SQUID Structures Research Articles

DNA Barcoding on Indian Ocean Squid, <I>Uroteuthis duvaucelii</I> (D’Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia

Highlight ResearchThe possibility of U. duvauceli be a polymorph cryptic species is further reinforced by the results of the present study.Phylogenetic analysis showed two separate clusters though did not perfectly segregate north to the south waters.Individuals in cluster II from the south coast showed the highest polymorphism levels by 40 segregating sites (S), compared to only 2-4 sites in that of cluster IFrequencies of A, C, G, and T in mitochondrial DNA of all specimens skewed toward A and T, with T being the most preferred and G being the least preferred nucleotideAll specimens showed no amino acid frequency for glutamic acid. Further, all four individuals in cluster II (south coast) were also have no amino acid frequencies for aspartic acid and valine as well.AbstractUroteuthis duvauceli (D’ Orbigny, 1835) also known as the Indian Ocean Squid is a highly important commercial marine organism along the Java coast, Indonesia. Based on genetic variation this species-complex are polymorphic and cryptic. In the present study, the genetic diversity and stock structure of loliginid squid U. duvauceli is investigated using a mitochondrial gene cytochrome oxidase subunit I (COI). Samples were collected by hand-jigging onboard of an 8hp small fisher-boat equipped with a few lamps during May to August 2015, May 2016 and August to November 2018. Sample collection started at dusk until midnight. The attractor was a weighed-quill attached to nylon string, manually immersed into the water and pulled quickly and continuously for about 3-5 minutes at each effort. The determination was conducted with BLAST. Phylogenetic analysis showed two separate clusters with 100% bootstrap value, in which cluster II from Palabuhanratu has divergences of 5.9 - 7.0%, compared to cluster I. Genetic variations exist within and among individuals over the locations. Palabuhanratu individuals have the highest polymorphism levels compared to other locations as shown by 40 segregating sites (S). Frequencies of A, C, G, and T in mtDNA of the 20 specimens U. duvauceli are biased toward A and T, with T being the most favoured and G being the least favoured nucleotide. All specimen showed no amino acid frequency for glutamic acid and all four individuals in cluster II (south coast) also have no amino acid frequencies for aspartic acid and valine as well.

Van der Waals ferromagnetic Josephson junctions

Superconductor-ferromagnet interfaces in two-dimensional heterostructures present a unique opportunity to study the interplay between superconductivity and ferromagnetism. The realization of such nanoscale heterostructures in van der Waals (vdW) crystals remains largely unexplored due to the challenge of making atomically-sharp interfaces from their layered structures. Here, we build a vdW ferromagnetic Josephson junction (JJ) by inserting a few-layer ferromagnetic insulator Cr2Ge2Te6 into two layers of superconductor NbSe2. The critical current and corresponding junction resistance exhibit a hysteretic and oscillatory behavior against in-plane magnetic fields, manifesting itself as a strong Josephson coupling state. Also, we observe a central minimum of critical current in some JJ devices as well as a nontrivial phase shift in SQUID structures, evidencing the coexistence of 0 and π phase in the junction region. Our study paves the way to exploring sensitive probes of weak magnetism and multifunctional building-blocks for phase-related superconducting circuits using vdW heterostructures.

Effects of hydroxyl radical induced oxidation on water holding capacity and protein structure of jumbo squid (Dosidicus gigas) mantle

SummaryProtein oxidation is considered as an important issue in food preservation process. In the present study, the potential influence of protein oxidation on water holding capacity and protein structure of jumbo squid (Dosidicus gigas) mantle was investigated. After the hydroxyl radical oxidation, it was found that the carbonyl, surface hydrophobicity and dityrosine content of myofibrillar protein significantly increased (P < 0.05), while the content of total sulphydryl decreased significantly (P < 0.01). Meanwhile, the fluorescence intensity of squid was weakened, and the maximum absorption peak of fluorescence red shift as the H2O2 concentration increased. The sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS‐PAGE) showed that not only the protein cross‐linking but also degradation could have occurred. The content of α‐helix decreased, the content of β‐sheet, β‐turn and the unordered structures increased after oxidation. In addition, oxidation resulted in a decrease in water holding capacity. Taken together, oxidation resulted in the damage of the myofibrillar structure, the increase in muscle loss rate and the decrease in water holding capacity.

Development of Magnetization Measurement Devices Using Micro-dc-SQUIDs and a Sr$$_2$$RuO$$_4$$ Microplate

We developed high-sensitivity magnetization measurement devices composed of micro-dc-SQUIDs and a superconducting Sr\(_2\)RuO\(_4\) microplate, aiming to investigate novel magnetic properties related to a spin-triplet chiral p-wave superconductor with a mesoscopic size. Micron-sized dc-SQUID was fabricated by thin Al electrodes, and the SQUID structure was improved to prevent magnetic fluxes from intruding into SQUID electrodes. A Sr\(_2\)RuO\(_4\) superconducting microplate was fabricated into the size as small as the SQUID loop using a focused ion beam and directly mounted on the SQUID with precise positioning for high-sensitivity magnetization measurements. In the preliminary magnetization measurements of this device, we observed vortices trapped into the plate and thus the lower critical field. The improved magnetization measurement device developed to exclude undesirable flux intrusion successfully enabled high-sensitivity detection of quantized vortex.

Flux qubit in a dc SQUID with the 4π period Josephson effect

We propose a superconducting flux qubit in a dc SQUID structure, formed by a conventional insulator Josephson junction and a topological nanowire Josephson junction with Majorana bound states. The zero-energy Majorana bound states transport 4π period Josephson currents in the nanowire junction. The interplay between this 4π period Josephson effect and the convectional 2π period Josephson effect in the insulator junction induces a double-well potential energy landscape in the SQUID. As a result, the two lowest-energy levels of the SQUID are isolated from the other levels. These two levels show counterpropagating supercurrents, thus can be used as a flux qubit. We reveal that this flux qubit has the merits of stability to external noises, tolerance to the deviation of system parameters, and scalability to large numbers. Furthermore, we demonstrate how to couple this flux qubit with the Majorana qubit by tuning the junction parameters, and how to use this coupling to manipulate the Majorana qubit.

Superconducting transition of Ru in SQUIDs with Nb/Ru/Sr2RuO4 junctions

We have measured transport properties and magnetic responses of direct current superconducting quantum interference devices(dc-SQUIDs) with Nb/Ru/Sr2RuO4 junctions on the same Ru inclusion of a Sr2RuO4-Ru eutectic crystal. We observed a superconducting transition of the Ru at 0.50 K and another transition with anomalous interference patterns of the SQUID at 0.40 K. The second transition led to change of the SQUID structure due to energy competition of alternative supercurrent paths. Phase shifts of the peak of the Fraunhofer diffraction pattern were observed below the transition temperatures, implying topological effects due to a chiral p-wave state or its competition with a s-wave state.

Nanoscale multifunctional sensor formed by a Ni nanotube and a scanning Nb nanoSQUID

Nanoscale magnets might form the building blocks of next generation memories. To explore their functionality, magnetic sensing at the nanoscale is key. We present a multifunctional combination of a scanning nanometer-sized superconducting quantum interference device (nanoSQUID) and a Ni nanotube attached to an ultrasoft cantilever as a magnetic tip. We map out and analyze the magnetic coupling between the Ni tube and the Nb nanoSQUID, demonstrate imaging of an Abrikosov vortex trapped in the SQUID structure - which is important in ruling out spurious magnetic signals - and reveal the high potential of the nanoSQUID as an ultrasensitive displacement detector. Our results open a new avenue for fundamental studies of nanoscale magnetism and superconductivity.

Trace elemental patterns in Humboldt squid statoliths from three geographic regions

Statolith trace elemental concentrations can be used as natural tracers to better understand life history and stock structure of squid. A highly variable Humboldt squid population was targeted to determine if ontogenic patterns could be revealed and to compare variations among squid collected from three geographic areas. Statoliths from Humboldt squid collected off Westport, WA; Oceanside, CA; and the Galapagos Islands were sampled for ten trace elements using laser ablation inductively coupled plasma mass spectrometry. Similar patterns were found for some elements despite geographic collection site distances indicating a potential to explain ontogenic shifts experienced by this species. Other elements displayed high variation in spatial pattern, which suggests the potential to distinguish among the squid collected from the three geographic regions and better understand stock structure. Within the California and Washington squid, eight of the elements varied in relation to calcium across the statolith with only yttrium and zirconium remaining statistically invariant. In addition to these two elements, copper and zinc also did not vary significantly across the statoliths collected from Galapagos squid. All elements demonstrate potential to influence a multivariate elemental fingerprint, which may provide a useful measure of population discrimination needed for stock assessment.

Interannual Variability in Mantle Length Structure, Recruitment, and Sex Ratio of Jumbo Squid,Dosidicus gigas, in the Central Gulf of California, Mexico

Changes in the number and abundance of the cohorts of jumbo squid are a demographic response associated with high variability in recruitment, and have implications for availability and accessibility to the fishing fleets. In this study, we analyzed the interannual changes in the size structure, recruitment, and sex ratio of jumbo squid Dosidicus gigas in the central Gulf of California, Mexico. Data were analyzed for the 2000 to 2009 fishing seasons (from March to November). The biological data were collected biweekly at the port of Santa Rosalía, Baja California Sur, during each fishing season. We recorded mantle length and mantle weight, and sex (male or female) was identified from morphochromatic properties of fresh gonads. We concluded that the mantle length structure of jumbo squid changed between 1 cohort and 3 cohorts from 2000 to 2009. In the study zone, the presence of 2 cohorts is common. The species shows positive allometric growth, and the females are more abundant than the males in the region. The comparison between the most important fishing grounds in the central Gulf of California (Santa Rosalia and Guaymas) showed similar patterns, such as the number of cohorts, sex ratios, growth pattern, and migration pattern identified between both coasts. We believe that this could be evidence of one population that is widely distributed in the central Gulf of California.

Interannual variability in size structure, age, and growth of jumbo squid (Dosidicus gigas) assessed by modal progression analysis

Abstract Keyl, F., Argüelles, J., and Tafur, R. 2011. Interannual variability in size structure, age, and growth of jumbo squid (Dosidicus gigas) assessed by modal progression analysis. – ICES Journal of Marine Science, 68: . A range of growth rates, longevity, maximum size, and number of annual cohorts have been documented for jumbo squid (Dosidicus gigas). Genetic and phenotypic plasticity have been mentioned as possible sources of the differences in maximum sizes. Here, a large dataset on length frequencies derived from the industrial jig fishery for the species off Peru from 1991 to 2007 was corrected for observation bias introduced by the fishing gear and used to analyse growth-related parameters by modal progression analysis (MPA). Mean growth rates of 33 cohorts varied interannually (11–44 mm month−1), as did longevity (11.1–32.1 months) and mean maximum size (273–1024 mm). Intra-annual difference in growth parameters was not significant. The number of cohorts per year fluctuated between 0 and 6. Fast-growing cohorts with medium longevity and large terminal size were found during moderately cool periods, and long-lived, slow-growing cohorts with small terminal size during extreme ecosystem conditions (El Niño and La Niña). The application of MPA to cephalopod populations has been rejected before, but the results presented suggest that a modified approach is appropriate if it allows for varying growth parameters and includes a correction for observation bias.

Crystal structure of squid rhodopsin

Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a G(q)-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cbeta. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 A resolution. Among seven transmembrane alpha-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of G(q)-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom.

Variability in the population structure of jumbo squid (Dosidicus gigas) in Santa Rosalía, central Gulf of California

Se describió la estructura poblacional del calamar gigante (Dosidicus gigas) en el área de Santa Rosalía (región central del Golfo de California) durante 2003 y 2004 y se analizó la variabilidad interanual en la estructura de tallas durante un periodo más amplio, de 1996|00E2|??2004 (excepto 2000|00E2|??2002). Los resultados evidenciaron claras diferencias en la madurez sexual y en la estructura de tallas, tanto de machos así como de hembras, entre 2003 y 2004. La población de calamar gigante observada en la temporada de pesca de 2003 reflejó altas proporciones de individuos maduros y de gran tamaño, mientras que la observada en 2004 estuvo compuesta mayoritariamente por individuos sexualmente inmaduros y de menor tamaño. Al expandir nuestro periodo de estudio se observó la existencia de una fuerte variabilidad interanual en la estructura de tallas del calamar gigante dentro del Golfo de California, lo cual también se vio reflejado en la talla de madurez. Los cambios en la estructura poblacional del calamar gigante parecen estar relacionados no sólo con la ocurrencia de eventos El Niño sino también con la intensidad o magnitud de los mismos. Por tal motivo se recomienda tener en cuenta esta variabilidad al momento de implementar cada año la estrategia de manejo a utilizar en la pesquería de calamar gigante del Golfo de California. Palabras clave: calamar gigante, Dosidicus gigas, estructura poblacional, variabilidad interanual, Golfo de California.
 
 This study describes the population structure of jumbo squid (Dosidicus gigas) in the area of Santa Rosalía (central Gulf of California) during the years 2003 and 2004, and analyzes the interannual variability in the size structure over a wider time period, 1996|00E2|??2004 (except 2000|00E2|??2002). The results revealed clear differences in the size structure and sexual maturity of males and females between 2003 and 2004. The jumbo squid population observed during the 2003 fishing season showed a high proportion of large and sexually mature individuals, whereas most specimens sampled during 2004 were smaller and immature. Expanding our time period, we observed a strong interannual variability in the size structure of jumbo squid within the Gulf of California, which was also reflected in the size at maturity. These changes in the population structure seem to be related to the occurrence and intensity of El Niño events. We recommend taking this variability into account at the beginning of each fishing season when the authorities establish the management strategy for the jumbo squid fishery in the Gulf of California.

Spatial patterns in the biology of the chokka squid, Loligo reynaudii on the Agulhas Bank, South Africa

Although migration patterns for various life history stages of the chokka squid (Loligo reynaudii) have been previously presented, there has been limited comparison of spatial variation in biological parameters. Based on data from research surveys; size ranges of juveniles, subadults and adults on the Agulhas Bank were estimated and presented spatially. The bulk of the results appear to largely support the current acceptance of the life cycle with an annual pattern of squid hatching in the east, migrating westwards to offshore feeding grounds on the Central and Western Agulhas Bank and the west coast and subsequent return migration to the eastern inshore areas to spawn. The number of adult animals in deeper water, particularly in autumn in the central study area probably represents squid spawning in deeper waters and over a greater area than is currently targeted by the fishery. The distribution of life history stages and different feeding areas does not rule out the possibility that discrete populations of L. reynaudii with different biological characteristics inhabit the western and eastern regions of the Agulhas Bank. In this hypothesis, some mixing of the populations does occur but generally squid from the western Agulhas Bank may occur in smaller numbers, grow more slowly and mature at a larger size. Spawning occurs on the western portion of the Agulhas Bank, and juveniles grow and mature on the west coast and the central Agulhas Bank. Future research requirements include the elucidation of the age structure of chokka squid both spatially and temporally, and a comparison of the statolith chemistry and genetic characterisation between adults from different spawning areas across the Agulhas Bank.

Population genetic structure of jumbo squid ( Dosidicus gigas) evaluated by RAPD analysis

The jumbo squid ( Dosidicus gigas) supports important fisheries, with the maximum landings being recorded in Mexico, Peru and Chile. To evaluate genetic structure and to measure the impact of temporal variation, randomly amplified polymorphic DNA (RAPD) data were generated and analysed from 210 samples from eight eastern Pacific sites and on two sample sets taken from the same location in consecutive years. The temporal variation was shown to have no significant effect on genetic diversity. In addition, a genetic structure was detected which divided the populations into northern and southern locations. There was marginal isolation by distance between populations. Like in other ommastrephids, genetic structure is considered evidence of an adaptive radiation.

Histological validation of the gonadal maturation stages of female jumbo squid (Dosidicus gigas) in the Gulf of California, Mexico.

The oocyte structure of jumbo squid (Dosidicus gigas) female gonads was analyzed to validate morphochromatic sexual maturation stages based on a six-phase s...

Statoliths as 'black boxes' (life recorders) in squid

The present study presents an overview of recent developments in statoliths studies. Statoliths are calcareous structures located in the equilibrium organs of cephalopods, which serve to detect body accelerations during movement in water. They are perfect ‘black boxes’ because they record a lot of information about the lives of squid and cuttlefish. For instance, it is possible to reveal the hatchling size and temperature of embryonic development, estimate age and growth rates of the animal with daily precision, date life transitions, analyse possible migratory routes and population structure of squid using trace element analysis, and even reveal how many spawning events a given animal has had by analysing statolith microstructure. Furthermore, because the paralarval statolith is embedded completely within the adult statolith, its features can be used to identify cephalopod paralarvae, which are sometimes very different from adult animals. The shape of statoliths is physiologically specific, which enables the determination of the movement pattern of the animal. Statoliths are usually one of the few remains of squid in fossil records, and their features can be used to infer ideas about the life styles of extinct species.

An allozyme investigation of the stock structure of arrow squid Nototodarus gouldi (Cephalopoda: Ommastrephidae) from Australia

AbstractAllozyme electrophoresis was used to examine the stock structure of arrow squid Nototodarus gouldi (McCoy 1888) from Australia. Samples collected from six localities around southern Australia, separated by distances of between 700 and 4300 km, were examined for allozyme variation at 48 loci. The data revealed no evidence of more than a single species among the 203 squid examined. Nine polymorphic loci were detected, although only three were sufficiently variable to provide real insight into the population structure of arrow squid. There were no significant deviations from Hardy–Weinberg expectations for any locus, population, or for the metapopulation. Pairwise comparisons of allele frequencies revealed minor evidence of stock structure, with the Iluka (north New South Wales) sample set displaying significant allelic differences from the Tasmanian sample set at Acyc and from the Ulladulla (south New South Wales) sample set at Sordh. F-statistics also provided weak support that the Australian metapopulation is not panmictic. Further studies are needed to delineate the degree of stock segregation within the Australian/New Zealand region in order to successfully manage the arrow squid fishery in these waters.

CLASSIFYING PREY HARD PART STRUCTURES RECOVERED FROM FECAL REMAINS OF CAPTIVE STELLER SEA LIONS (EUMETOPIAS JUBATUS)

AbstractFeces were collected from six Steller sea lions (Eumetopias jubatus) that consumed known amounts of Atka mackerel (Pleurogrammus monopterygius), Pacific herring (Clupea barengus), pink salmon (Oncorhynchus gorbuscha), walleye pollock (Theragra chalcogramma), and squid (Loligo opalacens). The goal was to determine the numbers and types of taxon‐specific hard parts that pass through the digestive tract and to develop correction factors for certain abundantly occurring structures. Over 20,000 fish and squid were consumed during 267 d of fecal collection. During this period, over 119,000 taxon‐specific hard parts, representing 56 different structures, were recovered. Skeletal structures and non‐skeletal structures accounted for 72% and 28% of all hard parts, respectively. The branchiocranium, axial skeleton, and dermocranium regions of the skeletal system accounted for the greatest number of hard parts recovered. Over 70% of all recovered hard parts were represented by one to six taxa specific structures for each prey type. The average number of hard parts (3.1–31.2) and structure types (2.0–17.7) recovered per individual prey varied across taxa and were used to derive correction factors (to reconstruct original prey numbers). A measure of the variability of hard part recovery among sea lions showed no difference for certain herring, pollock, and squid structures, however, there was a significant difference for salmon and Atka mackerel structures. Identifying all taxon‐ specific prey hard parts increases the likelihood of identifying and estimating the number of prey consumed.

Critical transitions in early life histories of short-finned squid, Illex illecebrosus as reconstructed from gladius growth

Early life growth of the short-finned squid, Illex illecebrosus (Mollusca: Cephalopoda), was reconstructed from periodic increments deposited on the gladius structure of squid collected in the Gulf Stream/Slope Water front and the Scotian Shelf. The general effects of environmental changes and lifestyle transitions in the variation of size-specific gladius growth was investigated. The offshore growth was exponential and at least six size-specific growth phases were distinguished. Paralarval growth ended at approximately 10 mm gladius length (GL). An important change in growth at 30–40 mm GL was associated with the shift from the macroplanktonic to micronektonic habitats and the transition from the Gulf Stream to Slope Water. The approximation to the Scotian Shelf/Slope Water Front was suggested as related to a growth transition at 68 mm GL. A change to linear growth occurred after the nektonic lifestyle was attained on shelf waters (90 mm GL).

Equivalent parameters of a Josephson junction in a microwave SQUID structure

The equivalent parameters of a Josephson junction in a microwave SQUID structure are calculated on the basis of relations obtained as a result of an analysis of the operation of an rf SQUID. This analysis is based on the sawtooth variation of the voltage on the resonator as a function of the constant flux bias. The quantitative characteristics permit regarding the Josephson junction as a linear impedance in the rf or microwave circuit, whose real and imaginary parts are controlled by the constant magnetic flux passing through the SQUID loop.