Lateral Pair Research Articles

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin.

β-Sheet is one of the major protein secondary structures. Oppositely charged residues are frequently observed across neighboring strands in antiparallel sheets, suggesting the importance of cross-strand ion pairing interactions. The charged amino acids Asp, Glu, Arg, and Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. To investigate the effect of side chain length of guanidinium- and carboxylate-containing residues on lateral cross-strand ion pairing interactions at non-hydrogen-bonded positions, β-hairpin peptides containing Zbb-Agx (Zbb = Asp, Glu, Aad in increasing length; Agx = Agh, Arg, Agb, Agp in decreasing length) sequence patterns were studied by NMR methods. The fraction folded population and folding energy were derived from the chemical shift deviation data. Peptides with high fraction folded populations involved charged residue side chain lengths that supported high strand propensity. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Minimal interaction was observed between residues with short side chains, most likely due to the diffused positive charge on the guanidinium group, which weakened cross-strand electrostatic interactions with the carboxylate side chain. Only the Aad-Arg/Agh interactions with long side chains clearly exhibited stabilizing energetics, possibly relying on hydrophobics. A survey of a non-redundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Arg < Glu-Arg, implying the need for matching long side chains. This suggested the need for long side chains on both guanidinium-bearing and carboxylate-bearing residues to stabilize the β-hairpin motif.

Experimental uncertainties of three-dimensional pair distribution function investigations exemplified on the diffuse scattering from a tris-tert-butyl-1,3,5-benzene tricarboxamide single crystal

Diffuse scattering from a substitutionally disordered tris-tert-butyl-1,3,5-benzene tricarboxamide single crystal is analyzed with the three-dimensional difference pair distribution function (3D-ΔPDF) method. The real structure of the crystal is shown to consist of infinite polar molecular stacks along thecaxis, which are laterally packed in a hexagonal fashion. The orientation of the stacks is disordered, but neighboring stacks strongly prefer antiparallel arrangements. Quantitative orientational pair correlation coefficients are determined for all lateral pairs separated by less than 100 Å. A careful analysis of the factors influencing the accuracy of the 3D-ΔPDF refinement is presented. It is shown that the effect of statistical errors is small compared to systematic errors coming from diffraction geometry distortions, reciprocal space resolution or incompletely corrected background. Various strategies for identifying and decreasing systematic errors are discussed. The impact of the systematic errors on the uncertainty of the results is not just specific for 3D-ΔPDF investigations but also relevant for other quantitative diffuse scattering modeling techniques.

Triassic-age salt tectonics of the Central North Sea

The framework of salt tectonics in the Central North Sea was set early in the Triassic. We defined and illustrated five major domains of differing salt tectonic style. The differing structural styles were all interpreted as having evolved under a component of lateral displacement pairing extensional and contractional structures, produced by some combination of decoupled rift extension and gravity sliding. However, the extensional structures are located toward the basin center and the contractional structures near the original updip limits of salt. This suggests a framework driven by gravity sliding of the sediments overlying the Zechstein away from the Central Graben. Possible mechanisms for structural relief away from the Central Graben are the Triassic focus of rifting lying further east at the Norwegian-Danish basin, footwall uplift of a Triassic Central Graben precursor and significant thermal doming occurring much earlier than had previously been thought. The mechanisms are not mutually exclusive and may have acted in concert.

Quantifying distortions in two-photon remote focussing microscope images using a volumetric calibration specimen

Remote focussing microscopy allows sharp, in-focus images to be acquired at high speed from outside of the focal plane of an objective lens without any agitation of the specimen. However, without careful optical alignment, the advantages of remote focussing microscopy could be compromised by the introduction of depth-dependent scaling artifacts. To achieve an ideal alignment in a point-scanning remote focussing microscope, the lateral (XY) scan mirror pair must be imaged onto the back focal plane of both the reference and imaging objectives, in a telecentric arrangement. However, for many commercial objective lenses, it can be difficult to accurately locate the position of the back focal plane. This paper investigates the impact of this limitation on the fidelity of three-dimensional data sets of living cardiac tissue, specifically the introduction of distortions. These distortions limit the accuracy of sarcomere measurements taken directly from raw volumetric data. The origin of the distortion is first identified through simulation of a remote focussing microscope. Using a novel three-dimensional calibration specimen it was then possible to quantify experimentally the size of the distortion as a function of objective misalignment. Finally, by first approximating and then compensating the distortion in imaging data from whole heart rodent studies, the variance of sarcomere length (SL) measurements was reduced by almost 50%.

Teaching chest X-ray reading for child tuberculosis suspects

Cape Town, South Africa. To improve the reading of chest X-rays (CXRs) in child tuberculosis (TB) suspects. We designed a reporting and recording form to assist in the diagnosis of childhood TB from CXRs. We then developed an image bank of antero-posterior and lateral CXR pairs, with each image pair assigned to one of four diagnostic categories. Finally, we designed and carried out a 1-day training course to teach clinicians how to read paediatric CXRs, with pre- and post-course assessments. Of the 27 participants included, 17 (63%) were women. The median age was 38 years (interquartile range [IQR] 32.5-43.5). The median pre-training score was 16.0/30 (IQR 13.0-18.0) and the median post-training score was 17.0 (IQR 13.5-21.0). Sensitivity (P = 0.09) and specificity (P = 0.06) to detect TB did not change as a result of the course; however, the Wilcoxon signed ranks paired-sample test indicated an increase in the participants' overall ability to read CXRs (P = 0.017). Teaching clinicians with a 1-day training course using a systematic approach and a standardised form led to a limited improvement in CXR reading ability.

Effect of Charged Amino Acid Side Chain Length on Lateral Cross-Strand Interactions between Carboxylate-Containing Residues and Lysine Analogues in a β-Hairpin

β-Sheets are one of the fundamental three-dimensional building blocks for protein structures. Oppositely charged amino acids are frequently observed directly across one another in antiparallel sheet structures, suggesting the importance of cross-strand ion pairing interactions. Despite the apparent electrostatic nature of ion pairing interactions, the charged amino acids Asp, Glu, Arg, Lys have different numbers of hydrophobic methylenes linking the charged functionality to the backbone. Accordingly, the effect of charged amino acid side chain length on cross-strand ion pairing interactions at lateral non-hydrogen bonded positions was investigated in a β-hairpin motif. The negatively charged residues with a carboxylate (Asp, Glu, Aad in increasing length) were incorporated at position 4, and the positively charged residues with an ammonium (Dap, Dab, Orn, Lys in increasing length) were incorporated at position 9. The fraction folded population and folding free energy were derived from the chemical shift deviation data. Double mutant cycle analysis was used to determine the interaction energy for the potential lateral ion pairs. Only the Asp/Glu-Dap interactions with shorter side chains and the Aad-Orn/Lys interactions with longer side chains exhibited stabilizing energetics, mostly relying on electrostatics and hydrophobics, respectively. This suggested the need for length matching of the interacting residues to stabilize the β-hairpin motif. A survey of a nonredundant protein structure database revealed that the statistical sheet pair propensity followed the trend Asp-Lys < Glu-Lys, also implying the need for length matching of the oppositely charged residues.

Fitting together: copulatory linking in some Neotropical Chrysomeloidea

Copulatory linking of male and female genitalic structures in 11 Neotropical species of Chrysomelidae and one species of Megalopodidae was studied by freezing and then dissecting pairs of beetles in copula. In Megalopus armatus (Megalopodidae) the male has a long endophallus with complex membranous protuberances and a terminal flagellum that probably reaches the spermatheca. In the subfamily Eumolpinae the females have telescoping ovipositors through which the male endophalli pass, reaching to or near the mouth of the spermathecal duct. A long thin flagellum is probably inserted into the spermathecal duct. The male endophalli are braced inside the female using various structures, including two pairs of lateral appendages and apical appendages (both lateral pairs sclerotized in Colaspis sanjoseana and only the basal pair in Brachypnoea irazuensis), a pair of membranous swellings (in Metaxyonycha amasia), and apical microspicules on the endophallus (in Xanthonia). In the subfamily Galerucinae, males of Metrioidea and Diabrotica (tribe Galerucini) have relatively short endophalli ornamented with sclerotized hooks, spines and needles. In Metrioidea elongata the long needle-like endophallic spines of the male were erected inside the female and penetrated the wall of her bursa. In the tribe Alticini, the male endophallus is very short and does not enter the female in two species, Alagoasa gemmata and Walterianella sp. Instead, the apical parts of the female bursae were everted, and were clamped by sclerites of the male median lobe. The male genitalia of Plectrotetra hirsuta reached deep into the female, to the median oviduct, far beyond the mouth of the spermathecal duct. Both rigid and membranous structures meshed in complex ways. When these observations are combined with published descriptions of mating in other Chrysomelidae, the great diversity of copulatory morphology in these families comes into sharper focus.

Caracterización Morfo Agronómica de Híbridos Provenientes del Cruzamiento entre Especies Diploides de Papa

&lt;p&gt;Se realizó la caracterización morfoagronómica de 2285 genotipos provenientes de 20 familias obtenidas a partir de cruzamientos entre progenitores diploides, cultivados y silvestres de las especies &lt;em&gt;Solanum tuberosum &lt;/em&gt;grupo Phureja, S&lt;em&gt;olanum stenotomun &lt;/em&gt;subsp. &lt;em&gt;stenotomun, Solanum stenotomun &lt;/em&gt;subsp. &lt;em&gt;goniocalyx y Solanum &lt;/em&gt;&lt;em&gt;bukasovii. &lt;/em&gt;El experimento fue establecido en el municipio de Facatativa (Cundinamarca) y se evaluaron 35 características en cinco etapas del cultivo. Para el registro de los datos se utilizó la guía para las caracterizaciones morfológicas básicas en colecciones de papas nativas del centro internacional de la papa. Al registrarse variables mixtas se utilizó la distancia genética de Gower. Se identificaron cinco grupos principales, en el grupo donde se ubicaron principalmente los cruzamientos entre variedades, se observó un aumento en la cantidad de pares de foliolos laterales, en el grupo donde se ubicó la variedad Guaneña y algunos cruzamientos de &lt;em&gt;S. stenotomun &lt;/em&gt;subsp. &lt;em&gt;goniocalix se &lt;/em&gt;observaron brotes violeta en forma predominante. Los cruzamientos de &lt;em&gt;S. bukasovii &lt;/em&gt;presentaron color de flor lila y/o morado intenso, hábito de crecimiento semiarrosetado y bajos rendimientos. En los cruzamientos de &lt;em&gt;S. stenotomum &lt;/em&gt;subsp &lt;em&gt;stenotonum &lt;/em&gt;se presentaron tubérculos de piel roja y ojos profundos.&lt;/p&gt;

Unifoliata-Afila interactions in pea leaf morphogenesis.

Processes of leaf morphogenesis provide the basis for the great diversity of leaf form among higher plants. The common garden pea (Pisum sativum) offers a developmental model system for understanding how gene and hormone interactions impart a large array of mutant leaf phenotypes. • To understand the role of auxin in AF and UNI gene function and their interaction, we compared the range of leaf phenotypes on afila (af) and unifoliata (uni) double mutants, examined the effects of these mutations on auxin levels, auxin transport, auxin response via DR5::GUS, and expression of auxin-regulated genes. • The adult leaves of af uni double mutants have leaflets and tendrils and typically possess two lateral pinna pairs and a terminal leaflet. The af mutants have higher auxin content, stronger auxin response, and higher expression of auxin responsive genes than wildtype. The uni mutant has reduced auxin content and transport, whereas the uni-tac mutant has higher auxin content and transport and reduced auxin response compared to wildtype. • Auxin concentration and response differences characterize the antagonistic relationship between AF and UNI in pea leaf development. The mechanism involves modulation of auxin mediated by one or both genes; UNI is expressed in and promotes high auxin levels, and AF suppresses auxin levels.

Cardamine calliphaea sp. nov. (Brassicaceae) from southwestern Greece

Cardamine calliphaea Kit Tan, G. Vold &amp; Giannopoulos sp. nov. (Brassicaceae) is illustrated and described as a new species endemic to Greece. It occurs in the prefectures of Ilia in western Peloponnese and Etolias‐Akarnanias in western Sterea Ellas and bears some resemblance to C. graeca, differing by its dense greyish–white indumentum and by the absence of leaf auricles. Affinities lie with C. glauca and C. plumieri from which it differs conspicuously, among other characters, by its imparipinnate leaves with the terminal leaflet smaller or equal in size to the lateral pairs.

Bi-unicondylar knee replacement laxity with changes to simulated soft tissue constraints

Unicondylar knee replacement systems have been shown to perform comparably to total knee replacements, while being much less surgically invasive. Proper ligament balancing, as well as knee laxity, has been shown to play an important role in optimizing kinematic behavior of these implant systems and improving long-term survival of the implant. This study investigates the effect of different simulated ligament laxity conditions of the anterior cruciate ligament and the posterior cruciate ligament on the resulting anteroposterior and mediolateral contact kinematics for medial and lateral pairs of UKR implants with flat and symmetric ultrahigh-molecular-weight polyethylene inserts during force-controlled ISO-14243-1 knee testing simulation. A novel method of capturing the tibiofemoral lowest point contact path was used to calculate the shear plane lowest point contact path kinematics in both the anteroposterior and the mediolateral directions. The results illustrated that multiple clinically relevant soft tissue configurations produce statistically different measured knee kinematics in unicondylar knee replacement systems than is seen in accepted "standard" knee simulator protocols with 95% confidence interval. The observed kinematic differences in anteroposterior and mediolateral movement from what was observed using standard wear testing protocols could aid in the development of unicondylar knee replacement design enhancements that are resistant to varying soft tissue deficiencies.

Impaired Default Mode Network on Resting-State fMRI in Children with Medically Refractory Epilepsy

Resting-state networks including the DMN have been shown to be abnormal in adults with temporal lobe epilepsy. However, little is known about the DMN in children with medically refractory epilepsy. The aim was to determine whether there was a difference in the DMN in children with medically refractory epilepsy relative to controls. Eleven children with medically refractory epilepsy and 11 age-matched healthy controls underwent resting-state fMRI. IC analysis was used to identify the DMN. A random-effects analysis was performed on the Z-maps of the DMN within each group and between groups. We calculated the temporal correlation coefficients of pairs of ROIs: PCC/PCUN, mPFC, and left and right lateral parietal cortices. The relations between z scores of temporal correlation coefficients of pairs of ROIs and clinical seizure parameters and IQ were assessed. The patients demonstrated decreased DMN connectivity in the PCC/PCUN, bilateral lateral parietal cortex, and anterior and midcingulate relative to controls. There was reduced connectivity between the mPFC-right lateral parietal cortex, the PCC/PCUN-left lateral parietal cortex, and the PCC/PCUN-right lateral parietal cortex pairs of ROIs in patients compared with controls. There were no significant correlations between the z scores of temporal correlation coefficients of the 6 pairs of ROIs in patients and age of seizure onset, duration of epilepsy, number of medications, seizure frequency, and IQ. We have found reduced connectivity in the DMN in children with medically refractory epilepsy. Further studies are needed to determine whether different seizure types have different effects on the DMN and whether the impaired connectivity is related to cognitive functions subserved by the DMN.

A PLIF and PIV study of liquid mixing enhanced by a lateral synthetic jet pair

In this paper, enhancement of mixing between two water streams of the same flow rate in a planar channel by means of a lateral synthetic jet pair is studied at a net flow Reynolds number of 83 using PLIF and PIV. The synthetic jet pair is operated 180° out-of-phase at a range of actuation frequencies and displacements, with the latter being characterized by the dimensionless stroke length. The extent of mixing is evaluated using PLIF data at a location further downstream in the mixing channel. It is found that at a fixed actuation frequency a higher dimensionless stroke length produces a better mixing, and as the actuation frequency increases a lower dimensionless stroke length is required to achieve a given mixing degree. At a sufficiently high frequency or dimensionless stroke length, a nearly homogenous mixing with a mixing degree greater than 0.9 can be obtained. A functional relationship between actuation frequency and dimensionless stroke length is also obtained by best fitting the experimental data, which can be used for selecting the synthetic jet operating conditions to ensure a good mixing. Furthermore, both PLIF and PIV results show that each synthetic jet actuation cycle produce two opposing vortex pairs, which play an important role in prompting mixing between the two fluid streams. The excellent mixing obtained at a high frequency or a high dimensionless stroke length is found to be largely caused by a strong interaction between these opposing vortex pairs.

Drilling a Better Pair: New Technologies in SAGD Directional Drilling

Summary The precise placement of well pairs is one of the most-crucial factors in the successful execution of a steam-assisted-gravity-drainage (SAGD) drilling program. A SAGD drilling program includes placing the producer well relative to the reservoir boundaries and twinning the producer with the injector well accurately. Delivering on these high expectations in unconsolidated formations (e.g., the McMurray oil sands in Canada) requires a strong focus on technological innovation. A common practice in drilling SAGD wells in northeast Alberta is to drill lateral SAGD pairs with conventional, steerable mud motors and logging-while-drilling (LWD) resistivity measurements. Although this combination has delivered success, certain limitations exist in terms of wellbore quality and placement. At a demonstration project by a major oil company, several industry firsts were implemented successfully, including a combination of the newest and most-cutting-edge directional, measurement, and LWD technology. The keystone of these industry firsts was the application of a soft-formation-modified, point-the-bit rotary-steerable system (RSS) used on 20 horizontal wells. Combined with an ultradeep azimuthal resistivity sensor, the RSS provided precise geosteering along the bottombed boundary in the producer wells, resulting in improved reservoir capture and characterization. More on-bottom time enabled more-efficient drilling and reduced well costs significantly. Highly smooth liner runs reflected the lack of tortuosity in the wellbore, made possible by the rotary bottomhole assembly (BHA). Improved directional control made uniform well separation possible between lateral pairs, thereby reducing the risk of hot spots and short circuiting during SAGD operations. The use of an even-walled power section above the RSS increased the bit rev/min for improved BHA responsiveness while minimizing casing and pipe wear. Overall, the results and lessons learned from the demonstration of these new techniques provide a clear indication of the progressive future of directional drilling in SAGD.

Estudios Sobre Rubiáceas Méxicanas XXXVII

Two new Randia species are described from the aculeata-complex, characterised by small leaves, flowers and fruits, the later with soft exocarpium. This group apparently has its diversification centre in Mexico represented actually by 19 species and 3 varieties. Randia crucis is a deciduous tree up to 6mhigh in Oaxaca, characterised by terminal pairs of spines and many-flowered lateral inflorescences with very small naked flowers and white tomentose hypanthium. Randia manglaris is a very special shrub of Veracruz, living in the mangrove bush, completely glabrous, characterised by lateral pairs of spines, few-flowered inflorescences and flowers with corolla lobes twice longer than the tube.

Shear Piezoresistance in MOSFET Devices Under General Operating Conditions

This paper describes the modeling and characterization of in-plane stress sensors based on the shear piezoresistance effect in field-effect-transistor (FET) inversion layers. FET test structures fabricated in a commercial 0.6-μm complementary MOS technology were subjected to in-plane shear and normal stresses. A complete set of inversion layer piezoresistive coefficients was extracted for gate, bulk, and inversion carrier potentials covering the entire operating range. Stress sensitivities of the pseudo-Hall voltage of rectangular 100-μm-long 3-μm-wide n- and p-MOSFETs with multiple lateral channel contact pairs were determined. The experimental values are compared to predictions from an analytical model treating the stress as a perturbation of the unstressed device. Strongly enhanced sensitivities associated with the large potential drop close to the pinch-off point are observed in saturation for lateral contact pairs near the drain. The inaccuracy of the model for sensor operation at |VG| = 5 V is better than 14% for n-type devices and 5% for p-type devices for lateral channel contact pairs distant from source and drain by more than 12.5 μm. For contact pairs 1 μm from the drain, due to degradation effects, the inaccuracies increase to 70% and 52% for n- and p-type devices, respectively.

Pair bonding and lateral neck-resting preferences in captive Caribbean flamingos (Phoenicopterus ruber)

When flamingos rest, they typically lay their head on their back and curve their neck to either the right or left of their body, with both individual and population-level lateral preferences for rightward neck resting when preferences are tracked over time (Anderson, Williams, & O'Brien, 2009). The present study attempted to replicate these previous neck-resting preferences, to examine how they changed over time, and to examine the possibility of a relationship between lateral neck-resting preference and pair bonding in captive Caribbean flamingos (Phoenicopterus ruber) housed at the Philadelphia Zoo (Philadelphia, PA, USA). Results successfully replicated the individual- and population-level lateral preferences for rightward neck resting, and demonstrated that these preferences were stable over time. Moreover, individual flamingos that demonstrated stronger pair bond strengths tended to differ less from their partners in terms of neck-resting preference than did those birds displaying weaker pair bond strengths, suggesting a relationship between laterality and social cohesion.

&lt;em&gt;Drosophila&lt;/em&gt; Pupal Abdomen Immunohistochemistry

The Drosophila pupal abdomen is an established model system for the study of epithelial morphogenesis and the development of sexually dimorphic morphologies 1-3. During pupation, which spans approximately 96 hours (at 25 °C), proliferating populations of imaginal cells replace the larval epidermis to generate the adult abdominal segments. These imaginal cells, born during embryogenesis, exist as lateral pairs of histoblast nests in each abdominal segment of the larvae. Four pairs of histoblast nests give rise to the adult dorsal cuticle (anterior and posterior dorsal nests), the ventral cuticle (ventral nests) and the spiracles associated with each segment (spiracle nests) 4. Upon puparation, these diploid cells (distinguishable by size from the larger polyploid larval epidermal cells- LECs) begin a stereotypical process of proliferation, migration and replacement of the LECs. Various molecular and genetic tools can be employed to investigate the contributions of genetic pathways involved in morphogenesis of the adult abdomen. Ultimate adult phenotypes are typically analyzed following dissection of adult abdominal cuticles. However, investigation of the underlying molecular processes requires immunohistochemical analyses of the pupal epithelium, which present unique challenges. Temporally dynamic morphogenesis and the interactions of two distinct epithelial populations (larval and imaginal) generate a fragile tissue prone to excessive cell loss during dissection and subsequent processing. We have developed methods of dissection, fixation, mounting and imaging of the Drosophila pupal abdominem epithelium for immunohistochemical studies that generate consistent high quality samples suitable for confocal or standard fluorescent microscopy.

&lt;em&gt;Drosophila&lt;/em&gt; Pupal Abdomen Immunohistochemistry

The Drosophila pupal abdomen is an established model system for the study of epithelial morphogenesis and the development of sexually dimorphic morphologies 1-3. During pupation, which spans approximately 96 hours (at 25 °C), proliferating populations of imaginal cells replace the larval epidermis to generate the adult abdominal segments. These imaginal cells, born during embryogenesis, exist as lateral pairs of histoblast nests in each abdominal segment of the larvae. Four pairs of histoblast nests give rise to the adult dorsal cuticle (anterior and posterior dorsal nests), the ventral cuticle (ventral nests) and the spiracles associated with each segment (spiracle nests) 4. Upon puparation, these diploid cells (distinguishable by size from the larger polyploid larval epidermal cells- LECs) begin a stereotypical process of proliferation, migration and replacement of the LECs. Various molecular and genetic tools can be employed to investigate the contributions of genetic pathways involved in morphogenesis of the adult abdomen. Ultimate adult phenotypes are typically analyzed following dissection of adult abdominal cuticles. However, investigation of the underlying molecular processes requires immunohistochemical analyses of the pupal epithelium, which present unique challenges. Temporally dynamic morphogenesis and the interactions of two distinct epithelial populations (larval and imaginal) generate a fragile tissue prone to excessive cell loss during dissection and subsequent processing. We have developed methods of dissection, fixation, mounting and imaging of the Drosophila pupal abdominem epithelium for immunohistochemical studies that generate consistent high quality samples suitable for confocal or standard fluorescent microscopy.

Sclerite fusion in the problematic early Cambrian spine-like fossil Stoibostrombus from South Australia

New collections of the problematic spine like fossil Stoibostrombus crenulatus Conway Morris & Bengtson from the Mt. Scott Range and Wilkawillina Gorge in the central Flinders Ranges, South Australia contain fused sclerite composites. In each fused specimen the spines are merged along their lateral margins and the orientation of the spines is almost identical. These new specimens confirm that Stoibostrombus spines were dermal sclerites, arranged in lateral pairs or transverse rows. The nature of the animal secreting the spines remains elusive, but available evidence suggest that it was an ecdysozoan animal, possibly a palaeoscolecid worm.