Identifying Subpopulations of Cells in Single-Cell Transcriptomic Data: A Bayesian Mixture Modeling Approach to Zero Inflation of Counts.

In the study of single-cell RNA-seq (scRNA-Seq) data, a key component of the analysis is to identify subpopulations of cells in the data. A variety of approaches to this have been considered, and although many machine learning-based methods have been developed, these rarely give an estimate of uncertainty in the cluster assignment. To allow for this, probabilistic models have been developed, but scRNA-Seq data exhibit a phenomenon known as dropout, whereby a large proportion of the observed read counts are zero. This poses challenges in developing probabilistic models that appropriately model the data. We develop a novel Dirichlet process mixture model that employs both a mixture at the cell level to model multiple populations of cells and a zero-inflated negative binomial mixture of counts at the transcript level. By taking a Bayesian approach, we are able to model the expression of genes within clusters, and to quantify uncertainty in cluster assignments. It is shown that this approach outperforms previous approaches that applied multinomial distributions to model scRNA-Seq counts and negative binomial models that do not take into account zero inflation. Applied to a publicly available data set of scRNA-Seq counts of multiple cell types from the mouse cortex and hippocampus, we demonstrate how our approach can be used to distinguish subpopulations of cells as clusters in the data, and to identify gene sets that are indicative of membership of a subpopulation.

A guide to the design of magnetic particle imaging tracers for biomedical applications.

Magnetic Particle Imaging (MPI) is a novel and emerging non-invasive technique that promises to deliver high quality images, no radiation, high depth penetration and nearly no background from tissues. Signal intensity and spatial resolution in MPI are heavily dependent on the properties of tracers. Hence the selection of these nanoparticles for various applications in MPI must be carefully considered to achieve optimum results. In this review, we will provide an overview of the principle of MPI and the key criteria that are required for tracers in order to generate the best signals. Nanoparticle materials such as magnetite, metal ferrites, maghemite, zero valent iron@iron oxide core@shell, iron carbide and iron-cobalt alloy nanoparticles will be discussed as well as their synthetic pathways. Since surface modifications play an important role in enabling the use of these tracers for biomedical applications, coating options including the transfer from organic to inorganic media will also be discussed. Finally, we will discuss different biomedical applications and provide our insights into the most suitable tracer for each of these applications.

Immune Cell Networks Uncover Candidate Biomarkers of Melanoma Immunotherapy Response.

The therapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types and their application to interrogate control of nivolumab response in advanced melanoma cohorts. The results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, 'immune hot' status, including T cell proliferation, correlates with response to first-line ICI therapy. Genes regulated in NK, dendritic, and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights CIITA and IKZF3 as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.

Occurrence of 1153 organic micropollutants in the aquatic environment of Vietnam.

The rapid increase in the number and volume of chemical substances being used in modern society has been accompanied by a large number of potentially hazardous chemicals being found in environmental samples. In Vietnam, the monitoring of chemical substances is mainly limited to a small number of known pollutants in spite of rapid economic growth and urbanization, and there is an urgent need to examine a large number of chemicals to prevent impacts from expanding environmental pollution. However, it is difficult to analyze a large number of chemicals using existing methods, because they are time consuming and expensive. In the present study, we determined 1153 substances to grasp a pollution picture of microcontaminants in the aquatic environment. To achieve this objective, we have used two comprehensive analytical methods: (1) solid-phase extraction (SPE) and LC-TOF-MS analysis, and (2) SPE and GC-MS analysis. We collected 42 samples from northern (the Red River and Hanoi), central (Hue and Danang), and southern (Ho Chi Minh City and Saigon-Dongnai River) Vietnam. One hundred and sixty-five compounds were detected at least once. The compounds detected most frequently (>40 % samples) at µg/L concentrations were sterols (cholesterol, beta-sitosterol, stigmasterol, coprostanol), phthalates (bis(2-ethylhexyl) phthalate and di-n-butyl phthalate), and pharmaceutical and personal care products (caffeine, metformin). These contaminants were detected at almost the same detection frequency as in developed countries. The results reveal that surface waters in Vietnam, particularly in the center of large cities, are polluted by a large number of organic micropollutants, with households and business activities as the major sources. In addition, risk quotients (MEC/PNEC values) for nonylphenol, sulfamethoxazole, ampicillin, acetaminophen, erythromycin and clarithromycin were higher than 1, which indicates a possibility of adverse effects on aquatic ecosystems.

Characterization of avian paramyxovirus serotype 14, a novel serotype, isolated from a duck fecal sample in Japan.

A hemagglutinating virus isolate designated 11OG0352, was obtained from a duck fecal sample. Genetic and virological analyses indicated that it might represent a novel serotype of avian paramyxovirus (APMV). Electron micrographs showed that the morphology of the virus particle was similar to that of APMV. The complete genome of this virus comprised 15,444 nucleotides complying with the paramyxovirus "rule of six" and contains six open reading frames (3'-N-P-M-F-HN-L-5'). The phylogenetic analysis of the whole genome revealed that the virus was a member of the genus Avulavirus, but that it was distinct from APMV-1 to APMV-13. Although the F-protein cleavage site was TREGK↓L, which resembles a lentogenic strain of APMV-1, the K residue at position -1 of the cleavage site was first discovered in APMV members. The phosphoprotein gene of isolate 11OG0352 contains a putative RNA editing site, 3'-AUUUUCCC-5' (negative sense) which sequence differs from that of other APMVs. The intracerebral pathogenicity index test did not detect virulence in infected chicks. In hemagglutination inhibition (HI) tests, an antiserum against this virus did not detectably react with other APMVs (serotypes 1-4, 6-9) except for low reciprocal cross-reactivity with APMV-6. We designated this isolate, as APMV-14/duck/Japan/11OG0352/2011 and propose that it is a novel APMV serotype. The HI test may not be widely applicable for the classification of a new serotype because of the limited availability of reference antisera against all serotypes and cross-reactivity data. The nucleotide sequence identities of the whole genome of 11OG0352 and other APMVs ranged from 46.3% to 56.1%. Such comparison may provide a useful tool for classifying new APMV isolates. However, the nucleotide sequence identity between APMV-12 and APMV-13 was higher (64%), which was nearly identical to the lowest nucleotide identity (67%) reported in subgroups within the serotype. Therefore, consensus criteria for using whole genome analysis should be established.

Sexual rest and post-meiotic sperm ageing in house mice.

Fertilization by aged sperm can result in adverse fitness consequences for both males and females. Sperm storage during male sexual rest could provide an environment for post-meiotic sperm senescence causing a deterioration in the quality of stored sperm, possibly impacting on both sperm performance (e.g. swimming ability) and DNA quality. Here, we compared the proportion of sperm with fragmented DNA, an indicator of structural damage of DNA within the sperm cell, among males that had been sexually rested for approximately 2 months, to that of males that had mated recently. We found no evidence of intra-epididymal sperm DNA damage or any impairment in sperm performance, and consequently no evidence of post-meiotic sperm senescence. Our results suggest that male house mice are likely to possess mechanisms that function to ensure that their sperm reserves remain stocked with 'young', viable sperm during periods of sexual inactivity. We also discuss the possibility that our experimental design leads to no difference in the age of sperm among males from the two mating treatments. Post-meiotic sperm senescence is especially relevant under sperm competition. Thus, we sourced mice from populations that differed in their levels of post-copulatory sexual selection, enabling us to gain insight into how selection for higher sperm production influences the rate of sperm ageing and levels of DNA fragmentation. We found that males from the population that produced the highest number of sperm also had the smallest proportion of DNA-fragmented sperm and discuss this outcome in relation to selection acting upon males to ensure that they produce ejaculates with high-quality sperm that are successful in achieving fertilizations under competitive conditions.

Hepatitis C virus dysregulates glucose homeostasis by a dual mechanism involving induction of PGC1α and dephosphorylation of FoxO1.

The maintenance of glucose homeostasis is a complex process in which the insulin signalling pathway plays a major role. Disruption of insulin-regulated glucose homeostasis is frequently observed in chronic hepatitis C (CHC) infection and might potentially contribute to type 2 diabetes mellitus (T2DM) development. Presently, the mechanism that links HCV infection to insulin resistance remains unclear. Previously, we have reported that HCV protein expression in HCV transgenic mice (B6HCV) leads to an overexpression of protein phosphatase 2A (PP2A) through an ER stress response. In the present work, we describe an association of FoxO1 hypophosphorylation and upregulation of both PGC-1α and G6Pase to phenotypic hyperglycaemia and insulin resistance in B6HCV mice. In vitro, we observed that PGC1α is concomitantly induced with PP2A. Moreover, we show that the enhanced PP2A expression is sufficient to inhibit insulin-induced FoxO1 phosphorylation via blockade of insulin-mediated Akt activation or/and through direct association and dephosphorylation of pS-FoxO1. Consequently, we found that the gluconeogenic gene glucose-6-phosphatase is upregulated. These observations were confirmed in liver biopsies obtained from CHC patients. In summary, our results show that HCV-mediated upregulation of PP2A catalytic subunit alters signalling pathways that control hepatic glucose homeostasis by inhibiting Akt and dephosphorylation of FoxO1.

Protein phosphatase 2A impairs IFNα-induced antiviral activity against the hepatitis C virus through the inhibition of STAT1 tyrosine phosphorylation.

Mammalian cells have developed several mechanisms to sense viruses and initiate adequate responses such as production of interferons. Interferons activate the antiviral response through the Jak-STAT signalling pathway. To establish a chronic infection, viruses need to counteract this barrier of defence. The hepatitis C and hepatitis B viruses are known to up-regulate the expression of protein phosphatase 2A (PP2A). In this study, we show that PP2Ac associates with Jak1/Tyk2/STAT1 and reduces Jak1/Tyk2/STAT1 phosphorylation resulting in an impairment of the IFNα-induced HCV antiviral response. Using the fully infectious HCV cell culture system (HCVcc), we demonstrate that the PP2A catalytic activity is not required to block the antiviral effect of IFNα, although it is needed to support HCVcc replication. Our data suggest an important contribution of virus-induced PP2Ac up-regulation in the establishment of a chronic infection.

Obese youths are not more likely to become depressed, but depressed youths are more likely to become obese.

BACKGROUND: Overweight/obesity and depression are both major public health problems among adolescents. However, the question of a link between overweight/obesity and depression remains unresolved in this age group. We examined whether obesity increases risk of depression, or depression increases risk of obesity, or whether there is a reciprocal effect. METHOD: A two-wave prospective cohort study of adolescents aged 11­17 years at baseline (n=4175) followed up a year later (n=3134) sampled from the Houston metropolitan area. Overweight was defined as 95th percentile >body mass index (BMI) < or = 85th percentile and obese as BMI >95th percentile. Three indicators of depression were examined: any DSM-IV mood disorder, major depression, and symptoms of depression. RESULTS: Data for the two-wave cohort indicated no evidence of reciprocal effects between weight and depression. Weight status predicted neither major depression nor depressive symptoms. However, mood disorders generally and major depression in particular increased risk of future obesity more than twofold. Depressed males had a sixfold increased risk of obesity. Females with depressive symptoms had a marginally increased risk of being overweight but not obese. CONCLUSIONS: Our findings, combined with those of recent meta-analyses, suggest that obese youths are not more likely to become depressed but that depressed youths are more likely to become obese.

Conversion of cortisone to cortisol and prostaglandin F2α production by the reproductive tract of cows at the late luteal stage in vivo.

Previous in vitro studies demonstrated that bovine endometrium has the capacity to convert inactive cortisone to biologically active cortisol (Cr) and that Cr inhibits cytokine-stimulated prostaglandin F(2α) (PGF) production. This study was carried out to test the hypothesis that bovine reproductive tract has the capacity to convert cortisone to Cr in vivo and to evaluate the effects of intravaginal application of exogenous cortisone on uterine PGF secretion during the late luteal stage. The temporal relationships between PGF and Cr levels in uterine plasma were also determined. Catheters were inserted into jugular vein (JV), uterine vein (UV), vena cava caudalis (VCC) and aorta abdominalis (AA) of six cows on Day 15 of the oestrous cycle (ovulation = Day 0) for frequent blood collection. On Day 16, the cows were divided randomly into two groups and infused intravaginally with vaseline gel (10 ml; control; n = 3) or cortisone dissolved in vaseline gel (100 mg; n = 3). Blood samples were collected at -2, -1, -0.5, 0, 0.5, 1, 1.5, 2, 3, 4, 5 and 6 h after treatments (0 h). Intravaginal application of cortisone increased plasma concentrations of Cr between 0.5 and 1.5 h in UV, at 0.5 h in VCC, at 1 h in JV and at 1.5 h in AA. The plasma concentrations of PGF in UV and of PGF metabolite in JV were greater at 0.5 and 1 h in the cortisone-treated animals than in control animals. The levels of PGF in UV blood plasma decreased after Cr reached its highest levels. The overall findings suggest that the female reproductive tract has the capacity to convert cortisone to Cr in vivo. Based on the temporal changes of PGF and Cr levels in the uterine plasma, a biphasic response in PGF secretion was found to be associated to the Cr increase induced by the cortisone treatment at the late luteal stage in non-pregnant cows.

Acute changes in the concentrations of prostaglandin F2α (PGF) and cortisol in uterine and ovarian venous blood during PGF-induced luteolysis in cows.

Prostaglandin F2α (PGF) is considered to be the main luteolysin in cattle. We have previously demonstrated that cortisol (Cr) suppresses PGF production in non-pregnant bovine endometrium. This study was carried out to test whether exogenous PGF increases ovarian and/or uterine PGF production and to determine the temporal relationship between PGF and Cr in ovarian and uterine circulations during PGF-induced luteolysis in cows. Catheters were inserted into the ovarian vein (OV), uterine vein (UV) and jugular vein (JV) of 10 cows on Day 9 of the oestrous cycle (Ovulation = Day 0) for frequent blood collection. On Day 10, the cows were divided randomly into two groups and treated with a luteolytic dose of a PGF analogue (cloprostenol) or saline solution. Blood samples were collected at -0.25, 0, 0.25, 0.5, 1 and 2 h and then at 2-h intervals until 12 h after treatment (0 h). The basal concentrations of PGF and Cr in OV and UV plasma were not significantly different. Injection of a PGF analogue induced more than twofold increases in the levels of PGF between 0.25 and 1 h in UV plasma, but not in OV plasma. PGF increased (p < 0.05) the concentrations of Cr in OV, UV and JV plasma between 0.5 and 1 h. The Cr levels in OV, UV and JV plasma were similar. The PGF levels in UV plasma decreased after Cr reached its highest levels. The overall results suggest that the uterus rather than the ovary increases PGF production in response to PGF injection. Based on the temporal changes of PGF and Cr in the ovarian and uterine circulations, Cr may act to reduce uterine PGF production in non-pregnant cows in vivo.

Fluorescence imaging efficiency of cold atoms in free fall.

A fluorescence detection scheme coupled to a highly sensitive nitrogen-cooled CCD camera is used to image the spatial distribution of a low-density falling rubidium atomic cloud released from an optical trap. The falling cloud passes through a thin probe laser beam tuned to resonance. The performance of the scheme is illustrated in the analysis of cold atomic clouds collimated by pinholes during their free fall under the influence of gravity. Clouds of approximately 10(4) atoms and with typically 10(6) at./cm(3) density are analyzed spatially with 24-mum resolution. This method is compared with different atomic cloud imaging techniques.

Biochemical effect and kinetics of thrombin inhibition by GYKI-14766.

The tripeptide aldehyde GYKI-14766 (D-MePhe-Pro-Arg-H) synthesized by Bajusz et al. in 1975 is a specific, reversible thrombin inhibitor. It was found effective in vitro in clotting time assays as well as in vivo in thrombosis models. To study the biochemical effects of the inhibitor various experimental setups were applied. First we measured the binding of thrombin to platelets using 125J-thrombin. KD was 55 nM. Second, 125J-thrombin was displaced by thrombin or by a GYKI-14766-thrombin-complex with similar efficacy. However, the binding of thrombin to the platelets increased the intracellular free Ca2+ concentration, but the inhibitor-thrombin complex did not influence it. Analyzing the kinetics of the reactions involved we found that the formation of the GYKI-14766-thrombin complex was slower than the triggering of the platelet Ca2+ signal by thrombin.