bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein polyglutamylation catalyzed by the bacterial Calmodulin-dependent pseudokinase SidJ
Authors: Sulpizio Alan , Minelli Marena E. , Wan Min , Burrowes Paul D. , Wu Xiaochun , Sanford Ethan , Shin Jung-Ho , Williams Byron , Goldberg Michael , Smolka Marcus B. , Mao Yuxin
Published: August 2019

Pseudokinases are considered to be the inactive counterparts of conventional protein kinases and comprise approximately 10% of the human and mouse kinomes. Here we report the crystal structure of theLegionella pneumophilaeffector protein, SidJ, in complex with the eukaryotic Ca2+-binding regulator, Calmodulin (CaM). The structure reveals that SidJ contains a protein kinase-like fold domain, which retains a majority of the characteristic kinase catalytic motifs. However, SidJ fails to demonstrate kinase activity. Instead, mass spectrometry and in vitro biochemical analysis demonstrate that SidJ modifies anotherLegionellaeffector SdeA, an unconventional phosphoribosyl ubiquitin ligase, by adding glutamate molecules to a specific residue of SdeA in a CaM-dependent manner. Furthermore, we show that SidJ-mediated polyglutamylation suppresses the ADP-ribosylation activity. Our work further implies that some pseudokinases may possess ATP-dependent activities other than conventional phosphorylation.
Gestural Communication of Wild Bonnet Macaques in the Bandipur National Park, Southern India
Authors: Gupta Shreejata , Sinha Anindya
Published: August 2019

Nonhuman primate gestures are believed to be crucial evolutionary precursors of human language. Comparative studies on primate gestures in an evolutionary framework have, however, remained largely restricted to the great apes and the potential flexibility and richness of gestural communication in monkeys, especially in the wild, continue to be virtually unknown. In this paper, we followed several criteria, adapted from ape gesture studies, to identify gestures and evaluate their contexts of usage in the repertoire of wild bonnet macaques Macaca radiata in the Bandipur National Park of southern India. This report is the first of its kind to systematically identify gestures in any wild, non-ape species, thus providing a platform for comparative studies across primate taxa, particularly in our efforts to trace out the phylogenetic origins of language-like markers in the primate lineage, earlier than in the great apes.
Higher-order chromatin organization defines Progesterone Receptor and PAX2 binding to regulate estradiol-primed endometrial cancer gene expression
Authors: La Greca Alejandro , Bellora Nicolás , Le Dily Francois , Jara Rodrigo , Oliete Javier Quilez , Villanueva José Luis , Vidal Enrique , Merino Gabriela , Fresno Cristóbal , Rieschle Inti Tarifa , Vallejo Griselda , Vicent Guillermo P. , Fernández Elmer , Beato Miguel , Saragüeta Patricia
Published: August 2019

Estrogen (E2) and Progesterone (Pg), via their specific receptors (ER and PR respectively), are major determinants in the development and progression of endometrial malignancies. Here, we have studied how E2 and the synthetic progestin R5020 affect genomic functions in Ishikawa endometrial cancer cells. Using ChIPseq in cells exposed to the corresponding hormones, we identified cell specific binding sites for ER (ERbs) and PR (PRbs), which mostly correspond to independent sites but both adjacent to sites bound by PAX2. Analysis of long-range interactions by Hi-C showed enrichment of regions co-bound by PR and PAX2 inside TADs that contain differentially progestin-regulated genes. These regions, which we call “progestin control regions” (PgCRs), exhibit an open chromatin state prior to the exposure to the hormone. Our observations suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with partner transcription factors to PgCRs, compartmentalizing hormone-independent open chromatin.
Cost-free lifespan extension via optimisation of gene expression in adulthood supports the developmental theory of ageing
Authors: Lind Martin I. , Carlsson Hanne , Ivimey-Cook Edward , Maklakov Alexei A.
Published: August 2019

Classic theory upholds that energy trade-offs between reproduction and somatic maintenance underpin the evolution of ageing and lifespan. In contrast, the developmental theory of ageing (DTA) suggests that organismal senescence is caused by dysregulated gene expression in adulthood due to decline in selection gradients with age. The DTA predicts that age-specific optimisation of gene expression can improve survival without fitness costs. Here we investigated consequences for survival, reproduction, egg size and fitness of early-life, adulthood and post-reproductive onset of RNAi knockdown of five well-described “longevity” genes involved in key biological processes inCaenorhabditis elegansnematodes: nutrient-sensing signalling via insulin/IGF-1 (age-1) and target-of-rapamycin (raga-1) pathways, global protein synthesis (ifg-1), global protein synthesis in somatic cells (ife-2) and mitochondrial respiration (nuo-6). Downregulation of these genes in adulthood and/or during post-reproductive period improves survival, while there was little evidence for a link between impaired reproduction and extended lifespan. Our findings demonstrate that hyper-function of diverse physiological processes after sexual maturation is detrimental for survival. Therefore, optimisation of gene expression in adult organisms can ameliorate ageing and increase fitness.
RIP1 kinase mediates angiogenesis by modulating macrophages in experimental neovascularization
Authors: Ueta Takashi , Ishihara Kenji , Notomi Shoji , Lee Jong-Jer , Maidana Daniel , Efstathiou Nikolaos , Murakami Yusuke , Hasegawa Eiichi , Azuma Kunihiro , Toyono Tetsuya , Paschalis Eleftherios , Aihara Makoto , Miller Joan W. , Vavvas Demetrios G.
Published: August 2019

Inflammation plays an important role in pathologic angiogenesis. Receptor-interacting protein 1 (RIP1) is highly expressed in inflammatory cells and is known to play an important role in the regulation of apoptosis, necroptosis, and inflammation, however its role in angiogenesis remains elusive. Here, we show that RIP1 is abundantly expressed in infiltrating macrophages during angiogenesis, and genetic or pharmacological inhibition of RIP1 kinase activity using kinase-inactive RIP1K45A/K45Amice or necrostatin-1 attenuates angiogenesis in laser-induced choroidal neovascularization (CNV), Matrigel plug angiogenesis, and alkali injury-induced corneal neovascularization in mice. The inhibitory effect on angiogenesis was mediated by caspase activation through a kinase-independent function of RIP1 and RIP3, and simultaneous caspase inhibition with RIP1 kinase inhibition abrogated the effects of RIP1 kinase inhibition on angiogenesisin vivo. Mechanistically, infiltrating macrophages are the key target for RIP1 kinase inhibition to attenuate pathological angiogenesis, and we observed that the inhibition of RIP1 kinase activity is associated with caspase activation in infiltrating macrophages and decreased expression of pro-angiogenic M2-like markers while M1 marker expressions were sustained. Similarly,in vitro, catalytic inhibition of RIP1 down-regulated M2 marker expressions in IL-4-activated bone marrow-derived macrophages, which was blocked by simultaneous caspase inhibition. Taken together, these results suggest a novel, non-necrotic function of RIP1 kinase activity and suggest that RIP1-mediated modulation of macrophage activation may represent a therapeutic target for the control of angiogenesis-related diseases.

Significance

Pathological angiogenesis has been implicated in diverse pathologies. Infiltrating macrophages, especially those activated to M2-like phenotype are critically important to support angiogenesis. Whereas the role of RIP1 kinase in the regulation of apoptosis, necroptosis, and inflammation have been well established, its role in angiogenesis remains elusive despite being abundantly expressed in angiogenesis-related infiltrating macrophages. This study demonstrated for the first time that RIP1 kinase inhibition attenuates angiogenesis in multiple mouse models of pathological angiogenesisin vivo. Mechanistically, the inhibitory effect on angiogenesis depends on RIP kinase inhibition-mediated caspase activation in infiltrating macrophages that suppresses M2-like polarization, thereby attenuating pathological angiogenesis.
A cold shock protein from a thermophile bacterium promotes the high-temperature growth of bacteria and fungi through binding to diverse RNA species
Authors: Zhou Zikang , Tang Hongzhi , Wang Weiwei , Zhang Lige , Su Fei , Wu Yuanting , Bai Linquan , Li Sicong , Sun Yuhui , Tao Fei , Xu Ping
Published: August 2019

High temperatures deleteriously affect cells by damaging cellular structures and changing the behavior of diverse biomolecules, and extensive research about thermophilic microorganisms has elucidated some of the mechanisms that can overcome these effects and allow thriving in high-temperature ecological niches. We here used functional genomics methods to screen out a cold-shock protein (CspL) from a high-productivity lactate producing thermophile strain (Bacillus coagulansstrain 2-6) grown at 37°C and 60°C. We subsequently made the highly striking finding that transgenic expression of CspL conferred massive increases in high temperature growth of other organisms includingE. coli(2.4-fold biomass increase at 45°C) and the eukaryoteS. cerevisiae(a 2.7-fold biomass increase at 34°C). Pursuing these findings, we used bio-layer interferometry assays to characterize the nucleotide-binding function of CspLin vitro, and used proteomics and RNA-Seq to characterize the global effects of CspL on mRNA transcript accumulation and used RIP-Seq to identifyin vivoRNA targets of this nucleotide-binding protein (e.g.rpoE, andrmf, etc.). Finally, we confirmed that a nucleotide-binding-dead variant form of CspL does not have increased growth rates or biomass accumulation effects at high temperatures. Our study thus establishes that CspL can function as a global RNA chaperone.
Intracellular Galectin-9 controls dendritic cell function by maintaining plasma membrane rigidity
Authors: Cano Laia Querol , Tagit Oya , van Duffelen Anne , Dieltjes Shannon , Buschow Sonja I. , Niki Toshiro , Hirashima Mitsuomi , Joosten Ben , van den Dries Koen , Cambi Alessandra , Figdor Carl G. , van Spriel Annemiek B.
Published: August 2019

Extracellular Galectins constitute a novel mechanism of membrane protein organisation at the cell surface. Although Galectins are also highly expressed intracellularly, their cytosolic functions are poorly understood. Here, we investigated the role of Galectin-9 in dendritic cell (DC) surface organisation and function. By combining functional, super-resolution and atomic force microscopy experiments to analyse membrane stiffness, we identified intracellular Galectin-9 to be indispensable for plasma membrane integrity and structure in DCs. Galectin-9 knockdown studies revealed intracellular Galectin-9 to directly control cortical membrane structure via modulating Rac1 activity, providing the underlying mechanism of Galectin-9-dependent actin cytoskeleton organisation. Consequent to its role in maintaining plasma membrane structure, phagocytosis studies revealed that Galectin-9 was essential for C-type lectin receptor-mediated pathogen uptake by human DCs. This was confirmed by the impaired phagocytic capacity of Galectin-9-null murine DCs. Together, this study demonstrates a novel role for intracellular Galectin-9 in modulating DC function, which may be evolutionary conserved.
Patterns of genetic variability in genomic regions with low rates of recombination
Authors: Becher Hannes , Jackson Benjamin C. , Charlesworth Brian
Published: August 2019

Surveys of DNA sequence variation have shown that the level of genetic variability in a genomic region is often strongly positively correlated with its rate of crossing over (CO) [1–3]. This pattern is caused by selection acting on linked sites, which reduces genetic variability and can also cause the frequency distribution of segregating variants to contain more rare variants than expected without selection (skew). These effects of selection may involve the spread of beneficial mutations (selective sweeps, SSWs), the elimination of deleterious mutations (background selection, BGS) or both together, and are expected to be stronger with lower rates of crossing over [1–3]. However, in a recent study of human populations, the skew was reduced in the lowest CO regions compared with regions with somewhat higher CO rates [4]. A similar pattern is seen in the population genomic studies ofDrosophila simulansdescribed here. We propose an explanation for this paradoxical observation, and validate it using computer simulations. This explanation is based on the finding that partially recessive, linked deleterious mutations can increase rather than reduce neutral variability when the product of the effective population size (Ne) and the selection coefficient against homozygous carriers of mutations (s) is ≤ 1, i.e. there is associative overdominance (AOD) rather than BGS [5]. We show that AOD can operate in a genomic region with a low rate of CO, opening up a new perspective on how selection affects patterns of variability at linked sites.
Effects of Shift Work on the Carotid Artery and Cerebral Blood Flow of Spontaneously Hypertensive Rats and Wistar-Kyoto Rats
Authors: Wang YunLei , Zhang Tong , Zhang YuGe , Yu Yan , Bai Fan , Zhang HaoJie , Chi YaFei , Gao Shan
Published: August 2019

Objective

The objective was to investigate the effects of shift-work (SW) on the carotid arteries.

Methods

This study used two inverted photoperiods (inverted light:dark [ILD]16:8 and ILD12:12) to create the SW model. We recorded the rhythm and performed serological tests, carotid ultrasound, magnetic resonance imaging, and carotid biopsy.

Results

SW induced elevated blood pressure and increased angiotensin-II, apolipoprotein E, blood glucose, and triglycerides. SW increased the carotid intima-media thickness. SW led to the development of carotid arterial thrombosis, reduced cerebral blood flow, and increased the number of collagen fibers, expression of angiotensin receptor and low-density lipoprotein receptor in the carotid arteries. SW decreased 3-hydroxy-3-methylglutaryl-CoA reductase and nitric oxide. SW induced the atherosclerotic plaque in the aorta. Multiple results of SHR were worse than WKY rats.

Conclusion

SW can induce metabolic disorders and elevated blood pressure. SW can cause intima-media thickening of the carotid artery and aorta atherosclerosis. SW may result in carotid arterial thrombosis and affect cerebral blood flow. Hypertension can aggravate the adverse effects of SW.
Unravelling the virome in birch: RNA-Seq reveals a complex of known and novel viruses
Authors: Rumbou Artemis , Candresse Thierry , Marais Armelle , Svanella-Dumas Laurence , Landgraf Maria , von Bargen Susanne , Büttner Carmen
Published: August 2019

High-throughput sequencing (HTS), combined with bioinformatics forde novodiscovery and assembly of plant virus or viroid genome reads, has promoted the discovery of abundant novel DNA and RNA viruses and viroids. However, the elucidation of a viral population in a single plant is rarely reported. In five birch trees of German and Finnish origin exhibiting symptoms of birch leaf-roll disease (BRLD), we identified in total five viruses, among which three are novel. The number of identified virus variants in each transcriptome ranged from one to five. The novel species are genetically - fully or partially - characterized, they belong to the generaCarlavirus, IdaeovirusandCapillovirusand they are tentatively namedbirch carlavirus,birch idaeovirus, andbirch capillovirus, respectively. The only virus systematically detected by HTS in symptomatic trees affected by the BRLD was the recently discovered birch leafroll-associated virus. The role of the new carlavirus in BLRD etiology seems at best weak, as it was detected only in one of three symptomatic trees. Continuing studies have to clarify the impact of the carlavirus to the BLRD. The role of theCapillovirusand theIdaeoviruswithin the BLRD complex and whether they influence plant vitality need to be investigated. Our study reveals the viral population in single birch trees and provides a comprehensive overview for the diversities of the viral communities they harbor.
Cannibalism as a feeding strategy for mantis shrimp Oratosquilla oratoria (De Haan, 1844) in the Tianjin coastal zone of Bohai Bay
Authors: Bo Qi-Kang , Lu Yun-Zhao , Mi Hui-Jing , Yu Yan-Guang , Gu De-Xian , You Hong-Zheng , Hao Shuang
Published: August 2019

A representative semi-enclosed bay of China, Bohai Bay has experienced severe interference in recent decades and is under threat from rapid human development. Although the mantis shrimp Oratosquilla oratoria plays an important role in the ecosystem and fishery, its feeding ecology and the impact of habitat changes on its feeding habits are poorly known. In this study, we sought to identify the prey consumed by O. oratoria through the separation of stomach contents and to describe its trophic ecology during maturation, from March to July, in the Tianjin coastal zone of Bohai Bay. A total of 594 specimens were collected and 347 (58.59%) stomachs were found to have food remains. More than half of the O. oratoria individuals had poor feeding activity, and the degree of feeding activity of females was higher than that of males, but there was no significant difference in the visual fullness index and the fullness weight index (FWI) between sexes for each month. And the feeding activities of O. oratoria were consistent over the study months. A total of 207 prey items yielded 231 readable sequences and 24 different taxa were identified. Prey detected in O. oratoria consisted mainly of crustaceans, which accounted for 71.86 % of the clones detected; 16.02% corresponded to fishes, 8.23% corresponded to mollusks and the remaining 3.90% corresponded to other marine organisms. Cannibalism (occured frequently, 69.08%) in this study was noticeably higher than that seen in previous studies and confirmed that cannibalism may be a significant feeding strategy in the mantis shrimp O. oratoria in the Tianjin coastal zone of Bohai Bay. The ecological environment in Bohai Bay has been affected by anthropogenic activities and the macrofaunal biodiversity and abundance have noticeably declined, which might make the food scarce for the mantis shrimp O. oratoria. Then, the starvation obviously increased cannibalistic tendencies.
Protein dynamics regulate distinct biochemical properties of cryptochromes in mammalian circadian rhythms
Authors: Fribourgh Jennifer L. , Srivastava Ashutosh , Sandate Colby R. , Michael Alicia K. , Hsu Peter L. , Rakers Christin , Nguyen Leslee T. , Torgrimson Megan R. , Parico Gian Carlo G. , Tripathi Sarvind , Zheng Ning , Lander Gabriel C. , Hirota Tsuyoshi , Tama Florence , Partch Carrie L.
Published: August 2019

Circadian rhythms are generated by a transcription-based feedback loop where CLOCK:BMAL1 drive transcription of their repressors (PER1/2, CRY1/2), which bind to CLOCK:BMAL1 to close the feedback loop with ~24-hour periodicity. Here we identify a key biochemical and structural difference between CRY1 and CRY2 that underlies their differential strengths as transcriptional repressors. While both cryptochromes bind the BMAL1 transactivation domain with similar affinity to sequester it from coactivators, CRY1 is recruited with much higher affinity to the PAS domain core of CLOCK:BMAL1, allowing it to serve as a stronger repressor that lengthens circadian period. We identify a dynamic loop in the secondary pocket that regulates differential binding of cryptochromes to the PAS domain core. Notably, PER2 binding remodels this loop in CRY2 to enhance its affinity for CLOCK:BMAL1, explaining why CRY2 forms an obligate heterodimer with PER2, while CRY1 is capable of repressing CLOCK:BMAL1 both with and without PER2.
An advantage for targets located horizontally to the cued location
Authors: Clevenger John , Yang Pei-Ling , Beck Diane M.
Published: August 2019

Over the years a number of researchers have reported enhanced performance of targets located horizontally to a cued location relative to those located vertically. However, many of these reports could stem from a known meridian asymmetry in which stimuli on the horizontal meridian show a performance advantage relative to those on the vertical meridian. Here we show a horizontal advantage for target and cue locations that reside outside the zone of asymmetry; that is, targets that appear horizontal to the cue, but above or below the horizontal meridian, are more accurate than those that appear vertical to the cue, but again either above or below the horizontal meridian (Experiments 1 and 4). This advantage does not extend to non-symmetrically located targets in the opposite hemifield (Experiment 2), nor horizontally located targets within the same hemifield (Experiment 3). These data raise the possibility that display designs in which the target and cue locations are positioned symmetrically across the vertical midline may be underestimating the cue validity effect.
Structural Basis of H2B Ubiquitination-Dependent H3K4 Methylation by COMPASS
Authors: Hsu Peter L. , Shi Hui , Leonen Calvin , Kang Jianming , Chatterjee Champak , Zheng Ning
Published: August 2019

The COMPASS complex represents the prototype of the SET1/MLL family of methyltransferases that controls gene transcription by H3K4 methylation (H3K4me). Although H2B monoubiquitination (H2Bub) is well-known as a prerequisite histone mark for COMPASS activity, how the H2Bub-H3K4me crosstalk is catalyzed by COMPASS remains unclear. Here, we report the cryo-EM structures of an extended COMPASS catalytic module (CM) bound to the H2Bub and free nucleosome. The COMPASS CM clamps onto the nucleosome disk-face via an extensive interface to capture the flexible H3 N-terminal tail. The interface also sandwiches a critical Set1 arginine-rich motif (ARM) that auto-inhibits COMPASS. Unexpectedly, without enhancing COMPASS-nucleosome interaction, H2Bub activates the enzymatic assembly by packing against Swd1 and alleviating the inhibitory effect of the Set1 ARM upon fastening it to the acidic patch. By unmasking the spatial configuration of the COMPASS-H2Bub-nucleosome assembly, our studies establish the structural framework for understanding the long-studied H2Bub-H3K4me histone modification crosstalk.
Comparison of a GC-Orbitrap-MS with Parallel GC-FID Capabilities for Metabolomics of Human Serum
Authors: Misra Biswapriya B. , Bassey Ekong , Olivier Michael
Published: August 2019

Gas chromatography mass spectrometry (GC-MS) platforms for use in high throughput and discovery metabolomics have heavily relied on time of flight (ToF), and low resolution quadrupole and ion trap mass spectrometers and are typically run in electron ionization (EI) modes for matching spectral libraries. Traditionally, detectors such as flame ionization detection (FID), have also helped in identification and quantification of compounds in complex samples for diverse clinical applications, i.e., fatty acids. We probed if combination of FID in line with a high-resolution instrument like a GC-Orbitrap-MS may confer advantages over traditional mass spectrometry using EI.

We used a commercially available human serum sample to enhance the chemical space of serum using an advanced high resolution mass spectrometry (HR-MS) platform (QExactive Orbitrap-MS) with an FID feature for confident metabolite identification to assess the suitability of the platform for routine clinical metabolomics research. Using the EI mode, we quantified 294 metabolites in human serum using GC-Orbitrap-MS. These metabolites belonged to 89 biological pathways in KEGG. Following a sample split, using an in-line FID analysis, 1117 peaks were quantified. Moreover, representative peaks from FID and their corresponding MS counterparts showed a good correspondence when compared for relative abundance.

Our study highlights the benefits of the use of a higher mass accuracy instrument for untargeted GC-MS-based metabolomics not only with EI mode but also orthogonal detection method such as FID, for robust and orthogonal quantification, in future studies addressing complex biological samples in clinical set ups.
Molecular characteristics of chronic hepatitis B virus infection among voluntary blood donors in Kinshasa, Democratic Republic of the Congo
Authors: Maindo Pati Moloko , Mudwahefa Didier Anzenza , Mukendi Jean-Pierre Kambala , Yuma Sylvain Ramazani , Muwonga Jérémie Masidi , Misinzo Gerald
Published: August 2019

Background

Hepatitis B represents a major global health problem. Despite the high endemicity of hepatitis B in Sub-Saharan Africa, little is known about the molecular characteristics of chronic hepatitis B virus (HBV) infection in Africa, and there are very few published studies that describe the genetic characteristics of HBV in asymptomatic adults in DRC. The present study aimed at determining the molecular diversity of chronic HBV infection in voluntary blood donors in Kinshasa, DRC.

Methods

Blood samples from 582 voluntary blood donors at the National Blood Transfusion Centre in Kinshasa, DRC, were screened for hepatitis B surface antigen (HBsAg) using enzyme-linked immunosorbent assay (ELISA). Partial amplification and sequencing of S gene in HBV-positive samples was conducted.

Results

The presence of HBsAg was detected in 6.9 % (40/582) blood donors. Phylogenetic analysis based on partial S gene nucleotide sequences of HBV showed that the majority (66.7 %, 10/15) of HBV strains clustered into genotype A, followed by the genotypes E (26.6 %, 4/15) and D (6.7 %, 1/15). Genotype A strains were classified into subgenotype A1, quasi-subgenotype A3, and subgenotype A4, with quasi-subgenotype A3 being predominant. One new genotype A strain did not cluster with any existing HBV/A subgenotype or quasi-subgenotype.

Conclusions

The present study highlights the high genetic variability of chronic HBV infection in DRC, and the possibility of a new HBV/A subgenotype, suggesting that HBV has a long evolutionary history in DRC. Further molecular characterization of complete HBV genomes is needed for a more accurate assessment of HBV genetic variability and its clinical significance in DRC, as partial sequences are not appropriate for determining HBV new subgenotypes.
Glycoproteomic measurement of site-specific polysialylation
Authors: Pelingon Ruby , Pegg Cassandra L. , Zacchi Lucia F. , Phung Toan K. , Howard Christopher B. , Xu Ping , Hardy Matthew P. , Owczarek Catherine M. , Schulz Benjamin L.
Published: August 2019

Polysialylation is the enzymatic addition of a highly negatively charged sialic acid polymer to the non-reducing termini of glycans. Polysialylation plays an important role in development, and is involved in neurological diseases, neural tissue regeneration, and cancer. Polysialic acid (PSA) is also a biodegradable and non-immunogenic conjugate to therapeutic drugs to improve their pharmacokinetics. PSA chains vary in length, composition, and linkages, while the specific sites of polysialylation are important determinants of protein function. However, PSA is difficult to analyse by mass spectrometry (MS) due to its high negative charge and size. Most analytical approaches for analysis of PSA measure its degree of polymerization and monosaccharide composition, but do not address the key questions of site specificity and occupancy. Here, we developed a high-throughput LC-ESI-MS/MS glycoproteomics method to measure site-specific polysialylation of glycoproteins. This method measures site-specific PSA modification by using mild acid hydrolysis to eliminate PSA and sialic acids while leaving the glycan backbone intact, together with protease digestion followed by LC-ESI-MS/MS glycopeptide detection. PSA-modified glycopeptides are not detectable by LC-ESI-MS/MS, but become detectable after desialylation, allowing measurement of site-specific PSA occupancy. This method is an efficient analytical workflow for the study of glycoprotein polysialylation in biological and therapeutic settings.

Graphical Abstract
The effects of intrinsic and extrinsic motivation on students learning effectiveness. Exploring the moderating role of gender
Authors: Zaccone Maria Cristina , Pedrini Matteo
Published: August 2019

Purpose

The purpose of this paper is to investigate the relationship between individual motivation – both intrinsic and extrinsic – and learning effectiveness; moreover, this paper also investigates whether this relationship is moderated by gender.

Design/methodology/approach

A quasi-experimental study was conducted. The research measured intrinsic motivation, extrinsic motivation and learning effectiveness among 1,491 students attending a course-work in informatics and computer basics in three different contexts: Burundi, Morocco and India.

Findings

Findings suggest that intrinsic motivation has a positive effect on learning effectiveness, while extrinsic motivation has a negative effect on learning effectiveness. It also shows that gender has a moderating role.

Originality/value

This research offers interesting contributions to the extant literature: first, it is the first to consider the moderating role of gender in the relationship between students’ motivation and learning effectiveness; second, it proposes the analysis of a rather broad data set with 1,491 students, thus providing strong empirical research based on a consistent data set.
The networked enterprise and legitimacy judgments: why digital platforms need leadership
Authors: Wang Chong , Cardon Peter Wilson
Published: August 2019

Purpose

In recent years, scholars, business practitioners and consultants frequently talk about building the networked enterprise. The purpose of this paper is to examine the connections between networked enterprises, organizational legitimacy and organizational performance.

Design/methodology/approach

A survey was developed that measured the following aspects of a networked enterprise: employees who network and communicate extensively via internal digital platforms across their organizations; leaders who actively use internal digital platforms to communicate with employees; leaders who actively communicate with stakeholders via external digital platforms; and an innovation culture. The survey measured the following forms of legitimacy judgments: moral; instrumental; and relational. Altogether, 501 executives and managers were surveyed (207 executives, 147 senior managers and 147 managers) in mid-to-large sized (over 500 employees) companies.

Findings

The analyses showed strong statistical significance for nearly all relationships. Internal communication on digital platforms, networked employee communication and an innovation culture all contributed to moral, instrumental and relational legitimacy. Leadership communication on external digital platforms (social media) was not a significant contributor to moral or relational legitimacy but was a significant contributor to instrumental legitimacy. Higher organization legitimacy was correlated with higher profit growth.

Practical implications

Leaders and communicators should prioritize a networked enterprise in several ways. They should actively communicate with employees on internal digital platforms. To be absent on internal digital platforms is a significant missed opportunity by leaders to build organizational legitimacy. Further, leaders and communicators should actively promote networked communication among employees as much as possible. Finally, leaders and communicators should communicate, model and reward an innovation culture.

Originality/value

There are no known scholarly studies that accomplish the following: empirically examine a model of networked enterprises comprised of vertical and horizontal communication and an innovation culture; and make connections between leadership communication on digital platforms in networked enterprises with legitimacy judgments. The large sample of contemporary executives and managers bolsters the strength of the findings.
Teaching through culture
Authors: Sturdivant Toni Denese , Alanís Iliana
Published: August 2019

Purpose

Oftentimes, attempts at culturally relevant early childhood practices are limited to diverse materials in the physical environment. The purpose of this study is to document the culturally relevant teaching practices, specifically for African American children, within a culturally diverse preschool classroom with a Black teacher.

Design/methodology/approach

The researchers used qualitative methodology to answer the following question: How does a Black preschool teacher enact culturally relevant practices for her African American students in a culturally diverse classroom? Data sources included field notes from classroom observations, transcripts from both formal and informal semi-structured interviews with a Master Teacher and photographs.

Findings

The authors found that the participant fostered an inclusive classroom community and a classroom environment that reflected the range of human diversity. She was intentional in her integration of culturally representative read alouds and lessons designed to incorporate students’ interests. Finally, she engaged families by facilitating their involvement in her curriculum. However, social justice aspects were absent during the time of the study.

Originality/value

This paper contributes to the literature in that it documents a high-quality early childhood classroom with a teacher, that is, actively trying to incorporate the cultures of her African American students. Many extant studies provide examples of superficial culturally relevant pedagogy (CRP) being enacting in early childhood classrooms or the focus is not specifically on African American children.
Predicted property investment returns: risk and growth models
Authors: French Nick
Published: August 2019

Purpose

The purpose of this paper is to discuss the principal measures of performance used in property and other investment types. In particular, the briefing will explore the relationship of the expected IRR with the initial return, highlighting the role of growth in the investment dynamic.

Design/methodology/approach

This education briefing is an overview of investment growth models with worked examples.

Findings

The analysis of property growth models is akin to the Fisher and Gordon growth models used in other finance markets.

Practical implications

This comparison of the models can work for all forms of investment. Similarly, instead of looking at the overall return as the measure of comparison (expected vs required), it is possible to work backwards and deduce market expectations and compare these with the investors view on those variables.

Originality/value

This is a review of existing models.
European energy security dilemma: major challenges and confrontation strategies
Authors: Elbassoussy Ahmed
Published: August 2019

Purpose

The purpose of this paper is to develop an integrated theoretical framework for energy security concept and to shed light on the policies and strategies applied by the European Union countries to confront the challenges that faces them.

Design/methodology/approach

The research paper uses Regional Security complexes theory, which mainly developed in Copenhagen school for security studies, that founded by Barry Buzan. This school tried to clarify the untraditional security aspects, through expanding its scope by adding new dimensions than military perspective.

Findings

Despite the consolidated efforts exerted by the European Union to assure safe levels of energy security, and their continuous pursuit to be liberated from Russian energy over dependence, but the results are still limited.

Originality/value

The value of this research paper stems from the fact that it encompass the theoretical aspect by shedding light on all the developments occurred to energy security concept, in addition to the Empirical side, by analyzing various European energy security challenges and their confrontation strategies.
A physiological model for predicting dynamics of tree stem‐wood non‐structural carbohydrates
Authors: Fang Jing , Lutz James A. , Shugart Hank H. , Yan Xiaodong
Published: August 2019

Non‐structural carbohydrates (NSC) are considered important in the metabolism of wood plants, and they are highly dynamic. Accurate and detailed modelling of NSC dynamics may increase the understanding of physiological processes.

We constructed a physiological model that simulates NSC dynamics from photosynthesis, transpiration and growth carbon demand. With this model, we tested the hypotheses that production, allocation and storage explain tree‐ and forest‐level carbohydrates balance, and especially that cambial activities explain the major portion of carbon consumption.

We applied this model at one plot in Harvard Forest, Massachusetts, USA. The predicted results of stem‐wood NSC dynamics of 20 deciduous broad‐leaved trees corresponded well with measurements. NSC (i.e. product from photosynthesis) allocations depended on thermal time and the development stage of each organ. Water movements driven by water potential gradients in whole‐trees also influenced tree growth, which was a necessary process for predicting the daily NSC dynamics.

Synthesis. This model combined wood growth at whole‐tree scale and carbohydrates balance at cellular scale with short‐term vegetation hydraulics. The model provides a foundation to further understand the complex interactions between environmental factors and tree carbon allocation.
Do independent treatment centers offer more value than general hospitals? The case of cataract care
Authors: Kruse Florien M. , Groenewoud Stef , Atsma Femke , van der Galiën Onno P. , Adang Eddy M. M. , Jeurissen Patrick P. T.
Published: August 2019

Objective

To identify differences between independent treatment centers (ITCs) and general hospitals (GHs) regarding costs, quality of care, and efficiency.

Data Sources

Anonymous claims data (2013‐2015) were used. We also obtained quality indicators from a semipublic platform.

Study Design

This study uses a comparative multilevel analysis, controlling for case mix, to evaluate the performance of ITCs and GHs for patients diagnosed with cataract.

Data Collection

Reimbursement claims were extracted from existing claims databases of the largest Dutch health insurer. Quality indicators were obtained by external agencies through a mixed‐mode survey.

Principal Findings

There are no stark differences in complexity of cases for cataract care. ITCs seem to perform surgeries more frequently per care pathway, but conduct a lower number of health care activities per surgical claim. Total average costs are lower in ITCs compared with GHs, but when adjusted for case mix, the differences in costs are lower. The findings with the adjusted quality differences suggest that ITCs outperform GHs on patient satisfaction, but patients’ outcomes are similar.

Conclusion

This finding supports the postulation—based on the focus factory theory—that ITCs can provide more value for cataract care than GHs.
Using Canola Oil Organogels as Fat Replacement in Liver Pâté
Authors: Barbut Shai , Marangoni Alejandro G. , Thode Uwe , Tiensa Brian E.
Published: August 2019

Five canola oil organogel formulations were used to replace pork fat in pâtés to increase unsaturated fat content, and to determine their effects on texture and sensory properties. While pâtés made with canola oil were softer than the control pork fat product at room temperature, pâtés made with gelled canola oil (organogel pâtés) had similar hardness values to the control. Back extrusion results (also a measure of spreadability) showed that pâté made with canola oil only was softer than the control at 4 °C, but the pâtés made with organogels were similar to the control. Organogel pâtés were perceived to have similar sensory hardness, oiliness, and juiciness as the control. Pâtés made with organogels showed higher oil loss, over time, compared to control; however, pâtés made with organogels containing glycerol monostearate showed lower oil loss after 24 hr (P < 0.05) compared to the other organogel treatments. Light microscopy showed that fat globule size was notably larger in pâtés made with organogels than in the pork fat and the canola oil control pâtés. The color of organogel pâtés was darker compared to pâtés made with pork fat or canola oil only. Sensory data showed that all fat replaced pâtés had very similar flavor profiles. Overall, organogel pâtés showed comparable textural, physical, and sensory properties to the traditional pâté made with pork fat, while reducing the saturated fat content by 60%.

Practical Application

Use of vegetable oil in highly emulsified liver pâté has been shown to be possible via the use of organogels prepared with ethylcellulose. This has been a challenge because some of the meat proteins are heat denatured prior to the emulsification process. Overall, the use of organogels, with specific hardness and oil retention values, is possible as demonstrated in this publication.
Sensory Shelf Life Estimation of Novel Fortified Blended Foods Under Accelerated and Real‐Time Storage Conditions
Authors: Chanadang Sirichat , Chambers Edgar
Published: August 2019

Fortified blended foods (FBFs), a staple of food aid around the world, must maintain desirable characteristics for long periods of storage. This study estimated the shelf life of FBFs, including a traditional FBF (nonextruded corn soy blend plus [CSB+]) and 13 novel extrusion cooked FBFs. All products were stored under accelerated and real‐time environments (real time = 30 °C and 65% relative humidity [RH], accelerated = 50 °C and 70% RH based on a Q10 factor of 2). Products were made into porridges and evaluated by a descriptive sensory panel for five times in each shelf life condition. Rancid and painty sensory characteristics were key determining factors for shelf life. Real‐time (RT) and accelerated shelf life (ASL) testing agreed that most novel extrusion cooked FBFs had shelf lives of at least 2 years, which is comparable to current CSB+. However, ASL testing failed to predict RT shelf life of two novel FBFs, which were estimated by RT testing to have a 2+ year shelf life. The results indicated that novel extrusion cooked FBFs have high potential for use as alternative complementary food and maintain quality for long storage periods. It is essential to conduct RT testing parallel with ASLT testing, especially for new products, to obtain a more precise estimation of products’ shelf life.

Practical Application

These findings show that extrusion cooked novel fortified blended foods made with extrusion generally can last up to or exceeding 24 months at ambient conditions as measured either real‐time or under accelerated conditions. This is plenty of time for storage, shipping, distribution, and home storage of such products by recipients. Thus, there should be no concerns about shelf life of these products for international distribution.
Nitrous oxide emissions associated with ammonia‐oxidizing bacteria abundance in fields of switchgrass with and without intercropped alfalfa
Authors: Pannu Manmeet W. , Meinhardt Kelley A. , Bertagnolli Anthony , Fransen Steven C. , Stahl David A. , Strand Stuart E.
Published: August 2019

The nitrogen (N) fertilizer required to supply a bioenergy industry with sufficient feedstocks is associated with adverse environmental impacts, including loss of oxidized reactive nitrogen through leaching and the production of the greenhouse gas nitrous oxide (N2O). We examined effects on crop yield, N fate and the response of ammonia‐oxidizing bacteria (AOB) and ammonia‐oxidizing archaea (AOA) to conventional fertilizer application or intercropping with N‐fixing alfalfa, for N delivery to switchgrass (Panicum virgatum), a potential bioenergy crop. Replicated field plots in Prosser, WA, were sampled over two seasons for reactive nitrogen, N2O gas emissions, and bacterial and archaeal ammonia monooxygenase gene (amoA) counts. Intercropping with alfalfa (70:30, switchgrass:alfalfa) resulted in reduced dry matter yields compared to fertilized plots, but three times lower N2O fluxes (≤ 4 g N2O‐N ha−1 d−1) than fertilized plots (12.5 g N2O‐N ha−1 d−1). In the fertilized switchgrass plots, AOA abundance was greater than AOB abundance, but only AOB abundance was positively correlated with N2O emissions, implicating AOB as the major producer of N2O emissions. A life cycle analysis of N2O emissions suggested the greenhouse gas emissions from cellulosic ethanol produced from switchgrass intercropped with alfalfa cultivation would be 94% lower than emissions from equivalent gasoline usage.
The Key: Education as a Tool and Weapon
Authors: Goodison Racquel
Published: August 2019

This essay utilizes autoethnography to explore myriad cultural and institutional practices that impacted the author’s education while she was growing up in Jamaica, West Indies. Informed by and through the use of some postcolonial theory, the information in this text is presented in the form of the creative nonfiction essay and chronicles the ways in which education is a path to economic well‐being as well as a lesson in acculturation.
Inherited retinal disease in Norway – a characterization of current clinical and genetic knowledge
Authors: Holtan Josephine Prener , Selmer Kaja Kristine , Heimdal Ketil Riddervold , Bragadóttir Ragnheiður
Published: August 2019

Purpose

The purpose of this study was to characterize current clinical and genetic knowledge of patients with inherited retinal disease in Norway and give an estimate of the prevalence. These data are necessary to identify patients eligible for new personalized medicines, to facilitate genetic counselling for their families and to plan clinical follow‐up.

Methods

A patient registry including clinical and genetic data was established. Clinical data were retrieved during 2003–2018. Genetic testing was performed in the period 2007–2018.

Results

The material included 866 patients with 41 clinical diagnoses at the cut‐off date. The most prevalent diseases were as follows: retinitis pigmentosa (54%), Stargardt macular dystrophy (6.5%) and Leber congenital amaurosis (5.2%). A genetic diagnosis was identified in 32% of patients. In total, 207 disease‐causing variants in 56 genes were reported. The most commonly reported disease‐causing genes were ABCA4, USH2A and BEST1. The estimated adjusted minimum prevalence of inherited retinal disease in the south‐east region of Norway was 1: 3,856 (2.6/10 000).

Conclusion

This population‐based study demonstrated an estimated prevalence for all inherited retinal diseases in south‐east Norway and described the distribution of clinical diagnoses, onset of symptoms, inheritance patterns and genetic data and thereby expands our knowledge of inherited retinal disease in Norway. The newly established registry and biobank will support patient feasibility for future clinical trials, treatment selection and counselling of families.
A ‘Decent Cuppa’: Worker Power and Consumer Power in the Sri Lankan Tea Sector
Authors: Thomas Huw
Published: August 2019

Consumers are increasingly seen as playing an important role in global labour governance through the establishment of voluntary certification programmes that promise better economic and social conditions for workers in global value chains. In the Sri Lankan tea sector, however, these private forms of governance (Rainforest Alliance (RA), UTZ Certified and the Ethical Tea Partnership (ETP)) at best have no effect and at worst are associated with indecent forms of work. Rather, conditions of work are defended by powerful trade unions that exercise structural power via their strategic position in the value chain and associational power through links with political parties and residual ethnic ties within and between nation‐states. It is evident that through close collaboration between the International Labour Organization (ILO) and the tea sector unions, workers are able to leverage institutional power through both national and international labour standards to reinforce decent work for those at the very bottom of the global value chain.