Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

Most genes in bacteria are experimentally uncharacterized and cannot be annotated with a specific function. Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed. Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility. We find that 2,350 genes have a pattern of fitness that is significantly different from random and 1,230 of these genes (37% of our total assayed genes) have enough signal to show strong biological correlations. We find that genes in all functional categories have phenotypes, including hundreds of hypotheticals, and that potentially redundant genes (over 50% amino acid identity to another gene in the genome) are also likely to have distinct phenotypes. Using fitness patterns, we were able to propose specific molecular functions for 40 genes or operons that lacked specific annotations or had incomplete annotations. In one example, we demonstrate that the previously hypothetical gene SO_3749 encodes a functional acetylornithine deacetylase, thus filling a missing step in S. oneidensis metabolism. Additionally, we demonstrate that the orphan histidine kinase SO_2742 and orphan response regulator SO_2648 form a signal transduction pathway that activates expression of acetyl-CoA synthase and is required for S. oneidensis to grow on acetate as a carbon source. Lastly, we demonstrate that gene expression and mutant fitness are poorly correlated and that mutant fitness generates more confident predictions of gene function than does gene expression. The approach described here can be applied generally to create large-scale gene-phenotype maps for evidence-based annotation of gene function in prokaryotes

Genome-scale metabolic reconstructions of multiple <i>Salmonella</i> strains reveal serovar-specific metabolic traits

Salmonella serovars colonize a wide range of hosts but the underlying genetic determinants remain poorly understood. Here, Seif et al. use a network-based computational analysis to link specific metabolic capabilities with host range and nutritional niche

Multicomponent Frailty Assessment Tools for Older People with Psychiatric Disorders: A Systematic Review

OBJECTIVE: To review evidence evaluating the use of multicomponent frailty assessment tools in assessing frailty in older adults with psychiatric disorders. // METHODS: A systematic literature review was conducted to identify all multicomponent frailty assessment tools (ie, a tool that assesses two or more indicators of frailty). The items of each frailty assessment tool were compared with Diagnostic and Statistical Manual of Mental Disorders, 5th edition (DSM‐5) diagnostic criteria for psychiatric disorders to assess construct overlap. Studies conducted in community, inpatient, and outpatient clinical settings were considered for inclusion. // PARTICIPANTS: Adults aged 60 years or older. // RESULTS: A total of 5639 records were identified following the removal of duplicates, from which 95 studies were included for review. Of the 48 multicomponent frailty assessment tools identified, no tool had been developed for, or validated in, older adult populations with a psychiatric disorder. Overall, 20 of 48 frailty assessment tools contained a psychological assessment domain, with 17 of 48 tools citing the presence of depressed mood and/or anxiety as a frailty indicator. Common areas of construct overlap in frailty assessment tools and DSM‐5 diagnostic criteria included weight loss (29 of 48) and fatigue (21 of 48). // CONCLUSIONS: Significant construct overlap exists between the indicators of frailty as conceptualized in existing frailty assessment tools and DSM‐5 diagnostic criteria for common psychiatric disorders including major depressive episode and generalized anxiety disorder that has the potential to confound frailty assessment results. Further research is necessary to establish a reliable and valid tool to assess frailty in this population

Cephalopods in neuroscience: regulations, research and the 3Rs

Cephalopods have been utilised in neurosci- ence research for more than 100 years particularly because of their phenotypic plasticity, complex and centralised nervous system, tractability for studies of learning and cellular mechanisms of memory (e.g. long-term potentia- tion) and anatomical features facilitating physiological studies (e.g. squid giant axon and synapse). On 1 January 2013, research using any of the about 700 extant species of ‘‘live cephalopods’’ became regulated within the European Union by Directive 2010/63/EU on the ‘‘Protection of Animals used for Scientific Purposes’’, giving cephalopods the same EU legal protection as previously afforded only to vertebrates. The Directive has a number of implications, particularly for neuroscience research. These include: (1) projects will need justification, authorisation from local competent authorities, and be subject to review including a harm-benefit assessment and adherence to the 3Rs princi- ples (Replacement, Refinement and Reduction). (2) To support project evaluation and compliance with the new EU law, guidelines specific to cephalopods will need to be developed, covering capture, transport, handling, housing, care, maintenance, health monitoring, humane anaesthesia, analgesia and euthanasia. (3) Objective criteria need to be developed to identify signs of pain, suffering, distress and lasting harm particularly in the context of their induction by an experimental procedure. Despite diversity of views existing on some of these topics, this paper reviews the above topics and describes the approaches being taken by the cephalopod research community (represented by the authorship) to produce ‘‘guidelines’’ and the potential contribution of neuroscience research to cephalopod welfare