Identification of a putative germ plasm in the amphipod Parhyale hawaiensis

Background: Specification of the germ line is an essential event during the embryonic development of sexually reproducing animals, as germ line cells are uniquely capable of giving rise to the next generation. Animal germ cells arise through either inheritance of a specialized, maternally supplied cytoplasm called 'germ plasm’ or though inductive signaling by somatic cells. Our understanding of germ cell determination is based largely on a small number of model organisms. To better understand the evolution of germ cell specification, we are investigating this process in the amphipod crustacean Parhyale hawaiensis. Experimental evidence from previous studies demonstrated that Parhyale germ cells are specified through inheritance of a maternally supplied cytoplasmic determinant; however, this determinant has not been identified. Results: Here we show that the one-cell stage Parhyale embryo has a distinct cytoplasmic region that can be identified by morphology as well as the localization of germ line-associated RNAs. Removal of this cytoplasmic region results in a loss of embryonic germ cells, supporting the hypothesis that it is required for specification of the germ line. Surprisingly, we found that removal of this distinct cytoplasm also results in aberrant somatic cell behaviors, as embryos fail to gastrulate. Conclusions: Parhyale hawaiensis embryos have a specialized cytoplasm that is required for specification of the germ line. Our data provide the first functional evidence of a putative germ plasm in a crustacean and provide the basis for comparative functional analysis of germ plasm formation within non-insect arthropods

ASGARD: An Open-Access Database of Annotated Transcriptomes for Emerging Model Arthropod Species

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics.Organismic and Evolutionary Biolog

Dynamics of a tunable superfluid junction

We study the population dynamics of a Bose-Einstein condensate in a double-well potential throughout the crossover from Josephson dynamics to hydrodynamics. At barriers higher than the chemical potential, we observe slow oscillations well described by a Josephson model. In the limit of low barriers, the fundamental frequency agrees with a simple hydrodynamic model, but we also observe a second, higher frequency. A full numerical simulation of the Gross-Pitaevskii equation giving the frequencies and amplitudes of the observed modes between these two limits is compared to the data and is used to understand the origin of the higher mode. Implications for trapped matter-wave interferometers are discussed.Comment: 8 pages, 7 figures; v3: Journal reference added, minor changes to tex

Dual-species quantum degeneracy of potassium-40 and rubidium-87 on an atom chip

In this article we review our recent experiments with a 40K-87Rb mixture. We demonstrate rapid sympathetic cooling of a 40K-87Rb mixture to dual quantum degeneracy on an atom chip. We also provide details on efficient BEC production, species-selective magnetic confinement, and progress toward integration of an optical lattice with an atom chip. The efficiency of our evaporation allows us to reach dual degeneracy after just 6 s of evaporation - more rapidly than in conventional magnetic traps. When optimizing evaporative cooling for efficient evaporation of 87Rb alone we achieve BEC after just 4 s of evaporation and an 8 s total cycle time.Comment: 8 pages, 4 figures. To be published in the Proceedings of the 20th International Conference on Atomic Physics, 2006 (Innsbruck, Austria

Evidence against a Germ Plasm in the Milkweed Bug Oncopeltus fasciatus, a Hemimetabolous Insect

Primordial germ cell (PGC) formation in holometabolous insects like Drosophila melanogaster relies on maternally synthesised germ cell determinants that are asymmetrically localised to the oocyte posterior cortex. Embryonic nuclei that inherit this "germ plasm" acquire PGC fate. In contrast, historical studies of basally branching insects (Hemimetabola) suggest that a maternal requirement for germ line genes in PGC specification may be a derived character confined principally to Holometabola. However, there have been remarkably few investigations of germ line gene expression and function in hemimetabolous insects. Here we characterise PGC formation in the milkweed bug Oncopeltus fasciatus, a member of the sister group to Holometabola, thus providing an important evolutionary comparison to members of this clade. We examine the transcript distribution of orthologues of 19 Drosophila germ cell and/or germ plasm marker genes, and show that none of them localise asymmetrically within Oncopeltus oocytes or early embryos. Using multiple molecular and cytological criteria we provide evidence that PGCs form after cellularisation at the site of gastrulation. Functional studies of vasa and tudor reveal that these genes are not required for germ cell formation, but that vasa is required in adult males for spermatogenesis. Taken together, our results provide evidence that Oncopeltus germ cells may form in the absence of germ plasm, consistent with the hypothesis that germ plasm is a derived strategy of germ cell specification in insects.Organismic and Evolutionary Biolog

Three-dimensional character of atom-chip-based rf-dressed potentials

We experimentally investigate the properties of radio-frequency-dressed potentials for Bose-Einstein condensates on atom chips. The three-dimensional potential forms a connected pair of parallel waveguides. We show that rf-dressed potentials are robust against the effect of small magnetic-field variations on the trap potential. Long-lived dipole oscillations of condensates induced in the rf-dressed potentials can be tuned to a remarkably low damping rate. We study a beam-splitter for Bose-Einstein condensates and show that a propagating condensate can be dynamically split in two vertically separated parts and guided along two paths. The effect of gravity on the potential can be tuned and compensated for using a rf-field gradient.Comment: 9 pages, 7 figure

RF spectroscopy in a resonant RF-dressed trap

We study the spectroscopy of atoms dressed by a resonant radiofrequency (RF) field inside an inhomogeneous magnetic field and confined in the resulting adiabatic potential. The spectroscopic probe is a second, weak, RF field. The observed line shape is related to the temperature of the trapped cloud. We demonstrate evaporative cooling of the RF-dressed atoms by sweeping the frequency of the second RF field around the Rabi frequency of the dressing field.Comment: 7 figures, 8 pages; to appear in J. Phys.

Fermions on atom chips

We review our recent and ongoing work with Fermi gases on an atom chip. After reviewing some statistical and thermodynamic properties of the ideal, non-interacting Fermi gas, and a brief description of our atom chip and its capabilities, we discuss our experimental approach to producing a potassium-40 degenerate Fermi gas (DFG) using sympathetic cooling by a rubidium-87 Bose-Einstein condensate on an atom chip. In doing so, we describe the factors affecting the loading efficiency of the atom chip microtrap. This is followed by a discussion of species selectivity in radio frequency manipulation of the Bose-Fermi mixture, which we explore in the context of sympathetic evaporative cooling and radio-frequency dressed adiabatic double-well potentials. Next, we describe the incorporation of a crossed-beam dipole trap into the atom chip setup, in which we generate and manipulate strongly interacting spin mixtures of potassium-40. Finally, we conclude with a brief discussion of future research directions with DFGs and atom chips.Comment: 33 pages, 10 figures. This article is to be included in a forthcoming, broader volume on atom chips; ISBN 978-3-527-40755-2. Wiley-VCH, Weinheim, German

Subdivision of arthropod cap-n-collar expression domains is restricted to Mandibulata

Background: The monophyly of Mandibulata - the division of arthropods uniting pancrustaceans and myriapods - is consistent with several morphological characters, such as the presence of sensory appendages called antennae and the eponymous biting appendage, the mandible. Functional studies have demonstrated that the patterning of the mandible requires the activity of the Hox gene Deformed and the transcription factor cap-n-collar (cnc) in at least two holometabolous insects: the fruit fly Drosophila melanogaster and the beetle Tribolium castaneum. Expression patterns of cnc from two non-holometabolous insects and a millipede have suggested conservation of the labral and mandibular domains within Mandibulata. However, the activity of cnc is unknown in crustaceans and chelicerates, precluding understanding of a complete scenario for the evolution of patterning of this appendage within arthropods. To redress these lacunae, here we investigate the gene expression of the ortholog of cnc in Parhyale hawaiensis, a malacostracan crustacean, and two chelicerates: the harvestman Phalangium opilio, and the scorpion Centruroides sculpturatus. Results: In the crustacean P. hawaiensis, the segmental expression of Ph-cnc is the same as that reported previously in hexapods and myriapods, with two distinct head domains in the labrum and the mandibular segment. In contrast, Po-cnc and Cs-cnc expression is not enriched in the labrum of either chelicerate, but instead is expressed at comparable levels in all appendages. In further contrast to mandibulate orthologs, the expression domain of Po-cnc posterior to the labrum is not confined within the expression domain of Po-Dfd. Conclusions: Expression data from two chelicerate outgroup taxa suggest that the signature two-domain head expression pattern of cnc evolved at the base of Mandibulata. The observation of the archetypal labral and mandibular segment domains in a crustacean exemplar supports the synapomorphic nature of mandibulate cnc expression. The broader expression of Po-cnc with respect to Po-Dfd in chelicerates further suggests that the regulation of cnc by Dfd was also acquired at the base of Mandibulata. To test this hypothesis, future studies examining panarthropod cnc evolution should investigate expression of the cnc ortholog in arthropod outgroups, such as Onychophora and Tardigrada

Distal-less and Dachshund Pattern both Plesiomorphic and Apomorphic Structures in Chelicerates: RNA Interference in the Harvestman Phalangium opilio (Opiliones)

The discovery of genetic mechanisms that can transform a morphological structure from a plesiomorphic (=primitive) state to an apomorphic (=derived) one is a cardinal objective of evolutionary developmental biology. However, this objective is often impeded for many lineages of interest by limitations in taxonomic sampling, genomic resources, or functional genetic methods. In order to investigate the evolution of appendage morphology within Chelicerata, the putative sister group of the remaining arthropods, we developed an RNA interference (RNAi) protocol for the harvestman Phalangium opilio. We silenced the leg gap genes Distal-less(Dll) and dachshund (dac) in the harvestman via zygotic injections of double-stranded RNA, and used in situ hybridization to confirm RNAi efficacy. Consistent with the conserved roles of these genes in patterning the proximo-distal axis of arthropod appendages, we observed that embryos injected with Dll dsRNA lacked distal parts of appendages and appendage-like structures, such as the labrum, the chelicerae, the pedipalps, and the walking legs, whereas embryos injected with dac dsRNA lacked the medial podomeres femur and patella in the pedipalps and walking legs. In addition, we detected a role for these genes in patterning structures that do not occur in well-established chelicerate models (spiders and mites). Dll RNAi additionally results in loss of the preoral chamber, which is formed from pedipalpal and leg coxapophyses, and the ocularium, a dorsal outgrowth bearing the eyes. In one case, we observed that an embryo injected with dac dsRNA lacked the proximal segment of the chelicera, a plesiomorphic podomere that expresses dac in wild type embryos. This may support the hypothesis that loss of the cheliceral dac domain underlies the transition to the two-segmented chelicera of derived arachnids.Organismic and Evolutionary Biolog