bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification and characterization of pleiotropic high-persistence mutations in the beta subunit of the bacterial RNA polymerase
Authors: Ostrer Lev , Ji Yinduo , Khodursky Arkady
Published: August 2020

Individual bacteria can escape killing by bactericidal antibiotics by becoming dormant. Such cells, also known as persisters, naturally occur in bacterial populations at a low frequency. Here we present the finding that antibiotic-resistance mutations in therpoBgene, encoding the beta subunit of RNA polymerase, increase the frequency of persisters by orders of magnitude. Furthermore, we show that: i) the persistent state depends on the (p)ppGpp transcriptional program and not on (p)ppGpp itself; ii) the high persistence (hip) is associated with increased populational heterogeneity in transcription; iii) indole overproduction, caused by transcriptional changes in thehipmutants, explains 50-80% of thehipphenotype. We report that the analogousrpoBmutations occur frequently in clinical isolates ofAcinetobacter baumannii, Mycobacterium tuberculosis and Staphylococcus aureus, and we demonstrate that one of thoserpoBmutations causes high persistence in MRSA. We also show that the RpoB-associatedhipphenotype can be reversed by inhibiting protein synthesis.

Importance

Persistence is an inevitable consequence of antibiotic usage. Although persistence is not a genetically heritable trait, here we demonstrate for the first time that antibiotic resistance, which is heritable, can promote persistence formation. Our finding that resistance to one antibiotic, rifampicin, can boost persistence to other antibiotics, such as ciprofloxacin and ampicillin, may help explain why certain chronic infections are particularly recalcitrant to antibiotic therapies. Out results also emphasize the need to assess the effects of combination antibiotic therapies on persistence.
Single cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium
Authors: Kirkwood PM , Gibson DA , Smith JR , Wilson-Kanamori JR , Kelepouri O , Esnal-Zufiaurre A , Dobie R , Henderson NC , Saunders PTK
Published: August 2020

The endometrium is a dynamic tissue that exhibits remarkable resilience to repeated episodes of differentiation, breakdown, regeneration and remodelling. Endometrial physiology relies on a complex interplay between the stromal and epithelial compartments with the former containing a mixture of fibroblasts, vascular and immune cells. There is evidence for rare populations of putative mesenchymal progenitor cells located in the perivascular niche of human endometrium, but the existence of an equivalent cell population in mouse is unclear.

In the current study we used thePdgfrb-BAC-eGFP transgenic reporter mouse in combination with bulk and single cell RNA sequencing (scRNAseq) to redefine the endometrial mesenchyme. Contrary to previous reports we show that CD146 is expressed in both PDGFRβ+ perivascular cells as well as CD31+ endothelial cells. Bulk RNAseq revealed cells in the perivascular niche which express high levels ofPdgfrbas well as genes previously identified in pericytes and/or vascular smooth muscle cells (Acta2, Myh11, Olfr78, Cspg4, Rgs4, Rgs5, Kcnj8, Abcc9). scRNAseq identified five subpopulations of cells including closely related pericytes/vascular smooth muscle cells and three subpopulations of fibroblasts. All three fibroblast populations were PDGFRα+/CD34+ but were distinct in their expression ofSpon2/Angptl7(fibroblast 1),Smoc2/Rgs2(fibroblast 2) andClec3b/Col14a1/Mmp3(fibroblast 3), with potential functions in regulation of immune responses, response to wounding and organisation of extracellular matrix respectively.

In conclusion, these data are the first to provide a single cell atlas of the mesenchymal cell landscape in mouse endometrium. By identifying novel markers for subpopulations of mesenchymal cells we can use mouse models investigate their contribution to endometrial function, compare with other tissues and apply these findings to further our understanding of human endometrium.

Highlights

GFP expression in the mouse endometrium, under the control of thePdgfrbpromoter, is restricted to two cell populations based on the intensity of GFP with GFPbrightcells close to the vasculature

Single cell RNAseq identified five subpopulations of GFP+ mesenchymal cells: pericytes, vascular smooth muscle cells (vSMC) and three closely related but distinct populations of fibroblasts

Bioinformatics revealed that pericytes and vSMC share functions associated with the circulatory system, actin-filament process and cell adhesion, and an apparent role for pericytes in smooth muscle cell migration and response to interferons

Comparisons between the fibroblast subpopulations suggest distinct roles in regulation of immune response, response to wound healing and collagen organisation.

Graphical Abstract
SARS-CoV-2 infection dynamics in lungs of African green monkeys
Authors: Speranza Emily , Williamson Brandi N. , Feldmann Friederike , Sturdevant Gail L. , Pérez-Pérez Lizzette , Mead-White Kimberly , Smith Brian J. , Lovaglio Jamie , Martens Craig , Munster Vincent J. , Okumura Atsushi , Shaia Carl , Feldmann Heinz , Best Sonja M. , de Wit Emmie
Published: August 2020

Detailed knowledge about the dynamics of SARS-CoV-2 infection is important for unraveling the viral and host factors that contribute to COVID-19 pathogenesis. Old-World nonhuman primates recapitulate mild-moderate COVID-19 cases, thereby serving as important pathogenesis models. We compared African green monkeys inoculated with SARS-CoV-2 or inactivated virus to study the dynamics of virus replication throughout the respiratory tract. RNA sequencing of single cells from the lungs and mediastinal lymph nodes allowed a high-resolution analysis of virus replication and host responses over time. Viral replication was mainly localized to the lower respiratory tract, with evidence of replication in the pneumocytes. Macrophages were found to play a role in initiating a pro-inflammatory state in the lungs, while also interacting with infected pneumocytes. Our dataset provides a detailed view of changes in host and virus replication dynamics over the course of mild COVID-19 and serves as a valuable resource to identify therapeutic targets.
SARS-CoV-2 Quasispecies provides insight into its genetic dynamics during infection
Authors: Sun Fengming , Wang Xiuhua , Tan Shun , Dan Yunjie , Lu Yanqiu , Zhang Juan , Xu Junli , Tan Zhaoxia , Xiang Xiaomei , Zhou Yi , He Weiwei , Wan Xing , Zhang Wei , Chen Yaokai , Tan Wenting , Deng Guohong
Published: August 2020

A novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has been pandemic worldwide. The genetic dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. However, no quasispecies data of SARS-CoV-2 have been reported yet. To explore quasispecies haplotypes and its transmission characteristics, we carried out single-molecule real-time (SMRT) sequencing of the full-length of SARS-CoV-2 spike gene within 14 RNA samples from 2 infection clusters, covering first-to third-generation infected-patients. We observed a special quasispecies structure of SARS-CoV-2 (modeled as ‘One-King’): one dominant haplotype (mean abundance ~70.15%) followed by numerous minor haplotypes (mean abundance < 0.10%). We not only discovered a novel dominant haplotype of F1040but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F1040and currently pandemic one G614) could potentially reveal adaptive and converse into the dominant one. However, minor haplotypes exhibited a high transmission bottleneck (~6% could be stably transmitted), and the new adaptive/dominant haplotypes were likely originated from genetic variations within a host rather than transmission. The evolutionary rate was estimated as 2.68-3.86 × 10−3per site per year, which was larger than the estimation at consensus genome level. The ‘One-King’ model and conversion event expanded our understanding of the genetic dynamics of SARS-CoV-2, and explained the incomprehensible phenomenon at the consensus genome level, such as limited cumulative mutations and low evolutionary rate. Moreover, our findings suggested the epidemic strains may be multi-host origin and future traceability would face huge difficulties.
rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated tool for Genome-Wide Association Study
Authors: Yin Lilin , Zhang Haohao , Tang Zhenshuang , Xu Jingya , Yin Dong , Zhang Zhiwu , Yuan Xiaohui , Zhu Mengjin , Zhao Shuhong , Li Xinyun , Liu Xiaolei
Published: August 2020

Along with the development of high-throughout sequencing technologies, both sample size and number of SNPs are increasing rapidly in Genome-Wide Association Studies (GWAS) and the associated computation is more challenging than ever. Here we present a Memory-efficient, Visualization-enhanced, and Parallel-accelerated R package called “rMVP” to address the need for improved GWAS computation. rMVP can: (1) effectively process large GWAS data; (2) rapidly evaluate population structure; (3) efficiently estimate variance components by EMMAX, FaST-LMM, and HE regression algorithms; (4) implement parallel-accelerated association tests of markers using GLM, MLM, and FarmCPU methods; (5) compute fast with a globally efficient design in the GWAS processes; and (6) generate various visualizations of GWAS related information. Accelerated by block matrix multiplication strategy and multiple threads, the association test methods embedded in rMVP are approximately 5-20 times faster than PLINK, GEMMA, and FarmCPU_pkg. rMVP is freely available athttps://github.com/xiaolei-lab/rMVP.
A Multi-pronged Screening Approach Targeting Inhibition of ETV6 PNT Domain Polymerization
Authors: Gerak Chloe A. N. , Zhang Si Miao , Balgi Aruna D. , Sadowski Ivan J. , Sessions Richard B. , McIntosh Lawrence P. , Roberge Michel
Published: August 2020

ETV6 is an ETS family transcriptional repressor for which head-to-tail polymerization of its PNT domain facilitates cooperative binding to DNA by its ETS domain. Chromosomal translocations frequently fuse the ETV6 PNT domain to one of several protein tyrosine kinases. The resulting chimeric oncoproteins undergo ligand-independent self-association, autophosphorylation, and aberrant stimulation of downstream signaling pathways leading to a variety of cancers. Currently, no small molecules inhibitors of ETV6 PNT domain polymerization are known and no assays targeting PNT domain polymerization have been described. In this study, we developed complementary experimental and computational approaches for identifying such inhibitory compounds. One mammalian cellular approach utilized a mutant PNT domain heterodimer system covalently attached to splitGaussialuciferase fragments. In this protein fragment complementation assay, inhibition of PNT domain heterodimerization reduces luminescence. A yeast assay took advantage of activation of the reporterHIS3gene upon heterodimerization of mutant PNT domains fused to DNA-binding and transactivation domains. In this two-hybrid screen, inhibition of PNT domain heterodimerization prevents cell growth in medium lacking histidine. The Bristol University Docking Engine (BUDE) was used to identify virtual ligands from the ZINC8 library predicted to bind the PNT domain polymerization interfaces. Over 75 hits from these three assays were tested by NMR spectroscopy for binding to the purified ETV6 PNT domain. Although none were found to bind, lessons learned from this study may facilitate future approaches for developing therapeutics that act against ETV6 oncoproteins by disrupting PNT domain polymerization.
Niche-derived soluble DLK1 promotes glioma stemness and growth
Authors: Grassi Elisa S. , Jeannot Pauline , Pantazopoulou Vasiliki , Berg Tracy J. , Pietras Alexander
Published: August 2020

Tumor cell behaviors associated with aggressive tumor growth such as proliferation, therapeutic resistance, and stemness are regulated in part by soluble factors derived from the tumor microenvironment. Tumor-associated astrocytes represent a major component of the glioma tumor microenvironment, and astrocytes have an active role in maintenance of normal neural stem cells in the stem cell niche, in part via secretion of soluble Delta-like Non-Canonical Notch Ligand 1 (DLK1). We found that astrocytes, when exposed to stresses of the tumor microenvironment such as hypoxia or ionizing radiation (IR), increased secretion of soluble DLK1. Tumor-associated astrocytes in a glioma mouse model expressed DLK1 in perinecrotic (hypoxic) and perivascular tumor areas. Glioma cells exposed to recombinant DLK1 displayed increased proliferation, enhanced sphere and colony formation abilities, and increased levels of stem cell marker genes. Mechanistically, DLK1-mediated effects on glioma cells involved increased and prolonged stabilization of Hypoxia-Inducible Factor 2alpha (HIF-2alpha), and inhibition of HIF-2alpha activity abolished effects of DLK1 in hypoxia. Forced expression of soluble DLK1 resulted in more aggressive tumor growth and shortened survival in a genetically engineered mouse model of glioma. Together, our data support DLK1 as a soluble mediator of glioma aggressiveness derived from the tumor microenvironment.

Graphical abstract

Highlights

Astrocytes secrete DLK1 after exposure to hypoxia or irradiation

Soluble DLK1 promotes stemness in glioma, in part by increasing HIF-2alpha stabilization.

High levels of soluble DLK1 are associated with tumor aggressiveness and lethality.
Human cytokine-induced memory-like NK cells preserve increased glycolysis but the glycolytic-dependence of their effector functions differ between stimuli
Authors: Terrén Iñigo , Orrantia Ane , Mosteiro Alba , Vitallé Joana , Zenarruzabeitia Olatz , Borrego Francisco
Published: August 2020

Natural Killer (NK) cells acquire memory-like properties following a brief stimulation with IL-12, IL-15 and IL-18. These IL-12/15/18-stimulated NK cells, also known as cytokine-induced memory-like (CIML) NK cells, have been revealed as a powerful tool in cancer immunotherapy due to their persistence in the host and their increased effector functions. Several studies have shown that NK cells modulate their metabolism in response to cytokine-stimulation and other stimuli, suggesting that there is a link between metabolism and cellular functions. In this paper, we have analyzed metabolic changes associated to IL-12/15/18-stimulation and the relevance of glycolytic pathway for NK cell effector functions. We have found that CIML NK cells are able to retain increased glycolytic machinery seven days after cytokine withdrawal. Furthermore, we found that glycolytic inhibition with 2-DG is stimuli-dependent and that differently affects to distinct effector functions. These findings may have implications in the design of NK cell-based cancer immunotherapies.
Dicer1 promotes Aβ clearance via blocking B2 RNA-mediated repression of apolipoprotein E
Authors: Wang Yan , Lian Meiling , Song Liping , Wu Shengzhou
Published: August 2020

Metabolism of β-amyloid is critical for healthy brain. Decreased clearance of β-amyloid is associated with ensued accumulation of amyloid peptide, culminating in formation of senile plaques, a neuropathological hallmark of Alzheimer’s disease(AD). Apolipoprotein E (APOE), a lipoprotein for phospholipid and cholesterol metabolism, is predominantly synthesized by glia in the central nervous system, controlling Aβ aggregation and metabolism. By use of stereotactic injection and a Morris water maze, we found that delivery of Dicer1-expressing adenovirus into the hippocampus of an animal model of AD mice APPswe/PSEN1deltaE9 significantly improved spatial memory. The effect was associated with reduced amyloid peptides in the hippocampus which were analyzed with immunofluorescence and enzyme-linked immunosorbent assay. With western blot, quantitative real-time PCR, fluorescencein situhybridization, and northern blot, Dicer1 overexpression increased apolipoprotein E (APOE) and concomitantly decreased B2 RNA in the hippocampus of the AD mice and in astrocyte cultures whereas transfection of B2 Mm2 RNA decreasedAPOEmRNA and protein levels in astrocyte cultures. Further, human or mouseAPOEmRNA was found containing Alu RNA or its equivalent, B2 Mm2 RNA, locating downstream of its 3’-untranslated region (UTR), respectively. The 3’-UTR or 3’-UTR in conjunction with the downstream Alu/B2 RNA were cloned into a luciferase reporter; with dual-luciferase assay, we found that simultaneous transfection of Dicer1 siRNA or Alu/B2 RNA decreased the corresponding luciferase activities which suggest that Alu RNA mediatedAPOEmRNA degradation. Altogether, Dicer1 expression mediated amyloid peptide clearance by increasing APOE via blocking B2 RNA-mediatedAPOEmRNA degradation.
Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response inArabidopsis thaliana
Authors: Rutley Nicholas , Poidevin Laetitia , Doniger Tirza , Tillet Richard , Rath Abhishek , Forment Javier , Luria Gilad , Schlauch Karen , Ferrando Alejandro , Harper Jeffery , Miller Gad
Published: August 2020

The male gametophyte is the most heat-sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinatingArabidopsis thalianapollen exposed to heat stress (HS), we identified 66 novel and 246 recently-annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison to HS in cauline leaves and other RNAseq experiments, indicated 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed 96% of the genes evolved recently inBrassicaceae. We found that 50 genes are putative targets of microRNAs, and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional, and play significant role in pollen biology, including the HS response.
What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes
Authors: Nagpal Sunil , Srivastava Divyanshu , Mande Sharmila S.
Published: August 2020

Topic modeling is frequently employed for discovering structures (or patterns) in a corpus of documents. Its utility in text-mining and document retrieval tasks in various fields of scientific research is rather well known. An unsupervised machine learning approach, Latent Dirichlet Allocation (LDA) has particularly been utilized for identifying latent (or hidden) topics in document collections and for deciphering the words that define one or more topics using a generative statistical model. Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a ‘Bag of Words’ to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Topic models were generated using ~47000 novel corona virus genomes (considered as documents), leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through coherence optimization. The document assumption for genomes also helped in identification of contextual nucleotide mutation signatures in the form of conventional N-grams (e.g. bi-grams and tri-grams). We validated the signatures obtained using LDA driven method against the previously reported recurrent mutations and phylogenetic clades for genomes. Additionally, we report the geographical distribution of the identified mutation signatures in SARS-CoV-2 genomes on the global map. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes).
When time really is money: in situ quantification of the strobilurin resistance mutation G143A in the wheat pathogen Blumeria graminis f. sp. tritici
Authors: Dodhia Kejal N , Cox Belinda A , Oliver Richard P , Lopez-Ruiz Francisco J
Published: August 2020

Background

There has been an inexorable increase in the incidence of fungicide resistance in plant pathogens in recent years. Control of diseases and the management of resistance would be greatly aided by rapid diagnostic methods. Quantitative allele specific PCR (ASqPCR) is an ideal technique for the analysis of fungicide resistance in the field as it can both detect and quantify the frequency of mutations associated with fungicide resistance. We have applied this technique to the fungal pathogenBlumeria graminisf. sp.tritici(Bgt), an obligate biotrophic fungus that causes wheat powdery mildew and is responsible for up to 25% yield loss annually. In Australia, strobilurin resistantBgtwas first discovered in samples from Tasmania and Victoria in 2016. Molecular analysis revealed a nucleotide transversion in the cytochromebc1 enzyme (cytb) complex, resulting in a substitution of alanine for glycine at position 143 (G143A) in Cytb.

Results

We have developed an in-field ASqPCR assay that can quantify both the resistant (A143) and sensitive (G143)cytballeles down to 1.67% in host andBgtDNA mixtures within 90 min of sample collection. Thein situanalysis of field samples collected during a survey in Tasmania revealed A143 frequencies ranging between 9-100%. We validated the analysis with a newly developed laboratory based digital PCR assay and found no significant differences between the two methods.

Conclusion

We have successfully developed an in-field quantification method, for a QoI resistant allele, by pairing an ASqPCR assay on a lightweight qPCR instrument with a quick DNA extraction method. The deployment of this type of methodologies in the field can contribute to the effective in-season management of fungicide resistance.
Oxidative stress induces cell death partially by decreasing both mRNA and protein levels of nicotinamide phosphoribosyltransferase in PC12 cells
Authors: Zhou Cuiyan , Ying Weihai
Published: August 2020

Numerous studies have indicated critical roles of NAD+deficiency in both aging and multiple major diseases. It is critical to investigate the mechanisms underlying the NAD+deficiency under the pathological conditions. It has been reported that there was a decreased level of Nicotinamide phosphoribosyltransferase (Nampt) – an important enzyme in the salvage pathway of NAD+synthesis – under certain pathological conditions, while the mechanisms underlying the Nampt decrease require investigation. In this study we used differentiated PC12 cells as a cellular model to investigate the effects of oxidative stress on both the mRNA and protein levels of Nampt, as well as the role of this effect in oxidative stress-induced cell death: First, Nampt plays significant roles in both the NAD+synthesis and survival of the cells under basal conditions; second, H2O2produced significant decreases in both the mRNA levels and the protein levels of Nampt; and third, H2O2induced cell death partially by producing the decreases in the mRNA and protein levels of Nampt, since the Nampt inhibitor or the Nampt activator significantly exacerbated or attenuated the H2O2-induced cell death, respectively. Collectively, our study has indicated that oxidative stress can decrease both the mRNA and protein levels of Nampt, which has indicated a novel mechanism underlying the NAD+deficiency in aging and under multiple pathological conditions. Our study has also indicated that the decreased Nampt levels contribute to the H2O2-induced cell death, suggesting a new mechanism underlying oxidative cell death.
LINE-1 ORF1p RIP-seq reveals widespread association with p-body enriched mRNAs
Authors: Briggs Erica M. , McKerrow Wilson , Mita Paolo , Boeke Jef D. , Logan Susan K. , Fenyö David
Published: August 2020

Background

Long INterspersed Element-1 (LINE-1) is an autonomous retroelement able to “copy-and-paste” itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer.

Results

Here, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in androgen sensitive and androgen independent cells, that we show are representative of LINE-1 copies expressed in prostate cancer before and after treatment. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of many of the identified ORF1p bound mRNAs also correlated with expression of LINE-1 RNA in prostate tumors from The Cancer Genome Atlas (TCGA).

Conclusion

Our results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells, suggesting an evolution of LINE-1 expression during prostate cancer progression. Additionally, our finding that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, suggest that ORF1p may play a role in non-LINE-1 RNA processing and regulation of specific transcripts in prostate tumors.
A Survey of the Kinome Pharmacopeia Reveals Multiple Scaffolds and Targets for the Development of Novel Anthelmintics
Authors: Knox Jessica , Zuercher William , Roy Peter J.
Published: August 2020

Over one billion people are currently infected with a parasitic nematode. Symptoms can include anemia, malnutrition, developmental delay, and in severe cases, death. Resistance is emerging to anthelmintic drugs used to treat nematode infection, prompting the need to develop new anthelmintics. Towards this end, we identified a set of kinases that may be targeted in a nematode-specific manner. We first screened 2040 inhibitors of vertebrate kinases for those that impair the model nematodeCaenorhabditis elegans. By determining whether the terminal phenotype induced by each kinase inhibitor matched that of the predicted target mutant inC. elegans, we identified 17 druggable nematode kinase targets. Of these, we found that nematode EGFR, MEK1, and PLK1 kinases have diverged from vertebrates within their drug-binding pocket. For each of these targets, we identified small molecule scaffolds that may be further modified to develop nematode-specific inhibitors. Nematode EGFR, MEK1, and PLK1 therefore represent key targets for the development of new anthelmintic medicines.

One sentence summary

Druggable Kinases as Anthelmintic Targets
Cytonuclear discordance in the crowned-sparrows,Zonotrichia atricapillaandZonotrichia leucophrys: a mitochondrial selective sweep?
Authors: Taylor Rebecca S. , Bramwell Ashley C. , Clemente-Carvalho Rute , Cairns Nicholas A. , Bonier Frances , Lougheed Stephen C.
Published: August 2020

The golden-crowned (Zonotrichia atricapilla) and white-crowned (Z. leucophrys) sparrows have been presented as a compelling case for rapid speciation. They display divergence in song and plumage with overlap in their breeding ranges implying reproductive isolation, but have almost identical mitochondrial genomes. Previous research proposed hybridization and subsequent mitochondrial introgression as an alternate explanation, but lacked robust nuclear gene trees to distinguish between introgression and incomplete lineage sorting. We test for signatures of these processes betweenZ. atricapillaandZ. leucophrys, and investigate the relationships amongZ. leucophryssubspecies, using mitochondrial sequencing and a reduced representation nuclear genomic dataset. Contrary to the paraphyly evident in mitochondrial gene trees, we confirmed the reciprocal monophyly ofZ. atricapillaandZ. leucophrysusing large panels of single nucleotide polymorphism (SNPs). The pattern of cytonuclear discordance is consistent with limited, historical hybridization and mitochondrial introgression, rather than a recent origin and incomplete lineage sorting between recent sister species. We found evidence of nuclear phylogeographic structure withinZ. leucophryswith two distinct clades. Altogether, our results support the true species status ofZ. atricapillaandZ. leucophrys, and indicate deeper divergences between the two species than inferred using mitochondrial markers. Our results demonstrate the limitations of relying solely on mitochondrial DNA for taxonomy, and raise questions about the possibility of selection on the mitochondrial genome during temperature oscillations (e.g. during the Pleistocene). Historical mitochondrial introgression facilitated by past environmental changes could cause erroneous dating of lineage splitting in other taxa when based on mitochondrial DNA alone.
Laboratory evolution of anticipatory gene regulation inEscherichia coli
Authors: Mahilkar Anjali , Mall Akshat , Saini Supreet
Published: August 2020

Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby they trigger response to a yet to appear cue, anticipating its actual arrival in the near future. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution ofE. coliin alternating environments of a pentose sugar, rhamnose, and an oxidative stress molecule, paraquat for more than 800 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation, whereby, exposure to rhamnose leads to partial induction of the oxidative stress response regulon. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Overall, we show that in niches where environmental stimuli have a cyclical nature, anticipatory regulation can evolve as an adaptive strategy, in a time course of a few hundred generations. This contributes to our understanding of how environment shapes the topology of regulatory networks in an organism.
An autonomous, but INSIG-modulated, role for the Sterol Sensing Domain in mallostery-regulated ERAD of yeast HMG-CoA reductase
Authors: Wangeline Margaret A , Hampton Randolph Y
Published: August 2020

HMG-CoA reductase (HMGR) undergoes feedback regulated degradation as part of sterol pathway control. Degradation of the yeast HMGR isozyme Hmg2 is controlled by the sterol pathway intermediate GGPP, which causes misfolding of Hmg2 to enhance its ERAD by the HRD pathway. GGPP-dependent reversible misfolding of Hmg2 is remarkably similar to classic allosteric control; we recently labeled this process mallostery to fuse the ideas of misfolding and allostery. We have evaluated the role of the Hmg2 sterol sensing domain (SSD) in mallostery, and the involvement of highly conserved INSIG proteins in SSD function. The SSD is a membrane-embedded motif found in many sterol-related proteins. The Hmg2 SSD was critical for in vivo regulated degradation of Hmg2, and required for mallosteric misfolding of GGPP as studied by in vitro limited proteolysis. The Hmg2 SSD functions in mallostery independently of conserved yeast INSIG proteins. However, this autonomous action of the SSD was modulated by INSIG, thus imposing a second layer of control on Hmg2 regulation. SSD-mediated mallostery occurs prior to HRD dependent ubiquitination, defining a pathway regulation involving SSD-mediated misfolding followed by HRD dependent ubiquitination. GGPP dependent misfolding occurred at a much slower rate in the absence of a functional SSD, indicating that the SSD functions to allow physiologically useful rate of GGPP response, and implying that the SSD is not a binding site for GGPP. We used unresponsive Hmg2 SSD mutants to test the importance of quaternary structure in mallosteric regulation: the presence of a non-responsive Hmg2 mutant strongly suppressed regulation of a co-expressed, normal Hmg2. Finally, we have found that GGPP regulated misfolding occurred in detergent solubilized Hmg2, indicating that the mallosteric response is an intrinsic feature of the Hmg2 multimer. The preserved response of Hmg2 when in micellar solution will allow next-level studies on the structural and biophysical features of this novel fusion of regulation and protein quality control.
Phenotypic reconstruction of the last universal common ancestor reveals a complex cell
Authors: Baidouri Fouad El , Venditti Chris , Suzuki Sei , Meade Andrew , Humphries Stuart
Published: August 2020

A fundamental concept in evolutionary theory is the last universal common ancestor (LUCA) from which all living organisms originated. While hypotheses regarding the phenotype of LUCA do exist, most are at best based on gene presence or absence. However, despite recent attempts to link genes and phenotypic traits in prokaryotes, it is still inherently difficult to predict phenotype based on the presence or absence of genes alone. Here, we apply a novel approach based on phylogenetically informed ancestral character reconstruction with 22 fundamental descriptors of prokaryotic cells to reconstruct LUCA’s phenotype. We infer that the last universal common ancestor of all living organisms was likely an ovoid cell with a large genome, which probably had a cell wall and was actively motile. Potentially obtaining energy from the oxidation of inorganic compounds, tolerant of saltwater and thriving at temperatures above 70°C, LUCA was probably found living freely in anaerobic conditions in water of neutral pH. Our results depict LUCA as likely to be a far more complex cell than has previously been proposed, challenging the evolutionary model of increased complexity through time in prokaryotes. Given current estimates for the emergence of LUCA we suggest that early life very rapidly evolved considerable cellular complexity.
Crystallographic evidence for unintended benzisothiazolinone 1-oxide formation from benzothiazinones through oxidation
Authors: Eckhardt Tamira , Goddard Richard , Lehmann Christoph , Richter Adrian , Sahile Henok Asfaw , Liu Rui , Tiwari Rohit , Oliver Allen G. , Miller Marvin J. , Seidel Rüdiger W. , Imming Peter
Published: August 2020

1,3-Benzothiazin-4-ones (BTZs) are a promising new class of drugs with activity against Mycobacterium tuberculosis, which have already reached clinical trials. A product obtained in low yield upon treatment of 8-nitro-2-(piperidin-1-yl)-6-(trifluoromethyl)-4H-benzothiazin-4-one with 3-chloroperbenzoic acid, in analogy to a literature report describing the formation of sulfoxide and sulfone derived from BTZ043 [Tiwari et al. (2015). ACS Med. Chem. Lett.
6, 128–133], is a ring-contracted benzisothiazolinone (BIT) 1-oxide, namely, 7-nitro-2-(piperidine-1-carbonyl)-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one 1-oxide, C14H12F3N3O5S, as revealed by X-ray crystallography. Single-crystal X-ray analysis of the oxidation product originally assigned as BTZ043 sulfone provides clear evidence that the structure of the purported BTZ043 sulfone is likewise the corresponding BIT 1-oxide, namely, 2-[(S)-2-methyl-1,4-dioxa-8-azaspiro[4.5]decane-8-carbonyl]-7-nitro-5-(trifluoromethyl)benzo[d]isothiazol-3(2H)-one 1-oxide, C17H16F3N3O7S. A possible mechanism for the ring contraction affording the BIT 1-oxides instead of the anticipated constitutionally isomeric BTZ sulfones and antimycobacterial activities thereof are discussed.
Is corporate disclosure of environmental performance indicators reliable or biased information? A look at the underlying drivers
Authors: Tadros Hani , Magnan Michel , Boulianne Emilio
Published: August 2020

Purpose

This study aims to examine the disclosure determinants of environmental performance indicators (EPIs) for a sample of US firms to understand if these disclosures are reliable or whether they are biased towards the reporting of positive information.

Design/methodology/approach

The study uses a panel data analysis to examine the association between firms’ EPIs disclosures and their environmental performances, and other economic and legitimacy factors.

Findings

The results show that firms’ disclosures are not associated with the level of environmental performance and that firms continue to provide EPI information even if they witness a decline in their environmental performance. The evidence suggests that firms’ environmental disclosures are reliable and indicative of their environmental performance.

Practical implications

The findings suggest that mandating EPI disclosures may increase the level of the information reported and reduce firms’ discretion over the disclosure of such information.

Originality/value

Reporting of EPIs is directly linked to firms’ environmental performances. By examining the association between EPI disclosures and environmental performance, the study contributes to the ongoing debate about firms’ reporting and whether it is informative to its stakeholders or whether firms use this type of information to legitimize their operations and portray it in a positive light.
Outcome and impact indicators for nanotechnology policies
Authors: Soltani Ali Mohammad , Tabatabaeian Seyed Habibollah , Hanafizadeh Payam , Bamdadsoofi Jahanyar
Published: August 2020

Purpose

The purpose of this paper is to suggest indicators for evaluating Iran national nanotechnology plan at the policy and program levels. Governments are required to evaluate their policies to be accountable to their audience and to improve their policies. The evaluation of nanotechnology policies both in academic and governmental institutions has been mainly confined to measuring the research and development outputs, while explicit models are required for evaluating national nanotechnology policies and programs. In other words, although policies are translated into several activities, it does not mean that the evaluation of activities results in holistic policy evaluation.

Design/methodology/approach

The present research uses a qualitative method to explore the process of developing a model for assessing nanotechnology policymaking in Iran. Expert opinions have been collected and analyzed by using local and international surveys to validate different elements of the model.

Findings

The model includes the evaluation time-frame, criteria and indicators for policy and program levels. Assessment at program and policy levels, as distinct from activity evaluation, measures the ultimate objectives of a policy intervention, based on which the outcome and impact indicators should be developed. This paper argues that the Iran national nanotechnology policy should be evaluated and revised triennially based on the model in which 46 outcome and impact indicators are included under three general criteria of appropriateness, efficiency and effectiveness. A number of these indicators should be evaluated annually or biannually.

Originality/value

The evaluation of nanotechnology plans has been mainly limited to assessing the research and development outputs that are related to the activity level. The main value of this work is developing outcome and impact indicators that are related to policy and program levels.
A systematic review on high performance organization
Authors: Do Thanh Tung , Mai Ngoc Khuong
Published: August 2020

Purpose

This paper aims to synthesize existing knowledge on high performance organization (HPO) in terms of definitions, contemporary trends and findings from empirical studies; from which areas for future research can be proposed.

Design/methodology/approach

This systematic literature review applies the matrix method to analyze major HPO literature in peer-reviewed English articles. A total of 73 articles have been found in 59 journals.

Findings

There are three key findings that emerged from this study. First, the research on HPO has been burgeoned in the past decades, generating several compelling studies in different contexts. The trend of HPO research is now shifting from theory development to theory validation. Second, HPO has been defined in various ways in the extant literature. However, they all address the importance of aligning the firms’ resources with the market demand and integrating various types of performance to measure HPO relative to competitors for a prolonged period. Third, an assessment of empirical HPO studies revealed gaps in terms of the research context, research design and the HPO’s nomological network.

Research limitations/implications

The literature search in this review targeted at only articles published in the English language; therefore, publications in other languages were not included.

Originality/value

The strength of this study is that it provided an updated systematic review of HPO literature, is therefore, valuable in providing an overall picture of the current state of HPO research and providing potential directions for future studies.
A consumption timecycle: contextually situated and temporally recurring experiences
Authors: Ryynänen Toni , Heinonen Visa
Published: August 2020

Purpose

Temporal consumption experiences have been conceptualised as universal, subjective or practice-based experiences. Little research, though, addresses such experiences in conjunction with the repeated and situational consumption events that bring them about. The purpose of this paper is to extend current knowledge by examining how the temporal and situational intertwine during consumption events. For this purpose, the concept of a consumption timecycle based on the research data is constructed.

Design/methodology/approach

The paper takes a longitudinal and researcher-led approach to study temporal consumption experiences. The data was collected through participant observations, video recordings and personal subjective introspections during three consecutive annual Nordic motorcycle consumer trade shows (2014–2016). The data was analysed using an interpretive approach.

Findings

The results demonstrate five temporalities that characterise a consumption timecycle as follows: emerging, core, intensifying, fading and idle-time temporalities. The features of these temporal experiences are presented in the conclusions section of the paper.

Research limitations/implications

Recalled temporal experiences are mediated experiences and they differ from lived experiences. The transferability or generalisability of the results might be limited, as the case is situated in the Nordic context.

Originality/value

The paper presents the novel concept of a consumption timecycle that extends current debates about consumer time. The consumption timecycle is contrasted with established temporal concepts in consumer and marketing research.
Comparing life review writing with active control groups: Results of a feasibility study
Authors: Schelly David , Ohl Alisha , Moronta Yessica , Nadres Ramona , Snyder Eric
Published: August 2020

Introduction

Life review writing can be used to improve depressive symptoms in well older adults, but it is unclear whether the reminiscing, writing, or socialising is associated with the improvements. This study assessed the feasibility of a controlled trial comparing life review writing with two active control groups designed to isolate the acts of (a) engaging in a meaningful leisure activity and (b) socialising.

Methods

Twenty‐four participants from a 100‐bed assisted living facility were enrolled in the study. Participants ranged in age from 70 to 98 years (M = 83.9, SD = 7.6). Eight 1‐hour weekly sessions were held, with participants assigned to one of three groups: (a) life review writing, (b) painting, or (c) coffee from around the world. At baseline, participants completed a demographic and health questionnaire, the Mini‐Cog, and the Geriatric Depression Scale Short Form (GDS‐15). The GDS‐15 was administered again at weeks 4 and 8, along with the health questionnaire at post‐test.

Results

Nearly 25% (N = 24) of the facility's residents attended at least one session, with an average attendance rate of 66.4%, or 5.3 sessions. However, to achieve this participation rate, our original plan to employ random assignment had to be abandoned. The groups were a partial success insofar as we successfully isolated engaging in a meaningful activity in the painting group, but the writing group engaged in less reminiscing than hoped. At post‐test, seven participants reported health, mood, and social life benefits. GDS‐15 scores fluctuated over time, with no significant improvement from pre‐ to post‐test.

Conclusion

The residents’ low willingness to be randomised creates a serious selection bias, but randomising volunteers into different activities runs counter to client‐centred therapy. To scrutinise the mechanisms of change of life review writing, we recommend comparing two writing groups: one that reminisces and one that does not.
Role of soy lecithin on emulsion stability of dairy beverages treated by ultrasound
Authors: Nyuydze Collette , Martínez‐Monteagudo Sergio I
Published: August 2020

The objective of this work was to evaluate the impact of soy lecithin during the formation and stability of oil‐in‐water ultrasound emulsions. Pre‐emulsions formulated with either 0%, 0.025% and 0.05% of soy lecithin were sonicated at different acoustic intensities (42–70 W/cm2) for 5 min. Dynamic rheology showed an improved stability of the ultrasound emulsions at high acoustic intensity and without soy lecithin, displaying a distinctive viscoelastic region and a behaviour of weak gel. During 21 days of storage at 4°C, the particle size slightly increased (470–500 nm), while the mechanical spectra remained unchanged. The outcomes of this investigation suggest that ultrasound can be used as manufacturing aid for the formulation of dairy‐based emulsions.