Showing 461 - 470 of 2039 Items
Bio-optical discrimination of diatoms from other phytoplankton in the surface ocean: Evaluation and refinement of a model for the Northwest Atlantic
Date: 2018-11-01
Creator: Sasha J. Kramer
Collin S. Roesler
Heidi M. Sosik
Access: Open access
- Diatoms dominate global silica production and export production in the ocean; they form the base of productive food webs and fisheries. Thus, a remote sensing algorithm to identify diatoms has great potential to describe ecological and biogeochemical trends and fluctuations in the surface ocean. Despite the importance of detecting diatoms from remote sensing and the demand for reliable methods of diatom identification, there has not been a systematic evaluation of algorithms that are being applied to this end. The efficacy of these models remains difficult to constrain in part due to limited datasets for validation. In this study, we test a bio-optical algorithm developed by Sathyendranath et al. (2004) to identify diatom dominance from the relationship between ratios of remote sensing reflectance and chlorophyll concentration. We evaluate and refine the original model with data collected at the Martha's Vineyard Coastal Observatory (MVCO), a near-shore location on the New England shelf. We then validated the refined model with data collected in Harpswell Sound, Maine, a site with greater optical complexity than MVCO. At both sites, despite relatively large changes in diatom fraction (0.8–82% of chlorophyll concentration), the magnitude of variability in optical properties due to the dominance or non-dominance of diatoms is less than the variability induced by other absorbing and scattering constituents of the water. While the original model performance was improved through successive re-parameterizations and re-formulations of the absorption and backscattering coefficients, we show that even a model originally parameterized for the Northwest Atlantic and re-parameterized for sites such as MVCO and Harpswell Sound performs poorly in discriminating diatom-dominance from optical properties.
Natural and experimental evolution of sexual conflict within Caenorhabditis nematodes
Date: 2015-05-22
Creator: Michael F. Palopoli
Colin Peden
Caitlin Woo
Ken Akiha
Megan, Ary
Lori Cruze
Jennifer L. Anderson
Patrick C. Phillips
Access: Open access
- Background: Although males and females need one another in order to reproduce, they often have different reproductive interests, which can lead to conflict between the sexes. The intensity and frequency of male-male competition for fertilization opportunities is thought to be an important contributor to this conflict. The nematode genus Caenorhabditis provides an opportunity to test this hypothesis because the frequency of males varies widely among species with different mating systems. Results: We find evidence that there is strong inter- and intra-sexual conflict within C. remanei, a dioecious species composed of equal frequencies of males and females. In particular, some C. remanei males greatly reduce female lifespan following mating, and their sperm have a strong competitive advantage over the sperm of other males. In contrast, our results suggest that both types of conflict have been greatly reduced within C. elegans, which is an androdioecious species that is composed of self-fertilizing hermaphrodites and rare males. Using experimental evolution in mutant C. elegans populations in which sperm production is blocked in hermaphrodites (effectively converting them to females), we find that the consequences of sexual conflict observed within C. remanei evolve rapidly within C. elegans populations experiencing high levels of male-male competition. Conclusions: Together, these complementary data sets support the hypothesis that the intensity of intersexual conflict varies with the intensity of competition among males, and that male-induced collateral damage to mates can evolve very rapidly within populations.
Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: Novel gene arrangement, truncated tRNA genes, and ancient divergence between species
Date: 2014-12-16
Creator: Michael F. Palopoli
Samuel Minot
Dorothy Pei
Alicia Satterly
Julie, Endrizzi
Access: Open access
- Background: Follicle mites of the genus Demodex are found on a wide diversity of mammals, including humans. surprisingly little is known, however, about the evolution of this association. Additional sequence information promises to facilitate studies of Demodex variation within and between host species. Here we report the complete mitochondrial genome sequences of two species of Demodex known to live on humans-Demodex brevis and D. folliculorum-which are the first such genomes available for any member of the genus. We analyzed these sequences to gain insight into the evolution of mitochondrial genomes within the Acariformes. We also used relaxed molecular clock analyses, based on alignments of mitochondrial proteins, to estimate the time of divergence between these two species. Results: Both Demodex genomes shared a novel gene order that differs substantially from the ancestral chelicerate pattern, with transfer RNA (tRNA) genes apparently having moved much more often than other genes. Mitochondrial tRNA genes of both species were unusually short, with most of them unable to encode tRNAs that could fold into the canonical cloverleaf structure. indeed, several examples lacked both D- and T-arms. Finally, the high level of sequence divergence observed between these species suggests that these two lineages last shared a common ancestor no more recently than about 87 mya. Conclusions: Among Acariformes, rearrangements involving tRNA genes tend to occur much more often than those involving other genes. The truncated tRNA genes observed in both Demodex species would seem to require the evolution of extensive tRNA editing capabilities and/or coevolved interacting factors. The molecular machinery necessary for these unusual tRNAs to function might provide an avenue for developing treatments of skin disorders caused by Demodex. The deep divergence time estimated between these two species sets a lower bound on the time that Demodex have been coevolving with their mammalian hosts, and supports the hypothesis that there was an early split within the genus Demodex into species that dwell in different skin microhabitats.
Noether’s theorem for plane domains with hyperelliptic double
Date: 1977-01-01
Creator: William H. Barker
Access: Open access
- This paper is motivated by the observation that Noether’s theorem for quadratic differentials fails for hyperelliptic Riemann surfaces. In this paper we provide an appropriate substitute for Noether’s theorem which is valid for plane domains with hyperelliptic double. Our result is somewhat more explicit than Noether’s, and, in contrast with the case of nonhyperelliptic surfaces, it provides a basis for the (even) quadratic differentials which holds globally for all domains with hyperelliptic double. An important fact which plays a significant role in these considerations is that no two normal differentials of the first kind can have a common zero on a domain with hyperelliptic double. © 1977 Pacific Journal of Mathematics. All rights reserved.
Non-Naturalism and Naturalism in Mathematics, Morality, and Epistemology
Date: 2018-05-01
Creator: Nicholas DiStefano
Access: Open access
Policy Making, Decision Making, and Advocacy: The U.S. Asylum System Since 9/11
Date: 2024-01-01
Creator: Clara Jergins
Access: Open access
- Immigration justice advocates and immigration restrictionists alike are unhappy with the way that the U.S. asylum system functions. This project seeks to develop a better understanding of policy changes and the politicized influence of the president and executive authorities over the asylum system since 9/11—in particular, these individuals’ ability to implement their policy preferences through the hiring and instruction of Asylum Officers and Immigration Judges. Through case studies of nonprofit organizations, it identifies the key points in the asylum process where asylum has been restricted, and the ways in which these restrictions can be responded to. On the basis of these factors, this project identifies four key changes, made by Congress, through which the asylum system could be improved: the establishment of an Article I immigration court, encoded testimonial and credibility standards, universal representation, and an end to asylum seeker detention. These changes are asserted to depoliticize the asylum process and to create a stable asylum system in which those that should qualify for asylum do qualify.
Prendersi Cura: Taking Care of Nature in Perugia, Italy
Date: 2024-03-20
Creator: Katharine Kurtz
Access: Open access
- Cities need more green spaces to adapt to climate change and facilitate community resilience. However, successfully managing green spaces is challenging. City governments consistently employ top-down management practices that limit the benefits, usage, and perception of such spaces as Nature. Further, current management practices overlook socio-cultural factors important to residents. Using the existing categories of urban green spaces (UGS) and informal green spaces (IGS), this article situates the cultural practice prendersi cura as a way to conceptualize successful, bottom-up green space management. The term prendersi cura, meaning “to take care of” in Italian, emerged through interviews in Perugia, Italy, and reflects the socio-ecological value of IGS and the disconnect between residents and city-managed UGS. This study employed mixed methods, combining 10 weeks of participant observation, 13 interviews, and GIS analysis to understand the relationship between Perugians and their green spaces. Results indicate that interviewees did not describe city-supported UGS (i.e. top-down green spaces like parks or historic gardens) as Nature, even if they were areas of dense vegetation and recognized by the City of Perugia in GIS analyses. In contrast, interviewees described IGS (i.e. community gardens, vacant lots, or potted plants) that were unrecognized in city GIS visualizations as Nature, indicating a stronger attachment to green spaces when interviewees had active roles in their management or witnessed community-based management practices. This paper demonstrates the importance of managing green spaces through a socio-ecological framework that considers user perceptions and cultural values. To allow greening initiatives to reach their full potential, it is critical to embrace local values and participation in management practices.
Prediction of a neuropeptidome for the eyestalk ganglia of the lobster Homarus americanus using a tissue-specific de novo assembled transcriptome
Date: 2017-03-01
Creator: Andrew E. Christie
Vittoria Roncalli
Matthew C. Cieslak
Micah G. Pascual
Andy, Yu
Tess J. Lameyer
Meredith E. Stanhope
Patsy S. Dickinson
Access: Open access
- In silico transcriptome mining is a powerful tool for crustacean peptidome prediction. Using homology-based BLAST searches and a simple bioinformatics workflow, large peptidomes have recently been predicted for a variety of crustaceans, including the lobster, Homarus americanus. Interestingly, no in silico studies have been conducted on the eyestalk ganglia (lamina ganglionaris, medulla externa, medulla interna and medulla terminalis) of the lobster, although the eyestalk is the location of a major neuroendocrine complex, i.e., the X-organ-sinus gland system. Here, an H. americanus eyestalk ganglia-specific transcriptome was produced using the de novo assembler Trinity. This transcriptome was generated from 130,973,220 Illumina reads and consists of 147,542 unique contigs. Eighty-nine neuropeptide-encoding transcripts were identified from this dataset, allowing for the deduction of 62 distinct pre/preprohormones. Two hundred sixty-two neuropeptides were predicted from this set of precursors; the peptides include members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon α, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, glycoprotein hormone β5, GSEFLamide, intocin, leucokinin, molt-inhibiting hormone, myosuppressin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families. The predicted peptides expand the H. americanus eyestalk ganglia neuropeptidome approximately 7-fold, and include 78 peptides new to the lobster. The transcriptome and predicted neuropeptidome described here provide new resources for investigating peptidergic signaling within/from the lobster eyestalk ganglia.
Distinct or shared actions of peptide family isoforms: II. Multiple pyrokinins exert similar effects in the lobster stomatogastric nervous system
Date: 2015-09-01
Creator: Patsy S. Dickinson
Sienna C. Kurland
Xuan Qu
Brett O. Parker
Anirudh, Sreekrishnan
Molly A. Kwiatkowski
Alex H. Williams
Alexandra B. Ysasi
Andrew E. Christie
Access: Open access
- Many neuropeptides are members of peptide families, with multiple structurally similar isoforms frequently found even within a single species. This raises the question of whether the individual peptides serve common or distinct functions. In the accompanying paper, we found high isoform specificity in the responses of the lobster (Homarus americanus) cardiac neuromuscular system to members of the pyrokinin peptide family: only one of five crustacean isoforms showed any bioactivity in the cardiac system. Because previous studies in other species had found little isoform specificity in pyrokinin actions, we examined the effects of the same five crustacean pyrokinins on the lobster stomatogastric nervous system (STNS). In contrast to our findings in the cardiac system, the effects of the five pyrokinin isoforms on the STNS were indistinguishable: they all activated or enhanced the gastric mill motor pattern, but did not alter the pyloric pattern. These results, in combination with those from the cardiac ganglion, suggest that members of a peptide family in the same species can be both isoform specific and highly promiscuous in their modulatory capacity. The mechanisms that underlie these differences in specificity have not yet been elucidated; one possible explanation, which has yet to be tested, is the presence and differential distribution of multiple receptors for members of this peptide family.
Related neuropeptides use different balances of unitary mechanisms to modulate the cardiac neuromuscular system in the American lobster, Homarus americanus
Date: 2015-01-01
Creator: Patsy S. Dickinson
Andrew Calkins
Jake S. Stevens
Access: Open access
- To produce flexible outputs, neural networks controlling rhythmic motor behaviors can be modulated at multiple levels, including the pattern generator itself, sensory feedback, and the response of the muscle to a given pattern of motor output. We examined the role of two related neuropeptides, GYSDRNYLRFamide (GYS) and SGRNFLRFamide (SGRN), in modulating the neurogenic lobster heartbeat, which is controlled by the cardiac ganglion (CG). When perfused though an isolated whole heart at low concentrations, both peptides elicited increases in contraction amplitude and frequency. At higher concentrations, both peptides continued to elicit increases in contraction amplitude, but GYS caused a decrease in contraction frequency, while SGRN did not alter frequency. To determine the sites at which these peptides induce their effects, we examined the effects of the peptides on the periphery and on the isolated CG. When we removed the CG and stimulated the motor nerve with constant bursts of stimuli, both GYS and SGRN increased contraction amplitude, indicating that each peptide modulates the muscle or the neuromuscular junction. When applied to the isolated CG, neither peptide altered burst frequency at low peptide concentrations; at higher concentrations, SGRN decreased burst frequency, whereas GYS continued to have no effect on frequency. Together, these data suggest that the two peptides elicit some of their effects using different mechanisms; in particular, given the known feedback pathways within this system, the importance of the negative (nitric oxide) relative to the positive (stretch) feedback pathways may differ in the presence of the two peptides.