bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional and translation shut-off in TBEV infected neural cells and involvement of viral C protein
Authors: Tykalová Hana , Selinger Martin , Štěrba Ján , Věchtová Pavlína , Kohl Alain , Schnettler Esther , Grubhoffer Libor 
Published: December 2019

Tick-borne encephalitis virus (TBEV, Flaviviridae) infection causes severe neurological disease and incapacitates more than 10 000 patients annually in the Eurasian region. Despite extensive studies, some areas of interaction of TBEV with the host cells remain undescribed. Here we investigated the interaction of TBEV and human neural DAOY HTB-186 cells on the transcriptional and translational level.
By labelling of nascent RNA and protein molecules in TBEV-infected DAOY cells, we showed that the virus-induced host translational shut-off. Moreover, TBEV interfered also with the expression of host ribosomal RNAs, in particular with the rRNA species transcribed by RNA polymerase I (18S rRNA, 28S rRNA, and their precursor 45-47S pre-rRNA). Synthesis of host rRNAs is an essential host cell process that is localized in the nucleus, namely nucleoli. By searching for virus factor that could be linked with these effects, we described so far unknown nucleolar localization of TBEV capsid protein C. More importantly, preliminary data from transfection of recombinant C protein led to the reduction in nascent protein synthesis indicating the link between TBEV capsid protein and shut-off phenomena which were described. Furthermore, we identified a potential nuclear localization signal, which seems not to be essential for the shut-down effect.
Taken together we described a brand new type of interaction between TBEV and host neural cells on the transcriptional and translational level and identified viral factor potentially responsible for the observed phenomena. However, further analyses are needed, and the particular mechanism of action remains still elusive.
Implications of vertical transmission of Alphaviruses in Aedes aegypti mosquitoes
Authors: Rodriguez Julio , Fazakerley John 
Published: December 2019

Mosquitoes are vectors for epidemic transmission of viruses of public and veterinary health. The mosquito vector is generally infected for life although, unlike the vertebrate counterpart, does not suffer a high fitness cost. Having a vector infected for the length of its life enables routes of viral transmission other than the classic infected bite (horizontal), including sexual (horizontal) and to the progeny (vertical). Vertical transmission is considered a route of transmission that allows for the persistence of the virus during adverse environmental periods (e.g., droughts, cold periods). Because Aedes aegypti and Aedes albopictus eggs are resistant to dessication, it is hypothesised that this attribute could promote arbovirus survival between transmission cycles, playing an important role in maintaining the pathogen.
Vertical transmission of arboviruses has been extensively documented for flaviviruses and bunyaviruses. However, there is very little and contradictory reports of vertical transmission of alphaviruses. In this research we establish the mechanisms of vertical transmission of the alphaviruses Semiliki Forest virus (SFV) and Ross river virus (RRV) and its implications in pathogen transmission of future generations.

Aedes aegypti mosquitoes were infected with SFV virus in different gonotrophic cycles. Their offspring was then reared and challenged with SFV, RRV and dengue virus (DENV). Offspring from infected parents showed significant reduction in viral load if infected with SFV or RRV but not with DENV.
Findings of this research highlight the importance of vertical transmission of alphaviruses in the general arbovirus infectious cycle.
St Abbs Head phlebovirus – a separate virus species or a strain of Uukuniemi phlebovirus?
Authors: Szemiel Agnieszka , Willett Brian , Ma Wing See 
Published: December 2019

St Abbs Head virus (SAHV), member of Phlebovirus genus (family Phenuiviridae, order Bunyavirales), belongs to the largest group of negative strand RNA viruses. All phleboviruses share a genome structure that comprises three segments of negative-sense or ambi-sense RNA. The viral genome is composed of the small (S), medium (M) and large (L) RNA segments. The S segment encodes the nucleocapsid (N) protein, the M segment encodes the precursor for the viral glycoproteins (Gn and Gc) and the L segment encodes the viral RNA-dependent RNA polymerase (RdRp). Some viruses within the genus also encode non-structural proteins within their S or M segments.
SAHV was isolated from a pool of Ixodes uriae ticks collected at a seabird colony in Berwickshire, Scotland in 1979. There were quite a few related bunyaviruses found in tick and bird samples on the East Coast of Scotland and England in the 70s and 80s. Recently we have sequenced a sample of SAHV using next generation sequencing technology. The results suggested that this virus is very closely related to the Uukuniemi phlebovirus (UUKV). To determine how similar are SAHV and UUKV, we compared virus growth in various mammalian, bird and tick cell lines.
SCHEEPDOG: programming electric cues to dynamically herd large-scale cell migration
Authors: Zajdel Tom J. , Shim Gawoon , Wang Linus , Rossello-Martinez Alejandro , Cohen Daniel J. 
Published: December 2019

AbstractDirected cell migration is critical across biological processes spanning healing to cancer invasion, yet no existing tools allow real-time interactive guidance over such migration. We present a new bioreactor that harnesses electrotaxis—directed cell migration along electric field gradients—by integrating four independent electrodes under computer control to dynamically program electric field patterns, and hence steer cell migration. Using this platform, we programmed and characterized multiple precise, two-dimensional collective migration maneuvers in renal epithelia and primary skin keratinocyte ensembles. First, we demonstrated on-demand, 90-degree collective turning. Next, we developed a universal electrical stimulation scheme capable of programming arbitrary 2D migration maneuvers such as precise angular turns and migration in a complete circle. Our stimulation scheme proves that cells effectively time-average electric field cues, helping to elucidate the transduction time scales in electrotaxis. Together, this work represents an enabling platform for controlling cell migration with broad utility across many cell types.
rMSIcleanup: An open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization
Authors: Baquer Gerard , Sementé LLuc , García-Altares María , Lee Young Jin , Chaurand Pierre , Correig Xavier , Ràfols Pere 
Published: December 2019

AbstractMass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove matrix-related signals based on its chemical formula and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classifym/zsignals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows.Resources availabilityThe R package presented in this publication is freely available under the terms of the GNU General Public License v3.0 athttps://github.com/gbaquer/rMSIcleanup. The datasets used in the experiments can be accessed upon request to the corresponding author.
Big data from small tissues: extraction of high-quality RNA for different plant tissue types during oilseedBrassicaspp. seed development for RNA-Sequencing
Authors: Siles Laura , Eastmond Peter , Kurup Smita 
Published: December 2019

AbstractObtaining high-quality RNA for gene expression analyses from different seed tissues is challenging due to the presence of various contaminants, such as polyphenols, polysaccharides and lipids which interfere with RNA extraction methods. At present, the available protocols for extracting RNA from seeds require high amounts of tissue and are mainly focused on extracting RNA from whole seeds. However, extracting RNA at the tissue level enables more detailed studies regarding tissue specific transcriptome during development. Seeds from heart stage embryo to mature developmental stages ofBrassica napusandB. oleraceawere sampled for isolation of the embryo, endosperm and seed coat tissues. Ovules and gynoecia wall tissue were also collected at the pre-fertilization stage. After testing several RNA extraction methods, E.Z.N.A. Plant RNA Kit and Picopure RNA Isolation kit extraction methods with some modifications, as well as the use of PVPP for seed coats and endosperms at green stages, resulted in high RNA concentrations with clear 28S and 18S bands and high RIN values. Here, we present efficient and reliable RNA extraction methods for different genotypes ofBrassicaspp for different tissue types during seed development. The high-quality RNA obtained by using these methodologies is suitable for RNA-Sequencing and gene expression analyses.
Sex Differences in Behavioral Responses during a Conditioned Flight Paradigm
Authors: Borkar Chandrashekhar D. , Dorofeikova Mariia , Le Quan-Son Eric , Vutukuri Rithvik , Vo Catherine , Hereford Daniel , Resendez Alexis , Basavanhalli Samhita , Sifnugel Natalia , Fadok Jonathan P. 
Published: December 2019

AbstractFemales exhibit greater susceptibility to trauma- and stress-related disorders compared to males; therefore, it is imperative to study sex differences in the mode and magnitude of defensive responses in the face of threat. To test for sex differences in defensive behavior, we used a modified Pavlovian fear conditioning paradigm that elicits clear transitions between freezing and flight behaviors within individual subjects. Female mice subjected to this paradigm exhibited higher percentages of freezing behavior compared to males, especially during the intertrial interval period. Female mice also exhibited more cued freezing in response to the conditioned stimuli in the last block of extinction training. Furthermore, there were sex differences in the expression of other adaptive behaviors during fear conditioning. Assaying rearing, grooming, and tail rattling behaviors during the conditioned flight paradigm yielded measurable differences across sessions and between males and females. Overall, these results provide insight into sex-dependent alterations in mouse behavior induced by fear conditioning.HighlightsMale and female mice do not differ in conditioned flight behavior.Female mice exhibit more freezing behavior.Rearing, self-grooming, and tail rattling behavior changes across days.Male mice exhibit more rearing and grooming behavior.Female mice exhibit more tail rattling behavior.
Retrograde transport of mannose-6-phosphate receptor depends on several sorting machineries as analyzed by sulfatable nanobodies
Authors: Buser Dominik P. , Spiess Martin 
Published: December 2019

AbstractRetrograde protein transport from the cell surface and endosomes to the trans-Golgi network (TGN) is essential for membrane homeostasis in general and for the recycling of mannose-6-phosphate receptors (MPRs) for sorting of lysosomal hydrolases in particular. Several different sorting machineries have been implicated in retrieval from early or late endosomes to the TGN, mostly for the cation-independent MPR (CIMPR), mainly by analysis of steady-state localization and by interaction studies. We employed a nanobody-based sulfation tool to more directly determine transport kinetics from the plasma membrane to the TGN – the site of sulfation – for the cation-dependent MPR (CDMPR) with and without silencing of candidate machinery proteins. The clathrin adaptor AP-1 that operates bidirectionally at the TGN-to-endosome interface, which had been shown to cause reduced sulfation when rapidly depleted, produced hypersulfation of nanobodies internalized by CDMPR upon long-term silencing, reflecting accumulation in the TGN. In contrast, knockdown of retromer (Vps26), epsinR, or Rab9 reduced CDMPR arrival to the TGN. No effect was observed upon silencing of TIP47. Most surprisingly, depletion of the GGA (Golgi-localized, γ-adaptin ear-containing, Arf-binding) proteins inhibited retrograde transport rather than TGN exit. This study illustrates the usefulness of derivatized, sulfation-competent nanobodies to analyze retrograde protein transport to identify the contributions of different machineries.
The functional organization of high-level visual cortex determines the representation of complex visual stimuli
Authors: Kliger Libi , Yovel Galit 
Published: December 2019

SummaryA hallmark of high-level visual cortex is its functional organization of neighboring clusters of neurons that are selective to single categories such as faces, bodies and objects. However, visual scenes are typically composed of multiple categories. How does category-selective cortex represent such complex stimuli? According to a normalization mechanism, the response of a single neuron to multiple stimuli is normalized by the response of its neighboring neurons (normalization pool). Here we show that category-selectivity, measured with fMRI, can provide an estimate for the heterogeneity of the normalization pool, which determines the response to multiple stimuli. These results provide a general framework for the varying representations of multiple stimuli that were reported in different regions of category-selective cortex in neuroimaging and single-unit recording studies. This type of organization may enable a dynamic and flexible representation of complex visual scenes that can be modulated by higher-level cognitive systems according to task demands.
Unraveling nanotopography of cell surface receptors
Authors: Franke Christian , Chum Tomáš , Kvíčalová Zuzana , Glatzová Daniela , Rodriguez Alvaro , Helmerich Dominic A. , Frank Otakar , Brdička Tomáš , van de Linde Sebastian , Cebecauer Marek 
Published: December 2019

ABSTRACTCells communicate with their environment via surface receptors, but nanoscopic receptor organization with respect to complex cell surface morphology remains unclear. This is mainly due to a lack of accessible, robust and high-resolution methods. Here, we present an approach for mapping the topography of receptors at the cell surface with nanometer precision. The method involves coating glass coverslips with glycine, which preserves the fine membrane morphology while allowing immobilized cells to be positioned close to the optical surface. We developed an advanced and simplified algorithm for the analysis of single-molecule localization data acquired in a biplane detection scheme. These advancements enable direct and quantitative mapping of protein distribution on ruffled plasma membranes with near isotropic 3D nanometer resolution. As demonstrated successfully for CD4 and CD45 receptors, the described workflow is a straightforward quantitative technique to study molecules and their interactions at the complex surface nanomorphology of differentiated metazoan cells.
TIMP-3 facilitates binding of target metalloproteinases to the endocytic receptor LRP-1 and promotes scavenging of MMP-1
Authors: Carreca Anna P. , Pravatà Veronica , Murphy Gillian , Nagase Hideaki , Troeberg Linda , Scilabra Simone D. 
Published: December 2019

ABSTRACTMatrix metalloproteinases (MMPs) and the related families of disintegrin metalloproteinases (ADAMs) and ADAMs with thrombospondin repeats (ADAMTSs) play a crucial role in the turnover of extracellular matrix (ECM) components and shedding of cell-surface molecules. The proteolytic activity of metalloproteinases is post-translationally regulated by their endogenous inhibitors, known as tissue inhibitors of metalloproteinases (TIMPs). Several MMPs, ADAMTSs and TIMPs have been reported to be endocytosed by the low-density lipoprotein receptor-related protein-1 (LRP-1). Different binding affinities of these proteins for the endocytic receptor correlate with different turnover rates which, together with differences in their mRNA expression, determines their nett extracellular levels.In this study, we used surface plasmon resonance to evaluate the affinity between LRP-1 and a number of MMPs, ADAMs, ADAMTSs, TIMPs and metalloproteinase/TIMP complexes. This identified MMP-1 as a new LRP-1 ligand. Among the proteins analysed, TIMP-3 bound to LRP-1 with highest affinity (KD= 1.68 nM). Additionally, we found that TIMP-3 can facilitate the clearance of its target metalloproteinases by bridging their binding to LRP-1. For example, the free form of MMP-1 was found to have aKDof 34.6 nM for LRP-1, while the MMP-1/TIMP-3 complex had a 7-fold higher affinity (KD= 4.96 nM) for the receptor. TIMP-3 similarly bridged binding of MMP-13 and MMP-14 to LRP-1. TIMP-1 and TIMP-2 were also found to increase the affinity of target metalloproteinases for LRP-1, albeit to a lesser extent. These findings suggest that LRP-1 scavenging of TIMP/metalloproteinase complexes may be a general mechanism by which inhibited metalloproteinases are removed from the extracellular environment.
Functional dynamics of dopamine synthesis during monetary reward and punishment processing
Authors: Hahn Andreas , Reed Murray B. , Pichler Verena , Michenthaler Paul , Rischka Lucas , Godbersen Godber M. , Wadsak Wolfgang , Hacker Marcus , Lanzenberger Rupert 
Published: December 2019

ABSTRACTPurposeIn the human brain endogenous dopamine release is commonly assessed by the PET competition model. Although thoroughly validated, cognitive processing yields low signal changes and the assessment of several task conditions requires repeated scanning. Using the framework of functional PET imaging we introduce a novel approach which leverages the incorporation of the radioligand 6-[18F]FDOPA into the dynamic fast-acting regulation of the corresponding enzyme activities by neuronal firing and neurotransmitter release. We demonstrate the feasibility of the approach by the assessment of widely described sex differences in dopamine neurotransmission.MethodsReward and punishment processing was behaviorally investigated in 36 healthy participants, where 16 underwent fPET and fMRI while performing the monetary incentive delay task. 6-[18F]FDOPA was applied as bolus+infusion during a single 50 min PET acquisition. Task-specific changes in dopamine synthesis were identified with the general linear model and quantified with the Gjedde-Patlak plot.ResultsMonetary gain induced 78% increase in nucleus accumbens dopamine synthesis vs. 49% for loss in men. Interestingly, the opposite was discovered in women (gain: 51%, loss: 78%). Behavioral modeling revealed direct associations of task-specific dopamine synthesis with reward sensitivity in men (rho = −0.7) and with punishment sensitivity in women (rho = 0.89). As expected, fMRI showed robust task-specific neuronal activation but no sex difference.ConclusionsOur findings provide a dopaminergic basis for well-known behavioral differences in reward and punishment processing between women and men. This has important implications in psychiatric conditions showing sex-specific prevalence rates, altered reward processing and dopamine signaling. The high temporal resolution and pronounced magnitude of task-specific changes make fPET a promising tool to investigate functional neurotransmitter dynamics during cognitive or emotional processing in various brain disorders.
Consumers’ perception of a traditional fermented beverage in Central Mexico
Authors: Rojas-Rivas Edgar , Viesca-González Felipe Carlos , Favila-Cisneros Héctor Javier , Cuffia Facundo 
Published: December 2019

Purpose
Pulque is a fundamental piece in the Mexican gastronomy and identifying consumers’ perception could help promote it and generate new opportunities of commercialization. The purpose of this paper is twofold: first, to explore the underlying factors that influence consumers’ perception toward pulque, and second, to identify groups of consumers according to their perception.

Design/methodology/approach
A questionnaire was designed and applied to 220 consumers within points of sales. Exploratory factor analysis (EFA) was undertaken and hierarchical cluster analysis (HCA) was used to identify different groups of consumers.

Findings
By means of EFA three factors were obtained: traditionality, bad reputation of pulquerías and functional beverage. In order to identify different consumption patterns among consumers, HCA was performed and three groups were identified: traditional, neo-consumers and neo-consumers in transition. The groups identified showed significant differences in their perception.

Practical implications
Pulque has recently gained interest in various consumer sectors, mainly among young consumers, who are consuming and promoting the beverage these days. In this sense, the results of this work could be used for its promotion and consumption in order to attract more consumers and make a contribution to the development of local economies.

Originality/value
This is the first work in Mexico to explore the perception of consumers toward pulque: the most important traditional fermented beverage in Central México. Results of this research suggest the appearance of a revaluation process among young consumers, more informed and with greater sensitivity toward traditional Mexican food, particularly in the case of pulque. Likewise, these results could be useful for producers and sellers to carry out commercial strategies and promote the drink.
Framework to analyze Sri Lanka disaster management mechanism
Authors: Randil Chameera , Siriwardana Chandana , Hewawasam Kalana 
Published: December 2019

Purpose
The purpose of this study is to develop a framework to assess the disaster management mechanism in Sri Lanka by means of the established indicators and newly derived indicators. This could be used to identify the parameters, which should be paid much attention to improving the resilience of the built environment.

Design/methodology/approach
This paper initially examines the effectiveness of the existing mechanism using data from a field study, by identifying the parameters needed to be considered based on the existing literature. Then the study continues on identifying new parameters of evaluation, covering a broad multidisciplinary scope inclusive of geographic, demographic, environmental, technological, social, economic and political perspectives. The identification process is based on regression relationships; hence, a framework will be developed to assess the resilience of the built environment.

Findings
The findings showed that the existing disaster management mechanism should be improved in terms of authoritative assistance while the humanitarian assistance is fulfilled to a satisfactory level as the resilience of the built environment is often community-based in Sri Lanka. Furthermore, resilience of a certain region could be effectively assumed with the indicators within the developed framework.

Originality/value
The existing evaluation criteria of the resilience framework in Sri Lanka is rather qualitative than quantitative. Therefore, this paper focuses on developing a framework where quantitative parameters are used to evaluate the existing mechanism from a number of responses from field surveys. In addition, recommendations for the key areas to be focused on developing the existing mechanism are stated.