Environmental shaping of codon usage and functional adaptation across microbial communities.

Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community

Brief Report: Correlates of Quality of Life-related Outcomes in Breast Cancer Patients Participating in the Pathfinders Pilot Study

In a pilot study, participation in the Pathfinders program was associated with reductions in distress and despair and improvements in quality of life (QOL) among advanced breast cancer patients. This paper explores the relationship between psychosocial resources invoked through the Pathfinders intervention and outcomes

Phase 2 pilot study of Pathfinders: a psychosocial intervention for cancer patients

Pathfinders is a multi-faceted psychosocial care program for cancer patients; it was developed in community oncology and adapted to the academic oncology setting. This prospective, single-arm, phase 2 pilot study examined the acceptability and feasibility of Pathfinders for women with metastatic breast cancer

Biomarkers in neuropsychiatry: a prospect for the twenty-first century?

The search for biomarkers to aid in the diagnosis and prognosis of psychiatric conditions and predict response to treatment is a focus of twenty-first century medicine. The current lack of biomarkers in routine use is attributable in part to the existing way mental health conditions are diagnosed, being based upon descriptions of symptoms rather than causal biological evidence. New ways of conceptualizing mental health disorders together with the enormous advances in genetic, epidemiological, and neuroscience research are informing the brain circuits and physiological mechanisms underpinning behavioural constructs that cut across current diagnostic DSM-5 categories. Combining these advances with ‘Big Data’, analytical approaches offer new opportunities for biomarker development. Here we provide an introductory perspective to this volume, highlighting methodological strategies for biomarker identification; ranging from stem cells, immune mechanisms, genomics, imaging, network science to cognition. Thereafter we emphasize key points made by contributors on affective disorders, psychosis, schizophrenia, and autism spectrum disorder. An underlying theme is how preclinical and clinical research are informing biomarker development and the importance of forward and reverse translation approaches. In considering the exploitation of biomarkers we note that there is a timely opportunity to improve clinical trial design informed by patient ‘biological’ and ‘psychological’ phenotype. This has the potential to reinvigorate drug development and clinical trials in psychiatry. In conclusion, we are poised to move from the descriptive and discovery phase to one where biomarker panels can be evaluated in real-life cohorts. This will necessitate resources for large-scale collaborative efforts worldwide. Ultimately this will lead to new interventions and personalized medicines and transform our ability to prevent illness onset and treat complex psychiatric disorders more effectively