Estimating Intraclonal Heterogeneity and Subpopulation Changes from Perturbational Bulk Gene Expression Profiles in LINCS L1000 CMap by Premnas

The connectivity among signatures upon perturbations curated in the CMap library provides a valuable resource for understanding therapeutic pathways and biological processes associated with the drugs and diseases. However, due to the nature of bulk-level expression profiling by the L1000 assay, intraclonal heterogeneity and subpopulation compositional change that could contribute to the responses to perturbations are largely neglected, hampering the interpretability and reproducibility of the connections. In this work, we proposed a computational framework, Premnas, to estimate the abundance of undetermined subpopulations from L1000 profiles in CMap directly according to an ad hoc subpopulation representation learned from a well-normalized batch of single-cell RNA-seq datasets by the archetypal analysis. By recovering the information of subpopulation changes upon perturbation, the potentials of searching for drug cocktails and drug-resistant/susceptible subpopulations with CMap L1000 were further explored and examined. The proposed framework enables a new perspective to understand the connectivity among cellular signatures and expands the scope of the CMAP and other similar perturbation datasets limited by the bulk profiling technology. The executable and source code of Premnas is freely available at https://github.com/jhhung/Premnas.

Prophages in the infant gut are largely induced, and may be functionally relevant to their hosts.

Background: Bacteriophages are the most abundant biological entity on the planet, and are key components of any ecosystem they are present in. The gut virome is increasingly being implicated in disease states although these studies largely focus on lytic phages in adults. Here we identify prophages from a large infant cohort and investigate their potential functions. Results: We identified 10645 vOTUs from 662 metagenomes. No core virome was found: the most prevalent vOTU was identified in 70% of the samples. The most abundant and prevalent group of phages are a novel group closely related to Bacteroides phage Hanky p00. Functional annotation of this group revealed the presence of genes in the dDTP-L-rhamnose pathway, possibly involved in the production of capsular polysaccharides. We also found an abundance of diversity generating retroelements in the phages. Additionally, paired virome data allowed us to show that the majority of prophages are induced in at least one sample and that this is not affected by the use of antibiotics in the 4 weeks prior to sampling. Conclusions: Prophages in the infant gut are largely unique to the individual and not shared. Most of them appear to be induced and so may be key drivers in shaping the bacterial microbiome. The most abundant group of phages are novel, and possess elements that may allow them to maintain differentially susceptible subpopulations of their host bacterium; whilst also containing diversity generating retroelements that could expand their host range. Prophages are important components of the infant gut that may have far reaching influences on the composition and function of the microbiome.

A Cumulative Framework for Identifying Overburdened Populations under the Toxic Substances Control Act: Formaldehyde Case Study

Extensive scholarship has demonstrated that communities of color, low-income communities, and Indigenous communities face greater environmental and health hazards compared to communities with more White or affluent people. Low-income, Indigenous, Black, and/or other populations of color are also more likely to lack access to health care facilities, healthy food, and adequate formal education opportunities. Despite the mountains of evidence that demonstrate the existence and significance of the elevated toxic social and environmental exposures experienced by these communities, the inclusion of these factors into chemical evaluations has been scarce. In this paper, we demonstrate a process built with publicly available data and simple geospatial techniques that could be utilized by the U.S. Environmental Protection Agency (USEPA) to incorporate cumulative approaches into risk assessments under the Toxic Substances Control Act. The use of these approaches, particularly as they relate to identifying potentially exposed and susceptible subpopulations, would help USEPA develop appropriate risk estimates and mitigation strategies to protect disproportionately burdened populations from the adverse effects of chemical exposures. By utilizing such approaches to inform risk evaluation and mitigation, USEPA can identify and protect those most burdened and impacted by toxic chemicals, and finally begin to close the gap of environmental health inequities.

Stability Analysis of HIV/AIDS Model with Educated Subpopulation

We had constructed mathematical model of HIV/AIDS with seven compartments. There were two different stages of infection and susceptible subpopulations. Two stages in infection subpopulation were an HIV-positive with consuming ARV such that this subpopulation can survive longer and an HIV-positive not consuming ARV. The susceptible subpopulation was divided into two, uneducated and educated susceptible subpopulations. The transmission coefficients from educated and uneducated subpopulations to infection stages were where (( and ) ( and )) In this paper, we consider the case of and were zero. We investigated local stability of the model solutions according to the basic reproduction number as a threshold of disease transmission. The disease-free and endemic equilibrium points were locally asymptotically stable when and respectively. To support the analytical results, numerical simulation was conducted.

Effect of non-antifungal agrochemicals on the pathogenic fungus Cryptococcus gattii

The chemical control of pests and weeds is employed to improve crop production and the quality of agricultural products. The intensive use of pesticides, however, may cause environmental contamination, thus altering microbial communities. Cryptococcus gattii is an environmental yeast and the causative agent of cryptococcosis in both humans and animals. Up to this day, the effects of agrochemicals on human pathogens living in nature are still widely unknown. In this work, we analyzed the susceptibility of C. gattii to nonfungicide agrochemicals (herbicides and insecticides). Microdilution and drug-combination susceptibility tests were performed for the herbicides flumioxazin (FLX), glyphosate (GLY), isoxaflutole (ISO), pendimethalin (PEND), and also for the insecticide fipronil (FIP). Moreover, these compounds were combined with the clinical antifungals amphotericin B and fluconazole. The MIC values found for the agrochemicals were the following: < 16 μg/ml, for flumioxazin; 128 to 256 μg/ml, for FIP, ISO, and PEND; and >256 μg/ml, for GLY. Synergistic and antagonistic interactions, depending on the strain and concentration tested, were also observed. All strains had undergone adaptation to increasing levels of agrochemicals, in order to select the less susceptible subpopulations. During this process, one C. gattii strain (196 L/03) tolerated high concentrations (50 to 900 μg/ml) of all pesticides assessed. Subsequently, the strain adapted to flumioxazin, isoxaflutole and pendimethalin showed a reduction in the susceptibility to agrochemicals and clinical antifungals, suggesting the occurrence of cross-resistance. Our data point to the risk of exposing C. gattii to agrochemicals existing in the environment, once it might impact the susceptibility of clinical antifungals.