A comparative study of synthetic winged peptides for absolute protein quantification

A proper internal standard choice is critical for accurate, precise, and reproducible mass spectrometry-based proteomics assays. Synthetic isotopically labeled (SIL) proteins are currently considered the gold standard. However, they are costly and challenging to obtain. An alternative approach uses SIL peptides or SIL "winged" peptides extended at C- or/and N-terminus with an amino acid sequence or a tag cleaved during enzymatic proteolysis. However, a consensus on the design of a winged peptide for absolute quantification is missing. In this study, we used human serum albumin as a model system to compare the quantitative performance of reference SIL protein with four different designs of SIL winged peptides: (i) commercially available SIL peptides with a proprietary trypsin cleavable tag at C-terminus, (ii) SIL peptides extended with five amino acid residues at C-terminus, (iii) SIL peptides extended with three and (iv) with five amino acid residues at both C- and N-termini. Our results demonstrate properties of various SIL extended peptides designs, e.g., water solubility and efficiency of trypsin enzymatic cleavage with primary influence on quantitative performance. SIL winged peptides extended with three amino acids at both C- and N-termini demonstrated optimal quantitative performance, equivalent to the SIL protein

A Climate Change Vulnerability Assessment of California's At-Risk Birds

Conservationists must develop new strategies and adapt existing tools to address the consequences of anthropogenic climate change. To support statewide climate change adaptation, we developed a framework for assessing climate change vulnerability of California's at-risk birds and integrating it into the existing California Bird Species of Special Concern list. We defined climate vulnerability as the amount of evidence that climate change will negatively impact a population. We quantified climate vulnerability by scoring sensitivity (intrinsic characteristics of an organism that make it vulnerable) and exposure (the magnitude of climate change expected) for each taxon. Using the combined sensitivity and exposure scores as an index, we ranked 358 avian taxa, and classified 128 as vulnerable to climate change. Birds associated with wetlands had the largest representation on the list relative to other habitat groups. Of the 29 state or federally listed taxa, 21 were also classified as climate vulnerable, further raising their conservation concern. Integrating climate vulnerability and California's Bird Species of Special Concern list resulted in the addition of five taxa and an increase in priority rank for ten. Our process illustrates a simple, immediate action that can be taken to inform climate change adaptation strategies for wildlife

Re-Shuffling of Species with Climate Disruption: A No-Analog Future for California Birds?

By facilitating independent shifts in species' distributions, climate disruption may result in the rapid development of novel species assemblages that challenge the capacity of species to co-exist and adapt. We used a multivariate approach borrowed from paleoecology to quantify the potential change in California terrestrial breeding bird communities based on current and future species-distribution models for 60 focal species. Projections of future no-analog communities based on two climate models and two species-distribution-model algorithms indicate that by 2070 over half of California could be occupied by novel assemblages of bird species, implying the potential for dramatic community reshuffling and altered patterns of species interactions. The expected percentage of no-analog bird communities was dependent on the community scale examined, but consistent geographic patterns indicated several locations that are particularly likely to host novel bird communities in the future. These no-analog areas did not always coincide with areas of greatest projected species turnover. Efforts to conserve and manage biodiversity could be substantially improved by considering not just future changes in the distribution of individual species, but including the potential for unprecedented changes in community composition and unanticipated consequences of novel species assemblages

Birds of Two Oceans? Trans-Andean and Divergent Migration of Black Skimmers (Rynchops niger cinerascens) from the Peruvian Amazon

We are grateful for assistance from John Terborgh, Antonio Guerra Rosas, Marcos Maguiña, Inés Nole, John Takekawa, Lisa Ferguson, Juan Kapeshi, Nikanor Kapeshi, Cathy Bykowsky, Chi (Tim) Lam, Scott Robinson, Fabrice Schmitt, and Cesar Flores. Alex Jahn, Ugo Mellone, Sergio Lambertucci and one anonymous reviewer provided comments that helped improve the manuscript.Seasonal flooding compels some birds that breed in aquatic habitats in Amazonia to undertake annual migrations, yet we know little about how the complex landscape of the Amazon region is used seasonally by these species. The possibility of trans-Andes migration for Amazonian breeding birds has largely been discounted given the high geographic barrier posed by the Andean Cordillera and the desert habitat along much of the Pacific Coast. Here we demonstrate a trans-Andes route for Black Skimmers (Rynchops niger cinerascens) breeding on the Manu River (in the lowlands of Manu National Park, Perú), as well as divergent movement patterns both regionally and across the continent. Of eight skimmers tracked with satellite telemetry, three provided data on their outbound migrations, with two crossing the high Peruvian Andes to the Pacific. A third traveled over 1800 km to the southeast before transmissions ended in eastern Paraguay. One of the two trans-Andean migrants demonstrated a full round-trip migration back to its tagging location after traveling down the Pacific Coast from latitude 9° South to latitude 37° S, spending the austral summer in the Gulf of Arauco, Chile. This is the first documentation of a trans-Andes migration observed for any bird breeding in lowland Amazonia. To our knowledge, this research also documents the first example of a tropical-breeding waterbird migrating out of the tropics to spend the non-breeding season in the temperate summer, this being the reverse pattern with respect to seasonality for austral migrants in general.Yeshttp://www.plosone.org/static/editorial#pee

Radical nephrectomy performed by open, laparoscopy with or without hand-assistance or robotic methods by the same surgeon produces comparable perioperative results

PURPOSE: Radical nephrectomy can be performed using open or laparoscopic (with or without hand assistance) methods, and most recently using the da Vinci Surgical Robotic System. We evaluated the perioperative outcomes using a contemporary cohort of patients undergoing radical nephrectomy by one of the above 4 methods performed by the same surgeon. MATERIALS AND METHODS: The relevant clinical information on 57 consecutive patients undergoing radical nephrectomy from September 2000 until July 2004 by a single surgeon was entered in a Microsoft Access DatabaseTM and queried. Following appropriate statistical analysis, p values < 0.05 were considered significant. RESULTS: Of 57 patients, the open, robotic, laparoscopy with or without hand assistance radical nephrectomy were performed in 18, 6, 21, and 12 patients, respectively. The age, sex, body mass index (BMI), incidence of malignancy, specimen and tumor size, tumor stage, Fuhrman grade, hospital stay, change in postoperative creatinine, drop in hemoglobin, and perioperative complications were not significantly different between the methods. While the estimated median blood loss, postoperative narcotic use for pain control, and hospital stay were significantly higher in the open surgery method (p < 0.05), the median operative time was significantly shorter compared to the robotic method (p = 0.02). Operating room costs were significantly higher in the robotic and laparoscopic groups; however, there was no significant difference in total hospital costs between the 4 groups. CONCLUSIONS: The study demonstrates that radical nephrectomy can be safely performed either by open, robotic, or laparoscopic with or without hand assistance methods without significant difference in perioperative complication rates. A larger cohort and longer follow up are needed to validate our findings and establish oncological outcomes

International Society of Urological Pathology (ISUP) Consensus Conference on Handling and Staging of Radical Prostatectomy Specimens. Working group 5: surgical margins.

Contains fulltext : 96027.pdf (publisher's version ) (Closed access)The 2009 International Society of Urological Pathology Consensus Conference in Boston, made recommendations regarding the standardization of pathology reporting of radical prostatectomy specimens. Issues relating to surgical margin assessment were coordinated by working group 5. Pathologists agreed that tumor extending close to the 'capsular' margin, yet not to it, should be reported as a negative margin, and that locations of positive margins should be indicated as either posterior, posterolateral, lateral, anterior at the prostatic apex, mid-prostate or base. Other items of consensus included specifying the extent of any positive margin as millimeters of involvement; tumor in skeletal muscle at the apical perpendicular margin section, in the absence of accompanying benign glands, to be considered organ confined; and that proximal and distal margins be uniformly referred to as bladder neck and prostatic apex, respectively. Grading of tumor at positive margins was to be left to the discretion of the reporting pathologists. There was no consensus as to how the surgical margin should be regarded when tumor is present at the inked edge of the tissue, in the absence of transected benign glands at the apical margin. Pathologists also did not achieve agreement on the reporting approach to benign prostatic glands at an inked surgical margin in which no carcinoma is present.1 januari 201