bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of COVID-19 non-pharmaceutical interventions on the lived experiences of people living in Thailand, Malaysia, Italy and the United Kingdom: a cross-country qualitative study
Authors: Schneiders Mira L. , Naemiratch Bhensri , Cheah Phaik Kin , Cuman Giulia , Poomchaichote Tassawan , Ruangkajorn Supanat , Stoppa Silvia , Osterrieder Anne , Cheah Phee-Kheng , Ongkili Darlene , Pan-ngum Wirichada , Mackworth-Young Constance R.S. , Cheah Phaik Yeong
Published: May 2021

This qualitative study explores the impact of non-pharmaceutical interventions (NPIs) on lived experiences during the first wave of the COVID-19 pandemic on people’s lives in Thailand, Malaysia, Italy and the United Kingdom. A total of 86 interviews were conducted with members of the public, including healthcare workers. Participants across countries held strong views on NPIs, with many feeling measures lacked clarity. Most participants reported primarily negative impacts of NPIs on their lives, including through separation, isolation and grief over missed milestones; work-related challenges and income loss; and poor mental health and wellbeing. Nonetheless, many also experienced inadvertent positive consequences, including more time at home to focus on what they most valued in life; a greater sense of connectedness; and benefits to working life. Commonly employed coping strategies focused on financial coping; psycho-emotional coping; social coping and connectedness; reducing and mitigating risks; and limiting exposure to the news. Importantly, the extent to which participants’ lived experiences were positive or negative, and their ability to cope was underpinned by individual, social and economic factors. In order to mitigate negative and unequal impacts of NPIs, COVID-19 policies will benefit from paying closer attention to the social, cultural and psychological—not just biological—vulnerabilities to, and consequences of public health measures.
Metabolomic profiling in small vessel disease identifies multiple associations with disease severity
Authors: Harshfield Eric L. , Sands Caroline J. , Tuladhar Anil M. , de Leeuw Frank-Erik , Lewis Matthew R. , Markus Hugh S.
Published: May 2021

Cerebral small vessel disease (SVD) is a major cause of vascular cognitive impairment and dementia. There are few treatments, largely reflecting limited understanding of the underlying pathophysiology. Metabolomics can be used to identify novel risk factors in order to better understand pathogenesis and to predict disease progression and severity.

We analysed data from 624 patients with symptomatic cerebral SVD from two prospective cohort studies. Serum samples were collected at baseline and patients underwent MRI scans and cognitive testing at regular intervals with up to 14 years of follow-up. Using ultra-performance liquid chromatography mass spectrometry and nuclear magnetic resonance spectroscopy, we obtained metabolic and lipidomic profiles from 369 annotated metabolites and 54,764 unannotated features and examined their association with respect to disease severity, assessed using MRI SVD markers, cognition, and future risk of all-cause dementia.

Over 100 annotated metabolites were significantly associated with SVD imaging markers, cognition, and progression to dementia. Decreased levels of multiple glycerophospholipids, sphingolipids, and sterol lipids were associated with increased SVD load as evidenced by higher white matter hyperintensities (WMH) volume, lower mean diffusivity normalised peak height (MDNPH), greater brain atrophy, and impaired cognition. Higher levels of several amino acids and nucleotides were associated with higher WMH volume, greater atrophy, and lower MDNPH. Lower baseline levels of carnitines and creatinine were associated with higher annualised change in peak width of skeletonised mean diffusivity (PSMD), and several metabolites, including lower levels of valine, caffeine, and VLDL analytes, were associated with future dementia incidence. Additionally, we identified 1,362 unannotated features associated with lower MDNPH and 2,474 unannotated features associated with increased WMH volume.

Our results show multiple distinct metabolic signatures that are associated with imaging markers of SVD, cognition, and conversion to dementia. Further research should assess causality and the use of metabolomic screening to improve the ability to predict future disease severity and dementia risk in SVD. The metabolomic profiles may also provide novel insights into disease pathogenesis and help identify novel treatment approaches.
Deep protein representations enable recombinant protein expression prediction
Authors: Martiny Hannah-Marie , Armenteros Jose Juan Almagro , Johansen Alexander Rosenberg , Salomon Jesper , Nielsen Henrik
Published: May 2021

A crucial process in the production of industrial enzymes is recombinant gene expression, which aims to induce enzyme overexpression of the genes in a host microbe. Current approaches for securing overexpression rely on molecular tools such as adjusting the recombinant expression vector, adjusting cultivation conditions, or performing codon optimizations. However, such strategies are time-consuming, and an alternative strategy would be to select genes for better compatibility with the recombinant host. Several methods for predicting soluble expression are available; however, they are all optimized for the expression host Escherichia coli and do not consider the possibility of an expressed protein not being soluble. We show that these tools are not suited for predicting expression potential in the industrially important host Bacillus subtilis. Instead, we build a B. subtilis-specific machine learning model for expressibility prediction. Given millions of unlabelled proteins and a small labeled dataset, we can successfully train such a predictive model. The unlabeled proteins provide a performance boost relative to using amino acid frequencies of the labeled proteins as input. On average, we obtain a modest performance of 0.64 area-under-the-curve (AUC) and 0.2 Matthews correlation coefficient (MCC). However, we find that this is sufficient for the prioritization of expression candidates for high-throughput studies. Moreover, the predicted class probabilities are correlated with expression levels. A number of features related to protein expression, including base frequencies and solubility, are captured by the model.
Mechanistic of Rac and Cdc42 synchronization at the cell edge by ARHGAP39-dependent signaling nodules and the impact on protrusion dynamics
Authors: Howell Michael , Delorme-Walker Violaine , Welch Christopher , Pathak Ritu , Hahn Klaus M. , DerMardirossian Céline
Published: May 2021

Compartmentalization of GTPase regulators into signaling nodules dictates the GTPase pathways selected. Rac and Cdc42 are synchronized at the cell edge for effective protrusion in motile cells but how their activity is coordinated remains elusive. Here, we discovered that ARHGAP39, a Rac and Cdc42 GTPase-activating protein, sequentially interacts with WAVE and mDia2 to control Rac/lamellipodia and Cdc42/filopodia protrusions, respectively. Mechanistically, ARHGAP39 binds to WAVE and, upon phosphorylation by Src kinase, inactivates Rac to promote Cdc42-induced filopodia formation. With our optimized FRET biosensor, we detected active Cdc42 at the filopodia tips that controls filopodia extension. ARHGAP39 is transported to filopodia tips by Myosin-X where it binds mDia2 and inactivates Cdc42 leading to filopodia retraction. Failure in lamellipodia to filopodia switch by defective ARHGAP39 impairs cell invasion and metastasis. Our study reveals that compartmentalization of ARHGAP39 within Rac/Cdc42 signaling nodules orchestrates the synchronization of lamellipodia/filopodia crosstalk and highlights the intricate regulation of leading edge dynamics in migrating cells.
T cell receptor (TCR) repertoire analysis reveals a highly conserved TCR repertoire in a bilateral tumor mouse model
Authors: Tsunoda Mikiya , Aoki Hiroyasu , Shimizu Haruka , Shichino Shigeyuki , Matsushima Kouji , Ueha Satoshi
Published: May 2021

Temporal analysis of the T cell receptor (TCR) repertoire has been used to monitor treatment-induced changes in antigen-specific T cells in patients with cancer. However, the lack of experimental models that allow temporal analysis of the TCR repertoire in the same individual in a homogeneous population limits the understanding of the causal relationship between changes in TCR repertoire and antitumor responses. A bilateral tumor model, where tumor cells were inoculated bilaterally into the backs of mice, could be used for temporal analysis of the TCR repertoire. This study examined the prerequisite for this strategy: the TCR repertoire is conserved between bilateral tumors with the same growth rate. Bilateral tumors with equivalent size and draining lymph nodes (dLNs) were collected 13 days after tumor inoculation to analyze the TCR repertoire of CD4+ and CD8+ T cells. The tumor-infiltrating T cell clones were highly conserved between the bilateral tumors, and the extent of clonal expansion was equivalent. In addition, the similarity between the bilateral tumors was equivalent to heterogeneity on one side of the tumor. The similarity of the TCR repertoire in the bilateral dLNs was markedly lower than that in the tumor, suggesting that tumor-reactive T cell clones induced independently in each dLN integrated during recirculation and then infiltrated the tumor. These findings suggest that our bilateral tumor model is suitable for temporal monitoring of the TCR repertoire to evaluate temporal and treatment-induced changes in tumor-reactive T cell clones.

Significance Statement

The bilateral subcutaneous tumor model, where tumor cells were inoculated bilaterally into the backs of mice, is a promising model for temporal analysis of the antitumor response in cancer immunotherapy. This study demonstrated a highly conserved TCR repertoire in bilateral tumors and provided the basis for using a bilateral tumor model for evaluating temporal and treatment-induced changes in tumor-responsive T cell clones in individual mice. In humans, accurate statistical analysis is hampered by various background factors, including cancer type and stage and history of treatment. Moreover, temporal tumor biopsy in patients is highly invasive. Our bilateral tumor model overcomes these clinical issues and is expected to be a valuable tool for the development of novel immune monitoring and therapeutic strategies.
Microfluidic Streptomyces Cultivation for Whole Lifecycle Characterization and Phenotypic Assays Enabled by Nanogap-stabilized Air-Water Interface
Authors: Chen Dongwei , Nie Mengyue , Tang Wei , Zhang Yuwei , Qiao Yuxin , Yun Juanli , Wang Jian , Lan Ying , Ma Liang , Chen Yihua , Du Wenbin
Published: May 2021

Streptomyces is a model filamentous prokaryote to study multicellular differentiation and a rich reservoir for antibiotics discovery. In their natural conditions, Streptomyces grows at the interface of porous soil, air, and water. The morphological development of Streptomyces is traditionally performed on agar plates and mostly studied at the population levels. However, the detailed lifecycle of Streptomyces has not been well studied due to its complexity and lack of research tools which can mimic their natural conditions in the soil. Here, we developed a simple assembled microfluidic device for cultivation and the entire lifecycle observation of Streptomyces development from single-cell level. The microfluidic device composed of a microchannel for loading samples and supplying nutrients, microwell arrays for seeding and growth of single spores, and air-filled chambers aside of the microwells that facilitate growth of aerial hyphae and spores. A unique feature of this device is that each microwell is surrounded by a 1.5 µm gap connected to an air-filled chamber which provide stabilized water-air interface. We used this device to observe the development of single Streptomyces spores and found that unlike those in bulk liquid culture, Streptomyces can differentiate at water-air interfaces in microscale liquid culture. Finally, we demonstrated that phenotypic A-Factor assay can be performed at defined time point of its lifecycle. This microfluidic device could become a robust tool for studying Streptomyces multi-cellular differentiation and interaction at single cell level.

IMPORTANCE

We describe a microfluidic device that mimics the natural porous environment for the growth and development of Streptomyces, the model system for bacterial multicellularity. The microfluidic device is used for cultivation and the entire lifecycle observation of Streptomyces development from single-cell level, including growth of aerial filaments. The aerial hyphae development of Streptomyces at the water-air interface was observed at real time in the microfluidic device. The early growth, opportunistic transformation (in the gap), and merging of aerial hyphae of Streptomyces in the microfluidic device were observed for the first time. It will play an important role in finding single-cell heterogeneity to study secondary metabolites related to the complex lifecycle of Streptomyces.
SCRaPL: hierarchical Bayesian modelling of associations in single cell multi-omics data
Authors: Maniatis Christos , Vallejos Catalina A , Sanguinetti Guido
Published: May 2021

Single-cell multi-omics assays offer unprecedented opportunities to explore gene regulation at cellular level. However, high levels of technical noise and data sparsity frequently lead to a lack of statistical power in correlative analyses, identifying very few, if any, significant associations between different molecular layers. Here we propose SCRaPL, a novel computational tool that increases power by carefully modelling noise in the experimental systems. We show on real and simulated multi-omics single-cell data sets that SCRaPL achieves higher sensitivity and better robustness in identifying correlations, while maintaining a similar level of false positives as standard analyses based on Pearson correlation.
Polygene control and trait dominance in death-feigning syndrome in the red flour beetle Tribolium castaneum
Authors: Matsumura Kentarou , Miyatake Takahisa
Published: May 2021

Death-feigning behavior is an anti-predator behavior in a wide range of animal taxa, and it often correlates with the movement (i.e. death-feigning syndrome). In the present study, we performed reciprocal crossing among strains with genetically longer (L strain) and shorter (S strain) duration of death feigning, and investigated related heritable factors in the F1 and F2 populations. We also investigated moving activity which negatively responded to artificial selection for death feigning in T. castaneum. Our results showed that death feigning occurred more frequently and for shorter periods in the F1 population. In the F2 population, death feigning and movement showed continuous segregation. The distribution of each trait value in the F2 generation was different from the distribution of trait values in the parental generation, and no individuals transgressing the distribution of trait values in the parental generation emerged in the F2 generation. Chi-square analysis of the observed death feigning and movement of F1 and F2 progenies rejected the hypothesis of mono-major gene inheritance. These results suggest that death-feigning syndrome is controlled in a polygenic manner. Our study indicated that reciprocal crossing experiments are useful in assessing the quantitative inheritance of behavioral traits.
Microgravity effect on murine T cells exposed to suborbital flight aboard Blue Origin’s New Shepard vehicle
Authors: Llanos Pedro J. , Andrijauskaite Kristina , Duraisamy Vijay Vishal , Gangadharan Sathya , Morris Jay , Wargovich Michael J.
Published: May 2021

Numerous scientific experiments have been conducted in space. However, the precise mechanisms mediating successful human body adaption to the hostile space environment are still not delineated. The cost and logistic challenges of sending biological payloads to International Space Station are forcing scientists to find alternative research platforms. In this study, we investigated whether brief exposure to microgravity during the suborbital flight aboard Blue Origin’s New Shepard rocket modulated the behavior of the gravity-sensitive murine T cells. We assessed the effect of suborbital environment on different T cell subsets, activation markers, functionality, and cytokine secretion capabilities. Thus, to optimize the potential response of T cells, we cultured them in interleukin IL-2 alone or combined with IL-12. We found that exposure to microgravity decreased the expression of T cells with CD4+ cells being more sensitive to suborbital flight as compared to CD8+ cells. Our data indicate that the functional capabilities of flown T cells were reduced. Also, our findings suggest that supplementing cells with IL-2 and IL-12 cytokines may restore microgravity-mediated cellular alterations. Finally, our study provides insights on the microgravity effect on the murine T cells by utilizing a novel suborbital research platform.
Homogeneous environmental selection overturns distance-decay relationship of soil prokaryotic community
Authors: Zhang Biao , Xue Kai , Zhou Shutong , Wang Kui , Liu Wenjing , Xu Cong , Cui Lizhen , Li Linfeng , Ran Qinwei , Hu Ronghai , Hao Yanbin , Cui Xiaoyong , Wang Yanfen
Published: May 2021

Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biomes on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4,000 km in both alpine and temperate biomes. Surprisingly, prokaryotic similarities increased with geographic distance after tipping points of 1,760 - 1,920 km, overturning the well-accepted distance-decay relationship and generating a significant U-shape pattern. Such U-shape pattern was likely due to decreased disparities in environmental heterogeneity along with geographic distance when across biomes, as homogeneous environmental selection dominated prokaryotic assembly based on βNTI analysis. Consistently, short-term environmental heterogeneity also followed the U-shape pattern spatially, mainly attributed to dissolved nutrients. In sum, these results demonstrate that homogeneous environmental selection via dissolved nutrients overwhelmed the “distance” effect when across biomes, subverting the previously well-accepted geographic pattern for microbes on a large scale.
Increasing temperature weakens the positive effect of genetic diversity on population growth
Authors: Singleton Alexandra L. , Votzke Samantha , Yammine Andrea , Gibert Jean P.
Published: May 2021

Genetic diversity and temperature increases associated with global climate change, are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species thermal optimum (i.e., the temperature at which population growth is maximal), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect almost completely disappears. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world.
Potent macrocycle inhibitors of the human SAGA deubiquitinating module
Authors: Morgan Michael , Ikenoue Tatsuya , Suga Hiroaki , Wolberger Cynthia
Published: May 2021

The SAGA transcriptional coactivator contains a four-protein subcomplex called the DUB module that removes ubiquitin from histone H2B-K120. The human DUB module contains the catalytic subunit, USP22, which is overexpressed in a number of cancers that are resistant to available therapies. We screened a massive combinatorial library of cyclic peptides and identified potent inhibitors of USP22. The top hit was highly specific for USP22 as compared to a panel of 44 other human DUBs. Cells treated with peptide had increased levels of H2B monoubiquitination, demonstrating the ability of the cyclic peptides to enter human cells and inhibit H2B deubiquitination. These macrocycle inhibitors are, to our knowledge, the first reported inhibitors of USP22/SAGA DUB module and show promise for development.
Fitness effects of CRISPR endonucleases inDrosophila melanogasterpopulations
Authors: Langmüller Anna M. , Champer Jackson , Lapinska Sandra , Xie Lin , Metzloff Matthew , Liu Jingxian , Xu Yineng , Clark Andrew G. , Messer Philipp W.
Published: May 2021

CRISPR/Cas9 systems provide a highly efficient and flexible genome editing technology with numerous potential applications in areas ranging from gene therapy to population control. Some proposed applications involve CRISPR/Cas9 endonucleases integrated into an organism’s genome, which raises questions about potentially harmful effects to the transgenic individuals. One application where this is particularly relevant are CRISPR-based gene drives, which promise a mechanism for rapid genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression inDrosophila melanogastercage populations by tracking allele frequencies of four different transgenic constructs, designed to disentangle direct fitness costs due to the integration, expression, and target-site activity of Cas9 from costs due to potential off-target cleavage. Using a maximum likelihood framework, we find a moderate level of fitness costs due to off-target effects but do not detect significant direct costs. Costs of off-target effects are minimized for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. Our results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.
Identification of mundulone and mundulone acetate as natural products with tocolytic efficacy in mono- and combination-therapy with current tocolytics
Authors: Siricilla Shajila , Hansen Christopher J. , Rogers Jackson H. , Simpson Carolyn L. , Crockett Stacey L. , Reese Jeff , Paria Bibhash C. , Herington Jennifer L.
Published: May 2021

Currently, there are a lack of FDA-approved tocolytics for the management of preterm labor. We previously observed that the isoflavones mundulone and mundulone acetate (MA) inhibit intracellular Ca2+-regulated myometrial contractility. Here, we further probed the potential of these natural products to be small molecule leads for discovery of novel tocolytics by: (1) examining uterine-selectivity by comparing concentration-response between human primary myometrial cells and a major off-target site, aortic vascular smooth muscle cells (VSMCs), (2) identifying synergistic combinations with current clinical tocolytics to increase efficacy or and reduce off-target side effects, (3) determining cytotoxic effects and (4) investigating the efficacy, potency and tissue-selectivity between myometrial contractility and constriction of fetal ductus arteriosus (DA), a major off-target of current tocolytics. Mundulone displayed significantly greater efficacy (Emax = 80.5% vs. 44.5%, p=0.0005) and potency (IC50 = 27 μM and 14 μM, p=0.007) compared to MA in the inhibition of intracellular-Ca2+ from myometrial cells. MA showed greater uterine-selectivity, compared to mundulone, based on greater differences in the IC50 (4.3 vs. 2.3 fold) and Emax (70% vs. 0%) between myometrial cells compared to aorta VSMCs. Moreover, MA demonstrated a favorable in vitro therapeutic index of 8.8, compared to TI = 0.8 of mundulone, due to its significantly (p<0.0005) smaller effect on the viability of myometrial (hTERT-HM), liver (HepG2) and kidney (RPTEC) cells. However, mundulone exhibited synergism with two current tocolytics (atosiban and nifedipine), while MA only displayed synergistic efficacy with only nifedipine. Of these synergistic combinations, only mundulone + atosiban demonstrated a favorable TI = 10 compared to TI=0.8 for mundulone alone. While only mundulone showed concentration-dependent inhibition of ex vivo mouse myometrial contractions, neither mundulone or MA affected mouse fetal DA vasoreactivity. The combination of mundulone and atosiban yielded greater tocolytic efficacy and potency on term pregnant mouse and human myometrial tissue compared to single-drugs. Collectively, these data highlight the difference in uterine‐selectivity of Ca2+‐mobilization, effects on cell viability and tocolytic efficacy between mundulone and MA. These natural products could benefit from medicinal chemistry efforts to study the structural activity relationship for further development into a promising single- and/or combination-tocolytic therapy for management of preterm labor.
Beyond resting state neuronal avalanches in the somatosensory barrel cortex
Authors: Mariani B. , Nicoletti G. , Bisio M. , Maschietto M. , Oboe R. , Suweis S. , Vassanelli S.
Published: May 2021

Since its first experimental signatures, the so called ‘critical brain hypothesis’ has been extensively studied. Yet, its actual foundations remain elusive. According to a widely accepted teleological reasoning, the brain would be poised to a critical state to optimize the mapping of the noisy and ever changing real-world inputs, thus suggesting that primary sensory cortical areas should be critical. We investigated whether a single barrel column of the somatosensory cortex of the anesthetized rat displays a critical behavior. Neuronal avalanches were recorded across all cortical layers in terms of both spikes and population local field potentials, and their behavior during spontaneous activity compared to the one evoked by a controlled single whisker deflection. By applying a maximum likelihood statistical method based on timeseries undersampling to fit the avalanches distributions, we show that neuronal avalanches are power law distributed for both spikes and local field potentials during spontaneous activity, with exponents that are spread along a scaling line. Instead, after the tactile stimulus, activity switches to an across-layers synchronization mode that appears to dominate during cortical representation of the single sensory input.
Syntrophy between fermentative and purple phototrophic bacteria for carbohydrate-based wastewater treatment
Authors: Cerruti Marta , Crosset-Perrotin Guillaume , Ananth Mythili , Rombouts Jules L. , Weissbrodt David G.
Published: May 2021

Fermentative chemoorganoheterotrophic bacteria (FCB) and purple photoorganoheterotrophic bacteria (PPB) are two interesting microbial guilds to process carbohydrate-rich wastewaters. Their interaction has been studied in axenic pure cultures or co-cultures. Little is known about their metabolic interactions in open cultures. We aimed to harness the competitive and syntrophic interactions between PPB and FCB in mixed cultures. We studied the effect of reactor regimes (batch or continuous, CSTR) and illumination modes (continuous irradiation with infrared light, dark, or light/dark diel cycles) on glucose conversions and the ecology of the process. In batch, FCB outcompeted (>80%) PPB, under both dark and infrared light conditions. In CSTR, three FCB populations of Enterobacteriaceae, Lachnospiraceae and Clostridiaceae were enriched (>70%), while Rhodobacteraceae relatives of PPB made 30% of the community. Fermentation products generated from glucose were linked to the dominant FCB. Continuous culturing at a dilution rate of 0.04 h-1 helped maintain FCB and PPB in syntrophy: FCB first fermented glucose into volatile fatty acids and alcohols, and PPB grew on fermentation products. Direct supply of carboxylates like acetate under infrared light enriched for PPB (60%) independent of reactor regimes. Ecological engineering of FCB- and PPB-based biorefineries can help treat and valorize carbohydrate-based waste feedstocks.

GRAPHICAL ABSTRACT
Light at the end of the tunnel: FRAP assay reveals that plant vacuoles start as a tubular network
Authors: Minina Elena A. , Scheuring David , Askani Jana , Krueger Falco , Schumacher Karin
Published: May 2021

Plant vacuoles play key roles in cellular homeostasis performing catabolic and storage functions, regulating pH and ion balance. The essential role of vacuoles for plant cell viability makes them a notoriously difficult subject to study impeding reaching the consensus on the mechanism of vacuolar establishment and the source of membrane material for it. Our previous suggestion of endoplasmic reticulum being the main membrane contributor for the tubular network of young vacuoles was recently challenged in a study proposing that young plant vacuoles comprise a set of individual vesicles that are formed de novo via homotypic fusion of multivesicular bodies (MVBs).

To resolve these seemingly contradictory observations we have carefully revaluated both hypotheses. Here we provide a systematic overview of successive vacuolar biogenesis stages in Arabidopsis root, starting from the youngest cells proximate to the quiescent center. We validate our previous conclusions by demonstrating that the vacuolar dye BCECF is fully suitable for studying the organelle’s morphology and provide 3D models of vacuoles at all developmental stages. Furthermore, we established a customized FRAP assay and proved that even at the earliest stages of biogenesis, vacuoles comprise a connected network. Finally, we summarized the new and pre-existing evidence substantiating that vacuolar structures cannot originate solely from MVBs.
Data Independent Acquisition Mass Spectrometry of the Human Lens Enhances Spatiotemporal Measurement of Fiber Cell Aging
Authors: Cantrell Lee S , Schey Kevin L
Published: May 2021

The ocular lens proteome undergoes post-translational and progressive degradation as fiber cells age. The oldest fiber cells and the proteins therein are present at birth and are retained through death. Transparency of the lens is maintained in part by the high abundance crystallin family proteins (up to 300 mg/mL), which establishes a high dynamic range of protein abundance. As a result, previous Data Dependent Analysis (DDA) measurements of the lens proteome are less equipped to identify the lowest abundance proteins. In an attempt to probe more deeply into the lens proteome, we measured the insoluble lens proteome of an 18-year-old human with DDA and newer Data Independent Analysis (DIA) methods. By applying library free DIA search methods, 4,564 protein groups, 48,474 peptides and 5,577 deamidation sites were detected: significantly outperforming the quantity of identifications in using DDA and Pan-Human DIA library searches. Finally, by segmenting the lens into multiple fiber cell-age related regions, we uncovered cell-age resolved changes in proteome composition and putative function.
Paternal chromosome elimination and X non-disjunction on asymmetric spindles inSciaramale meiosis
Authors: de Saint Phalle Brigitte , Oldenbourg Rudolf , Kubai Donna F. , Salmon E. D. , Gerbi Susan A.
Published: May 2021

Meiosis in maleSciarais unique with a single centrosome. A monopolar spindle forms in meiosis I, but a bipolar spindle forms in meiosis II. The imprinted paternal chromosomes are eliminated in meiosis I; there is non-disjunction of the X in meiosis II. Despite differences in spindle construction and chromosome behavior, both meiotic divisions are asymmetric, producing a cell and a small bud. Observations of live spermatocytes made with the LC-PolScope, differential interference contrast optics and fluorescence revealed maternal and paternal chromosome sets on the monopolar spindle in meiosis I and formation of an asymmetric monastral bipolar spindle in meiosis II where all chromosomes except the X congress to the metaphase plate. The X remains near the centrosome after meiosis I and stays with it as the spindle forms in meiosis II. Electron microscopy revealed amorphous material between the X and the centrosome. Immunofluorescence with an antibody against the checkpoint protein Mad2 stains the centromeres of the maternal X dyad in late meiosis I and in meiosis II where it fails to congress to the metaphase plate. Mad2 is also present throughout the paternal chromosomes destined for elimination in meiosis I, suggesting a possible role in chromosome imprinting. If Mad2 on the X dyad mediates a spindle checkpoint in meiosis II, it may delay metaphase to facilitate formation of the second half spindle through a non-centrosomal mechanism.
Alkaline intracellular pH activates AMPK-mTORC2 signaling to promote cell survival during growth factor limitation
Authors: Kazyken D , Lentz SI , Fingar DC
Published: May 2021

mTORC2 controls cell metabolism and promotes cell survival, yet its upstream regulation by diverse cellular cues remains poorly defined. While considerable evidence indicates that mTORC1 but not mTORC2 responds dynamically to amino acid levels, several studies reported activation of mTORC2 signaling by amino acids, a paradox that remains unresolved. Following amino acid starvation, we noted that addition of a commercial amino acid solution but not re-feeding with DMEM containing amino acids increased mTORC2 signaling. Interestingly, the pH of the amino acid solution was ∼ 10. These key observations enabled us to discover that alkaline intracellular pH (pHi) represents a previously unknown activator of mTORC2. Using a fluorescent pH-sensitive dye (cSNARF-1-AM) coupled to live-cell imaging, we demonstrate that alkaline extracellular pH (pHe) increases intracellular pHi, which increases mTORC2 catalytic activity and downstream signaling to Akt. Alkaline pHi also activates AMPK, a sensor of energetic stress. Functionally, alkaline pHi attenuates apoptosis caused by growth factor withdrawal, which requires AMPK in part and mTOR in full. Collectively, these findings reveal that alkaline pHi increases AMPK-mTORC2 signaling to promote cell survival during growth factor limitation. As elevated pHi represents an under-appreciated hallmark of cancer cells, alkaline pH sensing by AMPK-mTORC2 may contribute to tumorigenesis.

One Sentence Summary

Alkaline intracellular pH activates mTORC2
Chromatin loading of MCM hexamers is associated with di-/tri-methylation of histone H4K20 toward S phase entry
Authors: Hayashi-Takanaka Yoko , Hayashi Yuichiro , Hirano Yasuhiro , Miyawaki-Kuwakado Atsuko , Ohkawa Yasuyuki , Obuse Chikashi , Kimura Hiroshi , Haraguchi Tokuko , Hiraoka Yasushi
Published: May 2021

DNA replication is a key step in initiating cell proliferation. Loading hexameric complexes of minichromosome maintenance (MCM) helicase onto DNA replication origins during the G1 phase is essential for initiating DNA replication. Here, we examined MCM hexamer states during the cell cycle in human hTERT-RPE1 cells using multicolor immunofluorescence-based, single-cell plot analysis, and biochemical size fractionation. Experiments involving cell-cycle arrest at the G1 phase and release from the arrest revealed that a double MCM hexamer was formed via a single hexamer during G1 progression. A single MCM hexamer was recruited to chromatin in the early G1 phase. Another single hexamer was recruited to form a double hexamer in the late G1 phase. We further examined relationship between the MCM hexamer states and the methylation levels at lysine 20 of histone H4 (H4K20) and found that the double MCM hexamer state was correlated with di/trimethyl-H4K20 (H4K20me2/3). Inhibiting the conversion from monomethyl-H4K20 (H4K20me1) to H4K20me2/3 retained the cells in the single MCM hexamer state. Non-proliferative cells, including confluent cells or Cdk4/6 inhibitor-treated cells, also remained halted in the single MCM hexamer state. We propose that the single MCM hexamer state is a halting step in the determination of cell cycle progression.
Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-amino-5-methylphenyl)-2-(5-methyl-1H-pyrazol-3-yl)acetamide
Authors: Al Ati Gamal , Chkirate Karim , Mague Joel T. , Abad Nadeem , Achour Redouane , Essassi El Mokhtar
Published: May 2021

The title molecule, C13H16N4O, adopts an angular conformation. In the crystal a layer structure is generated by N—H...O and N—H...N hydrogen bonds together with C—H...π(ring) interactions. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H...H (53.8%), H...C/C...H (21.7%), H...N/N...H (13.6%), and H...O/O...H (10.8%) interactions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/ 6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO–LUMO energy gap is 5.0452 eV.
Regulatory compliance and environmental sustainability practices of manufacturing entrepreneurial ventures in Uganda
Authors: Sendawula Kasimu , Turyakira Peter , Ikiror Cathy Mbidde , Bagire Vincent
Published: May 2021

Purpose

The purpose of this paper is to establish whether all the dimensions of regulatory compliance matter for environmental sustainability practices of manufacturing small and medium entrepreneurial ventures (SMEVs) using evidence from Uganda.

Design/methodology/approach

This study is cross-sectional and correlational. Data was collected through a questionnaire survey of 106 manufacturing SMEVs. Data was analyzed using Statistical Package for Social Sciences (SPSS) version 23.

Findings

The results indicate that controls, legitimacy and deterrence do matter for environmental sustainability practices of the manufacturing SMEVs in Uganda, unlike social norms and values.

Originality/value

This study fosters the understanding of environmental sustainability practices, as it provides insights on whether all the dimensions of regulatory compliance do matter for environmental sustainability practices of manufacturing SMEVs in Uganda.
Entrepreneurial intentions on perceived behavioral control and personal attitude: moderated by structural support
Authors: Otchengco Jr. Alberto Magtoto , Akiate Yuri Walter Dulay
Published: May 2021

Purpose

This study aims to explore the association between the tricycle drivers’ personal attitude and perceived behavioral control and their entrepreneurial intention. Moreover, the study was conducted to determine whether such a relationship is moderated by structural support.

Design/methodology/approach

A total of 349 tricycle drivers in the Philippines were randomly selected and served as the respondents of this study. To determine if there is a significant relationship between the variables, structural equation modeling was used.

Findings

Tricycle drivers denoted that the more positive their perceived behavior control and personal attitude is, the greater their entrepreneurial intention is likely to be. Hence, the relationship of perceived behavioral control and personal attitude on entrepreneurial intention is moderated by perceived structural support.

Originality/value

By learning individuals’ perceived behavioral control, personal attitude and their entrepreneurial intention of specific classes of people, specifically tricycle drivers, it is possible to assess the feasibility of entrepreneurial efforts initiated by the government even before it is implemented, avoiding wastage of both times, resources and effort.
University-industry collaborations in Pakistan: current challenges and future opportunities
Authors: Malik Khaleel , Bashir Tariq , Ali Tariq Mahmood
Published: May 2021

Purpose

This paper aims to identify current challenges that hinder university–industry (U-I) collaboration in Pakistan and presents future opportunities for promoting such collaborations in developing countries.

Design/methodology/approach

This exploratory study presents new empirical evidence obtained from Pakistan via a questionnaire survey of 24 universities, 25 interviews with key stakeholders including industry managers and outputs from a high level workshop event.

Findings

Although there is limited evidence of U-I engagement in Pakistan, the findings show that a lack of coordination between government, universities and industrial firms has hindered knowledge transfer between universities and industry. Such steps as utilising intermediaries to help broker effective collaborations and building trust-based relationships can help in socialising these types of scientific activities.

Research limitations/implications

Any overall conclusions drawn from this exploratory study can only be tentative, as the findings represent a snapshot of current U-I collaboration initiatives in Pakistan.

Practical implications

Less stringent policy interventions from government entities, as well as more universities willing to invite industry input on their board of studies might enable co-development of some university curriculums with industry partners. U-I collaborations could also help to boost innovation efforts in developing country firms.

Originality/value

This paper also offers awareness into benefits of teaching activity collaboration with industry partners, which has been an under explored area of past U-I collaboration studies. The findings should be of interest for both innovation policy and higher education policy researchers.
Understanding the core elements of event portfolio strategy: lessons from Auckland and Dunedin
Authors: Antchak Vladimir , Lück Michael , Pernecky Tomas
Published: May 2021

Purpose

An event portfolio is a vital part of economic and socio-cultural processes designed around the use of public events in cities and destinations around the world. The purpose of this paper is to suggest a new research framework for comparative studies of diverse event portfolio strategies.

Design/methodology/approach

The discussion in this paper is based on a review of the literature and content analysis of event strategies from two New Zealand cities: Auckland and Dunedin.

Findings

The paper suggests an empirically tested framework for exploring event portfolios. It entails such dimensions as the event portfolio strategy, event portfolio focus, portfolio objectives and evaluation tools and event portfolio configuration.

Originality/value

This exploratory research provides a comparative analysis of diverse portfolio contexts and offers insights on developing sustainable event strategies while considering diverse local contexts. Core conditions and processes shaping event portfolio design and management are evaluated and strategic factors articulated.
Justice in arbitration: the consumer perspective
Authors: Ghodoosi Farshad , Sharif Monica M.
Published: May 2021

Purpose

Arbitration – a binding private third-party adjudication – has been the primary legal way for resolution of consumer disputes. Consumers, however, rarely use arbitration to resolve their disputes while evidence suggests that their disputes remain unresolved. Contrary to the current prevailing emphasis on who is winning in arbitration, this study aims to establish that consumers believe that the court is more just than arbitration, regardless of the outcome. This study further establishes that consumers’ perceived poor legitimacy and lack of familiarity, not cost calculation, are what drive their justice perception.

Design/methodology/approach

In three experimental studies, participants were presented with scenarios in which they were to envision themselves amid a consumer dispute. The scenarios were followed by survey questions that examined individuals’ perceptions of justice. Three mediating variables of legitimacy, cost and familiarity were also examined.

Findings

The results suggest that consumers hold a high perception of justice for court as opposed to arbitration. Even though a favorable outcome increases consumers’ perception of justice, the results suggest that consumers find courts to be fairer regardless of the outcome. Familiarity and legitimacy mediate this relationship, not cost.

Originality/value

Current research does not provide an adequate explanation for consumers’ underutilization of arbitration nor does it focus on correct factors. Studies in psychology and law primarily focus on ex post feelings of individuals after dispute resolution, ex post favorable outcomes and ex ante cost–benefit analysis. To the best of the authors’ knowledge, the present study for the first time analyzes ex ante consumer perception of justice.
A generalizable sentiment analysis method for creating a hotel dictionary: using big data on TripAdvisor hotel reviews
Authors: Bagherzadeh Sayeh , Shokouhyar Sajjad , Jahani Hamed , Sigala Marianna
Published: May 2021

Purpose

Research analyzing online travelers’ reviews has boomed over the past years, but it lacks efficient methodologies that can provide useful end-user value within time and budget. This study aims to contribute to the field by developing and testing a new methodology for sentiment analysis that surpasses the standard dictionary-based method by creating two hotel-specific word lexicons.

Design/methodology/approach

Big data of hotel customer reviews posted on the TripAdvisor platform were collected and appropriately prepared for conducting a binary sentiment analysis by developing a novel bag-of-words weighted approach. The latter provides a transparent and replicable procedure to prepare, create and assess lexicons for sentiment analysis. This approach resulted in two lexicons (a weighted lexicon, L1 and a manually selected lexicon, L2), which were tested and validated by applying classification accuracy metrics to the TripAdvisor big data. Two popular methodologies (a public dictionary-based method and a complex machine-learning algorithm) were used for comparing the accuracy metrics of the study’s approach for creating the two lexicons.

Findings

The results of the accuracy metrics confirmed that the study’s methodology significantly outperforms the dictionary-based method in comparison to the machine-learning algorithm method. The findings also provide evidence that the study’s methodology is generalizable for predicting users’ sentiment.

Practical implications

The study developed and validated a methodology for generating reliable lexicons that can be used for big data analysis aiming to understand and predict customers’ sentiment. The L2 hotel dictionary generated by the study provides a reliable method and a useful tool for analyzing guests’ feedback and enabling managers to understand, anticipate and re-actively respond to customers’ attitudes and changes. The study also proposed a simplified methodology for understanding the sentiment of each user, which, in turn, can be used for conducting comparisons aiming to detect and understand guests’ sentiment changes across time, as well as across users based on their profiles and experiences.

Originality/value

This study contributes to the field by proposing and testing a new methodology for conducting sentiment analysis that addresses previous methodological limitations, as well as the contextual specificities of the tourism industry. Based on the paper’s literature review, this is the first research study using a bag-of-words approach for conducting a sentiment analysis and creating a field-specific lexicon.