bluuebunny/crossref_metadata_2025 huggingface dataset:
Semaphorin 3A binding to chondroitin sulfate E enhances the biological activity of the protein, and cross-links and rigidifies glycosaminoglycan matrices
Authors: Djerbal Lynda , Vivès Romain R. , Lopin-Bon Chrystel , Richter Ralf P. , Kwok Jessica C.F. , Lortat-Jacob Hugues
Published: November 2019

Semaphorin 3A (Sema3A) is a secreted protein that signals to cells through binding to neuropilin and plexin receptors and provides neurons with guidance cues key for axon pathfinding, and also controls cell migration in several other biological systems. Sema3A interacts with glycosaminoglycans (GAGs), an interaction that could localize the protein within tissues and involves the C-terminal domain of the protein. This domain comprises several furin cleavage sites that are processed during secretion and in previous works have hampered recombinant production of full-length wild type Sema3A, and the biochemical analysis of Sema3A interaction with GAGs. In this work, we have developed a strategy to purify the full-length protein in high yield and identified two sequences in the C-terminal domain, KRDRKQRRQR and KKGRNRR, which confer to the protein sub nM affinity for chondroitin sulfate and heparan sulfate polysaccharides. Using chemically defined oligosaccharides and solid phase binding assays, we report that Sema3A recognizes a (GlcA-GalNAc4S6S)2motif but not a (GlcA2S-GalNAc6S)2motif and is thus highly specific for type E chondroitin sulfate. Functionally, we found that Sema3A rigidified CS-E films that mimic the GAG presentation within extracellular matrices (ECMs), suggesting that Sema3A may have a previously unidentified function to cross-link and thus stabilize GAG-rich ECMs. Finally, we demonstrated that the full-length Sema3A is more potent at inhibiting neurite outgrowth than the truncated or mutant forms that were previously purified and that the GAG binding sites are required to achieve full activity. The results suggest that Sema3A can rigidify and cross-link GAG matrices, implicating Sema3A could function as an extracellular matrix organizer in addition to binding to and signaling through its cognate cell surface receptors.
On the inference of a southern origin of the North American fireflyPhotinus pyralis
Authors: Catalán Ana , Höhna Sebastian , Lower Sarah E. , Duchen Pablo
Published: November 2019

The fireflyPhotinus pyralisinhabits a wide range of latitudinal and ecological niches, with populations living from temperate to tropical habitats. Its ample geographic distribution makes this species an ideal system for the study of local adaptation and demographic inference of wild populations. Therefore, in this study we modelled and inferred different demographic scenarios for North American populations ofP. pyralis, collected from Texas to New Jersey. To do this, we used a combination of ABC techniques (for multi-population/colonization analyses), and likelihood inference (dadi) for single-population demographic inference, which proved useful with our RAD data.We uncovered that the most ancestral North American population lays in Texas, which further colonized the Central region of the US and more recently the North Eastern coast. Our study confidently rejects a demographic scenario where the North Eastern populations colonized more southern populations until reaching Texas. Our results suggest thatP. pyralisoriginated in Central- or South America, followed by migration events that populated northern latitudes. Finally, modelling the demographic history of North AmericanP. pyralisserves as a null model of nucleotide diversity patterns, which will inform future studies of adaptation, not only inP. pyralis, but also in other North American taxa.
Neolithic genomes reveal a distinct ancient HLA allele pool and population transformation in Europe
Authors: Immel Alexander , Rinne Christoph , Meadows John , Barquera Rodrigo , Szolek András , Pierini Federica , Susat Julian , Böhme Lisa , Dose Janina , Bonczarowska Joanna , Drummer Clara , Fuchs Katharina , Ellinghaus David , Kässens Jan Christian , Furholt Martin , Kohlbacher Oliver , Schade-Lindig Sabine , Mathieson Iain , Franke Andre , Krause Johannes , Müller Johannes , Lenz Tobias L. , Nebel Almut , Krause-Kyora Ben
Published: November 2019

The Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.
Balancing cell populations endowed with a synthetic toggle switch via adaptive pulsatile feedback control
Authors: Guarino A. , Fiore D. , Salzano D. , di Bernardo M.
Published: November 2019

Controlling cells endowed with the genetic toggle switch has been suggested as a benchmark problem in synthetic biology. It has been shown that a carefully selected periodic forcing can balance a population of such cells in an undifferentiated state. The effectiveness of these control strategies, however, can be mined by the presence of stochastic perturbations and uncertainties typically observed in biological systems and is therefore not robust. Here, we propose the use of feedback control strategies to enhance robustness and performance of the balancing action by selecting in real-time both the amplitude and the duty-cycle of the inducer molecular signals affecting the toggle switch behavior. We show, via in-silico experiments and realistic agent-based simulations, the effectiveness of the proposed strategies even in presence of uncertainties and stochastic effects. In so doing, we confirm previous observations made in the literature about coherence of the population when pulsatile forcing inputs are used but, contrary to what proposed in the past, we leverage feedback control techniques to endow the balancing strategy with unprecedented robustness and stability properties. We compare via in-silico experiments different control solutions and show their advantages and limitations from an in-vivo implementation viewpoint.
Existence and functions of hypothalamic kisspeptin neuropeptide signaling system in a non-chordate deuterostome species
Authors: Wang Tianming , Cao Zheng , Shen Zhangfei , Yang Jingwen , Chen Xu , Yang Zhen , Xu Ke , Xiang Xiaowei , Yu Qiuhan , Song Yimin , Wang Weiwei , Tian Yanan , Sun Lina , Zhang Libin , tGuo Su , Zhou Naiming
Published: November 2019

The kisspeptin (Kp) system is a central modulator of the hypothalamic-pituitary-gonadal axis in vertebrates. Its existence outside the vertebrate lineage remains largely unknown. Here we report the identification and characterization of Kp system in the sea cucumber Apostichopus japonicus. The gene encoding the Kp precursor, generates two mature neuropeptides, AjKiss1a and AjKiss1b. The Kp receptors, AjKissR1 and AjKissR2, are strongly activated by synthetic A. japonicus and vertebrate Kps, triggering a rapid intracellular mobilization of Ca2+, followed by receptor internalization. AjKissR1 and AjKissR2 share similar intracellular signaling pathways via Gαq/PLC/PKC/MAPK cascade, when activated by C-terminal decapeptide (AjKiss1b-10). The A. japonicus Kp system functions in mutiple tissues which are closely related to reproduction and metabolism. Overall, our findings uncover for the first time, to our knowledge, the existence and function of the Kp system in a non-chordate species and provide new evidence to support the ancient origin of the hypothalamic neurosecretory system.
Transcriptional activation of cyclin D1 via HER2/HER3 contributes to cell survival and EGFR tyrosine kinase inhibitor resistance in non-small cell lung carcinoma
Authors: Liu Bin , Chen Deng , Chen Shipeng , Saber Ali , Haisma Hidde
Published: November 2019

Several different mechanisms are implicated in the resistance of lung cancer cells to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), and only few have been functionally investigated. Here, using genetically knocked out EGFR and TKI-resistant lung cancer cells, we show that loss of wild-type EGFR attenuates cell proliferation, migration and 3D-spherid formation, whereas loss of mutant EGFR or resistance to TKIs reinforces those processes. Consistently, disruption of wild-type EGFR leads to suppression of HER2/HER3, while mutant EGFR ablation or resistance to TKIs increases HER2/HER3 expression, compensating for EGFR loss. Furthermore, HER2/HER3 nuclear translocation mediates overexpression of cyclin D1, leading to tumor cell survival and drug resistance. Cyclin D1/CDK4/6 inhibition resensitizes erlotinib-resistant (ER) cells to erlotinib. Analysis of cyclin D1 expression in patients with non-small cell lung carcinoma (NSCLC) showed that its expression is negatively associated with overall survival and disease-free survival. Our results provide biological and mechanistic insights into targeting EGFR and TKI resistance.
Bulk and single-molecule analysis of a novel DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor
Authors: Wilkinson O.J. , Carrasco C. , Aicart-Ramos C. , Moreno-Herrero F. , Dillingham M.S.
Published: November 2019

DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterisedGeobacillus stearothermophilusBad, a novel bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5’ to 3’ ssDNA translocase and 5’ to 3’ helicase activity. Single molecule analysis reveals that Bad is a highly processive DNA motor capable of moving along DNA for distances of more than 4 kbp at a rate of ∼200 base pairs per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments also show that the enzyme loops DNA while translocating, which is an emerging feature of highly processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.
Competitive Inhibition of Cortisol by Prostaglandins at the Ligand Binding Domain of Glucocorticoid Receptors
Authors: Schaper Charles D.
Published: November 2019

Cortisol is a steroid hormone that binds to the glucocorticoid receptor with a diverse range of functions including metabolic, neurologic and immune responses. Prostglandins are lipid autacoids that participate in a wide range of functions including the inflammatory response and the vasoactivity of blood vessels and smooth muscle. Previously, a direct interaction between the two classes of biomolecules has not been studied, and here it is shown for the first time that there is competitive inhibition of cortisol and prostaglandins at the critical ligand binding domain of glucocorticoid receptors, which are found in nearly every cell and tissue in the human body. To assess molecular similarity that would enable competitive inhibition, it is first noted that cortisol (CORT, C21H30O5) and prostaglandin E2 (PGE2, C20H32O5) are of nearly the same molecular weight, and have nearly the same number of carbon, hydrogen and oxygen elements. The carbon-carbon double bonds on each of the two branches of PGE2, combined with the five-carbon cyclic centering structure, enable a conformational isomer of PGE2 to position the five oxygen-based functional groups at similar spatial positions as the corresponding five oxygen-based functional groups of CORT. Within the gene-regulating ligand binding domain (LBD) of the glucocorticoid receptor (GR), the average inter-molecular spacing of hydrogen bonding to the corresponding identical five functional groups is 1.778 Å for CORT versus 1.746 Å for PGE2. The conformational isomer of PGE2 within the LBD is at a lower energy state than CORT by 54.9%, indicating preference in stability. Both PGE2 and CORT exhibit a hydrophobic core within the LBD of GR, which is compatible with hydrophobic regions of the LBD. With the incorporation of two calcium ions into both PGE2 and CORT, the energy is further reduced by 58.9% and 113% respectively. PGE2 with calcium ion stabilization is lower by 15.5% in comparison to the equivalent arrangement of CORT. Because of the steroid ring structure of CORT, the spacing of the calcium ions is larger at 16.2Å, whereas PGE2, with just a single ring, collapses to 12.3Å. Analysis of experimental data associated with the adrenal response to an injection of lipopolysaccharide (LPS) is presented to indicate competitive inhibition of PGE2 is responsible for an observed lack of phosphorylation of the GR despite the presence of CORT. Competitive inhibition preventing normative cellular processing of cortisol, a stress hormone, by prostaglandins, which are associated with the inflammatory response, may be the causative source of certain signs and symptoms of disease, and thus is of significant medical importance.
Naturally occurring fluorescence protects the eutardigrade Paramacrobiotus sp. from ultraviolet radiation
Authors: Suma Harikumar R , Prakash Swathi , Giri Debasish , Mugesh Govindasamy , Eswarappa Sandeep M.
Published: November 2019

Naturally occurring fluorescence has been observed in multiple species ranging from bacteria to birds. In macroscopic animals such as birds and fishes, fluorescence provides a visual communication signal. However, the functional significance of this phenomenon is not known in most cases. Though photoprotection is attributed to fluorescence under ultraviolet (UV) light in some organisms, it lacks direct experimental evidence. Here, we have identified a new species of eutardigrade belonging to the genus Paramacrobiotus, which exhibits fluorescence under UV light. Using a natural variant of the same species that lacks fluorescence, we show that the fluorescence confers tolerance to lethal UV radiation. Remarkably, we could transfer this property to UV-sensitive Hypsibius exemplaris, another eutardigrade, and also to C. elegans, a nematode. Using high performance liquid chromatography (HPLC) we isolated the fluorescent compound from Paramacrobiotus sp. This compound has excitation maxima (λex) at 370 nm and emission maxima (λem) at 420-430 nm. We propose that Paramacrobiotus sp. uses a fluorescent shield that absorbs harmful UV radiation, and emits harmless blue light, thereby protecting itself from the lethal effects of UV radiation.

Summary statement

Tardigrades are well known for their tolerance to extreme environmental conditions. In this study, we have identified a new tardigrade species that employs a fluorescent shield to protect itself from the germicidal ultra violet radiation.
Single-cell immuno-mechanics: rapid viscoelastic changes are a hall-mark of early leukocyte activation
Authors: Zak Alexandra , Cortés Sara Violeta Merino , Sadoun Anaïs , Babataheri Avin , Dogniaux Stéphanie , Dupré-Crochet Sophie , Hudik Elodie , He Hai-Tao , Barakat Abdul I , Carrasco Yolanda R , Hamon Yannick , Puech Pierre-Henri , Hivroz Claire , Nüsse Oliver , Husson Julien
Published: November 2019

To accomplish their critical task of removing infected cells and fighting pathogens, leukocytes activate by forming specialized interfaces with other cells. Using an innovative micropipette rheometer, we show in three different cell types that when stimulated by microbeads mimicking target cells, leukocytes become up to ten times stiffer and more viscous. These mechanical changes initiate within seconds after contact and evolve rapidly over minutes. Remarkably, leukocyte elastic and viscous properties evolve in parallel, preserving a well-defined ratio that constitutes a mechanical signature specific to each cell type. The current results indicate that simultaneously tracking both elastic and viscous properties during an active cell process provides a new way to investigate cell mechanical processes. Our findings also suggest that dynamic immuno-mechanical measurements provide an identifier of leukocyte type and an indicator of the cell’s state of activation.
A multiscale framework for disentangling the roles of evenness, density and aggregation on diversity gradients
Authors: McGlinn Daniel J. , Engel Thore , Blowes Shane A. , Gotelli Nicholas J. , Knight Tiffany M. , McGill Brian J. , Sanders Nathan , Chase Jonathan M.
Published: November 2019

Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes changes in species diversity into three components of community structure: the species abundance distribution (SAD), the total community abundance, and the within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that ant species richness decreased along the elevational gradient because of changes in the SAD and in spatial aggregation, but not because of changes in the number of individuals. Specifically, with increasing elevation, species evenness was lower and species were less aggregated. These results do not support the more-individuals hypothesis; alternative hypotheses are required to explain why evenness and aggregation decrease with elevation. Our extension of MoB has the potential to elucidate the drivers of diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.
Evidence for the Involvement of Vernalization-related Genes in the Regulation of Cold-induced Ripening in ‘D’Anjou’ and ‘Bartlett’ Pear Fruit
Authors: Hewitt Seanna , Hendrickson Christopher A. , Dhingra Amit
Published: November 2019

European pear (Pyrus communis L.) cultivars require a genetically pre-determined duration of cold-temperature exposure to induce autocatalytic system 2 ethylene biosynthesis and subsequent fruit ripening. The physiological responses of pear to cold-temperature-induced ripening have been well characterized, but the molecular mechanisms underlying this phenomenon continue to be elucidated. This study employed established cold temperature conditioning treatments for ripening of two pear cultivars, ‘D’Anjou’ and ‘Bartlett’. Using a time-course transcriptomics approach, global gene expression responses of each cultivar were assessed at four different developmental stages during the cold conditioning process. Differential expression, functional annotation, and gene ontology enrichment analyses were performed. Interestingly, evidence for the involvement of cold-induced, vernalization-related genes and repressors of endodormancy release was found. These genes have not previously been described to play a role in fruit during the ripening transition. The resulting data provide insight into cultivar-specific mechanisms of cold-induced transcriptional regulation of ripening in European pear, as well as a unique comparative analysis of the two cultivars with very different cold conditioning requirements.
Time-of-day-dependent responses of cyanobacterial cellular viability against oxidative stress
Authors: Tanaka Kenya , Shimakawa Ginga , Nakanishi Shuji
Published: November 2019

As an adaptation to periodic fluctuations of environmental light, photosynthetic organisms have evolved a circadian clock. Control by the circadian clock of many cellular physiological functions, including antioxidant enzymes, metabolism and the cell cycle, has attracted attention in the context of oxidative stress tolerance. However, since each physiological function works in an integrated manner to deal with oxidative stress, whether or not cell responses to oxidative stress are under circadian control remains an open question. In fact, circadian rhythms of oxidative stress tolerance have not yet been experimentally demonstrated. In the present work, we applied an assay using methyl viologen (MV), which generates reactive oxygen species (ROS) under light irradiation, and experimentally verified the circadian rhythms of oxidative stress tolerance in photosynthetic cells of the cyanobacterium Synechococcus elongatus PCC7942, a standard model species for investigation of the circadian clock. Here, we report that ROS generated by MV treatment causes damage to stroma components and not to the photosynthetic electron transportation chain, leading to reduced cell viability. The degree of decrease in cell viability was dependent on the subjective time at which oxidative stress was applied. Thus, oxidative stress tolerance was shown to exhibit circadian rhythms. In addition, the rhythmic pattern of oxidative stress tolerance disappeared in mutant cells lacking the essential clock genes. Notably, ROS levels changed periodically, independent of the MV treatment. Thus, we demonstrate for the first time that in cyanobacterial cells, oxidative stress tolerance shows circadian oscillation.
Synergistic cues from diverse bacteria enhance multicellular development in a choanoflagellate
Authors: Ireland Ella V. , Woznica Arielle , King Nicole
Published: November 2019

Bacteria regulate the life histories of diverse eukaryotes, but relatively little is known about how eukaryotes interpret and respond to multiple bacterial cues encountered simultaneously. To explore how a eukaryote might respond to a combination of bioactive molecules from multiple bacteria, we treated the choanoflagellate Salpingoeca rosetta with two sets of bacterial cues, one that induces mating and the other that induces multicellular development. We found that simultaneous exposure to both sets of cues enhanced multicellular development in S. rosetta, eliciting both larger multicellular colonies and an increase in the number of colonies. Thus, rather than conveying conflicting sets of information, these distinct bacterial cues synergize to augment multicellular development. This study demonstrates how a eukaryote can integrate and modulate its response to cues from diverse bacteria, underscoring the potential impact of complex microbial communities on eukaryotic life histories.

Importance

Eukaryotic biology is profoundly influenced by interactions with diverse environmental and host-associated bacteria. However, it is not well understood how eukaryotes interpret multiple bacterial cues encountered simultaneously. This question has been challenging to address because of the complexity of many eukaryotic model systems and their associated bacterial communities. Here, we studied a close relative of animals, the choanoflagellate Salpingoeca rosetta, to explore how eukaryotes respond to diverse bacterial cues. We found that a bacterial chondroitinase that induces mating on its own can also synergize with bacterial lipids that induce multicellular “rosette” development. When encountered together, these cues enhance rosette development, resulting in the formation of more rosettes, each containing more cells than rosettes that form in the absence of the chondroitinase. These findings highlight how synergistic interactions among bacterial cues can influence the biology of eukaryotes.
Novel determination on root-knot nematodes; microspace, mineral profile and transduction of metabolic signals in tomato
Authors: García-Gaytán Víctor , Sánchez-Rodríguez Esteban , Ordaz-Ortiz José J. , Montero-Vargas Josaphat M. , Alonso-Pérez Olimpia , Rojas-Abarca Luis , Gómez-Cabrera Elena , Negrete-Guerrero Juan L.
Published: November 2019

Globally, nematodes are parasites that destroy many crops, however, their presence also serves as an indicator of the state of soil health. Tomato is a very studied, cultivated vegetable. In the micro-space of the knots we determine its pathogenesis. The macronutrients, micronutrients and beneficial elements present on root-knot nematodes were C>O> N (54.73, 37.57, and 3.55%), phosphorus (0.133%), Na>Ca>Mg>K cations (1.13, 1,032, 0.094, and 0.048%), S (0.247%), micronutrients Fe>Cl (0.163, 0.027%), and beneficial elements Si>Al (0.354, 0.985%). Progenesis of the chromatograms (ES+/ES-), 202 compounds were detected in the first polarity, in which 195 have at least one possible identification candidate, the second were 42 compounds, and 41 match with at least one compound. Putative compounds with the highest scores are reported in this research: kukoamina (57.6), furmecyclox (51.1), feruloylputrescina (55.3), N1-transferuloylagmatine (53.9), dehydrotomatin (49.8, 50.8, 52.3, 52.6), jurubine (54.8,51.6), etnangien (50.2), dehydromelilotoside (41.5), tomatine (55), minutissamide (51.7). Nematodes in state (J2), six nematodes within the knots with an average length of 1.16 mm, were found and their interaction with other microorganisms is possible. With the high concentrations of Na+ in the root, the concentration of the cation Mg2+ and K+ decreases; while the N does not present any change.
Do Muscle Synergies Improve Optimization Prediction of Muscle Activations During Gait?
Authors: Michaud Florian , Shourijeh Mohammad S. , Fregly Benjamin J. , Cuadrado Javier
Published: November 2019

Determination of muscle forces during motion can help to understand motor control, assess pathological movement, diagnose neuromuscular disorders, or estimate joint loads. Difficulty of in vivo measurement made computational analysis become a common alternative in which, as several muscles serve each degree of freedom, the muscle redundancy problem must be solved. Unlike static optimization (SO), synergy optimization (SynO) couples muscle activations across all time frames, thereby altering estimated muscle co-contraction. This study explores whether the use of a muscle synergy structure within a static optimization framework improves prediction of muscle activations during walking. A motion/force/EMG gait analysis was performed on five healthy subjects. A musculoskeletal model of the right leg actuated by 43 Hill-type muscles was scaled to each subject and used to calculate joint moments, muscle-tendon kinematics and moment arms. Muscle activations were then estimated using SynO with two to six synergies and traditional SO, and these estimates were compared with EMG measurements. SynO neither improved SO prediction of experimental activation patterns nor provided SO exact matching of joint moments. Finally, synergy analysis was performed on SO estimated activations, being found that the reconstructed activations produced poor matching of experimental activations and joint moments. As conclusion, it can be said that, although SynO did not improve prediction of muscle activations during gait, its reduced dimensional control space could be beneficial for applications such as functional electrical stimulation (FES) or motion control and prediction.
Early-life environmental enrichment generates persistent individualized behavior in mice
Authors: Zocher Sara , Schilling Susan , Grzyb Anna N. , Adusumilli Vijay S. , Lopes Jadna Bogado , Günther Sandra , Overall Rupert W. , Kempermann Gerd
Published: November 2019

Individuals differ in their response to environmental stimuli, but the stability of individualized behaviors and their associated changes in brain plasticity are poorly understood. We developed a novel model of enriched environment to longitudinally monitor 40 inbred mice exploring 35 connected cages over periods of three to six months. We show that behavioral individuality that emerged during the first three months of environmental enrichment persisted when mice were withdrawn from the enriched environment for three additional months. Behavioral trajectories were associated with stable inter-individual differences in adult hippocampal neurogenesis and persistent epigenetic effects on neuronal plasticity genes in the hippocampus. Using genome-wide DNA methylation sequencing, we show that one third of the DNA methylation changes were maintained after withdrawal from the enriched environment. Our results suggest that, even under the most constraint conditions controlling genes and environment, early-life experiences result in lasting individualized changes in behavior and brain plasticity.
A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea
Authors: Kirubakaran Tina Graceline , Andersen Øivind , Moser Michel , Arnyasi Mariann , McGinnity Philip , Lien Sigbjørn , Kent Matthew
Published: November 2019

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. Structurally, the genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig size of 686 Mb with a N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize in detail large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.
Neural adaptation to accented speech: prefrontal cortex aids attunement in auditory cortices
Authors: Blanco-Elorrieta Esti , Gwilliams Laura , Marantz Alec , Pylkkänen Liina
Published: November 2019

Speech is a complex and ambiguous acoustic signal that varies significantly within and across speakers. A prevalent and ubiquitous example of such variation is accented speech, to which humans adapt extremely rapidly. The goal of this study is to uncover the neurobiological bases of the attunement process that enables such fluent comprehension. Twenty-four native English participants listened to words spoken by an unaccented “canonical” American talker and two “accented” talkers, and performed a word-picture matching task, while magnetoencephalography (MEG) was recorded. Accented speech was created by including systematic phonological substitutions within the word (e.g. [s] → [sh]). Activity in the auditory cortex (superior temporal gyrus) was greater for accented speech, but, critically, this was not attenuated by exposure. By contrast, prefrontal regions showed an interaction between the presence of an accent and amount of exposure: while activity decreased for canonical speech over time, responses to accented speech remained consistently elevated. Grainger causality analyses further revealed that prefrontal responses serve to modulate activity in auditory regions, suggesting the recruitment of top-down processing to decode accented signal. In sum, our results show that accented speech does not elicit the same prefrontal reduction in amplitude over time that unaccented speech does, and points to a dynamic exchange of information between the prefrontal and auditory cortices in order to recalculate phonetic classification and subsequent identification of lexical items.

Significance statement

Human ability to adapt to different people’s idiosyncratic pronunciations is a hallmark of speech comprehension. This study aims to address whether adaptation to speakers’ accents manifests itself at the perceptual level (i.e. through adaptation of low-level neural responses in the auditory cortex) or at the post-perceptual level (i.e. higher-order regions correcting the sensory signal received from auditory cortex). Our results support the post-perceptual hypothesis: we found that responses in auditory cortex emitted an error-like signal that was invariant to exposure; whereas responses in the prefrontal cortex were modulated by exposure. These findings provide initial insight into accent adaptation, and illuminate the computational stages supporting speech comprehension more generally.
Open source digital library on open educational resources
Authors: Ahammad Nur
Published: November 2019

Purpose

This paper aims to explain the implementation procedure of DSpace at the Library of Independent University, Bangladesh. This paper shows how DSpace is promoting open educational resources (OER) movement and demonstrates the ease of implementing DSpace in an institution. Moreover, the purpose of this paper is to encourage library professionals to participate in the OER movement by implementing DSpace in their libraries.

Design/methodology/approach

The requirements for implementing DSpace have been shown in this paper. It also describes the system model of an academic repository (DSpace)/digital library (DL). In addition, the paper describes the legal issues for submitting an item in DSpace and self-submission process of an item as well as shows impact of DSpace on OER.

Findings

Open source software and Open Access Institutional Repository software has a fundamental role in promoting OER. DSpace is perfect for building a DL or an institutional repository in libraries, especially for developing country libraries because this demands low cost and it is easy to implement in libraries as well as is user-friendly.

Originality/value

This paper will help to understand the role of the library community and librarians about OER. It will also show the impact of DL on OER. In addition, this paper encourages librarians to participate in OER movement.
A weighted resource discovery approach in grid computing
Authors: Sabamoniri Saeed , Souri Alireza
Published: November 2019

Purpose

Grid computing is an effective environment for the execution of parallel applications that requires great computing power. This paper aims to present, based on the hierarchical architecture, an improved weighted resource discovery (WRD) algorithm to manage allocation of resources and minimize cost of communications between grid nodes.

Design/methodology/approach

A behavioral modeling method is addressed to prove the proposed method correctness. The behavioral model of the proposed algorithm is implemented by StarUML tool with two different model-checking mechanisms. Then, the resource discovery correctness is analyzed in terms of reachability condition, fairness condition and deadlock-free using NuSMV model checker.

Findings

The results show that WRD algorithm has better performance in requiring re-discovery process, the number of examined nodes in each request and discovering the free resources with high-bandwidth links.

Originality/value

To store information of resources, a new data structure called resource information table is proposed which facilitates resource finding of the algorithm. A behavioral modeling method is addressed to prove the proposed method correctness.
Political appearances
Authors: Buffam Bonar
Published: November 2019

Purpose

In Metro Vancouver, Vaisakhi celebrations are organized by local Sikh gurdwaras to mark the Punjabi harvest season and the anniversary of the Sikh Khalsa, which was formed in 1699. The purpose of this paper is to demonstrate how Vaisakhi celebrations have become mechanisms for state institutions to refigure and extend their racial authority over Sikh places and populations through their coordinated appearances at these public events. These appearances are analyzed to reveal how contemporary racial states are characterized by complex conditions of visibility and public identification that obscure and foreclose the racial conditions of their authority.

Design/methodology/approach

The data analyzed for this paper were generated through observational fieldwork at Vaisakhi celebrations and extensive archival and media research on the changing racial governance of Sikh and South Asian populations.

Findings

The results show that, in Metro Vancouver, racial modes of governance have created “post-racial” relations between the state’s public visages of diversity and accessibility and its expanded legal regulation of the social and political places of local Sikh populations.

Originality/value

The concept of political appearances is developed to explain how contemporary racial states reproduce and augment their authority through discursive practices of public engagement with minority populations as well as the specific aesthetic conditions of these engagements. The paper also offers important cautions against state practices that expand the presence of law enforcement within marginalized communities by showing how this enhanced visibility can engender forms of racialization.
Determinants of effective university–business collaboration
Authors: Alrajhi Ahmed Naser , Aydin Necati
Published: November 2019

Purpose

The attention to the university–business collaboration (UBC) for its role in the knowledge-based economy is growing in many countries. In this context, the purpose of this paper is to conduct two surveys to explore the causes of low collaboration between the private sector and academia in the Kingdom of Saudi Arabia.

Design/methodology/approach

The first survey covers nearly 50 companies to learn their perspectives. Using the findings of the first survey, a second survey was conducted of university researchers to understand the determinants of private and public funding of research and development projects. The survey provided two types of data, namely, categorical and continuous, which were subjected to reliability and normality tests. A linear regression analysis also was utilized to explore the role of different factors on the funded projects by the two sectors.

Findings

There is a perception among researchers that the private sector is woefully underestimating research capacity of Saudi universities. One interesting finding is that publishing in journals from the International Scientific Indexing (ISI) is a strong predictor for government funding, but not for private funding. From the private sector perspective, publishing in ISI-indexed journals is not sufficient evidence of research capability. Moreover, high teaching load is a major obstacle in acquiring private funding, but not so for public funding.

Practical implications

The paper provides two main recommendations to improve collaboration. First, universities should incentivize publishing in high-impact journals more than in ISI-indexed journals to increase the faculty’s research capabilities. Second, universities should reduce the teaching load of faculty involved in research projects, particularly those funded by the private sector.

Originality/value

The outcomes of this survey-based study are very valuable to the ecosystem of academia, business and government in general and for Saudi Arabia in particular, where there is a vital need to implement the right policies regarding UBC in the country.
Digital Rovaniemi: contemporary and future arctic tourist experiences
Authors: Varnajot Alix
Published: November 2019

Purpose

The purpose of this paper is to investigate tourists’ representations of the Arctic through the lens of the photo-sharing social network Instagram. The study focuses on the particular tourist experience of crossing the Arctic Circle in Rovaniemi, Finland, as in tourism, it represents the “official” entry to the Arctic. The study also aims at drawing assumptions about the future experiences of crossing the Arctic Circle, with the development of new technologies such as augmented and virtual realities.

Design/methodology/approach

Data were gathered with netnography methodologies on the Instagram social network. The first stage was the observational part and consisted of “lurking” at specific hashtags and locations, both referring to the Arctic Circle in Rovaniemi. Data were gathered in December 2018 and consisted of images and descriptions of Instagram posts published by users between June 1, 2018 and December 31, 2018, so data collection encompassed both summer and winter seasons. The second stage was the analysis part and involved interpretive understanding, and especially phenomenological sociology.

Findings

Results show that three dominant representations of the Arctic emerge when tourists cross the Arctic Circle. The region is either seen as a frozen fairytale wonderland due to the close proximity of the Christmas industry, as a far and northern destination participating in the realization of the self, and as a territory where summer weather conditions are not necessarily synonymous with the Arctic. In addition, the study acknowledges the future challenges of conceptualizing “Arctic tourism” due to the development of virtual reality technologies that could provide immersive Arctic experiences outside the region.

Originality/value

The paper investigates connections between social media studies and tourist experiences in the Arctic context. It also questions the future of Arctic tourist experiences with the development of new technologies enhancing experiences and, thus, potentially threatening the exceptionalism of the Arctic and what makes the region a unique tourism destination.
The regulations of shipping conferences in Taiwan referring to the EU to repeal the block exemption for liner conferences
Authors: Chiu Rong-Her
Published: November 2019

Purpose

The first well-known liner shipping conference was created for the UK/Calcutta trade in 1875. However, the European Union (EU) decided to abolish repeal the liner conferences system with effect from October 18 2008. This paper aims to study the governing regulations on shipping conferences in Taiwan along with investigating the impact on the EU to repeal conferences. The regulation on liner conferences in the USA is also briefly referred.

Design/methodology/approach

Literature review and questionnaire survey are used to conduct the study. This paper reviews important literature relating to the EU to repeal the conferences system and its impact on liner market competition to/from European trade routes, with discussions on the US and Taiwan regulations on shipping conferences. Questionnaire survey data, collected from published report and this research present shippers’ and carriers’ responses on the changes of regulations on liner conferences.

Findings

Shippers are strongly supporting the repeal of the conferences system. Academic research results basically reveal that the liner market will be more competitive in the trades to/from the USA and the EU after the repeal of the conferences. For Taiwan, its regulations are rather simple and loosely control over the liner conferences; therefore, if the shipping administration intends to enhance the inspection of the agreements of conferences and strategic alliances, more detailed regulations should be prepared, and the provisions of the EU or USA would be a good reference.

Practical implications

Through the discussions on the legal treatments of shipping conferences from the USA, the EU and Taiwan perspectives, this paper provides shipping researchers with not only a clear evolution of the liner conferences but also a deep understanding of the impact to repeal the conferences on liner market competition.

Originality/value

This paper reviews important literature and related legislations on liner conferences including the USA, the EU and Taiwan. The different responses on the EU to repeal the conferences system from shippers and carriers are discussed. The impact on liner market competition is presented.
Warming alters surface soil organic matter composition despite unchanged carbon stocks in a Tibetan permafrost ecosystem
Authors: Li Fei , Peng Yunfeng , Chen Leiyi , Yang Guibiao , Abbott Benjamin W. , Zhang Dianye , Fang Kai , Wang Guanqin , Wang Jun , Yu Jianchun , Liu Li , Zhang Qiwen , Chen Kelong , Mohammat Anwar , Yang Yuanhe
Published: November 2019

Climate warming can alter ecosystem carbon (C) balance and also the composition of soil organic matter (SOM), with important local and global implications. However, the extent to which rising temperature affects SOM composition in permafrost ecosystems remains poorly understood.

Here, we experimentally warmed a permafrost ecosystem by open‐top chambers (OTCs) on the Tibetan Plateau for 4 years to quantify the responses of C inputs via vegetation production, C losses via soil respiration and soil organic carbon (SOC) stocks in the top 30 cm. We also characterized the molecular composition of SOM using 13C nuclear magnetic resonance (NMR) and biomarker analyses.

The results indicated that warming treatment significantly increased root biomass, soil respiration, heterotrophic respiration and its contribution to soil respiration by 16.7%, 49.0%, 63.2% and 9.5% respectively. While we observed no change in SOC stocks, warming altered SOM composition in the 0–10 cm layer during the fourth experimental year. Warming increased the abundance of the alkyl C component (3.9%) and decreased aromatic C (5.1%), primarily lignin. The decrease in lignin‐derived compounds was attributable to the increased soil phenol oxidase activity.

Overall, the substantial increase in heterotrophic respiration and rapid degradation of relatively recalcitrant C components such as lignin demonstrate that Tibetan SOC stocks are vulnerable to climate warming, which could trigger positive C–climate feedback in a warmer world.

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