Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis

The oomycete pathogen, Pseudoperonospora cubensis, is the causal agent of downy mildew on cucurbits, and at present, no effective resistance to this pathogen is available in cultivated cucumber (Cucumis sativus). To better understand the host response to a virulent pathogen, we performed expression profiling throughout a time course of a compatible interaction using whole transcriptome sequencing. As described herein, we were able to detect the expression of 15,286 cucumber genes, of which 14,476 were expressed throughout the infection process from 1 day post-inoculation (dpi) to 8 dpi. A large number of genes, 1,612 to 3,286, were differentially expressed in pair-wise comparisons between time points. We observed the rapid induction of key defense related genes, including catalases, chitinases, lipoxygenases, peroxidases, and protease inhibitors within 1 dpi, suggesting detection of the pathogen by the host. Co-expression network analyses revealed transcriptional networks with distinct patterns of expression including down-regulation at 2 dpi of known defense response genes suggesting coordinated suppression of host responses by the pathogen. Comparative analyses of cucumber gene expression patterns with that of orthologous Arabidopsis thaliana genes following challenge with Hyaloperonospora arabidopsidis revealed correlated expression patterns of single copy orthologs suggesting that these two dicot hosts have similar transcriptional responses to related pathogens. In total, the work described herein presents an in-depth analysis of the interplay between host susceptibility and pathogen virulence in an agriculturally important pathosystem

Alternative Splicing of a Multi-Drug Transporter from Pseudoperonospora cubensis Generates an RXLR Effector Protein That Elicits a Rapid Cell Death

Pseudoperonospora cubensis, an obligate oomycete pathogen, is the causal agent of cucurbit downy mildew, a foliar disease of global economic importance. Similar to other oomycete plant pathogens, Ps. cubensis has a suite of RXLR and RXLR-like effector proteins, which likely function as virulence or avirulence determinants during the course of host infection. Using in silico analyses, we identified 271 candidate effector proteins within the Ps. cubensis genome with variable RXLR motifs. In extending this analysis, we present the functional characterization of one Ps. cubensis effector protein, RXLR protein 1 (PscRXLR1), and its closest Phytophthora infestans ortholog, PITG_17484, a member of the Drug/Metabolite Transporter (DMT) superfamily. To assess if such effector-non-effector pairs are common among oomycete plant pathogens, we examined the relationship(s) among putative ortholog pairs in Ps. cubensis and P. infestans. Of 271 predicted Ps. cubensis effector proteins, only 109 (41%) had a putative ortholog in P. infestans and evolutionary rate analysis of these orthologs shows that they are evolving significantly faster than most other genes. We found that PscRXLR1 was up-regulated during the early stages of infection of plants, and, moreover, that heterologous expression of PscRXLR1 in Nicotiana benthamiana elicits a rapid necrosis. More interestingly, we also demonstrate that PscRXLR1 arises as a product of alternative splicing, making this the first example of an alternative splicing event in plant pathogenic oomycetes transforming a non-effector gene to a functional effector protein. Taken together, these data suggest a role for PscRXLR1 in pathogenicity, and, in total, our data provide a basis for comparative analysis of candidate effector proteins and their non-effector orthologs as a means of understanding function and evolutionary history of pathogen effectors

Controlling the thermoelectric properties of organo-metallic coordination polymers through backbone geometry

Poly(nickel-benzene-1,2,4,5-tetrakis(thiolate)) (Ni-btt), an organometallic coordination polymer (OMCP) characterized by the coordination between benzene-1,2,4,5-tetrakis(thiolate) (btt) and Ni2+ ions, has been recognized as a promising p-type thermoelectric material. In this study, we employed a constitutional isomer based on benzene-1,2,3,4-tetrakis(thiolate) (ibtt) to generate the corresponding isomeric polymer, poly(nickel-benzene-1,2,3,4-tetrakis(thiolate)) (Ni-ibtt). Comparative analysis of Ni-ibtt and Ni-btt reveals several common infrared (IR) and Raman features attributed to their similar square-planar nickel–sulfur (Ni–S) coordination. Nevertheless, these two polymer isomers exhibit substantially different backbone geometries. Ni-btt possesses a linear backbone, whereas Ni-ibtt exhibits a more undulating, zig-zag-like structure. Consequently, Ni-ibtt demonstrates slightly higher solubility and an increased bandgap in comparison to Ni-btt. The most noteworthy dissimilarity, however, manifests in their thermoelectric properties. While Ni-btt exhibits p-type behavior, Ni-ibtt demonstrates n-type carrier characteristics. This intriguing divergence prompted further investigation into the influence of OMCP backbone geometry on the electronic structure and, particularly, the thermoelectric properties of these materials

Polarizable Anionic Sublattices Can Screen Molecular Dipoles in Noncentrosymmetric Inorganic-Organic Hybrids

We report the growth and photophysical characterization of two polar hybrid lead halide phases, methylenedianiline lead iodide and bromide, (MDA)Pb2I6 and (MDA)Pb2Br6, respectively. The phases crystallize in noncentrosymmetric space group Fdd2, which produces a highly oriented molecular dipole moment that gives rise to second harmonic generation (SHG) upon excitation at 1064 nm. While both compositions are isostructural, the size dependence of the SHG signal suggests that the bromide exhibits a stronger phase-matching response whereas the iodide exhibits a significantly weaker non-phase-matching signal. Similarly, fluorescence from (MDA)Pb2Br6 is observed around 630 nm below 75 K whereas only very weak luminescence from (MDA)Pb2I6 can be seen. We attribute the contrasting optical properties to differences in the character of the halide sublattice and postulate that the increased polarizability of the iodide ions acts to screen the local dipole moment, effectively reducing the local electric field in the crystals

mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection

Pseudoperonospora cubensis, an oomycete, is the causal agent of cucurbit downy mildew, and is responsible for significant losses on cucurbit crops worldwide. While other oomycete plant pathogens have been extensively studied at the molecular level, Ps. cubensis and the molecular basis of its interaction with cucurbit hosts has not been well examined. Here, we present the first large-scale global gene expression analysis of Ps. cubensis infection of a susceptible Cucumis sativus cultivar, ‘Vlaspik’, and identification of genes with putative roles in infection, growth, and pathogenicity. Using high throughput whole transcriptome sequencing, we captured differential expression of 2383 Ps. cubensis genes in sporangia and at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Additionally, comparison of Ps. cubensis expression profiles with expression profiles from an infection time course of the oomycete pathogen Phytophthora infestans on Solanum tuberosum revealed similarities in expression patterns of 1,576–6,806 orthologous genes suggesting a substantial degree of overlap in molecular events in virulence between the biotrophic Ps. cubensis and the hemi-biotrophic P. infestans. Co-expression analyses identified distinct modules of Ps. cubensis genes that were representative of early, intermediate, and late infection stages. Collectively, these expression data have advanced our understanding of key molecular and genetic events in the virulence of Ps. cubensis and thus, provides a foundation for identifying mechanism(s) by which to engineer or effect resistance in the host

Reference values for serum creatinine in children younger than 1 year of age

Reliable reference values of enzymatically assayed serum creatinine categorized in small age intervals are lacking in young children. The aim of this study was to determine reference values for serum creatinine during the first year of life and study the influence of gender, weight and height on these values. Serum creatinine determinations between 2003 and 2008 were retrieved from the hospital database. Strict exclusion criteria ensured the selection of patients without kidney damage. Correlation analysis was performed to evaluate the relation between height, weight and serum creatinine; the Mann–Whitney test was used to evaluate the relation between gender and serum creatinine. A broken stick model was designed to predict normal serum creatinine values. Mean serum creatinine values were found to decrease rapidly from 55 μmol/L on day 1 to 22 μmol/L in the second month of life; they then stabilized at 20 μmol/L until the seventh month, followed by a slight increase. No significant relation was found between serum creatinine and gender, weight and height. We present here reference values of serum creatinine in infants not at risk of decreased renal function. The absence of a relationship with gender, weight and height confirms that height-based equations to estimate glomerular filtration rate are less useful in patients of this age group

Mitigating the effects of COVID-19 on HIV treatment and care in Lusaka, Zambia: A before-after cohort study using mixed effects regression

Introduction The Zambian Ministry of Health (MoH) issued COVID-19 mitigation guidance for HIV care immediately after the first COVID-19 case was confirmed in Zambia on 18 March 2020. The Centre for Infectious Disease Research in Zambia implemented MoH guidance by: 1) extending antiretroviral therapy (ART) refill duration to 6 multi-month dispensation (6MMD) and 2) task-shifting communication and mobilisation of those in HIV care to collect their next ART refill early. We assessed the impact of COVID-19 mitigation guidance on HIV care 3 months before and after guidance implementation. Methods We reviewed all ART pharmacy visit data in the national HIV medical record for PLHIV in care having ≥1 visit between 1 January - 30 June 2020 at 59 HIV care facilities in Lusaka Province, Zambia. We undertook a before-after evaluation using mixed-effects Poisson regression to examine predictors and marginal probability of early clinic return (pharmacy visit >7 days before next appointment), proportion of late visit (>7 days late for next appointment) and probability of receiving a 6MMD ART refill. Results A total of 101 371 individuals (64% female, median age 39) with 130 486 pharmacy visits were included in the analysis. We observed a significant increase in the adjusted prevalence ratio (4.63; 95% CI 4.45 to 4.82) of early return before compared with after guidance implementation. Receipt of 6MMD increased from a weekly mean of 47.9% (95% CI 46.6% to 49.2%) before to 73.4% (95% CI 72.0% to 74.9%) after guidance implementation. The proportion of late visits (8-89 days late) was significantly higher before (18.8%, 95% CI17.2%to20.2%) compared with after (15.1%, 95% CI13.8%to16.4%) guidance implementation. Conclusions Timely issuance and implementation of COVID-19 mitigation guidance involving task-shifted patient communication and mobilisation alongside 6MMD significantly increased early return to ART clinic, potentially reducing interruptions in HIV care during a global public health emergency