Divergent Mode Research Articles

Divergent Evolutional Mode and Purifying Selection of the KIT Gene in European and Asian Domestic Pig Breeds.

The recent geographic expansion of wild boars and the even more recent development of numerous domestic pigs have spurred exploration on pig domestic origins. The porcine KIT gene has been showed to affect pleiotropic effects, blood parameters, and coat colour phenotypes, especially the white colour phenotype formation in European commercial breeds. Here, we described the use of SNPs to identify different selection patterns on the porcine KIT gene and the phylogenetic relationships of the inferred haplotypes. The phylogenetic tree revealed four clades in European and Asian wild and domestic pigs: two major clades with European and Asian origins and one minor clade with Iberian origins as well as the other minor clade in Asia, consistent with the major introgression of domestic Asian pigs in Europe around 18th -19th century. The domestication history of pigs, which occurred in the domestication centers (Europe and Asia), has also been demonstrated by mtDNA analysis. Furthermore, both Asian and European domestic pigs evolved under purifying selection. This study indicated that domestic pigs in Europe and Asia have different lineage origins but the porcine KIT gene was undergoing a purifying selection during their evolutional histories.

Archaeal and eukaryal translation initiation factor 1 differ in their RNA interacting loops

The archaeal translation initiation factor 1 (aIF1) is reported to be functionally homologous to the eukaryotic translation initiation factor 1 (eIF1). However, lack of a structural comparison between aIF1 and eIF1 has limited our understanding of the structural (dis)similarities. Herein, we have determined the three-dimensional crystal structure of an open reading frame PH1771.1 encoding aIF1 in Pyrococcushorikoshii OT3. Results reveal that although aIF1 has low sequence similarity with eIF1, high structural homology exists between the two proteins. Nonetheless, notable critical differences between aIF1 and eIF1 could still be perceived at the β1 -β2 basic loop, the acidic loop and the solvent-exposed surface. These differences might lead to a slightly divergent mode of action of aIF1 during archaeal translation initiation.

Molecular architecture of LSM14 interactions involved in the assembly of mRNA silencing complexes.

The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6. LSM14 binds DDX6 via a unique non-contiguous motif with distinct directionality as compared to other DDX6-interacting proteins. Together with mutational and proteomic studies, the LSM14-DDX6 structure reveals that LSM14 has adopted a divergent mode of binding DDX6 in order to support the formation of mRNA silencing complexes and P-body assembly.

Varifocal liquid lens actuated by laser-induced thermal Marangoni forces

This paper proposes a simple and easily implemented configuration of a varifocal liquid lens actuated by laser-induced thermal Marangoni forces. The lens consists of a sessile droplet of low-volatile liquid placed on a transparent solid surface. The focal length tunability is achieved by changing a local curvature of the droplet surface due to the thermocapillary displacement of liquid from the core part of the droplet to its edge caused by heating with a laser beam. Depending on the power of the laser beam, the droplet can operate as a varifocal convergent or varifocal divergent lens. In the convergent mode, the curvature of the droplet surface varies from an initial positive value to a near zero value (flat surface), whereas in the divergent mode, the curvature changes from a positive value to a negative value due to the formation of a thermocapillary dimple in the droplet.

Asteroseismic analysis of the pulsating subdwarf B star KIC 11558725: an sdB+WD system with divergent frequency multiplets and mode trapping observed by Kepler

Asteroseismic analysis of the pulsating subdwarf B star KIC 11558725: an sdB+WD system with divergent frequency multiplets and mode trapping observed by Kepler

Nonlinear dynamics and control of a laterally mass varying fighter aircraft

This paper presents dynamic analysis and nonlinear control of laterally mass varying combat aircraft based on a six degree-of-freedom model derived for a variable mass system. The objective is to investigate the effects of asymmetric lateral mass variation, due to mass ejection, from two different perspectives – the open loop dynamic behavior through bifurcation analysis; and the closed loop control performance while carrying out some demanding maneuvers. Bifurcation analysis reveals considerable coupling between the longitudinal and lateral-directional channels even for a modest lateral shift in the center-of-mass due to store ejection, which in turn is observed to give rise to a spiral-dive like divergent mode even at low angles-of-attack. Thereafter, the well-known high angle-of-attack cobra maneuver is implemented for the symmetric center-of-mass case using sliding mode control technique and using a new single loop control formulation in contrast with the conventional inner-outer loop formulation. The proposed single loop control formulation is further extended to handle the lateral movement of center-of-mass due to asymmetric store ejection using the asymmetric dynamics model proposed and derived in this paper.

Understanding Divergent Thermal Conductivity in Single Polythiophene Chains Using Green-Kubo Modal Analysis and Sonification.

We used molecular dynamics simulations and the Green-Kubo modal analysis (GKMA) method as well as sonification to study the modal contributions to thermal conductivity in individual polythiophene chains. The simulations suggest that it is possible to achieve divergent thermal conductivity in individual polythiophene chains of certain lengths, with periodic boundary conditions. Application of the GKMA method further allowed for exact pinpointing of the modes responsible for the anomalous behavior. The analysis showed that transverse vibrations in the plane of the aromatic rings at low frequencies ∼0.05 THz are primarily responsible for the divergence. Within the integration time, one mode in particular exhibits a thermal conductivity contribution greater than 100 W m-1 K-1. Further investigation showed that the divergence arises from persistent correlation between the three lowest frequency modes on chains that have exact multiples of 30 unit cells in length. Sonification of the mode heat fluxes revealed regions where the heat flux amplitude yields a somewhat sinusoidal envelope with a long period similar to the relaxation time. This characteristic in the divergent mode heat fluxes gives rise to the overall thermal conductivity divergence, which strongly supports earlier hypotheses that attribute the divergence to correlated phonon-phonon scattering/interactions as opposed to a lack of scattering/interaction among modes (e.g., infinite relaxation time/ballistic transport).

Institutionalization of Lifelong Learning in Europe and East Asia: from the Complexity Systems perspective

East Asia shows newly emerging experiments in lifelong learning that contrast with European experiences. The concepts and ideas share a similar platform, while the trajectories of institutionalization reveal great differences. It is because the idea of lifelong learning was coined by international agencies, like UNESCO, to share, it rather shows divergent mode of institutionalization in different contexts. In this article, I intend to grasp the particular characteristics of ‘institution formation’ in lifelong learning practices, especially shown in East Asian countries, including the Republic of Korea, Japan, and China. In so doing, I adopt social systems theories in interpreting the phenomena. Education is presumed to be a social system, or ‘autopoiesis’ that functionally differentiates and expands itself by self-referential reproduction. In this context, lifelong learning is a relative newcomer with new frameworks and ideas, which sometimes conflict with traditional education, and institutionalizes itself by competing the contested terrains of the system, most of which are preoccupied by early sectors of education. In this paper, I focus on how the ‘idea’ of lifelong learning embodies into the system, secures its own education spaces, and keeps expansive reproductions as a part of the education system in general.

Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony.

Plasmodium parasites, the causative agents of malaria, have evolved a unique cell division cycle in the clinically relevant asexual blood-stage of infection1. DNA replication commences approximately halfway through the intracellular development following invasion and parasite growth. The schizont stage is associated with multiple rounds of DNA replication and nuclear division without cytokinesis resulting in a multinucleated cell. Nuclei divide asynchronously through schizogony, with only the final round of DNA replication and segregation being synchronous and coordinated with daughter cell assembly2,3. However, the control mechanisms for this divergent mode of replication are unknown. Here we show that the Plasmodium-specific kinase PfCRK4 is a key cell cycle regulator that orchestrates the multiple rounds of DNA replication throughout schizogony in P. falciparum. PfCRK4 depletion led to a complete block in nuclear division and profoundly inhibited DNA replication. Quantitative phosphoproteomic profiling identified a set of PfCRK4-regulated phosphoproteins with greatest functional similarity to CDK2 substrates, particularly proteins involved in origin of replication firing. PfCRK4 was required for the initial and subsequent rounds of DNA replication during schizogony, and in addition was essential for development in the mosquito vector. Our results identified an essential S phase promoting factor of the unconventional P. falciparum cell cycle. PfCRK4 is required for both a prolonged period of the intraerythrocytic blood-stage of malaria infection, as well as for transmission, revealing a broad window for PfCRK4-targeted chemotherapeutics.

Prospects for Gamma-Ray Burst detection by the Cherenkov Telescope Array

The Large Area Telescope (LAT) on the Fermi satellite is expected to publish a catalogue with more than 100 Gamma-Ray Bursts (GRBs) detected above 100 MeV thanks to a new detection algorithm and a new event reconstruction. This work aims at revising the prospects for GRB alerts with the Cherenkov Telescope Array (CTA) based on the new LAT results. We start considering the simulation of the observations with the full CTA of two extremely bright events, the long GRB 130427A and the short GRB 090510, then we investigate how these GRBs would be observed by a particular configuration of the array with the telescopes pointing to different directions in what is called the “coupled divergent mode”.

Oncogenic events rather than antigen selection pressure may be the main driving forces for relapse in diffuse large B-cell lymphomas.

Little is known on the phylogenetic relationship between diagnostic and relapse clones of diffuse large B-cell lymphoma (DLBCL). We applied high throughput sequencing (HTS) of the VDJ locus of Immunoglobulin heavy chain (IGHV) on 14 DLBCL patients with serial samples, including tumor biopsies and/or peripheral blood mononuclear cells (PBMC). Phylogenetic data were consolidated with targeted sequencing and cytogenetics. Phylogeny clearly showed that DLBCL relapse could occur according either an early or a late divergent mode. These two modes of divergence were independent from the elapsed time between diagnosis and relapse. We found no significant features for antigen selection pressure in complementary determining region both at diagnosis and relapse for 9/12 pairs and a conserved negative selection pressure for the three remaining cases. Targeted HTS and conventional cytogenetics revealed a branched vs. linear evolution for 5/5 IGHV early divergent cases, but unexpected such "oncogenetic" branched evolution could be found in at least 2/7 IGHV late divergent cases. Thus, if BCR signaling is mandatory for DLBCL emergence, oncogenetic events under chemotherapy selection pressure may be the main driving forces at relapse. Finally, circulating subclones with divergent IGHV somatic hypermutations patterns from initial biopsy could be detected in PBMC at diagnosis for 4/6 patients and, for two of them, at least one was similar to the ones found at relapse. This study highlights that oncogenetic intraclonal diversity of DLBCL should be evaluated beyond the scope a single biopsy and represents a rationale for future investigations using peripheral blood for lymphoid malignancies genotyping. Am. J. Hematol. 92:68-76, 2017. © 2016 Wiley Periodicals, Inc.

Preliminary Study on Stability of a Hovering Bi-flap Flapping Wing Platform using Cycle-Averaged Linear Models

A preliminary study on the stability of a bi-flap flapping wing hovering platform is presented in this paper. The work includes the derivation of cycle-average linear longitudinal and lateral models, the experiment to determine the stability derivatives, and analysis on the identified system matrices. Also discussed in the paper is the validity of using a cycle-averaged model to represent the dynamics of the flapping wing platform, and the validity of using small perturbation theory to linearize the nonlinear model. Results show that the platform is unstable longitudinally and laterally about the hovering equilibrium. Longitudinally, the natural modes are short period unstable oscillatory mode, fast subsidence mode, and slow divergent mode. Laterally, the natural modes are neutral mode, fast subsidence mode, and long period unstable oscillatory mode.

Effects Of Various Contraction Modes With Equivalent Exercise Volume On Muscle Mtor Signaling

Although muscle contraction type (i.e. eccentric, concentric, or isometric contraction) affects the magnitude of mTORC1 activation and subsequent muscle protein synthesis, its regulatory mechanisms are still unknown. Previous studies have shown that eccentric contraction induced the highest mTORC1 activation and muscle protein synthesis as compared with other contraction modes. Although the magnitude of exercise volume (torque × contraction time) is critical in mTORC1 activation and muscle protein synthesis, no previous study was able to match the exercise volume between various contraction modes. PURPOSE: To investigate the effect of different contraction modes with equivalent exercise volume on mTOR signaling in rat skeletal muscle. METHODS: The male SD rats aged 11-week were randomly assigned to three groups designated as eccentric (ECC), concentric (CCN), or isometric contraction(ISO) groups. After a 12-h overnight fast, muscle contraction was performed on right gastrocnemius muscle by percutaneous electrical stimulation (100Hz, ∼30V, 3 sec stimulation × 10 contractions, with a 7 sec interval between contractions, per set, with 3 min rest intervals) by changing ankle joint angle (ISO: at 90°, ECC: 60°∼105°, CCN: 105°∼60°, with joint angular velocity at 15°/sec for ECC and CCN). To standardize to an equivalent exercise volume, the number of sets were modified between contraction modes (i.e. ECC: 3sets, CCN: 4sets, ISO: 5sets). Left gastrocnemius muscle served as the control. Animals were sacrificed and muscle samples were taken immediately and 3 hours after exercise. Western blotting analysis was used to measure phospholyration status of mTORC1 signaling. RESULTS: Erk1/2 and Akt phosphorylation significantly increased at immediately after contraction in all groups as compared to the control leg (p < 0.05), without significant group difference between groups. Furthermore, significant increase in p70S6K phosphorylation (∼11-fold above control) was observed in all three groups at 3h after the contraction, but no significant group differences were observed. CONCLUSIONS: Differential activation of mTORC1 by the electrical stimulation-induced divergent muscle contraction mode seems to be determined by the exercise volume and not by the contraction mode itself.

Energy and exergy analysis for a humidification–dehumidification desalination system integrated with multiple inserts

An experimental analysis is conducted to accelerate the productivity of the humidification dehumidification (HDH) desalination system. In the air heater region of the HDH desalination system, inserts namely (i) twisted tape in short length with tapered form, (ii) cut out conical turbulators integrated with internal fins arranged in convergent and divergent mode and (iii) half perforated circular inserts with an orientation angle of 45°, 90°, and 180° are tried out respectively with pitch ratio (PR) of 3, 4 and 5 to enhance the heat transfer rate in the air heater. Two types of packing materials, such as gunny bag and saw dust, are tested in the humidifier region accommodating the mass transfer rate. Also an attempt has been made to augment the overall heat transfer coefficient in the dehumidifier with spring insert for PR of 3 and 4. An energy and exergy analysis construed the quantity of effective utilization of energy with the modified HDH desalination system. The enhanced system produced 45% increase of productivity compared to conventional system of 0.340kg/h. For the same input power, the modified system enhanced the heat output and productivity equivalent to a power saving of 40% and 13% respectively.

Monte Carlo simulations of alternative sky observation modes with the Cherenkov Telescope Array

We investigate possible sky survey modes with the Middle Sized Telescopes (MST, aimed at covering the energy range from ∼100GeV to 10TeV) subsystem of the Cherenkov Telescope Array (CTA). We use the standard CTA tools, CORSIKA and sim_telarray, to simulate the development of gamma-ray showers, proton background and the telescope response. We perform simulations for the H.E.S.S.-site in Namibia, which is one of the candidate sites for the CTA experiment. We study two previously considered modes, parallel and divergent, and we propose a new, convergent mode with telescopes tilted toward the array center. For each mode we provide performance parameters crucial for choosing the most efficient survey strategy. For the non-parallel modes we study the dependence on the telescope offset angle. We show that use of both the divergent and convergent modes results in potential advantages in comparison with use of the parallel mode. The fastest source detection can be achieved in the divergent mode with larger offset angles (∼6° from the field of view center for the outermost telescopes), for which the time needed to perform a scan at a given sensitivity level is shorter by a factor of ∼2.3 than for the parallel mode. We note, however, the direction and energy reconstruction accuracy for the divergent mode is even by a factor of ∼2 worse than for other modes. Furthermore, we find that at high energies and for observation directions close to the center of the array field of view, the best performance parameters are achieved with the convergent mode, which favors this mode for deep observations of sources with hard energy spectra.

Embryonic development of the nervous system in the planarian Schmidtea polychroa

The development of a nervous system is a key innovation in the evolution of metazoans, which is illustrated by the presence of a common developmental toolkit for the formation of this organ system. Neurogenesis in the Spiralia, in particular the Platyhelminthes, is, however, poorly understood when compared with other animal groups. Here, we characterize embryonic neurogenesis in the freshwater flatworm Schmidtea polychroa and analyze the expression of soxB and a set of proneural bHLH genes, which are gene families with a well-established role in metazoan early neural development. We show that the nervous system is fully de novo assembled after the early embryo ingests the maternal nutrients. At early stages of neurogenesis, soxB1 genes are expressed in putative neural progenitor cells, whereas soxB2 and neural bHLH genes (achaete-scute, neuroD and beta3) are associated with late neurogenesis and the specification of neural subpopulations of the central and peripheral nervous system. Our findings are consistent with the role of proneural genes in other bilaterians, suggesting that the ancestral neural-specific gene regulatory network is conserved in triclads, despite exhibiting a divergent mode of development.

First and second sound in a two-dimensional harmonically trapped Bose gas across the Berezinskii–Kosterlitz–Thouless transition

We theoretically investigate first and second sound of a two-dimensional (2D) atomic Bose gas in harmonic traps by solving Landau’s two-fluid hydrodynamic equations. For an isotropic trap, we find that first and second sound modes become degenerate at certain temperatures and exhibit typical avoided crossings in mode frequencies. At these temperatures, second sound has significant density fluctuation due to its hybridization with first sound and has a divergent mode frequency towards the Berezinskii–Kosterlitz–Thouless (BKT) transition. For a highly anisotropic trap, we derive the simplified one-dimensional hydrodynamic equations and discuss the sound-wave propagation along the weakly confined direction. Due to the universal jump of the superfluid density inherent to the BKT transition, we show that the first sound velocity exhibits a kink across the transition. These predictions might be readily examined in current experimental setups for 2D dilute Bose gases with a sufficiently large number of atoms, where the finite-size effect due to harmonic traps is relatively weak.

Subthalamic deep brain stimulation improves auditory sensory gating deficit in Parkinson’s disease

ObjectiveWhile motor effects of dopaminergic medication and subthalamic nucleus deep brain stimulation (STN-DBS) in Parkinson’s disease (PD) patients are well explored, their effects on sensory processing are less well understood. Here, we studied the impact of levodopa and STN-DBS on auditory processing. MethodsRhythmic auditory stimulation (RAS) was presented at frequencies between 1 and 6Hz in a passive listening paradigm. High-density EEG-recordings were obtained before (levodopa ON/OFF) and 5months following STN-surgery (ON/OFF STN-DBS). We compared auditory evoked potentials (AEPs) elicited by RAS in 12 PD patients to those in age-matched controls. Tempo-dependent amplitude suppression of the auditory P1/N1-complex was used as an indicator of auditory gating. ResultsParkinsonian patients showed significantly larger AEP-amplitudes (P1, N1) and longer AEP-latencies (N1) compared to controls. Neither interruption of dopaminergic medication nor of STN-DBS had an immediate effect on these AEPs. However, chronic STN-DBS had a significant effect on abnormal auditory gating characteristics of parkinsonian patients and restored a physiological P1/N1-amplitude attenuation profile in response to RAS with increasing stimulus rates. ConclusionsThis differential treatment effect suggests a divergent mode of action of levodopa and STN-DBS on auditory processing. SignificanceSTN-DBS may improve early attentive filtering processes of redundant auditory stimuli, possibly at the level of the frontal cortex.

Effects of divergent resistance exercise contraction mode and dietary supplementation type on anabolic signalling, muscle protein synthesis and muscle hypertrophy.

Greater force produced with eccentric (ECC) compared to concentric (CONC) contractions, may comprise a stronger driver of muscle growth, which may be further augmented by protein supplementation. We investigated the effect of differentiated contraction mode with either whey protein hydrolysate and carbohydrate (WPH + CHO) or isocaloric carbohydrate (CHO) supplementation on regulation of anabolic signalling, muscle protein synthesis (MPS) and muscle hypertrophy. Twenty-four human participants performed unilateral isolated maximal ECC versus CONC contractions during exercise habituation, single-bout exercise and 12 weeks of training combined with WPH + CHO or CHO supplements. In the exercise-habituated state, p-mTOR, p-p70S6K, p-rpS6 increased by approximately 42, 206 and 213 %, respectively, at 1 h post-exercise, with resistance exercise per se; whereas, the phosphorylation was exclusively maintained with ECC at 3 and 5 h post-exercise. This acute anabolic signalling response did not differ between the isocaloric supplement types, neither did protein fractional synthesis rate differ between interventions. Twelve weeks of ECC as well as CONC resistance training augmented hypertrophy with WPH + CHO group compared to the CHO group (7.3 ± 1.0 versus 3.4 ± 0.8 %), independently of exercise contraction type. Training did not produce major changes in basal levels of Akt-mTOR pathway components. In conclusion, maximal ECC contraction mode may constitute a superior driver of acute anabolic signalling that may not be mirrored in the muscle protein synthesis rate. Furthermore, with prolonged high-volume resistance training, contraction mode seems less influential on the magnitude of muscle hypertrophy, whereas protein and carbohydrate supplementation augments muscle hypertrophy as compared to isocaloric carbohydrate supplementation .

Influence of divergent exercise contraction mode and whey protein supplementation on atrogin-1, MuRF1, and FOXO1/3A in human skeletal muscle

Knowledge from human exercise studies on regulators of muscle atrophy is lacking, but it is important to understand the underlying mechanisms influencing skeletal muscle protein turnover and net protein gain. This study examined the regulation of muscle atrophy-related factors, including atrogin-1 and MuRF1, their upstream transcription factors FOXO1 and FOXO3A and the atrogin-1 substrate eIF3-f, in response to unilateral isolated eccentric (ECC) vs. concentric (CONC) exercise and training. Exercise was performed with whey protein hydrolysate (WPH) or isocaloric carbohydrate (CHO) supplementation. Twenty-four subjects were divided into WPH and CHO groups and completed both single-bout exercise and 12 wk of training. Single-bout ECC exercise decreased atrogin-1 and FOXO3A mRNA compared with basal and CONC exercise, while MuRF1 mRNA was upregulated compared with basal. ECC exercise downregulated FOXO1 and phospho-FOXO1 protein compared with basal, and phospho-FOXO3A was downregulated compared with CONC. CONC single-bout exercise mediated a greater increase in MuRF1 mRNA and increased FOXO1 mRNA compared with basal and ECC. CONC exercise downregulated FOXO1, FOXO3A, and eIF3-f protein compared with basal. Following training, an increase in basal phospho-FOXO1 was observed. While WPH supplementation with ECC and CONC training further increased muscle hypertrophy, it did not have an additional effect on mRNA or protein levels of the targets measured. In conclusion, atrogin-1, MuRF1, FOXO1/3A, and eIF3-f mRNA, and protein levels, are differentially regulated by exercise contraction mode but not WPH supplementation combined with hypertrophy-inducing training. This highlights the complexity in understanding the differing roles these factors play in healthy muscle adaptation to exercise.