Influence of Northern Bobwhite Nest Site Selection on Nest Survival in an Agricultural Landscape

Working farms provide excellent potential for conserving northern bobwhite (Colinus virginianus) habitat in agricultural landscapes. Managing for areas of early successional vegetation can increase bobwhite abundance with little reduction in crop production on working farms, but the mechanisms behind the increase is not well known. Our objective was to determine nest site characteristics that may predict nest initiation and survival on agricultural lands to inform future management activities. We radio-collared 241 wild bobwhite on 1 farm with and 2 farms without bobwhite habitat management in southeastern North Carolina. Study sites consisted of a 1,740-ha farm with 9% of property actively managed for early successional cover using areas planted in native vegetation and fallow field borders, a 170-ha farm with 2% of property in early-successional field borders monitored in 2014, and a 395-ha farm with no previous early successional management efforts monitored in 2015. We monitored nests (n = 71) from 15 May to 30 September, 2014 and 2015. We compared vegetation cover between nests and paired reference sites within 250 m of each nest using a generalized linear mixed-effect model. We used measurements of vegetation cover types at nest sites as predictors of nest survival using the Program MARK nest survival model. Bobwhite on the farm with habitat management exhibited higher nest initiation (1 nest/2 marked individuals) than those on unmanaged farms (1 nest/4 marked individuals). On the managed farm, 76% of nests were located in fallow early successional vegetation. Percent forb cover (P = \u3c 0.001) was greater at nest sites on managed (μ = 53.61, SE = 4.32) than unmanaged (μ = 17.01, SE = 2.49) farms. Bobwhite selected nest sites with greater forb cover (β = 1.08, SE = 0.21) than reference sites. Daily nest survival was 0.962 (SE = 0.007) with no covariates that described variation in nest survival rates. Results indicate increasing fallow forb cover on agricultural lands can benefit nest initiation rates by increasing the cover bobwhite select for nesting

Molecular evolution of urea amidolyase and urea carboxylase in fungi

Background: Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms. Results: Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina. Conclusions: We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

Sequence simulation is an important tool in validating biological hypotheses as well as testing various bioinformatics and molecular evolutionary methods. Hypothesis testing relies on the representational ability of the sequence simulation method. Simple hypotheses are testable through simulation of random, homogeneously evolving sequence sets. However, testing complex hypotheses, for example, local similarities, requires simulation of sequence evolution under heterogeneous models. To this end, we previously introduced indel-Seq-Gen version 1.0 (iSGv1.0; indel, insertion/deletion). iSGv1.0 allowed heterogeneous protein evolution and motif conservation as well as insertion and deletion constraints in subsequences. Despite these advances, for complex hypothesis testing, neither iSGv1.0 nor other currently available sequence simulation methods is sufficient. indel-Seq-Gen version 2.0 (iSGv2.0) aims at simulating evolution of highly divergent DNA sequences and protein superfamilies. iSGv2.0 improves upon iSGv1.0 through the addition of lineage-specific evolution, motif conservation using PROSITE-like regular expressions, indel tracking, subsequence-length constraints, as well as coding and noncoding DNA evolution. Furthermore, we formalize the sequence representation used for iSGv2.0 and uncover a flaw in the modeling of indels used in current state of the art methods, which biases simulation results for hypotheses involving indels. We fix this flaw in iSGv2.0 by using a novel discrete stepping procedure. Finally, we present an example simulation of the calycin-superfamily sequences and compare the performance of iSGv2.0 with iSGv1.0 and random model of sequence evolution

The Emergence of the Infrared transient VVV-WIT-06

We report the discovery of an enigmatic large-amplitude (ΔKs> 10.5 mag) transient event in near-IR data obtained by the VISTA Variables in the Via Lactea (VVV) ESO Public Survey. The object (designated VVV-WIT-06) is located at R.A. = 17:07:18.917, decl. = -39:06:26.45 (J2000), corresponding to Galactic coordinates l = 347.14539, b = 0.88522. It exhibits a clear eruption, peaking at Ks = 9 mag during 2013 July and fading to Ks ~ 16.5 in 2017. Our late near-IR spectra show post-outburst emission lines, including some broad emission lines (upward of {FWHM} ~ 3000 k/s). We estimate a total extinction of A_V=10--15 mag in the surrounding field, and no progenitor was observed in ZYJHKs images obtained during 2010-2012 (down to Ks> 18.5 mag). Subsequent deep near-IR imaging and spectroscopy, in concert with the available multiband photometry, indicate that VVV-WIT-06 may be either: (I) the closest Type I SN observed in about 400 years, (II) an exotic high-amplitude nova that would extend the known realm of such objects, or (III) a stellar merger. In all of these cases, VVV-WIT-06 is a fascinating and curious astrophysical target under any of the scenarios considered.Peer reviewe

V496 Scuti: An Fe II nova with dust shell accompanied by CO emission

We present near-infrared and optical observations of the nova V496 Scuti 2009 covering various phases - pre-maximum, early decline and nebular - during the first 10 months of its discovery followed by limited observations in early part of 2011 April. The spectra follow the evolution of the nova when the lines had strong P Cygni profiles to a phase dominated by prominent emission lines. The notable feature of the near-IR spectra in the early decline phase is the rare presence of first overtone bands of carbon monoxide in emission. Later about 150 days after the peak brightness the IR spectra show clear dust formation in the expanding ejecta. Dust formation in V496 Sct is consistent with the presence of lines of elements with low ionization potentials like Na and Mg in the early spectra and the detection of CO bands in emission. The light curve shows a slow rise to the maximum and a slow decline indicating a prolonged mass loss. This is corroborated by the strengthening of P Cygni profiles during the first 30 days. In the spectra taken close to the optical maximum brightness, the broad and single absorption component seen at the time of discovery is replaced by two sharper components. During the early decline phase two sharp dips that show increasing outflow velocities are seen in the P Cygni absorption components of Fe II and H I lines. The spectra in 2010 March showed the onset of the nebular phase. Several emission lines display saddle-like profiles during the nebular phase. In the nebular stage the observed fluxes of [O III] and H-beta lines are used to estimate the electron number densities and the mass of the ejecta. The optical spectra show that the nova evolved in the P_fe A_o spectral sequence. The physical conditions in the ejecta are estimated. The absolute magnitude and the distance to the nova are estimated to be M_V = -7.0 +/- 0.2 and d = 2.9 +/- 0.3 kpc respectively.Comment: 14 pages, 9 figures and 6 Tables, Accepted for Publication in MNRA

Elemental Abundances in the Ejecta of Old Classical Novae from Late-Epoch Spitzer Spectra

We present Spitzer Space Telescope mid-infrared IRS spectra, supplemented by ground-based optical observations, of the classical novae V1974 Cyg, V382 Vel, and V1494 Aql more than 11, 8, and 4 years after outburst respectively. The spectra are dominated by forbidden emission from neon and oxygen, though in some cases, there are weak signatures of magnesium, sulfur, and argon. We investigate the geometry and distribution of the late time ejecta by examination of the emission line profiles. Using nebular analysis in the low density regime, we estimate lower limits on the abundances in these novae. In V1974 Cyg and V382 Vel, our observations confirm the abundance estimates presented by other authors and support the claims that these eruptions occurred on ONe white dwarfs. We report the first detection of neon emission in V1494 Aql and show that the system most likely contains a CO white dwarf.Comment: 22 pages, 12 figure

Evaluation of methods for detecting conversion events in gene clusters

Background: Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods. Results: We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events. Conclusions: Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution

Fecal Tests: From Blood to Molecular Markers

Detection of molecular markers for colorectal neoplasia in feces has the potential to improve performance of simple noninvasive screening tests for colorectal cancer. Most research has explored the value of DNA-based, RNA-based, and protein-based markers. In all cases there has been a trend to move from a single marker to a panel of markers to improve sensitivity. Unfortunately, no type of molecular marker has proved specific for neoplasia. DNA tests have been improved by combining mutation detection with assessment of DNA integrity plus epigenetic markers of neoplasia. RNA-based approaches are just beginning to explore the full power of transcriptomics. So far, no protein-based fecal test has proved better than fecal immunochemical tests for hemoglobin. Finally, no marker or panel of markers has yet been developed to the point where it has been evaluated in large unbiased population studies to assess performance across all stages of neoplasia and in all practical environments

Proteomic Analysis of Fusarium solani Isolated from the Asian Longhorned Beetle, Anoplophora glabripennis

Wood is a highly intractable food source, yet many insects successfully colonize and thrive in this challenging niche. Overcoming the lignin barrier of wood is a key challenge in nutrient acquisition, but full depolymerization of intact lignin polymers has only been conclusively demonstrated in fungi and is not known to occur by enzymes produced by insects or bacteria. Previous research validated that lignocellulose and hemicellulose degradation occur within the gut of the wood boring insect, Anoplophora glabripennis (Asian longhorned beetle), and that a fungal species, Fusarium solani (ATCC MYA 4552), is consistently associated with the larval stage. While the nature of this relationship is unresolved, we sought to assess this fungal isolate's ability to degrade lignocellulose and cell wall polysaccharides and to extract nutrients from woody tissue. This gut-derived fungal isolate was inoculated onto a wood-based substrate and shotgun proteomics using Multidimensional Protein Identification Technology (MudPIT) was employed to identify 400 expressed proteins. Through this approach, we detected proteins responsible for plant cell wall polysaccharide degradation, including proteins belonging to 28 glycosyl hydrolase families and several cutinases, esterases, lipases, pectate lyases, and polysaccharide deacetylases. Proteinases with broad substrate specificities and ureases were observed, indicating that this isolate has the capability to digest plant cell wall proteins and recycle nitrogenous waste under periods of nutrient limitation. Additionally, several laccases, peroxidases, and enzymes involved in extracellular hydrogen peroxide production previously implicated in lignin depolymerization were detected. In vitro biochemical assays were conducted to corroborate MudPIT results and confirmed that cellulases, glycosyl hydrolases, xylanases, laccases, and Mn- independent peroxidases were active in culture; however, lignin- and Mn- dependent peroxidase activities were not detected While little is known about the role of filamentous fungi and their associations with insects, these findings suggest that this isolate has the endogenous potential to degrade lignocellulose and extract nutrients from woody tissue