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.     

Patterns and mechanisms of invasive plant impacts on North American birds: a systematic review

Understanding how invasive plants affect biodiversity is a crucial conservation need. Numerous studies examine impacts of invasions on birds, but trends in these effects have not been synthesized. We reviewed 128 studies from North America to quantify the frequency of positive, negative, and neutral (non-significant) effects of invasive plants on avian ecology, and then evaluated support for proposed mechanisms of impacts. Our frequency-based approach enabled us to draw value from the full breadth of available literature, including articles that do not provide information necessary for meta-analyses and articles examining understudied phenomena. Total avian abundance and prevalence of individual bird species were usually unaffected by invasion, with 48.9 and 57.2% of tests showing neutral results, respectively. Avian richness decreased with invasion in 41.3% of tests. Although birds often preferred nesting in invasive vegetation (45.0% of tests), effects on nest survival were typically neutral (57.9%). Multiple metrics (e.g. body condition, fledgling survival) have received scant attention. Some of the patterns we highlight differ across ecological contexts, emphasizing the need to understand impact mechanisms. Several studies have directly linked invasion impacts to altered nest-site availability, habitat heterogeneity, and food supplies. There is mixed evidence that plant architecture impacts nest-site selection and nest predation. Our review highlights the nonuniform consequences of biological invasions. The high frequency of reported neutral effects suggests that invasions often have minimal impacts on birds, but positive and negative impacts certainly can arise. Managers considering eradicating invasive plants for avian conservation should monitor impacts locally to determine whether eradication will be beneficial.     

Complications in postbariatric body contouring: strategies for assessment and prevention

Massive weight loss patients present specific challenges to the plastic surgeon. Review of these issues may be valuable for the surgeon who does not specialize in this area. Obtaining excellent results involves a comprehensive perioperative approach, beginning with proper patient selection and appropriate expectations. Operative considerations such as hypothermia prevention and thromboembolic prophylaxis can play a role in improving outcomes and reducing morbidity. Appropriately focused postoperative care completes the surgical plan, leading to satisfying results for both patient and surgeon.     

Patterns of haemosporidian prevalence along a range expansion in introduced Kenyan house sparrows Passer domesticus

Avian haemosporidian infections (of the genera Haemoproteus, Plasmodium and Leucocytozoon) can regulate passerine populations. Thus, reduction in the number of avian haemosporidian infections in a population, for example in recently introduced hosts, may facilitate host establishment or spread (i.e. enemy release). Alternatively, colonizers could decrease competitive ability of native individuals in the novel range by increasing the prevalence of avian haemosporidians in that native passerine community (i.e. novel weapons). However, whether either or both of these phenomena will occur is difficult to predict because infection risk can be highly heterogeneous and dependent upon the interaction of biotic and abiotic factors at the microclimate level, especially because of the important role of vectors for these parasites. Here, we describe which factors best predicted avian haemosporidian prevalence in populations of house sparrows Passer domesticus introduced to Kenya. House sparrows inhabit an invasion gradient in Kenya; they were introduced via the eastern port city of Mombasa in ? 1950 and have since spread west‐ward across the country. This range expansion gave us the opportunity to examine how parasite prevalence changes over small spatiotemporal scales and what role is played by environmental and individual traits. Among all individuals, body mass was the strongest predictor of infection, with larger house sparrows being more likely to be infected. At the population level, capture month, precipitation (higher prevalence with more rainfall), and population age (increasing prevalence with increasing time since introduction) were important risk factors. Overall, haemosporidian prevalence in Kenyan house sparrows appears to be more strongly associated with individual characteristics rather than with time since introduction as was predicted, though this does not necessarily rule out a role for enemy release or novel weapons in this system.     

Phosphorylation and Degradation of Tomosyn-2 De-represses Insulin Secretion

The abundance and functional activity of proteins involved in the formation of the SNARE complex are tightly regulated for efficient exocytosis. Tomosyn proteins are negative regulators of exocytosis. Tomosyn causes an attenuation of insulin secretion by limiting the formation of the SNARE complex. We hypothesized that glucose-dependent stimulation of insulin secretion from β-cells must involve reversing the inhibitory action of tomosyn. Here, we show that glucose increases tomosyn protein turnover. Within 1 h of exposure to 15 mm glucose, ∼50% of tomosyn was degraded. The degradation of tomosyn in response to high glucose was blocked by inhibitors of the proteasomal pathway. Using ³²P labeling and mass spectrometry, we showed that tomosyn-2 is phosphorylated in response to high glucose, phorbol esters, and analogs of cAMP, all key insulin secretagogues. We identified 11 phosphorylation sites in tomosyn-2. Site-directed mutagenesis was used to generate phosphomimetic (Ser → Asp) and loss-of-function (Ser → Ala) mutants. The Ser → Asp mutant had enhanced protein turnover compared with the Ser → Ala mutant and wild type tomosyn-2. Additionally, the Ser → Asp tomosyn-2 mutant was ineffective at inhibiting insulin secretion. Using a proteomic screen for tomosyn-2-binding proteins, we identified Hrd-1, an E3-ubiquitin ligase. We showed that tomosyn-2 ubiquitination is increased by Hrd-1, and knockdown of Hrd-1 by short hairpin RNA resulted in increased abundance in tomosyn-2 protein levels. Taken together, our results reveal a mechanism by which enhanced phosphorylation of a negative regulator of secretion, tomosyn-2, in response to insulin secretagogues targets it to degradation by the Hrd-1 E3-ubiquitin ligase.     

Immunochemical studies on the metabolism of nitrosamines by ethanol-inducible cytochrome P-450

The ethanol-induced rabbit liver microsomal cytochrome P-450, P-450LM3a, has been shown previously to efficiently catalyze the demethylation of N-nitrosodimethylamine (NDMA) with a Km of 2.9 mM. Since the predominant Km in hepatic microsomes from ethanol-treated rabbits is 0.07 mM, the role of P-450LM3a in the activation of this carcinogen has been uncertain. In the present study, antibodies to P-450LM3a were shown to almost completely inhibit NDMA demethylation by the purified P-450 in a reconstituted system as well as the low-Km activity of liver microsomes from control or ethanol-treated rabbits. In contrast, the antibody did not inhibit the high-Km NDMA demethylase activity in the microsomes. These results indicate that P-450LM3a is the major P-450 responsible for the low-Km NDMA demethylase activity. In addition, evidence is provided for the existence of a cytochrome immunochemically similar to P-450LM3a in liver microsomes from rats, mice, and guinea pigs that effectively catalyzes the demethylation of NDMA.