bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective inhibition of PfATP6 by artemisinins and identification of new classes of inhibitors after expression in yeast
Authors: Moore Catherine M. , Wang Jigang , Lin Qingsong , Ferreira Pedro , Avery Mitchell A. , Elokely Khaled , Staines Henry M. , Krishna Sanjeev
Published: October 2021

Treatment failures with artemisinin combination therapies (ACTs) threaten global efforts to eradicate malaria. They highlight the importance of identifying drug targets and new inhibitors and of studying how existing antimalarial classes work.

Herein we report the successful development of an heterologous expression-based compound screening tool. Validated drug target P. falciparum calcium ATPase6 (PfATP6) and a mammalian ortholog (SERCA1a) were functionally expressed in yeast providing a robust, sensitive, and specific screening tool. Whole-cell and in vitro assays consistently demonstrated inhibition and labelling of PfATP6 by artemisinins. Mutations in PfATP6 resulted in fitness costs that were ameliorated in the presence of artemisinin derivatives when studied in the yeast model.

As previously hypothesised, PfATP6 is a target of artemisinins. Mammalian SERCA1a can be mutated to become more susceptible to artemisinins. The inexpensive, low technology yeast screening platform has identified unrelated classes of druggable PfATP6 inhibitors. Resistance to artemisinins may depend on mechanisms that can concomitantly address multi-targeting by artemisinins and fitness costs of mutations that reduce artemisinin susceptibility.
WGS analysis ofListeria monocytogenesfrom rural, urban, and farm environments in Norway: Genetic diversity, persistence, and relation to clinical and food isolates
Authors: Fagerlund Annette , Idland Lene , Heir Even , Møretrø Trond , Aspholm Marina , Lindbäck Toril , Langsrud Solveig
Published: October 2021

Listeria monocytogenesis a ubiquitous environmental bacterium associated with a wide variety of natural and man-made environments, such as soil, vegetation, livestock, food processing environments, and urban areas. It is also among the deadliest foodborne pathogens, and knowledge about its presence and diversity in potential sources is crucial to effectively track and control it in the food chain. Isolation ofL. monocytogenesfrom various rural and urban environments showed higher prevalence in agricultural and urban developments than in forest or mountain areas, and that detection was positively associated with rainfall. Whole genome sequencing (WGS) was performed for the collected isolates and forL. monocytogenesfrom Norwegian dairy farms and slugs, in total 218 isolates. The data was compared with available datasets from clinical and food associated sources in Norway collected within the last decade. Multiple examples of clusters of isolates with 0-8 wgMLST allelic differences were collected over time in the same location, demonstrating persistence ofL. monocytogenesin natural, urban and farm environments. Furthermore, several clusters with 6-20 wgMLST allelic differences containing isolates collected across different locations, times and habitats were identified, including nine clusters harbouring clinical isolates. The most ubiquitous clones found in soil and other natural and animal ecosystems (CC91, CC11, and CC37) were distinct from clones predominating among both clinical (CC7, CC121, CC1) and food (CC9, CC121, CC7, CC8) isolates. The analyses indicated that ST91 was more prevalent in Norway than other countries and revealed a high proportion of the hypovirulent ST121 among Norwegian clinical cases.

Importance

Listeria monocytogenesis a deadly foodborne pathogen that is widespread in the environment. For effective management, both public health authorities and food producers need reliable tools for source tracking, surveillance, and risk assessment. For this, whole genome sequencing (WGS) is regarded as the present and future gold standard. In the current study, we use WGS to show thatL. monocytogenescan persist for months and years in natural, urban and dairy farm environments. Notably, clusters of almost identical isolates, with genetic distances within the thresholds often suggested for defining an outbreak cluster, can be collected from geographically and temporally unrelated sources. The work highlights the need for a greater knowledge of the genetic relationships between clinical isolates and isolates ofL. monocytogenesfrom a wide range of environments, including natural, urban, agricultural, livestock, food production, and food processing environments, in order to correctly interpret and use results from WGS analyses.
Genomic diversity of hospital-acquired infections revealed through prospective whole genome sequencing-based surveillance
Authors: Mustapha Mustapha M. , Srinivasa Vatsala R. , Griffith Marissa P. , Cho Shu-Ting , Evans Daniel R. , Waggle Kady , Ezeonwuka Chinelo , Snyder Daniel J. , Marsh Jane W. , Harrison Lee H. , Cooper Vaughn S. , Van Tyne Daria
Published: October 2021

Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of healthcare resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAI using prospective whole genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here we describe the biodiversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of their genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 species groups. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal component analysis of accessory genes (PCA-A). Genetic distances between isolates and rates of evolution varied between different species, which has implications for the selection of distance cut-offs for outbreak analysis. Antimicrobial resistance genes and the sharing of mobile genetic elements between different species were frequently observed. Overall, this study describes the population structure of pathogens circulating in a single healthcare setting, and shows how investigating microbial population dynamics can inform genomic epidemiology studies.

Importance

Hospitalized patients are at increased risk of becoming infected with antibiotic-resistant organisms. We used whole-genome sequencing to survey and compare over 3,000 bacterial isolates collected from hospitalized patients at a large medical center over a two-year period. We identified nearly 100 different bacterial species, suggesting that patients can be infected with a wide variety of different organisms. When we examined how genetic relatedness differed between species, we found that different species are likely evolving at different rates within our hospital. This is significant because the identification of bacterial outbreaks in the hospital currently relies on genetic similarity cut-offs, which are often applied uniformly across organisms. Finally, we found that antibiotic resistance genes and mobile genetic elements were abundant among the bacterial isolates we sampled. Overall, this study provides an in-depth view of the genomic diversity and evolution of bacteria sampled from hospitalized patients, as well as genetic similarity estimates that can inform hospital outbreak detection and prevention efforts.
Listeria monocytogenes GlmR is an accessory uridyltransferase essential for cytosolic survival and virulence
Authors: Pensinger Daniel A. , Gutierrez Kimberly V. , Smith Hans B. , Vincent William J.B. , Stevenson David S. , Black Katherine A. , Perez-Medina Krizia M. , Dillard Joseph P. , Rhee Kyu Y. , Amador-Noguez Daniel , Huynh TuAnh N , Sauer John-Demian
Published: October 2021

The cytosol of eukaryotic host cells is an intrinsically hostile environment for bacteria. Understanding how cytosolic pathogens adapt to and survive in the cytosol is critical to developing novel therapeutic interventions for these pathogens. The cytosolic pathogen Listeria monocytogenes requires glmR (previously known as yvcK), a gene of unknown function, for resistance to cell wall stress, cytosolic survival, inflammasome avoidance and ultimately virulence in vivo. A genetic suppressor screen revealed that blocking utilization of UDP-GlcNAc by a non-essential wall teichoic acid decoration pathway restored resistance to cell wall stress and partially restored virulence of ΔglmR mutants. In parallel, metabolomics revealed that ΔglmR mutants are impaired in the production of UDP-GlcNAc, an essential peptidoglycan and wall teichoic acid (WTA) precursor. We next demonstrated that purified GlmR can directly catalyze the synthesis of UDP-GlcNAc from GlcNAc-1P and UTP, suggesting that it is an accessory uridyltransferase. Biochemical analysis of GlmR orthologues suggest that uridyltransferase activity is conserved. Finally, mutational analysis resulting in a GlmR mutant with impaired catalytic activity demonstrated that uridyltransferase activity was essential to facilitate cell wall stress responses and virulence in vivo. Taken together these studies indicate that GlmR is an evolutionary conserved accessory uridyltransferase required for cytosolic survival and virulence of L. monocytogenes.

Importance

Bacterial pathogens must adapt to their host environment in order to cause disease. The cytosolic bacterial pathogen Listeria monocytogenes requires a highly conserved protein of unknown function, GlmR (previously known as YvcK) to survive in the host cytosol. GlmR is important for resistance to some cell wall stresses and is essential for virulence. The ΔglmR mutant is deficient in production of an essential cell wall metabolite, UDP-GlcNAc, and suppressors which increase metabolite levels also restore virulence. Purified GlmR can directly catalyze the synthesis of UDP-GlcNAc and this enzymatic activity is conserved in pathogens from Firmicutes and Actinobacteria phyla. These results highlight the importance accessory cell wall metabolism enzymes in responding to cell wall stress in a variety of bacterial pathogens.
Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers
Authors: Wang Wei , Balfe Peter , Eyre David W , Lumley Sheila F , O’Donnell Denise , Warren Fiona , Crook Derrick W , Jeffery Katie , Matthews Philippa C , Klerman Elizabeth B , McKeating Jane A
Published: October 2021

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis with unprecedented challenges for public health. Vaccinations against SARS-CoV-2 have slowed the incidence of new infections and reduced disease severity. As the time-of-day of vaccination has been reported to influence host immune responses to multiple pathogens, we quantified the influence of SARS-CoV-2 vaccination time, vaccine type, age, sex, and days post-vaccination on anti-Spike antibody responses in healthcare workers. The magnitude of the anti-Spike antibody response associated with the time-of-day of vaccination, vaccine type, participant age, sex, and days post vaccination. These results may be relevant for optimizing SARS-CoV-2 vaccine efficacy.
Designing an evidence-based Bayesian network for estimating the risk versus benefits of AstraZeneca COVID-19 vaccine
Authors: Mayfield Helen J. , Lau Colleen L. , Sinclair Jane E. , Brown Samuel J. , Baird Andrew , Litt John , Vuorinen Aapeli , Short Kirsty R. , Waller Michael , Mengersen Kerrie
Published: October 2021

Uncertainty surrounding the risk of developing and dying from Thrombosis and Thromobocytopenia Syndrome (TTS) associated with the AstraZeneca (AZ) COVID-19 vaccine may contribute to vaccine hesitancy. A model is urgently needed to combine and effectively communicate the existing evidence on the risks versus benefits of the AZ vaccine. We developed a Bayesian network to consolidate the existing evidence on risks and benefits of the AZ vaccine, and parameterised the model using data from a range of empirical studies, government reports, and expert advisory groups. Expert judgement was used to interpret the available evidence and determine the structure of the model, relevant variables, data to be included, and how these data were used to inform the model.

The model can be used as a decision support tool to generate scenarios based on age, sex, virus variant and community transmission rates, making it a useful for individuals, clinicians, and researchers to assess the chances of different health outcomes. Model outputs include the risk of dying from TTS following the AZ COVID-19 vaccine, the risk of dying from COVID-19 or COVID-19-associated atypical severe blood clots under different scenarios. Although the model is focused on Australia, it can be easily adaptable to international settings by re-parameterising it with local data. This paper provides detailed description of the model-building methodology, which can used to expand the scope of the model to include other COVID-19 vaccines, booster doses, comorbidities and other health outcomes (e.g., long COVID) to ensure the model remains relevant in the face of constantly changing discussion on risks versus benefits of COVID-19 vaccination.
Personalized survival probabilities for SARS-CoV-2 positive patients by explainable machine learning
Authors: Zucco Adrian G. , Agius Rudi , Svanberg Rebecka , Moestrup Kasper S. , Marandi Ramtin Z. , MacPherson Cameron Ross , Lundgren Jens , Ostrowski Sisse R. , Niemann Carsten U.
Published: October 2021

Interpretable risk assessment of SARS-CoV-2 positive patients can aid clinicians to implement precision medicine. Here we trained a machine learning model to predict mortality within 12 weeks of a first positive SARS-CoV-2 test. By leveraging data on 33,928 confirmed SARS-CoV-2 cases in eastern Denmark, we considered 2,723 variables extracted from electronic health records (EHR) including demographics, diagnoses, medications, laboratory test results and vital parameters. A discrete-time framework for survival modelling enabled us to predict personalized survival curves and explain individual risk factors. Performances of weighted concordance index 0.95 and precision-recall area under the curve 0.71 were measured on the test set. Age, sex, number of medications, previous hospitalizations and lymphocyte counts were identified as top mortality risk factors. Our explainable survival model developed on EHR data also revealed temporal dynamics of the 22 selected risk factors. Upon further validation, this model may allow direct reporting of personalized survival probabilities in routine care.
Neural population dynamics underlying evidence accumulation in multiple rat brain regions
Authors: DePasquale Brian , Brody Carlos D. , Pillow Jonathan W.
Published: October 2021

Accumulating evidence to make decisions is a core cognitive function. Previous studies have tended to estimate accumulation using either neural or behavioral data alone. Here we develop a unified framework for modeling stimulus-driven behavior and multi-neuron activity simultaneously. We applied our method to choices and neural recordings from three rat brain regions — the posterior parietal cortex (PPC), the frontal orienting fields (FOF), and the anterior-dorsal striatum (ADS) — while subjects performed a pulse-based accumulation task. Each region was best described by a distinct accumulation model, which all differed from the model that best described the animal’s choices. FOF activity was consistent with an accumulator where early evidence was favored while the ADS reflected near perfect accumulation. Neural responses within an accumulation framework unveiled a distinct association between each brain region and choice. Choices were better predicted from all regions using a comprehensive, accumulation-based framework and different brain regions were found to differentially reflect choice-related accumulation signals: FOF and ADS both reflected choice but ADS showed more instances of decision vacillation. Previous studies relating neural data to behaviorally-inferred accumulation dynamics have implicitly assumed that individual brain regions reflect the whole-animal level accumulator. Our results suggest that different brain regions represent accumulated evidence in dramatically different ways and that accumulation at the whole-animal level may be constructed from a variety of neural-level accumulators.

Impact Statement

A computational framework for combining neural and behavioral data to infer latent dynamics underlying decision-making reveals distinct accumulation dynamics in different brain regions in the rat.
Selective Vulnerability of Tripartite Synapses in Amyotrophic Lateral Sclerosis
Authors: Broadhead MJ , Bonthron C , Waddington J , Smith WV , Lopez MF , Burley S , Valli J , Zhu F , Komiyama NH , Smith C , Grant SGN , Miles GB
Published: October 2021

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder. Separate lines of evidence suggest that synapses and astrocytes play a role in the pathological mechanisms underlying ALS. Given that astrocytes make specialised contacts with some synapses, called tripartite synapses, we hypothesise that tripartite synapses could act as the fulcrum of disease in ALS. To test this hypothesis, we have performed an extensive microscopy-based investigation of synapses and tripartite synapses in the spinal cord of ALS model mice and post-mortem human tissue from ALS cases. We reveal widescale synaptic changes at the early symptomatic stages of the SOD1G93a mouse model. Super-resolution microscopy reveals that large complex postsynaptic structures are lost in ALS mice. Most surprisingly, tripartite synapses are selectively lost while non-tripartite synapses remain in equal number to healthy controls. Finally, we also observe a similar selective loss of tripartite synapses in human post-mortem ALS spinal cords. From these data we conclude that tripartite synaptopathy is a key hallmark of ALS.
Regulation Mechanisms of the Dual ATPase in KaiC
Authors: Furuike Yoshihiko , Mukaiyama Atsushi , Koda Shinichi , Simon Damien , Ouyang Dongyan , Ito-Miwa Kumiko , Saito Shinji , Yamashita Eiki , Nishiwaki-Ohkawa Taeko , Terauchi Kazuki , Kondo Takao , Akiyama Shuji
Published: October 2021

KaiC is a dual ATPase, with one active site in its N-terminal domain and another in its C-terminal domain, that drives the circadian clock system of cyanobacteria through sophisticated coordination of the two sites. To elucidate the coordination mechanism, we studied the contribution of the dual ATPase activities in the ring-shaped KaiC hexamer and these structural bases for activation and inactivation. At the N-terminal active site, a lytic water molecule is sequestered between the N-terminal domains, and its reactivity to ATP is controlled by the quaternary structure of the N-terminal ring. The C-terminal ATPase activity is regulated mostly by water-incorporating voids between the C-terminal domains, and the size of these voids is sensitive to phosphoryl modification of S431. The N-terminal ATPase activity inversely correlates with the affinity of KaiC for KaiB, a clock protein constitutes the circadian oscillator together with KaiC and KaiA, and the complete dissociation of KaiB from KaiC requires KaiA-assisted activation of the dual ATPase. Delicate interactions between the N-terminal and C-terminal rings make it possible for the components of the dual ATPase to work together, thereby driving the assembly and disassembly cycle of KaiA and KaiB.

Significance Statement

KaiC, a core clock protein in the cyanobacterial circadian clock system, hydrolyzes ATP at two distinct sites in a slow but ordered manner to measure the circadian time scale. We used biochemical and structural biology techniques to characterize the properties and interplay of dual ATPase active sites. Our results show that the N-terminal and C-terminal ATPases communicate with each other through an interface between the N-terminal and C-terminal domains in KaiC. The dual ATPase sites are regulated rhythmically in a concerted or opposing manner dependent on the phase of the circadian clock system, controlling the affinities of KaiC for other clock proteins, KaiA and KaiB.
Reversing anterior insular cortex neuronal hypoexcitability attenuates compulsive behavior in juvenile rats
Authors: Jadhav Kshitij S. , Bernheim Aurélien P. , Aeschlimann Léa , Kirschmann Guylène , Decosterd Isabelle , Hoffman Alexander F. , Lupica Carl R. , Boutrel Benjamin
Published: October 2021

Development of self-regulatory competencies during adolescence is partially dependent on normative brain maturation. Here we report that juvenile rats as compared to adults exhibit impulsive and compulsive-like behavioral traits, the latter being associated with lower expression of mRNA levels of the immediate early gene zif268 in the anterior insula (AI). This observation suggests that deficits in AI function in juvenile rats could explain their immature pattern of interoceptive cue integration in rational decision-making and compulsive phenotype. In support of this, here we report hypoexcitability of juvenile layer-V pyramidal neurons in the AI, concomitant with reduced glutamatergic synaptic input to these cells. Chemogenetic activation of the AI attenuated the compulsive trait suggesting that delayed maturation of the AI results in suboptimal integration of sensory and cognitive information in adolescents and this contributes to inflexible behaviors in specific conditions of reward availability.
GATA4 regionalizes intestinal metabolism and barrier function to prevent immunopathology
Authors: Earley Zachary M. , Lisicka Wioletta , Sifakis Joseph J. , Aguirre-Gamboa Raúl , Kowalczyk Anita , Barlow Jacob T. , Shaw Dustin G. , Discepolo Valentina , Tan Ineke L. , Gona Saideep , Ernest Jordan D. , Matzinger Polly , Barreiro Luis B. , Morgun Andriy , Bendelac Albert , Ismagilov Rustem F. , Shulzhenko Natalia , Riesenfeld Samantha J. , Jabri Bana
Published: October 2021

Different regions of the gastrointestinal tract have distinct digestive and absorptive functions, which may be locally disrupted by infection or autoimmune disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. Here, we used mouse models, transcriptomics, and immune profiling to show that regional epithelial expression of the transcription factor GATA4 prevented adherent bacterial colonization and inflammation in the proximal small intestine by regulating retinol metabolism and luminal IgA. Loss of epithelial GATA4 expression increased mortality in mice infected with Citrobacter rodentium. In active celiac patients with villous atrophy, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. This study reveals broad impacts of GATA4-regulated intestinal regionalization and highlights an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.

One-sentence summary

Epithelial GATA4 regulates intestinal regionalization of bacterial colonization, metabolic pathways, and tissue immunity.
Effect of eribulin on angiogenesis and endothelial adhesion molecules
Authors: Abbona Andrea , Falletta Antonella , Paccagnella Matteo , Astigiano Simonetta , Martini Stefania , Denaro Nerina , Ruatta Fiorella , Barbieri Ottavia , Merlano Marco , Garrone Ornella
Published: October 2021

Tumor vasculature is an important component of the tumor microenvironment and deeply affect anticancer immune response. Eribulin is a non taxane inhibitor of the mitotic spindle. However, off-target effect interfering with the tumor vasculature have been reported. The mechanisms responsible of this effect is not clear.

We designed an in vitro study to investigate the effect of eribulin on neo-angiogenesis and on the adhesion molecules ICAM-1 and VCAM-1, with or without TGF-β. We also investigated the effects of paclitaxel and vinorelbine in the same experimental conditions.

Eribulin was able to up-regulate the epithelial markers VE-cadherin and CD-31 in the HUVEC and tube formation in HUVEC cultured in Matrigel. The drug effectively arrested tube formation even in presence of TGF-β. Eribulin counteracted the TGF-β induced change in cell shape from the endothelial cobblestone-like morphology to an elongated spindle-shaped morphology that is characteristic of EndMT.

We also observed that eribulin is able to upregulate ICAM-1 and to counteract its downregulation induced by TGF-β.

In this study, eribulin was able to inhibit the vasculature remodeling and the downregulation of ICAM-1 induced by TGF-β. These effects might have important therapeutic consequence if the drug will be administered with immunotherapy.
Absolute quantitation of serum antibody reactivity using the Richards growth model for antigen microspot titration
Authors: Papp Krisztián , Kovács Ágnes , Orosz Anita , Hérincs Zoltán , Randek Judit , Liliom Károly , Pfeil Tamás , Prechl József
Published: October 2021

In spite of its pivotal role in the characterization of humoral immunity, there is no accepted method for the absolute quantitation of antigen specific serum antibodies. We devised a novel method to quantify polyclonal antibody reactivity, which exploits protein microspot assays and employs a novel analytical approach. Microarrays with a density series of disease specific antigen were treated with different serum dilutions and developed for IgG and IgA binding. By fitting binding data of both dilution series to a product of two generalized logistic functions, we obtained estimates of antibody reactivity of two immunoglobulin classes simultaneously. These estimates are the antigen concentrations required for reaching the inflection point of thermodynamic activity coefficient of antibodies and the limiting activity coefficient of antigen. By providing universal chemical units, this approach may improve standardization of serological testing, the quality control of antibodies and the quantitative mapping of antibody-antigen interaction space.
FITTING OF HYPERELASTIC CONSTITUTIVE MODELS IN DIFFERENT SHEEP HEART REGIONS BASED ON BIAXIAL MECHANICAL PROPERTIES
Authors: Nemavhola Fulufhelo , Pandelani Thanyani , Ngwangwa Harry
Published: October 2021

Heart failure remains one of the leading causes of death especially among people over the age of 60 years worldwide. To develop effective therapy and suitable replacement materials for the heart muscle it is necessary to understand its biomechanical behaviour under load. This paper investigates the passive mechanical response of the sheep myocardia excised from three different regions of the heart. Due to the relatively higher cost and huge ethical demands in acquisition and testing of real animal heart models, this paper evaluates the fitting performances of five different constitutive models on the myocardial tissue responses. Ten sheep were sacrificed, and their hearts excised and transported within 3h to the testing biomechanical laboratory. The upper sections of the hearts above the short axes were carefully dissected out. Tissues were dissected from the mid-sections of the left ventricle, mid-wall and right ventricle for each heart. The epicardia and endocardia were then carefully sliced off each tissue to leave the myocardia. Stress-strain curves were calculated, filtered and resampled. The results show that Choi-Vito model was found to provide the best fit to the LV, the polynomial (Anisotropic) model to RV, the Four-Fiber Family model to RV, Holzapfel (2000) to RV, Holzapfel (2005) to RV and the Fung model to LV.
Detecting ice artefacts in processed macromolecular diffraction data with machine learning
Authors: Nolte Kristopher , Gao Yunyun , Stäb Sabrina , Kollmansberger Philip , Thorn Andrea
Published: October 2021

Contamination with diffraction from ice crystals can negatively affect, or even impede macromolecular structure determination and therefore, detecting the resulting artefacts in diffraction data is crucial. However, once the data have been processed, it can be very difficult to automatically recognize this problem. To address this, a set of convolutional neural networks named Helcaraxe has been developed which can detect ice diffraction artefacts in processed diffraction data from macromolecular crystals. The networks outperform previous algorithms and will be available as part of the AUSPEX webserver and CCP4-distributed software.

Synopsis

A program utilizing artificial learning and convolutional neural networks, named Helcaraxe, has been developed which can detect ice crystal artefacts in processed macromolecular diffraction data with unprecedented accuracy.
Plasticity in stomatal behavior across a gradient of water supply is consistent among field-grown maize inbred lines with varying stomatal patterning
Authors: Ding Risheng , Xie Jiayang , Mayfield-Jones Dustin , Zhang Yanqun , Kang Shaozhong , Leakey Andrew D.B.
Published: October 2021

Stomata regulate leaf CO2 assimilation (A) and water loss. The Ball–Berry and Medlyn models predict stomatal conductance (gs) with a slope parameter (m or g1) that reflects sensitivity of gs to A, atmospheric CO2 and humidity, and is inversely related to water use efficiency (WUE). This study addressed knowledge gaps about what the values of m and g1 are in C4 crops under field conditions, as well as how they vary among genotypes and with drought stress. m and g1 were unexpectedly consistent in four inbred maize genotypes across a gradient of water supply. This was despite genotypic variation in stomatal patterning, A and gs. m and g1 were strongly correlated with soil water content, moderately correlated with pre-dawn leaf water potential (Ψpd), and weakly correlated with midday leaf water potential (Ψmd). This implied that m and g1 respond to long-term water supply more than short-term drought stress. The conserved nature of m and g1 across anatomically diverse genotypes and water supplies suggests there is flexibility in structure-function relationships underpinning WUE. This evidence can guide simulation of maize gs across a range of water supply in the primary maize growing region and inform efforts to improve WUE.

Summary statement

Parameter values for models simulating stomatal conductance were unexpectedly consistent for anatomically and physiologically diverse genotypes of the model C4 crop maize when they were grown across a range of water supplies in the field.
RACK1 associates with RNA-binding proteins Vigilin and SERBP1 to control dengue virus replication
Authors: Brugier Alexis , Hafirrassou Mohamed-Lamine , Pourcelot Marie , Baldaccini Morgane , Couture Laurine , Kril Vasiliya , Kümmerer Beate M. , Gallois-Montbrun Sarah , Bonnet-Madin Lucie , Pfeffer Sébastien , Vidalain Pierre -Olivier , Delaugerre Constance , Meertens Laurent , Amara Ali
Published: October 2021

Dengue virus (DENV), a re-emerging virus transmitted byAedesmosquitoes, causes severe pathogenesis in humans. No effective treatment is available against this virus. We recently identified the scaffold protein RACK1 as a component of the DENV replication complex, a macromolecular complex essential for viral genome amplification. Here, we show that RACK1 is important for DENV infection. RACK1 mediates DENV replication through binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to a loss-of-function screen identified the RNA binding proteins Vigilin and SERBP1 as DENV host dependency factors. Vigilin and SERBP1 interact with DENV viral RNA (vRNA), forming a ternary complex with RACK1 to mediate viral replication. Overall, our results indicate that RACK1 recruits Vigilin and SERBP1, linking the DENV vRNA to the translation machinery for optimal translation and replication.
Co-expression Patterns Explain how a Basic Transcriptional Role for MYC Modulates Wnt and MAPK Pathways in Colon and Lung Adenocarcinomas
Authors: Kucherlapati Melanie Haas
Published: October 2021

Genome duplication begins at many epigenetically determined sites by pre-replication, pre-initiation, and replisome complexes; co-expression of their components must be optimally timed for S phase to occur. Oscillations of cyclin dependent kinases (Cdks) and regulator cyclins control cell cycling, many are pharmacological targets in cancer. This study examines gene expression relationships between drivers, cell cycle components, and a subset of proliferation genes in colon (COAD) and lung (LUAD) adenocarcinomas. Several known drivers of COAD and LUAD including APC, CTNNB1, KRAS, MYC, Braf, TP53, Rb1, and EGFR are also observed with focus on Wnt and MAPK signaling activation. Wnt signaling activation has relevance for immune checkpoint inhibitor therapy, as it provides cancer cells with escape mechanisms.

MYC and KRAS co-expressed directly with far fewer proliferation genes in LUAD than COAD, suggesting their expression is ectopic to S phase in lung tumors. APC indirectly co-expressed with the same factors in both COAD and LUAD, but was found co-expressed indirectly with MYC and mutated only in COAD. Other Wnt signaling components also co-expressed in low MYC context in COAD, had significantly higher mutation frequencies. These data suggest Wnt signaling activation to be the indirect result of decreased MYC availability in COAD, and ectopic overexpression of MYC in LUAD. Cyclins CCNH, CCNC, and CCNK, co-expressed with far fewer proliferation genes in LUAD. Conversely, Braf had direct co-expression with many proliferation factors in non EGFR activated LUAD. Proliferation in EGFR activated LUAD was completely deregulated with E2F(s) 4/5/6 expression, potentially explaining their low proliferative ability.
Repeated exposure to chlorpyrifos is associated with a dose-dependent chronic neurobehavioral deficit in adult rats
Authors: Ribeiro Ana C. R. , Hawkins Elisa , Jahr Fay M. , McClay Joseph L. , Deshpande Laxmikant S.
Published: October 2021

Organophosphate (OP) chemicals include commonly used pesticides and also chemical warfare agents, and mechanistically they are potent inhibitors of the cholinesterase (ChE) enzyme. While a chronic low-dose OP exposure does not produce acute cholinergic crises, epidemiological studies report long-term neuropsychiatric issues including depression and cognitive impairments in OP-exposed individuals. Chlorpyrifos (CPF) is one of the most widely used pesticides worldwide. Multiple laboratory studies have reported on either the long-term behavioral effect of a single, high-dose CPF or studied sub-chronic behavioral effects particularly the motor and cognitive effects of repeated low-dose CPF exposure. However, studies on chronic mood and depression-related morbidities following repeated sub-threshold CPF doses that would mimic occupationally-relevant OP exposures are lacking. Here, adult male rats were injected with CPF (1, 3, 5, or 10 mg/kg/d, s.c.) for 21-days. Dependent on the CPF dose, ChE activity was inhibited approximately 60-80% in the blood and about 20-50% in the hippocampus at 2-days after the end of CPF exposures. Following an 11-week washout period, CPF-treated rats exhibited a dose-dependent increase in signs of anhedonia (sucrose preference test), anxiety (open-field and elevated plus-maze), and despair (forced swim test) despite a complete recovery of ChE activity at this stage. We speculate that both cholinergic and non-cholinergic mechanisms could play a role in the development of chronic OP-related depressive outcomes. The proposed CPF exposure paradigm could provide an ideal model to further study molecular mechanisms underlying cause and effect relationships between environmental OP exposures and the development of chronic behavioral deficits.
Genetically distant bacteriophages elicit unique genomic changes in Enterococcus faecalis
Authors: Johnson Cydney N. , Araya Dennise Palacios , Schink Viviane , Islam Moutusee , Mangalea Mihnea R. , Decurtis Emily K. , Ngo Tuong-Vi Cindy , Palmer Kelli L. , Duerkop Breck A.
Published: October 2021

The human microbiota harbors diverse bacterial and bacteriophage (phage) communities. Bacteria evolve to overcome phage infection, thereby driving phage evolution to counter bacterial resistance. Understanding how phages promote genetic alterations in medically relevant bacteria is important as phages continue to become established biologics for the treatment of multidrug-resistant (MDR) bacterial infections. Before phages are used as standalone or combination antibacterial therapies, we must obtain a deep understanding of the molecular mechanisms of phage infection and how host bacteria alter their genomes to become resistant. We performed coevolution experiments using a single Enterococcus faecalis strain and two distantly related phages, to determine how phage pressure impacts the evolution of the E. faecalis genome. Whole genome sequencing revealed mutations previously demonstrated to be essential for phage infection. We also identified mutations in several genes previously unreported to be associated with phage infection in E. faecalis. Intriguingly, there was only one shared mutation in the E. faecalis genome in response to each of the two phages tested, demonstrating that infection by genetically distinct phages results in different host responses. This study shows that infection of the same host by disparate phages leads to evolutionary trajectories that result in distinct genetic changes. This implies that bacteria respond to phage pressure through host responses that are tailored to specific phages. This work serves as the basis for the study of E. faecalis genome evolution during phage infection and will inform the design of future therapeutics, such as phage cocktails, intended to target MDR E. faecalis.

IMPORTANCE

Studies characterizing the genome evolution of bacterial pathogens following phage selective pressure are lacking. Phage therapy is experiencing a rebirth in Western medicine. Such studies are critical for understanding how bacteria subvert phage infection and how phages evolve to counter such mutations. This study utilizes comparative genomic analyses to demonstrate how a pathogenic strain of Enterococcus faecalis responds to infection by two genetically distant phages. We show that genetic alterations in the E. faecalis genome accumulate in a manner that is specific to the infecting phage with little to no overlap in shared fixed mutations. This suggests that bacterial genome evolution in response to phage infection is uniquely tied to phage genotype, and sets a precedence for investigations into how phages drive bacterial genome evolution relevant to phage therapeutic applications.
Differential regulation of cranial and cardiac neural crest by Serum Response Factor
Authors: Dinsmore Colin J. , Soriano Philippe
Published: October 2021

Serum response factor (SRF) is an essential transcription factor that influences many cellular processes including cell proliferation, migration, and differentiation. SRF directly regulates and is required for immediate early gene (IEG) and actin cytoskeleton-related gene expression. SRF coordinates these competing transcription programs through discrete sets of cofactors, the Ternary Complex Factors (TCFs) and Myocardin Related Transcription Factors (MRTFs). The relative contribution of these two programs toin vivoSRF activity and mutant phenotypes is not fully understood. To study how SRF utilizes its cofactors during development, we generated a knock-inSrfαIallele in mice harboring point mutations that disrupt SRF-MRTF-DNA complex formation but leave SRF-TCF activity unaffected. HomozygousSrfαI/αImutants die at E10.5 with notable cardiovascular phenotypes, and neural crest conditional mutants succumb at birth to defects of the cardiac outflow tract but display none of the craniofacial phenotypes associated with complete loss of SRF in that lineage. Our studies further support an important role for MRTF mediating SRF function in cardiac neural crest and suggest new mechanisms by which SRF regulates transcription during development.
Causal Haplotype Block Identification in Plant Genome-Wide Association Studies
Authors: Wu Xing , Jiang Wei , Fragoso Chris , Huang Jing , Zhou Geyu , Zhao Hongyu , Dellaporta Stephen
Published: October 2021

Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) used in many GWAS that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects. In plants, the relatively small population size in GWAS and the high genetic diversity found many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods. HapFM uses genotype data to partition the genome into haplotype blocks, identifies haplotype clusters within each block, and then performs genome-wide haplotype fine-mapping to infer the causal haplotype blocks of trait. We benchmarked HapFM, GEMMA, BSLMM, and GMMAT in both simulation and real plant GWAS datasets. HapFM consistently resulted in higher mapping power than the other GWAS methods in simulations with high polygenicity. Moreover, it resulted in higher mapping resolution, especially in regions of high LD, by identifying small causal blocks in the larger haplotype block. In the Arabidopsis flowering time (FT10) datasets, HapFM identified four novel loci compared to GEMMA’s results, and its average mapping interval of HapFM was 9.6 times smaller than that of GEMMA. In conclusion, HapFM is tailored for plant GWAS to result in high mapping power on complex traits and improved mapping resolution to facilitate crop improvement.
Emergent phases of ecological diversity and dynamics mapped in microcosms
Authors: Hu Jiliang , Amor Daniel R. , Barbier Matthieu , Bunin Guy , Gore Jeff
Published: October 2021

Natural ecological communities display striking features, such as high biodiversity and a wide range of dynamics, that have been difficult to explain in a unified framework. Using experimental bacterial microcosms, we perform the first direct test of recent complex systems theory predicting that simple aggregate parameters dictate emergent behaviors of the community. As either the number of species or the strength of species interactions is increased, we show that microbial ecosystems transition between distinct qualitative dynamical phases in the predicted order, from a stable equilibrium where all species coexist, to partial coexistence, to emergence of persistent fluctuations in species abundance. Under the same conditions, high biodiversity and fluctuations allow and require each other. Our results demonstrate predictable emergent diversity and dynamics in ecological communities.

One-Sentence Summary

A phase diagram of ecological dynamics and diversity as a function of coarse-grained features of species interaction network.
Motor learning selectively strengthens cortical and striatal synapses of motor engram neurons
Authors: Hwang Fuu-Jiun , Roth Richard H. , Wu Yu-Wei , Sun Yue , Liu Yu , Ding Jun B.
Published: October 2021

Learning and consolidation of new motor skills require adaptations of neuronal activity and connectivity in the motor cortex and striatum, two key motor regions of the brain. Yet, how neurons undergo synaptic changes and become recruited during motor learning to form a memory engram remains an open question. Here, we train mice on a single-pellet reaching motor learning task and use a genetic approach to identify and manipulate behavior-relevant neurons selectively in the primary motor cortex (M1). We find that the degree of reactivation of M1 engram neurons correlates strongly with motor performance. We further demonstrate that learning-induced dendritic spine reorganization specifically occurs in these M1 engram neurons. In addition, we find that motor learning leads to an increase in the number and strength of outputs from M1 engram neurons onto striatal spiny projection neurons (SPNs) and that these synapses form local clusters along SPN dendrites. These results identify a highly specific synaptic plasticity during the formation of long-lasting motor memory traces in the corticostriatal circuit.

HIGHLIGHTS

– Motor performance is correlated with the reactivation of motor engram neurons

– Motor learning increases spine density and new spine survival selectively on M1 engram neurons

– Motor learning strengthens motor engram outputs to the striatum

– M1 engram outputs converge onto clusters of dendritic spines on striatal spiny projection neurons
Blood cytokine analysis suggests that SARS-CoV-2 infection results in a sustained tumour promoting environment in cancer patients
Authors: De Winter Fien HR , Hotterbeekx An , Huizing Manon , Konnova Angelina , Fransen Erik , Jongers Bart’s , Jairam Ravi Kumar , Van averbeke Vincent , Moons Pieter , Roelant Ella , Le Blon Debbie , Berghe Wim Vanden , Janssens Annelies , Lybaert Willem , Croes Lieselot , Vulsteke Christof , Malhotra-Kumar Surbhi , Goossens Herman , Berneman Zwi , Peeters Marc , van Dam Peter , Kumar-Singh Samir
Published: October 2021

Cytokines, chemokines and (angiogenic) growth factors (CCGs) have been shown to play an intricate role in the progression of both solid and haematological malignancies. Recent studies have shown that SARS-CoV-2 infection leads to worse outcome in cancer patients, especially in haematological malignancy patients. Here, we investigated how SARS-CoV-2 infection impacts the already altered CCG levels in solid or haematological malignancies, specifically whether there is a protective effect or rather a potentially higher risk for major COVID-19 complications in cancer patients due to elevated CCGs linked to cancer progression. Serially analysing immune responses with 55 CCGs in cancer patients under active treatment with or without SARS-CoV-2 infection, we first showed that cancer patients without SARS-CoV-2 infection (n=54) demonstrate elevated levels of 35 CCGs compared to the non-cancer, non-infected control group of health care workers (n=42). Of the 35 CCGs, 19 were common to both solid and haematological malignancy groups and comprised previously described cytokines such as IL-6, TNF-α, IL-1Ra, IL-17A, and VEGF, but also several less well described cytokines/chemokines such as Fractalkine, Tie-2, and T cell chemokine CTACK. Importantly, we show here that 7 CCGs are significantly altered in SARS-CoV-2 exposed cancer patients (n=52). Of these TNF-α, IFN-β, TSLP and sVCAM-1, identified to be elevated in haematological cancers, are also known tumour-promoting factors. Longitudinal analysis conducted over 3 months showed persistence of several tumour-promoting CCGs in SARS-CoV-2 exposed cancer patients. These data urge for increased vigilance for haematological malignancy patients as a part of long COVID follow-up.
Validity of the Web-based, Self-directed, NeuroCognitive Performance Test in MCI
Authors: Doraiswamy P. Murali , Goldberg Terry E. , Qian Min , Linares Alexandra R. , Nwosu Adaora , Nino Izael , D’Antonio Jessica , Philips Julia , Ndouli Charlie , Hellegers Caroline , Michael Andrew M. , Petrella Jeffrey R. , Andrews Howard , Sneed Joel , Devanand Davangere
Published: October 2021

Digital cognitive tests offer several potential advantages over established paper-pencil tests but have not yet been fully evaluated for the clinical evaluation of mild cognitive impairment. The NeuroCognitive Performance Test (NCPT) is a web-based, self-directed, modular battery intended for repeated assessments of multiple cognitive domains. Using a sample of 101 MCI subjects, we report in this study that the NCPT composite is significantly correlated with both a composite measure of established tests (r=0.77, p<0.0001) as well as with the ADAS-Cog (r=0.55, p<0.0001). Both test batteries had a similar factor structure that included a large “g” component with a high eigenvalue. Further, both the NCPT and established tests significantly (p< 0.01) predicted the UPSA and FAQ, measures of daily functioning. Despite limitations such as a relatively small sample, absence of control group and cross-sectional nature, these findings are consistent with the growing literature on the promise of self-directed, web-based cognitive assessments for MCI.