bluuebunny/crossref_metadata_2025 huggingface dataset:
Acidification of Cytoplasmic pH inEscherichia coliProvides a Strategy to Cope with Stress and Facilitates Development of Antibiotic Resistance
Authors: Reyes-Fernández Esmeralda Z. , Schuldiner Shimon
Published: February 2020

Awareness of the problem of antimicrobial resistance (AMR) has escalated, and drug-resistant infections are named among the most urgent issues facing clinicians today. Bacteria can acquire resistance to antibiotics by a variety of mechanisms that, at times, involve changes in their metabolic status, thus altering diverse biochemical reactions, many of them pH-dependent. In this work, we found that modulation of the cytoplasmic pH (pHi) ofEscherichia coliprovides a thus far unexplored strategy to support resistance. We show here that the acidification of the cytoplasmic pH is a previously unrecognized consequence of the activation of themarRABoperon. The acidification itself contributes to the full implementation of the resistance phenotype. We measured the pHiof two resistant strains, developed in our laboratory, that carry mutations inmarRthat activate themarRABoperon. The pHiof both strains is lower than that of the wild type strain. Inactivation of themarRABresponse in both strains weakens resistance, and pHiincreases back to wild type levels. Likewise, we showed that exposure of wild type cells to weak acids that caused acidification of the cytoplasm induced a resistant phenotype, independent of themarRABresponse. We speculate that the decrease of the cytoplasmic pH brought about by activation of themarRABresponse provides a signaling mechanism that modifies metabolic pathways and serves to cope with stress and to lower metabolic costs.

SIGNIFICANCE

The decreasing effectiveness of antibiotics in treating common infections has quickened in recent years, and resistance has spread worldwide. There is an urgent need to understand the mechanisms underlying acquisition and maintenance of resistance, and here we identify a novel element in the chain of events leading to a full-fledged clinically relevant state. TheEscherichia colimultiple antibiotic resistance (mar) regulon is induced by a variety of signals and modulates the activity of dozens of target genes involved in resistance to antibiotics. We report here a thus far unidentified result of this activation: acidification of the cytoplasmic pH. Manipulation of the cytoplasmic pH with weak acids and bases, independently of themarresponse, shows that the acidification significantly increases resistance.
Can routine laboratory tests discriminate 2019 novel coronavirus infected pneumonia from other community-acquired pneumonia?
Authors: Pan Yunbao , Ye Guangming , Zeng Xiantao , Liu Guohong , Zeng Xiaojiao , Jiang Xianghu , Zhao Jin , Chen Liangjun , Guo Shuang , Deng Qiaoling , Hong Xiaoyue , Yang Ying , Li Yirong , Wang Xinghuan
Published: February 2020

Background

The clinical presentation of 2019 Novel Coronavirus (2019-nCov) infected pneumonia (NCIP) resembles that of other etiologies of community-acquired pneumonia (CAP). We aimed to identify clinical laboratory features to distinguish NCIP from CAP.

Methods

We compared the ability of the hematological and biochemical features of 84 patients with NCIP at hospital admission and 316 patients with CAP. Parameters independently predictive of NCIP were calculated by multivariate logistic regression. The receiver operating characteristic (ROC) curves were generated and the area under the ROC curve (AUC) was measured to evaluate the discriminative ability.

Results

Most hematological and biochemical indexes of patients with NCIP were significantly different from patients with CAP. Nine laboratory parameters were identified to be highly predictive of a diagnosis of NCIP by multivariate analysis. The AUCs demonstrated good discriminatory ability for red cell distribution width (RDW) with an AUC of 0.88 and Hemoglobin (HGB) with an AUC of 0.82. Red blood cell (RBC), albumin (ALB), eosinophil (EO), hematocrit (HCT), alkaline phosphatase (ALP), and white blood cell (WBC) had fair discriminatory ability. Combinations of any two parameters performed better than did the RDW alone.

Conclusions

Routine laboratory examinations may be helpful for the diagnosis of NCIP. Application of laboratory tests may help to optimize the use of isolation rooms for patients when they present with unexplained febrile respiratory illnesses.
The Evolution of Mass Cell Suicide in Bacterial Warfare
Authors: Granato Elisa T. , Foster Kevin R.
Published: February 2020

Behaviours that reliably cause the death of an actor are typically strongly disfavoured by natural selection, and yet many bacteria undergo cell lysis to release anti-competitor toxins [1–4]. This behaviour is most easily explained if only a few cells die to release toxins and help their clonemates, but the number of cells that actually lyse during bacterial warfare is unknown. The challenge is that one cannot distinguish cells that have undergone programmed suicide from those that were simply killed by a competitor’s toxin. We developed a two-colour fluorescence reporter assay inEscherichia colito overcome this problem. Surprisingly, this revealed conditions where nearly all cells undergo programmed lysis. Adding a DNA-damaging toxin (DNase colicin) to a focal strain causes it to engage in mass cell suicide where around 85% of cells lyse to release their own toxin. Time-lapse 3D confocal microscopy revealed that self-lysis occurs at even higher frequencies (~94%) at the interface between competing colonies. We sought to understand how such high levels of cell suicide could be favoured by natural selection. ExposingE. colithat do not perform lysis to the DNase colicin revealed that mass lysis only occurs when cells are going to die anyway from toxin exposure. From an evolutionary perspective, this renders the behaviour cost-free as these cells have zero reproductive potential. This explains how mass cell suicide can evolve, as any small benefit to surviving clonemates can lead to the strategy being favoured by natural selection. Our findings have strong parallels to the suicidal attacks of social insects [5–8], which are also performed by individuals with low reproductive potential, suggesting convergent evolution in these very different organisms.

HIGHLIGHTS

A novel assay can detectEscherichia coliundergoing cell suicide to release toxins

We quantified the frequency of suicidal self-lysis during competitions

Under some conditions, nearly all cells will self-lyse to release toxins

Self-lysis makes evolutionary sense as cells will die anyway from competitors’ toxins
Genetic Profiling of Protein Burden and Nuclear Export Overload
Authors: Kintaka Reiko , Makanae Koji , Kato Hisaaki , Ohnuki Shinsuke , Ohya Yoshikazu , Andrews Brenda , Boone Charles , Moriya Hisao
Published: February 2020

Overproduction (op) of proteins triggers cellular defects. One of the defined consequences of protein overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion mutants of nonessential genes and temperature-sensitive mutants of essential genes, in the budding yeastSaccharomyces cerevisiae. To dissect interactions specific to the protein burden, we also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, probably through the formation of intracellular aggregates, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
Two alveolin network proteins are essential for the subpellicular microtubules assembly and conoid anchoring to the apical pole of matureToxoplasma gondii
Authors: Tosetti Nicolò , Dos Santos Pacheco Nicolas , Bertiaux Eloïse , Maco Bohumil , Bournonville Lorène , Hamel Virginie , Guichard Paul , Soldati-Favre Dominique
Published: February 2020

Toxoplasma gondiibelongs to the coccidian sub-group of Apicomplexa that possess an apical complex harboring a conoid, made of unique tubulin polymer fibers. This enigmatic and dynamic organelle extrudes in extracellular invasive parasites and is associated to the apical polar ring (APR), a microtubule-organizing center for the 22 subpellicular microtubules (SPMTs). The SPMTs are linked to the Inner Membrane Complex (IMC), a patchwork of flattened vesicles, via an intricate network of small filaments composed of alveolins proteins. Here, we capitalize on super-resolution techniques including stimulated emission depletion (STED) microscopy and ultrastructure expansion microscopy (U-ExM) to localize the Apical Cap protein 9 (AC9) and its close partner AC10, identified by BioID, to the alveolin network and intercalated between the SPMTs. Conditional depletion of AC9 or AC10 using the Auxin-induced Degron (AiD) system uncovered a severe loss of fitness. Parasites lacking AC9 or AC10 replicate normally but are defective in microneme secretion and hence fail to invade and egress from infected cells. Remarkably, a series of crucial apical complex proteins (MyoH, AKMT, FRM1, CPH1, ICMAP1 and RNG2) are lost in the mature parasites although they are still present in the forming daughter cells. Electron microscopy on intracellular or deoxycholate-extracted parasites revealed that the mature parasite mutants are conoidless. Closer examination of the SPMTs by U-ExM highlighted the disassembly of the SPMTs in the apical cap region that is presumably at the origin of the catastrophic loss of APR and conoid. AC9 and AC10 are two critical components of the alveolin network that ensure the integrity of the whole apical complex inT. gondiiand likely other coccidians.
Accelerated single cell seeding in relapsed multiple myeloma
Authors: Landau Heather , Yellapantula Venkata , Diamond Benjamin T. , Rustad Even H. , Maclachlan Kylee H. , Gundem Gunes , Medina-Martinez Juan , Arango Ossa Juan , Levine Max , Zhou Yangyu , Kappagantula Rajya , Baez Priscilla , Attiye Marc , Makohon-Moore Alvin , Zhang Lance , Boyle Eileen M , Ashby Cody , Blaney Patrick , Patel Minal , Zhang Yanming , Dogan Ahmet , Chung David , Giralt Sergio , Lahoud Oscar B. , Peled Jonathan U. , Scordo Michael , Shah Gunjan , Hassoun Hani , Korde Neha S. , Lesokhin Alexander M. , Lu Sydney , Mailankody Sham , Shah Urvi , Smith Eric , Hultcrantz Malin L. , Ulaner Gary A. , van Rhee Frits , Morgan Gareth , Ola Landgren C. , Papaemmanuil Elli , Iacobuzio-Donahue Christine , Maura Francesco
Published: February 2020

The malignant progression of multiple myeloma is characterized by the seeding of cancer cells in different anatomic sites followed by their clonal expansion. It has been demonstrated that this spatial evolution at varying anatomic sites is characterized by genomic heterogeneity. However, it is unclear whether each anatomic site at relapse reflects the expansion of pre-existing but previously undetected disease or secondary seeding from other sites. Furthermore, genomic evolution over time at spatially distinct sites of disease has not been investigated in a systematic manner.

To address this, we interrogated 25 samples, by whole genome sequencing, collected at autopsy from 4 patients with relapsed multiple myeloma and demonstrated that each site had a unique evolutionary trajectory characterized by distinct single and complex structural variants and copy number changes. By analyzing the landscape of mutational signatures at these sites and for an additional set of 125 published whole exomes collected from 51 patients, we demonstrate the profound mutagenic effect of melphalan and platinum in relapsed multiple myeloma. Chemotherapy-related mutagenic processes are known to introduce hundreds of unique mutations in each surviving cancer cell. These mutations can be detectable by bulk sequencing only in cases of clonal expansion of a single cancer cell bearing the mutational signature linked to chemotherapy exposure thus representing a unique single-cell genomic barcode linked to a discrete time window in each patient’s life. We leveraged this concept to show that multiple myeloma systemic seeding is accelerated at clinical relapse and appears to be driven by the survival and subsequent expansion of a single myeloma cell following treatment with high dose melphalan therapy and autologous stem cell transplant.
High-resolution animal tracking with integration of environmental information in aquatic systems
Authors: Francisco Fritz A , Nührenberg Paul , Jordan Alex
Published: February 2020

Acquiring high resolution quantitative behavioural data underwater often involves installation of costly infrastructure, or capture and manipulation animals. Aquatic movement ecology can therefore be limited in scope of taxonomic and ecological coverage. Here we present a novel deep-learning based, multi-individual tracking approach, which incorporates Structure-from-Motion in order to determine the 3D location, body position and the visual environment of every recorded individual. The application is based on low-cost cameras and does not require the animals to be confined or handled in any way. Using this approach, single individuals, small heterospecific groups and schools of fish were tracked in freshwater and marine environments of varying complexity. Further, we established accuracy measures, resulting in positional tracking errors as low as 1.09 ± 0.47 cm (RSME) in underwater areas up to 500 m2. This cost-effective and open-source framework allows the analysis of animal behaviour in aquatic systems at an unprecedented resolution. Implementing this versatile approach, quantitative behavioural analysis can employed in a wide range of natural contexts, vastly expanding our potential for examining non-model systems and species.
Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models
Authors: Ni Ruiqing , Dean-Ben Xose Luis , Kirschenbaum Daniel , Rudin Markus , Chen Zhenyue , Crimi Alessandro , Voigt Fabian F. , Nilsson K. Peter R. , Helmchen Fritjof , Nitsch Roger , Aguzzi Adriano , Razansky Daniel , Klohs Jan
Published: February 2020

Deposition of beta-amyloid (Aβ) deposits is one major histopathological hallmark of Alzheimer’s disease (AD). Here, we introduce volumetric multi-spectral optoacoustic tomography (vMSOT), which covers 10×10×10 mm3 field-of-view, capable of 3D whole mouse brain imaging. We show for the first time the optoacoustic properties of oxazine-derivative AOI987 probe, which binds to Aβ, and the application of vMSOT for the quantification of brain-wide Aβ deposition. Administration of AOI987 to two common transgenic mouse strains of AD amyloidosis led to a retention of the probe in Aβ-laden brain regions. Co-registered of vMSOT data to a brain atlas revealed strain-specific pattern of AOI987 uptake. A comparison with ex vivo light-sheet microscopy in cleared mouse brains showed a good correspondence in Aβ distribution. Lastly, we demonstrate the specificity of the AOI987 probe by immunohistochemistry. vMSOT with AOI987 facilitates preclinical brain region-specific studies of Aβ spread and accumulation, and the monitoring of putative treatments targeting Aβ.
Biogenic Amine Neurotransmitters Promote Eicosanoid Production And Protein Homeostasis
Authors: Joshi Kishore K. , Matlack Tarmie L. , Pyonteck Stephanie , Menzel Ralph , Rongo Christopher
Published: February 2020

Multicellular organisms use multiple pathways to restore protein homeostasis (proteostasis) in response to adverse physiological conditions, changing environment, and developmental aging. The nervous system can regulate proteostasis in different tissues, but it is unclear how it mobilizes proteostasis pathways to offset physiological decline. Here we show thatC. elegansemploys the humoral biogenic amine neurotransmitters dopamine, serotonin, and tyramine to regulate proteostasis and the activity of the Ubiquitin Proteasome System (UPS) in epithelial tissues. Mutants for biogenic amine synthesis show decreased poly-ubiquitination and turnover of a GFP-based UPS substrate. Using RNA-seq, we determined the expression profile of genes regulated by biogenic amine signaling. We find that biogenic amines promote the expression of a subset of cytochrome P450 monooxygenases involved in eicosanoid production from polyunsaturated fatty acids (PUFAs). Mutants for these P450s share the same UPS phenotype observed in biogenic amine mutants. The production of n-3 PUFAs is required for UPS substrate turnover, whereas mutants that accumulate n-3 PUFAs show accelerated turnover of this GFP-based substrate. Our results suggest that neurosecretory sensory neurons release biogenic amines to modulate the lipid signaling profile, which in turn activates stress response pathways to maintain proteostasis.
Search for top-down and bottom-up drivers of latitudinal trends in insect herbivory in oak trees in Europe
Authors: Valdés-Correcher Elena , Moreira Xoaquín , Augusto Laurent , Barbaro Luc , Bouget Christophe , Bouriaud Olivier , Branco Manuela , Centenaro Giada , Csóka György , Damestoy Thomas , Dobrosavljević Jovan , Duduman Mihai-Leonard , Dulaurent Anne-Maïmiti , Eötvös Csaba B. , Faticov Maria , Ferrante Marco , Fürjes-Mikó Ágnes , Galmán Andrea , Gossner Martin M. , Hampe Arndt , Harvey Deborah , Howe Andrew Gordon , Kadiri Yasmine , Kaennel-Dobbertin Michèle , Koricheva Julia , Kozel Alexander , Kozlov Mikhail V. , Löveï Gábor L. , Lupaştean Daniela , Milanović Slobodan , Mrazova Anna , Opgennoorth Lars , Pitkänen Juha-Matti , Popova Anna , Popović Marija , Prinzing Andreas , Queloz Valentin , Roslin Tomas , Sallé Aurélien , Sam Katerina , Scherer-Lorenzen Michael , Schuldt Andreas , Selikhovkin Andrey , Suominen Lassi , Tack Ayco J. M. , Tahadlova Marketa , Thomas Rebecca , Castagneyrol Bastien
Published: February 2020

Aim

The strength of species interactions is traditionally expected to become stronger toward the Equator. However, recent studies have reported opposite or inconsistent latitudinal trends in the bottom-up (plant quality) and top-down (natural enemies) forces driving insect herbivory, possibly because these forces have rarely been studied concomitantly. This makes previous attempts to understand the effect of large scale climatic gradients on insect herbivory unsuccessful.

Location

Europe

Time period

2018-2019

Major taxa studied

Quercus robur

Methods

We used scholar-based citizen science to simultaneously test for latitudinal variation in plant-herbivore-natural enemy interactions. We further investigated the underlying climatic factors associated with variation in herbivory, leaf chemistry and attack rates inQuercus roburacross its complete latitudinal range in Europe. We quantified insect herbivory and the occurrence of specialist herbivores as well as leaf chemistry and bird attack rates on dummy caterpillars on 261 oak trees.

Results

Climatic factors rather than latitudeper sewere the best predictors of the large-scale (geographical) variation in the incidence of gall-inducers and leaf-miners as well as of leaf nutritional quality. However, insect herbivory, plant chemical defences (leaf phenolics) and bird attack rates were not influenced by latitude or climatic factors. The incidence of leaf-miners increased with increasing concentrations of hydrolysable tannins and decreased with those of condensed tannins, whereas the incidence of gall-inducers increased with increasing leaf soluble sugar concentration and decreased with increasing leaf C:N ratios. However, neither other traits nor bird attack rates varied with insect herbivory.

Main conclusions

These findings help to refine our understanding of the bottom-up and top-down mechanisms driving geographical variation in plant-herbivore interactions, and urge for further examination of the drivers of insect herbivory on trees.
Key histone chaperones have distinct roles in replisome progression and genomic stability
Authors: Tsirkas Ioannis , Dovrat Daniel , Lei Yang , Kalyva Angeliki , Lotysh Diana , Li Qing , Aharoni Amir
Published: February 2020

Replication-coupled (RC) nucleosome assembly is an essential process in eukaryotic cells in order to maintain chromatin structure during DNA replication. The deposition of newly synthesized H3/H4 histones during DNA replication is facilitated by specialized histone chaperones. Although the contribution of these histone chaperones to genomic stability has been thoroughly investigated, their effect on replisome progression is much less understood. By exploiting a time-lapse microscopy system for monitoring DNA replication in individual live cells, we examined how mutations in key histone chaperones includingCAC1,RTT106,RTT109andASF1, affect replication fork progression. Our experiments revealed that mutations inCAC1orRTT106that directly deposit histones on the DNA, slowdown replication fork progression. In contrast, analysis of cells mutated in the intermediaryASF1orRTT109histone chaperones revealed that replisome progression is not affected. We found that mutations in histone chaperones includingASF1andRTT109lead to extended G2/M duration, elevated number of RPA foci and in some cases, increased spontaneous mutation rate. Our research suggests that histone chaperones have distinct roles in enabling high replisome progression and maintaining genome stability during cell cycle progression.

Author Summary

Histone chaperones (HC) play key roles in maintaining the chromatin structure during DNA replication in eukaryotic cells. Despite extensive studies on HCs, little is known regarding their importance for replication fork progression during S-phase. Here, we utilized a live-cell imaging approach to measure the progression rates of single replication forks in individual yeast cells mutated in key histone chaperones. Using this approach, we show that mutations inCAC1orRTT106HCs that directly deposit histones on the DNA lead to slowdown of replication fork progression. In contrast, mutations inASF1orRTT109HCs that transfers H3/H4 toCAC1orRTT106, do not affect replisome progression but lead to post replication defects. Our results reveal distinct functions of HCs in replication fork progression and maintaining genome stability.
Coupling of conformational switches in calcium sensor unraveled with local Markov models and transfer entropy
Authors: Hempel Tim , Plattner Nuria , Noé Frank
Published: February 2020

Proteins often have multiple switching domains that are coupled to each other and to binding of ligands in order to realize signaling functions. Here we investigate the C2A domain of Synaptotagmin-1 (Syt-1), a calcium sensor in the neurotransmitter release machinery and a model system for the large family of C2 membrane binding domains. We combine extensive molecular dynamics (MD) simulations and Markov modeling in order to model conformational switching domains, their states and their dependence on bound calcium ions. Using transfer entropy, we characterize how the switching domains are coupled via directed or allosteric mechanisms and give rise to the calcium sensing function of the protein. Our switching mechanism contributes to the understanding of the neurotransmitter release machinery and the proposed methodological approach serves as a template to analyze conformational switching domains and study their coupling in macromolecular machines in general.
Evaluation of a new probiotic concept for broilers
Authors: Jørgensen S. L. , Poulsen L. L. , Bisgaard M. , Christensen H.
Published: February 2020

Probiotics were introduced as a spray directly in the hatcher when chickens started to leave the eggs which potentially could reduce the horizontal transmission and colonization with pathogenic bacteria. The single introduction of probiotics could limit the cost compared to multiple introductions with feed and/or water. A mixture of five probiotic strains belonging toEscherichia coli, Enterococcus faecalis, Lactobacillus agilisandLactobacillus rhamnosuswas tested with two independent flocks of broilers (Ross 308). For each experiment, a comparison was made to an untreated control flock on the same farm. At day 14 of production the probiotic strains were re-isolated from ileum of euthanized chickens. The first week mortality was slightly increased in the probiotic flock (0.42%) compared to the control (0.35%) in experiment 1, however, it was higher in the control flock (1.45%) compared to the probiotic flock (1.12%) in experiment 2. The average weight of chickens that could be slaughtered for consumption was increased by 3.5% in the probiotic flocks compared to the control flocks, resulting in a 1.9% higher total weight of slaughtered chickens in the probiotics treated flocks compared to the control as a mean of the two experiments. The number of condemned animals was within the normal range for the production system and could not directly be related to effects of probiotics. Although one probiotic strain ofE. coliwas isolated from dead animals, the probiotics did not affect the proportion of chickens which died due toE. coliduring the first week compared to the control.

Primary audience

plant managers, veterinarians, nutritionists
Gut microbiome, diet and symptom interactions in irritable bowel syndrome
Authors: Tap Julien , Störsrud Stine , Nevé Boris Le , Cotillard Aurélie , Pons Nicolas , Doré Joël , Öhman Lena , Törnblom Hans , Derrien Muriel , Simren Magnus
Published: February 2020

While several studies have documented associations between dietary habits and microbiota composition and function in healthy subjects, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially in relation to symptoms. Here, we used a novel approach that combined data from 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for IBS patients (N=149) and healthy subjects (N=52). Paired microbiota and food-based trees allowed to detect new association between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. IBS patients with severe symptoms had a diet enriched in food items of poorer quality, a high abundance of gut microbial enzymes involved in hydrogen metabolism in correlation with animal carbohydrate (mucin/meat-derived) metabolism. Our study provides unprecedented resolution of diet-microbiota-symptom interactions and ultimately paves the way for personalized nutritional recommendations.
The evolution of mechanisms to produce phenotypic heterogeneity in microorganisms
Authors: Cooper Guy Alexander , Liu Ming , Peña Jorge , West Stuart Andrew
Published: February 2020

In bacteria and other microorganisms, the cells within a population often show extreme phenotypic variation. Different species use different mechanisms to determine how distinct phenotypes are allocated between individuals, including coordinated, random, and genetic determination. However, it is not clear if this diversity in mechanisms is adaptive—arising because different mechanisms are favoured in different environments—or is merely the result of non-adaptive artifacts of evolution. We use theoretical models to analyse the relative advantages of the two dominant mechanisms to divide labour between reproductives and helpers in microorganisms. We show that coordinated specialisation is more likely to evolve over random specialisation in well-mixed groups when: (i) social groups are small; (ii) helping is more “essential”; and (iii) there is a low metabolic cost to coordination. We find analogous results when we allow for spatial structure with a more detailed model of cellular filaments. More generally, this work shows how diversity in the mechanisms to produce phenotypic heterogeneity could have arisen as adaptations to different environments.
Inference of sexual selection from pairwise contests
Authors: Yu Thomas , Clark Andrew G.
Published: February 2020

Sexual selection, whether mediated by male-male competition, female choice, or male choice, is often realized through a series of pairwise contests. Experimental evolutionists have long applied male-choice and female-choice experiments to quantify the relative mating abilities of genotypes, an important component of fitness. Here, we consider Drosophila mate-choice experiments and apply two mathematical models, the Bradley-Terry and the Élő models, which have been explicitly designed to quantify the merits of contestants and establish a ranking based on results from pairwise contests. Methods such as the Bradley-Terry model and Élő ratings also provide a way to predict the outcome of contests that have not yet taken place. Leave-one-out validation approaches allow us to assess the utility of these models to quantify relative fitnesses, how well the models fit the data, and how well they perform at prediction. After applying these methods to Drosophila mate-choice experiments, we interpret the results in terms of sexual selection, and discuss the implications of departures of the data from good fits to the models.
Functional remodeling of lysosomes by type I interferon modifies host defense
Authors: Zhang Hailong , Zoued Abdelrahim , Liu Xu , Sit Brandon , Waldor Matthew K.
Published: February 2020

Organelle remodeling is critical for cellular homeostasis, but host factors that control organelle function during microbial infection remain largely uncharacterized. Here, a genome-scale CRISPR/Cas9 screen in intestinal epithelial cells with the prototypical intracellular bacterial pathogenSalmonellaled us to discover that type I interferon (IFN-I) remodels lysosomes. Even in the absence of infection, IFN-I signaling modified the localization, acidification, protease activity and proteomic profile of lysosomes. Proteomic and genetic analyses revealed that multiple IFN-I-stimulated genes includingIfitm3, Slc15a3, andCnpcontribute to lysosome acidification. IFN-I-dependent lysosome acidification stimulated intracellularSalmonellavirulence gene expression, leading to rupture of theSalmonella-containing vacuole and host cell death. Moreover, IFN-I signaling promotedin vivo Salmonellapathogenesis in the intestinal epithelium, whereSalmonellainitiates infection. Our findings explain how an intracellular bacterial pathogen co-opts epithelial IFN-I signaling. We propose that IFN-I control of lysosome function broadly impacts host defense against diverse viral and microbial pathogens.
Modelling FtsZ nucleation, hydrolysis and treadmilling activity with Monte Carlo methods
Authors: Corbin L. , Erickson H.P.
Published: February 2020

Bacterial cell division is tightly coupled to the dynamic behavior of FtsZ, a tubulin homolog. Recent experimental workin vitroandin vivohas attributed FtsZ’s assembly dynamics to treadmilling, where subunits add to the bottom and dissociate from the top of protofilaments. However, the molecular mechanisms producing treadmilling have yet to be characterized and quantified. We have developed a Monte Carlo model for FtsZ assembly that explains treadmilling and assembly nucleation by the same mechanisms. A key element of the model is a conformational change from R (relaxed), which is highly favored for monomers, to T (tense), which is favored for subunits in a protofilament. This model was created in MATLAB. Kinetic parameters were converted to probabilities of execution during single, small time steps, and these were used to stochastically determine FtsZ dynamics. Our model is able to accurately describe the results of severalin vitroandin vivostudies for a variety of FtsZ flavors. With standard conditions, the model FtsZ polymerized and produced protofilaments that treadmilled at 28 nm/s, hydrolyzed GTP at 2.8 to 4.2 GTP min-1FtsZ-1, and had an average length of 25 to 54 subunits, all similar to experimental results. Adding a bottom capper resulted in shorter protofilaments and higher GTPase, similar to the effect of the known the bottom capper protein MciZ. The model could match nucleation kinetics of several flavors of FtsZ using the same parameters as treadmilling and varying only the R to T transition of monomers.

SIGNIFICANCE

FtsZ assembly dynamics are now known to be governed by treadmilling, where subunits add to the bottom and dissociate from the top of protofilaments. We have generated a Monte Carlo model of treadmilling based on (a) a conformational transition of FtsZ subunits between two states, and (b) stochastic GTP hydrolysis. Importantly, the nucleation of new protofilaments is explained by the same mechanisms as treadmilling. We have determined kinetic parameters that match a wide range of experimental data. The model is available to users for their ownin silicoexperiments.
Epigenetic silencing of clustered tDNAs in Arabidopsis
Authors: Hummel Guillaume , Berr Alexandre , Graindorge Stéfanie , Cognat Valérie , Ubrig Elodie , Pflieger David , Molinier Jean , Drouard Laurence
Published: February 2020

Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) andcis-elements,trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. Our data highlight that the combination of both genomic environment and epigenomic landscape contribute to fine tune the differential expression of dispersed versus clustered tDNAs in Arabidopsis.
Disappeared supramolecular isomer reappears with perylene guest
Authors: Park In-Hyeok , Dey Atanu , Sasaki Kenta , Ohba Masaaki , Lee Shim Sung , Vittal Jagadese J.
Published: February 2020

Among different types of polymorphism, disappearing polymorphism deals with the metastable kinetic form which can not be reproduced after its first isolation. In the world of coordination polymers (CPs) and metal–organic frameworks (MOFs), despite the fact that many types of supramolecular isomerism exist, we are unaware of disappearing supramolecular isomerism akin to disappearing polymorphism. This work reports a MOF with dia topology that could not be reproduced, but subsequent synthesis yielded another supramolecular isomer, a double-pillared-layer MOF. When perylene was added in the same reaction, the disappeared dia MOF reappeared with perylene as a guest in the channels. Interestingly, the photoluminescence of the dia MOF with a perylene guest is dominated by the emission of the guest molecule. The influence of guest molecules on the stabilization of the supramolecular isomers of a MOF opens up a strategy to access MOFs with different structures.
The differentiated effect of information on the sensorial appreciation of wine
Authors: Saïdi Monia , Giraud Georges
Published: February 2020

Purpose

This paper investigates how giving additional information to consumers changes their appreciation of wine, and how this effect changes with their knowledge of wine and their characteristics.

Design/methodology/approach

A survey of 415 French consumers was carried-out in 2014, focusing on the sensory evaluation of 37 red Bourgogne wines. Two sensorial evaluations (visual, and smell & taste) are investigated, first without any information about the wine and then with the presentation of the wine bottle with its labels.

Findings

The majority of participants are significantly influenced by the information displayed. The influence of information depends on their initial knowledge and individual characteristics (gender, age, and home area). This influence is robust, whatever be the means of evaluation.

Research limitations/implications

The study was carried out with red Bourgogne wines and focused on the village and regional appellations, with a low and medium price range. The results need a broader investigation to be generalizable.

Practical implications

Information does not have the same influence depending on individual characteristics and on knowledge of wine. Promoting different wines to different consumers who do not have the same knowledge and do not use the same distribution channels is challenging as consumers do not all have the same expectations of red Bourgogne wines. The results provide directions for better targeting consumers through the information on the bottle labels.

Originality/value

By cross-tabulating sensory tastings and knowledge tests, this research contributes to measuring the holistic effect of information on the hedonic appreciation of wine across a significant range of consumers issued from two big cities.
Factors affecting business graduates' employability–empirical evidence using partial least squares (PLS)
Authors: Hossain Md Moazzem , Alam Manzurul , Alamgir Mohammed , Salat Amirus
Published: February 2020

Purpose

The purpose of this paper is to examine the relationship between skills and employability of business graduates. The study also examines the moderating effect of ‘social mobility factors’ in the ‘skills–employability’ relationship.

Design/methodology/approach

A quantitative positivist approach was undertaken to test the hypotheses. Business graduates from two universities in a developing country responded to a questionnaire about their perceptions of different sets of employability factors. Partial least squares (PLS)-based structural equation modelling (SEM) was used to examine the relationships between skills and employability of business graduates.

Findings

The findings show that both soft skills and technical skills are positively related to employability, which is consistent with prior studies. The findings also indicate that social mobility factors play a significant role in employability.

Research limitations/implications

The study is based on data from two public universities, and its findings need to be interpreted with care as universities differ in their size, area of concentration and ownership structure.

Practical implications

The findings advance the evidence of graduate employability of business students. Based on these results, university authorities, policymakers, teachers and business graduates will benefit from the findings related to students preparedness for the competitive global job market.

Originality/value

The study's findings contribute to business graduates' skill set development in the developing countries that share a similar education system, culture and values.
Impacts of remittances on financial development
Authors: Azizi SeyedSoroosh
Published: February 2020

Purpose

The purpose of this paper is to examine the impacts of international remittances on financial development in developing countries.

Design/methodology/approach

The focus is on a panel of 124 developing countries for the period 1990–2015. The empirical evidence is based on the instrumental variable-fixed effect model.

Findings

Results obtained in this study indicate that a 10 percent increase in the remittance to GDP ratio leads to 1.7 percent increase in domestic credit to private sector, 1.9 percent increase in bank credit, 1.2 percent increase in bank deposit, and 0.8 percent increase in liquid liabilities. The positive impact of remittances on financial development in developing countries is particularly important because financial development fosters long-run growth and reduces poverty.

Originality/value

To address the endogeneity of remittances, the study estimates bilateral remittances and use them to create weighted gross national income per capita and real interest rates of remittance-sending countries. To the best of the author’s knowledge, this is the first study to assess the endogeneity of remittances in this way.
Pricing decisions, competition and liquidity constraints
Authors: Amountzias Chrysovalantis
Published: February 2020

Purpose

This study investigates the pricing decisions of the UK wholesale and retail food, beverages and tobacco sector over 2007–2016 using 19 four-digit level NACE Rev.2 classification industries.

Design/methodology/approach

The Hall (1988) and Roeger (1995) model is employed to estimate the price-cost margin for the aggregate sector and each constituent industry.

Findings

The results suggest the presence of weak imperfect competitive conduct as the markup value is close to perfect competition. Moreover, it is found that industries with higher market share and liquidity reserves tend to charge a lower markup, validating the presence of price wars and competitive incentives in the sector.

Originality/value

This paper contributes to the literature of pricing decisions and how access to available liquidity may affect the selling price of products. The pricing strategies also depend on the market structure as firms operating in more competitive sectors may start price wars more often than their counterparts in more concentrated sectors. Therefore, this study adds value to the investigation of pricing decisions under liquidity constraints across the UK wholesale and retail food, beverages and tobacco firms.
The structure of an innovation ecosystem: foundations for future research
Authors: Dias Sant´Ana Tomás , de Souza Bermejo Paulo Henrique , Moreira Marina Fiqueiredo , de Souza Wagner Vilas Boas
Published: February 2020

Purpose

The concept of an innovation ecosystem, based on the idea of business ecosystem, has increasingly grown in the literature on strategy, innovation, and entrepreneurship. However, not all innovation ecosystems have the same architectural models or internal collaboration, and existing research rarely deconstructs an ecosystem of innovation and examines its structure. The objective of this article is to systematize the discussion about the structure of an innovation ecosystem and offer a foundation for future research.

Design/methodology/approach

Using the Web of Science database as the source for the articles, this paper presents a systematic review of the literature on the structure of the innovation ecosystems. The period of analysis spanned from January 1993 to August 2019. Two methods, bibliometric analysis and content analysis, were used to structure the systematic review.

Findings

The results of the content analysis showed that the main classifications related to the structure of an innovation ecosystem are the ecosystem life cycle (birth, expansion, leadership, and self-renewal), the classification according to the ecosystem level (macroscopic, medium, and microscopic), and the layered structure (core–periphery structure, triple-layer structure, triple-layer core–periphery structure, and framework 6C). The results also showed that studies in the field are concentrated around a small group of authors, and few studies have discussed the structure of an ecosystem.

Research limitations/implications

This study includes only peer-reviewed articles from the Web of Science database.

Originality/value

This article contributes to innovation ecosystem theory by exploring the characteristics that influence ecosystem structure. In addition to the theoretical contribution, the triple-layer core–periphery framework and the 6C framework set a benchmark for future research on innovation ecosystems.
Repurchase intentions in Y generation: mediation of trust and e-satisfaction
Authors: Trivedi Shrawan Kumar , Yadav Mohit
Published: February 2020

Purpose

Research on online businesses has focused on the adoption of e-commerce and initial purchase behavior; repurchase intention and its antecedents remain underresearched. The present study develops an empirical model to explore the extent to which trust and e-satisfaction mediate the effect of vendor-specific attributes and customer intention to repurchase from the same online platform.

Design/methodology/approach

The proposed model is tested and validated in the context of Generation Y in India. A self-administrated online survey was employed, and the students aged between 20 and 35 at universities in Northern India are selected as subject. The data is analyzed using SPSS 20.0 and AMOS 20.0, where structural equation modeling is used to examine the model and test the hypothesis.

Findings

The results of this study suggest that trust mediates fully between security concerns, privacy concerns, and repurchase intention. E-satisfaction mediates between security and ease of use (EOU).

Practical implications

This study reveals the fact that security, EOU, and privacy concerns are the critical determinants that have the most impact on consumer's purchasing behavior. Gen Y consumers of India need some strong security features, an easy-to-use interface, a trusted privacy policy. Furthermore, it may be beneficial to observe e-satisfaction and trust as a mediator when identifying potential problems; online satisfaction is essential for the group in this study, and the results show that it impacts on the relation between repurchase intention and some determinant of repurchase intentions.

Originality/value

This research determines the impact of security, privacy concerns, EOU on the online repurchasing behavior of Gen Y in India. The mediation effect of e-satisfaction and trust has also been determined.
“They love death as we love life”: The “Muslim Question” and the biopolitics of replacement
Authors: Bracke Sarah , Hernández Aguilar Luis Manuel
Published: February 2020

This article approaches the analytic of the “Muslim Question” through the prism of the discursive and conspiratorial use of demographics as an alleged threat to Europe. It argues that concerns about “Muslim demographics” within Europe have been entertained, mobilized, and deployed to not only construct Muslims as problems and dangers to the present and future of Europe, but also as calls to revive eugenic policies within the frame of biopower. The article begins by sketching the contours of the contemporary “Muslim Question” and proceeds with a critical engagement with the literature positing a deliberate and combative strategy by “Muslims” centered on birth rates—seen by these authors as a tactical warfare—to allegedly replace European “native” populations. The analysis continues by focusing on two images juxtaposing life and death as imagined within the replacement discourse, and that capture that discourse in powerful albeit disturbing ways. Finally, the article proposes reading the population replacement discourse as a deployment of biopolitics and one of its many techniques, namely, eugenics.