Outer Pair Research Articles

Misidentification of mysis stages of Xiphopenaeus kroyeri (Heller, 1862) and Rimapenaeus Pérez-Farfante and Kensley, 1997 (Decapoda: Penaeidae) in the western Atlantic

Studies in the western Atlantic have relied primarily on the key of Cook (1966) to identify and discriminate early life stages (ELS) of Xiphopenaeus kroyeri (Heller, 1862) and Rimapenaeus spp. Perez-Farfante and Kensley, 1997, even though larvae had not been reared successfully past the zoea phase at that time. We surveyed the penaeid literature for descriptions of reared mysis stages of X. kroyeri and Rimapenaeus, compared characters with those of Cook (1966), and found that Cook had reversed illustrations and criteria to discriminate taxa. We also examined plankton-collected mysis stages and identified new characters and previously unrecognized differences between taxa. Mysis stages of X. kroyeri have a slender median spine laterally near the posterior margin of pleomere five, not those of Rimapenaeus, although some early first myses of Rimapenaeus may have a vestigial spine laterally on pleomere five. Rimapenaeus has single dorsomedian spines on pleomeres four through six with the spine on pleomeres five and six >40% (usually about 50%) of fifth pleomere length as measured along the dorsal midline. Rimapenaeus lacks a pterygiostomial spine, although a spine on the distal margin of the developing antennal peduncle near the ventrolateral border of the carapace can be confused with a pterygiostomial spine. Xiphopenaeus kroyeri has a pterygiostomial spine and single dorsomedian spines on pleomeres four through six with the spine on pleomeres five and six <35% (usually about 25%) of fifth pleomere length. Xiphopenaeus kroyeri also has a gap about the width of one spine between the longest and adjacent outer pairs of furcal spines along the posterior margin of the telson, whereas Rimapenaeus has contiguous furcal spines. Differences in spine length dorsally on pleomeres five and six, and the presence or absence of a pterygiostomial spine should be used to discriminate taxa because the low hepatic spine and median spine laterally on pleomere five can be difficult to detect in X. kroyeri, even with a biological stain applied. Likely misidentification of mysis stages and possible overexploitation of X. kroyeri and Rimapenaeus spp. stocks in the western Atlantic emphasizes the need to re-assess information on ELS and the necessity of accurate identifications.

Analysis Methods of Power Characteristics for Hydraulic Pressing of the Traction Drive Device

Analysis Methods of Power characteristics for hydraulic pressing of the traction drive device are studied. The operating principle of hydraulic pressing of the traction drive device is analyzed, Probe into the rule of variation of the inner and outer Friction Pairs about the traction coefficient and the transmission ratio, A mathematical model of transmission traction characteristics is built up based of the Elasto-hydrodynamic lubrication theory, to explore the power characteristics of the friction pairs under different slip roll ratio and normal loading force, and the transmission of the input power and output power under different total sliding rate and loading force. The results showed that the transmission power of hydraulic pressing of the traction drive device is increasing when the normal loading force is increasing under some sliding Rate, but the transmission power tend to stable when the shearing stress is close to limiting shearing stress；and with the Sliding Rate increasing the transmission power increase under some normal loading force, but the transmission power eventually tend to stable when the Shearing Stress is close to limiting shearing stress.

Two New Genera and Three New Combinations in Neotropical Capparaceae

Two new genera and three new combinations are proposed herein for Neotropical Capparaceae: Caphexandra, a monospecific genus of shrubs or small trees from southern Mexico to Panama, distinguished by the branchlets with subterminal small cataphylls on the raceme axis, calyces with closed aestivation in bud with the outer pair of sepals enclosing the dimorphic inner pair, asymmetric corollas with large unguiculate petals, long (2–5 mm) narrowly-lanceolate floral nectaries, and six stamens arranged in one whorl, which at anthesis forms adaxially an hemiorbicular arc opposite to the gynophore. Caphexandra is represented only by the new combination C. heydeana, a species of horticultural interest herein transferred from Capparis, and Preslianthus, a genus of shrubs or trees from Nicaragua to Brazil, characterized by a stellate pubescence, and flowers with stamens conspicuously accrescent just before anthesis. Preslianthus comprises the following two species, herein proposed as new combinations, also transferred from Capparis: Preslianthus detonsus and Preslianthus pittieri. Capparis schunkei is synonymyzed under P. pittieri. The new genera are illustrated and their relationships discussed.

The Membrane Interface Dictates Different Anchor Roles for “Inner Pair” and “Outer Pair” Tryptophan Indole Rings in Gramicidin A Channels

We investigated the effects of substituting two of the four tryptophans (the "inner pair" Trp(9) and Trp(11) or the "outer pair" Trp(13) and Trp(15)) in gramicidin A (gA) channels. The conformational preferences of the doubly substituted gA analogues were assessed using circular dichroism spectroscopy and size-exclusion chromatography, which show that the inner tryptophans 9 and 11 are critical for the gA's conformational preference in lipid bilayer membranes. [Phe(13,15)]gA largely retains the single-stranded helical channel structure, whereas [Phe(9,11)]gA exists primarily as double-stranded conformers. Within this context, the (2)H NMR spectra from labeled tryptophans were used to examine the changes in average indole ring orientations, induced by the Phe substitutions and by the shift in conformational preference. Using a method for deuterium labeling of already synthesized gAs, we introduced deuterium selectively onto positions C2 and C5 of the remaining tryptophan indole rings in the substituted gA analogues for solid-state (2)H NMR spectroscopy. The (least possible) changes in orientation and overall motion of each indole ring were estimated from the experimental spectra. Regardless of the mixture of backbone folds, the indole ring orientations observed in the analogues are similar to those found previously for gA channels. Both Phe-substituted analogues form single-stranded channels, as judged from the formation of heterodimeric channels with the native gA. [Phe(13,15)]gA channels have Na(+) currents that are ~50% and lifetimes that are ~80% of those of native gA channels. The double-stranded conformer(s) of [Phe(9,11)]gA do not form detectable channels. The minor single-stranded population of [Phe(9,11)]gA forms channels with Na(+) currents that are ~25% and single-channel lifetimes that are ~300% of those of native gA channels. Our results suggest that Trp(9) and Trp(11), when "reaching" for the interface, tend to drive both monomer folding (to "open" a channel) and dimer dissociation (to "close" a channel). Furthermore, the dipoles of Trp(9) and Trp(11) are relatively more important for the single-channel conductance than are the dipoles of Trp(13) and Trp(15).

Optimum Utilization of Edge Pairs

Summary Nearly all of Husky's SAGD projects in the Lloydminster, Saskatchewan area are in reservoirs with bottomwater. While operating several projects in this region, Husky observed that in some reservoir settings, the outer SAGD pair had significantly decreased performance compared to inner SAGD pairs. When the outer pair was shut in to improve overall pilot performance, the performance of the now exposed adjacent pair rapidly decreased. It was hypothesized that operating the edge pairs protected inner pairs from the detrimental effects of bottomwater. Numerical simulation runs have confirmed this behaviour. The conclusions reached are that in many bottomwater settings, poorer-performing edge SAGD pairs protect and preserve the performance of inner SAGD pairs; and this should be taken into consideration during facilities' design, development of operational strategy, and production forecasting.

Resonances in the three-body problem with equal masses

Numerical simulations of near-resonant motions occurring in planar rotating systems of three bodies with equal masses are presented for the cases of prograde and retrograde motions of the inner and outer pairs. The ratios n: m of the initial periods of these pairs are within 1 ≤ m ≤ n ≤ 7. It is shown that, as a rule, retrograde are more stable than prograde motions. The k loop structures oriented inwards for prograde and outwards for retrograde motions are revealed. Empirical relations between k and n are found for the main resonances n: 1 and n: 2.

Physical parameters and dynamical properties of the multiple star o and

An analysis of the physical characteristics, orbital parameters, and dynamical stability of the multiple Be star HD 217675 (o And) is presented. Observations on the 6-m SAO and 1.5-m RTT telescopes are used to refine the orbital parameters of the subsystems. The spectral types, absolute magnitudes, and masses of the components are estimated. The total mass of the system is 18 ± 2 Mdb. It is shown that the configuration of the system is 2 + 2, where one of the subsystems is a spectral binary with a period of 33 d and the outer pair has a period of 117 yr. The parameters of the second inner subsystem are uncertain, making it difficult to draw firm conclusions about the stability of this multiple star.

Maxillary Fragment Stabilization After Le Fort I Fracture With 1 Screw Pair per Plate

The aim of the present study was to determine whether plates with only 1 screw pair can be used for Le Fort I fracture management. Good postoperative results motivated the direct application of mandible fixation principles to the fractured midface region without additional experimental research. However, the amount and distribution of the forces in the midface region is different from those on the mandible. Testing was conducted on plastic anatomic models. The validity of the experimental model was tested before the fixation techniques were compared. Standard miniplates and miniscrews were used for fixation of the maxilla. The model surface strain analysis was conducted using the noncontact object grating method, which enabled the surface strain measurement without direct influence on the measured model. In 2 screw pair fixation, the outer screw pair has little effect on the local strain distribution, but it lowers the contact forces along the crack. One screw pair fixation is stable enough for fixation, but it has a greater strain peak at the crack edges. Our results showed that 1 screw pair per plate was enough for stable fixation, and 2 or more screw pairs should only be used when the bone fragment at the fracture site cannot sufficiently transmit forces along the crack.

Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

EcoRV, a restriction enzyme in Escherichia coli, destroys invading foreign DNA by cleaving it at the center step of a GATATC sequence. In the EcoRV–cognate DNA crystallographic complex, a sharp kink of 50° has been found at the center base-pair step (TA). Here, we examine the interplay between the intrinsic propensity of the cognate sequence to kink and the induction by the enzyme by performing all-atom molecular dynamics simulations of EcoRV unbound and interacting with three DNA sequences: the cognate sequence, GATATC (TA); the non-cognate sequence, GAATTC (AT); and with the cognate sequence methylated on the first adenine GACH3TATC (TA-CH3). In the unbound EcoRV, the cleft between the two C-terminal subdomains is found to be open. Binding to AT narrows the cleft and forms a partially bound state. However, the intrinsic bending propensity of AT is insufficient to allow tight binding. In contrast, the cognate TA sequence is easier to bend, allowing specific, high-occupancy hydrogen bonds to form in the complex. The absence of cleavage for this methylated sequence is found to arise from the loss of specific hydrogen bonds between the first adenine of the recognition sequence and Asn185. On the basis of the results, we suggest a three-step recognition mechanism. In the first step, EcoRV, in an open conformation, binds to the DNA at a random sequence and slides along it. In the second step, when the two outer base pairs, GAxxTC, are recognized, the R loops of the protein become more ordered, forming strong hydrogen-bonding interactions, resulting in a partially bound EcoRV–DNA complex. In the third step, the flexibility of the center base pair is probed, and in the case of the full cognate sequence the DNA bends, the complex strengthens and the protein and DNA interact more closely, allowing cleavage.

DNA BARCODING OF CHLORARACHNIOPHYTES USING NUCLEOMORPH ITS SEQUENCES1

Chlorarachniophytes are a small group of marine photosynthetic protists. They are best known as examples of an intermediate stage of secondary endosymbiosis: their plastids are derived from green algae and retain a highly reduced nucleus, called a nucleomorph, between the inner and outer pairs of membranes. Chlorarachniophytes can be challenging to identify to the species level, due to their small size, complex life cycles, and the fact that even genus-level diagnostic morphological characters are observable only by EM. Few species have been formally described, and many available culture collection strains remain unnamed. To alleviate this difficulty, we have developed a barcoding system for rapid and accurate identification of chlorarachniophyte species in culture, based on the internal transcribed spacer (ITS) region of the nucleomorph rRNA cistron. Although this is a multicopy locus, encoded in both subtelomeric regions of each chromosome, interlocus variability is low due to gene conversion by homologous recombination in this region. Here, we present barcode sequences for 39 cultured strains of chlorarachniophytes (>80% of currently available strains). Based on barcode data, other published molecular data, and information from culture records, we were able to recommend names for 21 out of the 24 unidentified, partially identified, or misidentified chlorarachniophyte strains in culture. Most strains could be assigned to previously described species, but at least two to as many as five new species may be present among cultured strains.

A simple method to reduce infection of ventriculoperitoneal shunts

Postoperative shunt infection is the most common and feared complication of ventriculoperitoneal (VP) shunt placement for treatment of hydrocephalus. The rate of shunt infection is highest in the 1st postoperative month. The most common organisms responsible for shunt infection include coagulase-negative Staphylococcus and Staphylococcus aureus. This suggests a transfer of patient's skin flora via the surgeons' glove as a possible means of infection. The authors conducted a study to determine if the rate of postoperative shunt infections could be reduced simply by changing gloves before handling the shunt catheter. A total of 111 neonates born with congenital hydrocephalus requiring a VP shunt were enrolled retrospectively and divided into 2 groups: a control group of 54 neonates treated with standard protocol VP shunt placement (Group A) and a treatment group of 57 neonates in whom, after initially double gloving, the outer pair of gloves was removed before handling the shunt catheter (Group B). Shunt infection rates were compared up to 6 months postoperatively. There was a statistically significant reduction of infection rate from 16.33% in Group A (control) to 3.77% in Group B (p = 0.0458). The study shows that a changing of gloves before handling the shunt catheter may be a simple and cost-effective way to reduce the burden of postoperative shunt infections.

Density Functional Study of the Thermodynamics of Hydrogen Production by Tetrairon Hexathiolate, Fe4[MeC(CH2S)3]2(CO)8, a Hydrogenase Model

The tetranuclear iron complex Fe(4)[MeC(CH(2)S)(3)](2)(CO)(8) (1) functions like a hydrogenase to catalyze proton reduction to H(2) in the presence of 2,6-dimethylpyridinium acid (LutH(+)). Experimentally, at the first reduction potential (-1.22 V vs Fc/Fc(+)), the concentration of LutH(+) decreases slowly, while at the second reduction potential, which is sufficient to reduce 1(-) (-1.58 V vs Fc/Fc(+)), the concentration of LutH(+) decreases more rapidly. Here, density functional theory predicts both reduction potentials (E(0)) and proton-transfer free energies relative to LutH(+) for numerous intermediates and several important transition states as a basis for developing thermodynamics cycles for routes to hydrogen production by 1. At the less negative potential, one-electron reduction of 1 is followed by protonation to form a bridging hydride complex; then, a second one-electron reduction is followed by a second protonation, an ECEC process. This doubly reduced and doubly protonated species has a structure with bridging hydrides between both outer Fe-Fe pairs and can produce H(2) and regenerate 1 only by bringing the two hydrogens into proximity through a high-energy intermediate or transition state, a result consistent with the experimentally slow uptake of LutH(+) at this potential. In contrast, at the more negative (lower) reduction potential the two-electron-reduced species, 1(2-), which has bridging carbonyls between both Fe-Fe pairs, is protonated at a terminal Fe position to form a species that produces H(2) by rapidly picking up a second proton and regenerating 1 in an EECC process. Thus, the latter route avoids the high-energy intermediates and transition states necessarily accessed by the former route, a result that explains the more rapid uptake of LutH(+) at the second more negative potential. Although both routes arrive at a doubly reduced, singly protonated species in the third step of these processes, the calculations predict that a high barrier prevents the rapid interconversion of these two nearly isoenergetic species. The calculations confirm the importance of terminal metal hydrides, rather than bridging hydrides, for rapid H(2) production and show in detail how the bridging CO maintains the terminal hydride structure at the lower reduction potential even though the bridging hydride conformation is more stable. These results provide clues for designing new biomimic electrocatalysts and further evidence for the terminal Fe-H mechanism in [FeFe]-hydrogenase. The calculations also predict that at even lower reduction potentials, new more highly reduced intermediate species can be accessed that could lead to alternative routes to H(2).

Is the curvature of the flagellum involved in the apparent cooperativity of the dynein arms along the “9+2” axoneme?

In a recent study [Cibert, 2008. Journal of Theoretical Biology 253, 74-89], by assuming that walls of microtubules are involved in cyclic compression/dilation equilibriums as a consequence of cyclic curvature of the axoneme, it was proposed that local adjustments of spatial frequencies of both dynein arms and beta-tubulin monomers facing series create propagation of joint probability waves of interaction (JPI) between these two necessary partners. Modeling the occurrence of these probable interactions along the entire length of an axoneme between each outer doublet pair (without programming any cooperative dialog between molecular complexes) and the cyclic attachment of two facing partners, we show that such constituted active couples are clustered. Along a cluster the dynein arms exhibit a small phase shift with respect to the order according to which they began their cycle after being linked to a beta-tubulin monomer. The number of couples included in these clusters depends on the probability of interaction between the dynein arms and the beta-tubulin, on the location of the outer doublet pairs around the axonemal cylinder, and on the local bending of the axoneme; around the axonemal cylinder, the faster and the larger the sliding, the shorter the clusters. This mechanism could be involved in the apparent cooperativity of molecular motors and the beta-tubulin monomers, since it is partially controlled by local curvature, and the cluster length is inversely proportional to the sliding activity of the outer doublet pairs they link.

Bending of the “9+2” axoneme analyzed by the finite element method

Many data demonstrate that the regulation of the bending polarity of the “9+2” axoneme is supported by the curvature itself, making the internal constraints central in this process, adjusting either the physical characteristics of the machinery or the activity of the enzymes involved in different pathways. Among them, the very integrated Geometric Clutch model founds this regulation on the convenient adjustments of the probability of interaction between the dynein arms and the β-tubulin monomers of the outer doublet pairs on which they walk. Taking into consideration (i) the deviated bending of the outer doublets pairs (Cibert, C., Heck, J.-V., 2004. Cell Motil. Cytoskeleton 59, 153–168), (ii) the internal tensions of the radial spokes and the tangential links (nexin links, dynein arms), (iii) a theoretical 5 μm long proximal segment of the axoneme and (iv) the short proximal segment of the axoneme, we have reevaluated the adjustments of these intervals using a finite element approach. The movements we have calculated within the axonemal cylinder are consistent with the basic hypothesis that found the Geometric Clutch model, except that the axonemal side where the dynein arms are active increases the intervals between the two neighbor outer doublet pairs. This result allows us to propose a mechanism of bending reversion of the axoneme, involving the concerted ignition of the molecular engines along the two opposite sides of the axoneme delineated by the bending plane.

On the dynamics of multiple systems of hot super-Earths and Neptunes: tidal circularization, resonance and the HD 40307 system

[Abridged] We consider the dynamics of a system of hot super-Earths or Neptunes such as HD 40307. We show that, as tidal interaction with the central star leads to small eccentricities, the planets in this system could be undergoing resonant coupling even though the period ratios depart significantly from very precise commensurability. In a three planet system, this is indicated by the fact that resonant angles librate or are associated with long term changes to the orbital elements. We propose that the planets in HD 40307 were in a strict Laplace resonance while they migrated through the disc. After entering the disc inner cavity, tidal interaction would cause the period ratios to increase from two but with the inner pair deviating less than the outer pair, counter to what occurs in HD 40307. However, the relationship between these pairs that occurs in HD 40307 might be produced if the resonance is impulsively modified by an event like a close encounter shortly after the planetary system decouples from the disc. We find this to be in principle possible for a small relative perturbation on the order of a few 1.d-3 but then we find that evolution to the present system in a reasonable time is possible only if the masses are significantly larger than the minimum masses and tidal dissipation is very effective. On the other hand we found that a system like HD 40307 with minimum masses and more realistic tidal dissipation could be produced if the eccentricity of the outermost planet was impulsively increased to about 0.15. The form of resonantly coupled tidal evolution we consider here is quite general and could be of greater significance for systems with inner planets on significantly shorter orbital periods characteristic of for example CoRoT 7 b.

Characterization of Periplastidal Compartment–Targeting Signals in Chlorarachniophytes

Secondary plastids are acquired by the engulfment and retention of eukaryotic algae, which results in an additional surrounding membrane or pair of membranes relative to the more familiar primary plastids of land plants. In most cases, the endocytosed alga loses its eukaryotic genome as it becomes integrated, but in two algal groups, the cryptophytes and chlorarachniophytes, the secondary plastids retain a vestigial nucleus in the periplastidal compartment (PPC), the remnant eukaryotic cytoplasm between the inner and the outer membrane pairs. Many essential housekeeping genes are missing from these reduced genomes, suggesting that they are now encoded in the host nucleus and their products are targeted to the PPC. One such nucleus-encoded, PPC-targeted protein, the translation elongation factor like (EFL) was recently identified in chlorarachniophytes. It bears an N-terminal-targeting sequence comprising a signal peptide and a transit peptide-like sequence (TPL) similar to the plastid-targeted proteins of chlorarachniophytes as well as a hydrophilic C-terminal extension rich in lysine and aspartic acid. Here, we characterize the function of the N- and C-terminal extensions of PPC-targeted EFL in transformed chlorarachniophyte cells. Using green fluorescent protein as a reporter molecule, we demonstrate that several negatively charged amino acids within the TPL are essential for accurate targeting to the PPC. Our findings further reveal that the C-terminal extension functions as a PPC retention signal in combination with an N-terminal plastid-targeting peptide, which suggests that plastid and PPC proteins may be sorted in the PPC.

A new diagnostic system for ultra-sensitive and specific detection and quantification of Candidatus Liberibacter asiaticus, the bacterium associated with citrus Huanglongbing

An ultra-sensitive and quantitative diagnostic system by combining nested PCR and TaqMan® PCR in a single tube was developed for detection of “ Candidatus Liberibacter asiaticus”. The procedure involves two PCR steps using the species-specific outer and inner primer pairs. Different annealing temperatures allow both the first and the second rounds of PCR to be performed sequentially in the same closed tube. The first PCR with outer primers was performed at a higher annealing temperature and with limited amount of primers to prevent interference with the inner primers during the second round of PCR. The specificity of the dual primer TaqMan® is high because the fluorescent signal can only be generated from the TaqMan® probes that are homologous to the product amplified by the outer and inner primers. This new detection system can reliably detect as few as single copies of target DNA. The sensitivity of the dual primer system is comparable to the conventional two-tube nested PCR, but it eliminates the potential risk of cross contamination commonly associated with conventional nested PCR. This one-tube dual primer TaqMan® PCR method is gel-free with reduced handling time and is cost effective. At the same time, this system provides significantly increased sensitivity, improved reliability and high through-put capability suitable for routine, large scale diagnoses of clinical plant tissue and insect samples. The technique described here is generic and can be applied to the detection of other plant pathogenic bacteria.

DUAL-STAGE RECONNECTION DURING SOLAR FLARES OBSERVED IN HARD X-RAY

In this Letter, we present hard X-ray (HXR) observation by the Reuven Ramaty High Energy Solar Spectroscopic Imager of the 2003 October 29 X10 flare. Two pairs of HXR conjugate footpoints have been identified during the early impulsive phase. This geometric configuration is very much in the manner predicted by the tether-cutting scenario first proposed by Moore & Roumeliotis. The HXR light curves show that the outer pair of footpoints disappeared much faster than the other pair. This temporal behavior further confirms that this event is a good example of the tether-cutting model. In addition, we reconstructed a three-dimensional magnetic field based on the nonlinear force-free extrapolation and found that each pair of HXR footpoints were indeed linked by corresponding magnetic field lines.

Heart of the Beat (the Flagellar Beat, that Is)

Heart of the Beat (the Flagellar Beat, that Is)

Simulation of Cyclic Dynein-Driven Sliding, Splitting, and Reassociation in an Outer Doublet Pair

A regular cycle of dynein-driven sliding, doublet separation, doublet reassociation, and resumption of sliding was previously observed by Aoyama and Kamiya in outer doublet pairs obtained after partial dissociation of Chlamydomonas flagella. In the work presented here, computer programming based on previous simulations of oscillatory bending of microtubules was extended to simulate the cycle of events observed with doublet pairs. These simulations confirm the straightforward explanation of this oscillation by inactivation of dynein when doublets separate and resumption of dynein activity after reassociation. Reassociation is augmented by a dynein-dependent “adhesive force” between the doublets. The simulations used a simple mathematical model to generate velocity-dependent shear force, and an independent elastic model for adhesive force. Realistic results were obtained with a maximum adhesive force that was 36% of the maximum shear force. Separation between a pair of doublets is the result of a buckling instability that also initiates a period of uniform sliding that enlarges the separation. A similar instability may trigger sliding initiation events in flagellar bending cycles.