Eutrophication has no short-term effect on the Cymbastela stipitata holobiont

Levels of nitrogen in coastal areas have been rapidly increasing due to accumulative inputs of sewage and terrigenous sediments carrying fertilizers. Sponges have an immense filtering capacity and may be directly impacted (positively or negatively) by elevated concentrations of nitrogen. Sponges also host a wide diversity of microbes involved in nitrogen metabolism, yet little is known about the effects of nitrogen loading on these symbiotic partnerships. Manipulative experiments were undertaken to examine the potential effects of excess nitrogen (up to 240 μM) on microbial symbiosis in the abundant sponge species Cymbastela stipitata. Microbial composition and activity were examined using 454-pyrotag sequencing of DNA- and RNA-derived samples. Despite the high levels of nitrogen exposure (up to 124-fold above ambient), sponges appeared visibly unaffected at all treatment concentrations. At the phylum level, the microbial community was consistent between all sponge samples regardless of nitrogen treatment, with Cyanobacteria and Thaumarchaeota being the dominant taxa. Higher microbial diversity was observed at the operational taxonomic units (OTU) level (97% sequence similarity), with only 40% of OTUs shared between samples from all treatments. However, a single cyanobacterial OTU dominated the community of all individuals (average 73.5%) and this OTU did not vary with nitrogen treatment. The conserved microbial community in all sponges irrespective of nitrogen treatment highlights the stability of the sponge-microbe relationship and indicates that the holobiont is resistant to short pulses of nitrogen at levels mimicking sewage effluent

Phytoplasmas in Australian grapevines - detection, differentiation and associated diseases

Phytoplasmas associated with Australian grapevine yellows (AGY) symptoms were detected using the polymerase chain reaction (PCR). To optimise the diagnostic, nested PCRs were compared with single PCRs using different primer pairs. Grapevine DNA known to be AGY phytoplasma positive was serially diluted and subjected to nested and single round PCR tests to determine which was the most sensitive. Samples taken over two growing seasons were used to determine the optimum sampling time for phytoplasma detection. The specificity of primer pairs was determined using phytoplasmas detected in Australian grapevines and overseas reference grapevine phytoplasmas. DNA extracted from grapevine exhibiting a range of symptoms was screened for phytoplasmas. Two different phytoplasmas were amplified in the PCR and they were identified using specific PCR primers and by restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and 16S rRNA/23S rRNA spacer region. RFLP analysis confirmed that one phytoplasma was the AGY phytoplasma and the other phytoplasma was indistinguishable from the tomato big bud (TBB) phytoplasma. The AGY phytoplasma was associated with AGY symptoms but was occasionally detected in asymptomatic vines and those with late season leaf curl (LSLC) and restricted growth (RG) symptoms. The TBB phytoplasma was detected in some vines with LSLC symptoms and very occasionally in vines with AGY symptoms. A 'variant' of the AGY phytoplasma was also detected in vines showing typical AGY symptoms

Comet C/2004 Q2 (MACHHOLZ): Parent Volatiles, a Search for Deuterated Methane, and Constraint on the CH4 Spin Temperature

High-dispersion (l/dl ~ 25,000) infrared spectra of Comet C/2004 Q2 (Machholz) were acquired on Nov. 28-29, 2004, and Jan. 19, 2005 (UT dates) with NIRSPEC at the Keck-2 telescope on Mauna Kea. We detected H2O, CH4, C2H2, C2H6, CO, H2CO, CH3OH, HCN, and NH3 and we conducted a sensitive search for CH3D. We report rotational temperatures, production rates, and mixing ratios (with respect to H2O) at heliocentric distances of 1.49 AU (Nov. 2004) and 1.21 AU (Jan. 2005). We highlight three principal results: (1) The mixing ratios of parent volatiles measured at 1.49 AU and 1.21 AU agree within confidence limits, consistent with homogeneous composition in the mean volatile release from the nucleus of C/2004 Q2. Notably, the relative abundance of C2H6/C2H2 is substantially higher than those measured in other comets, while the mixing ratios C2H6/H2O, CH3OH/H2O, and HCN/H2O are similar to those observed in comets, referred to as "organics-normal". (2) The spin temperature of CH4 is > 35-38 K, an estimate consistent with the more robust spin temperature found for H2O. (3) We obtained a 3s upper limit of CH3D/CH4 < 0.020 (D/H < 0.005). This limit suggests that methane released from the nucleus of C/2004 Q2 is not dominated by a component formed in extremely cold (near 10 K) environments. Formation pathways of both interstellar and nebular origin consistent with the measured D/H in methane are discussed. Evaluating the relative contributions of these pathways requires further modeling of chemistry including both gas-phase and gas-grain processes in the natal interstellar cloud and in the protoplanetary disk.Comment: Accepted by The Astrophysical Journa

Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH -Mutant Molecular Profiles

Cholangiocarcinoma (CCA) is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance

Integrated genomic characterization of pancreatic ductal adenocarcinoma

We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic drivers, including GNAS, BRAF, CTNNB1, and additional RAS pathway genes. A subset of tumors harbored multiple KRAS mutations, with some showing evidence of biallelic mutations. Protein profiling identified a favorable prognosis subset with low epithelial-mesenchymal transition and high MTOR pathway scores. Associations of non-coding RNAs with tumor-specific mRNA subtypes were also identified. Our integrated multi-platform analysis reveals a complex molecular landscape of PDAC and provides a roadmap for precision medicine

Dolutegravir twice-daily dosing in children with HIV-associated tuberculosis: a pharmacokinetic and safety study within the open-label, multicentre, randomised, non-inferiority ODYSSEY trial

Background: Children with HIV-associated tuberculosis (TB) have few antiretroviral therapy (ART) options. We aimed to evaluate the safety and pharmacokinetics of dolutegravir twice-daily dosing in children receiving rifampicin for HIV-associated TB. Methods: We nested a two-period, fixed-order pharmacokinetic substudy within the open-label, multicentre, randomised, controlled, non-inferiority ODYSSEY trial at research centres in South Africa, Uganda, and Zimbabwe. Children (aged 4 weeks to <18 years) with HIV-associated TB who were receiving rifampicin and twice-daily dolutegravir were eligible for inclusion. We did a 12-h pharmacokinetic profile on rifampicin and twice-daily dolutegravir and a 24-h profile on once-daily dolutegravir. Geometric mean ratios for trough plasma concentration (Ctrough), area under the plasma concentration time curve from 0 h to 24 h after dosing (AUC0–24 h), and maximum plasma concentration (Cmax) were used to compare dolutegravir concentrations between substudy days. We assessed rifampicin Cmax on the first substudy day. All children within ODYSSEY with HIV-associated TB who received rifampicin and twice-daily dolutegravir were included in the safety analysis. We described adverse events reported from starting twice-daily dolutegravir to 30 days after returning to once-daily dolutegravir. This trial is registered with ClinicalTrials.gov (NCT02259127), EudraCT (2014–002632-14), and the ISRCTN registry (ISRCTN91737921). Findings: Between Sept 20, 2016, and June 28, 2021, 37 children with HIV-associated TB (median age 11·9 years [range 0·4–17·6], 19 [51%] were female and 18 [49%] were male, 36 [97%] in Africa and one [3%] in Thailand) received rifampicin with twice-daily dolutegravir and were included in the safety analysis. 20 (54%) of 37 children enrolled in the pharmacokinetic substudy, 14 of whom contributed at least one evaluable pharmacokinetic curve for dolutegravir, including 12 who had within-participant comparisons. Geometric mean ratios for rifampicin and twice-daily dolutegravir versus once-daily dolutegravir were 1·51 (90% CI 1·08–2·11) for Ctrough, 1·23 (0·99–1·53) for AUC0–24 h, and 0·94 (0·76–1·16) for Cmax. Individual dolutegravir Ctrough concentrations were higher than the 90% effective concentration (ie, 0·32 mg/L) in all children receiving rifampicin and twice-daily dolutegravir. Of 18 children with evaluable rifampicin concentrations, 15 (83%) had a Cmax of less than the optimal target concentration of 8 mg/L. Rifampicin geometric mean Cmax was 5·1 mg/L (coefficient of variation 71%). During a median follow-up of 31 weeks (IQR 30–40), 15 grade 3 or higher adverse events occurred among 11 (30%) of 37 children, ten serious adverse events occurred among eight (22%) children, including two deaths (one tuberculosis-related death, one death due to traumatic injury); no adverse events, including deaths, were considered related to dolutegravir. Interpretation: Twice-daily dolutegravir was shown to be safe and sufficient to overcome the rifampicin enzyme-inducing effect in children, and could provide a practical ART option for children with HIV-associated TB