Decision tree-driven tandem mass spectrometry for shotgun proteomics

Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.     

Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan

Cells are organized into distinct compartments to perform specific tasks with spatial precision. In neurons, presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion. Activity-dependent changes in the abundance of presynaptic proteins are thought to endow synapses with different functional states; however, relatively little is known about the rules that govern changes in the composition of presynaptic terminals. We describe a genetic strategy to systematically analyze protein localization at Caenorhabditis elegans presynaptic specializations. Nine presynaptic proteins were GFP-tagged, allowing visualization of multiple presynaptic structures. Changes in the distribution and abundance of these proteins were quantified in 25 mutants that alter different aspects of neurotransmission. Global analysis of these data identified novel relationships between particular presynaptic components and provides a new method to compare gene functions by identifying shared protein localization phenotypes. Using this strategy, we identified several genes that regulate secretion of insulin-like growth factors (IGFs) and influence lifespan in a manner dependent on insulin/IGF signaling.     

Eicosapentaenoic-acid-derived isoprostanes: synthesis and discovery of two major isoprostanes

The stereospecific synthesis of two all-syn-EPA-derived isoprostanes (iPs), 5-epi-8,12-iso-iPF(3alpha)-VI 17 and 8,12-iso-iPF(3alpha)-VI 18, has been accomplished. These two synthetic probes have been used to discover and identify their presence in human urine. The eventual quantitative measurement of these two iPs may be a valuable index of oxidative stress in people with eicosapentaenoic acid- (EPA) and docosahexaenoic acid- (DHA) enriched phospholipids.     

Mechanisms and innovations: Traumatic brain injury: Can the consequences be stopped?

Traumatic brain injury is a leading cause of morbidity and death in both industrialized and developing countries. To date, there is no targeted pharmacological treatment that effectively limits the progression of secondary injury. The delayed progression of deterioration of grey and white matter gives hope that a meaningful intervention can be applied in a realistic timeframe following initial trauma. In this review we discuss new insights into the subcellular mechanisms of secondary injury that have highlighted numerous potential targets for intervention.We provide an overview of traumatic brain injury and, in particular, the mechanisms of secondary injury and emerging novel concepts for future intervention strategies. Understanding these processes in greater detail can identify feasible time frame for treatment and targets for meaningful interventions.Severe traumatic brain injury continues to be a leading cause of death and morbidity in North America.^1–8 The incidence of mild traumatic brain injury is high, and it is a major management problem for clinicians and a considerable source of frustration for patients. The economic and social burden of traumatic brain injury has implications on a global scale, with incidences in developing countries rising as the rate of vehicle use outpaces the development of safety infrastructure.^9,10 In addition, traumatic brain injury is now a major focus of casualty care in combat areas, as it is the principal cause of mortality and morbidity especially because of the recent surge in the use of low-cost, yet powerful, explosive devices directed at civilian and military personnel.¹¹Extensive literature aimed at understanding the tissue, cellular, inflammatory and subcellular processes following traumatic brain injury have proven unequivocally that these pathophysiological events are delayed and progressive in nature. Although the greatest impact on survival and outcome to date may be attributed to systemic and intracranial physiologic management (e.g., fluid resuscitation, intracranial pressure monitoring), future mitigation of the progression of secondary injury will likely be through molecular, gene and pharmacologic interventions. The prospect of gene therapy and pharmacologic treatments require physicians to be familiar with the subcellular mechanisms of brain injury.     

Oxidative stress in diseases of the human cornea

Intense exposure to light, robust metabolic activity, and high oxygen tension render the human eye particularly vulnerable to oxidative damage and the list of ophthalmological disorders implicating reactive oxygen and nitrogen species is rapidly expanding. Here, we review the roles of oxidative stress in the etiopathogeneses and pathophysiology of diseases of the human cornea including pterygium, keratoconus, trauma and chemical injury, and a host of inflammatory, metabolic, degenerative, and iatrogenic conditions. Data from animal and tissue culture experimentation germane to these conditions are also adduced.     

Behavioral and electrophysiological indices of negative affect predict cocaine self-administration

The motivation to seek cocaine comes in part from a dysregulation of reward processing manifested in dysphoria, or affective withdrawal. Learning is a critical aspect of drug abuse; however, it remains unclear whether drug-associated cues can elicit the emotional withdrawal symptoms that promote cocaine use. Here we report that a cocaine-associated taste cue elicited a conditioned aversive state that was behaviorally and neurophysiologically quantifiable and predicted subsequent cocaine self-administration behavior. Specifically, brief intraoral infusions of a cocaine-predictive flavored saccharin solution elicited aversive orofacial responses that predicted early-session cocaine taking in rats. The expression of aversive taste reactivity also was associated with a shift in the predominant pattern of electrophysiological activity of nucleus accumbens (NAc) neurons from inhibitory to excitatory. The dynamic nature of this conditioned switch in affect and the neural code reveals a mechanism by which cues may exert control over drug self-administration.     

Soft-tissue injuries of the fingertip: methods of evaluation and treatment. An algorithmic approach

LEARNING OBJECTIVES: After studying this article, the participant should be able to: 1. Understand the anatomy of the fingertip. 2. Describe the methods of evaluating fingertip injuries. 3. Discuss reconstructive options for various tip injuries. SUMMARY: The fingertip is the most commonly injured part of the hand, and therefore fingertip injuries are among the most frequent injuries that plastic surgeons are asked to treat. Although microsurgical techniques have enabled replantation of even very distal tip amputations, it is relatively uncommon that a distal tip injury will be appropriate for replantation. In the event that replantation is not pursued, options for distal tip soft-tissue reconstruction must be considered. This review presents a straightforward method for evaluating fingertip injuries and provides an algorithm for fingertip reconstruction.