Publications by authors named "Tara Edwards"

30 Publications

  • Page 1 of 1

ATP released by Candida albicans is associated with reduced skin infectivity.

J Invest Dermatol 2021 Mar 27. Epub 2021 Mar 27.

Departments of Dermatology and Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2021.03.010DOI Listing
March 2021

Nonpeptidergic neurons suppress mast cells via glutamate to maintain skin homeostasis.

Cell 2021 Mar 18. Epub 2021 Mar 18.

Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address:

Cutaneous mast cells mediate numerous skin inflammatory processes and have anatomical and functional associations with sensory afferent neurons. We reveal that epidermal nerve endings from a subset of sensory nonpeptidergic neurons expressing MrgprD are reduced by the absence of Langerhans cells. Loss of epidermal innervation or ablation of MrgprD-expressing neurons increased expression of a mast cell gene module, including the activating receptor, Mrgprb2, resulting in increased mast cell degranulation and cutaneous inflammation in multiple disease models. Agonism of MrgprD-expressing neurons reduced expression of module genes and suppressed mast cell responses. MrgprD-expressing neurons released glutamate which was increased by MrgprD agonism. Inhibiting glutamate release or glutamate receptor binding yielded hyperresponsive mast cells with a genomic state similar to that in mice lacking MrgprD-expressing neurons. These data demonstrate that MrgprD-expressing neurons suppress mast cell hyperresponsiveness and skin inflammation via glutamate release, thereby revealing an unexpected neuroimmune mechanism maintaining cutaneous immune homeostasis.
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http://dx.doi.org/10.1016/j.cell.2021.03.002DOI Listing
March 2021

Evaluation of COVID-19 coagulopathy; laboratory characterization using thrombin generation and nonconventional haemostasis assays.

Int J Lab Hematol 2021 Feb 5;43(1):123-130. Epub 2020 Sep 5.

Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.

Introduction: Patients with COVID-19 are known to have a coagulopathy with a thrombosis risk. It is unknown whether this is due to a generalized humoral prothrombotic state or endothelial factors such as inflammation and dysfunction. The aim was to further characterize thrombin generation using a novel analyser (ST Genesia, Diagnostica Stago, Asnières, France) and a panel of haematological analytes in patients with COVID-19.

Methods: Platelet poor plasma of 34 patients with noncritical COVID-19 was compared with 75 patients with critical COVID-19 (as defined by WHO criteria) in a retrospective study by calibrated automated thrombography and ELISA. Patients were matched for baseline characteristics of age and gender.

Results: Critical patients had significantly increased fibrinogen, CRP, interleukin-6 and D-dimer compared to noncritical patients. Thrombin generation, in critical patients, was right shifted without significant differences in peak, velocity index or endogenous thrombin potential. Tissue plasminogen activator (tPA), tissue factor pathway inhibitor (TFPI) and vascular endothelial growth factor (VEGF) were significantly increased in the critical versus noncritical patients. Critically ill patients were on haemodiafiltration (31%; heparin used in the circuit) or often received escalated prophylactic low-molecular weight heparin.

Conclusion: These results confirm increased fibrinogen and D-dimer in critical COVID-19-infected patients. Importantly, disease severity did not increase thrombin generation (including thrombin-antithrombin complexes and prothrombin fragment 1 + 2) when comparing both cohorts; counter-intuitively critical patients were hypocoaguable. tPA, TFPI and VEGF were increased in critical patients, which are hypothesized to reflect endothelial dysfunction and/or contribution of heparin (which may cause endothelial TFPI/tPA release).
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http://dx.doi.org/10.1111/ijlh.13329DOI Listing
February 2021

An IL-17F.S65L Knock-In Mouse Reveals Similarities and Differences in IL-17F Function in Oral Candidiasis: A New Tool to Understand IL-17F.

J Immunol 2020 08 29;205(3):720-730. Epub 2020 Jun 29.

Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA 15261;

Oropharyngeal candidiasis (OPC) is an opportunistic infection of the oral mucosa caused by the commensal fungus IL-17R signaling is essential to prevent OPC in mice and humans, but the individual roles of its ligands, IL-17A, IL-17F, and IL-17AF, are less clear. A homozygous IL-17F deficiency in mice does not cause OPC susceptibility, whereas mice lacking IL-17A are moderately susceptible. In humans, a rare heterozygous mutation in IL-17F (IL-17F.S65L) was identified that causes chronic mucocutaneous candidiasis, suggesting the existence of essential antifungal pathways mediated by IL-17F and/or IL-17AF. To investigate the role of IL-17F and IL-17AF in more detail, we exploited this "experiment of nature" by creating a mouse line bearing the homologous mutation in IL-17F (Ser65Leu) by CRISPR/Cas9. Unlike mice that are resistant to OPC, mice showed increased oral fungal burdens similar to mice. In contrast to humans, however, disease was only evident in homozygous, not heterozygous, mutant mice. The mutation was linked to modestly impaired CXC chemokine expression and neutrophil recruitment to the infected tongue but not to alterations in oral antimicrobial peptide expression. These findings suggest mechanisms by which the enigmatic cytokine IL-17F contributes to host defense against fungi. Moreover, because these mice do not phenocopy mice, they may provide a valuable tool to interrogate IL-17F and IL-17AF function in vivo in other settings.
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http://dx.doi.org/10.4049/jimmunol.2000394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7369233PMC
August 2020

Contemporaneity of , , and early in South Africa.

Science 2020 04;368(6486)

Department of Biology, University of Florence, Florence, Italy.

Understanding the extinction of and origins of and in South Africa has been hampered by the perceived complex geological context of hominin fossils, poor chronological resolution, and a lack of well-preserved early specimens. We describe, date, and contextualize the discovery of two hominin crania from Drimolen Main Quarry in South Africa. At ~2.04 million to 1.95 million years old, DNH 152 represents the earliest definitive occurrence of , and DNH 134 represents the earliest occurrence of a cranium with clear affinities to These crania also show that , , and were contemporaneous at ~2 million years ago. This high taxonomic diversity is also reflected in non-hominin species and provides evidence of endemic evolution and dispersal during a period of climatic variability.
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http://dx.doi.org/10.1126/science.aaw7293DOI Listing
April 2020

Dog owner's accuracy measuring different volumes of dry dog food using three different measuring devices.

Vet Rec 2019 11 13;185(19):599. Epub 2019 Aug 13.

Department of Clinical Studies, University of Guelph, Ontario Veterinary College, Guelph, Ontario, Canada.

Prior research demonstrates significant inaccuracy when repeatedly measuring the same amount of dry dog food using a dry-food measuring cup, bringing into question the accuracy of measuring devices. This study aimed to determine dog owners' accuracy when measuring different volumes of dry dog food using different types of measuring devices. One hundred dog owners, randomly assigned one of three measuring devices (a one-cup dry-food measuring cup, a two-cup graduated-liquid measuring cup or a two-cup commercial food scoop), were asked to measure ¼, ½ and 1 cup of dry dog food. Accuracy was assessed with an electronic gram scale by comparing measured volumes with the correct weight in grams. Individual accuracy ranged from -47.83% to 152.17% across devices and volumes. Measuring accuracy was found to be associated with the volume of food measured (p<0.001) and the type of measuring device used (p<0.001). Findings highlight approaches for decreasing excess intake of calories by dogs, including promotion of tactics to improve measurement accuracy (eg, gram scales, volume-calibrated dry-food measuring devices), especially for measuring small volumes.
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http://dx.doi.org/10.1136/vr.105319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902066PMC
November 2019

Cutaneous TRPV1 Neurons Trigger Protective Innate Type 17 Anticipatory Immunity.

Cell 2019 08 25;178(4):919-932.e14. Epub 2019 Jul 25.

Department of Dermatology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA; Pittsburgh Center for Pain Research, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address:

Cutaneous TRPV1 neurons directly sense noxious stimuli, inflammatory cytokines, and pathogen-associated molecules and are required for innate immunity against some skin pathogens. Important unanswered questions are whether TRPV1 neuron activation in isolation is sufficient to initiate innate immune responses and what is the biological function for TRPV1 neuron-initiated immune responses. We used TRPV1-Ai32 optogenetic mice and cutaneous light stimulation to activate cutaneous neurons in the absence of tissue damage or pathogen-associated products. We found that TRPV1 neuron activation was sufficient to elicit a local type 17 immune response that augmented host defense to C. albicans and S. aureus. Moreover, local neuron activation elicited type 17 responses and augmented host defense at adjacent, unstimulated skin through a nerve reflex arc. These data show the sufficiency of TRPV1 neuron activation for host defense and demonstrate the existence of functional anticipatory innate immunity at sites adjacent to infection that depends on antidromic neuron activation.
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http://dx.doi.org/10.1016/j.cell.2019.06.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788801PMC
August 2019

MicroRNA-guided regulation of heat stress response in wheat.

BMC Genomics 2019 Jun 13;20(1):488. Epub 2019 Jun 13.

Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada.

Background: With rising global temperature, understanding plants' adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed.

Results: Sequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins.

Conclusion: The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies.
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http://dx.doi.org/10.1186/s12864-019-5799-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567507PMC
June 2019

Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the mushroom body.

Dis Model Mech 2019 03 25;12(3). Epub 2019 Mar 25.

Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada

Technology has led to rapid progress in the identification of genes involved in neurodevelopmental disorders such as intellectual disability (ID), but our functional understanding of the causative genes is lagging. Here, we show that the SWI/SNF chromatin remodelling complex is one of the most over-represented cellular components disrupted in ID. We investigated the role of individual subunits of this large protein complex using targeted RNA interference in post-mitotic memory-forming neurons of the mushroom body (MB). Knockdown flies were tested for defects in MB morphology, short-term memory and long-term memory. Using this approach, we identified distinct roles for individual subunits of the SWI/SNF complex. Bap60, Snr1 and E(y)3 are required for pruning of the MBγ neurons during pupal morphogenesis, while Brm and Osa are required for survival of MBγ axons during ageing. We used the courtship conditioning assay to test the effect of MB-specific SWI/SNF knockdown on short- and long-term memory. Several subunits, including Brm, Bap60, Snr1 and E(y)3, were required in the MB for both short- and long-term memory. In contrast, Osa knockdown only reduced long-term memory. Our results suggest that individual components of the SWI/SNF complex have different roles in the regulation of structural plasticity, survival and functionality of post-mitotic MB neurons. This study highlights the many possible processes that might be disrupted in SWI/SNF-related ID disorders. Our broad phenotypic characterization provides a starting point for understanding SWI/SNF-mediated gene regulatory mechanisms that are important for development and function of post-mitotic neurons.
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http://dx.doi.org/10.1242/dmm.037325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451433PMC
March 2019

Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt's Farm, Cradle of Humankind (South Africa).

PeerJ 2019 14;7:e6202. Epub 2019 Jan 14.

Centre for Anthropological Research, University of Johannesburg, Johannesburg, Gauteng, South Africa.

Bolt's Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner's rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947-1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke's map to try and relocate the original fossil deposits. However, Peabody's map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody's original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (, ) and partial skeletons of the extinct felid . We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt's Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt's Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of in some pits implying ages of <2.3 Ma, whereas more primitive suids () hint at a terminal Pliocene age for other deposits. This study highlights that Bolt's Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material.
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http://dx.doi.org/10.7717/peerj.6202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336010PMC
January 2019

Mechanical properties of silicone based composites as a temperature insensitive ballistic backing material for quantifying back face deformation.

Forensic Sci Int 2018 Apr 31;285:1-12. Epub 2018 Jan 31.

U.S. Army Research Laboratory, 4600 Deer Creek Loop, Aberdeen Proving Ground, MD 21005, USA. Electronic address:

This paper describes a new witness material for quantifying the back face deformation (BFD) resulting from high rate impact of ballistic protective equipment. Accurate BFD quantification is critical for the assessment and certification of personal protective equipment, such as body armor and helmets, and ballistic evaluation. A common witness material is ballistic clay, specifically, Roma Plastilina No. 1 (RP1). RP1 must be heated to nearly 38°C to pass calibration, and used within a limited time frame to remain in calibration. RP1 also exhibits lot-to-lot variability and is sensitive to time, temperature, and handling procedures, which limits the BFD accuracy and reproducibility. A new silicone composite backing material (SCBM) was developed and tested side-by-side with heated RP1 using quasi-static indentation and compression, low velocity impact, spherical projectile penetration, and both soft and hard armor ballistic BFD measurements to compare their response over a broad range of strain rates and temperatures. The results demonstrate that SCBM mimics the heated RP1 response at room temperature and exhibits minimal temperature sensitivity. With additional optimization of the composition and processing, SCBM could be a drop-in replacement for RP1 that is used at room temperature during BFD quantification with minimal changes to the current RP1 handling protocols and infrastructure. It is anticipated that removing the heating requirement, and temperature-dependence, associated with RP1 will reduce test variability, simplify testing logistics, and enhance test range productivity.
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http://dx.doi.org/10.1016/j.forsciint.2018.01.014DOI Listing
April 2018

Identification of a novel synaptic protein, TMTC3, involved in periventricular nodular heterotopia with intellectual disability and epilepsy.

Hum Mol Genet 2017 11;26(21):4278-4289

Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada, N6A 5C1.

Defects in neuronal migration cause brain malformations, which are associated with intellectual disability (ID) and epilepsy. Using exome sequencing, we identified compound heterozygous variants (p.Arg71His and p. Leu729ThrfsTer6) in TMTC3, encoding transmembrane and tetratricopeptide repeat containing 3, in four siblings with nocturnal seizures and ID. Three of the four siblings have periventricular nodular heterotopia (PVNH), a common brain malformation caused by failure of neurons to migrate from the ventricular zone to the cortex. Expression analysis using patient-derived cells confirmed reduced TMTC3 transcript levels and loss of the TMTC3 protein compared to parental and control cells. As TMTC3 function is currently unexplored in the brain, we gathered support for a neurobiological role for TMTC3 by generating flies with post-mitotic neuron-specific knockdown of the highly conserved Drosophila melanogaster TMTC3 ortholog, CG4050/tmtc3. Neuron-specific knockdown of tmtc3 in flies resulted in increased susceptibility to induced seizures. Importantly, this phenotype was rescued by neuron-specific expression of human TMTC3, suggesting a role for TMTC3 in seizure biology. In addition, we observed co-localization of TMTC3 in the rat brain with vesicular GABA transporter (VGAT), a presynaptic marker for inhibitory synapses. TMTC3 is localized at VGAT positive pre-synaptic terminals and boutons in the rat hypothalamus and piriform cortex, suggesting a role for TMTC3 in the regulation of GABAergic inhibitory synapses. TMTC3 did not co-localize with Vglut2, a presynaptic marker for excitatory neurons. Our data identified TMTC3 as a synaptic protein that is involved in PVNH with ID and epilepsy, in addition to its previously described association with cobblestone lissencephaly.
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http://dx.doi.org/10.1093/hmg/ddx316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886076PMC
November 2017

Optimal Feedback Controlled Assembly of Perfect Crystals.

ACS Nano 2016 07 11;10(7):6791-8. Epub 2016 Jul 11.

Department of Chemical & Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.

Perfectly ordered states are targets in diverse molecular to microscale systems involving, for example, atomic clusters, protein folding, protein crystallization, nanoparticle superlattices, and colloidal crystals. However, there is no obvious approach to control the assembly of perfectly ordered global free energy minimum structures; near-equilibrium assembly is impractically slow, and faster out-of-equilibrium processes generally terminate in defective states. Here, we demonstrate the rapid and robust assembly of perfect crystals by navigating kinetic bottlenecks using closed-loop control of electric field mediated crystallization of colloidal particles. An optimal policy is computed with dynamic programming using a reaction coordinate based dynamic model. By tracking real-time stochastic particle configurations and adjusting applied fields via feedback, the evolution of unassembled particles is guided through polycrystalline states into single domain crystals. This approach to controlling the assembly of a target structure is based on general principles that make it applicable to a broad range of processes from nano- to microscales (where tuning a global thermodynamic variable yields temporal control over thermal sampling of different states via their relative free energies).
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http://dx.doi.org/10.1021/acsnano.6b02400DOI Listing
July 2016

Reconfigurable multi-scale colloidal assembly on excluded volume patterns.

Sci Rep 2015 Sep 2;5:13612. Epub 2015 Sep 2.

Chemical &Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218.

The ability to create multi-scale, periodic colloidal assemblies with unique properties is important to emerging applications. Dynamically manipulating colloidal structures via tunable kT-scale attraction can provide the opportunity to create particle-based nano- and microstructured materials that are reconfigurable. Here, we report a novel tactic to obtain reconfigurable, multi-scale, periodic colloidal assemblies by combining thermoresponsive depletant particles and patterned topographical features that, together, reversibly mediate local kT-scale depletion interactions. This method is demonstrated in optical microscopy experiments to produce colloidal microstructures that reconfigure between well-defined ordered structures and disordered fluid states as a function of temperature and pattern feature depth. These results are well described by Monte Carlo simulations using theoretical depletion potentials that include patterned excluded volume. Ultimately, the approach reported here can be extended to control the size, shape, orientation, and microstructure of colloidal assemblies on multiple lengths scales and on arbitrary pre-defined pattern templates.
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http://dx.doi.org/10.1038/srep13612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557032PMC
September 2015

Diversity within the genus Elymus (Poaceae: Triticeae) II: analyses of variation within 5S nrDNA restrict membership in the genus to species with StH genomes.

Mol Genet Genomics 2016 Feb 12;291(1):217-25. Epub 2015 Aug 12.

Ottawa-Carleton Institute of Biology, University of Ottawa, PO Box 450, Station A, Ottawa, ON, K1N 6N5, Canada.

The genus Elymus is a repository for a large number of species that have been difficult to classify by traditional techniques due to their remarkable levels of polymorphism. Following the genome analyses of Yen and Yang (Genus Elymus 5:58-362, 2013), we used sequences of the nr5SDNA to investigate diversity within those 24 species having St and H haplomes (Baum et al. Mol Genet Genomics 290:329-42, 2015) and for which the genome status was known. The present work extends this analysis to include eight species for which there was no information on genomic status. Our results show that these eight have nr5SDNA sequences that can be assigned to unit classes of orthologous sequences found in St and H haplomes, suggesting that the presence of St and H haplomes is characteristic of the genus. We then carried out a set of canonical discriminant analyses based on 247 DNA new sequences from these 8 species plus the 1054 sequences previously identified from 24 Elymus species. Sequences were analyzed to answer the following questions: Do the species integrate or are they different? Are the tetraploids different from the higher-ploid species? Are the species united within sections, or the same within regions? How do the species fare when divided according to sections? The main results of the canonical discriminant analyses are that the species are united within the tetraploids and within the hexaploids, within each region and within each section. In addition, a series of classificatory discriminant analyses showed that the identification tests are different, although not sufficiently useful for the discrimination of all the species. We also demonstrate the power of our approach by showing that the voucher for Elymus mobilis is not Elymus at all, but Leymus.
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http://dx.doi.org/10.1007/s00438-015-1096-5DOI Listing
February 2016

Direct Measurement of Macromolecule-Coated Colloid-Mucus Interactions.

Langmuir 2015 Aug 11;31(33):9076-85. Epub 2015 Aug 11.

Chemical & Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.

We report measurements of macromolecule-coated colloids interacting with mucus to understand colloidal particle diffusion near mucus-coated surfaces. Total internal reflection microscopy is used to measure colloids with adsorbed poly(ethylene glycol) (PEG), bovine serum albumin (BSA), and polyelectrolyte bilayers (PEB) interacting with mucus to obtain kT-scale energy landscapes and nanometer-scale diffusivity landscapes. Energy landscapes are quantified as a superposition of van der Waals, steric, and tethering potentials, and diffusivity landscapes are modeled by considering lubrication in the presence of permeable layers. PEG- and BSA-coated colloids have soft repulsion with mucus that could enable diffusion of small particles within mucus pores. PEB-coated colloids display attractive tethers to mucus that produce irreversible binding. Different interaction potentials for each particle coating confirm that the ζ-potential is not a successful predictor of particle-mucus interactions and diffusion. Diffusivity landscapes show thick mucus layers are permeable to the solvent and dominate particle-mucus hydrodynamic interactions relative to the thin, impermeable particle coatings. Our results show direct measurements and models to understand how particle coating properties (e.g., elasticity, porosity) control particle interactions and transport near mucus films to potentially aid the design of better particle-based therapeutics and diagnostics.
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http://dx.doi.org/10.1021/acs.langmuir.5b01460DOI Listing
August 2015

Modeling depletion mediated colloidal assembly on topographical patterns.

J Colloid Interface Sci 2015 Jul 6;449:270-8. Epub 2014 Dec 6.

Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, United States. Electronic address:

This work reports a model and Monte Carlo simulations of excluded volume mediated interactions between colloids and topographically patterned substrates in the presence of thermosensitive depletants. The model is matched to experiments to yield density, free energy, and potential energy landscapes that quantitatively capture particle microstructures varying from immobilized non-close packed configurations to random fluid states. A numerical model of local excluded volume affects is developed to enable computation of local depletion attraction in the presence of arbitrary geometries. Our findings demonstrate a quantitative modeling method to interpret and predict how surface patterns mediate local depletion interactions, which enables the design of colloidal based materials and devices.
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http://dx.doi.org/10.1016/j.jcis.2014.12.002DOI Listing
July 2015

Colloidal crystal grain boundary formation and motion.

Sci Rep 2014 Aug 20;4:6132. Epub 2014 Aug 20.

Chemical &Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218.

The ability to assemble nano- and micro- sized colloidal components into highly ordered configurations is often cited as the basis for developing advanced materials. However, the dynamics of stochastic grain boundary formation and motion have not been quantified, which limits the ability to control and anneal polycrystallinity in colloidal based materials. Here we use optical microscopy, Brownian Dynamic simulations, and a new dynamic analysis to study grain boundary motion in quasi-2D colloidal bicrystals formed within inhomogeneous AC electric fields. We introduce "low-dimensional" models using reaction coordinates for condensation and global order that capture first passage times between critical configurations at each applied voltage. The resulting models reveal that equal sized domains at a maximum misorientation angle show relaxation dominated by friction limited grain boundary diffusion; and in contrast, asymmetrically sized domains with less misorientation display much faster grain boundary migration due to significant thermodynamic driving forces. By quantifying such dynamics vs. compression (voltage), kinetic bottlenecks associated with slow grain boundary relaxation are understood, which can be used to guide the temporal assembly of defect-free single domain colloidal crystals.
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http://dx.doi.org/10.1038/srep06132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138518PMC
August 2014

Controlling colloidal particles with electric fields.

Langmuir 2014 Sep 19;30(36):10793-803. Epub 2014 Mar 19.

Chemical & Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.

In this instructional review, we discuss how to control individual colloids and ensembles of colloids using electric fields. We provide background on the electrokinetic transport mechanisms and kT-scale equilibrium colloidal interactions that enable such control. We also describe the experimental configurations, microscopy methods, image analyses, and material systems for which these mechanisms have been successfully employed. Methods are presented for creating various structures including colloidal chains, quasi-2D colloidal crystals, and 3D colloidal crystals. We also describe electric-field-mediated feedback control of the colloidal crystal size as well as colloidal crystal assembly and disassembly. Finally, we discuss future extensions of these methods that aim to incorporate accurate colloidal crystallization dynamic models into electric-field-mediated feedback control to allow rapid assembly, disassembly, and repair of defect-free colloidal structures.
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http://dx.doi.org/10.1021/la500178bDOI Listing
September 2014

Self-consistent colloidal energy and diffusivity landscapes in macromolecular solutions.

Langmuir 2013 Oct 27;29(40):12337-41. Epub 2013 Sep 27.

Chemical & Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.

We report a dynamic analysis to simultaneously measure colloidal forces and hydrodynamic interactions in the presence of both adsorbed and unadsorbed macromolecules. A Bayesian inference method is used to self-consistently obtain the position-dependent potential energy (i.e., energy landscape) and diffusivity (i.e., diffusivity landscape) from measured colloidal trajectories normal to a wall. Measurements are performed for particles and surfaces with adsorbed polyethylene oxide (PEO) copolymer as a function of unadsorbed PEO homopolymer concentration. Energy landscapes are well described by a steric repulsion between adsorbed brushes and depletion attraction due to unadsorbed macromolecules. Diffusivity landscapes show agreement with predicted short-range permeable brush models and long-range mobilities determined by the bulk solution viscosity. Lower than expected mobilities in the vicinity of overlapping depletion layers are attributed to interactions of adsorbed and unadsorbed macromolecules altering nonconservative lubrication forces.
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http://dx.doi.org/10.1021/la403261mDOI Listing
October 2013

Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the US Great Basin, China, and Armenia.

FEMS Microbiol Ecol 2013 Aug 11;85(2):283-92. Epub 2013 Apr 11.

School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA.

Despite its importance in the nitrogen cycle, little is known about nitrite oxidation at high temperatures. To bridge this gap, enrichment cultures were inoculated with sediment slurries from a variety of geothermal springs. While nitrite-oxidizing bacteria (NOB) were successfully enriched from seven hot springs located in US Great Basin, south-western China, and Armenia at ≤ 57.9 °C, all attempts to enrich NOB from > 10 hot springs at ≥ 61 °C failed. The stoichiometric conversion of nitrite to nitrate, chlorate sensitivity, and sensitivity to autoclaving all confirmed biological nitrite oxidation. Regardless of origin, all successful enrichments contained organisms with high 16S rRNA gene sequence identity (≥ 97%) with Nitrospira calida. In addition, Armenian enrichments also contained close relatives of Nitrospira moscoviensis. Physiological properties of all enrichments were similar, with a temperature optimum of 45-50 °C, yielding nitrite oxidation rates of 7.53 ± 1.20 to 23.0 ± 2.73 fmoles cell(-1) h(-1), and an upper temperature limit between 60 and 65 °C. The highest rates of NOB activity occurred with initial NO2 - concentrations of 0.5-0.75 mM; however, lower initial nitrite concentrations resulted in shorter lag times. The results presented here suggest a possible upper temperature limit of 60-65 °C for Nitrospira and demonstrate the wide geographic range of Nitrospira species in geothermal environments.
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http://dx.doi.org/10.1111/1574-6941.12117DOI Listing
August 2013

Depletion-mediated potentials and phase behavior for micelles, macromolecules, nanoparticles, and hydrogel particles.

Langmuir 2012 Oct 18;28(39):13816-23. Epub 2012 Sep 18.

Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.

We report a simple depletion potential that captures measured potentials and phase behavior for micrometer-sized colloids in the presence of unadsorbing charged micelles, charged nanoparticles, nonionic macromolecules, and nonionic hydrogel particles. Total internal reflection microscopy (TIRM) is used to measure net potentials between colloids and surfaces, and video microscopy (VM) is used to measure quasi-2D phase behavior in the same material systems. A modified Asakura-Oosawa (AO) depletion potential is developed to accurately quantify particle-wall potentials and interfacial crystallization via particle-particle potentials in Monte Carlo (MC) simulations. The modified AO potential includes effective depletant sizes, accurate osmotic equations of state, and partition coefficients. Partition coefficients are used as the sole adjustable fitting parameter, although an approach to their theoretical prediction from depletant density profiles is also presented. Our results demonstrate a model that accurately captures depletion interactions and phase behavior in a variety of material systems.
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http://dx.doi.org/10.1021/la302805nDOI Listing
October 2012

The metabolism of histamine in the Drosophila optic lobe involves an ommatidial pathway: β-alanine recycles through the retina.

J Exp Biol 2012 Apr;215(Pt 8):1399-411

Department of Psychology and Neuroscience, Life Sciences Centre, Dalhousie University, Halifax, Canada, B3H 4J1.

Flies recycle the photoreceptor neurotransmitter histamine by conjugating it to β-alanine to form β-alanyl-histamine (carcinine). The conjugation is regulated by Ebony, while Tan hydrolyses carcinine, releasing histamine and β-alanine. In Drosophila, β-alanine synthesis occurs either from uracil or from the decarboxylation of aspartate but detailed roles for the enzymes responsible remain unclear. Immunohistochemically detected β-alanine is present throughout the fly's entire brain, and is enhanced in the retina especially in the pseudocone, pigment and photoreceptor cells of the ommatidia. HPLC determinations reveal 10.7 ng of β-alanine in the wild-type head, roughly five times more than histamine. When wild-type flies drink uracil their head β-alanine increases more than after drinking l-aspartic acid, indicating the effectiveness of the uracil pathway. Mutants of black, which lack aspartate decarboxylase, cannot synthesize β-alanine from l-aspartate but can still synthesize it efficiently from uracil. Our findings demonstrate a novel function for pigment cells, which not only screen ommatidia from stray light but also store and transport β-alanine and carcinine. This role is consistent with a β-alanine-dependent histamine recycling pathway occurring not only in the photoreceptor terminals in the lamina neuropile, where carcinine occurs in marginal glia, but vertically via a long pathway that involves the retina. The lamina's marginal glia are also a hub involved in the storage and/or disposal of carcinine and β-alanine.
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http://dx.doi.org/10.1242/jeb.060699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3309881PMC
April 2012

Organization and metamorphosis of glia in the Drosophila visual system.

J Comp Neurol 2012 Jul;520(10):2067-85

Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS, Canada.

The visual system of Drosophila is an excellent model for determining the interactions that direct the differentiation of the nervous system's many unique cell types. Glia are essential not only in the development of the nervous system, but also in the function of those neurons with which they become associated in the adult. Given their role in visual system development and adult function we need to both accurately and reliably identify the different subtypes of glia, and to relate the glial subtypes in the larval brain to those previously described for the adult. We viewed driver expression in subsets of larval eye disc glia through the earliest stages of pupal development to reveal the counterparts of these cells in the adult. Two populations of glia exist in the lamina, the first neuropil of the adult optic lobe: those that arise from precursors in the eye-disc/optic stalk and those that arise from precursors in the brain. In both cases, a single larval source gives rise to at least three different types of adult glia. Furthermore, analysis of glial cell types in the second neuropil, the medulla, has identified at least four types of astrocyte-like (reticular) glia. Our clarification of the lamina's adult glia and identification of their larval origins, particularly the respective eye disc and larval brain contributions, begin to define developmental interactions which establish the different subtypes of glia.
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http://dx.doi.org/10.1002/cne.23071DOI Listing
July 2012

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae).

Genome 2010 Mar;53(3):180-202

Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Neatby Building, Ottawa, ON, Canada.

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host-parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.
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http://dx.doi.org/10.1139/g09-096DOI Listing
March 2010

The functional organisation of glia in the adult brain of Drosophila and other insects.

Prog Neurobiol 2010 Apr 29;90(4):471-97. Epub 2010 Jan 29.

Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, NS, Canada, B3H 4J1.

This review annotates and categorises the glia of adult Drosophila and other model insects and analyses the developmental origins of these in the Drosophila optic lobe. The functions of glia in the adult vary depending upon their sub-type and location in the brain. The task of annotating glia is essentially complete only for the glia of the fly's lamina, which comprise: two types of surface glia-the pseudocartridge and fenestrated glia; two types of cortex glia-the distal and proximal satellite glia; and two types of neuropile glia-the epithelial and marginal glia. We advocate that the term subretinal glia, as used to refer to both pseudocartridge and fenestrated glia, be abandoned. Other neuropiles contain similar glial subtypes, but other than the antennal lobes these have not been described in detail. Surface glia form the blood brain barrier, regulating the flow of substances into and out of the nervous system, both for the brain as a whole and the optic neuropiles in particular. Cortex glia provide a second level of barrier, wrapping axon fascicles and isolating neuronal cell bodies both from neighbouring brain regions and from their underlying neuropiles. Neuropile glia can be generated in the adult and a subtype, ensheathing glia, are responsible for cleaning up cellular debris during Wallerian degeneration. Both the neuropile ensheathing and astrocyte-like glia may be involved in clearing neurotransmitters from the extracellular space, thus modifying the levels of histamine, glutamate and possibly dopamine at the synapse to ultimately affect behaviour.
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http://dx.doi.org/10.1016/j.pneurobio.2010.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847375PMC
April 2010

Transcriptional orchestration of the regulated secretory pathway in neurons by the bHLH protein DIMM.

Curr Biol 2010 Jan 31;20(1):9-18. Epub 2009 Dec 31.

Department of Psychology, Life Sciences Centre, Dalhousie University, Halifax, NS B3H 4J1, Canada.

Background: The Drosophila basic helix-loop-helix (bHLH) gene dimmed (dimm) promotes a neurosecretory/neuroendocrine phenotype in cells but is not associated with specific neuropeptides or neurohormones. Rather, it is expressed by those peptidergic neurons that project long axons and appear to produce large amounts of secretory peptides. Here, we genetically transform nonpeptidergic neurons in Drosophila to study DIMM's action mechanisms.

Results: Nonpeptidergic neurons normally fail to accumulate ectopic neuropeptides. We now show that they will do so when they are also forced to express ectopic DIMM. Furthermore, mass spectrometry shows that photoreceptors, which are normally nonpeptidergic, fail to process an ectopic neuropeptide precursor to make bioactive peptides but will do so efficiently when DIMM is co-misexpressed. Likewise, photoreceptors, which normally package the fast neurotransmitter histamine within small clear synaptic vesicles, produce numerous large dense-core vesicles (LDCVs) when they misexpress DIMM. These novel LDCVs accumulate ectopic neuropeptide when photoreceptors co-misexpress a neuropeptide transgene. DIMM-expressing photoreceptors no longer accumulate histamine and lose synaptic organelles critical to their normal physiology.

Conclusions: These findings indicate that DIMM suppresses conventional fast neurotransmission and promotes peptidergic neurosecretory properties. We conclude that DIMM normally provides a comprehensive transcriptional control to direct the differentiation of dedicated neuroendocrine neurons.
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http://dx.doi.org/10.1016/j.cub.2009.11.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831871PMC
January 2010

Photoreceptor neurons find new synaptic targets when misdirected by overexpressing runt in Drosophila.

J Neurosci 2009 Jan;29(3):828-41

Department of Biology, Life Sciences Centre, Dalhousie University, Halifax, Nova Scotia, Canada.

As a neuron differentiates, it adopts a suite of features specific to its particular type. Fly photoreceptors are of two types: R1-R6, which innervate the first optic neuropile, the lamina; and R7-R8, which innervate the second, the medulla. Photoreceptors R1-R6 normally have large light-absorbing rhabdomeres, express Rhodopsin1, and have synaptic terminals that innervate the lamina. In Drosophila melanogaster, we used the yeast GAL4/UAS system to drive exogenous expression of the transcription factor Runt in subsets of photoreceptors, resulting in aberrant axonal pathfinding and, ultimately, incorrect targeting of R1-R6 synaptic terminals to the medulla, normally occupied by terminals from R7 and R8. Even when subsets of their normal R1-R6 photoreceptor inputs penetrate the lamina, to terminate in the medulla, normal target cells within the lamina persist and maintain expression of cell-specific markers. Some R1-R6 photoreceptors form reciprocal synaptic inputs with their normal lamina targets, whereas supernumerary terminals targeted to the medulla also form synapses. At both sites, tetrad synapses form, with four postsynaptic elements at each release site, the usual number in the lamina. In addition, the terminals at both sites are invaginated by profiles of glia, at organelles called capitate projections, which in the lamina are photoreceptor sites of vesicle endocytosis. The size and shape of the capitate projection heads are identical at both lamina and medulla sites, although those in the medulla are ectopic and receive invaginations from foreign glia. This uniformity indicates the cell-autonomous determination of the architecture of its synaptic organelles by the presynaptic photoreceptor terminal.
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http://dx.doi.org/10.1523/JNEUROSCI.1022-08.2009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823086PMC
January 2009

Drosophila tan encodes a novel hydrolase required in pigmentation and vision.

PLoS Genet 2005 Nov 18;1(5):e63. Epub 2005 Nov 18.

Department of Ecology and Evolution, State University of New York, Stony Brook, New York, United States of America.

Many proteins are used repeatedly in development, but usually the function of the protein is similar in the different contexts. Here we report that the classical Drosophila melanogaster locus tan encodes a novel enzyme required for two very different cellular functions: hydrolysis of N-beta-alanyl dopamine (NBAD) to dopamine during cuticular melanization, and hydrolysis of carcinine to histamine in the metabolism of photoreceptor neurotransmitter. We characterized two tan-like P-element insertions that failed to complement classical tan mutations. Both are inserted in the 5' untranslated region of the previously uncharacterized gene CG12120, a putative homolog of fungal isopenicillin-N N-acyltransferase (EC 2.3.1.164). Both P insertions showed abnormally low transcription of the CG12120 mRNA. Ectopic CG12120 expression rescued tan mutant pigmentation phenotypes and caused the production of striking black melanin patterns. Electroretinogram and head histamine assays indicated that CG12120 is required for hydrolysis of carcinine to histamine, which is required for histaminergic neurotransmission. Recombinant CG12120 protein efficiently hydrolyzed both NBAD to dopamine and carcinine to histamine. We conclude that D. melanogaster CG12120 corresponds to tan. This is, to our knowledge, the first molecular genetic characterization of NBAD hydrolase and carcinine hydrolase activity in any organism and is central to the understanding of pigmentation and photoreceptor function.
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http://dx.doi.org/10.1371/journal.pgen.0010063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1285064PMC
November 2005

The extraretinal eyelet of Drosophila: development, ultrastructure, and putative circadian function.

J Neurosci 2002 Nov;22(21):9255-66

Zoological Institute/Animal Physiology, University of Tübingen, D-72076 Tübingen, Germany.

Circadian rhythms can be entrained by light to follow the daily solar cycle. In Drosophila melanogaster a pair of extraretinal eyelets expressing immunoreactivity to Rhodopsin 6 each contains four photoreceptors located beneath the posterior margin of the compound eye. Their axons project to the region of the pacemaker center in the brain with a trajectory resembling that of Bolwig's organ, the visual organ of the larva. A lacZ reporter line driven by an upstream fragment of the developmental gap gene Krüppel is a specific enhancer element for Bolwig's organ. Expression of immunoreactivity to the product of lacZ in Bolwig's organ persists through pupal metamorphosis and survives in the adult eyelet. We thus demonstrate that eyelet derives from the 12 photoreceptors of Bolwig's organ, which entrain circadian rhythmicity in the larva. Double labeling with anti-pigment-dispersing hormone shows that the terminals of Bolwig's nerve differentiate during metamorphosis in close temporal and spatial relationship to the ventral lateral neurons (LN(v)), which are essential to express circadian rhythmicity in the adult. Bolwig's organ also expresses immunoreactivity to Rhodopsin 6, which thus continues in eyelet. We compared action spectra of entrainment in different fly strains: in flies lacking compound eyes but retaining eyelet (so(1)), lacking both compound eyes and eyelet (so(1);gl(60j)), and retaining eyelet but lacking compound eyes as well as cryptochrome (so(1);cry(b)). Responses to phase shifts suggest that, in the absence of compound eyes, eyelet together with cryptochrome mainly mediates phase delays. Thus a functional role in circadian entrainment first found in Bolwig's organ in the larva is retained in eyelet, the adult remnant of Bolwig's organ, even in the face of metamorphic restructuring.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6758046PMC
November 2002