bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of aNidoviralesOrf1a N7-guanine cap Methyltransferase signature-sequence as a genetic marker of large genomeTobaniviridae
Authors: Ferron François , Debat Humberto Julio , Decroly Etienne , Canard Bruno
Published: May 2019

Members of theNidoviralesorder have (+)RNA genomes amongst the largest in size in the RNA virus world. Expression of their genes is promoted through reading of genomic RNA and mRNA transcripts by the ribosome of the infected cell. The 5’-end of these RNAs is supposedly protected by an RNA-cap structure (m7GpppNm) whose most synthesis steps remain elusive. In Eukaryotes, the RNA-cap structure is methylated by RNA methyltransferases (MTases) at the RNA-cap N7-guanine position as well as the 2’-O methyl position of the first transcribed nucleotide. InCoronaviridae, two separate enzymes (nsp14 and nsp16) perform the N7-guanine and the 2’-OH methylation, respectively. One salient feature of theNidoviralesN7-guanine MTase nsp14 is that it is the only example of non-Rossman fold viral MTase known so far. Conversely, all otherNidoviralesnsp16-like MTases have a canonical Rossman fold. ManyNidoviralesmembers lack either any RNA MTase signature sequence (e.g.,Arteriviridae), or lack a N7-guanine MTase signature sequence (e.g.,Tobaniviridae,Euroniviridae,Roniviridae,Medioniviridae). Both nsp14-and nsp16-like enzyme genes are usually located in Orf1b encoding for the replication machinery. Here, we report the discovery of a putative Rossman fold RNA MTase in the Orf1a of tenTobaniviridaemembers. Multiple sequence alignments and structural analyses identify this novel gene as a typical RNA-cap N7-guanine MTase with substrate specificity and active-site organization similar to the canonical eukaryotic RNA-cap N7-guanine MTase.
Dissociable effects of visual crowding on the perception of colour and motion
Authors: Greenwood John A. , Parsons Michael J.
Published: May 2019

Our ability to recognise objects in peripheral vision is fundamentally limited by crowding, the deleterious effect of clutter that disrupts the recognition of features ranging from orientation and colour to motion and depth. Prior research is equivocal on whether this reflects a singular process that disrupts all features simultaneously or multiple processes that affect each independently. We examined crowding for motion and colour, two features that allow a strong test of feature independence. ‘Cowhide’ stimuli were presented 15 degrees in peripheral vision, either in isolation or surrounded by flankers to give crowding. Observers reported either the target direction (clockwise/counterclockwise from upwards) or its hue (blue/purple). We first established that both features show systematic crowded errors (predominantly biased towards the flanker identities) and selectivity for target-flanker similarity (with reduced crowding for dissimilar target/flanker elements). The multiplicity of crowding was then tested with observers identifying both features: a singular object-selective mechanism predicts that when crowding is weak for one feature and strong for the other that crowding should be all-or-none for both. In contrast, when crowding was weak for colour and strong for motion, errors were reduced for colour but remained for motion, and vice versa with weak motion and strong colour crowding. This double dissociation reveals that crowding disrupts certain combinations of visual features in a feature-specific manner, ruling out a singular object-selective mechanism. The ability to recognise one aspect of a cluttered scene, like colour, thus offers no guarantees for the correct recognition of other aspects, like motion.

Significance statement

Our peripheral vision is primarily limited by crowding, the disruption to object recognition that arises in clutter. Crowding is widely assumed to be a singular process, affecting all of the features (orientation, motion, colour, etc.) within an object simultaneously. In contrast, we observe a double dissociation whereby observers make errors regarding the colour of a crowded object whilst correctly judging its direction, and vice versa. This dissociation can be reproduced by a population-coding model where the direction and hue of target/flanker elements are pooled independently. The selective disruption of some object features independently of others rules out a singular crowding mechanism, posing problems for high-level crowding theories, and suggesting that the underlying mechanisms may be distributed throughout the visual system.
Disruption of the CSF-1-CSF-1R axis alters cerebellar microglia and is associated with motor and social interaction defects
Authors: Kana Veronika , Desland Fiona A. , Casanova-Acebes Maria , Ayata Pinar , Badimon Ana , Nabel Elisa , Yamamuro Kazuhiko , Sneeboer Marjolein , Tan I-Li , Flanigan Meghan E. , Rose Samuel A. , Chang Christie , Leader Andrew , Bouris Hortense Le , Sweet Eric , Tung Navpreet , Wroblewska Aleksandra , Lavin Yonit , See Peter , Baccarini Alessia , Ginhoux Florent , Chitu Violeta , Stanley E. Richard , Russo Scott J. , Yue Zhenyu , Brown Brian D. , Joyner Alexandra L. , De Witte Lotje , Morishita Hirofumi , Schaefer Anne , Merad Miriam
Published: May 2019

Microglia, the brain resident macrophages, critically shape forebrain neuronal circuits. However, their precise function in the cerebellum is unknown. Here we show that human and mouse cerebellar microglia express a unique molecular program distinct from forebrain microglia. Cerebellar microglial identity was driven by the CSF-1R ligand CSF-1, independently of the alternate CSF-1R ligand, IL-34. Accordingly, CSF-1 depletion from Nestin+cells led to severe depletion and transcriptional alterations of cerebellar microglia, while microglia in the forebrain remained intact. Strikingly, CSF-1 deficiency and alteration of cerebellar microglia were associated with reduced Purkinje cells, altered neuronal function, and defects in motor learning and social novelty interactions. These findings reveal a novel CSF-1-CSF-1R signaling-mediated mechanism that contributes to motor function and social behavior.

Microglia are a heterogeneous population whose identity and function are dictated by signals from their microenvironment. Kana et al. show that CSF-1 signaling is critical for maintaining cerebellar microglial transcriptional identity and homeostasis, and that altering the CSF-1 – CSF-1R axis leads to motor and behavioral defects.
Genetic risk underlying psychiatric and cognitive symptoms in Huntington’s Disease
Authors: Ellis Natalie , Tee Amelia , McAllister Branduff , Massey Thomas , McLauchlan Duncan , Stone Timothy , Correia Kevin , Loupe Jacob , Kim Kyung-Hee , Barker Douglas , Hong Eun Pyo , Chao Michael J. , Long Jeffrey D. , Lucente Diane , Vonsattel Jean Paul G. , Pinto Ricardo Mouro , Elneel Kawther Abu , Ramos Eliana Marisa , Mysore Jayalakshmi Srinidhi , Gillis Tammy , Wheeler Vanessa C. , Medway Christopher , Hall Lynsey , Kwak Seung , Sampaio Cristina , Ciosi Marc , Maxwell Alastair , Chatzi Afroditi , Monckton Darren G. , Orth Michael , Landwehrmeyer G. Bernhard , Paulsen Jane S. , Shoulson Ira , Myers Richard H. , van Duijn Erik , Rickards Hugh , MacDonald Marcy E. , Lee Jong-min , Gusella James F. , Jones Lesley , Holmans Peter
Published: May 2019

Huntington’s disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the HTT gene. It is diagnosed following a standardized exam of motor control and often presents with cognitive decline and psychiatric symptoms. Recent studies have detected genetic loci modifying the age at onset of motor symptoms in HD, but genetic factors influencing cognitive and psychiatric presentations are unknown. We tested the hypothesis that psychiatric and cognitive symptoms in HD are influenced by the same common genetic variation as in the general population by constructing polygenic risk scores from large genome-wide association studies of psychiatric and neurodegenerative disorders, and of intelligence, and testing for correlation with the presence of psychiatric and cognitive symptoms in a large sample (n=5160) of HD patients. Polygenic risk score for major depression was associated specifically with increased risk of depression in HD, as was schizophrenia risk score with psychosis and irritability. Cognitive impairment and apathy were associated with reduced polygenic risk score for intelligence. In general, polygenic risk scores for psychiatric disorders, particularly depression and schizophrenia, are associated with increased risk of the corresponding psychiatric symptoms in HD, suggesting a common genetic liability. However, the genetic liability to cognitive impairment and apathy appears to be distinct from other psychiatric symptoms in HD. No associations were observed between HD symptoms and risk scores for other neurodegenerative disorders. These data provide a rationale for treatments effective in depression and schizophrenia to be used to treat depression and psychotic symptoms in HD.
Community structure – ecosystem function relationships in the Congo Basin methane cycle depend on the physiological scale of function
Authors: Meyer Kyle M. , Hopple Anya M. , Klein Ann M. , Morris Andrew H. , Bridgham Scott , Bohannan Brendan J. M.
Published: May 2019

Belowground ecosystem processes can be highly variable and difficult to predict using microbial community data. Here we argue that this stems from at least three issues: 1) complex covariance structure of samples (with environmental conditions or spatial proximity) can make distinguishing biotic drivers a challenge, 2) communities can control ecosystem processes through multiple mechanisms, making the identification of these controls a challenge and 3) ecosystem function assessments can be broad in physiological scale, encapsulating multiple processes with unique microbially mediated controls. We test these assertions using methane (CH4)-cycling processes in soil samples collected along a wetland-to-upland habitat gradient in the Congo Basin. We perform our measurements of function under controlled laboratory conditions and include environmental covariates in statistical analyses to aid in identifying biotic drivers. We divide measurements of microbial communities into four attributes (abundance, activity, composition, and diversity) that represent different forms of community control. Lastly, our process measurements differ in physiological scale, including broader processes (gross methanogenesis and methanotrophy) that involve more mediating groups, to finer processes (hydrogenotrophic methanogenesis and high-affinity CH4oxidation) with fewer mediating groups. We observed that finer scale processes can be more readily predicted from microbial community structure than broader scale processes. In addition, the nature of those relationships differed, with broad processes limited by abundance while fine-scale processes were associated with diversity and composition. These findings demonstrate the importance of carefully defining the physiological scale of ecosystem function and performing community measurements that represent the range of possible controls on ecosystem processes.
Dissection of central clock function inDrosophilathrough cell-specific CRISPR-mediated clock gene disruption
Authors: Delventhal Rebecca , Pantalia Meghan , O’Connor Reed M. , Ulgherait Matthew , Kim Han X. , Basturk Maylis , Canman Julie C. , Shirasu-Hiza Mimi
Published: May 2019

InDrosophila, ~150 neurons expressing molecular clock proteins regulate circadian behavior. Sixteen of these clock neurons secrete the neuropeptide Pdf and have been called “master pacemakers” because they are essential for circadian rhythms. A subset of Pdf+neurons (the morning oscillator) regulates morning activity and communicates with other non-Pdf+neurons, including a subset called the evening oscillator. It is assumed that the molecular clock in Pdf+neurons is required for these functions. To test this, we developed and validated Gal4-UAS based CRISPR tools for cell-specific disruption of key molecular clock components,periodandtimeless. While loss of the molecular clock in both the morning and evening oscillators eliminates circadian locomotor activity, the molecular clock in either oscillator alone is sufficient for circadian locomotor activity. This suggests that clock neurons do not act in a hierarchy but as a distributed network to regulate circadian activity.
Diffuse TBI-induced expression of anxiety-like behavior coincides with altered glutamatergic function, TrkB protein levels and region-dependent pathophysiology in amygdala circuitry
Authors: Beitchman Joshua A. , Griffiths Daniel R. , Hur Yerin , Ogle Sarah B. , Hair Caitlin E. , Morrison Helena W. , Lifshitz Jonathan , Adelson P. David , Thomas Theresa Currier
Published: May 2019

Up to 50% of traumatic brain injury (TBI) survivors demonstrate persisting affective symptoms indicative of limbic system dysregulation, yet the pathophysiology underlying the symptoms is unclear. We hypothesize that TBI-induced pathophysiologic changes within distinct amygdala nuclei contribute to the expression of late-onset anxiety-like behavior. Adult, male Sprague-Dawley rats underwent midline fluid percussion injury or sham surgery. Anxiety-like behavior was assessed at 7 and 28 days post-injury (DPI) followed by assessment of real-time glutamate neurotransmission in the basolateral amygdala (BLA) and central nucleus of the amygdala (CeA) using glutamate-selective microelectrode arrays. In separate animal cohorts, the presence of neuropathology, astrocytosis, and microglial activation were assessed at 1, 7, and 28DPI. Protein levels of glutamatergic transporters (Glt-1, GLAST) and presynaptic modulators of glutamate release (mGluR2, TrkB, BDNF, and glucocorticoid receptors) were quantified using automated capillary western techniques at 28DPI. The expression of anxiety-like behavior at 28DPI coincided with decreased glutamate release and slower glutamate clearance in the CeA, not BLA. Changes in glutamate neurotransmission were independent of protein levels of glutamate transporters and mGluR2 receptors, neuropathology, and astrocytosis. At 1DPI, microglia in the CeA demonstrated a neuroinflammatory response. BDNF and TrkB were decreased at 28DPI in the amygdala. These data indicate that diffuse axonal injury instigates sequences of molecular, structural and functional changes in the amygdala that contribute to circuit dysregulation relevant to the expression of affective disorders. Translationally, diffuse axonal injury can influence severity and incidence of affective symptoms and should be addressed in the history of patients with affective disorders.
Lexical landscapes as largein silicodata for examining advanced properties of fitness landscapes
Authors: Meszaros Victor A. , Miller-Dickson Miles D. , Ogbunugafor C. Brandon
Published: May 2019

In silicoapproaches have served a central role in the development of evolutionary theory for generations. This especially applies to the concept of the fitness landscape, one of the most important abstractions in evolutionary genetics, and one which has benefited from the presence of large empirical data sets only in the last decade or so. In this study, we propose a method that allows us to generate enormous data sets that walk the line betweenin silicoand empirical: word usage frequencies as catalogued by the Google ngram corpora. These data can be codified or analogized in terms of a multidimensional empirical fitness landscape towards the examination of advanced concepts—adaptive landscape by environment interactions, clonal competition, higher-order epistasis and countless others. We argue that the greaterLexical Landscapesapproach can serve as a platform that offers an astronomical number of fitness landscapes for exploration (at least) or theoretical formalism (potentially) in evolutionary biology.
Methods Matter -- Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors
Authors: Rumachik Neil G. , Malaker Stacy A. , Poweleit Nicole , Maynard Lucy H. , Adams Christopher M. , Leib Ryan D. , Cirolia Giana , Thomas Dennis , Stamnes Susan , Holt Kathleen , Sinn Patrick , May Andrew P. , Paulk Nicole K.
Published: May 2019

Different manufacturing approaches have been used in the production of recombinant adeno-associated virus (rAAV). The two leading approaches are transiently transfected human HEK293 cells and live baculovirus infection ofSf9insect cells. Unexplained differences in vector performance have been seen clinically and preclinically. Thus, we performed for the first time a highly controlled comparative production analysis varying only the host cell species but keeping all other rAAV production parameters the same. We demonstrate that host cell species is critical for determining vector potency. Given these key findings, we then sought to deeply characterize differences in rAAVs when produced by these two manufacturing platforms with multiple analytical approaches including: proteomic profiling by mass spectrometry, isoelectric focusing, cryo-EM, denaturation assays, genomic and epigenomic sequencing of packaged genomes, human cytokine profiling, and comparative functional transduction assessmentsin vitroandin vivo, including in humanized liver mice. Using these tools we’ve made two major discoveries: 1) rAAV capsids have post-translational modifications (PTMs) including glycosylation, acetylation, phosphorylation, methylation and deamidation, and these PTMs differ between platforms; 2) rAAV genomes are methylated during production, and these methylation marks are also differentially deposited between platforms. In addition, our data also demonstrate that host cell protein impurities differ between platforms and can have their own PTMs including potentially immunogenic N-linked glycans. We show that human-produced rAAVs are more potent than baculovirus-Sf9vectors in various cell typesin vitro(P< 0.05-0.0001), in various mouse tissuesin vivo(P< 0.03-0.0001), and in human liverin vivo(P< 0.005). Collectively, our findings were reproducible across vendors, including commercial manufacturers, academic core facilities, and individual laboratory preparations. These vector differences may have clinical implications for rAAV receptor binding, trafficking, expression kinetics, expression durability, vector immunogenicity as well as cost considerations.
Distinct sensorimotor feedback loops for dynamic and static control of primate precision grip
Authors: Oya Tomomichi , Takei Tomohiko , Seki Kazuhiko
Published: May 2019

Volitional limb motor control involves dynamic and static muscle actions. It remains elusive how such distinct actions are controlled through separated or shared neural circuits. Here we explored the potential separation for dynamic and static controls in the primate hand actions, by investigating the neuronal coherence between local 1eld potentials (LFPs) of the spinal cord and the forelimb electromyographic activity (EMGs), and LFPs of the motor cortex and the EMGs during the performance of a precision grip in macaque monkeys. We observed the emergence of beta-range coherence with EMGs at spinal cord and motor cortex in the separated phases; spinal coherence during the grip phase and cortical coherence during the hold phase. Further, both of the coherence were influenced by bidirectional interactions with reasonable latencies as beta oscillatory cycles. These results indicate that dedicated feedback circuits comprising spinal and cortical structures underlie dynamic and static controls of dexterous hand actions.
Overexpression ofMedicago sativa glutamate-semialdehyde aminotransferase(GSA) gene in tobacco increased photosynthesis efficiency
Authors: Ghasemzadeh Maryam , Khozeai Mahdi , Amiri Hamzeh
Published: May 2019

To investigate the effect of increasedglutamate-semialdehyde aminotransferase (GSA)on photosynthetic capacity and growth, tobacco (Nicoliana tabacumL. Xanti) plants with increased levels of glutamate-semialdehyde aminotransferase protein were produced. This was achieved using a cassette composed of a full-lengthMedicago sativecDNA under the control of the cauliflower mosaic virus 35S promoter. The results revealed distinct impacts of GSA activity on photosynthesis rate and growth inGSAover expression tobacco plants. In transgenic plants with increased GSA activity, an increase in soluble and insoluble sugars accumulation was evident. Total biomass, leaf area, plant height and internode 3-4 were increased inGSAsense plants, compared with equivalent wild-type tobacco plants. Moreover, transgenic tobacco plants with increased GSA activity exhibit higher levels of 5-aminolevulinic acid (ALA) accumulation and increased in content of chlorophyll and carotenoids pigments. Collectively, our data suggest that higher level of GSA activity gives an advantage to photosynthesis, growth in tobacco plants. This work also provides a case study that an individual enzyme in the biosynthesis of chlorophyll pathway may serve as a useful target for genetic engineering to improve photosynthesis and growth in plants.

Highlight

Overexpression ofglutamate-semialdehyde aminotransferase (GSA) increasephotosynthetic capacity, growth in tobacco.
Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
Authors: Thiergart Thorsten , Durán Paloma , Ellis Thomas , Garrido-Oter Ruben , Kemen Eric , Roux Fabrice , Alonso-Blanco Carlos , Ågren Jon , Schulze-Lefert Paul , Hacquard Stéphane
Published: May 2019

Factors that drive continental-scale variation in root microbiota and plant adaptation are poorly understood. We monitored root-associated microbial communities in Arabidopsis thaliana and co-occurring grasses at 17 European sites across three years. Analysis of 5,625 microbial community profiles demonstrated strong geographic structuring of the soil biome, but not of the root microbiota. Remarkable similarity in bacterial community composition in roots of A. thaliana and grasses was explained by the presence of a few diverse and geographically widespread taxa that disproportionately colonize roots across sites. In a reciprocal transplant between two A. thaliana populations in Sweden and Italy, we uncoupled soil from location effects and tested their respective contributions to root microbiota variation and plant adaptation. The composition of the root microbiota was affected by location and soil origin, and to a lesser degree by host genotype. The filamentous eukaryotes were particularly strongly affected by location. Strong local adaptation between the two A. thaliana populations was observed, with difference in soil properties and microbes of little importance for the observed magnitude of adaptive differentiation. Our results suggest that, across large spatial scales, climate is more important than are soil conditions for plant adaptation and variation in root-associated filamentous eukaryotic communities.
A rationally designed and highly versatile epitope tag for nanobody-based purification, detection and manipulation of proteins
Authors: Götzke Hansjörg , Kilisch Markus , Martínez-Carranza Markel , Sograte-Idrissi Shama , Rajavel Abirami , Schlichthaerle Thomas , Engels Niklas , Jungmann Ralf , Stenmark Pål , Opazo Felipe , Frey Steffen
Published: May 2019

Specialized epitope tags are widely used for detecting, manipulating or purifying proteins, but often their versatility is limited. Here, we introduce the ALFA-tag, a novel, rationally designed epitope tag that serves an exceptionally broad spectrum of applications in life sciences while outperforming established tags like the HA, FLAG or myc tags. The ALFA-tag forms a small and stable α-helix that is functional irrespective of its position on the target protein in prokaryotic and eukaryotic hosts. We developed a nanobody (NbALFA) binding ALFA-tagged proteins from native or fixed specimen with low picomolar affinity. It is ideally suited for super-resolution microscopy, immunoprecipitations and Western blotting, and also allows in-vivo detection of proteins. By solving the crystal structure of the complex we were able to design a nanobody mutant (NbALFAPE) that permits efficient one-step purifications of native ALFA-tagged proteins, complexes and even entire living cells using peptide elution under physiological conditions.
Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure
Authors: Suma Antonio , Stopar Alex , Nicholson Allen W. , Castronovo Matteo , Carnevale Vincenzo
Published: May 2019

We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
Live-cell STED microscopy of mitochondrial cristae
Authors: Stephan Till , Roesch Axel , Riedel Dietmar , Jakobs Stefan
Published: May 2019

Mitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for light microscopy. Relying on a cell line stably expressing the mitochondrial protein Cox8A fused to the SNAP-tag and using STED (stimulated emission depletion) super-resolution microscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells.
Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells
Authors: Kohyama Shunshi , Yoshinaga Natsuhiko , Yanagisawa Miho , Fujiwara Kei , Doi Nobuhide
Published: May 2019

Min system, which determines the cell division plane of bacteria, uses the localization change of protein (Min wave) emerged by a reaction-diffusion coupling. Although previous studies have shown that cell-sized space and boundaries modulate shape and speed of Min waves, its effects on Min wave emergence was still elusive. Here, by using a fully confined microsized space as a mimic of live cells, we revealed that confinement changes conditions for Min wave emergence. In the microsized space, an increase of surface-to-volume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary to produce stable Min wave generations. Furthermore, we showed that the cell-sized space more strictly limits parameters for wave emergence because confinement inhibits instability and excitability of the system. These results illuminate that confinement of reaction-diffusion systems works as a controller of spatiotemporal patterns in live cells.
Paraoxonase and acylated homoserine lactones in urine from patients with urinary tract infections
Authors: Lafleur John , Amdur Richard L.
Published: May 2019

Paraoxonases are mammalian enzymes that have a number of roles including the inhibition of bacterial virulence and biofilm formation by microorganisms that quorum sense with acylated homoserine lactones. Paraoxonases have previously been reported to inhibit P. aeruginosa biofilm formation in mammalian airways and skin. An innate immune role for paraoxonases in urinary tract infection has not previously been reported. We performed western blots for paraoxonase1 in urine from patients with urinary tract infection; we also tested urinary tract infection urine for the presence of acylated homoserine lactones using a cellular reporter system. We report here that paraoxonase1 was not found with our western blot assay in the urine of normal control patients; in those with urinary tract infection, paraoxonase1 was associated with E. coli UTI. Acylated homoserine lactones, but not paraoxonases, were found in the bulk urine of those with P. aeruginosa urinary tract infection. We hypothesize that paraoxonase may play a similar innate immune role in infected urine as has previously described in skin and airways.
Trypanosoma bruceiJ protein 2 functionally cooperates with the cytosolic Hsp70.4 and Hsp70 proteins
Authors: Bentley Stephen J. , Boshoff Aileen
Published: May 2019

The etiological agent of African trypanosomiasis,Trypanosoma brucei, has been identified to possess an expanded and diverse group of heat shock proteins, that have been implicated in cytoprotection, differentiation, and subsequently progression and transmission of the disease. Heat shock protein 70 is a highly conserved and ubiquitous molecular chaperone that is important in maintaining protein homeostasis in the cell. Its function is regulated by a wide range of co-chaperones; and inhibition of these functions and interactions with co-chaperones are emerging as potential therapeutic targets for numerous diseases. This study sought to biochemically characterize the cytosolic Hsp70 and Hsp70.4 proteins and to investigate if they form a functional partnership with the Type I J-protein, Tbj2. The cytosolic localisation of the proteins was confirmed by accessing the TrypTag endogenous tagging microscopy database. Expression of TbHsp70 was shown to be heat inducible, whilst TbHsp70.4 was constitutively expressed. The basal ATPase activities of TbHsp70.4 and TbHsp70 were stimulated by Tbj2. It was further determined that Tbj2 forms a functional partnership with TbHsp70 and TbHsp70.4 as the J-protein was shown to stimulate the ability of both proteins to mediate the refolding of chemically denatured β-galactosidase. This study provides further insight into this important class of proteins which may contribute to the development of new therapeutic strategies to combat African Trypanosomiasis.
Landscape of tumor-infiltrating immune cells in human immunogenic cancers:B cells are inversely associated with CD8T cells, but positively correlated with Treg cells
Authors: Chae Young Kwang , Bae William Han , Jung Minji , Kim Young Suk , Anker Jonathan Forrest , Tamragouri Keerthi , Matsangou Maria , Giles Francis Joseph
Published: May 2019

The composition of tumor-infiltrating immune cells may be a strong predictor of cancer treatment responses and survival outcomes. While B cells have been suggested to suppress T cell cytotoxicity in preclinical studies, it has been less understood whether B cells will exert immune-regulatory roles in human cancers. We explored immune cell landscapes in six human immunogenic cancers, including bladder cancer, head and neck cancer, lung adenocarcinoma, lung squamous cell carcinoma, melanoma, and renal cell carcinoma by calculating gene expression patterns of immune cell-specific metagenes in a total of 2951 cancers. We demonstrated that tumor-infiltrating activated B cells was correlated with regulatory T cell (Treg) infiltration, but had an inverse association with activated CD8 T cell infiltration consistently across all six human cancers. Tumors infiltrated by activated B cells (ActB+ tumors) demonstrated an elevated expression of regulatory cytokines and immune checkpoints, compared to tumors without infiltration by activated B cells (ActB-tumors). Activated B infiltration was not significantly associated with survival outcomes.

Précis

This human cancer tissue analysis showed that tumor infiltration by activated B cells correlates with decreased infiltration by activated CD8 T cells in immunogenic solid tumors, implicating B cell inhibition may enhance T cell-mediated cytotoxicity.
A general approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes
Authors: Paull Michael L. , Johnston Tim , Ibsen Kelly N. , Bozekowski Joel D. , Daugherty Patrick S.
Published: May 2019

Antibodies are essential to functional immunity, yet the epitopes targeted by antibody repertoires remain largely uncharacterized. To aid in characterization, we developed a generalizable strategy to identify antibody-binding epitopes within individual proteins and entire proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a random library and identified the peptides using next-generation sequencing. To identify antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We used the enrichment over background of these k-mers in the antibody-binding peptide dataset to identify antibody-binding epitopes. As a positive control, we used this approach, termed K-mer Tiling of Protein Epitopes (K-TOPE), to identify epitopes targeted by monoclonal and polyclonal antibodies of well-characterized specificity, accurately recovering their known epitopes. K-TOPE characterized a commonly targeted antigen fromRhinovirus A, identifying three epitopes recognized by antibodies present in 83% of sera (n = 250). An analysis of 2,908 proteins from 400 viral taxa that infect humans revealed seven enterovirus epitopes and five Epstein-Barr virus epitopes recognized by >30% of specimens. Analysis ofStaphylococcusandStreptococcusproteomes similarly revealed six epitopes recognized by >40% of specimens. These common viral and bacterial epitopes exhibited excellent agreement with previously mapped epitopes. Additionally, we identified 30 HSV2-specific epitopes that were 100% specific against HSV1 in novel and previously reported antigens. The K-TOPE approach thus provides a powerful new tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires.
A beamline-compatible STED microscope for combined visible-light and X-ray studies of biological matter
Authors: Bernhardt Marten , Nicolas Jan-David , Osterhoff Markus , Mittelstädt Haugen , Reuss Matthias , Harke Benjamin , Wittmeier Andrew , Sprung Michael , Köster Sarah , Salditt Tim
Published: May 2019

A dedicated stimulated emission depletion (STED) microscope had been designed and implemented into the Göttingen Instrument for Nano-Imaging with X-rays (GINIX) at the synchrotron beamline P10 of the PETRA III storage ring (DESY, Hamburg). The microscope was installed on the same optical table used for X-ray holography and scanning small-angle X-ray scattering (SAXS). Scanning SAXS was implemented with the Kirkpatrick–Baez (KB) nano-focusing optics of GINIX, while X-ray holography used a combined KB and X-ray waveguide optical system for full-field projection recordings at a defocus position of the object. The STED optical axis was aligned (anti-)parallel to the focused synchrotron beam and was laterally displaced from the KB focus. This close proximity between the STED and the X-ray probe enabled in situ combined recordings on the same biological cell, tissue or any other biomolecular sample, using the same environment and mounting. Here, the instrumentation and experimental details of this correlative microscopy approach are described, as first published in our preceding work [Bernhardt et al. (2018), Nat. Commun.
9, 3641], and the capabilities of correlative STED microscopy, X-ray holography and scanning SAXS are illustrated by presenting additional datasets on cardiac tissue cells with labeled actin cytoskeleton.
Crystal structure and Hirshfeld surface analysis of (Z)-6-[(2-hydroxy-5-nitroanilino)methylidene]-4-methylcyclohexa-2,4-dien-1-one
Authors: Kansiz Sevgi , Dege Necmi , Aydin Alev Sema , Ağar Erbil , Matushko Igor P.
Published: May 2019

The title compound, C14H12N2O4, is a Schiff base that exists in the keto–enamine tautomeric form and adopts a Z configuration. The molecule is almost planar, the rings making a dihedral angle of 4.99 (7)°. The molecular structure is stabilized by an intramolecular N—H...O hydrogen bond forming an S(6) ring motif. In the crystal, inversion-related molecules are linked by pairs of O—H...O hydrogen bonds, forming dimers with an R
2
2(18) ring motif. The dimers are linked by pairs of C—H...O contacts with an R
2
2(10) ring motif, forming ribbons extended along the [2\overline{1}0] direction. Hirshfeld surface analysis, two-dimensional fingerprint plots and the molecular electrostatic potential surfaces were used to analyse the intermolecular interactions present in the crystal, indicating that the most important contributions for the crystal packing are from H...H (33.9%), O...H/H...O (29.8%) and C...H/H...C (17.3%) interactions.
Mediterranean Diet adherence in emerging adults in Izmir
Authors: Genc Mahmut , Genc Seda
Published: May 2019

Purpose

The purpose of this paper is to evaluate the adherence and abandonment of the Turkish emerging adults in an Izmir University located at western Mediterranean coast of Turkey and to assess potential associations with anthropometric characteristics.

Design/methodology/approach

A cross-sectional survey (n=494, 18–27 years) carried out in 2017 among emerging adults in University. KIDMED Index was used to assess the degree of adherence Mediterranean Diet (MedDiet). The associations of KIDMED scores with demographic, residency and anthropometric were separately reported. The data were collected through standardized questionnaires directly from participants.

Findings

The average KIDMED score was calculated 4.86±2.5. Optimum adherence to the MedDiet was found only in 13.0 percent of participants, whereas 32.6 percent had poor adherence levels. Considering self-reported anthropometric data, the BMI values of the population was calculated as 22.3±3.9 kg/m2. In population, 13.9 percent of the subjects were underweight, while 16.0 percent were overweight and 3.9 percent obese. A significant association was found between BMI and KIDMED scores both in genders and residency.

Originality/value

This is the first study reporting the level of adherence to the MedDiet among Turkish emerging adults in terms of residency during education and the first KIDMED study conducted in Izmir located at Aegean Sea. The results support previously proposed transition concept by several scholar from different Mediterranean countries: it was found that only 13 percent of young adults having desired dietary habits in an Aegean city with local traditional cuisine highly affected by Cretan cuisine. These results are significant for University managements and health authorities in order to take actions for returning this transition contrariwise beginning with these groups.
Consumers’ willingness to buy dairy product imitations (analogues) based on structural equation modelling
Authors: Izsó Tekla , Szabó-Bódi Barbara , Somogyi László , Kasza Gyula
Published: May 2019

Purpose

Replacement of milk fat with vegetable fats (e.g. coconut oil or palm fat) in sour cream is a well-established practice among producers – these products are called sour cream imitations or sour cream analogues. Although sour cream imitations are legitimate products, consumers might be confused by them. The purpose of this paper is to assess the familiarity of sour cream imitations, the opinion of consumers, and to map the factors that may affect purchasing decision.

Design/methodology/approach

A quantitative consumer survey (n=1,000) has been conducted in 2017 based on personal interviews. Data were analysed by descriptive statistics and partial least squares structural equation modelling.

Findings

Results showed that the majority of Hungarian consumers have already purchased a sour cream imitation. In total, 69.65 per cent of them bought the imitation product accidentally: packaging and placement on the shelves were mentioned as major reasons. And 44.68 per cent of the respondents consider this product category to be misleading. Path modelling revealed that the perceived price-value ratio of the product and the respondent’s culinary skill, knowledge, consciousness and general preference of sour cream have a significant impact on the willingness to buy of sour cream imitations.

Originality/value

Sour cream imitations are accepted as reasonable cheaper alternatives to sour cream as it has been revealed by descriptive statistical methods and structural equation modelling. However, producers and retailers should avoid misleading packaging and product placement. General communication to broaden consumer knowledge would be also important. The study provides evidence-based input for producers, retailers, marketing experts and policy makers on consumer behaviour regarding food product analogues.
Relationships along the organic supply chain
Authors: Baron Haley , Dimitri Carolyn
Published: May 2019

Purpose

Since the implementation of the National Organic Program in 2002, the US organic market has grown in both scale and scope, consequently placing pressure on the organic supply chain. The crucial role of matching consumer demand for final products with farm-level production falls to certified organic handlers, the intermediary firms that process, manufacture and distribute organic products. Locating certified organic commodities and products that meet their needs, in a timely manner, is costly and challenging. The paper aims to discuss these issues.

Design/methodology/approach

A mixed-methods study was designed to better understand organic sector supply chain relationships in the USA. Data were collected from certified organic handlers via survey and semi-structured interviews. Those interviewed were randomly selected from 153 survey respondents who expressed an interest in being interviewed. This paper presents an analysis of interviews with 26 certified organic handlers regarding the relationships with their suppliers.

Findings

Three key concepts characterize the relationships between handlers and their suppliers: closeness, support and commitment. Nearly all handler supplier relationships possess some degree of closeness, where the handler expresses interest in their supplier. The relationships follow a spectrum of intensity, where the least engaged handlers provide little support and commitment, and the most engaged handlers provide support and commitment through a long-term relationship or contract.

Originality/value

Research into the organic supply chain is challenging to undertake, given the proprietary nature of the relationships. As the organic market continues to grow, the relationships along the supply chain will need to evolve to allow firms to meet consumer demand.
The antecedents and consequences of financial literacy: a meta-analysis
Authors: Santini Fernando De Oliveira , Ladeira Wagner Junior , Mette Frederike Monika Budiner , Ponchio Mateus Canniatti
Published: May 2019

Purpose

The purpose of this paper is to determine the antecedents and consequences of financial literacy by using meta-analytic techniques.

Design/methodology/approach

The authors conducted a meta-analysis of 44 valid studies, which generated a total of 690 observations (effect sizes).

Findings

The findings showed that the factors influencing financial literacy were as follows: educational level, financial attitude, financial knowledge, financial behaviour, gender, household income and investments. The consequences of financial literacy were the behaviour of incurring avoidable credit and checking fees, credit score, and the willingness to take investment risks. The authors also find some methodological, cultural, economic and theoretical moderations effects between financial literacy and antecedent/consequent constructs.

Research limitations/implications

This meta-analysis reviewed the relationships found worldwide in the literature on financial literacy. The authors also identified new avenues for future research. Some specific limitations, such as the non-use of qualitative studies, are registered.

Originality/value

This research tested the impact of the antecedents, consequences and moderators of financial literacy via a meta-analytical review. This meta-analysis contributes to the marketing and financial literature by offering a set of empirical generalisations about the direct and moderation effects investigated.
A systematic literature review of the evolution of pedagogy in entrepreneurial education research
Authors: Hägg Gustav , Gabrielsson Jonas
Published: May 2019

Purpose

The purpose of this paper is to create a better understanding of how entrepreneurial education research has evolved with regard to pedagogy over the past decades.

Design/methodology/approach

The authors employed systematic review methodology to enable an in-depth analysis of the literature in a process that was both replicable and transparent. Guided by the research purpose, the systematic review of 395 articles published between January 1980 and December 2018 was influenced by a configurative approach aimed at interpreting and understanding the phenomenon under study.

Findings

The analysis suggests that the scholarly discourse on pedagogy in entrepreneurial education research has developed over time from teacher-guided instructional models to more constructivist perspectives. A shift in the literature was also observed, where scholarly discussions moved from addressing the issue of teachability to a greater emphasis on learnability. Contemporary discussions centre on the theoretical and philosophical foundations of experience-based teaching and learning.

Originality/value

The study illustrates how entrepreneurial education has evolved into a distinct research theme, characterized by a practice-oriented research agenda that emphasizes the need to connect teaching to “real-world” environments. The practice-oriented agenda has led to continued societal interest in promoting entrepreneurial education, while at the same time creating low academic legitimacy.