bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid endothelial infection, endothelialitis and vascular damage characterise SARS-CoV-2 infection in a human lung-on-chip model
Authors: Thacker Vivek V , Sharma Kunal , Dhar Neeraj , Mancini Gian-Filippo , Sordet-Dessimoz Jessica , McKinney John D
Published: August 2020

Severe cases of COVID-19 present with hypercoagulopathies and systemic endothelialitis of the lung microvasculature. The dynamics of vascular damage, and whether it is a direct consequence of endothelial infection or an indirect consequence of immune cell mediated cytokine storms is unknown. This is in part becausein vitromodels are typically epithelial cell monocultures or fail to recapitulate vascular physiology. We use a vascularised lung-on-chip model where, consistent with monoculture reports, low numbers of SARS-CoV-2 virions are released apically from alveolar epithelial cells. However, rapid infection of the underlying endothelial layer leads to the generation of clusters of endothelial cells with low or no CD31 expression, a progressive loss of endothelial barrier integrity, and a pro-coagulatory microenvironment. These morphological changes do not occur if these cells are exposed to the virus apically. Viral RNA persists in individual cells, which generates a response that is skewed towards NF-KB mediated inflammation, is typified by IL-6 secretion even in the absence of immune cells, and is transient in epithelial cells but persistent in endothelial cells. Perfusion with Tocilizumab, an inhibitor of trans IL-6 signalling slows the loss of barrier integrity but does not prevent the formation of endothelial cell clusters with reduced CD31 expression. SARS-CoV-2 mediated endothelial cell damage occurs despite a lack of rapid viral replication, in a cell-type specific manner and independently of immune-cell mediated cytokine storms, whose effect would only exacerbate the damage.
VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss
Authors: Peng Jiguang , Xiang Jiale , Jin Xiangqian , Meng Junhua , Song Nana , Chen Lisha , Tayoun Ahmad Abou , Peng Zhiyu
Published: August 2020

Purpose

The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study aimed to semi-automate the HL ACMG/AMP rules.

Methods

VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7.

Results

We benchmarked VIP-HL using 50 variants where 83 rules were activated by the HL expert panel. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.

Conclusion

VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other.
Continuous variable response, kinetic gating and connectivity that govern IS topology are perturbed in hyperinsulinemia
Authors: Shukla Namrata , Kadam Shantanu , Padinhateeri Ranjith , Kolthur-Seetharam Ullas
Published: August 2020

Understanding kinetic control of biological processes is as important as identifying components that constitute pathways. Insulin-signaling (IS) is central for almost all metazoans and its perturbations are associated with various diseases and aging. While temporal phosphorylation changes and kinetic constants have provided some insights, constant or variable parameters that establish and maintain signal topology are poorly understood. Our iterative experimental and mathematical simulation-based approaches reveal novel kinetic parameters that encode concentration and nutrient dependent information. Further, we find that pulsatile fasting insulin rewires IS akin to memory and in anticipation of a fed response. Importantly, selective kinetic gating of signals and maximum connectivity, between metabolic and growth-factor arms under normo-insulinemic states, maintains network topology. In addition to unraveling kinetic constraints that determine cascade architecture, our findings will help in identifying novel therapeutic strategies that conserve coupling between metabolic and growth-factor arms, which is lost in diseases and conditions of hyperinsulinemia.
CD40 provides immune privilege to the bone marrow hematopoietic niche
Authors: Bassani Barbara , Gulino Alessandro , Portararo Paola , Botti Laura , Cappetti Barbara , Chiodoni Claudia , Bolli Niccolò , Ciciarello Marilena , Joehrens Korinna , Anagnostopoulos Ioannis , Na Il-Kang , Curti Antonio , Tripodo Claudio , Colombo Mario P. , Sangaletti Sabina
Published: August 2020

Allogeneic bone marrow transplantation remains the only therapeutic option for a wide range of hematological malignancies despite the risk of possible adverse, immune-related events, such as infection and acute graft-versus-host disease (aGVHD). aGVHD is characterized by T-cell activation, defective B-cell development and osteoblastic niche destruction in bone marrow (BM) among other issues. Transplant conditioning regimens cause excessive inflammatory cytokines production and impaired regulatory T-cell control of aberrant T-cell activation. Here, we show that mesenchymal cells (MSCs) upregulated CD40 upon irradiation at the expense of mesenchymal markers, and that CD40 endows MSC of regulatory function on Treg homeostasis and fitness. Transplantation of wild type hematopoietic cells into a CD40-null recipient reduces Treg numbers allowing persistent T-cell activation and pro-inflammatory cytokines production causing, impaired B-lymphopoiesis. These evidences find correlation in aGVHD patients showing the loss of CD40+ BM-MSCs along with reduction in cells of the B-lineage. Modeling aGVHD in mice we show that the elimination of CD40+ BM-MSCs relies on their higher expression of MHC-I molecules. Indeed, aGVHD mice compared to MHC-matched controls showed the loss of MHC-I + radio-resistant host BM-MSCs. Our data point to CD40+ MHC-I+BM-MSCs as a key regulator of BM tolerogenic niches.

Key points

CD40 regulates BM immunological tolerance following total body irradiation (TBI) and transplantation (BMT).

Loss of CD40+MHC-IhighBM-MSCs is associated to BM manifestation of aGVHD in human and murine model.
Agromonas: a rapid disease assay forPseudomonas syringaegrowth in agroinfiltrated leaves
Authors: Buscaill Pierre , Sanguankiattichai Nattapong , Lee Yoon Joo , Kourelis Jiorgos , Preston Gail , van der Hoorn Renier A. L.
Published: August 2020

The lengthy process to generate transformed plants is a limitation in current research on the interactions of the model plant pathogenPseudomonas syringaewith plant hosts. Here we present an easy method called agromonas, where we quantifyP. syringaegrowth in agroinfiltrated leaves ofNicotiana benthamianausing a cocktail of antibiotics to selectP. syringaeon plates. As a proof of concept, we demonstrate that transient expression of PAMP receptors reduces bacterial growth and that transient depletion of a host immune gene and transient expression of a T3 effector increaseP. syringaegrowth in agromonas assays. We show that we can rapidly achieve structure-function analysis of immune components and test the function of immune hydrolases. The agromonas method is easy, fast and robust for routine disease assays with variousPseudomonasstrains without transforming plants or bacteria. The agromonas assay offers reliable opportunity for further comprehensive analysis of plant immunity.

One sentence summary

Agromonas is a rapid and robust disease assay to monitorPseudomonas syringaegrowth in agroinfiltrated leaves expressing immune components and their suppressors.
Development of Putative Isospecific Inhibitors for HDAC6 using Random Forest, QM-Polarized docking, Induced-fit docking, and Quantum mechanics
Authors: Joel Ireoluwa Yinka , Adigun Temidayo Olamide , Bankole Olukayode Olusola , Ajibola Ahmeedah Ololade , Ofeniforo Emmanuel Bankole , Auta Faith Beyaan , Ozojiofor Ugochukwu Okechukwu , Remi-Esan Ifelolu Adeseye , Akande Aminat Ifeoluwa
Published: August 2020

Histone deacetylases have been recognized as a potential target for epigenetic aberrance reversal in the various strategies for cancer therapy, with HDAC6 implicated in various forms of tumor growth and cancers. Diverse inhibitors of HDAC6 has been developed, however, there is still the challenge of iso-specificity and toxicity. In this study, we trained a Random forest model on all HDAC6 inhibitors curated in the ChEMBL database (3,742). Upon rigorous validations the model had an 85% balanced accuracy and was used to screen the SCUBIDOO database; 7785 hit compounds resulted and were docked into HDAC6 CD2 active-site. The top two compounds having a benzimidazole moiety as its zinc-binding group had a binding affinity of −78.56kcal/mol and −78.21kcal/mol respectively. The compounds were subjected to exhaustive docking protocols (Qm-polarized docking and Induced-Fit docking) in other to elucidate a binding hypothesis and accurate binding affinity. Upon optimization, the compounds showed improved binding affinity (−81.42kcal/mol), putative specificity for HDAC6, and good ADMET properties. We have therefore developed a reliable model to screen for HDAC6 inhibitors and suggested a series of benzimidazole based inhibitors showing high binding affinity and putative specificity for HDAC6.
A spiking neural program for sensory-motor control during foraging in flying insects
Authors: Rapp Hannes , Nawrot Martin Paul
Published: August 2020

Foraging is a vital behavioral task for living organisms. Behavioral strategies and abstract mathematical models thereof have been described in detail for various species. To explore the link between underlying neural circuits and computational principles we present how a biologically detailed neural circuit model of the insect mushroom body implements sensory processing, learning and motor control. We focus on cast & surge strategies employed by flying insects when foraging within turbulent odor plumes. Using a spike-based plasticity rule the model rapidly learns to associate individual olfactory sensory cues paired with food in a classical conditioning paradigm. We show that, without retraining, the system dynamically recalls memories to detect relevant cues in complex sensory scenes. Accumulation of this sensory evidence on short time scales generates cast & surge motor commands. Our generic systems approach predicts that population sparseness facilitates learning, while temporal sparseness is required for dynamic memory recall and precise behavioral control. Our work successfully combines biological computational principles with spike-based machine learning. It shows how knowledge transfer from static to arbitrary complex dynamic conditions can be achieved by foraging insects and may serve as inspiration for agent-based machine learning.
Human Embryonic Stem Cell-derived Lung Organoids: a Model for SARS-CoV-2 Infection and Drug Test
Authors: Pei Rongjuan , Feng Jianqi , Zhang Yecheng , Sun Hao , Li Lian , Yang Xuejie , He Jiangping , Xiao Shuqi , Xiong Jin , Lin Ying , Wen Kun , Zhou Hongwei , Chen Jiekai , Rong Zhili , Chen Xinwen
Published: August 2020

The coronavirus disease 2019 (COVID-19) pandemic is caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is spread primary via respiratory droplets and infects the lungs. Currently widely used cell lines and animals are unable to accurately mimic human physiological conditions because of the abnormal status of cell lines (transformed or cancer cells) and species differences between animals and humans. Organoids are stem cell-derived self-organized three-dimensional culturein vitroand model the physiological conditions of natural organs. Here we demonstrated that SARS-CoV-2 infected and extensively replicated in human embryonic stem cells (hESCs)-derived lung organoids, including airway and alveolar organoids. Ciliated cells, alveolar type 2 (AT2) cells and rare club cells were virus target cells. Electron microscopy captured typical replication, assembly and release ultrastructures and revealed the presence of viruses within lamellar bodies in AT2 cells. Virus infection induced more severe cell death in alveolar organoids than in airway organoids. Additionally, RNA-seq revealed early cell response to SARS-CoV-2 infection and an unexpected downregulation of ACE2 mRNA. Further, compared to the transmembrane protease, serine 2 (TMPRSS2) inhibitor camostat, the nucleotide analog prodrug Remdesivir potently inhibited SARS-CoV-2 replication in lung organoids. Therefore, human lung organoids can serve as a pathophysiological model for SARS-CoV-2 infection and drug discovery.
PU.1 drives specification of pluripotent stem cell-derived endothelial cells to LSEC-like cells
Authors: De Smedt Jonathan , van Os Elise Anne , Talon Irene , Ghosh Sreya , Toprakhisar Burak , Da Costa Rodrigo Furtado Madeiro , Zaunz Samantha , Vazquez Marta Aguirre , Boon Ruben , Baatsen Pieter , Smout Ayla , Verhulst Stefaan , van Grunsven Leo A. , Verfaillie Catherine M.
Published: August 2020

To date there is no representativein vitromodel for liver sinusoidal endothelial cells (LSECs), as primary LSECs dedifferentiate very fast in culture and no combination of cytokines or growth factors can induce an LSEC fate in (pluripotent stem cell-derived) endothelial cells (ECs). Furthermore, the transcriptional programs driving an LSEC fate have not yet been described. Here, we first present a computational workflow (CenTFinder) that can identify transcription factors (TFs) that are crucial for modulating pathways involved in cell lineage specification. UsingCenTFinder, we identified several novel LSEC-specific protein markers such as FCN2 and FCN3, which were validated by analysis of previously published single-cell RNAseq data. We also identified PU.1 (encoded by theSPI1gene) as a major regulator of LSEC-specific immune functions. We show thatSPI1overexpression (combined with the general EC transcription factorETV2) in human pluripotent stem cells (PSCs) induces ECs with an LSEC-like phenotype. The ETV2-SPI1-ECs display increased expression of LSEC markers such as CD32B and MRC1 as well as several of the proposed novel markers. More importantly, ETV2-SPI1-ECs acquire LSEC functions, including uptake of FSA-FITC as well as labelled IgG. In conclusion, we present theCenTFindercomputational tool to identify key regulatory TFs within specific pathways, in this work pathways of lineage specification, and we demonstrate its use by the identification and validation of PU.1 as a master regulator for LSEC fating.
Regulation ofCYP94B1by WRKY33 controls apoplastic barrier formation in the roots leading to salt tolerance
Authors: Krishnamurthy Pannaga , Vishal Bhushan , Ho Wan Jing , Lok Felicia Chien Joo , Lee Felicia Si Min , Kumar Prakash P
Published: August 2020

Salinity is an environmental stress that causes decline in crop yield.Avicennia officinalisand other mangroves have adaptations such as ultrafiltration at the roots aided by apoplastic cell-wall barriers to thrive in saline conditions. We studied a Cytochrome P450 gene,AoCYP94B1fromA. officinalisand itsArabidopsisorthologAtCYP94B1that are involved in apoplastic barrier formation, and are induced by 30 minutes of salt treatment in the roots. Heterologous expression ofAoCYP94B1inatcyp94b1 Arabidopsismutant and wild-type rice conferred increased NaCl tolerance to seedlings by enhancing root suberin deposition. Histochemical staining and GC-MS/MS quantification of suberin precursors confirmed the role of CYP94B1 in suberin biosynthesis. Using chromatin immunoprecipitation, yeast one-hybrid and luciferase assays, we identified AtWRKY33 as the upstream regulator ofAtCYP94B1inArabidopsis. In addition,atwrky33mutants exhibited reduced suberin and salt sensitive phenotypes, which were rescued by expressing35S::AtCYP94B1inatwrky33mutant. This further confirms that the regulation ofAtCYP94B1by AtWRKY33 is part of the salt tolerance mechanism, and our findings can help in generating salt tolerant crops.

One sentence summary

AtWRKY33 transcription factor regulatesAtCYP94B1to increase plant salt tolerance by enhanced suberin deposition in the endodermal cells ofArabidopsisroots
Bioinformatic Analysis Reveals That Some Mutations May Affect On Both Spike Structure Damage and Ligand Binding Site
Authors: Aktas Emre
Published: August 2020

There are some mutations are known related to SARS-CoV-2. Together with these mutations known, I tried to show other newly mutations regionally. According to my results which 4326 whole sequences are used, I found that some mutations occur only in a certain region, while some other mutations are found in each regions. Especially in Asia, more than one mutation(three different mutations are found in QLA46612 isolated from South Korea) was seen in the same sequence. Although I detected a huge number of mutations (more than seventy in Asia) by regions, some of them were predicted that damage spike’s protein structure by using bioinformatic tools.The predicted results are G75V(isolated from North America), T95I(isolated from South Korea), G143V(isolated from North America), M177I(isolated Asia), L293M(isolated from Asia), P295H(isolated from Asia), T393P(isolated from Europe), P507S(isolated from Asia), D614G(isolated from all regions) respectively. Also, in this study, I tried to show how possible binding sites of ligands change if the spike protein structure is damaged and whether more than one mutation affects ligand binding was estimated using bioinformatics tools. Interestingly, mutations that predicted to damage the structure do not affect ligand binding sites, whereas ligands’ binding sites were affected in those with multiple mutations.Focusing on mutations may opens up the window to exploit new future therapeutic targets.
The psychophysics of visual search with heterogeneous distractors
Authors: Mihali Andra , Ma Wei Ji
Published: August 2020

Visual search is one of the most ecologically important perceptual task domains. One research tradition has studied visual search using simple, parametric stimuli and a signal detection theory or Bayesian modeling framework. However, this tradition has mostly focused on homogeneous distractors (identical to each other), which are not very realistic. In a different tradition, Duncan and Humphreys (1989) conducted a landmark study on visual search with heterogeneous distractors. However, they used complex stimuli, making modeling and dissociation of component processes difficult. Here, we attempt to unify these research traditions by systematically examining visual search with heterogeneous distractors using simple, parametric stimuli and Bayesian modeling. Our experiment varied multiple factors that could influence performance: set size, task (N-AFC localization vs detection), whether the target was revealed before or after the search array (perception versus memory), and stimulus spacing. We found that performance robustly decreased with increasing set size. When examining within-trial summary statistics, we found that the minimum target-to-distractor feature difference was a stronger predictor of behavior than the mean target-to-distractor difference and than distractor variance. To obtain process-level understanding, we formulated a Bayesian optimal-observer model. This model accounted for all summary statistics, including when fitted jointly to localization and detection. We replicated these results in a separate experiment with reduced stimulus spacing. Together, our results represent a critique of Duncan and Humphrey’s descriptive approach, bring visual search with heterogeneous distractors firmly within the reach of quantitative process models, and affirm the “unreasonable effectiveness” of Bayesian models in explaining visual search.
Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome
Authors: Albrecht Tessa , White Samantha , Layton Marylee , Stenglein Mark , Haley Scott , Nachappa Punya
Published: August 2020

The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.
An Ensemble Learning Approach for Cancer Drug Prediction
Authors: Mandera Darsh , Ritz Anna
Published: August 2020

Predicting the response to a particular drug for specific cancer, despite known genetic mutations, still remains a huge challenge in modern oncology and precision medicine. Today, prescribing a drug for a cancer patient is based on a doctor’s analysis of various articles and previous clinical trials; it is an extremely time-consuming process. We developed a machine learning classifier to automatically predict a drug given a carcinogenic gene mutation profile. Using the Breast Invasive Carcinoma Dataset from The Cancer Genome Atlas (TCGA), the method first selects features from mutated genes and then applies K-Fold, Decision Tree, Random Forest and Ensemble Learning classifiers to predict best drugs. Ensemble Learning yielded prediction accuracy of 66% on the test set in predicting the correct drug. To validate that the model is general-purpose, Lung Adenocarcinoma (LUAD) data and Colorectal Adenocarcinoma (COADREAD) data from TCGA was trained and tested, yielding prediction accuracies 50% and 66% respectively. The resulting accuracy indicates a direct correlation between prediction accuracy and cancer data size. More importantly, the results of LUAD and COADREAD show that the implemented model is general purpose as it is able to achieve similar results across multiple cancer types. We further verified the validity of the model by implementing it on patients with unclear recovery status from the COADREAD dataset. In every case, the model predicted a drug that was administered to each patient. This method will offer oncologists significant time-saving compared to their current approach of extensive background research, and offers personalized patient care for cancer patients.
Ectopic expression of a maize gene is induced by Composite Insertions generated through Alternative Transposition
Authors: Su Weijia , Zuo Tao , Peterson Thomas
Published: August 2020

Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status and generating small RNAs. In this study, we demonstrated thatAc/fActransposable elements are able to induce ectopic gene expression by duplicating and shuffling enhancer elements.Ac/fAcelements belong to thehATfamily of Class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events which involve the termini of two different, nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations and Composite Insertions (CIs). We identified over 50 independent cases of CIs generated byAc/fAcalternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maizepericarp color 2 (p2)gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearbyp1gene, suggesting that the CI-induced activation ofp2is effected by mobilization of thep1enhancer. This is further supported by analysis of a mutant in which the CI is excised andp2expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate Composite Insertions that can control gene expression.

When Barbara McClintock originally identified and characterized Transposable Elements (TEs) in maize, she termed them “Controlling Elements” due to their effects on gene expression. Here we show that maizeAc/DsTEs can acquire a genomic enhancer and generate Composite Insertions (CIs) that activate expression of a nearby gene. CIs are structurally variable elements that include TE termini enclosing sequences from an original donor locus, and are formed when the termini of two nearby TEs transpose during S phase from a replicated to unreplicated site. In this way, TEs may acquire genomic enhancers to generate Controlling Elements as described by McClintock.
Mycobacterium tuberculosisSufR Responds to Nitric oxide via its 4Fe-4S cluster and Regulates Fe-S cluster Biogenesis for Persistence in Mice
Authors: Anand Kushi , Tripathi Ashutosh , Shukla Kaustubh , Malhotra Nitish , Jamithireddy Anil Kumar , Jha Rajiv Kumar , Chaudhury Susmit Narayan , Rajmani Raju S , Ramesh Arati , Nagaraja Valakunja , Gopal Balasubramanian , Nagaraju Ganesh , Narain Seshayee Aswin Sai , Singh Amit
Published: August 2020

The persistence ofMycobacterium tuberculosis(Mtb) is a major problem in managing tuberculosis (TB). Host-generated nitric oxide (NO) is perceived as one of the signals byMtbto reprogram metabolism and respiration for persistence. However, the mechanisms involved in NO sensing and reorganizingMtb’s physiology are not fully understood. Since NO damages Fe-S clusters of essential enzymes, the mechanism(s) involved in regulating iron-sulfur (Fe-S) cluster biogenesis could helpMtbpersist in host tissues. Here, we show that a transcription factor SufR (Rv1460) senses NO via its 4Fe-4S cluster and promotes persistence ofMtbby mobilizing the Fe-S cluster biogenesis system;sufoperon (Rv1460-Rv1466). Analysis of anaerobically purified SufR by UV-visible spectroscopy, circular dichroism, and iron-sulfide estimation confirms the presence of a 4Fe-4S cluster. Atmospheric O2and H2O2gradually degrade the 4Fe-4S cluster of SufR. Furthermore, electron paramagnetic resonance (EPR) analysis demonstrates that NO directly targets SufR 4Fe-4S cluster by forming a protein-bound dinitrosyl-iron-dithiol complex. DNase I footprinting, gel-shift, andin vitrotranscription assays confirm that SufR directly regulates the expression of thesufoperon in response to NO. Consistent with this, RNA- sequencing ofMtbΔsufRdemonstrates deregulation of thesufoperon under NO stress. Strikingly, NO inflicted irreversible damage upon Fe-S clusters to exhaust respiratory and redox buffering capacity ofMtbΔsufR. Lastly,MtbΔsufRfailed to recover from a NO-induced non-growing state and displayed persistence defect inside immune-activated macrophages and murine lungs in a NO-dependent manner. Data suggest that SufR is a sensor of NO that supports persistence by reprogramming Fe-S cluster metabolism and bioenergetics.

Highlights

Mycobacterium tuberculosis(Mtb) induces the expression ofsufoperon for Fe-S cluster biogenesis in response to nitric oxide (NO).

We found that a transcription factor SufR senses NO via its 4Fe-4S cluster and regulates the expression of thesufoperon for Fe-S cluster biogenesis.

SufR-regulated Fe-S cluster biogenesis confers respiratory and redox features that promote recovery ofMtbfrom NO stress.

SufR activity is required to support the NO-dependent persistence ofMtbin macrophages and mice.
Is there a genetic correlation between movement and immobility in field populations of a beetle?
Authors: Matsumura Kentarou , Miyatake Takahisa
Published: August 2020

Genetic correlations among behavioural traits are often controlled by pleiotropic genes. Many studies suggest the existence of genetic correlations among behavioural traits based on artificial selection experiments in the laboratory. However, few studies have examined whether behavioural correlations in the laboratory are maintained in the field, where natural selection works. Artificial selection experiments showed a behavioural correlation among death feigning, walking movement, and locomotor activity in the red flour beetle (Tribolium castaneum). This study investigated whether this behavioural correlation is observed in wildT. castaneumpopulations. We also collected beetles from various regions in Japan and investigated the geographic variation in these traits. There was geographic variation in the three behavioural traits. However, these behavioural traits were not correlated. The results suggest that the genetic correlations among behavioural traits are not maintained in the field. Therefore, the results derived from laboratory experiments may be overestimated. The same correlation between traits was not believed to arise in the field, as the indoor results may have been caused by unrealistic selection pressures. Further laboratory and field investigations are both needed.
Antagonism of STAT3 signalling by Ebola virus
Authors: Harrison Angela R. , Dearnley Megan , Todd Shawn , Green Diane , Marsh Glenn A. , Moseley Gregory W.
Published: August 2020

Many viruses target signal transducers and activators of transcription (STAT) 1 and 2 to antagonise antiviral interferon (IFN) signalling, but targeting of signalling by other STATs/cytokines, including STAT3/interleukin (IL-) 6 that regulate processes important to Ebola virus (EBOV) haemorrhagic fever, is poorly defined. We report that EBOV potently inhibits STAT3 responses to IL-6 family cytokines, and that this is mediated by the IFN-antagonist VP24. Mechanistic analysis indicates that VP24 effects a unique strategy combining distinct karyopherin-dependent and karyopherin-independent mechanisms to antagonise STAT3-STAT1 heterodimers and STAT3 homodimers, respectively. This appears to reflect distinct mechanisms of nuclear trafficking of the STAT3 complexes, revealed for the first time by our analysis of VP24 function. These findings are consistent with major roles for global inhibition of STAT3 signalling in EBOV infection, and provide new insights into the molecular mechanisms of STAT3 nuclear trafficking, significant to pathogen-host interactions, cell physiology and pathologies such as cancer.

Author summary

Ebola virus (EBOV) continues to pose a significant risk to human health globally, causing ongoing disease outbreaks with case-fatality rates between 40 and 60%. Suppression of immune responses is a critical component of EBOV haemorrhagic fever, but understanding of EBOV impact on signalling by cytokines other than interferon is limited. We find that infectious EBOV inhibits interleukin-6 cytokine signallingviaantagonism of STAT3. The antagonistic strategy uniquely combines two distinct mechanisms, which appear to reflect differing nuclear trafficking mechanisms of critical STAT3 complexes. This provides fundamental insights into the mechanisms of pathogenesis of a lethal virus, and biology of STAT3, a critical player in immunity, development, growth and cancer.
Niche mediated integrin signaling supports steady state hematopoiesis in spleen
Authors: Mehatre Shubham Haribhau , Roy Irene Mariam , Biswas Atreyi , Prit Devila , Schouteden Sarah , Huelsken Joerg , Verfaillie Catherine M. , Khurana Satish
Published: August 2020

Outside-in integrin signaling regulates cell fate decisions in a variety of cell types, including hematopoietic stem cells (HSCs). Our earlier published studies showed that interruption of Periostin (POSTN) and Integrin-αv (ITGAV) interaction induces faster proliferation in HSCs with developmental stage dependent functional effects. Here, we examined the role of POSTN-ITGAV axis in lympho-hematopoietic activity in spleen that hosts rare population of HSCs, the functional regulation of which is not clearly known.Vav-iCremediated deletion ofItgavin hematopoietic system led to higher proliferation rates, resulting in increased frequency of primitive HSCs in adult spleen. However, in vitro CFU-C assays demonstrated a poorer differentiation potential followingItgavdeletion. This also led to a decrease in the white pulp area with a significant decline in the B-cell numbers. Systemic deletion of its ligand, POSTN, phenocopied the effects noted inVav-Itgav−/−mice. Histological examination ofPostndeficient spleen also showed increase in the spleen trabecular areas. Surprisingly, these were the myofibroblasts of the trabecular and capsular areas that expressed high levels of POSTN within the spleen tissue. In addition, vascular smooth muscle cells also expressed POSTN. Through CFU-S12assays, we showed that hematopoietic support potential of stroma inPostndeficient splenic hematopoietic niche was defective. Overall, we demonstrate that POSTN-ITGAV interaction plays important role in spleen lympho-hematopoiesis.
The identity of human tissue-emigrant CD8+T cells
Authors: Buggert Marcus , Vella Laura A. , Nguyen Son , Wu Vincent , Sekine Takuya , Perez-Potti André , Maldini Colby R. , Manne Sasikanth , Darko Samuel , Ransier Amy , Kuri-Cervantes Leticia , Japp Alberto Sada , Brody Irene Bukh , Ivarsson Martin A. , Hertwig Laura , Antel Jack P. , Johnson Matthew E. , Okoye Afam , Picker Louis , Vahedi Golnaz , Sparrelid Ernesto , Llewellyn-Lacey Sian , Gostick Emma , Björkström Niklas , Bar-Or Amit , Dori Yoav , Naji Ali , Canaday David H. , Laufer Terri M. , Wells Andrew D. , Price David A. , Frank Ian , Douek Daniel C. , Wherry E. John , Itkin Maxim G. , Betts Michael R.
Published: August 2020

Lymphocyte migration is essential for human adaptive immune surveillance. However, our current understanding of this process is rudimentary, because most human studies to date have been restricted to immunological analyses of blood and various tissues. To address this issue, we used an integrated approach to characterize tissue-emigrant immune cells in thoracic duct lymph (TDL). In humans and non-human primates, lymphocytes were by far the most abundant immune lineage population in efferent lymph, and a vast majority of these lymphocytes were T cells. Cytolytic CD8+T cell subsets were clonotypically discrete and selectively confined to the intravascular circulation, persisting for months after inhibition of S1P-dependent tissue egress by FTY-720. In contrast, non-cytolytic CD8+T cell subsets with stem-like epigenetic and transcriptional signatures predominated in tissues and TDL. Collectively, these data provide an atlas of the migratory immune system and define the nature of tissue-emigrant CD8+T cells that recirculate via TDL.
On-demand correction for X-ray response non-uniformity in microstrip detectors by a data-driven approach
Authors: Kato Kenichi , Shigeta Kazuya
Published: August 2020

A statistical approach, which was previously developed to correct scattering data for X-ray response non-uniformity (XRNU) in microstrip detectors, has been improved to significantly reduce the correcting time. The improved algorithm has succeeded in increasing the utilization rate of data acquired for reference intensity to 98%. As a result, the correcting time was reduced from half a day to half an hour, which was shorter than the typical measuring time of a sample. Moreover, the present approach was found to yield better correction results than the previous one. The data-driven approach enabled the on-demand correction for XRNU according to the detector and experimental settings. The present study will encourage the correction of scattering data for XRNU in area detectors.
Combining Laue diffraction with Bragg coherent diffraction imaging at 34-ID-C
Authors: Pateras Anastasios , Harder Ross , Cha Wonsuk , Gigax Jonathan G. , Baldwin J. Kevin , Tischler Jon , Xu Ruqing , Liu Wenjun , Erdmann Mark J. , Kalt Robert , Sandberg Richard L. , Fensin Saryu , Pokharel Reeju
Published: August 2020

Measurement modalities in Bragg coherent diffraction imaging (BCDI) rely on finding a signal from a single nanoscale crystal object which satisfies the Bragg condition among a large number of arbitrarily oriented nanocrystals. However, even when the signal from a single Bragg reflection with (hkl) Miller indices is found, the crystallographic axes on the retrieved three-dimensional (3D) image of the crystal remain unknown, and thus localizing in reciprocal space other Bragg reflections becomes time-consuming or requires good knowledge of the orientation of the crystal. Here, the commissioning of a movable double-bounce Si (111) monochromator at the 34-ID-C endstation of the Advanced Photon Source is reported, which aims at delivering multi-reflection BCDI as a standard tool in a single beamline instrument. The new instrument enables, through rapid switching from monochromatic to broadband (pink) beam, the use of Laue diffraction to determine crystal orientation. With a proper orientation matrix determined for the lattice, one can measure coherent diffraction patterns near multiple Bragg peaks, thus providing sufficient information to image the full strain tensor in 3D. The design, concept of operation, the developed procedures for indexing Laue patterns, and automated measuring of Bragg coherent diffraction data from multiple reflections of the same nanocrystal are discussed.
Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering
Authors: Chen Yen-Lin , Pollack Lois
Published: August 2020

Macromolecular structures can be determined from solution X-ray scattering. Small-angle X-ray scattering (SAXS) provides global structural information on length scales of 10s to 100s of Ångstroms, and many algorithms are available to convert SAXS data into low-resolution structural envelopes. Extension of measurements to wider scattering angles (WAXS or wide-angle X-ray scattering) can sharpen the resolution to below 10 Å, filling in structural details that can be critical for biological function. These WAXS profiles are especially challenging to interpret because of the significant contribution of solvent in addition to solute on these smaller length scales. Based on training with molecular dynamics generated models, the application of extreme gradient boosting (XGBoost) is discussed, which is a supervised machine learning (ML) approach to interpret features in solution scattering profiles. These ML methods are applied to predict key structural parameters of double-stranded ribonucleic acid (dsRNA) duplexes. Duplex conformations vary with salt and sequence and directly impact the foldability of functional RNA molecules. The strong structural periodicities in these duplexes yield scattering profiles with rich sets of features at intermediate-to-wide scattering angles. In the ML models, these profiles are treated as 1D images or features. These ML models identify specific scattering angles, or regions of scattering angles, which correspond with and successfully predict distinct structural parameters. Thus, this work demonstrates that ML strategies can integrate theoretical molecular models with experimental solution scattering data, providing a new framework for extracting highly relevant structural information from solution experiments on biological macromolecules.
Crystal structures of [(N,N-dimethylamino)methyl]ferrocene and (R
p,R
p)-bis{2-[(dimethylamino)methyl]ferrocenyl}dimethylsilane
Authors: Krupp Anna , Wegge Jessica , Otte Felix , Kleinheider Johannes , Wall Helene , Strohmann Carsten
Published: August 2020

The title compound [(N,N-dimethylamino)methyl]ferrocene, [Fe(C5H5)(C8H12N)], (1), is an interesting starting material for the synthesis of planar chiral 1,2-disubstituted ferrocenes, as demonstrated by the preparation of (R
p,R
p)-bis{2-[(dimethylamino)methyl]ferrocenyl}dimethylsilane, [Fe2(C5H5)2(C18H18N2Si)], (2), from the lithiated derivative of 1. The configuration of the lithium compound is unchanged after the substitution reaction and the chirality is preserved in space group P212121. In both compounds, the Cp rings adopt eclipsed conformations. Hirshfeld surface analysis was used to investigate the intermolecular interactions, and showed that H...H (van der Waals) interactions dominate in both structures with contact percentages of 83.9 and 88.4% for 1 and 2, respectively.
Crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the di-enol tautomeric form of the compound 3,3′-[(2-sulfanylidene-1,3-dithiole-4,5-diyl)bis(sulfanediyl)]bis(pentane-2,4-dione)
Authors: Cordero Giménez Keysha T. , Soto Díaz Victoria Y. , González Espiet Jean C. , Lavín Flores Alexis , Bas Concepción Jesbaniris , Rivera Cruz Kevin E. , Rodríguez Ayala Dara L. , Piñero Cruz Dalice M.
Published: August 2020

The reaction between [TBA]2[Zn(dmit)2] and 3-chloro-2,4-pentanedione yielded single crystals of the title compound, (3E,3′E)-3,3′-[(2-sulfanylidene-1,3-dithiole-4,5-diyl)bis(sulfanediyl)]bis(4-hydroxypent-3-en-2-one), C13H14O4S5, after solvent evaporation. The title compound crystallizes in the triclinic space groupP\overline{1} with two molecules related by an inversion center present in the unit cell. The central thione ring moiety contains a carbon–carbon double bond covalently linked to two sulfoxide substituents located outside of the plane of the ring. The S—C—C—S torsion angles are −176.18 (8) and −0.54 (18)°. Intramolecular hydrogen bonds occur within the two dione substituents (1.67–1.69 Å). Adjacent asymmetric units are linked by C—H...S (2.89–2.90 Å), S...S [3.569 (1) Å] and O...H [2.56–2.66 Å between non-stacked thione rings] short contacts.
Crystal structures of tolfenamic acid polymorphic forms I and II with precise hydrogen-atom positions for nuclear magnetic resonance studies
Authors: Blade Helen , Blundell Charles D. , Vitorica-Yrezabal Iñigo J.
Published: August 2020

The structures of tolfenamic acid [TFA; 2-(3-chloro-2-methylanilino)benzoic acid, C14H12ClNO2] polymorph forms I and II have been redetermined [compare Andersen et al. (1989). J. Chem. Soc., Perkin Trans. 2, pp. 1443–1447] with improved precision using high-resolution X-ray diffraction data and Hirshfield atom refinement in order to better define both hydrogen-atom locations and their associated bond lengths. Covalent bond lengths to hydrogen were found to be significantly longer throughout both structures, especially for the anilino H atom, which is involved in an important intramolecular N—H...O hydrogen bond to the carboxylic acid group. This hydrogen bond is shown to clearly perturb the electron density around both oxygen atoms in the latter group. The extended structures of both polymorphs feature carboxylic acid inversion dimers. These structures provide an improved foundation for nuclear magnetic resonance studies in both solution and the solid state.
1-Hydroxy-3,4-dimethoxy-10-methylacridin-9-one
Authors: Araújo Rodrigo S. A. de , Zondegoumba Ernestine N. T. , Tankoua Whisthler L. D. , Nyassé Barthelemy , Mendonça-Junior Francisco J. B. , De Simone Carlos A.
Published: August 2020

There are two independent molecules in the asymmetric unit of the title compound, C16H15NO4, which was isolated from fruits of Zanthoxylum leprieurii. The atoms of the three rings of each molecule are close to coplanar with the largest deviations from the least-squares planes being 0.084 (3) Å and 0.069 (2) Å. Each molecule features an intramolecular O—H...·O hydrogen bond. In the crystal, C—H...·O hydrogen-bonding interactions link the molecules into a three-dimensional network.
Incorporating the human facet of security in developing systems and services
Authors: Naqvi Bilal , Clarke Nathan , Porras Jari
Published: August 2020

Purpose

The purpose of this paper is to present an integrative framework for handling the security and usability conflicts during the system development lifecycle. The framework has been formulated while considering key concerns raised after conducting a series of interviews with practitioners from the industry. The framework is aimed at assisting system designers and developers in making reasonably accurate choices when it comes to the trade-offs between security and usability. The outcomes of using the framework are documented as design patterns, which are disseminated among the community of system designers and developers for use in other but similar contexts.

Design/methodology/approach

A design science research approach was used to develop the integrative framework for usable security. Interviews were conducted for identification of the key concerns; however, the framework was validated during a workshop. Moreover, to validate the patterns’ template and the usable security pattern identified after instantiating the framework, a survey instrument was used.

Findings

It is important to consider the usability aspect in the development of security systems; otherwise, the systems, despite being secure against attacks, would be susceptible to user mistakes leading to compromises. It is worthwhile to handle usable security concerns right from the start of system development life cycle. Design patterns can help the developers in assessing the usability of their security options.

Practical implications

Practical implications

The framework would assist the designers and developers in handling the security and usability conflicts right from the start of the system development life cycle. The patterns documented after using the framework would help not only the designers and developers working in the industry but also freelancers.

Originality/value

The authors present a novel framework to handle the security and usability conflicts during the system development life cycle. The development process of the framework was driven by the concerns raised after a series of interviews with the practitioners from industry. The framework presented in this paper was validated during a workshop in which it was exposed for review and comments by the participants from the industry. To demonstrate the use of patterns in general and the framework in particular, a case study featuring smart grids from the domain of cyber-physical systems is presented, which (to the best of the authors’ knowledge) features the first work relevant to usable security in the domain of cyber-physical systems.