bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-wide association mapping and systems-level analysis reveal genetic architecture and physiological mechanisms linked with tolerance to flooding during germination in rice
Authors: Entila Frederickson D. , Pacleb Myrish A. , Ella Evangelina S. , Ismail Abdelbagi M.
Published: May 2021

Rice is the staple food of more than half of the world’s population; yet, it faces numerous challenges to meet the rising food demands and worsening climates. An urgent global imperative is to address imminent food shortages through intensive and sustainable agri-food systems and steady genetic gains. Intensification of rice production through direct-seeded rice (DSR) has been progressively practiced but is hindered by poor germination of existing high-yielding varieties in flooded soils. Identifying donors of anaerobic germination (AG) tolerance in rice will expedite the development of varieties suitable for DSR and will lead to enhanced and sustained agricultural productivity. This study aims to dissect the genetic architecture and physiological mechanisms of AG tolerance using systems biology and omics approaches. A Rice Diversity Panel (343 accessions) consisting of 5 subpopulations was screened for AG tolerance under greenhouse conditions, mapped through genome-wide association study (GWAS), and profiled for metabolites. Analyses revealed that most of the AG-tolerant varieties are japonicas with few indicas) and aus. Tolerant japonicas employed better root growth or rapid shoot extension, while tolerant indicas exhibited only the latter. A total of 51 significant GWAS peaks were detected across the genome, some of which were co-localized with known quantitative trait loci while others were novel, more so tolerance was found to involve different genetic controls across subpopulations. AG stress causes distinct biochemical signatures for tolerant genotypes and the profiles contrast among subpopulations implicating divergent metabolic adjustments, including shifts in sugars, intermediates, amino acids, antioxidants, and hormones. This study provides a systems-level approach for underpinning physiological mechanisms of AG tolerance; elucidating phenotypic heterogeneity, genetic architecture, transcriptomic networks, and metabolic landscapes from a genome-wide perspective.

ONE SENTENCE SUMMARY

The integration of GWA mapping, gene network analysis and, non-targeted metabolite profiling elucidates genetic architecture and physiological mechanisms of tolerance to germination and early seedling growth under anaerobic conditions in rice.
Extracellular vesicles from neuronal cells promote neural induction of mESCs through cyclinD1
Authors: Song Lu , Tian Xinran , Schekman Randy
Published: May 2021

Extracellular vesicles (EVs) that are thought to mediate the transport of proteins and RNAs involved in intercellular communication. Here, we show dynamic changes in the buoyant density and abundance of extracellular vesicles that are secreted by PC12 cells stimulated with nerve growth factor (NGF), N2A cells treated with retinoic acid to induce neural differentiation and mESCs differentiated into neuronal cells. EVs secreted from in vitro differentiated cells promote neural induction of mouse embryonic stem cells (mESCs). Cyclin D1 enriched within the EVs derived from differentiated neuronal cells contributes to this induction. EVs purified from cells overexpressing cyclin D1 are more potent in neural induction of mESC cells. Depletion of cyclin D1 from the EVs reduced the neural induction effect. Our results suggest that extracellular vesicles regulate neural development through sorting of cyclin D1.

Extracellular vesicles (EVs) may mediate intercellular communication through the transfer of cargo molecules. Here, we report that cyclinD1 is sorted into EVs during neuronal differentiation and that these EVs help to promote the neural induction of mouse embryonic stem cells.
A novel approach to the functional classification of retinal ganglion cells
Authors: Hilgen Gerrit , Kartsaki Evgenia , Kartysh Viktoriia , Cessac Bruno , Sernagor Evelyne
Published: May 2021

Retinal neurons are remarkedly diverse based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal electrophysiology. Our novel strategy allows grouping of cells sharing gene expression and understanding how these cell classes respond to basic and complex visual scenes. Our approach consists of several consecutive steps. First, the spike firing frequency is increased in RGCs co-expressing a certain gene (Scnn1a or Grik4) using excitatory DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) in order to single out activity originating specifically from these cells. Their spike location is then combined with post hoc immunostaining, to unequivocally characterize their anatomical and functional features. We grouped these isolated RGCs into multiple clusters based on spike train similarities. Using this novel approach. we were able to extend the pre-existing list of Grik4 expressing RGC types to a total of 8 and, for the first time, we provide a phenotypical description of 13 Scnn1a-expressing RGCs. The insights and methods gained here can guide not only RGC classification but neuronal classification challenges in other brain regions as well.
Edaravone activates the GDNF/RET neurotrophic signaling pathway and protects mRNA-induced motor neurons from iPS cells
Authors: Li Qian , Feng Yi , Xue Yingchao , Zhan Xiping , Fu Yi , Gui Gege , Zhou Weiqiang , Richard Jean-Philippe , Taga Arens , Li Pan , Mao Xiaobo , Maragakis Nicholas J. , Ying Mingyao
Published: May 2021

Background

Spinal cord motor neurons (MNs) from human iPS cells (iPSCs) have wide applications in disease modeling and therapeutic development for amyotrophic lateral sclerosis (ALS) and other MN-associated neurodegenerative diseases. We need highly efficient MN differentiation strategies for generating iPSC-derived disease models that closely recapitulate the genetic and phenotypic complexity of ALS. An important application of these models is to understand molecular mechanisms of action of FDA-approved ALS drugs that only show modest clinical efficacy. Novel mechanistic insights will help us design optimal therapeutic strategies together with predictive biomarkers to achieve better efficacy.

Methods

We induce efficient MN differentiation from iPSCs in 4 days using synthetic mRNAs coding two transcription factors (Ngn2 and Olig2) with phosphosite modification. These MNs after extensive characterization were applied in electrophysiological and neurotoxicity assays as well as transcriptomic analysis, to study the neuroprotective effect and molecular mechanisms of edaravone, an FDA-approved drug for ALS, for improving its clinical efficacy.

Results

We generate highly pure and functional mRNA-induced MNs (miMNs) from normal and ALS iPSCs, as well as embryonic stem cells. Edaravone alleviates H2O2-induced neurotoxicity and electrophysiological dysfunction in miMNs, demonstrating its neuroprotective effect that was also found in the glutamate-induced miMN neurotoxicity model. Guided by the transcriptomic analysis, we show a previously unrecognized effect of edaravone to induce the GDNF receptor RET and the GDNF/RET neurotrophic signaling in vitro and in vivo, suggesting a clinically translatable strategy to activate this key neuroprotective signaling. Notably, edaravone can replace required neurotrophic factors (BDNF and GDNF) to support long-term miMN survival and maturation, further supporting the neurotrophic function of edaravone-activated signaling. Furthermore, we show that edaravone and GDNF combined treatment more effectively protects miMNs from H2O2-induced neurotoxicity than single treatment, suggesting a potential combination strategy for ALS treatment.

Conclusions

This study provides methodology to facilitate iPSC differentiation and disease modeling. Our discoveries will facilitate the development of optimal edaravone-based therapies for ALS and potentially other neurodegenerative diseases.

Graphic Abstract
An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche
Authors: Rujano Maria Alexandra , Briand David , Ðelić Bojana , Spéder Pauline
Published: May 2021

Neural stem cells (NSCs) are embedded in a multi-layered, intricate cellular microenvironment supporting their activity, the niche. Whilst shape and function are inseparable, the morphogenetic aspects of niche development are poorly understood. Here, we use the formation of the glial network of a NSC niche to investigate acquisition of architectural complexity. Cortex glia (CG) in Drosophila regulate neurogenesis and build a reticular structure around NSCs. We first show that individual CG cells grow tremendously to ensheath several NSC lineages, eventually spanning the entire tissue while partitioning the NSC population. Elaborate proliferative mechanisms convert these cells into syncytia rich in cytoplasmic bridges. Unexpectedly, CG syncytia further undergo homotypic cell-cell fusion, relying on defined molecular players of cell fusion such as cell surface receptors and actin regulators. Exchange of cellular components is however dynamic in space and time, a previously unreported unique mechanism. This atypical cell fusion remodels cellular borders, restructuring the CG syncytia. Ultimately, the coordination of growth and fusion builds the multi-level architecture of the niche, and creates a modular, spatial partition of the NSC population. Our findings provide novel insights into how a niche forms and organises while developing intimate contacts with a stem cell population.
Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa)
Authors: Carlson Craig H. , Stack George M. , Jiang Yu , Taşkıran Bircan , Cala Ali R. , Toth Jacob A. , Philippe Glenn , Rose Jocelyn K.C. , Smart Christine D. , Smart Lawrence B.
Published: May 2021

The breeding of hybrid cultivars of hemp (Cannabis sativaL.) is not well described, especially the segregation and inheritance of traits that are important for yield. A total of 23 families were produced from genetically diverse parents to investigate the inheritance of morphological traits and their association with biomass accumulation and cannabinoid yield. In addition, a novel classification method for canopy architecture was developed. The strong linear relationship between wet and dry biomass provided an accurate estimate of final dry stripped floral biomass. Of all field and aerial measurements, basal stem diameter was determined to be the single best selection criterion for final dry stripped floral biomass yield. Along with stem diameter, canopy architecture and stem growth predictors described the majority of the explainable variation of biomass yield. Within-family variance for morphological and cannabinoid measurements reflected the heterozygosity of the parents. While selfed populations suffered from inbreeding depression, hybrid development in hemp will require at least one inbred parent to achieve uniform growth and biomass yield. Nevertheless, floral phenology remains a confounding factor in selection because of its underlying influence on biomass production highlighting the need to understand the genetic basis for flowering time in the breeding of uniform cultivars.

Highlight

Stem and canopy architecture traits are superior predictors of floral biomass yield and offer a good indication of hybrid uniformity in field plantings of genetically diverse cannabinoid hemp populations.
Synthetic Nanobody-Functionalized Nanoparticles for Accelerated Development of Rapid, Accessible Detection of Viral Antigens
Authors: Chen Xiahui , Kang Shoukai , Ikbal Ashif , Zhao Zhi , Pan Yuxin , Zuo Jiawei , Gu Liangcai , Wang Chao
Published: May 2021

Successful control of emerging infectious diseases requires accelerated development of fast, affordable, and accessible assays to be widely implemented at a high frequency. Here we present a generalizable assay platform, nanobody-functionalized nanoparticles for rapid, electronic detection (Nano2RED), demonstrated in the detection of Ebola and COVID-19 antigens. To efficiently generate high-quality affinity reagents, synthetic nanobody co-binders and mono-binders with high affinity, specificity, and stability were selected by phage display screening of a vastly diverse, rationally randomized combinatorial library, bacterially expressed and site-specifically conjugated to gold nanoparticles (AuNPs) as multivalent in-solution sensors. Without requiring fluorescent labelling, washing, or enzymatic amplification, these AuNPs reliably transduce antigen binding signals upon mixing into physical AuNP aggregation and sedimentation processes, displaying antigen-dependent optical extinction readily detectable by spectrometry or simple electronic circuitry. With nanobodies against an Ebola virus secreted glycoprotein (sGP) and a SARS-CoV-2 spike protein receptor binding domain (RBD) as targets, Nano2RED showed a high sensitivity (limit of detection of ∼10 pg/mL for sGP and ∼40 pg/mL for RBD in diluted human serum), a high specificity, and a large dynamic range (∼7 logs). Unlike conventional assays where slow mass transport for surface binding limits the assay time, Nano2RED features fast antigen diffusion at micrometer scale, and can be accelerated to deliver results within a few minutes. The rapid detection, low material cost (estimated < $0.01 per test), inexpensive and portable readout system (< $5 and < 100 cm3), and digital data output, make Nano2RED particularly suitable for screening of patient samples with simplified operation and accelerated data transmission. Our method is widely applicable for prototyping diagnostic assays for other antigens from new emerging viruses.
Making the invisible visible: New perspectives on the intersection of human-environment interactions of clinical teams in intensive care
Authors: Visram Sheena , Potts Laura , Sebire Neil J , Rogers Yvonne , Broughton Emma , Chigaru Linda , Nambyiah Pratheeban
Published: May 2021

Understanding human behaviour is essential to the adoption practices for new technologies that promote safer care. This requires capturing the detail of clinical workflows to inform the design of new interactions including those with touchless technologies that decipher human-speech, gesture and motion and allow for interactions that are free of contact. Many environments in hospitals are sub-optimally designed, with a poor layout of work surfaces, cumber-some equipment that requires space and effort to manoeuvre, designs that require healthcare staff to reach awkwardly and medical devices that require extensive touch. This suggests there is a need to better understand how they can be designed. Here, we employ a new approach by installing a single 360° camera into a clinical environment to analyse touch patterns and human-environment interactions across a clinical team to recommend design considerations for new technologies with potential to reduce avoidable touch.
The impact of COVID-19 pandemic on the provision of ambulatory care for patients with chronic neurological diseases in Japan: evaluation of an administrative claims database
Authors: Sato Kenichiro , Mano Tatsuo , Niimi Yoshiki , Iwata Atsushi , Toda Tatsushi , Iwatsubo Takeshi
Published: May 2021

Background

The COVID-19 pandemic has affected not only the emergency medical system, but also patients’ regular ambulatory care. The number of patients visiting outpatient internal medicine clinics decreased during March–April 2020 compared to 2019. Moreover, the ban on telephone re-examination for outpatient clinics in lieu of ambulatory care for chronic diseases has been lifted since March 2020. In this context, we investigate the impact of the COVID-19 pandemic on ambulatory care at Japanese outpatient clinics for patients with chronic neurological diseases during the first half of 2020.

Methods

We collected data from the administrative claims database by DeSC Healthcare. Serial changes in the frequency of subsequent outpatient visits to clinics or hospitals (excluding large hospitals with beds >200) for chronic ambulatory care of epilepsy, migraine, Parkinson’s disease (PD), and Alzheimer’s disease were measured. We also evaluated the utilization rate of telephone re-examination at outpatient clinics.

Results

Since April 2020, the monthly count of outpatient clinic visits for epilepsy or PD decreased slightly but significantly. The use of telephone re-examination was facility-dependent, and it was used in less than 5% of all outpatient clinic visits for the examined neurological diseases in May 2020. The utilization rate of telephone re-examination was not associated with age or the neurological diseases of interest.

Conclusion

The impact of the COVID-19 pandemic on ambulatory care for several chronic neurological diseases may have been relatively limited, in terms of the frequency or type of outpatient visit, during the first half of 2020 in Japan.
Outlier detection in multimodal MRI identifies rare individual phenotypes among 20,000 brains
Authors: Ma Zhiwei , Reich Daniel S. , Dembling Sarah , Duyn Jeff H. , Koretsky Alan P.
Published: May 2021

Outliers in neuroimaging represent spurious data or the data of unusual phenotypes that deserve special attention such as clinical follow-up. Outliers have usually been detected in a supervised or semi-supervised manner for labeled neuroimaging cohorts. There has been much less work using unsupervised outlier detection on large unlabeled cohorts like the UK Biobank brain imaging dataset. Given its large sample size, rare imaging phenotypes within this unique cohort are of interest, as they are often clinically relevant and could be informative for discovering new processes. Here we developed a two-level outlier detection and screening methodology to characterize individual outliers of multiple different brain imaging phenotypes from 20,000 UK Biobank subjects. In primary screening, every subject was parameterized with an outlier score per imaging phenotype to quantitate the degree of outlierness. This approach enabled the assessment of test-retest reliability via outlier scores, which ranged from excellent reliability for ventricular volume, white matter lesion volume, and fractional anisotropy, to good reliability for mean diffusivity and cortical thickness. Resting-state functional connectivity was eliminated for individual-level outlier screening due to its low test-retest reliability of outlier scores. In secondary screening, the extreme outliers (1110 subjects) were examined individually, and those arising from data collection/processing errors were eliminated. A subgroup (108 subjects) of the remaining non-artifactual outliers were radiologically reviewed, and radiological findings were identified in 98%. This study establishes an unsupervised framework for investigating rare individual imaging phenotypes within a large neuroimaging cohort.
High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning
Authors: Li Zhengda , Wang Shiyuan , Sun Meng , Jin Minjun , Khain Daniel , Yang Qiong
Published: May 2021

Many biological oscillators exhibit widely tunable frequency in adapting to environmental changes. Although theoretical studies have proposed positive feedback as a mechanism underlying an oscillator’s large tunability, there have been no experiments to test it. Here, applying droplet microfluidics, we created a population of synthetic cells, each containing a cell-cycle oscillator and varying concentrations of cyclin B mRNAs for speed-tuning and positive-feedback inhibitors for modulating network interactions, allowing a continuous mapping of the cell-cycle period landscape in response to network perturbation. We found that although the cell cycle’s high tunability to cyclin B can reduce with Wee1 inhibition, the reduction is not as great as theoretically predicted, and another positive-feedback regulator, PP2A, may provide additional machinery to ensure the robustness of cell cycle period tunability. Remarkably, we discovered polymorphic responses of cell cycles to the PP2A inhibition. Droplet cells display a monomodal distribution of oscillations peaking at either low or high PP2A activity or a bimodal distribution with both low and high PP2A peaks. We explain such polymorphism by a model of two interlinked bistable switches of Cdk1 and PP2A where cell cycles exhibit two different oscillatory modes in the absence or presence of PP2A bistability.
C. elegans PEZO-1 is a Mechanosensitive Ion Channel Involved in Food Sensation
Authors: Millet Jonathan RM , Romero Luis O , Lee Jungsoo , Bell Briar , Vásquez Valeria
Published: May 2021

PIEZO channels are force sensors essential for physiological processes, including baroreception and proprioception. The Caenorhabditis elegans genome encodes an ortholog gene of the Piezo family, pezo-1, which is expressed in several tissues, including the pharynx. This myogenic pump is an essential component of the C. elegans alimentary canal, whose contraction and relaxation are modulated by mechanical stimulation elicited by food content. Whether pezo-1 encodes a mechanosensitive ion channel and contributes to pharyngeal function remain unknown. Here, we leverage genome editing, genetics, microfluidics, and electropharyngeogram recording to establish that pezo-1 is expressed in the pharynx, including in a proprioceptive-like neuron, and regulates pharyngeal function. Knockout (KO) and gain-of-function (GOF) mutants reveal that pezo-1 is involved in fine-tuning pharyngeal pumping frequency, sensing osmolarity, and food mechanical properties. Using pressure-clamp experiments in primary C. elegans embryo cultures, we determine that pezo-1 KO cells do not display mechanosensitive currents, whereas cells expressing wild-type or GOF PEZO-1 exhibit mechanosensitivity. Moreover, infecting the Spodoptera frugiperda cell line with a baculovirus containing the G-isoform of pezo-1 (among the longest isoforms) demonstrates that pezo-1 encodes a mechanosensitive channel. Our findings reveal that pezo-1 is a mechanosensitive ion channel that regulates food sensation in worms.
The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2
Authors: Suthapot Praewa , Xiao Tiaojiang , Felsenfeld Gary , Hongeng Suradej , Wongtrakoongate Patompon
Published: May 2021

Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by RNA helicases, which comprise a diverse class of RNA remodeling enzymes. We show here that expression of the DEAD boxcontaining RNA helicases DDX5 and DDX17 is abundant throughout retinoic acid-induced neural differentiation of the human pluripotent stem cell (hPSC) line NTERA2, and is mostly localized within the nucleus. Using ChIP-seq, we identify that the two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis- and differentiation-related genes in both hPSCs and their neural derivatives. Further, RNA-seq analyses indicate both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes. We show that the two RNA helicases are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and expression of key neurogenic transcription factors during neural differentiation. Importantly, DDX5 and DDX17 are important for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons. Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.
How much pollen do solitary bee larvae consume? : Or establishing realistic exposure estimates of solitary bee larvae via pollen for the use in risk assessment
Authors: Pamminger Tobias , Schneider Christof , Maas Raffael , Bergtold Matthias
Published: May 2021

Bees foraging in agricultural habitats can be exposed to plant protection products. In order to limit the risk of adverse events to occur a robust risk assessment is needed, which requires reliable estimates for the expected exposure. Especially the exposure pathways to developing solitary bees are not well described and in the currently proposed form rely on limited information. To address this topic, we used a published data set on the volume of pollen solitary bees provide for their larvae to build two scaling models predicting the amount of protein and pollen developing solitary bees need based on adult body weight. We test our models using both literature and experimental data, which both support the validity of the presented models. Using scaling models in the bee risk assessment could complement existing risk assessment approaches, facilitate the further development of accurate risk characterization for solitary bees and ultimately will help to protect them during their foraging activity in agricultural settings.
The genetic architecture of phenotypic diversity in the betta fish (Betta splendens)
Authors: Zhang Wanchang , Wang Hongru , Brandt Débora Y. C. , Hu Beijuan , Sheng Junqing , Wang Mengnan , Luo Haijiang , Guo Shujie , Sheng Bin , Zeng Qi , Peng Kou , Zhao Daxian , Jian Shaoqing , Wu Di , Wang Junhua , van Esch Joep H. M. , Shi Wentian , Ren Jun , Nielsen Rasmus , Hong Yijiang
Published: May 2021

The Betta fish displays a remarkable variety of phenotypes selected during domestication. However, the genetic basis underlying these traits remain largely unexplored. Here, we report a high-quality genome assembly and re-sequencing of 727 individuals representing diverse morphologies of the betta fish. We show that current breeds have a complex domestication history with extensive introgression with wild species. Using GWAS, we identify the genetic basis of multiple traits, including several coloration phenotypes, sex-determination which we map toDMRT1, and the long-fin phenotype which maps toKCNJ15. We identify a polygenic signal related to aggression with many similarities to human psychiatric traits, involving genes such asCACNB2andDISC1. Our study provides a resource for developing the Betta fish as a genetic model for morphology and behavior in vertebrates.
Cell Surface Glycan Engineering Reveals that Matriglycan Alone can Recapitulate Dystroglycan Binding and Function
Authors: Osman Sheikh M. , Capicciotti Chantelle J. , Liu Lin , Praissman Jeremy , Mead Daniel G. , Brindley Melinda A. , Willer Tobias , Campbell Kevin P. , Moremen Kelley W. , Wells Lance , Boons Geert-Jan
Published: May 2021

α-Dystroglycan (α-DG) is uniquely modified on O-mannose sites by a repeating disaccharide (-Xylα1,3-GlcAβ1,3-)n termed matriglycan, which is a receptor for laminin-G domain-containing proteins and employed by old-world arenaviruses for infection. Using chemoenzymatically synthesized matriglycans printed as a microarray, we demonstrated length-dependent binding to Laminin, Lassa virus GP1, and the clinically-important antibody IIH6. Utilizing an enzymatic engineering approach, an N-linked glycoprotein was converted into a IIH6-positive Laminin-binding glycoprotein. Engineering of the surface of cells deficient for either α-DG or O-mannosylation with matriglycans of sufficient length recovered infection with a Lassa-pseudovirus. Finally free matriglycan in a dose and length dependent manner inhibited viral infection of wildtype cells. These results indicate that matriglycan alone is necessary and sufficient for IIH6 staining, Laminin and LASV GP1 binding, and Lassa-pseudovirus infection and support a model in which it is a tunable receptor for which increasing chain length enhances ligand-binding capacity.

Graphical Abstract
Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers
Authors: Lemma Roza Berhanu , Fleischer Thomas , Martinsen Emily , Ledsaak Marit , Kristensen Vessela , Eskeland Ragnhild , Gabrielsen Odd Stokke , Mathelier Anthony
Published: May 2021

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesized that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF-binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
Vaccination-induced rapid protection against bacterial pneumonia via training alveolar macrophage in mice
Authors: Gu Hao , Zeng Xi , Peng Liusheng , Xiang Chuanying , Zhou Yangyang , Zhang Xiaomin , Zhang Jixin , Wang Ning , Guo Gang , Li Yan , Liu Kaiyun , Gu Jiang , Zeng Hao , Zhuang Yuan , Li Haibo , Zhang Jinyong , Zhang Weijun , Zou Quanming , Shi Yun
Published: May 2021

Vaccination strategies for rapid protection against multidrug-resistant bacterial infection are very important, especially for hospitalized patients who have high risk of exposure to these bacteria. However, few such vaccination strategies exist due to a shortage of knowledge supporting their rapid effect. Here we demonstrated a single intranasal immunization of inactivated whole cell (IWC) of Acinetobacter baumannii elicits rapid protection against A. baumannii-infected pneumonia via training of innate immune response in Rag1-/- mice. Immunization-trained alveolar macrophages (AMs) showed enhanced TNF-α production upon restimulation. Adoptive transfer of immunization-trained AMs into naive mice mediated rapid protection against infection. Elevated TLR4 expression on vaccination-trained AMs contributed to rapid protection. Moreover, immunization-induced rapid protection was also seen in Pseudomonas aeruginosa and Klebsiella pneumoniae pneumonia models, but not in Staphylococcus aureus and Streptococcus pneumoniae model. Our data reveal that a single intranasal immunization induces rapid and efficient protection against certain Gram-negative bacterial pneumonia via training AMs response, which highlights the importance and the possibility of harnessing trained immunity of AMs to design rapid-effecting vaccine.
A Facile Alternative Sustainable Process for the Extraction and Purification of Microbial Melanin
Authors: Ghadge Vishal , Kumar Pankaj , Maity Tapan K. , Prasad Kamalesh , Shinde Pramod B.
Published: May 2021

Conventional techniques for the extraction of the melanin encounter several disadvantages such as poor extraction efficiency, excessive use of acid and alkali, and lengthy time duration. To extract melanin in a more sustainable manner, herein suitability of an aqueous solution of quaternary ammonium hydroxide known as tetrabutylammonium hydroxide (40% w/w TBAOH in water) to extract and purify the pigment from the endophyte Streptomyces hyderabadensis 7VPT5-5R was investigated. The solvent could extract 5.54±0.03 g/L of pure melanin against 3.31± 0.02 g/L of pure melanin by conventional method from bacterial culture resulting 66% increase in the yield of the pigment. The quaternary ammonium based solvent was further recycled for 5 consecutive cycles and production of melanin with yield ranging from 5.54±0.03 g/L to 5.47± 0.02 g/L was obtained. The yield of the pigment was 38−40% higher in the recycled solvent in comparison to the melanin yield extracted by conventional method. Considering the efficiency of the solvent for effective extraction and purification of melanin and its recyclability potential, it can be considered as a sustainable solvent for the extraction of the pigments from bacterial culture. Furthermore, the developed method for extraction of melanin from microorganisms as a sustainable source would help in reducing the cost of melanin leading to its efficient utilization in diverse fields.
SARS-CoV-2 receptor ACE2 identifies immuno-hot tumors in breast cancer
Authors: Mei Jie , Cai Yun , Xu Rui , Yu Xinqian , Chen Lingyan , Ma Tao , Gao Tianshu , Gao Fei , Zhu Yichao , Zhang Yan
Published: May 2021

Angiotensin-converting enzyme 2 (ACE2) is known as a host cell receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is identified to be dysregulated in multiple tumors. Although the characterization of abnormal ACE2 expression in malignancies has been preliminarily explored, in-depth analysis of ACE2 in breast cancer (BRCA) has not been elucidated. A systematic pan-cancer analysis was conducted to assess the expression pattern and immunological role of ACE2 based on RNA-sequencing (RNA-seq) data downloaded from The Cancer Genome Atlas (TCGA). Next, correlations between ACE2 expression immunological characteristics in the BRCA tumor microenvironment (TME) were evaluated. Also, the role of ACE2 in predicting the clinical features and the response to therapeutic options in BRCA was estimated. These findings were subsequently validated in another public transcriptomic cohort as well as a recruited cohort. ACE2 was lowly expressed in most cancers compared with adjacent tissues. ACE2 was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), cancer immunity cycles, immune checkpoints, and tumor mutation burden (TMB). Besides, high ACE2 levels indicated the triple-negative breast cancer (TNBC) subtype of BRCA, lower response to endocrine therapy and higher response to chemotherapy, anti-ERBB therapy, antiangiogenic therapy and immunotherapy. To sum up, ACE2 correlates with an inflamed TME and identifies immuno-hot tumors, which may be used as an auxiliary biomarker for the identification of immunological characteristics in BRCA.
Atoh8 is a regulator of intestinal microfold cell (M cell) differentiation
Authors: George Joel Johnson , Martin-Diaz Laura , Ojanen Markus , Viiri Keijo
Published: May 2021

Intestinal microfold cells (M cells) are a dynamic lineage of epithelial cells that initiate mucosal immunity in the intestine. They are responsible for the uptake and transcytosis of microorganisms, pathogens and other antigens in the gastrointestinal tract. A mature M cell expresses a receptor Gp2 which binds to pathogens and aids in the uptake. Due to the rarity of these cells in the intestine, its development and differentiation remains yet to be fully understood. We recently demonstrated that polycomb repressive complex 2 (PRC2) is an epigenetic regulator of M cell development and 12 novel transcription factors including Atoh8 were revealed to be regulated by the PRC2. Here, we show that Atoh8 acts as a regulator of M cell differentiation; absence of Atoh8 led to a significant increase in the number of Gp2+ mature M cells and other M cell associated markers. Atoh8 null mice showed an increase in transcytosis capacity of luminal antigens. Increase in M cell population has been previously reported to be detrimental to mucosal immunity because some pathogens like orally acquired prions have been able to exploit the transcytosis capacity of M cells to infect the host; mouse with increased population of M cells are also susceptible to Salmonella infections. Our study here demonstrates that the population density of intestinal M-cell in the Peyer’s patch is regulated by the PRC2 regulated Atoh8.
Innovative GenExpA software for selecting suitable reference genes for reliable normalization of gene expression in melanoma
Authors: Hoja-Łukowicz Dorota , Maciążek Dawid , Kościelniak Piotr , Janik Marcelina E.
Published: May 2021

The algorithms commonly used to select the best stable reference gene in RT-qPCR data analysis have their limitations. We showed that simple selection of the reference gene or pair of genes with the lowest stability value from the pool of potential reference genes - a commonly used approach - is not sufficient to accurately and reliably normalize the target gene transcript and can lead to biologically incorrect conclusions. For reliable assessment of changes in a target gene expression level, we propose our innovative GenExpA software, which works in a manner independent of the experimental model and the normalizer used. GenExpA software selects the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and in the set of daughter models assigned to it. The reliability of references is validated based on the consistency of the statistical analyses of normalized target gene expression levels through all models, described by the coherence score (CS). The use of the CS value imparts a new quality to qPCR analysis because it clarifies how low the stability value of reference must be in order for biologically correct conclusions to be drawn. We tested our method on qPCR data for theB4GALTgenes family in melanoma, which is characterized by a high mutation rate, and in melanocytes. GenExpA is available athttps://github.com/DorotaHojaLukowicz/GenExpAorhttps://www.sciencemarket.pl/baza-programow-open-source#oferty.

Highlights

GenExpA – next-generation software for normalizer selection and validation

The GenExpA tool defines how low the stability value of the reference should be

The GenExpA tool determines the level of gene expression analysis robustness

The GenExpA tool increases the speed of analysis and reduces cost
COVID-19 and the governmentality of emergency food in the City of Turin
Authors: Sargiacomo Massimo , Corazza Laura , D'Andreamatteo Antonio , Dumay John , Guthrie James
Published: May 2021

Purpose

This paper shows the accounting, accountability and calculative practices associated with emergency food allocations by the City of Turin through a program to feed the vulnerable during COVID-19.

Design/methodology/approach

This is a single case study framed by Foucault's governmentality concept. The data was collected through interviews with key institutional actors and triangulated against decrees, circulars, ordinances and other publicly available documents.

Findings

The accounting tools of governmentality are always incomplete. Sometimes unique situations and crises help us to revise and improve the tools we have. Other times, they demand entirely new tools.

Research limitations/implications

Accounting needs both things to count and a context to count them. In the case of food assistance, what is counted is people. In Turin's case, many people had never been counted – either because there was no need or because they were unaccounted for by choice. Now, the government was accountable for the welfare of both. Thus, new classification systems emerged, as did organisational and accounting solutions.

Originality/value

Although the accounting-for-disasters literature is diverse, studies too often favour the macro social, economic and political issues surrounding crises, neglecting the micro issues associated with governmentality and calculative practices.
Speak softly and carry a big stick: How contract representatives deal with problems
Authors: Daley Dennis M.
Published: May 2021

The contracting process is fraught with difficulties. While successful completion of a contract is the goal, problems and challenges often arise. This requires skills in negotiation or mediation. Dealing with these problems, even if it means recommending contract termination, is part of the job of the contract representatives who oversee the specific projects. Data from the Contracting Officer Representatives survey conducted by the U.S. Merit Systems Protection Board (2005) is used. An index of perceived outcomes (deliverables or services were timely, of high quality, complete, contributed to the agency mission, fair and reasonable, and of good value) was constructed. Roughly, half the respondents indicated that they had had to deal with a problem or challenge. Problem-solving actions (discussions with contactors and other governmental officials, the submission of official documentations, and the recommendation of non-payment or termination sanctions) were submitted to a regression analysis (R2 = .19). From a dozen options, only discussion of the problem with contractors and with their own supervisors along with the recommendation of contract termination registered some meaningful importance (Standardized Betas .1 to .2).
Stock price reaction on ISO 9001 certification announcement: evidence from Indonesia
Authors: Kiryanto Kiryanto , Kartika Indri , Zaenudin Zaenudin
Published: May 2021

Purpose

Certification information published by a company will be responded by the market. Therefore, the purpose of this study is to examine the impact of ISO 9001 certification on the stock market reaction as indicated by stock returns reaction of companies in Indonesia.

Design/methodology/approach

This study used event study method with the period of 13 days. It consists of 6 days before and after ISO 9001 certification announcement and 1 day at the time of the event. It analyzed by using pair sample t-test and one sample t-test. The stock return data is obtained from companies that are ISO 9001 certified and it tested for their stock reactions before and after the certification.

Findings

The results of empirical research showed that the average and companies cumulative abnormal returns in Indonesia react quickly and positively on the first day after ISO 9001 certification announcement. This study proved the differences between abnormal returns before and after the ISO 9001 certification announcement period.

Research limitations/implications

The company's success in implementing ISO 9001 will have an impact on investment in the capital market with a positive response from stock market players. The implication of this study is the further research can examine directly the impact of ISO 9001 implementation on investor behavior in the capital market.

Originality/value

Based on the development of the literature review, this is the first study which examined the impact of ISO 9001 certification announcement on investor reactions in the short term. Therefore, companies in Indonesia need to implement a quality management system for investors in Indonesia.
Exploring how digital kiosk customer experience enhances shopping value, self-mental imagery and behavioral responses
Authors: Lao Aurély , Vlad Mariana , Martin Annabel
Published: May 2021

Purpose

This research analyzes how the dimensions of the customer experience derived from using a digital kiosk during the store visit influence shopping value, self-mental imagery and the behavioral intentions of buying and word of mouth. Mediation effects of utilitarian, hedonic and social shopping values are examined, as well as the mediating effect of self-mental imagery.

Design/methodology/approach

Two empirical studies were conducted to test the research hypotheses. A first analysis was carried out using a sample of 115 customers from several retail sectors. For the second study, 200 customers of one of the largest international sporting goods retailers were interviewed immediately after their store visit.

Findings

The results confirm significant influences of each dimension of the digital kiosk customer experience (sensorial, pragmatic, cognitive, social) on shopping value and self-mental imagery. They highlight strongest effects as well as the quasi-generalized mediating role of these values, and this self-mental imagery in the relations between the components of the experience and the behavioral intentions.

Research limitations/implications

The studies were carried out in only one country (France). It would be also useful to consider variations in shopping motives and in involvement between retail sectors. Highlighted relationships should be deepened by experiments intended to identify the psychological mechanisms and emotions capable of mediating influences of customer experience on shopping value.

Practical implications

The results encourage both advice on the design of digital kiosks and the specifications of their content and several recommendations about the widespread introduction of kiosks or similar new technologies.

Originality/value

This research highlights influences of each of components of customer experience when using an interactive kiosk on shopping values and self-mental imagery, and central roles of these in understanding influences of the customer experience on behavioral responses.
The prospects for dark (troubles) tourism in Belfast, NI
Authors: Ironside Greg , James Kieran
Published: May 2021

Purpose

The purpose of this paper is to investigate the prospects of Belfast as a Tourism City with a special focus on dark (troubles) tourism.

Design/methodology/approach

This paper uses two surveys – one for overseas-based potential tourists and one for Northern Ireland residents; one focus group with potential tourists; and three interviews, one with a Belfast MP and two with tour-guide operators, one from each side of the Northern Ireland divide. This paper is less theoretical than exploratory.

Findings

Generally, there is strong and widespread support for the concept of troubles tourism. Stakeholders must ensure that troubles tourism is intelligently and sensitively handled and builds up communities.

Originality/value

This is a relatively new and under-researched area. Belfast has been rarely looked at in urban-tourism studies. Findings have applicability for other post-conflict and divided countries, such as the countries of the former Yugoslavia.