bluuebunny/crossref_metadata_2025 huggingface dataset:
Structure of bacterial phospholipid transporter MlaFEDB with substrate bound
Authors: Coudray Nicolas , Isom Georgia L. , MacRae Mark R. , Saiduddin Mariyah N. , Bhabha Gira , Ekiert Damian C.
Published: June 2020

In double-membraned bacteria, phospholipids must be transported across the cell envelope to maintain the outer membrane barrier, which plays a key role in antibiotic resistance and pathogen virulence. The Mla system has been implicated in phospholipid trafficking and outer membrane integrity, and includes an ABC transporter complex, MlaFEDB. The transmembrane subunit, MlaE, has minimal sequence similarity to other ABC transporters, and the structure of the entire inner membrane MlaFEDB complex remains unknown. Here we report the cryo-EM structure of the MlaFEDB complex at 3.05 Å resolution. Our structure reveals that while MlaE has many distinct features, it is distantly related to the LPS and MacAB transporters, as well as the eukaryotic ABCA/ABCG families. MlaE adopts an outward-open conformation, resulting in a continuous pathway for phospholipid transport from the MlaE substrate-binding site to the pore formed by the ring of MlaD. Unexpectedly, two phospholipids are bound in the substrate-binding pocket of MlaFEDB, raising the possibility that multiple lipid substrates may be translocated each transport cycle. Site-specific crosslinking confirms that lipids bind in this pocketin vivo. Our structure provides mechanistic insight into substrate recognition and transport by the MlaFEDB complex.
Calmodulin binds to the N-terminal domain of the cardiac sodium channel Nav1.5
Authors: Wang Zizun , Vermij Sarah H. , Sottas Valentin , Shestak Anna , Ross-Kaschitza Daniela , Zaklyazminskaya Elena V. , Hudmon Andy , Pitt Geoffrey S. , Rougier Jean-Sébastien , Abriel Hugues
Published: June 2020

The cardiac voltage-gated sodium channel Nav1.5 conducts the rapid inward sodium current crucial for cardiomyocyte excitability. Loss-of-function mutations in its geneSCN5Aare linked to cardiac arrhythmias such as Brugada Syndrome (BrS). Several BrS-associated mutations in the Nav1.5 N-terminal domain exert a dominant-negative effect (DNE) on wild-type channel function, for which mechanisms remain poorly understood. We aim to contribute to the understanding of BrS pathophysiology by characterizing three mutations in the Nav1.5 N-terminal domain (NTD): Y87C–here newly identified–, R104W and R121W. In addition, we hypothesize that the calcium sensor protein calmodulin is a new NTD binding partner.

Recordings of whole-cell sodium currents in TsA-201 cells expressing WT and variant Nav1.5 showed that Y87C and R104W but not R121W exert a DNE on WT channels. Biotinylation assays revealed reduction in fully glycosylated Nav1.5 at the cell surface and in whole-cell lysates. Localization of Nav1.5 WT channel with the ER however did not change in the presence of variants, shown by transfected and stained rat neonatal cardiomyocytes. We next demonstrated that calmodulin binds Nav1.5 N-terminus usingin silicomodeling, SPOTS, pull-down and proximity ligation assays. This binding is impaired in the R121W variant and in a Nav1.5 construct missing residues 80-105, a predicted calmodulin binding site.

In conclusion, we present the first evidence that calmodulin binds to the Nav1.5 NTD, which seems to be a determinant for the DNE.
Analysis of costs and strategies for using academic research in a private dental college to develop commercially viable products
Authors: Chandra Rampalli Viswa , Raju Devaraju Rama
Published: June 2020

Background & objectives

The study had two aims. 1) Analysis of research projects done in our institution from 2014-2019 to identify products with a potential for commercialization and 2) To understand the effect of product-development variables on research projects to improve the quality of future commercialization-oriented trials.

Methods

338 clinical trials were grouped into 188 projects under the headings irrigants, diagnostic devices, surgical devices, biomaterials and gels. Trials per project, capital, material costs, labour and the cycle timespertrial were calculated. To understand the effect these variables, five hypotheses were generated to test whether greater number of trials, successes, higher capital, more investigators per trial and a longer trial duration will result in a product worthy of commercialization.

Results

22 projects had products with a potential for commercialization. Except labour and cycle time (p>0.05), all variables showed significant differences across all projects. Three products were identified as having potential for actual commercialization. It was observed that greater number of trials (χ2=4.6793; p=0.030528) and successes (χ2=20.8134; p<0.00001) in a project along with a higher capital (χ2=12.2662; p=0.000461) will generate a product worthy of commercialization.

Interpretation & conclusions

The results seem to suggest that in trials for commercialization, emphasis must be placed on implementing multiple, well-designed clinical trials on a device or product to successfully identify whether it is commercialization-worthy or not. Due attention must be given to the financial aspects of the projects as deficiencies may result in negative impact on the flow and outcomes of a clinical trial.
Environmental rhythms orchestrate neural activity at multiple stages of processing during memory encoding: Evidence from event-related potentials
Authors: Hickey Paige , Barnett-Young Annie , Patel Aniruddh D. , Race Elizabeth
Published: June 2020

Accumulating evidence suggests that rhythmic temporal structures in the environment influence memory formation. For example, stimuli that appear in synchrony with the beat of background, environmental rhythms are better remembered than stimuli that appear out-of-synchrony with the beat. This rhythmic modulation of memory has been linked to entrained neural oscillations which are proposed to act as a mechanism of selective attention by amplifying early sensory responses to events that coincide with the beat. The current study aimed to further test this hypothesis by using event-related potentials (ERPs) to investigate the locus of stimulus processing at which rhythm temporal cues operate in the service of memory formation. Participants incidentally encoded a series of visual objects while passively listening to background, instrumental music with a steady beat. Objects either appeared in-synchrony or out-of-synchrony with the background beat. Participants were then given a surprise subsequent memory test (in silence). The timing of stimulus presentation during encoding (in-synchrony or out-of-synchrony with the background beat) influenced canonical ERPs associated with post-perceptual selection and orienting attention in time. Importantly, post-perceptual ERPs also differed according to whether or not participants demonstrated a mnemonic benefit for in-synchrony compared to out-of-synchrony stimuli, and were related to the magnitude of the rhythmic modulation of memory across participants. These results support two prominent theories in the field, the Dynamic Attending Theory and the Oscillation Selection Hypothesis, which propose that neural responses to rhythm act as a core mechanism of selective attention that optimize processing at specific moments in time. Furthermore, they reveal that in addition to acting as a mechanism of early attentional selection, rhythm influences later, post-perceptual cognitive processes as events are transformed into memory.
NetBoxR: Automated Discovery of Biological Process Modules by Network Analysis in R
Authors: Liu Eric Minwei , Luna Augustin , Dong Guanlan , Sander Chris
Published: June 2020

Large-scale sequencing projects, such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), have accumulated a variety of high throughput sequencing and molecular profiling data, but it is still challenging to identify potentially causal genetic mutations in cancer as well as in other diseases in an automated fashion. We developed the NetBoxR package written in the R programming language, that makes use of the NetBox algorithm to identify candidate cancer-related processes. The algorithm makes use of a networkbased approach that combines prior knowledge with a network clustering algorithm, obviating the need for and the limitation of functionally curated gene sets. A key aspect of this approach is its ability to combine multiple data types, such as mutations and copy number alterations, leading to more reliable identification of functional modules. We make the tool available in the Bioconductor R ecosystem for applications in cancer research and cell biology.

Availability and implementation

The NetBoxR package is free and open-sourced under the GNU GPL-3 license R package available athttps://www.bioconductor.org/packages/release/bioc/html/netboxr.html

Contact

lium2@mskcc.org;aluna@jimmy.harvard.edu;sander.research@gmail.com

Supplementary information

None
Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain
Authors: van de Vossenberg Bart T.L.H. , Visser Michael , Bruinsma Maaike , Koenraadt Harrie M.S. , Westenberg Marcel , Botermans Marleen
Published: June 2020

Tomato brown rugose fruit virus (ToBRFV) is a Tobamovirus that was first observed in 2014 and 2015 on tomato plants in Israel and Jordan causing discolorations and deformation of leaves and fruits. Apart from tomato, damage in pepper fruits has been reported. Since the first description, the virus has been found on all continents except Oceania and Antarctica.

In October 2019, the Dutch National Plant Protection Organization received a tomato sample suspected to be infected with ToBRFV as part of an official specific survey of tomato fruit growers in the Netherlands carried out July to October 2019. During the survey 124 companies were visited and inspected for possible ToBRFV symptoms. Of the 47 samples tested, one sample tested positive with ELISA and test plants, which was verified using real-time RT-PCR and Illumina RNAseq data. A follow-up survey was initiated to determine the extent of ToBRFV presence in the Dutch tomato horticulture and identify possible linkages between ToBRFV genotypes, companies and epidemiological traits. We used Nextstrain to visualize these potential connections.

Genomic diversity of ToBRFV isolates found in the Netherlands group in three main clusters which are hypothesized to represent three sources. No correlation was found between genotypes, companies and epidemiological traits such as rootstock and scion varieties, seed batches and nurseries, and the source(s) of the Dutch outbreak remain unknown.

This paper describes a Nextstrain build containing ToBRFV genomes up to and including November 2019. The NPPO-NL has committed itself to maintain and improve the build. Sharing data with this interactive online tool will enable the regulatory plant virology field to better understand and communicate the diversity and spread of this new virus. Other organizations are stimulated to share data or materials for inclusion in the Nextstrain build, which can be accessed at //40.91.255.14/ToBRFV/20191231.
Analysis of opticin binding to collagen fibrils identifies a single binding site in the gap region and a high specificity towards thin heterotypic fibrils containing collagens II, and XI or V/XI
Authors: Hansen Uwe , Holmes David F. , Bruckner Peter , Bishop Paul N.
Published: June 2020

Opticin is a class III member of the extracellular matrix small leucine-rich repeat protein/proteoglycan (SLRP) family found in vitreous humour and cartilage. It was first identified associated with the surface of vitreous collagen fibrils and several other SLRPs are also known to bind collagen fibrils and it some cases alter fibril morphology. The purpose of this study was to investigate the binding of opticin to the collagen II-containing fibrils found in vitreous and cartilage. Electron microscopic studies using gold labelling demonstrated that opticin binds vitreous and thin cartilage collagen fibrils specifically at a single site in the gap region of the collagen D-period corresponding to the e2 stain band; this is the first demonstration of the binding site of a class III SLRP on collagen fibrils. Opticin did not bind thick cartilage collagen fibrils from cartilage or tactoids formedin vitrofrom collagen II, but shows high specificity for thin, heterotypic collagen fibrils containing collagens II, and XI or V/XI. Vitreous collagen fibrils from opticin null and wild-type mice were compared and no difference in fibril morphology or diameter was observed. Similarly,in vitrofibrillogenesis experiments showed that opticin did not affect fibril formation. We propose that when opticin is bound to collagen fibrils, rather than influencing their morphology it instead hinders the binding of other molecules to the fibril surfaces and/or act as an intermediary bridge linking the collagen fibrils to other non-collagenous molecules.
GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization
Authors: Ren Lixin , Gao Caixia , Duren Zhana , Wang Yong
Published: June 2020

The DNA methyltransferases (DNMTs) (DNMT3A, DNMT3B, and DNMT3L) are primarily responsible for the establishment of genomic locus-specific DNA methylation patterns, which play an important role in gene regulation and animal development. However, this important protein family’s binding mechanism, i.e., how and where the DNMTs bind to genome, is still missing in most tissues and cell lines. This motivates us to explore DNMTs and TF’s cooperation and develop a network regularized logistic regression model, GuidingNet, to predict DNMTs’ genome-wide binding by integrating gene expression, chromatin accessibility, sequence, and protein-protein interaction data. GuidingNet accurately predicted methylation experimental data validated DNMTs’ binding, outperformed single data source based method and sparsity regularized methods, and performed well in within and across tissue prediction for several DNMTs in both human and mouse. Importantly, GuidingNet can reveal transcription co-factors assisting DNMTs for methylation establishment. This provides biological understanding in the DNMTs’ binding specificity in different tissues and demonstrate the advantage of network regularization. In addition, GuidingNet achieves good performance for chromatin regulators’ binding other than DNMTs and serves as a useful method for studying chromatin regulator binding and function. The GuidingNet is freely available athttps://github.com/AMSSwanglab/GuidingNet.

Author summary

DNA methyltransferases (DNMTs) are in charge of the addition of methyl groups to cytosine residues by binding to DNA specific region. However, DNMTs do not have DNA binding domains to recognize specific DNA sequences and an urging question is how DNMTs recognize their binding sites in the genome in different tissues. Here, we propose a network regularized logistic regression model, GuidingNet, for predicting DNMT’ genome-wide binding by integrating gene expression, chromatin accessibility, sequence, and protein-protein interaction data. The main contribution is to hypothesize that DNMTs interact with transcription factors and are guided by the TF network to bind to DNA, and methylate DNA GuidingNet captures the mechanism of DNMT binding in different tissue contexts and predict DNMTs’ binding well.
Species composition and risk of transmission ofAedes-borne arboviruses around some Yellow hotspot areas in Northern Ghana
Authors: Joannides Joannitta , Dzodzomenyo Mawuli , Azerigyik Faustus , Agbosu Eudocia Esinam , Pratt Deborah , Osei Nyarkoh Joseph , Pwalia Rebecca , Kwame Amlalo Godwin , Appawu Maxwell A. , Takashi Hayashi , Iwanaga Shiroh , Buchwald Andrea , Rochford Rosemary , Boakye Daniel , Koram Kwadwo , Bonney Kofi , Dadzie Samuel Kweku
Published: June 2020

Aedes-borne viral diseases mainly Yellow Fever (YF), Dengue (DEN), Zika (ZIK) and Chikungunya (CHK) have contributed to many deaths’ in the world especially in Africa. There have been major outbreaks of these diseases in West Africa. YF outbreaks have occurred in Ghana. Although Ghana has not recorded any outbreak of DEN, ZIK and CHK, the risk is high due to its proximity to West African countries where outbreaks have been recently been recorded. This study assessed the risk of transmission of Yellow fever (YFV), Dengue (DENV), Chikungunya (CHKV) and Zika (ZIKV) viruses in Larabanga and Mole Game Reserve areas in Northern Ghana. The immature and adult stages ofAedesmosquitoes were collected from Larabanga and Mole Game Reserve area. There was a significant (P>0.001) number of mosquitoes collected during the rainy season than the dry season. A total of 1,930Aedesmosquitoes were collected during the rainy season and morphologically identified. Of these, 1,915 (99.22%) wereAedes aegyptiand 15 (0.22%) wereAedes vittatus. During the dry season, 27Aedes aegyptimosquitoes were collected. A total of 415Ae. aegyptimosquitoes were molecularly identified to subspecies level of whichAedes (Ae) aegypti aegyptiwas the predominant subspecies. BothAe. aegypti aegypti and Ae aegypti formosusexist in sympatry in the area. AllAedespools (75) were negative for DENV, ZIKV and CHKV when examined by RT-PCR. Three Larval indices namely House Index, HI (percentage of houses positive forAedeslarvae or pupae), Container Index, CI (the percentage of containers positive forAedeslarvae or pupae) and Breteau Index, BI (the number of positive containers (with larvae and/or pupae per 100 inspected houses) were assessed as a measure for risk of transmission. The HI, CI and BI for both sites were as follows; Mole game reserve (HI, 42.1%, CI, 23.5% and BI, 100 for rainy season and 0 for all indices for dry season) and Larabanga (39%, 15.5% and 61 for rainy season and 2.3%, 1.3% and 2.3 for dry season). The spatial distribution ofAedesbreeding sites in both areas indicated thatAedeslarvae were breeding in areas with close proximity to humans. Lorry tires were the main source ofAedeslarvae in all the study areas. Information about the species composition and the potential role ofAedesmosquitoes in future outbreaks of the diseases that they transmit is needed to design efficient surveillance and vector control tools.
Target tracking behaviour of the praying mantisSphrodromantis lineola(Linnaeus) is driven by looming-type motion-detectors
Authors: Rind F. Claire , Jones Lisa , Tarawneh Ghaith , Read Jenny F. M.
Published: June 2020

We designed visual stimuli to characterise the motion-detectors that underlie target tracking behaviour in the mantis. The first was a small, moving, stripy, bug-like target, made by opening a moving, Gabor-filtered window onto an extended, moving, sinewave pattern. The mantis tracked this bug-like target, but the likelihood of tracking the bug depended only on the temporal frequency of its motion. In contrast, optomotor responses to the extended moving sinewave pattern alone depended on both spatial and temporal frequency of the pattern, as expected from classical, correlation-based motion-detectors. In another experiment, we used small moving objects that were made up of chequerboard patterns of randomly arranged dark squares, and found objects with smaller sized chequers were tracked relatively less. Response suppression like this, when the internal detail of an object increases, suggests the presence of lateral inhibition between inputs to the motion-detectors for target tracking. Finally, wide-field motion of a chequerboard background near the target, balanced so no optomotor responses were evoked, suppressed tracking proportionally both to the nearness of the background to the target and to the size its dark chequered squares. Backgrounds with smaller sized squares produced more suppression. This effect has been used as a demonstration of lateral inhibition in detectors for looming-motion and makes their response greatest to an expanding outer edge, an image produced by an approaching object. Our findings point to a new role for a looming-type motion-detector in mantis target tracking. We also discuss the suitability of several large lobula-complex neurons for this role.

Summary Statement

Lateral inhibition shown by motion-detectors underlying target tracking by the praying mantisSphrodromantis lineola(Linnaeus).
Online milk composition analysis with an on-farm near-infrared sensor
Authors: Diaz-Olivares Jose A. , Adriaens Ines , Stevens Els , Saeys Wouter , Aernouts Ben
Published: June 2020

On-farm monitoring of milk composition can support close control of the udder and metabolic health of individual dairy cows. In previous studies, near-infrared (NIR) spectroscopy applied to milk analysis has proven useful for predicting the main components of raw milk (fat, protein, and lactose). In this contribution, we present and evaluate a precise tool for online milk composition analysis on the farm. For each milking, the online analyzer automatically collects and analyses a representative milk sample. The system acquires the NIR transmission spectra of the milk samples in the wavelength range from 960 to 1690 nm and performs a milk composition prediction afterward.

Over a testing period of 8 weeks, the sensor collected 1165 NIR transmittance spectra of raw milk samples originating from 36 cows for which reference chemical analyses were performed for fat, protein, and lactose. For the same online sensor system, two calibration scenarios were evaluated: training post-hoc prediction models based on a representative set of calibration samples (n= 319) acquired over the entire testing period, and training real-time prediction models exclusively on the samples acquired in the first week of the testing period (n= 308).

The obtained prediction models were thoroughly tested on all the remaining samples not included in the calibration sets (nrespectively 846 and 857). For the post-hoc prediction models, this resulted in an overall prediction error (root-mean-squared error of prediction, RMSEP) smaller than 0.08% (all % are inw/w) for milk fat (range 1.5-6.3%), protein (2.6-4.3%) and lactose (4-5.1%), while for the real-time prediction models the RMSEP was smaller than 0.09% for milk fat and lactose, and smaller than 0.11% for protein. The milk lactose predictions could be further improved by taking into account a cow-specific bias. The presented online sensor system using the real-time prediction approach can thus be used for detailed and autonomous on-farm monitoring of milk composition after each individual milking, as its accuracy is well within the ICAR requirements for on-farm milk analyzers and even meet the ICAR standards for laboratory analysis systems for fat and lactose. For this real-time prediction approach, a drift was observed in the predictions, especially for protein. Therefore, further research on the development of online calibration maintenance techniques is required to correct for this model drift and further improve the performance of this sensor system.
Masserstein: robust linear deconvolution by optimal transport
Authors: Ciach Michał , Miasojedow Błażej , Skoraczyński Grzegorz , Majewski Szymon , Startek Michał , Valkenborg Dirk , Gambin Anna
Published: June 2020

A common theme in many applications of computational mass spectrometry is fitting a linear combination of reference spectra to an experimental one in order to estimate the quantities of different ions, potentially with overlapping isotopic envelopes. In this work, we study this procedure in an abstract setting, in order to develop new approaches applicable to a diverse range of experiments. We introduce an application of a new spectral dissimilarity measure, known in other fields as the Wasserstein or the Earth Mover’s distance, in order to overcome the sensitivity of ordinary linear regression to measurement inaccuracies. Usinga a data set of 200 mass spectra, we demonstrate that our approach is capable of accurate estimation of ion proportions without extensive pre-processing required for state-of-the-art methods. The conclusions are further substantiated using data sets simulated in a way that mimics most of the measurement inaccuracies occurring in real experiments. We have implemented our methods in a Python 3 package, freely available athttps://github.com/mciach/masserstein.
Maintenance of Metabolic Plasticity Despite Relaxed Selection in a Long-Term Evolution Experiment withEscherichia coli
Authors: Grant Nkrumah A. , Maddamsetti Rohan , Lenski Richard E.
Published: June 2020

Abstract

Traits that are unused in a given environment are subject to processes that tend to erode them, leading to reduced fitness in other environments. Although this general tendency is clear, we know much less about why some traits are lost while others are retained, and about the roles of mutation and selection in generating different responses. We addressed these issues by examining populations of a facultative anaerobe,Escherichia coli, that have evolved for >30 years in the presence of oxygen, with relaxed selection for anaerobic growth and the associated metabolic plasticity. We asked whether evolution led to the loss, improvement, or maintenance of anaerobic growth, and we analyzed gene expression and mutational datasets to understand the outcomes. We identified genomic signatures of both positive and purifying selection on aerobic-specific genes, while anaerobic-specific genes showed clear evidence of relaxed selection. We also found parallel evolution at two interacting loci that regulate anaerobic growth. We competed the ancestor and evolved clones from each population in an anoxic environment, and we found that anaerobic fitness had not decayed, despite relaxed selection. In summary, relaxed section does not necessarily reduce an organism’s fitness in other environments. Instead, the genetic architecture of the traits under relaxed selection and their correlations with traits under positive and purifying selection may sometimes determine evolutionary outcomes.
Clustering-mediated activation of Cdc42 GTPase antagonized by GAPs in fission yeast
Authors: Lamas Iker , Weber Nathalie , Martin Sophie G
Published: June 2020

The small GTPase Cdc42 is critical for cell polarization in eukaryotic cells. In rod-shaped fission yeastSchizosaccharomyces pombecells, active GTP-bound Cdc42 promotes polarized growth at cell poles, while inactive Cdc42-GDP localizes ubiquitously also along cell sides. Zones of Cdc42 activity are maintained by positive feedback amplification involving the formation of a complex between Cdc42-GTP, the scaffold Scd2 and the guanine nucleotide exchange factor (GEF) Scd1, which promotes the activation of more Cdc42. Here, we use the CRY2-CIB1 optogenetic system to recruit and cluster a cytosolic Cdc42 allele at the plasma membrane and show that this leads to its moderate activation also on cell sides. Surprisingly, activation of CRY2-Cdc42 does not individually depend on Scd1 or the GEF Gef1. We show that activated Cdc42 clusters at cell sides are able to recruit Scd1, dependent on the scaffold Scd2. However, Cdc42 activity is not amplified by positive feedback and does not lead to morphogenetic changes, due to antagonistic activity of the GTPase activating protein Rga4 on cell sides. Thus, the cell architecture is robust to moderate activation of Cdc42 at cell sides.
Antibiotic tolerance, persistence, and resistance of the evolved minimal cell,Mycoplasma mycoidesJCVI-Syn3B
Authors: Hossain Tahmina , Deter Heather S. , Peters Eliza J. , Butzin Nicholas C.
Published: June 2020

Antibiotic resistance is a growing problem, but bacteria can evade antibiotic treatment via tolerance and persistence. Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. Hence, persistence is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections. Here, we used the synthetically developed minimal cellMycoplasma mycoidesJCVI-Syn3B to examine essential mechanisms of antibiotic survival. The minimal cell contains only 473 genes, and most genes are essential. Its reduced complexity helps to reveal hidden phenomenon and fundamental biological principles can be explored because of less redundancy and feedback between systems compared to natural cells. We found that Syn3B evolves antibiotic resistance to different types of antibiotics expeditiously. The minimal cell also tolerates and persists against multiple antibiotics. It contains a few already identified persister-related genes, although lacking many systems previously linked to persistence (e.g. toxin-antitoxin systems, ribosome hibernation genes, etc.).
Insights into the structure and role of seed-borne bacteriome during maize germination
Authors: dos Santos Lidiane Figueiredo , Souta Julie Fernandes , de Paula Soares Cleiton , da Rocha Letícia Oliveira , Santos Maria Luiza Carvalho , de Matos Clicia Grativol Gaspar , Roesch Luiz Fernando Wurdig , Olivares Fabio Lopes
Published: June 2020

Seed germination events modulate microbial community composition, which ultimately influences seed to seedling growth performance. Here we assess the seed-borne bacteria community in disinfected and non-disinfected maize seeds and seedlings. Using a gnotobiotic system, sodium hypochlorite (1.25%, 30 min) treated-seeds showed a reduction of bacteria population size and an increase of bacteria community diversity associated with selective suppression of Burkholderia related taxon. The shift in the bacteria community composition in disinfested-seeds negatively affects germination speed, seedling growth, and reserve mobilization rates in comparison with non-disinfected maize seeds. A synthetic bacteria community formed by twelve isolates (9 Burkholderia spp.; 2 Bacillus spp. and 1 Staphylococcus sp.) obtained from natural microbiota of maize seeds herein were capable of recovering germination and seedling growth when reintroduced in disinfected seeds. Overall results showed that changes in bacterial community composition and selective reduction of Burkholderia related members dominance interfere with germination events and initial growth of the maize plantlets. By cultivation-dependent and independent approaches, we deciphered seed-maize microbiome structure, bacterial niches location, and bacterial taxon with relevant roles in seedlings growth performance. A causal relationship between seed microbial community succession and germination performance open opportunities in seed technologies to build-up microbial communities to boost plant growth and health.

One sentence summary

partial removal of the seed-borne microbiota negatively affects maize seedling growth performance and altered bacteria community structure. Partial microbial recomposition, mainly with Burkholderia-related isolates, restores the germination phenotype of disinfested seeds.
Analysis of coagulation factor IX in bioreactor cell culture medium predicts yield and quality of the purified product
Authors: Zacchi Lucia F. , Recinos Dinora Roche , Pegg Cassandra L. , Phung Toan K. , Napoli Mark , Aitken Campbell , Sandford Vanessa , Mahler Stephen M. , Lee Yih Yean , Schulz Benjamin L. , Howard Christopher B.
Published: June 2020

Coagulation factor IX (FIX) is a highly complex post-translationally modified human serum glycoprotein and a high-value biopharmaceutical. The quality of recombinant FIX (rFIX), especially complete γ-carboxylation, is critical for rFIX clinical efficacy. Changes in bioreactor operating conditions can impact rFIX production and occupancy and structure of rFIX post-translational modifications (PTMs). We hypothesized that monitoring the bioreactor cell culture supernatant with Data Independent Acquisition Mass Spectrometry (DIA-MS) proteomics would allow us to predict product yield and quality after purification. With the goal of optimizing rFIX production, we developed a suite of MS proteomics analytical methods and used these to investigate changes in rFIX yield, γ-carboxylation, other PTMs, and host cell proteins during bioreactor culture and after purification. Our methods provided a detailed overview of the dynamics of site-specific PTM occupancy and abundance on rFIX during production, which accurately predicted the efficiency of purification and the quality of the purified product from different culture conditions. In addition, we identified new PTMs in rFIX, some of which were near the GLA domain and could impact rFIX GLA-dependent purification efficiency and protein function. The workflows presented here are applicable to other biologics and expression systems, and should aid in the optimization and quality control of upstream and downstream bioprocesses.
Effects of industry-level factors, brand credibility and brand reputation on brand trust in safe food: evidence from the safe vegetable sector in Vietnam
Authors: Ngo Hai Minh , Liu Ran , Moritaka Masahiro , Fukuda Susumu
Published: June 2020

Purpose

While the essential role of brand trust toward consumer decision to purchase food products has been well addressed, there has been still little research on its influential factors. The primary purpose of this study was to explore factors affecting consumer trust in brands of safe vegetables.

Design/methodology/approach

Structural equation modeling technique was applied to test the hypothetical relationships based on a sample of 361 consumers from a face-to-face interview in the urban areas of Hanoi city, Vietnam, in March and April 2018.

Findings

The authors' findings show that both brand credibility and brand reputation positively affected brand trust. The trustworthiness of a safe vegetable system had a more important role than the competence in building brand trust. While the effects of system trustworthiness on brand trust were found directly and indirectly (through brand credibility), system competence only had an indirect influence on brand trust via brand reputation. Notably, while risk recall directly reduced brand trust, risk information caused a directly positive effect on brand trust. In addition, the impact of food hazards on brand trust was indirect through brand credibility.

Practical implications

Based on our results, the Vietnamese government and stakeholders in the safe vegetable chain should improve brand trust based on fulfilling comprehensive traceability, expanding the brand reputation and providing an appropriate risk communication strategy to the public.

Originality/value

This study is one of the first attempts to model and evaluate factors affecting brand trust in the food sector directly and indirectly.
Consumer perception of local food products in Hungary
Authors: Szegedyné Fricz Ágnes , Ittzés András , Ózsvári László , Szakos Dávid , Kasza Gyula
Published: June 2020

Purpose

The purpose of this paper is to examine the role of local origin of food in the Hungarian population's decisions regarding food purchase and to identify under which conditions consumers consider food to be a local product.

Design/methodology/approach

The study was based on a representative quantitative consumer survey (n = 1,000). Cluster analysis was used to define different consumer groups.

Findings

In general, consumers perceive that local products have positive characteristics that distinguish them from not locally sourced foodstuffs. The results prove that the accessibility of local food products differs to a great extent in towns and regions. In towns with local markets, the ratio of recognition and acceptance of local products is higher. Based on the attitudes and behaviour of respondents towards local products, five clusters were separated and described.

Research limitations/implications

Although the sample's representativeness of three demographic factors was ensured, some general limitations resulted from the sampling methodology.

Practical implications

Based on the study findings, the authors encourage farmers' market operators to actively study the purchasing habits, attitudes and expectations of the consumer groups described in the study and to exchange information to promote the development of an economically successful local food supply system.

Originality/value

This empirical representative study is suitable to describe the knowledge, attitudes and behaviour of Hungarian consumers related to local food products. Consumer perception about local food varies internationally; therefore, national level studies are important to understand the viability of short food supply chains.
Design of hardened flip-flop using Schmitt trigger-based SEM latch in CNTFET technology
Authors: Badugu Divya Madhuri , S. Sunithamani , Shaik Javid Basha , Vobulapuram Ramesh Kumar
Published: June 2020

Purpose

The purpose of this paper is to design novel hardened flip-flop using carbon nanotube field effect transistors (CNTFETs).

Design/methodology/approach

To design the proposed flip-flop, the Schmitt trigger-based soft error masking and unhardened latches have been used. In the proposed design, the novel mechanism, i.e. hysteresis property is used to enhance the hardness of the single event upset.

Findings

To obtain the simulation results, all the proposed circuits are extensively simulated in Hewlett simulation program with integrated circuit emphasis software. Moreover, the results of the proposed latches are compared to the conventional latches to show performance improvements. It is noted that the proposed latch shows the performance improvements up to 25.8%, 51.2% and 17.8%, respectively, in terms of power consumption, area and power delay product compared to the conventional latches. Additionally, it is observed that the simulation result of the proposed flip-flop confirmed the correctness with its respective functions.

Originality/value

The novel hardened flip-flop utilizing ST based SEM latch is presented. This flip-flop is significantly improves the performance and reliability compared to the existing flip-flops.
Human resource outsourcing: the impact on organizational learning
Authors: Pandey Peeyush
Published: June 2020

Purpose

The construct of Organizational Learning has been studied through various perspectives but still there is a dearth of literature on how the organization’s outsourcing activities impact the learning process, specifically human resource outsourcing. This paper intends to link these two concepts.

Design/methodology/approach

Several research articles related to Organizational learning and outsourcing have been read and reviewed. Based on the understanding from the literature the insights are summarised and discussed.

Findings

This paper demonstrates linkage between organizational learning and human resource outsourcing by putting forth the impact human resource outsourcing can have on organizational learning from both positive and negative lenses.

Originality/value

Not many studies have established the linkage between two important constructs- Organizational Learning and Human Resource Outsourcing. This paper intends to bridge this gap in the literature by highlighting both positive and negative aspects of HR Outsourcing on the learning capabilities of the organizations.
Experience and attitude towards luxury brands consumption in an emerging market
Authors: Jhamb Deepika , Aggarwal Arun , Mittal Amit , Paul Justin
Published: June 2020

Purpose

Conventionally, consumers perceive luxury products as a means of displaying their wealth and prosperity. Consumption of luxury products has usually been considered the prerogative of the Western world. Although there are a number of studies capturing the pre-purchase and purchase behaviour of consumers, there is a dearth of quality studies that have been conducted in this field to understand the post-purchase behaviour of consumers towards luxury brands, especially in the context of young shoppers in an emerging market context. Studying the post-purchase behaviour of shoppers is important to understand their experience with the brand. A negative experience could lead to a post-purchase dissonance, which in turn could lead to an unbalanced or distorted attitude towards the brand and other marketing stimuli. Keeping this in consideration, the purpose of this study is to explore the experiences and attitudes of young shoppers in India towards luxury consumption.

Design/methodology/approach

The study captured responses from young shoppers of Chandigarh and its satellite cities located in the relatively prosperous northwest region of India. The data were collected from 200 participants through a structured questionnaire that was based on an adapted “Attitude towards the concept of luxury” scale by Dubois and Laurent (1994) and “Brand Experience” Scale by Brakus et al. (2009). The structural equation modeling technique was applied to test the proposed model.

Findings

The empirical results indicate that sensory, intellectual, behavioural and affective experience play a significant role in building the attitude of consumers towards luxury brands.

Research limitations/implications

The study selected university students from Chandigarh (India) Tricity region as target respondents, which may limit the generalisability of the results to other target respondents in different regions of India or other countries.

Practical implications

The study is useful for researchers, academicians, marketers and retailers of luxury brands, as it gives fresh insights into understanding the consumer behaviour of a young segment towards the consumption of luxury brands in the post-purchase scenario, especially in the context of an emerging market.

Originality/value

The uniqueness of the study lies in the fact that it examines the post-purchase behaviour of a segment consisting of young, educated and aspirational individuals in one of the world’s fastest-growing major economies.
Brand image as the competitive edge for hospitals in medical tourism
Authors: Cham Tat Huei , Cheng Boon Liat , Low Mei Peng , Cheok Jason Boon Chuan
Published: June 2020

Purpose

Following promising growth of the international medical tourism industry, competitions within the global market have escalated tremendously with increased involvement by numerous healthcare providers to acquire a share of its disposable income. The brand reputation would hereby play a determining role as a competitive strategy. Specifically, this paper aims to investigate the impact of social and marketing aspects on the brand image of medical tourism-based hospitals, alongside its relationship toward service quality. In turn, the influence of perceived service quality on satisfaction and the perceived value was examined, in view of further potential behavioral intention among medical tourists on healthcare providers in Malaysia.

Design/methodology/approach

The data were collected through a survey questionnaire among medical tourists, with 596 successful cases collected via 6 major private hospitals at 3 popular Malaysian medical tourism locations. Data analysis was then performed using both SPSS and Smart PLS software.

Findings

The findings from the present study acknowledged the importance of both social (e.g. social media and word-of-mouth communications) and marketing (e.g. hospital advertisement and price perception) aspects toward establishing brand image among medical tourism-based hospitals. Consequently, the brand image would influence perceived service quality among medical tourists; further entail positive impact on behavioral intention, with satisfaction and perceived value as mediators between both factors. Following PLS predict analysis confirming this model’s high predictive capability, it demonstrated close representation to actual medical tourism scenario in Malaysia.

Originality/value

This study is one of the very few studies that explored the minimally investigated territory on the consequential importance of hospital branding within the medical tourism industry; specifically through extending the literature on the influence of social and marketing efforts toward the formation of brand image.
Familiness, social capital and market orientation in the family firm
Authors: Martín-Santana Josefa D. , Cabrera-Suárez M. Katiuska , Déniz-Déniz M. de la Cruz
Published: June 2020

Purpose

This paper aims to analyse if the family influence on the firm and the relational dynamics inside the family and the firm could create specific familiness resources, which lead to a stronger market orientation (MO) of the family firms (FFs).

Design/methodology/approach

This study is based on a cross-industry sample of 374 managers in 174 Spanish FFs. Structural equation modelling is used to test the research hypotheses.

Findings

The climate of family relationships is going to affect the firm’s MO through the influence that this climate has on two relational social capital variables, one in the family area (the identification of the family managers with the FF) and the other in the business area (the level of trust between the members [family and non-family] of the top management teams [TMTs]).

Research limitations/implications

This study contributes to the literature on the under-researched topic of MO in the FFs by going beyond earlier studies focusing on FFs’ explicit attributes, such as their names, as potential explanatory variables of their marketing behaviour. This study also proposes and analyses new internal antecedents of MO based on the social capital of the firm.

Practical implications

Business families should promote the adequate governance mechanisms to enhance the quality of family social capital to promote the firms’ social capital and ultimately their MO. With the same aim, family managers should try to orientate their leadership behaviour to transmit their own organizational identification to the rest of the firm’s employees. Also, open communication and shared values should be promoted within TMTs to reinforce firms’ social capital that leads to MO.

Originality/value

This paper integrates social capital literature with MO literature. It also contributes to the literature on FFs, and specifically to the issue of familiness, by analyzing the effect of specific FF characteristics on MO.
Social benefits valuation of hosting non-mega sporting events
Authors: Zawadzki Krystian
Published: June 2020

Purpose

In the study, an attempt was made to estimate the social benefits resulting from three non-mega sporting events organized in Ergo Arena located on the border of two cities in Poland. By attributing a value to intangible social benefits, the intangible effect was determined and compared to the expenditure incurred in the construction of Ergo Arena Hall.

Design/methodology/approach

In order to value social intangible effects of three non-mega sporting events the Contingent Valuation Method was applied. Each time, the Contingent Valuation Method study covered the area of the two cities: Gdańsk and Sopot and was conducted on a sample of 500 people – 250 per city. The mean values of Willingness-to-Pay were used in order to obtain aggregate values of intangible benefits. Finally, the aggregate results were compared to expenditure incurred in connection with the construction of Ergo Arena Hall.

Findings

It appeared that intangible effects were eagerly valued by the residents of Gdańsk and Sopot. The aggregated value of all three sporting events was estimated at PLN 8.8 million. The obtained results question the equal share of both cities in financing but confirm that under certain circumstances, hosting non-mega sporting events may justify the use of public funds. In the case of the two cities, the reasonable reason for the employment of public means is the size of Gdańsk compared to Sopot.

Originality/value

The paper fulfils the research gap which arises regarding Willingness-to-Pay in estimating the intangible social effects of non-mega sporting events and considering these effects in the net effect valuation. The findings have implications for policy makers since they show to what extent it may be justified to use public means in order to host non-mega sporting events.