Peppy: Proteogenomic Search Software

Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have been limited to small genomes, as large genomes can prove impractical due to the required amount of computer memory and computation time. We present Peppy, a software tool designed to perform every necessary task of proteogenomic searches quickly, accurately and automatically. The software generates a peptide database from a genome, tracks peptide loci, matches peptides to MS/MS spectra and assigns confidence values to those matches. Peppy automatically performs a decoy database generation, search and analysis to return identifications at the desired false discovery rate threshold. Written in Java for cross-platform execution, the software is fully multithreaded for enhanced speed. The program can run on regular desktop computers, opening the doors of proteogenomic searching to a wider audience of proteomics and genomics researchers. Peppy is available at http://geneffects.com/peppy

Families of Quintic Calabi-Yau 3-Folds with Discrete Symmetries

At special loci in their moduli spaces, Calabi-Yau manifolds are endowed with discrete symmetries. Over the years, such spaces have been intensely studied and have found a variety of important applications. As string compactifications they are phenomenologically favored, and considerably simplify many important calculations. Mathematically, they provided the framework for the first construction of mirror manifolds, and the resulting rational curve counts. Thus, it is of significant interest to investigate such manifolds further. In this paper, we consider several unexplored loci within familiar families of Calabi-Yau hypersurfaces that have large but unexpected discrete symmetry groups. By deriving, correcting, and generalizing a technique similar to that of Candelas, de la Ossa and Rodriguez-Villegas, we find a calculationally tractable means of finding the Picard-Fuchs equations satisfied by the periods of all 3-forms in these families. To provide a modest point of comparison, we then briefly investigate the relation between the size of the symmetry group along these loci and the number of nonzero Yukawa couplings. We include an introductory exposition of the mathematics involved, intended to be accessible to physicists, in order to make the discussion self-contained.Comment: 54 pages, 3 figure

When Reintroductions are Augmentations: The Genetic Legacy of Fishers (Martes Pennanti) in Montana

Fishers (Martes pennanti) were purportedly extirpated from Montana by 1930 and extant populations are assumed to be descended from translocated fishers. To determine the lineage of fisher populations, we sequenced 2 regions of the mitochondrial DNA genome from 207 tissue samples from British Columbia, Minnesota, Wisconsin, and Montana. In northwestern Montana, fishers share haplotypes with samples from the upper Midwest and British Columbia; in west-central Montana, we detected haplotypes found in British Columbia samples, but also detected a control region and cytochrome-b haplotype not found in source populations. Based on the unique haplotypes found in west-central Montana, we propose that individuals with these haplotypes are descended from a relic population. Fishers in northwestern Montana are likely descended from fishers from the Midwest and British Columbia

Expected Limits on the Ocean Acidification Buffering Potential of a Temperate Seagrass Meadow

Ocean acidification threatens many marine organisms, especially marine calcifiers. The only global‐scale solution to ocean acidification remains rapid reduction in CO2 emissions. Nevertheless, interest in localized mitigation strategies has grown rapidly because of the recognized threat ocean acidification imposes on natural communities, including ones important to humans. Protection of seagrass meadows has been considered as a possible approach for localized mitigation of ocean acidification due to their large standing stocks of organic carbon and high productivity. Yet much work remains to constrain the magnitudes and timescales of potential buffering effects from seagrasses. We developed a biogeochemical box model to better understand the potential for a temperate seagrass meadow to locally mitigate the effects of ocean acidification. Then we parameterized the model using data from Tomales Bay, an inlet on the coast of California, USA which supports a major oyster farming industry. We conducted a series of month‐long model simulations to characterize processes that occur during summer and winter. We found that average pH in the seagrass meadows was typically within 0.04 units of the pH of the primary source waters into the meadow, although we did find occasional periods (hours) when seagrass metabolism may modify the pH by up to ±0.2 units. Tidal phasing relative to the diel cycle modulates localized pH buffering within the seagrass meadow such that maximum buffering occurs during periods of the year with midday low tides. Our model results suggest that seagrass metabolism in Tomales Bay would not provide long‐term ocean acidification mitigation. However, we emphasize that our model results may not hold in meadows where assumptions about depth‐averaged net production and seawater residence time within the seagrass meadow differ from our model assumptions. Our modeling approach provides a framework that is easily adaptable to other seagrass meadows in order to evaluate the extent of their individual buffering capacities. Regardless of their ability to buffer ocean acidification, seagrass meadows maintain many critically important ecosystem goods and services that will be increasingly important as humans increasingly affect coastal ecosystems

Spatial and temporal variability of solar penetration depths in the Bay of Bengal and its impact on SST during the summer monsoon

Chlorophyll has long been known to influence air–sea gas exchange and CO2 drawdown. But chlorophyll also influences regional climate through its effect on solar radiation absorption and thus sea surface temperature (SST). In the Bay of Bengal, the effect of chlorophyll on SST has been demonstrated to have a significant impact on the Indian summer (southwest) monsoon. However, little is known about the drivers and impacts of chlorophyll variability in the Bay of Bengal during the southwest monsoon. Here we use observations of downwelling irradiance measured by an ocean glider and three profiling floats to determine the spatial and temporal variability of solar absorption across the southern Bay of Bengal during the 2016 summer monsoon. A two-band exponential solar absorption scheme is fitted to vertical profiles of photosynthetically active radiation to determine the effective scale depth of blue light. Scale depths of blue light are found to vary from 12 m during the highest (0.3–0.5 mg m−3) mixed-layer chlorophyll concentrations to over 25 m when the mixed-layer chlorophyll concentrations are below 0.1 mg m−3. The Southwest Monsoon Current and coastal regions of the Bay of Bengal are observed to have higher mixed-layer chlorophyll concentrations and shallower solar penetration depths than other regions of the southern Bay of Bengal. Substantial sub-daily variability in solar radiation absorption is observed, which highlights the importance of near-surface ocean processes in modulating mixed-layer chlorophyll. Simulations using a one-dimensional K-profile parameterization ocean mixed-layer model with observed surface forcing from July 2016 show that a 0.3 mg m−3 increase in chlorophyll concentration increases sea surface temperature by 0.35 ∘C in 1 month, with SST differences growing rapidly during calm and sunny conditions. This has the potential to influence monsoon rainfall around the Bay of Bengal and its intraseasonal variability

BoBBLE: ocean-atmosphere interaction and its impact on the South Asian monsoon

The Bay of Bengal (BoB) plays a fundamental role in controlling the weather systems that make up the South Asian summer monsoon system. In particular,the southern BoB has cooler sea surface temperature (SST) that influence ocean-atmosphere interaction and impact on the monsoon. Compared to the southeast, the southwestern BoB is cooler, more saline, receives much less rain, and is influenced by the Summer Monsoon Current(SMC). To examine the impact of these features on the monsoon, the BoB Boundary Layer Experiment (BoBBLE) was jointly undertaken by India and the UK during June–July 2016. Physical and bio-geochemical observations were made using a CTD, five ocean gliders, a uCTD, a VMP, two ADCPs, Argo floats, drifting buoys, meteorological sensors and upper air radiosonde balloons. The observations were made along a zonal section at 8◦N between 85.3◦E and 89◦E with a 10-day time series at 89◦E, 8◦N. This paper presents the new observed features of the southern BoB from the BoBBLE field program, supported by satellite data. Key results from the BoBBLE field campaign show the Sri Lanka Dome and the SMC in different stages of their seasonal evolution and two freshening events during which salinity decreased in the upper layer leading to the formation of thick barrier layers. BoBBLE observations were taken during a suppressed phase of the intraseasonal oscillation; they captured in detail the warming of the ocean mixed layer and preconditioning of the atmosphere to convection

A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities

Peppy, the proteogenomic / proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial probabilities: the probability that a fragment ion will randomly align with a peptide ion, the probability that the aligning ions will be selected from subsets of the most intense peaks, and the probability that the intensities of fragment ions identified as y-ions are greater than those of their counterpart b-ions. The scores produced by the method act as global confidence scores, which facilitate the accurate comparison of results and the estimation of false discovery rates. Peppy has been integrated into the meta-search engine PepArML to produce meaningful comparisons with Mascot, MSGF+, OMSSA, X!Tandem, k-Score and s-Score. For two of the four data sets examined with the PepArML analysis, Peppy exceeded the accuracy performance of the other scoring systems. Peppy is available for download at http://geneffects.com/peppy