bluuebunny/crossref_metadata_2025 huggingface dataset:
Tet2negatively regulates memory fidelity
Authors: Zengeler Kristine E. , Gettens Caroline P. , Smith Hannah C. , Caron Mallory M. , Zhang Xinyuan , Howard Alexandra H. , Boitnott Andrea R. , Gogliettino Alex R. , Reda Anas , Malachowsky Beth G. , Zhong Chun , Song Hongjun , Kaas Garrett A. , Kennedy Andrew J.
Published: November 2019

Despite being fully differentiated, DNA methylation is dynamically regulated in post-mitotic glutamatergic neurons in the CA1 of the hippocampus through competing active DNA methylation and de-methylation, a process that regulates neuronal plasticity. Active DNA methylation after learning is necessary for long-term memory formation, and active DNA de-methylation by the TET enzymes has been implicated as a counter-regulator of that biochemical process. We demonstrate thatTet2functions in the CA1 as a negative regulator of long-term memory, whereby its knockdown across the CA1 or haploinsufficiency in glutamatergic neurons enhances the fidelity of hippocampal-dependent spatial and associative memory. Loci of altered DNA methylation were then determined using whole genome bisulfite sequencing from glutamatergicTet2haploinsufficient CA1 tissue, which revealed hypermethylation in the promoters of genes known to be transcriptionally regulated after experiential learning. This study demonstrates a link betweenTet2activity at genes important for memory formation in CA1 glutamatergic neurons and memory fidelity.
Inhibition of TXNRD or SOD1 overcomes NRF2-mediated resistance to β-lapachone
Authors: Torrente Laura , Prieto Nicolas , Falzone Aimee , Boothman David A. , Haura Eric B. , DeNicola Gina M.
Published: November 2019

Alterations in the NRF2/KEAP1 pathway result in the constitutive activation of NRF2, leading to the aberrant induction of antioxidant and detoxification enzymes, including NQO1. The NQO1 bioactivatable agent β-lapachone can target cells with high NQO1 expression but relies in the generation of reactive oxygen species (ROS), which are actively scavenged in cells with NRF2/KEAP1 mutations. However, whether NRF2/KEAP1 mutations influence the response to β-lapachone treatment remains unknown. To address this question, we assessed the cytotoxicity of β-lapachone in a panel of NSCLC cell lines bearing either wild-type or mutant KEAP1. We found that, despite overexpression of NQO1, KEAP1 mutant cells were resistant to β-lapachone due to enhanced detoxification of ROS, which prevented DNA damage and cell death. To evaluate whether specific inhibition of the NRF2-regulated antioxidant enzymes could abrogate resistance to β-lapachone, we systematically inhibited the four major antioxidant cellular systems using genetic and/or pharmacologic approaches. We demonstrated that inhibition of the thioredoxin-dependent system or copper-zinc superoxide dismutase (SOD1) could abrogate NRF2-mediated resistance to β-lapachone, while depletion of catalase or glutathione was ineffective. Interestingly, inhibition of SOD1 selectively sensitized KEAP1 mutant cells to β-lapachone exposure. Our results suggest that NRF2/KEAP1 mutational status might serve as a predictive biomarker for response to NQO1-bioactivatable quinones in patients. Further, our results suggest SOD1 inhibition may have potential utility in combination with other ROS inducers in patients with KEAP1/NRF2 mutations.

Highlights

Aberrant activation of NRF2 in non-small cell lung cancer promotes resistance to β-lapachone via the antioxidant defense.

Inhibition of the thioredoxin-dependent system and superoxide dismutase 1 increase sensitivity to β-lapachone treatment.

Mutations in the NRF2/KEAP1 pathway might serve as predictive biomarker for response to β-lapachone in patients.
Dynamic evolution of cervical cancer mutations during chemoradiation using novel sampling approach
Authors: Chapman Bhavana V. , Karpinets Tatiana , Sims Travis T. , Biegert Greyson , Wu Xiaogang , Delgado Medrano Andrea Y. , Eifel Patricia J. , Jhingran Anuja , Lin Lilie L. , Ramondetta Lois M. , Futreal Andrew M. , Jazaeri Amir A. , Frumovitz Michael , Schmeler Kathleen M. , Yue Jingyan , Mitra Aparna , Yoshida-Court Kyoko , Solley Travis , Mathew Geena , Ahmed-Kaddar Mustapha , Zhang Jianhua , Klopp Ann H. , Colbert Lauren E.
Published: November 2019

Objective

The aim of this study was to validate a whole exome sequencing approach to longitudinally characterize the tumor mutational profile of cervical cancer patients undergoing chemoradiation (CRT).

Experimental Design

Cervical cancer tumor specimens from twenty-seven patients undergoing chemoradiation were collected before and throughout CRT and whole exome sequencing (WES) was performed to characterize individual mutations and alterations in unique genes. WES data were analyzed from cervical cancer patients in The Cancer Genome Atlas (TCGA) as a comparison group.

Results

Over 93% of mutated genes detected at baseline were present in TCGA. Tumor purity from collected swabs correlated with MRI tumor volumes during the course of treatment (R2=0.969). CDK4/CDK6/cyclin D1-related gene mutations involved in the ERK1/2, p16INK4, and p53 pathway and G1/S checkpoint most commonly persisted at the end of CRT.

Conclusion

This non-invasive swab technique to serially sample tumor during CRT will allow new discoveries of dynamic tumor mutational profile changes during chemoradiation for mucosal tumors. Mutations that survived or increased during the initial weeks of radiation treatment are potential drivers of radiation resistance including the CDL4/CDK6/cyclin D1-related pathway.

Statement of Translational Relevance

There are no established biomarkers to predict chemoradiation (CRT) response for cervical cancer patients. Serial biopsies cannot be performed due to risks of bleeding and fistula. We used a novel non-invasive swab-based biopsy technique to obtain serial samples from a cohort of twenty-seven patients through the course of treatment, and validated this approach to obtain whole exome sequencing data. We analyzed dynamic tumor mutation profiles during CRT. Results from this study show that mutations in CDK4/CDK6/cyclin D1-related genes increased at the end of CRT, suggesting this pathway as a potential driver of radiation resistance.
The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5’ cap modulates protein expression in living cells
Authors: Sikorski Pawel J. , Warminski Marcin , Kubacka Dorota , Ratajczak Tomasz , Nowis Dominika , Kowalska Joanna , Jemielity Jacek
Published: November 2019

7-Methylguanosine 5’-cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5’-terminal nucleotides and additional methylations (2’-O-methylation and m6A). Currently available 5’-capping methods do not address this diversity. We report trinucleotide 5’-cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (± 2’-O-methylation). HPLC-purified mRNAs carrying these 5’ caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa, and JAWS II). In all cases the highest expression was achieved for mRNAs carrying 5’-terminal A and m6A, whereas the lowest was observed for G and Gm. The 2’-O-methylation of the first transcribed nucleotide (cap 1) significantly increased expression compared to cap 0 only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.
An improved whole life cycle culture protocol for the hydrozoan genetic model Clytia hemisphaerica
Authors: Lechable Marion , Jan Alexandre , Weissbourd Brandon , Uveira Julie , Gissat Loann , Collet Sophie , Gilletta Laurent , Chevalier Sandra , Leclère Lucas , Peron Sophie , Barreau Carine , Lasbleiz Régis , Houliston Evelyn , Momose Tsuyoshi
Published: November 2019

The jellyfish species Clytia hemisphaerica (Cnidaria, Hydrozoa) has emerged as a new experimental model animal in the last decade. Favorable characters include a fully transparent body suitable for microscopy, daily gamete production and a relatively short life cycle. Furthermore, whole genome sequence assembly and efficient gene editing techniques using CRISPR/Cas9 have opened new possibilities for genetic studies. The quasi-immortal vegetatively-growing polyp colony stage provides a practical means to maintain mutant strains. In the context of developing Clytia as a genetic model, we report here an improved whole life cycle culture method including an aquarium tank system designed for culture of the tiny jellyfish form. We have compared different feeding regimes using Artemia larvae as the food and demonstrate that the stage-dependent feeding control is the key for rapid and reliable medusa and polyp rearing. Metamorphosis of the planula larvae into a polyp colony can be efficiently induced using a new synthetic peptide. The optimized procedures detailed here make it practical to generate new genetically modified Clytia strains and to safely maintain their whole life cycle in the laboratory.
The inhibition of cellular toxicity of amyloid-beta by dissociated transthyretin
Authors: Cao Qin , Anderson Daniel H. , Liang Wilson , Chou Joshua , Saelices Lorena
Published: November 2019

The protective effect of transthyretin (TTR) on cellular toxicity of amyloid-beta (Aβ) has been previously reported. TTR is a tetrameric carrier of thyroxine in blood and cerebrospinal fluid, whose pathogenic aggregation causes systemic amyloidosis. In contrast, many reports have shown that TTR binds amyloid-beta (Aβ), associated with Alzheimer’s disease, alters its aggregation, and inhibits its toxicity bothin vitroandin vivo. In this study, we question whether TTR amyloidogenic ability and its anti-amyloid inhibitory effect are associated. Our results indicate that the dissociation of the TTR tetramer, required for its amyloid pathogenesis, is also necessary to prevent cellular toxicity from Aβ oligomers. These findings suggest that the Aβ binding site of TTR may be hidden in its tetrameric form. Aided by computational docking and peptide screening, we identified a TTR segment that is capable of altering Aβ aggregation and toxicity, mimicking TTR cellular protection. This segment inhibits Aβ oligomer formation and also promotes the formation of non-toxic, non-amyloid, amorphous aggregates which are more sensitive to protease digestion. This segment also inhibits seeding of Aβ catalyzed by Aβ fibrils extracted from the brain of an Alzheimer’s patient. Our results suggest that mimicking the inhibitory effect of TTR with peptide-based therapeutics represents an additional avenue to explore for the treatment of Alzheimer’s disease.

Significance statement

The pathological landmarks of Alzheimer’s disease are the formation of amyloid plaques and neurofibrillary tangles. Amyloid plaques contain fibrous structures made of aggregated amyloid-beta (Aβ). In 1982, Shirahama and colleagues observed the presence of transthyretin (TTR) in these plaques. TTR is a tetrameric protein whose aggregation causes transthyretin amyloidosis. However, TTR protects Aβ from aggregating and causing toxicity to neurons. In this study, we show that the dissociation of TTR tetramers is required to inhibit cellular toxicity caused by Aβ. In addition, we identified a minimum segment of TTR that inhibits Aβ aggregation and cellular toxicity by the formation of amorphous aggregates that are sensitive to proteases, similar to the natural effect of TTR found by others in vivo.
AGTR1 is overexpressed in neuroendocrine neoplasms, regulates secretion and may serve as a target for molecular imaging and therapy
Authors: Exner Samantha , Schuldt Claudia , Sachindra Sachindra , Du Jing , Heing-Becker Isabelle , Licha Kai , Wiedenmann Bertram , Grötzinger Carsten
Published: November 2019

Peptide receptor targeting has proven to be a pivotal tool for diagnostic imaging and radioligand therapy of neuroendocrine neoplasms (NENs), which frequently express somatostatin receptors (SSTRs) on their cell surface. However, up to 30 % of NEN patients do not benefit from SSTR-based approaches, others develop a resistance. Consequently, alternative cell surface targets need to be identified. In this study, cell-based dynamic mass redistribution and calcium mobilization screening using a 998-compound library identified and confirmed angiotensin II (ATII) as a strong activator of cellular signaling in NEN cells. Expression analyses of the ATII receptor type 1 (AGTR1) revealed an upregulation of both mRNA levels (RT-qPCR) and radioligand binding (autoradiography) in pancreatic (n=42) and small-intestinal (n=71) NEN tissues compared to healthy controls (n=25). The two NEN cell lines BON (pancreas) and H727 (lung) with elevated AGTR1 expression exhibited concentration-dependent calcium mobilization and chromogranin A secretion upon stimulation with ATII, blocked by AGTR1 antagonism and Gαq inhibition. To assess the applicability of AGTR1 for optical in vivo imaging, the receptor ligand saralasin was coupled to the near-infrared dye indotricarbocyanine and tested for its biodistribution in a NMRI Foxn1nu/Foxn1nu mouse model bearing AGTR1-positive BON and negative QGP-1 xenograft tumors. Near-infrared fluorescent imaging showed a significantly higher uptake in BON tumors 3-6 hours after injection. This successful targeting in an NEN model establishes AGTR1 as an interesting target in this tumor entity, paving the way for the development of translational chelator-based probes for diagnostic PET imaging and peptide receptor radioligand therapy.
Host lipid alterations afterMacrophomina phaseolinainfection contribute to charcoal rot disease susceptibility in grain sorghum: Evidence from transcriptomic and lipidomic data
Authors: Bandara Ananda Y. , Weerasooriya Dilooshi K. , Liu Sanzhen , Little Christopher R.
Published: November 2019

Lipids are involved in central metabolic processes and confer basic configuration to cellular and subcellular membranes. Lipids also play a role in determining the outcome of plant-pathogen interactions. Lipid based links that delineate either host resistance or susceptibility against necrotrophic microorganisms are poorly investigated and described.Macrophomina phaseolina(MP) is an important necrotrophic fungus which causes diseases in over 500 plant species including charcoal rot in sorghum.

We used RNA sequencing and automated direct infusion electrospray ionization-triple quadrupole mass spectrometry (ESI-MS/MS) to quantitatively profile the transcriptomes and lipidomes of a known charcoal rot resistant (SC599) and susceptible (Tx7000) sorghum genotype in response to MP inoculation.

We found that MP is capable of significantly decreasing the phosphatidylserine, phytosterol, and ox-lipid contents in the susceptible genotype while significantly increasing its stigmasterol:sitosterol and monogalactosyldiacylglycerol: digalactosyldiacylglycerol ratios. None of the above was significantly affected in the resistant genotype, except for the significantly increased ox-lipid content.

Our transcriptome and functional lipidome findings suggested the lethal impacts of MP inoculation on plastid- and cell- membrane integrity and the lipid based signaling capacity of the charcoal rot susceptible sorghum genotype, Tx7000. Findings also suggested the strong oxidative stress experienced by Tx7000 under MP inoculation and shed light on the potential lipid classes involved in induced charcoal rot disease susceptibility.
Lin28a/let-7Pathway Modulates theHoxCode viaPolycombRegulation during Axial Patterning in Vertebrates
Authors: Sato Tempei , Kataoka Kensuke , Ito Yoshiaki , Yokoyama Shigetoshi , Inui Masafumi , Mori Masaki , Takahashi Satoru , Akita Keiichi , Takada Shuji , Ueno-Kudoh Hiroe , Asahara Hiroshi
Published: November 2019

The body plan along the anteroposterior axis and regional identities are specified by the spatiotemporal expression ofHoxgenes. Multistep controls are required for their unique expression patterns; however, the molecular mechanisms behind the tight control ofHoxgenes are not fully understood. In this study, we demonstrated that theLin28a/let-7reciprocal regulatory pathway is critical for vertebral specification.Lin28a−/−mice exhibited homeotic transformations of vertebrae which were caused by the global dysregulation of posteriorHoxgenes. The accumulation oflet-7-family microRNAs inLin28a−/−mice resulted in the reduction of PRC1 occupancy at theHoxcluster loci by targetingCbx2. Consistently, Lin28a loss in embryonic stem-like cells led to aberrant induction of posteriorHoxgenes, which was rescued by the knockdown oflet-7-family microRNAs. These results suggest thatLin28/let-7pathway is possibly involved in the modulation of the “Hoxcode” viaPolycombregulation during axial patterning in vertebrates.
Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)
Authors: Gardner Elliot M. , Johnson Matthew G. , Pereira Joan T. , Ahmad Puad Aida Shafreena , Arifiani Deby , Sahromi  , Wickett Norman J. , Zerega Nyree J.C.
Published: November 2019

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. While codon partitioning did not result in any substantial topological differences, the inclusion of flanking non-coding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of datasets increased convergence between analysis methods but did not reduce gene tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. While the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of datasets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution.
Towards the molecular architecture of the peroxisomal receptor docking complex
Authors: Lill Pascal , Hansen Tobias , Wendscheck Daniel , Klink Bjoern Udo , Jeziorek Tomasz , Miehling Jonas , Bender Julian , Drepper Friedel , Girzalsky Wolfgang , Warscheid Bettina , Erdmann Ralf , Gatsogiannis Christos
Published: November 2019

Import of yeast peroxisomal matrix proteins is initiated by cytosolic receptors, which specifically recognize and bind the respective cargo proteins. At the peroxisomal membrane, the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with Pex17p. Previous data suggest that this interaction triggers the formation of an import pore for further translocation of the cargo. The mechanistic principles are however unclear, mainly because structures of higher order assemblies are still lacking. Here, using an integrative approach, we provide the first structural characterization of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer environment and reveal its subunit organization. Our data show that three copies of Pex14p and a single copy of Pex17p assemble to form a 20 nm rod-like particle. The different subunits are arranged in a parallel manner, showing interactions along their complete sequences and providing receptor binding-sites on both membrane sides. The long rod facing the cytosol is mainly formed by the predicted coiled-coil domains of Pex14p and Pex17p, possibly providing the necessary structural support for the formation of the import pore. Further implications of Pex14p/Pex17p for formation of the peroxisomal translocon are discussed.
SIRT2-knockdown Rescues GARS-induced Charcot-Marie-Tooth Neuropathy
Authors: Shen Chao , Qi Qian , Qin Yicai , Zhou Dejian , Chen Xinyuan , Qi Yun , Yan Zhiqiang , Lin Xinhua , Lin Jinzhong , Yu Wei
Published: November 2019

Charcot-Marie-Tooth disease is the most common inherited peripheral neuropathy. Dominant mutations in glycyl-tRNA synthetase (GARS) gene cause peripheral nerve degeneration and lead to CMT disease type 2D. Mutations in GARS (GARSCMT2D) show partial loss-of-function features, suggesting that tRNA-charging deficits play a role in disease pathogenesis, but the underlying mechanisms are not fully understood. In this study we report that wild-type GARS tightly binds the NAD+-dependent deacetylase SIRT2 and inhibits its deacetylation activity, resulting in the hyperacetylated α-tubulin, the major substrate of SIRT2. Previous studies showed that acetylation of α-tubulin protects microtubules from mechanical breakage and keep axonal transportation. However, CMT2D mutations in GARS can not inhibit SIRT2 deacetylation, which leads to decrease acetylated α-tubulin and severe axonal transport deficits. Genetic reduction of SIRT2 in the Drosophila model rescues the GARS–induced axonal CMT neuropathy and extends the life span. Our findings demonstrate the pathogenic role of SIRT2-dependent α-tubulin deacetylation in mutant GARS-induced neuropathies and provide new perspectives for targeting SIRT2 as a potential therapy against hereditary axonopathies.
Neonatal endotoxin stimulation was associated with long- term innate immune markers and an anti-allergic response in bronchiolar epithelium in spite of allergen challenge
Authors: García Luciana N , Leimgruber Carolina , Nicola Juan P. , Quintar Amado A , Maldonado Cristina A
Published: November 2019

Asthma is a heterogeneous disease underlying different medical processes, being the allergic asthma, with an early-onset in childhood, the most common type. In this phenotype, the continuous exposure to allergens produces a Th2-driven airway remodeling process that leads to symptoms and pathophysiological changes in asthma. Strategies as the avoidance of aeroallergen exposure in early life have been tested to prevent asthma, without a clear success. Alongside, several mouse models of aeroallergen challenge have dissected potential homeostatic responses by which environmental microbial stimulation reduces the subsequent allergic inflammation in the offspring. This suggests the onset of underlying preventive mechanisms in the beginning of asthma that have not been fully recognized. In this study, we aimed to evaluate if neonatal LPS-induced stimulus in epithelial host defenses could contribute to the prevent asthma in adult Balb/c mice. For this purpose, we studied the response of bronchiolar club cells (CC) that are situated in the crossroads of the host defense and allergic inflammation, and express specific pro and antiallergic proteins. LPS stimulus in the neonatal life intensified the production of TLR-4, TNFα, and natural anti-allergic products (CCSP and SPD), changes that contributed to prevent asthma triggering in adulthood. At epithelial level, CC skipped the mucous metaplasia, declining the overproduction of mucin via the EGFR pathway and the mice expressed normal breathing patterns in front of OVA challenge. Furthermore, the overexpression of TSLP, an epithelial pro-Th2 cytokine was blunted and normal TSLP and IL-4 levels were found in bronchoalveolar lavage (BAL). Complementing this shift, we also detected lower eosinophilia in BAL while an increase in phagocytes as well as in regulatory cells (CD4+CD25+FOXP3+ and CD4+IL-10+) was seen, whit an elevation in IL-12 and TNFα secretion. Summarizing, our study pointed to stable asthma-preventive effects promoted by neonatal LPS-stimulation; the main finding was the increase of several anti-Th2 specific proteins at epithelial level, together with an important diminution of pro-Th2 TSLP, conditions that promoted changes in the local immune response with Treg. We thus evidenced several anti-allergic dynamic mechanisms overlying in the epithelium that could be favored in an adequate epidemiological environment
TCF7L2 plays a complex role in human adipose progenitor biology which may contribute to genetic susceptibility to type 2 diabetes
Authors: Verma Manu , Loh Nellie Y. , Vasan Senthil K. , van Dam Andrea D. , Todorčević Marijana , Neville Matt J. , Karpe Fredrik , Christodoulides Constantinos
Published: November 2019

Non-coding genetic variation at TCF7L2 is the strongest genetic determinant of type 2 diabetes (T2D) risk in humans. TCF7L2 encodes a transcription factor mediating the nuclear effects of WNT signalling in adipose tissue (AT). Here we mapped the expression of TCF7L2 in human AT and investigated its role in adipose progenitor (AP) biology. APs exhibited the highest TCF7L2 mRNA abundance compared to mature adipocytes and adipose-derived endothelial cells. Obesity was associated with reduced TCF7L2 transcript levels in subcutaneous abdominal AT but increased expression in APs. In functional studies, TCF7L2 knockdown (KD) in APs led to dose-dependent activation of WNT/β-catenin signaling, impaired proliferation and dose-dependent effects on adipogenesis. Whilst partial KD enhanced adipocyte differentiation, complete KD impaired lipid accumulation and adipogenic gene expression. Overexpression of TCF7L2 accelerated adipogenesis. Transcriptome-wide profiling revealed that TCF7L2 can modulate multiple aspects of AP biology including extracellular matrix secretion, immune signalling and apoptosis. The T2D-risk allele at rs7903146 was associated with reduced AP TCF7L2 expression and enhanced AT insulin sensitivity. Our study highlights a complex role for TCF7L2 in AP biology and suggests that in addition to regulating pancreatic insulin secretion, genetic variation at TCF7L2 may also influence T2D risk by modulating AP function.
A fully phased accurate assembly of an individual human genome
Authors: Porubsky David , Ebert Peter , Audano Peter A. , Vollger Mitchell R. , Harvey William T. , Munson Katherine M. , Sorensen Melanie , Sulovari Arvis , Haukness Marina , Ghareghani Maryam ,   Human Genome Structural Variation Consortium, Lansdorp Peter M. , Paten Benedict , Devine Scott E. , Sanders Ashley D. , Lee Charles , Chaisson Mark J.P. , Korbel Jan O. , Eichler Evan E. , Marschall Tobias
Published: November 2019

The prevailing genome assembly paradigm is to produce consensus sequences that “collapse” parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing (Strand-seq)1,2 and combine them with high-fidelity (HiFi) long sequencing reads3, in a novel reference-free workflow for diploid de novo genome assembly. Employing this strategy, we produce completely phased de novo genome assemblies separately for each haplotype of a single individual of Puerto Rican origin (HG00733) in the absence of parental data. The assemblies are accurate (QV > 40), highly contiguous (contig N50 > 25 Mbp) with low switch error rates (0.4%) providing fully phased single-nucleotide variants (SNVs), indels, and structural variants (SVs). A comparison of Oxford Nanopore and PacBio phased assemblies identifies 150 regions that are preferential sites of contig breaks irrespective of sequencing technology or phasing algorithms.
Reactomics: using mass spectrometry as a reaction detector
Authors: Yu Miao , Petrick Lauren
Published: November 2019

Untargeted metabolomics analysis captures chemical reactions among small molecules. Common mass spectrometry-based metabolomics workflows first identify the small molecules significantly associated with the outcome of interest, then begin exploring their biochemical relationships to understand biological fate (environmental studies) or biological impact (physiological response). We suggest an alternative by which biochemical relationships can be directly retrieved through untargeted high-resolution paired mass distance (PMD) analysis without a priori knowledge of the identities of participating compounds. Retrieval is done using high resolution mass spectrometry as a chemical reaction detector, where PMDs calculated from the mass spectrometry data are linked to biochemical reactions obtained via data mining of small molecule and reaction databases, i.e. ‘Reactomics’. We demonstrate applications of reactomics including PMD network analysis, source appointment of unknown compounds, and biomarker reaction discovery as a complement to compound discovery analyses used in traditional untargeted workflows. An R implementation of reactomics analysis and the reaction/PMD databases is available as the pmd package (https://yufree.github.io/pmd/).
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells
Authors: Kowalczyk Gabriel J. , Cruz J. Agustin , Guo Yue , Zhang Qiuhong , Sauerwald Natalie , Lee Robin E. C.
Published: November 2019

Many biological processes are regulated by single molecules and molecular assemblies within cells that are visible by microscopy as punctate features, often diffraction limited. Here we present detecting-NEMO (dNEMO), a computational tool optimized for accurate and rapid measurement of fluorescent puncta in fixed-cell and time-lapse images. The spot detection algorithm uses the à trous wavelet transform, a computationally inexpensive method that is robust to imaging noise. By combining automated with manual spot curation in the user interface, fluorescent puncta can be carefully selected and measured against their local background to extract high quality single-cell data. Integrated into the workflow are segmentation and spot-inspection tools that enable almost real-time interaction with images without time consuming pre-processing steps. Although the software is agnostic to the type of puncta imaged, we demonstrate dNEMO using smFISH to measure transcript numbers in single cells in addition to the transient formation of IKK/NEMO puncta from time-lapse images of cells exposed to inflammatory stimuli.
Host cholesterol dependent activation of VapC12 toxin enriches persister population duringMycobacterium tuberculosisinfection
Authors: Talwar Sakshi , Pandey Manitosh , Sharma Chandresh , Kutum Rintu , Lum Josephine , Carbajo Daniel , Goel Renu , Poidinger Michael , Dash Debasis , Singhal Amit , Pandey Amit Kumar
Published: November 2019

A worldwide increase in the frequency of multidrug-resistant and extensively drug-resistant cases of tuberculosis is mainly due to therapeutic noncompliance associated with a lengthy treatment regimen. Depending on the drug susceptibility profile, the treatment duration can extend from 6 months to 2 years. This protracted regimen is attributed to a supposedly non-replicating and metabolically inert subset of theMycobacterium tuberculosis(Mtb) population, called ‘persisters’. The mechanism underlying stochastic generation and enrichment of persisters is not fully known. We have previously reported that the utilization of host cholesterol is essential for mycobacterial persistence. In this study, we have demonstrated that cholesterol-induced activation of a ribonuclease toxin (VapC12) inhibits translation by targeting proT tRNA in Mtb. This results in cholesterol-specific growth modulation that increases the frequency of the generation of persisters in a heterogeneous Mtb population. Also, a null mutant strain of this toxin (ΔvapC12) failed to persist and demonstrated an enhanced growth phenotype in a guinea pig model of Mtb infection. Thus, we have identified a novel strategy through which cholesterol-specific activation of a toxin–antitoxin (TA) module in Mtb enhances persister formation during infection. In addition to identifying the mechanism, the study provides opportunity for targeting persisters, a new paradigm facilitating tuberculosis drug development.
A novel (3,6)-connected CdII coordination polymer based on an ether-linked tricarboxylate ligand: synthesis, topology and luminescence sensing properties in aqueous solution
Authors: Yu Yu'e , Chen Yuqian , Mi Xiuna , Wang Suna , Lu Jing
Published: November 2019

A novel three-dimensional coordination polymer, namely, poly[[diaquabis(μ-4,4′-bipyridine)bis{μ3-5-[(2-carboxyphenoxy)methyl]isophthalato}tricadmium(III)] dimethylformamide monosolvate 2.5-hydrate], {[Cd3(C16H9O7)2(C10H8N2)2(H2O)2]·2C3H7NO·5H2O}
n
, was obtained by the reaction of ether-linked 5-[(2-carboxyphenoxy)methyl]isophthalic acid (H3
L) with CdII salts in the presence of 4,4′-bipyridine (bpy) under solvothermal conditions. In this complex, the CdII centres are connected by the carboxylate ligands to form two-dimensional wave-like layers, which are pillared by bpy ligands and extended into a rare three-dimensional (3,6)-connected sqc27 framework. The complex demonstrated good water stability and strong luminescence emissions. It not only possesses excellent luminescence sensing activities toward Fe3+ and Cr2O7
2− in aqueous solution, but can also distinguish between Cr2O7
2− and CrO4
2− by luminescence. Furthermore, it could be simply and quickly regenerated at least five times. A study of the sensing mechanism indicated that luminescence quenching may be related to the energy competition between the complex and sensing analytes.
“Saying yes to everything”: Slung Low’s mission in a time of rapid change
Authors: Perry Rachel
Published: November 2019

Purpose

This study explores what it means to be a mission-driven arts organisation (MDAO) in the UK. Drawing on literature relating to artistic risk and rupture, mission and vision, and arts participation, the purpose of this paper is to shed light on how Slung Low, a theatre organisation with a core staff of five, creates large and complex initiatives and seeks to make a difference to its local community.

Design/methodology/approach

Using a case study approach, this interpretive study makes use of qualitative data to offer context-specific knowledge about how MDAOs create new initiatives including: interviews with members of the Slung Low team; attendance at company meetings; analysis of internal organisational documents, company website and artistic director’s blog; and articles about Slung Low from the local, national and theatre industry press. Data was gathered through a research collaboration with Slung Low which is supported by Paul Hamlyn Foundation.

Findings

The results offer fresh insight into how MDAOs take a positive approach to rupture and rapid change. The study finds that by embracing risk and committing to an ambitious and provocative mission, small-scale arts organisations can achieve artistic, cultural and social objectives which far exceed their size.

Research limitations/implications

This paper offers an organisational perspective on the research questions and so participants were not interviewed on this occasion. However, the participant view will be the subject of further research with Slung Low.

Originality/value

This research paper provides insight into one of the UK’s most innovative theatre companies during a period of monumental change, and advances knowledge on mission-driven organisations by offering reflections on what it means to be an arts organisation which places rupture, risk and usefulness at the heart of its mission.
Study on the corrosion resistance performance of PbO2-ZrO2 nanocomposite electrode in NaCl electrolyte solution
Authors: Teng Ganggang , Wei Feng , Yao Yingwu
Published: November 2019

Purpose

This paper aims to improve the corrosion resistance performance and stability of PbO2 electrodes in chloride wastewater.

Design/methodology/approach

The morphology of PbO2-ZrO2 nanocomposite electrodes was observed by scanning electron microscopy (SEM). The open circuit potential (OCP) curves, anodic polarization curves, electrochemical impedance spectra, accelerated life tests, weight-loss tests and reusability tests were used to study the corrosion resistance properties and stability of PbO2-ZrO2 nanocomposite electrodes in NaCl solution.

Findings

SEM showed that the surface morphology of PbO2-ZrO2 nanocomposite electrodes became compacted and smooth. Electrochemical tests showed that ZrO2 nanoparticles could increase the OCP, corrosion potential and charge transfer resistance, and decrease the corrosion current density in 3.5 Wt. per cent NaCl electrolyte solution. Besides, PbO2-ZrO2 nanocomposite electrodes showed high reusability for acetamiprid degradation, the accelerated service life could reach 146 h, which was almost 3.3 times longer than that of PbO2 electrodes (44 h), weight-loss tests showed that the corrosion resistance for PbO2-ZrO2 nanocomposite electrodes was 2.3 times as compared to PbO2 electrodes.

Originality/value

By the codeposition of ZrO2 nanoparticles, the corrosion resistance performance and stability of PbO2 electrodes in NaCl electrolyte were improved.
Enhancing cognitive and entrepreneurship competencies through EBL
Authors: Kholilah  , Wafaretta Vega , Syariati Dian
Published: November 2019

Purpose

Entrepreneurship-based learning (EBL) is one of the student-center learningmethods that can answer learning challenges in the era of industrial revolution 4.0. EBL is expected to improve students’ competencies and make students more adaptable to the changes in the world of work in the future. The paper aims to discuss this issue.

Design/methodology/approach

This study uses quasi-experiments and divides classes into project class and control class. The project consists of making business proposals, conducting business, liquidating the partnership, and recording business transaction using the Xero platform. The Wilcoxon Signed Ranks Test, Mann–Whitney Test and independent t-test were carried out to test whether there are differences of cognitive abilities and entrepreneurial (general, social and functional) competencies between the project class and control class.

Findings

The results of the study shows there are differences of understanding of partnership accounting and the achievement of social and functional entrepreneurial competencies between the project class and control class.

Research limitations/implications

This study implies in using EBL to improve entrepreneurial skills for students beyond cognitive abilities.

Originality/value

The novelty of this research is the implementation of EBL in partnership accounting topics.
Rhetorical strategies and emotions in political marketing management
Authors: Ortigueira-Sánchez Luis Camilo , Cárdenas-Egúsquiza Ana Lucía
Published: November 2019

Purpose

The purpose of this paper is to analyze how political marketing management in terms of communication practices influence the voters’ emotional responses as they observe and listen to the discourse of a political leader.

Design/methodology/approach

An experiment was conducted, in which participants watched the last debate of the campaign leading up the Peruvian presidential elections held in June 2016. During the experiment, the Emotient FACET technology codifies the facial micro-expressions of participants.

Findings

The results reveal that a voter’s political tendencies influence the intensity of their positive emotions, when the political leader communicated a challenging message. Rhetorical strategies and non-verbal behaviors accompany this type of message in order to emphasize the discourse and persuade the audience.

Practical implications

The findings suggest that the gender gap in attitudes toward female politicians exists and could change the relationship found, influencing negative emotions instead of positive emotions. The implications of the findings for achieving political success are discussed.

Originality/value

The study makes a methodological contribution, employing an experimental protocol based on Emotient FACET technology in a political context, thereby enabling more direct and objective measurement of voters’ emotional responses.
Investigation of process and product parameters for physico-chemical properties of low Glycemic Index water chestnut and barley flour-based extruded snacks
Authors: Beigh Mushtaq , Hussain Syed Zameer , Qadri Tahiya , Naseer Bazila , Raja Tariq , Naik Haroon
Published: November 2019

Purpose

Keeping in view the diabetes status that has affected about 415 million people globally and is the leading cause of death in many countries along with therising demand for low Glycemic Index (GI) foods, the purpose of this paper is to optimize the extrusion process for the development of low GI snacks from underutilized crops like water chestnut and barley.

Design/methodology/approach

The extrusion parameters (screw speed and barrel temperature), feed moisture and water chestnut flour, barley flour proportion, were varied and their effects on system and product responses (specific mechanical energy, water absorption index, water solubility index, bulk density, expansion ratio and breaking strength) were studied.

Findings

All the system and product responses were significantly affected by independent variables. Response surface and regression models were established to determine the responses as function of process variables. Models obtained were highly significant with high coefficient of determination (R2=0.88). The optimum processing conditions obtained by numerical optimization for the development of snacks were 90°C barrel temperature, 300 rpm screw speed, 14 per cent feed moisture and WCF-to-BF ratio as 90:10. Shelf life studies confirmed that the developed snacks can be safely stored in HDPE bags for a period of six months under ambient conditions.

Originality/value

Water chestnut and barley flour did not blend till date for extrusion cooking. Such snacks shall be a viable food option for diabetic people and can act as laxative due to high fibre and β-glucan content from barley.
Agile business process management
Authors: Badakhshan Peyman , Conboy Kieran , Grisold Thomas , vom Brocke Jan
Published: November 2019

Purpose

Business Process Management (BPM) is key for successful organisational management. However, BPM techniques are often criticized for their inability to deal with continuous and significant change and uncertainty. Following recent calls to make BPM more agile and flexible towards change, this study presents the results of a systematic literature review (SLR) of agile concepts in BPM. Analysing and synthesising previous works and drawing on agility research in the field of IS, this paper introduces a framework for agile BPM. Integrating different components that define agility in the context of BPM, this framework offers a number of important implications. On the theoretical side, the authors argue that the concept of agile BPM departs in some important ways from traditional BPM research. This, in turn, points to various opportunities for future research. On the practical side, the authors suggest that emerging technologies, such as process mining, embody important features that help organisations to be more responsive to change. The paper aims to discuss these issues.

Design/methodology/approach

To assess the state of the art of agility in the BPM research, the authors conducted an SLR. More specifically, the authors drew on the approach of vom Brocke et al. (2009, 2015), which consists of five steps: defining the scope of the review; conceptualising the topic; searching for literature; analysing and synthesising literature; and developing a research agenda.

Findings

This study presents the results of a systematic review of agile concepts in BPM. This study then proposes a resulting research framework that can be used to strengthen the concept of agile BPM and provides an agenda for research in this rapidly growing and increasingly necessary area of BPM.

Originality/value

In this paper, the authors establish a shared understanding of agile BPM and develop an agile BPM framework that represents the current state as well as implications for research and practice in agile BPM.
An optimized security solution based on trust value for multithreaded wireless body area network communication
Authors: Saha Sanchari , K. Anvekar Dinesh
Published: November 2019

Purpose

Security of wireless body area network communication is highly important as it directly impacts human life. This paper aims to focus on battlefield application area of WBAN for implementing security where data must be protected against various possible attacks before delivering over a public network.

Design/methodology/approach

Providing a strong security system is still a research challenge due to low computational power of used sensors for protecting transmission data. In this paper, the authors have proposed an optimized security solution for multithreaded wireless body area network (MWBAN) using trust-based distributed group key management technique to overcome the drawbacks of existing elliptical curve cryptography-homomorphism (ECC-Homomorphism) scheme as well as coded cooperative data exchange group key management (CCDE_GKM) scheme.

Findings

The proposed optimized security solution is implemented for a particular deployment strategy and test runs are conducted. It is found that when number of attack nodes increased to 25, compared to ECC–Homomorphism and CCDE_GKM for the proposed trust-based distributed group key management technique there is an improvement in performance parameters such as throughput is dropped to only 10.11 Kbps, average delay is just 3.4 s, energy consumption is maximum 29 joules, packet loss is only 12.3 per cent, 90.9 per cent truly can detect attack, only 8.9 per cent false attack detection and 84 per cent true negative detection.

Social implications

Medical care can be provided to human beings with much ease and flexibility via remote monitoring. The user can be at any place, can do his/her everyday work while remotely being monitored of their health parameters and secured transmission of their data to the health-care center for medical service in need.

Originality/value

This paper presents an optimized security solution for MWBAN using trust-based distributed group key management technique where bilinear pairing theory is used as major cryptographic base. Optimal key is selected based on trust value and also attack nodes are detected based on trust value to control participation in communication.
A new positioning method for remotely operated vehicle of the nuclear power plant
Authors: Dong Mingjie , Li Jianfeng , Chou Wusheng
Published: November 2019

Purpose

The purpose of this study is to develop a new positioning method for remotely operated vehicle (ROV) in the nuclear power plant. The ROV of the nuclear power plant is developed to inspect the reactor cavity pools, the component pools and spent-fuel storage pools. To enhance the operational safety, the ability of localizing the ROV is indispensable.

Design/methodology/approach

Therefore, the positioning method is proposed based on the MEMS inertial measurement unit and mechanical scanning sonar in this paper. Firstly, the ROV model and on board sensors are introduced in detail. Then the sensor-based Kalman filter is deduced for attitude estimation. After that, the positioning method is proposed that divided into static positioning and dynamic positioning. The improved iterative closest point-Kalman filter is deduced to estimate the global position by the whole circle scanning sonar data in static, and the relative positioning method is proposed by the small scale scanning sonar data in dynamic.

Findings

The performance of the proposed method is verified by comparing with the visual positioning system. Finally, the effectiveness of the proposed method is proved by the experiment in the reactor simulation pool of the Daya Bay Nuclear Power Plant.

Originality/value

The research content of this manuscript is aimed at the specific application needs of nuclear power plants and has high theoretical significance and application value.