s): Liu, BY; Zhu, Q; Riley, WJ; Zhao, L; Ma, H; Van Gordon, M; Larsen, L | Abstract: Water availability has historically been one of the most significant threats to African regional social and economic well-being. Over the Sahel region, a megadrought during the 1960s and 1970s induced by an abrupt and substantial rainfall reduction caused widespread famine and death. The postdrought recovery, which is still ongoing, has been characterized by gradual increases in rainfall, but with dramatic fluctuations. The large negative human impacts, slow recovery, and variability raise important questions of why and how rainfall dynamics evolve and interact with other components of the regional climate system. Here we provide an observational assessment of rainfall interactions mechanisms (informed by directional transfer of information entropy) that regulate Sahel rainfall. We quantitatively demonstrate that (1) sea surface temperature over the Gulf of Guinea controls moisture advection and transport to the West Sahel region and (2) strong bidirectional interactions exist between local vegetation dynamics and rainfall patterns. Then we assess the directional interaction patterns from nine state-of-the-art Earth System Models (ESMs). We find that most ESMs are able to represent either the unidirectional control of sea surface temperature on precipitation or the bidirectional interaction between vegetation and precipitation. However, none of the ESMs represents both interactive patterns. The GFDL and IPSL-CM5A-LR models successfully reproduced observed patterns over ~50% of the West Sahel region but were not accurate in reproducing observed precipitation regional trends or interannual variation. We propose that the directional information transfer is a powerful mechanistic benchmark to assess model fidelity at the process level.

// Candice C. Poon 1 , Paul M.K. Gordon 2 , Katherine Liu 1 , Runze Yang 1 , Susobhan Sarkar 1 , Reza Mirzaei 1 , Shiekh Tanveer Ahmad 3 , Martha L. Hughes 1 , V. Wee Yong 1, * and John J.P. Kelly 1, * 1 Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada 2 Centre for Health Genomics and Informatics, University of Calgary, Calgary, AB, Canada 3 Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada * These authors contributed equal supervision to this work Correspondence to: John J.P. Kelly, email: jjkelly@ucalgary.ca Keywords: glioblastoma; microglia; macrophages; isocitrate dehydrogenase; single-cell RNA sequencing Received: January 11, 2019 Accepted: March 04, 2019 Published: May 03, 2019 ABSTRACT Microglia and macrophages are the largest component of the inflammatory infiltrate in glioblastoma (GBM). However, whether there are differences in their representation and activity in the prognostically-favorable isocitrate dehydrogenase (IDH)-mutated compared to -wild type GBMs is unknown. Studies on human specimens of untreated IDH-mutant GBMs are rare given they comprise 10% of all GBMs and often present at lower grades, receiving treatments prior to dedifferentiation that can drastically alter microglia and macrophage phenotypes. We were able to obtain large samples of four previously untreated IDH-mutant GBM. Using flow cytometry, immunofluorescence techniques with automated segmentation protocols that quantify at the individual-cell level, and comparison between single-cell RNA-sequencing (scRNA-seq) databases of human GBM, we discerned dissimilarities between GBM-associated microglia and macrophages (GAMMs) in IDH-mutant and -wild type GBMs. We found there are significantly fewer GAMM in IDH-mutant GBMs, but they are more pro-inflammatory, suggesting this contributes to the better prognosis of these tumors. Our pro-inflammatory score which combines the expression of inflammatory markers (CD68/HLA-A, -B, -C/TNF/CD163/IL10/TGFB2), Iba1 intensity, and GAMM surface area also indicates that more pro-inflammatory GAMMs are associated with longer overall survival independent of IDH status. Interrogation of scRNA-seq databases demonstrates microglia in IDH-mutants are mainly pro-inflammatory, while anti-inflammatory macrophages that upregulate genes such as FCER1G and TYROBP predominate in IDH-wild type GBM. Taken together, these observations are the first head-to-head comparison of GAMMs in treatment-naive IDH-mutant versus -wild type GBMs. Our findings highlight biological disparities in the innate immune microenvironment related to IDH prognosis that can be exploited for therapeutic purposes.