Intercellular network structure and regulatory motifs in the human hematopoietic system.

The hematopoietic system is a distributed tissue that consists of functionally distinct cell types continuously produced through hematopoietic stem cell (HSC) differentiation. Combining genomic and phenotypic data with high-content experiments, we have built a directional cell-cell communication network between 12 cell types isolated from human umbilical cord blood. Network structure analysis revealed that ligand production is cell type dependent, whereas ligand binding is promiscuous. Consequently, additional control strategies such as cell frequency modulation and compartmentalization were needed to achieve specificity in HSC fate regulation. Incorporating the in vitro effects (quiescence, self-renewal, proliferation, or differentiation) of 27 HSC binding ligands into the topology of the cell-cell communication network allowed coding of cell type-dependent feedback regulation of HSC fate. Pathway enrichment analysis identified intracellular regulatory motifs enriched in these cell type- and ligand-coupled responses. This study uncovers cellular mechanisms of hematopoietic cell feedback in HSC fate regulation, provides insight into the design principles of the human hematopoietic system, and serves as a foundation for the analysis of intercellular regulation in multicellular systems

Food Acceptability in Field Studies with US Army Men and Women: Relationship with Food Intake and Food Choice After Repeated Exposures

Laboratory data with single exposures showed that palatability has a positive relationship with food intake. The question addressed in this study is whether this relationship also holds over repeated exposures in non-laboratory contexts in more natural environments. The data were collected in four field studies, lasting 4–11 days with 307 US Army men and 119 Army women, and comprised 5791 main meals and 8831 snacks in total. Acceptability was rated on the nine point hedonic scale, and intake was registered in units of 1/4, 1/2, 3/4, or 1 or more times of the provided portion size. Correlation coefficients between individual acceptability ratings and intakes varied from 0.22 to 0.62 for the main meals (n=193–2267), and between 0.13 and 0.56 for the snacks (n=304–2967). The likelihood of choosing a meal for the second time was positively related to the acceptability rating of the meal when it was consumed for the first time. The results reinforce the importance of liking in food choice and food intake/choice behavior. However, the magnitude of the correlation coefficients between acceptability ratings and food intake suggest that environmental factors also have an important role in determining intake and choice

Models predict change in plasma triglyceride concentrations and long-chain n-3 polyunsaturated fatty acid proportions in healthy participants after fish oil intervention

Introduction: Substantial response heterogeneity is commonly seen in dietary intervention trials. In larger datasets, this variability can be exploited to identify predictors, for example genetic and/or phenotypic baseline characteristics, associated with response in an outcome of interest. Objective: Using data from a placebo-controlled crossover study (the FINGEN study), supplementing with two doses of long chain n-3 polyunsaturated fatty acids (LC n-3 PUFAs), the primary goal of this analysis was to develop models to predict change in concentrations of plasma triglycerides (TG), and in the plasma phosphatidylcholine (PC) LC n-3 PUFAs eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA), after fish oil (FO) supplementation. A secondary goal was to establish if clustering of data prior to FO supplementation would lead to identification of groups of participants who responded differentially. Methods: To generate models for the outcomes of interest, variable selection methods (forward and backward stepwise selection, LASSO and the Boruta algorithm) were applied to identify suitable predictors. The final model was chosen based on the lowest validation set root mean squared error (RMSE) after applying each method across multiple imputed datasets. Unsupervised clustering of data prior to FO supplementation was implemented using k-medoids and hierarchical clustering, with cluster membership compared with changes in plasma TG and plasma PC EPA + DHA. Results: Models for predicting response showed a greater TG-lowering after 1.8 g/day EPA + DHA with lower pre-intervention levels of plasma insulin, LDL cholesterol, C20:3n-6 and saturated fat consumption, but higher pre-intervention levels of plasma TG, and serum IL-10 and VCAM-1. Models also showed greater increases in plasma PC EPA + DHA with age and female sex. There were no statistically significant differences in PC EPA + DHA and TG responses between baseline clusters. Conclusion: Our models established new predictors of response in TG (plasma insulin, LDL cholesterol, C20:3n-6, saturated fat consumption, TG, IL-10 and VCAM-1) and in PC EPA + DHA (age and sex) upon intervention with fish oil. We demonstrate how application of statistical methods can provide new insights for precision nutrition, by predicting participants who are most likely to respond beneficially to nutritional interventions

miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells

SummaryTo investigate miRNA function in human acute myeloid leukemia (AML) stem cells (LSC), we generated a prognostic LSC-associated miRNA signature derived from functionally validated subpopulations of AML samples. For one signature miRNA, miR-126, high bioactivity aggregated all in vivo patient sample LSC activity into a single sorted population, tightly coupling miR-126 expression to LSC function. Through functional studies, miR-126 was found to restrain cell cycle progression, prevent differentiation, and increase self-renewal of primary LSC in vivo. Compared with prior results showing miR-126 regulation of normal hematopoietic stem cell (HSC) cycling, these functional stem effects are opposite between LSC and HSC. Combined transcriptome and proteome analysis demonstrates that miR-126 targets the PI3K/AKT/MTOR signaling pathway, preserving LSC quiescence and promoting chemotherapy resistance

Ecological compatibility of GM crops and biological control

Insect-resistant and herbicide-tolerant genetically modified (GM) crops pervade many modern cropping systems (especially field-cropping systems), and present challenges and opportunities for developing biologically based pest-management programs. Interactions between biological control agents (insect predators, parasitoids, and pathogens) and GM crops exceed simple toxicological relationships, a priority for assessing risk of GM crops to non-target species. To determine the compatibility of biological control and insect-resistant and herbicide-tolerant GM crop traits within integrated pest-management programs, this synthesis prioritizes understanding the bi-trophic and prey/host-mediated ecological pathways through which natural enemies interact within cropland communities, and how GM crops alter the agroecosystems in which natural enemies live. Insect-resistant crops can affect the quantity and quality of non-prey foods for natural enemies, as well as the availability and quality of both target and non-target pests that serve as prey/hosts. When they are used to locally eradicate weeds, herbicide-tolerant crops alter the agricultural landscape by reducing or changing the remaining vegetational diversity. This vegetational diversity is fundamental to biological control when it serves as a source of habitat and nutritional resources. Some inherent qualities of both biological control and GM crops provide opportunities to improve upon sustainable IPM systems. For example, biological control agents may delay the evolution of pest resistance to GM crops, and suppress outbreaks of secondary pests not targeted by GM plants, while herbicide-tolerant crops facilitate within-field management of vegetational diversity that can enhance the efficacy of biological control agents. By examining the ecological compatibility of biological control and GM crops, and employing them within an IPM framework, the sustainability and profitability of farming may be improved

Genomic investigations of unexplained acute hepatitis in children

Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children

Does the type of culture medium used influence birthweight of children born after IVF?

STUDY QUESTION: Do culture media influence birthweight of children born after IVF? SUMMARY ANSWER: Some studies have observed a significant effect of culture media on birthweight, while others have not, but since most studies compared different culture media, conventional meta-analysis was not possible. WHAT IS KNOWN ALREADY: Animal studies suggest that in vitro culture of embryos can have a significant effect on the birthweight of offspring when compared with in vivo developed embryos. The type of culture medium (or certain components of the medium) used is one of the causal factors. STUDY DESIGN, SIZE, DURATION: We reviewed all available literature reporting on a relation between culture medium and birthweight in human studies and a selection of animal studies. PARTICIPANTS/MATERIALS, SETTING, METHODS: An extensive literature search on Pubmed and Medline was performed with relevant search criteria relating to IVF, birthweight and culture medium. MAIN RESULTS AND THE ROLE OF CHANCE: Eleven studies reporting on a relationship between culture medium and birthweight in human were included in this review. Five of these found significant differences in birthweight when offspring born after culture in different culture media were compared. The remaining studies did not find differences in birthweight after changing culture medium. LIMITATIONS, REASONS FOR CAUTION: The number of human studies is limited and different culture media with different compositions are compared which makes a comparison between the studies difficult, if not impossible. Furthermore, most study designs were retrospective with consecutive use of different culture media and limited sample sizes, which makes bias of the results likely. WIDER IMPLICATIONS OF THE FINDINGS: If it could be confirmed that the type of culture medium used does indeed influence phenotypic characteristics (such as birthweight) of children born after IVF, it would underline the importance of monitoring the health of IVF children in relation to aspects of the laboratory techniques used during embryo culture