bluuebunny/crossref_metadata_2025_split huggingface dataset:
BASILIScan: a tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins
Authors: Barski Michał S 
Published: July 2018

AbstractBackgroundIntrinsic structural disorder is a common property of many proteins, especially in eukaryotic and virus proteomes. The tendency of some proteins or protein regions to exist in a disordered state usually precludes their structural characterisation and renders them especially difficult for experimental handling after recombinant expression.ResultsA new intuitive, publicly-available computational resource, called BASILIScan, is presented here. It provides a BLAST-based search for close homologues of the protein of interest, integrated with a simultaneous prediction of intrinsic disorder together with a robust data viewer and interpreter. This allows for a quick, high-throughput screening, scoring and selection of closely-related yet highly structured homologues of the protein of interest. Comparative parallel analysis of the conservation of extended regions of disorder in multiple sequences is also offered. The use of BASILIScan and its capacity for yielding biologically applicable predictions is demonstrated. Using a high-throughput BASILIScan screen it is also shown that a large proportion of the human proteome displays homologous sequences of superior intrinsic structural order in many related species.ConclusionThrough the swift identification of intrinsically stable homologues and poorly conserved disordered regions by the BASILIScan software, the chances of successful recombinant expression and compatibility with downstream applications such as crystallisation can be greatly increased.
Inferring interaction partners from protein sequences using mutual information
Authors: Bitbol Anne-Florence 
Published: July 2018

AbstractSpecific protein-protein interactions are crucial in most cellular processes. They enable multiprotein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between proteins result in coevolution between the interacting partners, and thus in correlations between their sequences. Pairwise maximum-entropy based models have enabled successful inference of pairs of amino-acid residues that are in contact in the three-dimensional structure of multi-protein complexes, starting from the correlations in the sequence data of known interaction partners. Recently, algorithms inspired by these methods have been developed to identify which proteins are specific interaction partners among the paralogous proteins of two families, starting from sequence data alone. Here, we demonstrate that a slightly higher performance for partner identification can be reached by an approximate maximization of the mutual information between the sequence alignments of the two protein families. This stands in contrast with structure prediction of proteins and of multiprotein complexes from sequence data, where pairwise maximum-entropy based global statistical models substantially improve performance compared to mutual information. Our findings entail that the statistical dependences allowing interaction partner prediction from sequence data are not restricted to the residue pairs that are in direct contact at the interface between the partner proteins.Author summarySpecific protein-protein interactions are at the heart of most intra-cellular processes. Mapping these interactions is thus crucial to a systems-level understanding of cells, and has broad applications to areas such as drug targeting. Systematic experimental identification of protein interaction partners is still challenging. However, a large and rapidly growing amount of sequence data is now available. Recently, algorithms have been proposed to identify which proteins interact from their sequences alone, thanks to the co-variation of the sequences of interacting proteins. These algorithms build upon inference methods that have been used with success to predict the three-dimensional structures of proteins and multi-protein complexes, and their focus is on the amino-acid residues that are in direct contact. Here, we propose a simpler method to identify which proteins interact among the paralogous proteins of two families, starting from their sequences alone. Our method relies on an approximate maximization of mutual information between the sequences of the two families, without specifically emphasizing the contacting residue pairs. We demonstrate that this method slightly outperforms the earlier one. This result highlights that partner prediction does not only rely on the identities and interactions of directly contacting amino-acids.
Effect of feeding and thermal stress on photosynthesis, respiration and the carbon budget of the scleractinian coral Pocillopora damicornis
Authors: Lyndby Niclas Heidelberg , Holm Jacob Boiesen , Wangpraseurt Daniel , Grover Renaud , Rottier Cécile , Kühl Michael , Ferrier-Pagès Christine 
Published: July 2018

AbstractStudying carbon dynamics in the coral holobiont provides essential knowledge of nutritional strategies and is thus central to understanding coral ecophysiology. In this study, the first aim was to investigate the effect of daily feeding and thermal stress on oxygen (O2) rates measured at polyp-scale with microsensors and at whole fragment scale using incubation methods. The second aim was to assess the carbon budget of the symbiotic association using H13CO3, under the different conditions. Micro- and macro-scale measurements revealed enhanced O2 evolution rates for fed compared to unfed corals. However, gross O2 production in fed corals was increased at high temperature on a macroscale but not on a microscale basis, likely due to a heterogeneous distribution of photosynthesis over the coral surface. Starved corals always exhibited reduced photosynthetic activity at high temperature, which suggests that the nutritional status of the coral host is a key limiting factor for coral productivity under thermal stress. Quantification of photosynthate translocation and carbon budgets showed very low incorporation rates, for both symbionts and host (0.03 - 0.6 μg C cm-2 h-1) equivalent to only 0.008 - 0.6 %, of the photosynthetically fixed carbon for P. damicornis, in all treatments. Carbon loss (via respiration and/or mucus release) was about 41 - 47 % and 52 - 76% of the fixed carbon for starved and fed corals, respectively. Such high loss of translocated carbon suggests that P. damicornis is nitrogen and/or phosphorus limited. Heterotrophy might thus cover a larger portion of the nutritional demand for P. damicornis than previously assumed. Our results suggest that active feeding plays a fundamental role in metabolic dynamics and bleaching susceptibility of corals.
Short-term insurance versus long-term bet-hedging strategies as adaptations to variable environments
Authors: Haaland Thomas Ray , Wright Jonathan , Tufto Jarle , Ratikainen Irja Ida 
Published: July 2018

AbstractUnderstanding how organisms adapt to environmental variation is a key challenge of biology. Central to this are bet-hedging strategies that maximize geometric mean fitness across generations, either by being conservative or diversifying phenotypes. Theoretical models of bet-hedging and the multiplicative fitness effects of environmental variation across generations have traditionally assumed that environmental conditions are constant within lifetimes. However, behavioral ecology has revealed adaptive responses to additive fitness effects of environmental variation within lifetimes, either through insurance or risk-sensitive strategies. Here we explore whether the effects of adaptive insurance interact with the evolution of bet-hedging by varying the position and skew of fitness functions within and between lifetimes. When insurance causes the optimal phenotype to shift from the peak to down the less steeply decreasing side of the fitness function, then conservative bet-hedging does not generally evolve on top of this, even if diversifying bet-hedging can. Canalization to reduce phenotypic variation within a lifetime is almost always favored, except when the tails of the fitness function are steeply convex and produce a novel risk-sensitive increase in phenotypic variance akin to diversifying bet-hedging. Importantly, using skewed fitness functions, we provide the first example of how conservative and diversifying bet-hedging strategies might coexist.
Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation
Authors: Macpherson Jamie A. , Theisen Alina , Masino Laura , Fets Louise , Driscoll Paul C. , Encheva Vesela , Snijders Ambrosius P. , Martin Stephen R. , Kleinjung Jens , Barran Perdita E. , Fraternali Franca , Anastasiou Dimitrios 
Published: July 2018

ABSTRACTAllosteric regulation is central to the role of the glycolytic enzyme pyruvate kinase M2 (PKM2) in cellular metabolism. Multiple activating and inhibitory allosteric ligands regulate PKM2 activity by controlling the equilibrium between high activity tetramers and low activity dimers and monomers. However, it remains elusive how allosteric inputs upon simultaneous binding of different ligands are integrated to regulate PKM2 activity. Here, we show that, in the presence of the allosteric inhibitor L-phenylalanine (Phe), the activator fructose 1,6-bisphosphate (FBP) can induce PKM2 tetramerisation, but fails to maximally increase enzymatic activity. Guided by a new computational framework we developed to identify residues that mediate FBP-induced allostery, we generated two PKM2 mutants, A327S and C358A, in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings demonstrate a role for residues involved in FBP-induced allostery in enabling the integration of allosteric input from Phe and reveal a mechanism that underlies the co-ordinate regulation of PKM2 activity by multiple allosteric ligands.
ALSgeneScanner: a pipeline for the analysis and interpretation of DNA NGS data of ALS patients
Authors: Iacoangeli Alfredo , Al Khleifat Ahmad , Sproviero William , Shatunov Aleksey , Jones Ashley R , Opie-Martin Sarah , Naselli Ersilia , Fogh Isabella , Hodges Angela , Dobson Richard J , Newhouse Stephen J , Al-Chalabi Ammar 
Published: July 2018

AbstractAmyotrophic lateral sclerosis (ALS, MND) is a neurodegenerative disease of upper and lower motor neurons resulting in death from neuromuscular respiratory failure, typically within two years of first symptoms. Genetic factors are an important cause of ALS, with variants in more than 25 genes having strong evidence, and weaker evidence available for variants in more than 120 genes. With the increasing availability of Next-Generation sequencing data, non-specialists, including health care professionals and patients, are obtaining their genomic information without a corresponding ability to analyse and interpret it. Furthermore, the relevance of novel or existing variants in ALS genes is not always apparent. Here we present ALSgeneScanner, a tool that is easy to install and use, able to provide an automatic, detailed, annotated report, on a list of ALS genes from whole genome sequence data in a few hours and whole exome sequence data in about one hour on a readily available mid-range computer. This will be of value to non-specialists and aid in the interpretation of the relevance of novel and existing variants identified in DNA sequencing data.
Tbx1 and Foxi3 genetically interact in the third pharyngeal pouch endoderm required for thymus and parathyroid development
Authors: Hasten Erica , Morrow Bernice E 
Published: July 2018

SummaryThe mechanisms required for segmentation of the pharyngeal apparatus to individual arches are not precisely delineated in mammalian species. Here, using conditional mutagenesis, we found that two transcription factor genes, Tbx1, the gene for 22q11.2 deletion syndrome and Foxi3, genetically interact in the third pharyngeal pouch endoderm for thymus and parathyroid gland development. We found that Tbx1 is autonomously required for the endoderm to form a temporary multilayered epithelium while invaginating. E-cadherin for adherens junctions remains expressed and cells in the apical boundary express ZO-1. Foxi3 is required autonomously to modulate proliferation and promote later restoration of the endoderm to a monolayer once the epithelia meet after invagination. Completion of this process cooccurs with expression of Alcam needed to stabilize adherens junctions and extracellular, Fibronectin. These processes are required in the third pharyngeal pouch to form the thymus and parathyroid glands, disrupted in 22q11.2 deletion syndrome patients.
Salinity shock in Jatropha curcas leaves is more pronounced during recovery than during stress time
Authors: Silva-Santos Leonardo , Corte-Real Natália , Dias-Pereira Jaqueline , Figueiredo Regina C.B.Q. , Endres Lauricio , Pompelli Marcelo F. 
Published: July 2018

AbstractTo verify the possible morphological and ultrastructural differences in the Jatropha curcas leaves, in response to high-intensity salt stress, three genotypes were evaluated (CNPAE183, JCAL171 and CNPAE218). In all the genotypes, 750mM NaCl, added to the nutrient solution, was applied to test its salt tolerance. For the analysis, the leaves were collected at three time points: (i) before stress (time 0 hour); (ii) during stress time (time 50 hours); and (iii) in the recovery period (time 914 hours) when the stressed plants recovered and demonstrated measurements of net photosynthetic with values similar to those demonstrated by the control plants. We showed that regardless of the genotype, saline shock caused an increase in the thickness of the mesophyll, and after the removal of NaCl, the thicker mesophyll remained in the JCAL171 and CNPAE218 genotypes, while the values observed in the CNPAE183 genotype were similar to those before stress. Scanning electron microscopy indicated that the stomata of CNPAE183 are smaller and have a stomatal index higher than the values demonstrated in JCAL171 and CNPAE218. Therefore, among the genotypes analysed, CNPAE183 demonstrates that it could be considered a promising genotype for future studies of genetic improvement that seek elite genotypes tolerant to salinity.HighlightsThis manuscript present the following highlights:The mesophyll thickness contributes to provide a smaller path for the CO2 to Rubisco J. curcas may reduce mesophyll air spaces as a strategy to mitigate low gas exchange Leaves modulate the expansion of stomata differently than other epidermal cells Smaller stomata with greater pore aperture are more abundant on the abaxial surface CNPAE183 is a candidate for studies in search of elite genotypes tolerant to salinity
Multiple Mechanisms Inactivate the LIN-41 RNA-Binding Protein to Ensure A Robust Oocyte-to-Embryo Transition inCaenorhabditis elegans
Authors: Spike Caroline A. , Huelgas-Morales Gabriela , Tsukamoto Tatsuya , Greenstein David 
Published: July 2018

ABSTRACTIn the nematodeCaenorhabditis elegans,the conserved LIN-41 RNA-binding protein is a translational repressor that coordinately controls oocyte growth and meiotic maturation. LIN-41 exerts these effects, at least in part, by preventing the premature activation of the cyclin-dependent kinase CDK-1. Here we investigate the mechanism by which LIN-41 is rapidly eliminated upon the onset of meiotic maturation. Elimination of LIN-41 requires the activities of CDK-1 and multiple SCF-type ubiquitin ligase subunits, including the conserved substrate adaptor protein SEL-10/Fbw7/Cdc4, suggesting that LIN-41 is a target of ubiquitin-mediated protein degradation. Within the LIN-41 protein, two non-overlapping regions, Deg-A and Deg-B, are individually necessary for LIN-41 degradation; both contain several potential phosphodegron sequences, and at least one of these sites is required for LIN-41 degradation. Finally, Deg-A and Deg-B are sufficient, in combination, to mediate SEL-10-dependent degradation when transplanted into a different oocyte protein. Although LIN-41 is a potent inhibitor of protein translation and M-phase entry, the failure to eliminate LIN-41 from early embryos does not result in the continued translational repression of LIN-41 oocyte mRNA targets. Based on these observations, we propose a molecular model for the elimination of LIN-41 by SCFSEL-10and suggest that LIN-41 is inactivated before it is degraded. Furthermore, we provide evidence that another RNA-binding protein, the GLD-1 tumor suppressor, is regulated similarly. Redundant mechanisms to extinguish translational repression by RNA-binding proteins may both control and provide robustness to irreversible developmental transitions, including meiotic maturation and the oocyte-to-embryo transition.
Acetic acid activates distinct taste pathways in Drosophila to elicit opposing, state-dependent feeding responses
Authors: Devineni Anita V. , Sun Bei , Zhukovskaya Anna , Axel Richard 
Published: July 2018

ABSTRACTTaste circuits are genetically determined to elicit an innate appetitive or aversive response, ensuring that animals consume nutritious foods and avoid the ingestion of toxins. We have examined the response of the fruit fly Drosophila melanogaster to acetic acid, a tastant that can be a metabolic resource but can also be toxic to the fly. Our data reveal that flies accommodate these conflicting attributes of acetic acid by virtue of a hunger-dependent switch in their behavioral response to this stimulus. Fed flies show taste aversion to acetic acid, likely a response to its potential toxicity, whereas starved flies show a robust appetitive response that may reflect their overriding need for calories. These opposing responses are mediated by two different classes of taste neurons. Acetic acid activates both the sugar and bitter pathways, which have opposing effects on feeding behavior. Hunger shifts the response from aversion to attraction by enhancing the appetitive sugar pathway as well as suppressing the aversive bitter pathway. Thus a single tastant can drive opposing behaviors by activating distinct taste pathways modulated by internal state.
Mechanisms for zinc and proton inhibition of the GluN1/GluN2A NMDA receptor
Authors: Jalali-Yazdi Farzad , Chowdhury Sandipan , Yoshioka Craig , Gouaux Eric 
Published: July 2018

SummaryN-Methyl-D-aspartate receptors (NMDARs) play essential roles in memory formation, neuronal plasticity and brain development with their dysfunction linked to a range of disorders from ischemia to schizophrenia. Zinc and pH are physiological allosteric modulators of NMDARs with GluN2A containing receptors inhibited by nanomolar concentrations of divalent zinc and by excursions to low pH. Despite the widespread importance of zinc and proton modulation of NMDARs, the molecular mechanism by which these ions modulate receptor activity has proven elusive. Here, we use cryo-electron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under a range of physiologically relevant zinc and proton concentrations. We show how zinc binding to the amino terminal domain elicits structural changes that are transduced though the ligand-binding domain and result in constriction of the ion channel gate.
Development of probiotic yogurt by incorporation of milk protein concentrate (MPC) and ‎microencapsulated Lactobacillus paracasei ‎ in gellan-caseinate mixture
Authors: Moghaddas Kia Ehsan , Ghasempour Zahra , Ghanbari Soheila , Pirmohammadi Rasool , Ehsani Ali 
Published: July 2018

Purpose
The purpose of this paper is to evaluate effects of simultaneous supplementation of milk protein concentrate (MPC) as texture modifier and microencapsulated Lactobacillus paracasei (L. paracasei) (entrapped in gellan–caseinate) on physico-chemical, sensorial and microbial characteristics of yogurt during storage time.

Design/methodology/approach
L. paracasei cells were encapsulated through unique pH triggered gelation technique using combination of sodium caseinate-gellan gum as protective shell material. MPC was also used to improve physico-chemical indices of probiotic yogurt at different levels (0–3 percent).

Findings
The results showed that yogurt samples containing encapsulated L. paracasei showed lower post-acidification and higher viability. Samples containing encapsulated L. paracasei showed less syneresis amount, due to possible hydration of shell material, also application of MPC could reduce this attribute during storage time. The numbers of probiotic bacteria were remained above the recommended therapeutic minimum throughout the samples.

Practical implications
The findings suggest a practical ingredient in probiotic dairy product. Simultaneous usage of this kind of encapsulation via MPC enhanced sensorial and physical properties of probiotic yogurt while of no reduction in viable counts survival.

Originality/value
This study revealed usage of microcapsules of L. paracasei prepared by the gelation of sodium caseinate-gellan gum could be a suitable manner for delivery of probiotics in fermented dairy products like yogurt.
The role of big data in shaping ambidextrous business process management
Authors: Dezi Luca , Santoro Gabriele , Gabteni Heger , Pellicelli Anna Claudia 
Published: July 2018

PurposeThe purpose of this paper is to explore how big data can shape ambidextrous business process management (BPM) in terms of exploitation and exploration.Design/methodology/approachA qualitative methodology involving case studies has been chosen to explore the impact of big data deployment on exploitative and explorative business processes.FindingsThe results of case studies offer some opportunities and challenges for service firms related to both the exploitative and the explorative aspects of BPM driven by big data.Originality/valueThe deployment of big data in business processes has attracted a large amount of interest recently. However, these studies are mostly conceptual, so empirical research about this complex relationship is quite rare, especially research with specific arguments regarding exploitative and explorative activities. This paper aims to fill this gap by offering empirical evidence for big data-driven business processes.
The dynamic information spill-over effect of WTI crude oil prices on China’s traditional energy sectors
Authors: Zhang Yue-Jun , Wu Yao-Bin 
Published: July 2018

Purpose
The purpose of this paper is to explore the dynamic influence of WTI crude oil returns on the stock returns of China’s traditional energy sectors, including oil and gas exploitation, coal mining and processing, petroleum processing and coking, electricity, heat production and supply and mining services.

Design/methodology/approach
Hong’s information spill-over test and the DP Granger causality test are applied to investigate the relationship between the two markets. Moreover, a rolling window is introduced into the above two tests to capture time-varying characteristics of the influence of WTI crude oil returns.

Findings
The empirical results indicate that, first, there exists significant bidirectional linear causality between WTI crude oil returns and China’s traditional energy sectoral stock returns, but the nonlinear causality appears weaker. Second, the influence of WTI crude oil returns on traditional energy sectoral stock returns has time-varying characteristics and industry heterogeneity both in the linear and nonlinear cases. Finally, the decline of WTI crude oil prices may strengthen its linear influence on the stock returns of traditional energy sectors, while the excessive rise of market values in traditional energy sectors may weaken the linear and nonlinear influence of WTI on them.

Originality/value
The general nexus between international crude oil market and China’s traditional energy stock market is explored both in the linear and nonlinear perspectives. In particular, the dynamic linear and nonlinear influence of WTI crude oil returns on China’s traditional energy sectoral stock returns and its industry heterogeneity are analysed in detail.