A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.

Genome-scale metabolic models (GEMs) cover the entire list of metabolic genes in an organism and associated reactions, in a tissue/condition non-specific manner. RNA-seq provides crucial information to make the GEMs condition-specific. Integrative Metabolic Analysis Tool (iMAT) and Integrative Network Inference for Tissues (INIT) are the two most popular algorithms to create condition-specific GEMs from human transcriptome data.

A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer.

Background: Prioritizing candidate drugs based on genome-wide expression data is an emerging approach in systems pharmacology due to its holistic perspective for preclinical drug evaluation. In the current study, a network-based approach was proposed and applied to prioritize plant polyphenols and identify potential drug combinations in breast cancer. We focused on MEK5/ERK5 signalling pathway genes, a recently identified potential drug target in cancer with roles spanning major carcinogenesis processes.

Brain-wide transcriptome-based metabolic alterations in Parkinson's disease: human inter-region and human-experimental model correlations.

Alterations in brain metabolism are closely associated with the molecular hallmarks of Parkinson's disease (PD). A clear understanding of the main metabolic perturbations in PD is therefore important. Here, we retrospectively analysed the expression of metabolic genes from 34 PD-control post-mortem human brain transcriptome data comparisons from literature, spanning multiple brain regions.

A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data.

Background: Narrow spectrum of action through limited molecular targets and unforeseen drug-related toxicities have been the main reasons for drug failures at the phase I clinical trials in complex diseases. Most plant-derived compounds with medicinal values possess poly-pharmacologic properties with overall good tolerability, and, thus, are appropriate in the management of complex diseases, especially cancers. However, methodological limitations impede attempts to catalogue targeted processes and infer systemic mechanisms of action.

Working together.

Heart attacks have a ripple effect on how other organs exchange biomolecules that help the heart respond to injury.

Anticarcinogenic effects of halofuginone on lung-derived cancer cells.

Malignant mesothelioma is a rare but aggressive form of malignancy, which is difficult to diagnose and is resistant to current chemotherapeutic treatment options. Molecular techniques have been used to investigate the mechanisms of action and the beneficial therapeutic effects of halofuginone (HF) in several cancers but not malignant mesotheliomas. In this study, the antiproliferative and apoptotic effects of HF were investigated through its ability to deregulate EGFR downstream signalling cascade proteins in the pathologically aggressive malignant mesothelioma and non-small-cell lung cancer cells.

Factors influencing use of long-acting versus short-acting contraceptive methods among reproductive-age women in a resource-limited setting.

Background: Unplanned pregnancy remains a common problem in many resource-limited settings, mostly due to limited access to modern family planning (FP) services. In particular, use of the more effective long-acting reversible contraceptive (LARC) methods (i.e.

Validation of an improved method for detection of Campylobacter jejuni in foods.

Campylobacter jejuni ATCC 29428 and 33560 were inoculated separately into beef muscle, ground beef, and chicken skin to yield approximately 10 to 100 CFU/g of food sample. The samples were stored at 4 degrees C for 10 d. On days 0, 3, 7, and 10, enrichment cultures in Bolton broth supplemented with antibiotics, with and without blood supplementation were made for each sample, for 24 and 48 h following the Food and Agricultural Products Center (FAPC) and the Food and Drug Administration (FDA) protocols.

Water usage patterns in low-income urban communities in Uganda: implications for water supply surveillance.

The selection of water sources by poor households in three urban areas in Uganda is shown to be complex, with a range of communal water sources used. In all towns, significant numbers of households used multiple sources. An aggregated estimate of the level of use in the largest town, Kampala, showed little difference in the number of households collecting water from piped and non-piped sources.