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Throughout the vascular tree, endothelial cells function as the interface between circulation and underlying tissues. They act not only as gatekeepers but are also designed to gauge and adapt to circulating factors for regulation of vascular tone, development, and repair. The severity of many diseases, such as cardiovascular disease and diabetes, hinge on endothelial function and the ability to initiate vascularization of hypoxic tissues. Vascular morphogenesis requires a delicate molecular gradient of Notch signaling in endothelial cells to pattern correct angiogenic sprouting. This process is controlled, at least in part, by the distribution of ligands (Dll4 and Jagged1). How Jagged1 (Jag1) expression is compartmentalized in the vascular plexus remains unclear. Understanding the molecular regulators for this process can help our understanding of drivers toward endothelial dysfunction. Here, we showed that mRNA decay protein Zinc-finger protein 36 (ZFP36) is robustly induced in vitro in various human primary endothelial cells (ECs) downstream of canonical vascular endothelial growth factor (VEGF) signaling. This induction, observed at the mRNA and protein level, is uniquely specific to ZFP36 and not shared by other family members ZFP36L1 nor ZFP36L2, which have already been linked to vascular development. This induction was also observed to be primarily facilitated through VEGF receptor 2 (VR2) as receptor inhibition blunted ZFP36 induction. We identified Jag1 mRNA as direct target of zinc finger protein 36 (ZFP36) via crosslinking-immunoprecipitation and verified conserved Jag1 regulation in human primary ECs. Human ECs lacking ZFP36 achieved with CRISPR KO, displayed high levels of JAG1 and increased angiogenic sprouting in vitro. Similarly, in mice with tamoxifen induced endothelial specific vascular endothelial-cadherin Cre-mediated KO of Zfp36, endothelial cells displayed mispatterned and increased levels of JAG1 in the developing retinal vascular plexus. Abnormal levels of JAG1 at the sprouting front altered Notch1 signaling, increasing the number of tip cells; a phenotype that was rescued by crossing the EC specific Zfp36 KO with Jag1 KO mice to achieve haploinsufficiency of Jag1.Additionally, we tested the significance of ZFP36 induction in the broad context of molecular drivers of endothelial plasticity: metabolism, kinase signaling, and shear stress. We were unable to confirm several metabolic targets identified in mouse embryonic fibroblasts (MEFs) in our human primary ECs in vitro. However, conserved sensitivity to changes in kinase activity, confirmed through inhibitor studies, suggests that these discrepancies in targets could be a result of cell specific targets for ZFP36 mRNA binding and regulation. Microenvironment can further play a role in ZFP36 mediated endothelial transcript regulation as we show that shear stress is able to suppress overall ZFP36 expression.Our findings reveal an important feedforward loop, whereby VEGF stimulates ZFP36, consequently suppressing Jag1 to enable adequate levels of Notch signaling during sprouting angiogenesis.

Six varieties of watermelon (Sugar baby, Sugar dragon, Kaolack, Crimson sweet, Koloss and baby doll) were evaluated in the field to assess the genetic parameters associated with morphological traits in the watermelon genotypes. The experiment was laid out in Randomized Complete Block Design (RCBD) in three replications. There were variations in number of branches per plant, vine length, number of days to 50% flowering, number of male flowers, number of fruits per plant and fruit weight per plant. Low response to selection and genetic variation was observed in most traits. The number of days to 50% flowering had the highest heritability estimates (97%), genetic gain of 15.84% and genetic advance of 5.33. Fruit weight per plant had high heritability estimates of 89%, moderate genetic gain of 46.20% and genetic advance of 2.31. Moderate broad sense heritability estimates ranging from 55% for number of male flowers per plant to 63% for number of fruits per plant. Mean branch number had the highest genetic gain of 49.33% but moderate heritability estimates of 58.91% signifying moderate response of selection. Koloss and Kaolack had the highest genetic performance for fruits yield than Baby doll and other varieties plant in the humid environment. Therefore, Koloss and Kaolack is recommended in the humid ecology and should be cultivated in the ecological zone.

The presence of a characteristic chimeric fusion as the initiating genomic event is one defining feature of Spitz neoplasms. Characterization of specific subtypes of Spitz neoplasms allows for better recognition facilitating diagnosis. Data on clinical outcomes of the specific tumor types may help in predicting behavior. In this study we present the largest series to date on ROS1 fusion Spitz neoplasms. We present the clinical, morphologic, and genomic features of 17 cases. We compared the morphologic features of these 17 cases to a cohort of 99 other non-ROS1 Spitz neoplasms to assess for features that may have high specificity for ROS1 fusions. These tumors consisted of ten Spitz nevi and seven Spitz tumors. None of the cases met criteria for a diagnosis of Spitz melanoma. Morphologically, the ROS1 fusion tumors of this series were characterized by a plaque-like or nodular silhouette, often densely cellular intraepidermal melanocyte proliferation, frequent pagetosis, tendency toward spindle cell cytomorphology, low grade nuclear atypia, and floating nests with occasional transepidermal elimination. However, there was a significant range in microscopic appearances, including two cases with morphologic features of a desmoplastic Spitz nevus. Different binding partners to ROS1 were identified with PWWP2A and TPM3 being the most common. No case had a recurrence or metastasis. Our findings document that most ROS1 fusion Spitz neoplasms have some typical characteristic microscopic features, while a small proportion will have features overlapping with other genomic subtypes of Spitz neoplasms. Preliminary evidence suggests that they tend to be indolent or low grade neoplasms.

X-Linked Dystonia-Parkinsonism (XDP) is a neurodegenerative disease affecting individuals with ancestry to the island of Panay in the Philippines. In recent years there has been considerable progress at elucidating the genetic basis of XDP and candidate disease mechanisms in patient-derived cellular models, but the neural substrates that give rise to XDP in vivo are still poorly understood. Previous studies of limited XDP postmortem brain samples have reported a selective dropout of medium spiny neurons within the striatum, although neuroimaging of XDP patients has detected additional abnormalities in multiple brain regions beyond the basal ganglia. Given the need to fully define the CNS structures that are affected in this disease, we created a brain bank in Panay to serve as a tissue resource for detailed studies of XDP-related neuropathology. Here we describe this platform, from donor recruitment and consent to tissue collection, processing, and storage, that was assembled within a predominantly rural region of the Philippines with limited access to medical and laboratory facilities. Thirty-six brains from XDP individuals have been collected over an initial 4 years period. Tissue quality was assessed based on histologic staining of cortex, RNA integrity scores, detection of neuronal transcripts in situ by fluorescent hybridization chain reaction, and western blotting of neuronal and glial proteins. The results indicate that this pipeline preserves tissue integrity to an extent compatible with a range of morphologic, molecular, and biochemical analyses. Thus the algorithms that we developed for working in rural communities may serve as a guide for establishing similar brain banks for other rare diseases in indigenous populations. Supplementary Information The online version contains supplementary material available at 10.1007/s00702-020-02286-9.

Two distinct studies have shown that RET fusions are found in 3%-4% of Spitz neoplasms. RET fusions have been well described in papillary thyroid cancer, non-small-cell lung cancer, breast cancer, and soft-tissue mesenchymal tumors as well as some other neoplasms. However, there are no comprehensive descriptions to date of the characteristic morphologic, clinical, or genomic findings in RET fusion Spitz neoplasms. In this study, we identified 5 cases of RET fusion Spitz neoplasms. These tumors showed characteristic morphologic features which included plaque-like silhouette and monotonous epithelioid cytology with expansile and dyscohesive nesting. Four of 5 patients including 1 diagnosed as Spitz melanoma had clinical follow-up all of which was uneventful. Furthermore, we describe the genomic sequences in 4 of these cases, 2 of which have previously described KIF5B-RET fusion and 2 of which had a novel LMNA-RET fusion. We believe this report significantly contributes to our current knowledge regarding Spitz neoplasms and describes characteristics features which can help with recognition of the RET subgroup of Spitz.

This is a radiomics study investigating the ability of texture analysis of MRF maps to improve differentiation between intra-axial adult brain tumors and to predict survival in the glioblastoma cohort. Magnetic resonance fingerprinting (MRF) acquisition was performed on 31 patients across 3 groups: 17 glioblastomas, 6 low-grade gliomas, and 8 metastases. Using regions of interest for the solid tumor and peritumoral white matter on T1 and T2 maps, second-order texture features were calculated from gray-level co-occurrence matrices and gray-level run length matrices. Selected features were compared across the three tumor groups using Wilcoxon rank-sum test. Receiver operating characteristic curve analysis was performed for each feature. Kaplan-Meier method was used for survival analysis with log rank tests. Low-grade gliomas and glioblastomas had significantly higher run percentage, run entropy, and information measure of correlation 1 on T1 than metastases (p

Plant associations with soil microbiota can modulate tree seedling growth and survival via mutualistic or antagonistic interactions. It is uncertain, however, whether soil microbiota influence seedling growth of coastal trees when exposed to extreme flooding regimes. We evaluated the role of soil microbes in promoting baldcypress (Taxodium distichum) seedling performance under different inundation scenarios and determined the influence of flooding on the colonization of in planta beneficial microbes. Seedlings reared in sterile and non-sterile soil were exposed to three different flooding regimes historically experienced in Louisiana swamps. Seedling growth was assessed, and the colonization by beneficial symbionts such as arbuscular mycorrizhal fungi (AMF), and dark septate endophytes (DSE) was evaluated in harvested roots. Seedlings grown in sterile soil had six times higher growth than seedlings reared in non-sterile soil. As a result, we evaluated pathogen load in the roots by assessing oomycete colonization. Flooding influenced the in planta colonization of DSE and oomycetes, but did not affect the colonization of mutualist AMF fungi. DSE and oomycetes were rarer in flooded conditions, while AMF remained abundant. Seedling biomass production was not correlated with in planta fungal colonization or pathogen load. Soil microbiota can negatively influence baldcypress seedling growth, and no growth benefit was evidenced from the root colonization of mutualist fungi. Flooding can modify baldcypress-fungal interactions by diminishing colonization of DSE. Overall, baldycpress seedlings were more sensitive to the presence of microbiota than flooding, and thus restoration efforts should focus on having a better understanding of plant–microbe interactions in swamps.

As rising sea levels alter coastal ecosystems, there is a pressing need to examine the effects of saltwater intrusion on coastal communities. Using 16S Illumina profiling, we characterized the communities of baldcypress tree (Taxodium distichum) root endosphere and rhizosphere soil bacteria. Our study utilized established sites along salinity and flooding gradients in the United States of Georgia, Louisiana, and South Carolina. We hypothesized that environmental variables, namely salinity and water level, as well as distance between sites would be correlated with baldcypress-associated rhizosphere and root endosphere bacterial communities. We found that geographic distance correlated with rhizosphere but not root endosphere bacterial communities, suggesting that the trees may have stabilized their endosphere communities via recruitment of a more specific suite of taxa from the surrounding soil. Mean water level, mean salinity, and the volume of woody debris were associated with both endosphere and rhizosphere bacterial communities in baldcypress trees. The density of host trees was also associated with endosphere community composition. Our study is the first to use 16S Illumina sequencing to characterize bacterial communities in baldcypress trees— a key restoration species in coastal swamp ecosystems under threat from rising sea levels.

Circadian rhythms are endogenous and entrainable daily patterns of physiology and behavior. Molecular mechanisms underlie circadian rhythms, characterized by an ~24-h pattern of gene expression of core clock genes. Although it has long been known that breathing exhibits circadian rhythms, little is known concerning clock gene expression in any element of the neuromuscular system controlling breathing. Furthermore, we know little concerning gene expression necessary for specific respiratory functions, such as phrenic motor plasticity. Thus, we tested the hypotheses that transcripts for clock genes ( Bmal1, Clock, Per1, and Per2) and molecules necessary for phrenic motor plasticity ( Htr2a, Htr2b, Bdnf, and Ntrk2) oscillate in regions critical for phrenic/diaphragm motor function via RT-PCR. Tissues were collected from male Sprague-Dawley rats entrained to a 12-h light-dark cycle at 4 zeitgeber times (ZT; n = 8 rats/group): ZT5, ZT11, ZT17, and ZT23; ZT0 = lights on. Here, we demonstrate that 1) circadian clock genes ( Bmal1, Clock, Per1, and Per2) oscillate in regions critical for phrenic/diaphragm function, including the caudal medulla, ventral C3–C5 cervical spinal cord, and diaphragm; 2) the clock protein BMAL1 is localized within CtB-labeled phrenic motor neurons; 3) genes necessary for intermittent hypoxia-induced phrenic/diaphragm motor plasticity ( Htr2b and Bdnf) oscillate in the caudal medulla and ventral C3–C5 spinal cord; and 4) there is higher intensity of immunofluorescent BDNF protein within phrenic motor neurons at ZT23 compared with ZT11 ( n = 11 rats/group). These results suggest local circadian clocks exist in the phrenic motor system and confirm the potential for local circadian regulation of neuroplasticity and other elements of the neural network controlling breathing.

Proteins with a functionalized C-terminus such as a C-terminal thioester are key to the synthesis of larger proteins via expressed protein ligation. They are usually made by recombinant fusion to intein. Although powerful, the intein fusion approach suffers from premature hydrolysis and low compatibility with denatured conditions. To totally bypass the involvement of an enzyme for expressed protein ligation, here we showed that a cysteine in a recombinant protein was chemically activated by a small molecule cyanylating reagent at its N-side amide for undergoing nucleophilic acyl substitution with amines including a number of L- and D-amino acids and hydrazine. The afforded protein hydrazides could be used further for expressed protein ligation. We demonstrated the versatility of this activated cysteine-directed protein ligation (ACPL) approach with the successful synthesis of ubiquitin conjugates, ubiquitin-like protein conjugates, histone H2A with a C-terminal posttranslational modification, RNAse H that actively hydrolyzed RNA, and exenatide that is a commercial therapeutic peptide. The technique, which is exceedingly simple but highly useful, expands to a great extent the synthetic capacity of protein chemistry and will therefore make a large avenue of new research possible.

BackgroundMerkel cell carcinoma (MCC) is a rare skin cancer with 46% disease-associated mortality and half of patients unresponsive to immune checkpoint inhibitors.1 2 MCC and melanomas often display decreased MHC class I (MHC-I) expression on the surface of cells, which prevents antigen recognition by T cells (”signal 1”) and hampers immune activation. We therefore sought to genetically reprogram cells to express their own costimulatory molecules (”signal 2”) and immunostimulatory cytokines (”signal 3”) to increase MHC-I expression and drive a targeted immune response.MethodsWe used biodegradable poly(beta-amino ester) nanoparticles (NPs) to co-deliver plasmids encoding a signal 2 molecule (4-1BBL) and two signal 3 molecules (IL-12 and IFNγ) to cancer cells. For in vitro evaluation of NPs we used two patient-derived MCC cell lines with low baseline MHC-I expression; MCC13 and UISO. Co-culture experiments were performed with human PBMCs or primary human natural killer (NK) cells. All in vitro analysis was performed 7 days following PBMC or NK cell addition. For in vivo evaluation, subcutaneous B16F10 mouse melanoma tumors were implanted in C57BL/6J mice and NPs were administered by direct injection into the tumor with and without intraperitoneal injection of αPD1. Tumors were harvested for analysis on day 16.ResultsTransfection with particles delivering the three plasmids to MCC13 and UISO increased MHC-I expression (mean fluorescence intensity) 1.6- and 5.0-fold, respectively, and MHC-II expression increased 1.6- and 6.3-fold, respectively (figure 1). In co-culture with human PBMCs, signal 2/3 particles resulted in increased leukocyte proliferation (4.6- and 6.1-fold increase, respectively) and led to significantly reduced MCC viability (10.6 and 1.6% vs control particles)(figure 2). When MCC13 cells were co-cultured with primary human NK cells, NK cell expansion increased 355-fold with 4-1BBL/IL-12 particles compared to control particles and was accompanied by 2.5% MCC13 cell viability, indicating a potent innate immune response with signal 2/3 NP administration in vitro (figure 3). Following evaluation of NPs in vivo, assessment of MHC-I and MHC-II expression in the melanoma tumors found increased expression with signal 2/3 NPs compared to control NPs (figure 4). When signal 2/3 NPs were administered in combination with αPD1 treatment, 4-1BBL/IL-12 NPs with αPD1 demonstrated improved survival compared to αPD1 treatment with control NPs (p=0.0010) (figure 5).Abstract 222 Figure 1Administration of signal 2/3 NPs to MCC13 and UISO cells led to increases in MHC-I and MHC-II expression after 7 days. MHC-I expression in transfected cells (red) and MHC-II expression in transfected cells (blue) compared to untreated control (black)Abstract 222 Figure 2Co-culture of transfected MCC cells with human PBMCs led to increases in CD45+ cells and reduced MCC cell viability after 7 daysAbstract 222 Figure 3Co-culture of 4-1BBL/IL-12 transfected MCC13 cells with isolated CD56+ NK cells demonstrated robust NK-cell expansion and low MCC cell viability after 7 daysAbstract 222 Figure 4Direct intratumoral injection with signal 2 and 3 NPs led to increases in MHC-I and MHC-II in cancer cells in vivo.Abstract 222 Figure 5NPs were administered intratumorally ± intraperitoneal aPD1 on day 9, 11, and 13 following B16F10 melanoma tumor implantation. 4-1BBL/IL12 particles in combination with αPD1 demonstrated a significant improvement in survival compared to control particles (Luc) with αPD1 (p=0.0010)ConclusionsTogether, these results show the ability of signal 2/3 NPs to reprogram MCC and melanoma cells, leading to increased MHC-I expression in vitro and in vivo, eliciting a productive immune response against cancer cells.ReferencesHughes MP, Hardee ME, Cornelius LA, Hutchins LF, Becker JC, Gao L. Merkel cell carcinoma: epidemiology, target, and therapy. Curr Dermatol 2014;46–53.Nghiem PT, Bhatia S, Lipson EJ, Kudchadkar RR, Miller NJ, Annamalai L, Berry S, Chartash EK, Daud A, Fling SP, Friedlander PA, Kluger HM, Kohrt HE, Lundgren L, Margolin K, Mitchell A, Olencki T, Pardoll DM, Reddy SA, Shantha EM, Sharfman WH, Sharon E, Shemanski LR, Shinohara MM, Sunshine JC, Taube JM, Thompson JA, Townson SM, Yearley JH, Topalian SL, Cheever MA. PD-1 blockade with pembrolizumab in advanced merkel-cell carcinoma. N Engl J Med 2016;374:2542–2552.

The wide spectrum of SARS-CoV-2 variants with phenotypes impacting transmission and antibody sensitivity necessitates investigation of the immune response to different spike protein versions. Here, we compare the neutralization of variants of concern, including B.1.617.2 (Delta) and B.1.1.529 (Omicron) in sera from individuals exposed to variant infection, vaccination, or both. We demonstrate that neutralizing antibody responses are strongest against variants sharing certain spike mutations with the immunizing exposure. We also observe that exposure to multiple spike variants increases the breadth of variant cross-neutralization. These findings contribute to understanding relationships between exposures and antibody responses and may inform booster vaccination strategies., SUMMARY This study characterizes neutralization of eight different SARS-CoV-2 variants, including Delta and Omicron, with respect to nine different prior exposures, including vaccination, booster, and infections with Delta, Epsilon, and others. Different exposures were found to confer substantially differing neutralization specificity.

Aims: This study was designed to evaluate the effects of Efavirenz-based highly active antiretroviral therapy (EFVb-HAART, Efavirenz/Lamivudine/Tenofovir) with emphasis on survival, longevity, climbing ability, and reproductive capacity in D. melanogaster. Methods: The experiments were carried out at the Africa Center of Excellence in Phytomedicine Research and Development (ACEPRD), University of Jos, Nigeria between January 2017 and August 2018. D. melanogaster (both sexes) 1-4 days old were exposed to different concentrations of EFVb-HAART (range 10-1200 mg) in the fly food for initial 7 days to determine the LD50, then 5 day fly exposure to 93.11 mg, 46.56 mg, 23.28 mg or 11.64 mg for negative geotaxis assay, and acetylcholinesterase (AChE) activity. Furthermore, 28-day fly survival and longevity were determined. Statistical significance was presumed at P< 0.05. Results: The LD50 of EFVb-HAART in D. melanogaster was 93.11 mg. The HAART exposed flies showed significantly (P

We report the synthesis and characterization of a new self-assembled VO2-L metallogel. Gel formation was investigated by dissolving VO2-L in various solvents and it was found that water/methanol (1 : 9 (v/v) ratio) induces gel formation. The single crystal X-ray structure of the VO2-L metallogel exhibits C–H⋯O and N–H⋯O hydrogen bonding interactions and pi–pi stacking. The VO2-L xerogel obtained after removing the solvents was found to exhibit outstanding performance in catalysis. Bromoperoxidase-like activity of the VO2-L metallogel was also reported. The present catalytic studies are simple and proceed under mild conditions.

Pompe disease is caused by mutations in the gene encoding the lysosomal glycogen-metabolizing enzyme, acid-alpha glucosidase (GAA). Tongue myofibers and hypoglossal motoneurons appear to be particularly susceptible in Pompe disease. Here we used intramuscular delivery of adeno-associated virus serotype 9 (AAV9) for targeted delivery of an enhanced form of GAA to tongue myofibers and motoneurons in 6-month-old Pompe (Gaa−/−) mice. We hypothesized that addition of a glycosylation-independent lysosomal targeting tag to the protein would result in enhanced expression in tongue (hypoglossal) motoneurons when compared to the untagged GAA. Mice received an injection into the base of the tongue with AAV9 encoding either the tagged or untagged enzyme; tissues were harvested 4 months later. Both AAV9 constructs effectively drove GAA expression in lingual myofibers and hypoglossal motoneurons. However, mice treated with the AAV9 construct encoding the modified GAA enzyme had a >200% increase in the number of GAA-positive motoneurons as compared to the untagged GAA (p < 0.008). Our results confirm that tongue delivery of AAV9-encoding GAA can effectively target tongue myofibers and associated motoneurons in Pompe mice and indicate that the effectiveness of this approach can be improved by addition of the glycosylation-independent lysosomal targeting tag. Keywords: hypoglossal, tongue, Pompe, gene therapy, GAA, AAV, lysosomal storage disease, motoneuron, genioglossus, respiratory

Objective: To screen the toxic effect of Mangifera indica aqueous leaf extract in Drosophila melanogaster. Materials and Methods: Phytochemical screening was carried out. 20 Adult flies were exposed to 7.5 mg, 15 mg, 30 mg, 45 mg and 100 mg /10 g diet for acute toxicity (168hrs) while 50 flies were exposed to 2.5 mg, 5 mg and 10 mg/10 g diet for sub chronic (28 days). All concentrations were prepared in 1000µl of distilled water and replicated three (3) times. Diet+1000µl of Distilled water served as control. Fecundity/developmental toxicity, Climbing and AChE activities were carried out by exposing flies to the sub-chronic concentrations for 5 days. Results: Phytochemical screening revealed the presence of alkaloids, phenols, flavonoids, tannins, saponins and terpenoids. The acute toxicity test showed 100% mortality at 100 mg/ 10 g diet and 168hrs LC50 was 72.4 mg/10 g diet. The sub chronic toxicity test showed decrease in flies survival along concentration with a least survival at 10 mg/10 g diet. There was a slight reduction and elevation in the Climbing and AChE activities respectively but not statistically significant (p>0.05) compared to control. At 5 mg and 10 mg/10 g diet there was a delay in the development with few emerged flies. Conclusion: From the Results, it can be concluded that Mangiferaindica aqueous leaf extract may be toxic at high dose from 72.4 mg/10 g diet and might have an adverse effect on the development and survival of flies at sub chronic concentration as low as 2.5 mg/10g diet.

Little is known about the microbiota that form symbioses with wetland plants. We describe how endophytes from leaves and roots of baldcypress trees changed along a nutrient gradient and differed in wastewater treated versus untreated wetlands. Cultured bacterial and fungal endophytes were most abundant and diverse in baldcypress roots (compared to leaves) for both treated and untreated wetlands. Bacterial endophyte abundance increased with increasing distance from the wastewater outfall pipe, while fungal endophytes decreased with increasing distance from the wastewater outfall pipe—showing a greater abundance of fungi where nutrients were greatest. Bacterial endophyte abundance and species richness were greater in the wastewater-treatment compared to untreated wetlands, but diversity metrics suggested this was due to incomplete sampling at some sites. Community composition of endophytes in the treated wetland differed from some but not all of the communities observed in untreated wetlands. Since baldcypress is a key restoration species for declining swamps in the southeastern US, our descriptive work provides a foundation for future studies to understand the functional roles of plant-microbial interactions and community patterns.

Objective: To evaluate in vivo antioxidant activity of Mangifera indica cold aqueous leaf extract. Methods: A number of 50 adult flies were exposed to graded concentrations of Mangifera indca cold aqueous leaf extract, 2.5 mg/10 g diet, 5 mg/10 g diet and 10 mg/10 g diet for 5 days. Each concentration was prepared in 200 µl of distilled water and replicated five times. 10 g diet with 200 µl distilled water served as control. Mortality reading was taken at 24 hours interval. The flies were homogenized, centrifuged and the supernatant was used to assay for Glutathione-S-transferase (GST), Catalase (CAT) and Total thiol content. Results: The % mortality of flies after 5 days showed 32.5%, 0%, 15.5% and 37% in the control (10 g diet with 200 µl of distilled water), 2.5 mg/10 g diet, 5 mg/10 g diet and 10 mg/ 10 g diet respectively. There was elevation in total thiol content and high GST and CAT activity in 2.5 mg/10 g diet and 5 mg/10 g diet treated flies. Conclusion: The 100% and 85% survival of 2.5 mg/10 g and 5 mg/10 g diet-treated flies respectively and increase of fly antioxidant system after 5 days exposure at these concentrations may suggest protective activity of Mangifera indica in D. melanogaster.

The invasion of exotic species in aquatic environments is one of the several disturbance factors responsible for altering the dynamics of fish communities. The golden mussel Limnoperna fortunei was first recorded in the upper Uruguay river, Brazil, in 2012 and, since then, it has been needed to discuss and evaluate how this invasive species interferes with the dynamics of the ten most abundant fishes of this region. Literature lacks works that investigate how to model and control the effect of such kind of invasion. This paper proposes a polynomial-nonlinear state-space representation to model the dynamics of the these fish communities, whose parameters are identified with the use of Least Squares procedures, considering in loci collected data from 2007 to 2016. This work also evaluates quantitatively, by relying on simulation results, how the (sudden) presence of the golden mussel medelled with the aquatic life of the upper Uruguay river. The obtained model allows some ambitious automatic control objectives. Using a Nonlinear Model Predictive Control (NMPC) approach, an automatic controller is designed to determine how much and how often the golden mussel should be removed from the water in order for the most affected species to once again exhibit sustainable life conditions, in terms of its K Condition Factor and abundance. The NMPC strategy is synthesized considering performance constraints and piecewise-constant control trajectories. By relying on simulation results, this work elucidates how an automatic controller could be implemented as management policies established by environmental agencies to gradually restore the fish ecological balance of the upper Uruguay river, previously unsettled by an exotic invasor.

CellMiner (http://discover.nci.nih.gov/cellminer) and CellMinerCDB (https://discover.nci.nih.gov/cellminercdb/) are web-based applications for mining publicly available genomic, molecular, and pharmacologic datasets of human cancer cell lines including the NCI-60, Cancer Cell Line Encyclopedia, Genomics of Drug Sensitivity in Cancer, Cancer Therapeutics Response Portal, NCI/DTP small cell lung cancer, and NCI Almanac cell line sets. Here, we introduce our RNA sequencing (RNA-seq) data for the NCI-60 and their access and integration with the other databases. Correlation to transcript microarray expression levels for identical genes and identical cell lines across CellMinerCDB demonstrates the high quality of these new RNA-seq data. We provide composite and isoform transcript expression data and demonstrate diversity in isoform composition for individual cancer- and pharmacologically relevant genes, including HRAS, PTEN, EGFR, RAD51, ALKBH2, BRCA1, ERBB2, TP53, FGFR2, and CTNND1. We reveal cell-specific differences in the overall levels of isoforms and show their linkage to expression of RNA processing and splicing genes as well as resultant alterations in cancer and pharmacologic gene sets. Gene–drug pairings linked by pathways or functions show specific correlations to isoforms compared with composite gene expression, including ALKBH2-benzaldehyde, AKT3-vandetanib, BCR-imatinib, CDK1 and 20-palbociclib, CASP1-imexon, and FGFR3-pazopanib. Loss of MUC1 20 amino acid variable number tandem repeats, which is used to elicit immune response, and the presence of the androgen receptor AR-V4 and -V7 isoforms in all NCI-60 tissue of origin types demonstrate translational relevance. In summary, we introduce RNA-seq data to our CellMiner and CellMinerCDB web applications, allowing their exploration for both research and translational purposes. Significance: The current study provides RNA sequencing data for the NCI-60 cell lines made accessible through both CellMiner and CellMinerCDB and is an important pharmacogenomics resource for the field.

Ets1 is emerging as a key transcription factor that is required to prevent autoimmunity in mice and humans. Ets1 is expressed in both B and T cells, and mice lacking Ets1 are characterized by excess B and T cell activation, leading to enhanced formation of Ab-secreting cells and high titers of autoantibodies. In humans, genome-wide association studies have detected associations of single nucleotide polymorphisms in the human ETS1 gene with autoimmune diseases, including lupus. An increased fraction of CD4+ T cells from Ets1−/− mice have an activated effector-memory phenotype, and there are aberrations in differentiation that contribute to the autoimmune phenotype. In vitro studies of B cells suggest that Ets1 may have B cell–intrinsic effects as well. To confirm B cell–intrinsic roles for Ets1, we crossed CD19-Cre mice to mice with a floxed allele of Ets1. Mice with a B cell–specific deletion of Ets1 show increases in B cell activation, numbers of Ab-secreting cells, and levels of autoantibodies, despite the fact that T cells are normal. However, when compared with conventional Ets1 knockout mice, mice with B cell–specific loss of Ets1 have a significantly milder phenotype. These results demonstrate that Ets1 is required in B cells to prevent autoimmune responses but that loss of Ets1 activity in other cell types is required for maximal autoimmune phenotypes.

Klebsiella pneumoniae (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO3-2)-resistance (ter) operon as strongly associated with infection. However, TeO3-2 is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between ter and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the ter locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the ter operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available ter operon-encoding Kp plasmids, indicating that the ter operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the ter operon is dispensable during bacteremia, 2) the ter operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for ter. Furthermore, using 16S rRNA gene sequencing, we show that the ter operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a ter mutant. These findings indicate that the ter operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings., Author summary The bacterial pathogen Klebsiella pneumoniae is of substantial public health concern due to its ability to cause serious antibiotic-resistant infections. These infections frequently occur in healthcare settings, especially in patients with detectable gut colonization by K. pneumoniae. Importantly, infectious K. pneumoniae strains are often detected in the gut of patients with K. pneumoniae disease, indicating that the gut is a reservoir of infectious K. pneumoniae. Our previous work interrogating the genetic underpinnings of K. pneumoniae disease in colonized patients identified a strong association between K. pneumoniae infection and the presence of an enigmatic genetic locus known as the ter operon. We found that this operon is not needed for pneumonia and bacteremia, and therefore, we explored the importance of the ter operon in the gut. K. pneumoniae lacking ter function was at a disadvantage in the gut, thus explaining the connection between the ter operon and infection in hospitalized patients. Interestingly, the advantage conferred by the ter operon in the gut was associated with the presence of specific indigenous gut microbiota and the presence of short-chain fatty acids, which are metabolized by the host and gut microbiota. This work demonstrates that the ter operon is a microbiome-dependent gut fitness factor and suggests that indigenous gut bacteria may limit colonization by infectious K. pneumoniae.

BackgroundSequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities.MethodsSARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants.ResultsA total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to “West Coast” variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%).ConclusionsThe increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants.SummaryWe observed a growing prevalence and elevated attack rate for “West Coast” SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

The spiny mouse (Acomys species) has emerged as an exciting research organism due to its remarkable ability to undergo scarless regeneration of skin wounds and ear punches. Excitingly, Acomys species demonstrate scar-free healing in a wide-range of tissues beyond the skin. In this perspective article, we discuss published findings from a variety of tissues to highlight how this emerging research organism could shed light on numerous clinically relevant human diseases. We also discuss the challenges of working with this emerging research organism and suggest strategies for future Acomys-inspired research.

Limnoperna fortunei is an invasive alien species (IAS) that cause serious ecological and economic problems in Brazilian freshwater environments. Due to its high dispersion capacity and the lack of new records in peer-reviewed journals we carried out an extensive survey to update the distribution of L. fortunei in the Brazilian hydrographic basins. We also performed a detailed investigation of its distribution in the Upper Uruguay River basin using a molecular method. We presented new records, showing the invasion in new basins and a wide distribution in the basins previously infested. Additionally, we confirmed that the Upper Uruguay River is fully colonized by the golden mussel, being distributed in the lentic, lotic, and transitional lotic/lentic environments presented in this region. This update is an important tool for the implementation of guidelines and the development of safety protocols and sanitary barriers to avoid the dispersion of this IAS to new environments.. Resumo: Limnoperna fortunei é uma espécie exótica invasora que causa sérios problemas ecológicos e econômicos em ambientes de água doce do Brasil. Devido à sua elevada capacidade de dispersão e à falta de novos registros em publicações científicas, o objetivo deste estudo foi realizar uma extensa pesquisa para entender e alertar sobre o atual cenário de distribuição de L. fortunei nas bacias hidrográficas brasileiras. Também realizamos uma investigação mais detalhada sobre a distribuição da espécie na bacia do Alto Rio Uruguai, utilizando um método molecular. Apresentamos novos registros de ocorrência da espécie, mostrando a invasão em novas bacias e uma ampla distribuição nas bacias anteriormente infestadas. Além disso, confirmamos que o Alto Rio Uruguai está totalmente colonizado pelo mexilhão-dourado, estando distribuído pelos ambientes lênticos, lóticos e de transição existentes na região. Esta atualização se mostra como uma importante ferramenta para a implementação de diretrizes e o desenvolvimento de protocolos de segurança e barreiras sanitárias para evitar a dispersão desta espécie invasora em novos ambientes.

Estimates of the prevalence of dementia among Latinos in the United States vary from 5% to over 12.9% depending upon the measurement of cognitive impairment employed, the age of the sample, and specific nation of origin (Gonzalez et al., 2019; Haan, Mungas, Gonzalez, Ortiz, & Jagust, 2003; Langa et al., 2017; Matthews et al., 2019; Mehta & Yeo, 2017). Because of life-long structural disadvantage, including low levels of education, a lack of health insurance, low income, and low levels of savings, Latinos are more likely than non-Latino whites to develop mild cognitive impairment at earlier ages and dementia (Fitten et al., 2014; Mehta & Yeo, 2017). These structural risks in combination with longer life expectancies at birth and at age 65 mean that older Latinos will spend more years with serious cognitive impairment (Garcia et al., 2018). As a consequence, they will need dementia care for a longer time. Such care places great practical and financial strain on families and increasingly requires that they find some alternative sources. The increase in the number of older persons with mild and serious cognitive impairment also places serious fiscal strains on states. The benefits of longer life, then, are accompanied by greater burdens on families and the need for the state to provide affordable and culturally-appropriate alternatives.

Environmental cues, such as physical forces and heterotypic cell interactions play a critical role in cell function, yet their collective contributions to transcriptional changes are unclear. Focusing on endothelial cells, we performed broad individual sample analysis to identify transcriptional drifts associated with environmental changes that were independent of genetic background. Global gene expression profiling by RNA-seq, ATACseq, and protein expression by LC-MS directed proteomics distinguished endothelial cells in vivo from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes. In contrast, co-culture of endothelial cells with smooth muscle cells normalized approximately 9% of the original in vivo signature. Our findings highlight specific genes and pathways that rely on contextual information and physical forces.

Neuroinflammation plays a pathogenic role in neurodegenerative diseases and recent findings suggest that it may also be involved in X-linked Dystonia-Parkinsonism (XDP) pathogenesis. Previously, fibroblasts and neuronal stem cells derived from XDP patients demonstrated hypersensitivity to TNF-α, dysregulation in NFκB signaling, and an increase in several pro-inflammatory markers. However, the role of inflammatory processes in XDP patient brain remains unknown. Here we demonstrate that there is a significant increase in astrogliosis and microgliosis in human post-mortem XDP prefrontal cortex (PFC) compared to control. Furthermore, there is a significant increase in histone H3 citrullination (H3R2R8R17cit3) with a concomitant increase in peptidylarginine deaminase 2 (PAD2) and 4 (PAD4), the enzymes catalyzing citrullination, in XDP post-mortem PFC. While there is a significant increase in myeloperoxidase (MPO) levels in XDP PFC, neutrophil elastase (NE) levels are not altered, suggesting that MPO may be released by activated microglia or reactive astrocytes in the brain. Similarly, there was an increase in H3R2R8R17cit3, PAD2 and PAD4 levels in XDP-derived fibroblasts. Importantly, treatment of fibroblasts with Cl-amidine, a pan inhibitor of PAD enzymes, reduced histone H3 citrullination and pro-inflammatory chemokine expression, without affecting cell survival. Taken together, our results demonstrate that inflammation is increased in XDP post-mortem brain and fibroblasts and unveil a new epigenetic potential therapeutic target.

Vascular epiphytes contribute up to 35% of the plant diversity and foliar biomass of flowering plants. The family Bromeliaceae is a monophyletic group of plants native to the Neotropics. Epiphytic bromeliads form associations with distinct groups of organisms but their relationship with foliar fungal endophytes remain underexplored. In this study we examined the relationship of foliar fungal endophytes to host photosynthetic pathways and associated ecophysiological traits. We sampled the fungal endophyte communities of 67 host individuals in six epiphytic bromeliad species differing in C3 and crassulacean acid metabolism (CAM) photosynthetic pathways. We tested whether endophyte assemblages were associated with ecophysiological leaf traits related to host photosynthetic pathways. Our results indicate that (1) C3 and CAM bromeliads host dissimilar endophyte assemblages, (2) endophyte communities in C3 bromeliads are characterized by variable relative abundances of fungal orders, conversely, CAM associated endophyte communities were characterized by consistent relative abundances of fungal orders, and (3) endophyte communities in bromeliads are distributed along a continuum of leaf toughness and leaf water content. Taken together, our study suggests that host physiology and associated ecophysiological traits of epiphytic bromeliads may represent biotic filters for communities of fungal endophytes in the tropics.

Plant roots assemble in two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi, unlike rhizosphere fungi, were correlated with host density and canopy cover, suggesting that hosts can impose selective filters on fungi colonizing their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns, e.g. highest endosphere diversity (hump-shaped) and lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure of the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.

The dog provides a large animal model of familial dilated cardiomyopathy for the study of important aspects of this common familial cardiovascular disease. We have previously demonstrated a form of canine dilated cardiomyopathy in the Doberman pinscher breed that is inherited as an autosomal dominant trait and is associated with a splice site variant in the pyruvate dehydrogenase kinase 4 (PDK4) gene, however, genetic heterogeneity exists in this species as well and not all affected dogs have the PDK4 variant. Whole genome sequencing of a family of Doberman pinchers with dilated cardiomyopathy and sudden cardiac death without the PDK4 variant was performed. A pathologic missense variant in the titin gene located in an immunoglobulin-like domain in the I-band spanning region of the molecule was identified and was highly associated with the disease (p

BackgroundSARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) testing remains the cornerstone of laboratory-based identification of patients with COVID-19. As the availability and speed of SARS-CoV-2 testing platforms improve, results are increasingly relied upon to inform critical decisions related to therapy, use of personal protective equipment, and workforce readiness. However, early reports of RT-PCR test performance have left clinicians and the public with concerns regarding the reliability of this predominant testing modality and the interpretation of negative results. In this work, two independent research teams report the frequency of discordant SARS-CoV-2 test results among initially negative, repeatedly tested patients in regions of the United States with early community transmission and access to testing.MethodsAll patients at the University of Washington (UW) and Stanford Health Care undergoing initial testing by nasopharyngeal (NP) swab between March 2nd and April 7th, 2020 were included. SARS-CoV-2 RT-PCR was performed targeting the N, RdRp, S, and E genes and ORF1ab, using a combination of Emergency Use Authorization laboratory-developed tests and commercial assays. Results through April 14th were extracted to allow for a complete 7-day observation period and an additional day for reporting.ResultsA total of 23,126 SARS-CoV-2 RT-PCR tests (10,583 UW, 12,543 Stanford) were performed in 20,912 eligible patients (8,977 UW, 11,935 Stanford) undergoing initial testing by NP swab; 626 initially test-negative patients were re-tested within 7 days. Among this group, repeat testing within 7 days yielded a positive result in 3.5% (4.3% UW, 2.8% Stanford) of cases, suggesting an initial false negative RT-PCR result; the majority (96.5%) of patients with an initial negative result who warranted reevaluation for any reason remained negative on all subsequent tests performed within this window.ConclusionsTwo independent research teams report the similar finding that, among initially negative patients subjected to repeat SARS-CoV-2 RT-PCR testing, the occurrence of a newly positive result within 7 days is uncommon. These observations suggest that false negative results at the time of initial presentation do occur, but potentially at a lower frequency than is currently believed. Although it is not possible to infer the clinical sensitivity of NP SARS-CoV-2 RT-PCR testing using these data, they may be used in combination with other reports to guide the use and interpretation of this common testing modality.

The invasion of exotic species in aquatic environments is one of the several factors responsible for altering the dynamics of fish communities. The golden mussel Limnoperna fortunei was first recorded in the upper Uruguay river, Brazil in 2012 and since then there is an open need to discuss and evaluate how this invasive species interferes with the life of the ten must abundant fishes of this region. In order to achieve this, this work uses two different nonlinear state-space models to describe the dynamics of the K condition factor and abundance of these communities, whose parameters are identified by extended Least Squares procedures, considering real, in locus collected data. One model is polynomially nonlinear on the states and the other is linear, while both are output-nonlinear. This work also evaluates quantitatively how the (sudden) presence of the golden mussel medelled with the aquatic life of the upper Uruguay river, with the aid of high-fidelity simulation results. The methodology points to significant changes in five distinct fish communities, which was also partially observed in nature. Moreover, preliminary results regarding control techniques are also presented to illustrate how environmental policies could act to prevent a biological catastrophe due to this invasor.

Despite the availability of antifungal treatments, fungal infections are still causing morbidity all around the globe with unacceptably high mortality rates. A major driver for the rising incidence of serious fungal infections is due to a substantial increase in immunocompromised individuals with autoimmune diseases, cancers and transplants. Because of growing resistance in fungus to frontline triazole antifungals and the association of fungal disease with the immunocompromised host, adjunctive host-directed therapy is seen as a promising choice to improve patient outcomes. Immunotherapeutic treatments being explored as adjunct therapies to existing antifungal treatments include cytokine therapy, monoclonal antibodies and cellular immunotherapy. In this review, we give a brief overview of potential immunotherapies and recent developments in the field, which are needed to tackle the growing problem of fungal diseases.

Summary CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, NCI-SCLC, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics and gene regulatory network analyses, and exploration of pharmacogenomic determinants and drug signatures. It leverages overlaps of cell lines and drugs across databases to examine reproducibility and expand pathway analyses. We illustrate the value of CellMinerCDB for elucidating gene expression determinants, such as DNA methylation and copy number variations, and highlight complexities in assessing mutational burden. We demonstrate the value of CellMinerCDB in selecting drugs with reproducible activity, expand on the dominant role of SLFN11 for drug response, and present novel response determinants and genomic signatures for topoisomerase inhibitors and schweinfurthins. We also introduce LIX1L as a gene associated with mesenchymal signature and regulation of cellular migration and invasiveness., Graphical Abstract, Highlights • CellMinerCDB integrates pharmacogenomic data of the major cancer cell line databases • It seamlessly enables genomic and drug data exploration within and across databases • It tests genomic data reproducibility and proposes drug response determinants • We expand the GDSC drug panel and advance LIX1L as a novel mesenchymal gene, Genomics; Bioinformatics; Biological Database; Cancer Systems Biology

Background We recently reported a 56% objective response rate in patients with advanced Merkel cell carcinoma (MCC) receiving pembrolizumab. However, a biomarker predicting clinical response was not identified. Methods Pretreatment FFPE tumor specimens (n = 26) were stained for CD8, PD-L1, and PD-1 by immunohistochemistry/immunofluorescence (IHC/IF), and the density and distribution of positive cells was quantified to determine the associations with anti-PD-1 response. Multiplex IF was used to test a separate cohort of MCC archival specimens (n = 16), to identify cell types expressing PD-1. Results Tumors from patients who responded to anti-PD-1 showed higher densities of PD-1+ and PD-L1+ cells when compared to non-responders (median cells/mm2, 70.7 vs. 6.7, p = 0.03; and 855.4 vs. 245.0, p = 0.02, respectively). There was no significant association of CD8+ cell density with clinical response. Quantification of PD-1+ cells located within 20 μm of a PD-L1+ cell showed that PD-1/PD-L1 proximity was associated with clinical response (p = 0.03), but CD8/PD-L1 proximity was not. CD4+ and CD8+ cells in the TME expressed similar amounts of PD-1. Conclusions While the binomial presence or absence of PD-L1 expression in the TME was not sufficient to predict response to anti-PD-1 in patients with MCC, we show that quantitative assessments of PD-1+ and PD-L1+ cell densities as well as the geographic interactions between these two cell populations correlate with clinical response. Cell types expressing PD-1 in the TME include CD8+ T-cells, CD4+ T-cells, Tregs, and CD20+ B-cells, supporting the notion that multiple cell types may potentiate tumor regression following PD-1 blockade. Electronic supplementary material The online version of this article (10.1186/s40425-018-0404-0) contains supplementary material, which is available to authorized users.

Understanding variation in leaf functional traits-including rates of photosynthesis and respiration and concentrations of nitrogen and phosphorus-is a fundamental challenge in plant ecophysiology. When expressed per unit leaf area, these traits typically increase with leaf mass per area (LMA) within species but are roughly independent of LMA across the global flora. LMA is determined by mass components with different biological functions, including photosynthetic mass that largely determines metabolic rates and contains most nitrogen and phosphorus, and structural mass that affects toughness and leaf lifespan (LL). A possible explanation for the contrasting trait relationships is that most LMA variation within species is associated with variation in photosynthetic mass, whereas most LMA variation across the global flora is associated with variation in structural mass. This hypothesis leads to the predictions that (i) gas exchange rates and nutrient concentrations per unit leaf area should increase strongly with LMA across species assemblages with low LL variance but should increase weakly with LMA across species assemblages with high LL variance and that (ii) controlling for LL variation should increase the strength of the above LMA relationships. We present analyses of intra- and interspecific trait variation from three tropical forest sites and interspecific analyses within functional groups in a global dataset that are consistent with the above predictions. Our analysis suggests that the qualitatively different trait relationships exhibited by different leaf assemblages can be understood by considering the degree to which photosynthetic and structural mass components contribute to LMA variation in a given assemblage.

Plant endophytic microbes, accustomed to the Macondo oil-spill environment, may be ideal candidates for crude-oil degradation, bioremediation and endophyte-assisted phytoremediation. We tested both single strain and bacteria consortia for their ability to degrade weathered crude oil, over 25 days, and found the single strain Pseudomonas putida (P. putida) exhibited the best performance for degrading all alkanes from C14 to C32 and 61.01% of the Total Petroleum Hydrocarbons (TPHs), but bacterial consortia did not degrade as much of the n-alkanes as the single strain, with TPHs degradation ranging from 28.4% to 51.5%. This is the first time the endophyte P. putida has been shown to improve the degradation of crude oil, demonstrating the potential of this strain to benefit biological remediation. We did not find any correlation between bio-surfactant production and oil degradation.

Merkel cell carcinoma (MCC) is a rare but lethal cancer with the highest case-by-case fatality rate among all skin cancers. Eighty percent of cancers are associated with the Merkel cell polyomavirus (MCPyV). Twenty percent of MCCs are virus negative. Recent epidemiological data suggest that there are important, clinically relevant differences between these two subtypes of MCC. Recent studies in cancer genomics, mouse genetics, and virology experiments have transformed our understanding of MCC pathophysiology. Importantly, dramatic differences in the genetics of these two MCC subtypes suggest fundamental differences in their pathophysiology. We review these recent works and find that they provocatively suggest that MCPyV-positive and MCPyV-negative MCCs arise from two different cells of origin: the MCPyV-negative MCC from epidermal keratinocytes and the MCPyV-positive MCC from dermal fibroblasts. If true, this would represent the first cancer that we are aware of that evolves from cells of origin from two distinct germ layers: MCPyV-negative MCCs from ectodermal keratinocytes and MCPyV-positive MCCs from mesodermal fibroblasts. Future epigenetic experiments may prove valuable in confirming these distinct lineages for these MCC subtypes, especially for the clinical importance the cell of origin has on MCC treatment and prevention.

Summary Maintaining proteostasis is key to resisting stress and promoting healthy aging. Proteostasis is necessary to preserve stem cell function, but little is known about the mechanisms that regulate proteostasis during stress in stem cells, and whether disruptions of proteostasis contribute to stem cell aging is largely unexplored. We determined that ex-vivo-cultured mouse and human hematopoietic stem cells (HSCs) rapidly increase protein synthesis. This challenge to HSC proteostasis was associated with nuclear accumulation of Hsf1, and deletion of Hsf1 impaired HSC maintenance ex vivo. Strikingly, supplementing cultures with small molecules that enhance Hsf1 activation partially suppressed protein synthesis, rebalanced proteostasis, and supported retention of HSC serial reconstituting activity. Although Hsf1 was dispensable for young adult HSCs in vivo, Hsf1 deficiency increased protein synthesis and impaired the reconstituting activity of middle-aged HSCs. Hsf1 thus promotes proteostasis and the regenerative activity of HSCs in response to culture stress and aging.

The baldcypress midge (Taxodiomyia cupressi and Taxodiomyia cupressiananassa) forms a gall that originates from leaf tissue. Female insects may inoculate galls with fungi during oviposition, or endophytes from the leaf tissue may grow into the gall interior. We investigated fungal diversity inside of baldcypress galls, comparing the gall communities to leaves and comparing fungal communities in galls that had successful emergence versus no emergence of midges or parasitoids. Galls of midges that successfully emerged were associated with diverse gall fungal communities, some of which were the same as the fungi found in surrounding leaves. Galls with no insect emergence were characterized by relatively low fungal diversity.

Introductory paragraphGut colonization by the pathogen Klebsiella pneumoniae (Kp) is consistently associated with subsequent Kp disease1-5, and patients are predominantly infected with their colonizing strain1,2. However, colonizing strains likely vary in their potential to cause infection. We previously identified the plasmid-encoded tellurium resistance (ter) operon as highly associated with infection when compared to asymptomatic colonization in hospitalized patients1. The ter operon bestows resistance to the toxic compound tellurite oxide (TeO3−2), but this is unlikely to be its physiological function, as tellurium and TeO3−2 are exceedingly rare. Here we show that terC is necessary and terZABCDEF is sufficient for phenotypic TeO3−2 resistance. Next, we demonstrate that ter is encoded on a diverse group of plasmids without known plasmid-encoded virulence genes, suggesting an independent role in infection. Finally, our studies indicate that ter is a gut fitness factor, and its fitness advantage is conferred only when specific gut microbiota constituents are present. Collectively, these data reveal the Kp ter operon that is highly associated with human infection likely acts early in pathogenesis as a horizontally-transferrable fitness factor promoting robust gut colonization in the presence of the indigenous microbiota.

The identification of autoantigens remains a critical challenge for understanding and treating autoimmune diseases. Autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic form of autoimmunity, presents as widespread autoimmunity with T and B cell responses to multiple organs. Importantly, autoantibody discovery in APS1 can illuminate fundamental disease pathogenesis, and many of the antigens found in APS1 extend to common autoimmune diseases. Here, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from an APS1 cohort and discovered multiple common antibody targets. These novel autoantigens exhibit tissue-restricted expression, including expression in enteroendocrine cells and dental enamel. Using detailed clinical phenotyping, we find novel associations between autoantibodies and organ-restricted autoimmunity, including between anti-KHDC3L autoantibodies and premature ovarian insufficiency, and between anti-RFX6 autoantibodies and diarrheal-type intestinal dysfunction. Our study highlights the utility of PhIP-Seq for interrogating antigenic repertoires in human autoimmunity and the importance of antigen discovery for improved understanding of disease mechanisms.

Premise There is growing recognition that intraspecific genetic variation in plants can influence associated soil microbial communities, but the functional bridges linking plant genotype with microbial community structure are not well understood. This deficit is due in part to a prevailing focus on characterizing relationships between microbial communities and functional trait variation among plant species or across plant communities, rather than within a single species. Methods We examined whether and how spatiotemporal variation in salt marsh rhizosphere microbial communities reflect plant provenance (genotypic variation) and associated trait variation within an ecosystem engineer, Spartina alterniflora. We planted S. alterniflora from four genetically distinct source populations in replicate sets of experimental plots across a shoreline in southeastern Louisiana, USA. After 2 years, we measured functional plant traits and profiled microbial communities. Results Bacterial and fungal α-diversity and richness were significantly higher in winter than in summer and corresponded to plant trait variation associated with provenance. Notably, 20% of the variation in fungal community composition was explained by trait differences while bacterial community structure did not reflect plant provenance or trait variation. However, evidence was found suggesting that bacterial communities are indirectly shaped by the influence of plant provenance on soil physicochemical properties. Conclusions This study illustrates that intraspecific genetic and corresponding trait variation in an ecosystem engineer can shape rhizosphere microbial communities, with fungal communities being more responsive than bacteria to the influence of plant provenance and associated trait variation. Our results highlight the potential relevance of plant intraspecific variation in plant-microbe-soil feedbacks shaping naturally depauperate ecosystems like salt marshes.

SUMMARY Low protein synthesis is a feature of somatic stem cells that promotes regeneration in multiple tissues. Modest increases in protein synthesis impair stem cell function, but the mechanisms by which this occurs are largely unknown. We determine that low protein synthesis within hematopoietic stem cells (HSCs) is associated with elevated proteome quality in vivo. HSCs contain less misfolded and unfolded proteins than myeloid progenitors. Increases in protein synthesis cause HSCs to accumulate misfolded and unfolded proteins. To test how proteome quality affects HSCs, we examine Aarssti/sti mice that harbor a tRNA editing defect that increases amino acid misincorporation. Aarssti/sti mice exhibit reduced HSC numbers, increased proliferation, and diminished serial reconstituting activity. Misfolded proteins overwhelm the proteasome within Aarssti/sti HSCs, which is associated with increased c-Myc abundance. Deletion of one Myc allele partially rescues serial reconstitution defects in Aarssti/sti HSCs. Thus, HSCs are dependent on low protein synthesis to maintain proteostasis, which promotes their self-renewal., In Brief Stem cells in multiple tissues depend on low protein synthesis to promote regeneration. Hidalgo San Jose et al. demonstrate that low protein synthesis promotes hematopoietic stem cell function by restricting the biogenesis of misfolded proteins. Misfolded proteins impair stem cell quiescence and self-renewal by overwhelming the proteasome and disrupting proteostasis., Graphical Abstract

While the endosymbiotic communities recruited by plants are known to vary among host species and across environmental gradients, the drivers of community assembly remain poorly understood. We tested the hypothesis that establishment of an endosymbiotic bacterial community is driven primarily by the influence of the abiotic environment on biotic interactions between plant and soil bacteria. We planted sterile Jatropha curcas seedlings at three field sites in Panama and in a greenhouse with soil from those sites. After allowing sufficient time for endosymbiont colonization, we sequenced bacterial 16S rRNA to study the endophytic bacterial community in root and leaf tissue. We compared the communities between field and greenhouse plants and examined associations among the endosymbionts, the soil microbial community, and local abiotic factors. We found that endosymbiont richness and community composition varied between the greenhouse and field, despite plants being grown in the same soil. Plants in each field site harbored a distinct bacterial community, determined by soil microbes and select environmental variables, particularly major plant nutrients. Jatropha curcas can harbor a wide variety of endosymbiotic communities, and the composition of these communities is a product of the local environment. Fertility and agricultural practices may determine the fate of plant symbionts and therefore plant properties modulated through those symbionts.

The spiny mouse (Acomys cahirinus)appears to be unique among mammals by showing little scarring or fibrosis after skin or muscle injury, but theAcomysresponse to spinal cord injury (SCI) is unknown. We tested the hypothesis thatAcomyswould have molecular and immunohistochemical evidence of reduced spinal inflammation and fibrosis following SCI as compared to C57BL/6 mice (Mus), which similar to all mammals studied to date exhibits spinal scarring following SCI. Initial experiments used two pathway-focused RT-PCR gene arrays (“wound healing” and “neurogenesis”) to evaluate tissue samples from the C2-C6 spinal cord 3-days after a C3/C4 hemi-crush injury (C3Hc). Based on the gene array, specific genes were selected for RT-qPCR evaluation using species-specific primers. The results supported our hypothesis by showing increased inflammation and fibrosis related gene expression (Serpine 1, Plau, Timp1)inMusas compared toAcomys(P(Bmp2, GDNF, Shh)inAcomyscompared toMus(PAcomys(PAcomys. Collectively, the molecular and histologic results support the hypothesis thatAcomyshas reduced spinal inflammation and fibrosis following SCI. We suggest thatAcomysmay be a useful comparative model to study adaptive responses to SCI.HighlightsSpiny mice (Acomys cahirinus)and C57BL/6 (Mus) were studied after spinal injuryRT-PCR gene arrays suggested different molecular response inAcomysRTq-PCR with species-specific primers showed increased neurogenesis-related signalingHistology indicates reduced scarring and fibrosis inAcomysAcomysmay be a useful comparative model to study SCI

Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.