bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies
Authors: Du Xiao , Li Lili , Liang Fan , Liu Sanyang , Zhang Wenxin , Sun Shuai , Sun Yuhui , Fan Fei , Wang Linying , Liang Xinming , Qiu Weijin , Fan Guangyi , Wang Ou , Yang Weifei , Zhang Jiezhong , Xiao Yuhui , Wang Yang , Wang Depeng , Qu Shoufang , Chen Fang , Huang Jie
Published: August 2020

The importance of structural variants (SVs) on phenotypes and human diseases is now recognized. Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed, few benchmarking procedures are available to confidently assess their performances in biological and clinical research. To facilitate the validation and application of those approaches, our work established an Asian reference material comprising identified benchmark regions and high-confidence SV calls. We established a high-confidence SV callset with 8,938 SVs in an EBV immortalized B lymphocyte line, by integrating four alignment-based SV callers [from 109× PacBio continuous long read (CLR), 22× PacBio circular consensus sequencing (CCS) reads, 104× Oxford Nanopore long reads, and 114× optical mapping platform (Bionano)] and onede novoassembly-based SV caller using CCS reads. A total of 544 randomly selected SVs were validated by PCR and Sanger sequencing, proofing the robustness of our SV calls. Combining trio-binning based haplotype assemblies, we established an SV benchmark for identification of false negatives and false positives by constructing the continuous high confident regions (CHCRs), which cover 1.46Gb and 6,882 SVs supported by at least one diploid haplotype assembly. Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology, disease, and clinical diagnosis.
Conformational changes and channel gating induced by CO2binding to Connexin26
Authors: Brotherton Deborah H. , Savva Christos G. , Ragan Timothy J. , Linthwaite Victoria L. , Cann Martin J. , Dale Nicholas , Cameron Alexander D.
Published: August 2020

CO2is the inevitable by-product of oxidative metabolism. Many physiological processes such as breathing1and cerebral blood flow2are sensitive to CO2. Historically, the physiological actions of CO2have been regarded as being mediated exclusivelyviachanges in pH. Here, we change this consensus by showing that the gap junction protein Connexin26 (Cx26) acts as a receptor for CO2showing sensitivity to modest changes in PCO2around the physiological norm3-6. Mass spectrometry analysis7shows that CO2carbamylates specific lysines on a regulatory loop of Cx26 at high, but not at low levels of PCO2. By means of high resolution cryo-EM, we have solved structures of Cx26 gap junctions at 1.9, 2.2 and 2.1 Å for PCO2of 90, 55 and 20 mmHg respectively, all at pH 7.4. Classification of the particles at each level of PCO2, shows the transmembrane helices and N-terminal helix flexing at the dynamic cytoplasmic side of the protein. Gating of Cx26 gap junctions by CO2involves movements of the N-terminus to plug the channel at high PCO2. We therefore provide mechanistic detail for a new paradigm by which CO2can directly control breathing8and other key physiological functions9.
Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks
Authors: Müller Maik , Gräbnitz Fabienne , Barandun Niculò , Shen Yang , Vetterli Stefan U. , Mondal Milon , Prudent James R. , Severin Yannik , van Oostrum Marc , Hofmann Raphael , Sarott Roman , Nesvizhskii Alexey I. , Carreira Erick M. , Bode Jeffrey , Snijder Berend , Robinson John A. , Loessner Martin J. , Oxenius Annette , Wollscheid Bernd
Published: August 2020

Delineating the molecular nanoscale organization of the surfaceome is pre-requisite for understanding cellular signaling. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would open up theranostic opportunities and the possibility to engineer extracellular signaling. Here, we developed an optoproteomic technology termed LUX-MS that exploits singlet oxygen generators (SOG) for the light-triggered identification of acute protein interactions on living cells. Using SOG-coupled antibodies, small molecule-drugs, biologics and intact viral particles, we show that not only ligand-receptor interactions can be decoded across organisms, but also the surfaceome receptor nanoscale organization ligands engage in with direct implications for drug action. Furthermore, investigation of functional immunosynapses revealed that intercellular signaling inbetween APCs and CD8+T cells can be mapped now providing insights into T cell activation with spatiotemporal resolution. LUX-MS based decoding of surfaceome signaling architectures provides unprecedented molecular insights for the rational development of theranostic strategies.
Analysis of fungal genomes reveals commonalities of intron loss/gain and functions in intron-poor species
Authors: Lim Chun Shen , Weinstein Brooke N. , Roy Scott W. , Brown Chris M.
Published: August 2020

Current evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. However, some extant eukaryotes have few introns, raising the question as to why these few introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species support the idea that massive intron loss has occurred in multiple clades. The intron densities estimated in the fungal ancestral states differ from zero to 8.28 introns per one kbp of protein-coding gene. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 introns/kbp on average, respectively), but also in diverse smuts and allies (e.g.Ustilago maydis, Meira miltonrushiiandMalassezia globosahave 0.06, 0.10 and 0.20 introns/kbp, respectively). To investigate the roles of introns, we searched for their special characteristics using 1302 orthologous genes from eight intron-poor fungi. Notably, most of these introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression.
Obesity promotes glucocorticoid-dependent muscle atrophy in male C57BL/6J mice
Authors: Gunder Laura C. , Harvey Innocence , Redd JeAnna R. , Davis Carol S. , AL-Tamimi Ayat , Brooks Susan V. , Bridges Dave
Published: August 2020

Glucocorticoids promote muscle atrophy by inducing a class of proteins called atrogenes, resulting in reductions in muscle size and strength. In this work, we evaluated whether a mouse model with pre-existing diet-induced obesity had altered glucocorticoid responsiveness. We observed that all animals treated with the synthetic glucocorticoid dexamethasone had reduced strength, but that obesity exacerbated this effect. These changes were concordant with more pronounced reductions in muscle size, particularly in Type II muscle fibers, and potentiated induction of atrogene expression in the obese mice relative to lean mice. Furthermore, we show that the reductions in lean mass do not fully account for the dexamethasone-induced insulin resistance observed in these mice. Together these data suggest that obesity potentiates glucocorticoid-induced muscle atrophy.
Mechanically induced cytoskeletal remodeling in trabecular meshwork cells requires TRPV4 - Rho signaling interactions
Authors: Lakk Monika , Križaj David
Published: August 2020

Intraocular pressure (IOP) is dynamically regulated by the trabecular meshwork (TM), a mechanosensitive tissue that protects the eye from injury through dynamic regulation of aqueous humor outflow from the anterior chamber of the eye. IOP-dependent increases in TM stiffness and contractility drive open angle glaucoma but the mechanotransduction mechanisms that regulate these processes remain poorly understood. We used fluorescence imaging and biochemical analyses to investigate cytoskeletal and focal adhesion remodeling in human TM cells stimulated with cyclic strain. The cells showed enhanced F-actin polymerization, increased number and size of focal adhesions, and activation of the Rho-associated protein kinase (ROCK). Stretch-induced activation of the small GTPase RhoA, and tyrosine phosphorylations of focal adhesion proteins paxillin, focal adhesion kinase (FAK), vinculin and zyxin were time-dependently inhibited by HC-067047, an antagonist of transient receptor potential vanilloid 4 (TRPV4) channels, and the ROCK inhibitor Y-27632. TRPV4 and ROCK activation were required for zyxin translocation and increase in the number/size of focal adhesions in stretched cells. Y-27632 blocked actin polymerization without affecting calcium influx induced by membrane stretch and the TRPV4 agonist GSK1016790A. These results reveal that mechanical tuning of TM cells requires parallel activation of TRPV4, integrins and ROCK, with chronic stress leading to sustained remodeling of the cytoskeleton and focal complexes.
Age-related alterations in prelimbic cortical neuronArcexpression vary by behavioral state and cortical layer
Authors: Hernandez Abbi R. , Truckenbrod Leah M. , Barrett Maya E. , Lubke Katelyn N. , Clark Benjamin J. , Burke Sara N.
Published: August 2020

Prefrontal cortical and medial temporal lobe connectivity is critical for higher cognitive functions that decline in older adults. Likewise, these cortical areas are among the first to show anatomical, functional, and biochemical alterations in advanced age. The prelimbic subregion of the prefrontal cortex and the perirhinal cortex of the medial temporal lobe are densely reciprocally connected and well-characterized as undergoing age-related neurobiological changes that correlate with behavioral impairment. Despite this fact, it remains to be determined how changes within these brain regions manifest as alterations in their functional connectivity. In our previous work, we observed an increased probability of age-related dysfunction for perirhinal cortical neurons that projected to the prefrontal cortex in old rats compared to neurons that were not identified as projection neurons. The current study was designed to investigate the extent to which aged prelimbic cortical neurons also had altered patterns ofArcexpression during behavior, and if this was more evident in those cells that had long-range projections to the perirhinal cortex. The expression patterns of the immediate-early geneArcwere quantified in behaviorally characterized rats that also received the retrograde tracer cholera toxin B (CTB) in the perirhinal cortex to identify projection neurons to this region. As in our previous work, the current study found that CTB+ cells were more active than those that did not have the tracer. Moreover, there were age-related reductions in prelimbic cortical neuronArcexpression that correlated with a reduced ability of aged rats to multitask. Unlike the perirhinal cortex, however, the age-related reduction inArcexpression was equally likely in CTB+ and CTB− negative cells. Thus, the selective vulnerability of neurons with long-range projections to dysfunction in old age may be a unique feature of the perirhinal cortex. Together, these observations identify a mechanism involving prelimbic-perirhinal cortical circuit disruption in cognitive aging.
Aggression is induced by resource limitation in the monarch caterpillar
Authors: Collie Joseph , Granela Odelvys , Brown Elizabeth , Keene Alex C.
Published: August 2020

Food represents a limiting resource for the growth and developmental progression of many animal species. As a consequence, competition over food, space, or other resources can trigger territoriality and aggressive behavior. Throughout their early development stages, insect larvae eat voraciously and limited food availability can potently impact their viability through metamorphosis. In the monarch butterfly,Danaus plexippus,caterpillars feed predominantly on milkweed, raising the possibility that access to milkweed is critical for growth and survival. Here, we characterize the role of food availability on aggression in monarch caterpillars. We find that monarch caterpillars display stereotyped aggressive lunges that increase during development, peaking during the 4thand 5thinstar stages. Detailed behavioral analysis reveals that aggressive actions are most likely to occur when the target is feeding and increases the probability that the target will leave the food source. To determine the relationship between food availability and the initiation of an aggressive encounter, we provided groups of caterpillars differing amounts of food availability and measured aggressive behavior. The number of lunges toward a conspecific caterpillar was significantly increased under conditions of low food availability, suggesting resource defense may trigger aggression. We find that aggression occurs independently of light, suggesting the visual system is dispensable for the induction of aggression. These findings establish monarch caterpillars as a model for investigating interactions between resource availability and aggressive behavior under ecologically relevant conditions and set the stage for future investigations into the neuroethology of aggression in this system.
Chronic Exposure to Palmitic Acid Downregulates AKT in Beta-Cells through Activation of mTOR
Authors: Aggarwal Richa , Peng Zhechu , Zeng Ni , Silva Joshua , He Lina , Chen Jingyu , Debebe Anketse , Stiles Eileen X. , Chen Chien-Yu , Stiles Bangyan L.
Published: August 2020

High circulating lipids occurring in obese individuals and insulin resistant patients are considered a contributing factor to Type 2 Diabetes (T2D). Exposure to high lipids initially causes the beta-cells to expand in population. Long-term exposure to high lipids however is associated with failure of beta-cells and the development of T2D. To prevent the failure of beta-cells and development of Type 2 Diabetes, this study focuses on understanding the molecular mechanisms that underlie this biphasic response of beta-cells to lipid exposure. Using palmitic acid (PA) in cultured beta-cells and islets, we demonstrated that chronic exposure to lipids leads to reduced viability and inhibition of cell cycle progression concurrent with downregulation of a pro-growth/survival kinase AKT, independent of glucose. This AKT downregulation by PA treatment is correlated with a consistent induction of mTOR/S6K activity concurrent with AKT downregulation. Inhibiting mTOR activity restores AKT activity and allows beta-cells to gain proliferation capacity that are lost after high fat diet exposure. In summary, we elucidated a novel mechanism for which lipid exposure may cause the dipole effects on beta-cell growth, where mTOR acts as a lipid sensor. These mechanisms can be novel targets for future therapeutic developments.
Knowledge, attitudes and practices (KAP) towards COVID-19 among Palestinians during the COVID-19 outbreak: A cross-sectional survey
Authors: Qutob Nouar , Awartani Faisal
Published: August 2020

Coronavirus disease 2019 (COVID-19) is a highly contagious illness that spreads rapidly through human-to-human transmission. On March 5, the government of Palestine declared a state of emergency in order to curb the spread of the virus, a declaration that it extended for a fifth time on July 5th. The degree to which a population complies with corresponding safety measures is surely affected by the people’s knowledge, attitudes and practices (KAP) towards the disease. To explore this hypothesis, we gathered data from 1,731 Palestinians between April 19thand May 1st, 2020 through a KAP questionnaire. The participant pool represented a stratified sample of Palestinians living across a number of governorates in the Gaza Strip and the West Bank, with 36.5% from Gaza and (63.5%) from the West Bank. Gender was almost equally distributed within the sample with (51%) male respondents and (49%) female respondent. The questionnaire included 17 questions about participants’ knowledge and awareness of COVID- 19, 17 questions regarding the safety measures they had taken in the wake of the outbreak and 3 questions asking them to assess the efficacy of the government’s response to the pandemic. The overall correct mean of the knowledge was 79.26+-0.35. Most participants expressed confidence that Covid-19 would be successfully controlled and that Palestine could win the battle against Covid-19, though 62% believed that stricter measurements must be applied. Based on the results of this study, we conclude that health education programs aimed at improving the public’s understanding of COVID-19 are important in helping the population maintain appropriate practices, and that findings such as those discussed in this report may provide valuable feedback to lawmakers working to stop the spread of the virus.
FITs: Forest of imputation trees for recovering true signals in single-cell open chromatin profiles
Authors: Sharma Rachesh , Pandey Neetesh , Mongia Anchal , Mishra Shreya , Majumdar Angshul , Kumar Vibhor
Published: August 2020

The advent of single-cell open-chromatin profiling technology has facilitated the analysis of heterogeneity of activity of regulatory regions at single-cell resolution. However, stochasticity and availability of low amount of relevant DNA cause high drop-out rate and noise in single-cell open-chromatin profiles. We introduce here a robust method called as Forest of Imputation Trees (FITs) to recover original signals from highly sparse and noisy single-cell open-chromatin profiles. FITs makes a forest of imputation trees to avoid bias during the restoration of read-count matrices. It resolves the challenging issue of recovering open chromatin signals without blurring out information at genomic sites with cell-type-specific activity. FITs is generalized for wider applicability, especially for highly sparse read-count matrices. The superiority of FITs in recovering signals of minority cells also makes it highly useful for single-cell open-chromatin profile fromin vivosamples.

First made online as thesis work athttps://repository.iiitd.edu.in/xmlui/handle/123456789/807
Investigation of white spot syndrome virus (WSSV) infection in wild crustaceans in the Bohai Sea
Authors: Xu Tingting , Shan Xiujuan , Li Yingxia , Yang Tao , Teng Guangliang , Wu Qiang , Wang Chong , Tang Kathy F.J. , Zhang Qingli , Jin Xianshi
Published: August 2020

The ecological risks of white spot syndrome virus (WSSV), an important aquatic pathogen, has been causing increasing concern recently. A continuous survey on the prevalence of WSSV in the wild crustaceans of the Bohai Sea was conducted in present study. The result of loop-mediated isothermal amplification detection showed that WSSV positivity rates of sampling sites were determined to be 76.73%, 55.0% and 43.75% in 2016, 2017 and 2018, respectively. And the WSSV positivity rates of samples were 17.43%, 12.24% and 7.875% in 2016, 2017 and 2018, respectively. Meanwhile, the investigation revealed that 11 wild species from the sea were identified to be WSSV positive. The WSSV infection in wild crustacean species was confirmed by transmission electron microscopy analysis. The results of this study suggest that WSSV had been colonized in wild species offshore and the impact caused by WSSV to the wild marine ecosystem cannot be ignored.
The retinoic acid receptor drives neuroinflammation and fine tunes the homeostasis of interleukin-17-producing T cells
Authors: Agerholm Rasmus , Rizk John , Kadekar Darshana , Borch Annie , Hadrup Sine Reker , Bekiaris Vasileios
Published: August 2020

The vitamin A metabolite retinoic acid (RA) and its receptor (RAR) are one of the key interactions regulating cellular immunity and neural signaling. Whether endogenous RA-RAR interactions contribute to the development of neuroinflammation and diseases like multiple sclerosis, remains to be elucidated. Herein, we used the murine experimental autoimmune encephalomyelitis (EAE) model and an established genetic RAR silencing approach to decipher its role in pathogenic T cell responses. We show that RAR is necessary for the development of interleukin(IL)-17-driven, cell-mediated immunopathology in the brain and that it fine tunes the homeostasis of IL-17-producing gamma delta (γδT17) and CD4+T cells (TH17). At steady-state, RAR was required in the γδT17 compartment to sustain optimal cell numbers and maintain expression of genes involved in cell cycle progression. In contrast, RAR negatively regulated T helper-17 (TH17) cell homeostasis. Our data show that RAR is required during the early phases of EAE in order to induce a γδT17 response and that its activity is necessary throughout the course of the disease to allow TH17 and γδT17 cells to infiltrate the brain. This is correlated with failure of RAR deficient cells to express surface integrin-alpha4, a major brain homing molecule. Collectively, our work demonstrates that endogenous RA-RAR interactions are important for the homeostasis of IL-17-producing T cells and necessary for their pathogenicity during neuroinflammation.

One sentence summary

Retinoic acid receptor activity was required on IL-17-producing CD4+and γδ T cells to induce their neuropathogenicity, and to regulate both positively and negatively their homeostasis.
Action potentials induce biomagnetic fields in Venus flytrap plants
Authors: Fabricant Anne , Iwata Geoffrey Z. , Scherzer Sönke , Bougas Lykourgos , Rolfs Katharina , Jodko-Władzińska Anna , Voigt Jens , Hedrich Rainer , Budker Dmitry
Published: August 2020

Upon stimulation, plants elicit electrical signals that can travel within a cellular network analogous to the animal nervous system. It is well-known that in the human brain, voltage changes in certain regions result from concerted electrical activity which, in the form of action potentials (APs), travels within nerve-cell arrays. Electrophysiological techniques like electroencephalography1, magnetoencephalography2, and magnetic resonance imaging3,4are used to record this activity and to diagnose disorders. In the plant kingdom, two types of electrical signals are observed: all-or-nothing APs of similar amplitudes to those seen in humans and animals, and slow-wave potentials of smaller amplitudes. Sharp APs appear restricted to unique plant species like the “sensitive plant”,Mimosa pudica, and the carnivorous Venus flytrap,Dionaea muscipula5,6. Here we ask the question, is electrical activity in the Venus flytrap accompanied by distinct magnetic signals? Using atomic optically pumped magnetometers7,8, biomagnetism in AP-firing traps of the carnivorous plant was recorded. APs were induced by heat stimulation, and the thermal properties of ion channels underlying the AP were studied. The measured magnetic signals exhibit similar temporal behavior and shape to the fast de- and repolarization AP phases. Our findings pave the way to understanding the molecular basis of biomagnetism, which might be used to improve magnetometer-based noninvasive diagnostics of plant stress and disease.
UPRmtscales mitochondrial network expansion with protein synthesis via mitochondrial import
Authors: Shpilka Tomer , Du YunGuang , Yang Qiyun , Melber Andrew , Naresh Nandhitha U. , Lavelle Joshua , Liu Pengpeng , Weidberg Hilla , Li Rui , Yu Jun , Zhu Lihua Julie , Strittmatter Lara , Haynes Cole M.
Published: August 2020

As organisms develop, individual cells generate mitochondria to fulfill physiologic requirements. However, it remains unknown how mitochondrial network expansion is scaled to cell growth and impacted by environmental cues. The mitochondrial unfolded protein response (UPRmt) is a signaling pathway mediated by the transcription factor ATFS-1 which harbors a mitochondrial targeting sequence (MTS)1. Here, we demonstrate that ATFS-1 mediates an adaptable mitochondrial expansion program that is active throughout normal development. Developmental mitochondrial network expansion required the relatively inefficient MTS2in ATFS-1, which allowed the transcription factor to be responsive to parameters that impact protein import capacity of the entire mitochondrial network. Increasing the strength of the ATFS-1 MTS impaired UPRmtactivity throughout development due to increased accumulation within mitochondria. The insulin-like signaling-TORC13and AMPK pathways affected UPRmtactivation4,5in a manner that correlated with protein synthesis. Manipulation to increase protein synthesis caused UPRmtactivation. Alternatively, S6 kinase inhibition had the opposite effect due to increased mitochondrial accumulation of ATFS-1. However, ATFS-1 with a dysfunctional MTS6constitutively increased UPRmtactivity independent of TORC1 function. Lastly, expression of a single protein with a strong MTS, was sufficient to expand the muscle cell mitochondrial network in an ATFS-1-dependent manner. We propose that mitochondrial network expansion during development is an emergent property of the synthesis of highly expressed mitochondrial proteins that exclude ATFS-1 from mitochondrial import, causing UPRmtactivation. Mitochondrial network expansion is attenuated once ATFS-1 can be imported.
Mutations of SARS-CoV-2 nsp14 exhibit strong association with increased genome-wide mutation load
Authors: Eskier Doğa , Suner Aslı , Oktay Yavuz , Karakülah Gökhan
Published: August 2020

SARS-CoV-2 is a betacoronavirus responsible for human cases of COVID-19, a pandemic with global impact that first emerged in late 2019. Since then, the viral genome has shown considerable variance as the disease spread across the world, in part due to the zoonotic origins of the virus and the human host adaptation process. As a virus with an RNA genome that codes for its own genomic replication proteins, mutations in these proteins can significantly impact the variance rate of the genome, affecting both the survival and infection rate of the virus, and attempts at combating the disease. In this study, we analyzed the mutation densities of viral isolates carrying frequently observed mutations for four proteins in the RNA synthesis complex over time in comparison to wildtype isolates. Our observations suggest mutations in nsp14, an error-correcting exonuclease protein, have the strongest association with increased mutation load in both regions without selective pressure and across the genome, compared to nsp7, 8, and 12, which form the core polymerase complex. We propose nsp14 as a priority research target for understanding genomic variance rate in SARS-CoV-2 isolates, and nsp14 mutations as potential predictors for high mutability strains.
The Nutrient and Energy Pathway Requirements for Surface Motility of Nonpathogenic and UropathogenicEscherichia coli
Authors: Sudarshan Sushmita , Hogins Jacob , Ambagaspitiye Sankalya , Zimmern Philippe , Reitzer Larry
Published: August 2020

UropathogenicE. coli(UPEC) is the causative pathogen for most uncomplicated urinary tract infections. Flagellar-mediated motility is essential for virulence and colonization for ascending urinary tract infections. The appendage requirement for surface motility depends on the strain: nonpathogenicE. coli(NPEC) lab strains use pili, NPEC hypermotile derivatives use flagella, and UPEC strains use flagella.E. coliflagella-dependent surface motility had been previously shown to require glucose and amino acids. We examined the nutritional and pathway requirements of the NPEC strain W3110 for pili-dependent surface motility, which have not been previously examined. We then compared these requirements to those for two strains with flagella-dependent surface motility: a variant of W3110, W3110-J1, in which the synthesis of the activator of flagella synthesis has been upregulated and the UPEC strain UTI89. The glucose requirement for W3110 was higher than that for either W3110-J1 or UTI89. The pathways required for motility were also different. W3110, but not UTI89, required the Embden-Meyerhof-Parnas pathway via PfkA; conversely, UTI89, but not W3110, required the Entner-Doudoroff pathway, acetogenesis, and the TCA cycle. Glucose did not control flagella synthesis for W3110-J1 and UTI89. The differing requirements for surface motility are likely to reflect major metabolic differences between strains. The metabolic requirements for UTI89 motility suggest a specific adaptation to the urinary tract environment.

IMPORTANCE

Urinary tract infections affect over 50% of women andE. coliis the most common uropathogen. Virulence requires both pili and flagella, and both appendages can contribute to surface motility. Previous studies ofE. colisurface motility did not consider the appendage requirement and the ability to switch the surface appendage. The nutrient and pathway requirements for surface motility of a non-pathogenicE. colistrain with either pili- or flagella-dependent surface motility and the uropathogen UTI89 were examined. Pili-dependent surface motility required glycolysis, while flagella-dependent motility required the TCA cycle and oxidative phosphorylation and was less dependent on glycolysis. The distinctive nutrient and pathway requirements for UTI89 motility probably result from metabolic adaptations to the urinary tract.
Response of mycorrhizae to herbivory and soil moisture in a semiarid grazing ecosystem
Authors: Tiruvaimozhi Yadugiri V , Bagchi Sumanta , Sankaran Mahesh
Published: August 2020

Arbuscular mycorrhizal fungal (AMF) symbioses with plants can be influenced by top-down forces such as grazing, and also by bottom-up forces such as soil resource availability, both of which are being altered by anthropogenic and global change drivers. While the influence of each of these factors on AMF symbioses has been widely studied, explicit tests of the relative strengths of top-down versus bottom-up influences on these ubiquitous plant root symbioses are few. We studied AMF colonization responses of four species of graminoids (3 grassesElymus longae-aristatus,Leymus secalinusandStipa orientalis, and a sedgeCarex melanantha) common to semiarid high-altitude rangelands of the Spiti region, Trans-Himalaya, to changes in a top-down driver, grazing intensity (through short-term clipping and long-term grazer exclusion experiments), and a bottom-up driver, water availability (using irrigation treatments, and by evaluating responses to annual precipitation levels across years). Over three years, AMF colonization in all four host species was influenced by precipitation, with the highest and lowest AMF colonization levels corresponding to years with the lowest and highest rainfall, respectively. However, responses to long-term grazer exclusion differed among host species, and across years: while some species showed decreases in AMF colonization levels under grazing, others showed increases from ungrazed control levels, and these responses changed, even reversed, across years. Responses to short-term clipping and irrigation treatments also differed among hosts, with some species responding to irrigation alone, some to clipping and irrigation combined, and others showing no changes in AMF colonization from control levels in any of the treatments. In our study, long-term changes in water availability influenced AMF colonization levels, while short-term responses were host specific. Responses to above-ground tissue loss, however, differed among host species both in the long- and short-term. Overall, this study demonstrates that while AMF colonization levels correspond to annual precipitation levels in this semiarid ecosystem, host species also play a role in influencing plant-AMF interactions in these rangelands, with colonization levels and responses to abiotic factors changing with host species.
New models to study plasma cells in mouse based on the restriction of IgJ expression to antibody secreting cells
Authors: Ayala Maria Victoria , Bonaud Amélie , Bender Sébastien , Lambert Jean-Marie , Lechouane Fabien , Carrion Claire , Cogné Michel , Pascal Virginie , Sirac Christophe
Published: August 2020

Plasma cells (PC) represent the last stage of B cell development and are mainly characterized by their capacity of secreting large quantities of antibodies. They can be implicated in a broad-spectrum of neoplastic disorders, including Multiple Myeloma, Waldenstrom macroglobulinemia or Monoclonal Gammopathy of Clinical Significance, all characterized by the abnormal proliferation of a PC clone. Up to date, there are only few reporter models to specifically follow PC development, migration and homing in mouse and none allowing the genetic manipulation of these cells. We created a transgenic mouse model in which a green fluorescent protein gene was placed under the control of the well-characterized regulatory elements of the murine immunoglobulin J (IgJ) chain locus. Thanks to this model, we demostrated that IgJ is an early and specific marker of antibody secreting cells (ASCs) and appears before the expression of CD138, making it a good candidate to targeted genetic modifications of plasma cells. Therefore, a conditional deletion model using a Tamoxifen-dependent Cre recombinase inserted into the IgJ locus was characterized. Using a reporter model, we showed that, in contrast with existing models of B cell lineage genetic modification, the activity of the CRE recombinase only affects ASCs after tamoxifen treatment. Additionally, we used this model in a functionalin vitroassay, to show that Ig modifications directly affect plasma cell survival. These two new mouse models, IgJGFPand IgJCreERT2represent exquisite tools to study PCs. In pathology, the IgJCreERT2model opens new frontiers forin vivogenetic modifications of PCs to better reflect the pathophysiology of PC-related diseases.
ATF3 drives senescence by reconstructing accessible chromatin profiles
Authors: Zhang Chao , Zhang Xuebin , Guan Yiting , Huang Xiaoke , Zhang Lijun , Tian Xiao-Li , Tao Wei
Published: August 2020

Chromatin architecture and gene expression profile undergo tremendous reestablishment during senescence. However, the regulatory mechanism between chromatin reconstruction and gene expression in senescence remain elusive. The chromatin accessibility is an excellent perspective to reveal the latent regulatory elements. Thus, we depicted the landscapes of chromatin accessibility and gene expression during HUVECs senescence. We found that chromatin accessibilities are re-distributed during senescence. The senescence related increased accessible regions (IARs) and the decreased accessible regions (DARs) are mainly distributed in distal intergenic regions. The DARs are correlated with the function declines caused by senescence, whereas the IARs are involved in the regulation for senescence program. Moreover, the heterochromatin contributes most of IARs in senescent cells. We identified that the AP-1 transcription factors, especially ATF3 is responsible for driving chromatin accessibility reconstruction in IARs. In particular, DNA methylation is negatively correlated with chromatin accessibility during senescence. AP-1 motifs with low DNA methylation may improve their binding affinity in IARs and further opens the chromatin nearby. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program. And we identified a cellular senescence regulator, AP-1, which promotes senescence through organizing the accessibility profile in IARs.
Synthesis by deamination reaction and crystal structure at 120 K of (16Z,19E)-18-oxo-N-(pyridin-2-yl)-6,7,9,10-tetrahydro-18H-dibenzo[h,o][1,4,7]trioxacyclohexadecine-17-carboxamide
Authors: Wodajo Ayalew T. , Tran Thi Thanh Van , Truong Hong Hieu , Tskhovrebov Alexander G. , Le The Duan , Khrustalev Victor N. , Le Tuan Anh
Published: August 2020

The title compound, C27H24N2O5, is a product of the deamination reaction from aza-14-crown-4 ether containing the γ-piperidone subunit. The title molecule contains a 16-membered macrocycle with the conformation of the C—O—C—C—O—C—C—O—C polyether chain being t–g
(-)–t–t–g
(+)–t (t = trans, 180°; g = gauche, ±60°). The dihedral angle between the planes of the benzene rings fused to the aza-14-crown-4-ether moiety is 31.11 (14)°. The cavity size inside the macrocycle is 4.72 Å. The macrocycle is significantly flattened as a result of the extended conjugated system. Steric repulsion between the pyridylcarboxamide fragment and the benzene ring results in a slight deviation of macrocycle from planarity. The structure also features intramolecular hydrogen bonding, which results in a deviation of the angle between the planes of amide and pyridyl groups from planarity: this angle is 16.32 (18)°. In the crystal, the molecules are linked into infinite zigzag chains via intermolecular C—H...π contacts. The chains are bound into layers parallel to (100) by weak intermolecular C—H...O hydrogen bonds.
Who is attracted to socially responsible organizations? Roles of job applicants' volunteer experience and motives
Authors: Choi Byoung Kwon , Moon Hyoung Koo , Joo Young Ran
Published: August 2020

Purpose

Based on the multiple domain perspective and self-identity theory, this study aims to investigate the effect of job applicants' volunteer experience on their attraction to organizations that engage in corporate social responsibility (CSR). Moreover, it examines the mediating effect of the CSR work role definition in this relationship and proposes a moderated mediation model of how the effect of volunteer experience on organizational attractiveness through the CSR work role definition differs according to other- and self-oriented motives.

Design/methodology/approach

Hypotheses were tested with a moderated mediation model using a scenario-based questionnaire with a sample of 146 undergraduate students in South Korea.

Findings

Job applicants' volunteer experience was positively related to attraction to socially responsible organizations, and the CSR work role definition mediated this relationship. The conditional indirect effect of job applicants' volunteer experience on their attraction to socially responsible organizations through the CSR work role definition was significant only for job applicants with lower other- and self-oriented motives.

Practical implications

The study findings suggest that organizations performing CSR should examine whether job applicants have experience with volunteering activities and the motives behind their participation in such activities.

Originality/value

This study contributes to a comprehensive understanding of how job applicants are attracted to organizations that perform CSR and when such attraction is significant by considering their perception of the CSR work role definition and motives for volunteering activities.
Pivot or pirouette? Turning to emergency remote teaching in the COVID-19 pandemic
Authors: Whitakker Louise , Kleyn Nicola , Pearson Hayley
Published: August 2020

Learning outcomes

Learning outcomes are as follows: Students will be able to demonstrate the need to understand the uncertainty faced in a crisis; demonstrate how dynamic capabilities allow an organisation to respond effectively in a time of crisis and deep uncertainty; explore how strong dynamic capabilities are required to maintain continuity of operations by enabling a shift in the current business model; and evaluate methods of mobilising resources to address needs and possible opportunities presented in a crisis.

Case overview/synopsis

Gordon Institute of Business Science (GIBS), a South African-based business school and the one of the top ranked business schools in Africa, faced a crisis in the midst of the COVID-19 pandemic. With the announcement of a national lock down, under strict conditions, and the immediate closure of the GIBS campus, the Academic Programmes had to radically shift their mode of delivery to enable students to continue with their respective programmes. When the situation was further exacerbated by the breaking of the undersea cable, the Executive Director of Academic Programmes, Professor Louise Whittaker faced the difficult decision on what to do next. The case illustrates the need for strong dynamic capabilities to foster organisational agility and to respond effectively in times of deep uncertainty or crises.

Complexity academic level

The case is positioned at a postgraduate level and would be ideal as a teaching case for business students on a Master of Business Administration programme, a specialised Master in Philosophy programme or selected executive education programmes for general managers or senior executives.

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS: 11 Strategy.
Why people need privacy? The role of privacy fatigue in app users' intention to disclose privacy: based on personality traits
Authors: Tang Jie , Akram Umair , Shi Wenjing
Published: August 2020

Purpose

Mobile Applications (App) privacy has become a prominent social problem. Compared with privacy concerns, this study examines a relatively novel concept of privacy fatigue and explores its effect on the users’ intention to disclose their personal information via mobile Apps. In addition, the personality traits are proposed as antecedents that will induce the personal perception of privacy fatigue and privacy concerns differently.

Design/methodology/approach

Data were collected from 426 respondents. Structure equation modeling was used to test the hypotheses.

Findings

The findings describe that App users’ intention toward personal information disclosure is determined by privacy fatigue and privacy concerns, but the former has a greater impact. With minor exceptions, the two factors are also influenced by different personality traits. Specifically, neuroticism has positive effects on privacy fatigue, but agreeableness and extraversion have presented the opposite results on the two variables.

Practical implications

This research is very scarce to examine the joint effects of privacy fatigue, privacy concerns and personality traits on App users’ disclosing intention. In doing so, these results will be of benefit to App providers and platform managers and can be the basis for a variety of follow-up studies.

Originality/value

While previous research just focuses on privacy concerns, this study explores the critical roles of privacy fatigue and opens up a new avenue of emotion-attitude analysis that can further increase the specificity and richness of users’ privacy research. Additionally, implications for personality traits as antecedents in the impact of App users’ privacy emotions and attitudes are discussed.
Crop diversity benefits carabid and pollinator communities in landscapes with semi‐natural habitats
Authors: Aguilera Guillermo , Roslin Tomas , Miller Kirsten , Tamburini Giovanni , Birkhofer Klaus , Caballero‐Lopez Berta , Lindström Sandra Ann‐Marie , Öckinger Erik , Rundlöf Maj , Rusch Adrien , Smith Henrik G. , Bommarco Riccardo
Published: August 2020

In agricultural landscapes, arthropods provide essential ecosystem services such as biological pest control and pollination. Intensified crop management practices and homogenization of landscapes have led to declines among such organisms. Semi‐natural habitats, associated with high numbers of these organisms, are increasingly lost from agricultural landscapes but diversification by increasing crop diversity has been proposed as a way to reverse observed arthropod declines and thus restore ecosystem services. However, whether or not an increase in the diversity of crop types within a landscape promotes diversity and abundances of pollinating and predaceous arthropods, and how semi‐natural habitats might modify this relationship, are not well understood.

To test how crop diversity and the proportion of semi‐natural habitats within a landscape are related to the diversity and abundance of beneficial arthropod communities, we collected primary data from seven studies focusing on natural enemies (carabids and spiders) and pollinators (bees and hoverflies) from 154 crop fields in Southern Sweden between 2007 and 2017.

Crop diversity within a 1‐km radius around each field was positively related to the Shannon diversity index of carabid and pollinator communities in landscapes rich in semi‐natural habitats. Abundances were mainly affected by the proportion of semi‐natural habitats in the landscape, with decreasing carabid and increasing pollinator numbers as the proportion of this habitat type increased. Spiders showed no response to either crop diversity or the proportion of semi‐natural habitats.

Synthesis and applications. We show that the joint effort of preserving semi‐natural habitats and promoting crop diversity in agricultural landscapes is necessary to enhance communities of natural enemies and pollinators. Our results suggest that increasing the diversity of crop types can contribute to the conservation of service‐providing arthropod communities, particularly if the diversification of crops targets complex landscapes with a high proportion of semi‐natural habitats.
Greenhouse gas emissions are affected by land use type in two agroforestry systems: Results from an incubation experiment
Authors: Li Ping , Lang Man , Zhu Sixi , Bork Edward W. , Carlyle Cameron N. , Chang Scott X.
Published: August 2020

In order to better understand factors affecting greenhouse gas (GHG) emissions in Canadian agroforestry systems, we conducted a laboratory incubation study to assess N2O, CO2 and CH4 emissions from soils in response to land use (forestland vs. cropland) and agroforestry system type (hedgerow vs. shelterbelt) in central Alberta, Canada. Emissions of N2O were lower in soils from forestland than cropland, and forest soils acted as a net sink of atmospheric CH4 while cropland soils were weak sources of CH4. However, the forest soil had higher CO2 emission rates than the cropland soil within both agroforestry systems. Soil CH4 oxidation was higher in soil from hedgerow (consisted of natural forest vegetation) than from shelterbelt system (planted forest vegetation), while the former also had lower N2O emissions. Overall, soil CO2 emissions were significantly higher from hedgerow than from shelterbelt systems. Emissions of N2O were positively related with gross nitrification rates and soil pH, and negatively related with gross N immobilization rates. The CO2 emissions were positively related with water‐soluble organic C contents, while CH4 emissions were positively related with clay content, but negatively with gross N immobilization rates and soil organic C content. The global warming potential was higher in forestland soil than in cropland soil within agroforestry systems, and higher in forestland soil of the hedgerow compared to that in shelterbelts. Our results suggest that we need to select land uses or agroforestry systems that have a higher potential of mitigating GHG emissions from soils.