bluuebunny/crossref_metadata_2025 huggingface dataset:
Oligogenic risk model for Gilles de la Tourette syndrome reveals a genetic continuum of tic disorders
Authors: Borczyk Malgorzata , Fichna Jakub P , Piechota Marcin , Gołda Sławomir , Zięba Mateusz , Hoinkis Dzesika , Cięszczyk Paweł , Korostyński Michal , Janik Piotr , Żekanowski Cezary
Published: December 2021

Gilles de la Tourette syndrome (GTS) and other Tic Disorders (TDs) have a substantial genetic component with their heritability estimated at between 60 and 80%. Here we propose an oligogenic risk model of TDs using whole-genome sequencing (WGS) data from a group of Polish GTS patients, their families, and control samples (n = 278). The model is based on the overrepresentation of coding and non-coding genetic variants in and in the vicinity of genes selected from a set of 84 genes previously indicated as putatively associated with GTS. In the discovery phase, based on a variant burden test between unrelated GTS cases (n = 37) and a database of local allele frequencies 10 genes were selected for the model (CHADL,DRD2,MAOA,PCDH10,HTR2A,SLITRK5,SORCS3,KCNQ5,CDH9,andCHD8). Variants in these genes (n = 7654) with a median minor allele frequency in the non-Finnish European population of 0.02 were integrated into an additive classifier. This risk model was then applied to healthy and GTS-affected individuals from 23 families and 100 unrelated healthy samples from the Polish population (AUC-ROC=0.62, p=0.02). Application of the oligogenic model to a group of patients with other tic disorders revealed a continuous increase of the oligogenic score with healthy individuals with the lowest mean, then patients with other tic disorders, then GTS patients, and finally with severe GTS cases with the highest oligogenic score. Results were also overlapped with Psychiatric Genomics Consortium (PGC) GWAS data and we found no significant overlap between the common variant signal and our oligogenic model (p=0.21). Therefore obtained results were compared with the polygenic risk score built from the PGC GWAS data, which revealed a significant contribution of common variant background in severe GTS cases. Overall, we leveraged WGS data to construct a GTS/TDs risk model based on variants that may cooperatively contribute to the etiology of these disorders. This study provides evidence that typical and severe adult GTS as well as other tic disorders may exist on a single spectrum in terms of their genetic background.
Population Optimally Immunized after Accounting for Type-Specific COVID-19 Vaccine Waning Intervals: State-Level Prevalence and Trends
Authors: Pathak Elizabeth B. , Salemi Jason L.
Published: December 2021

BACKGROUND

COVID-19 vaccines exhibit real-world waning effectiveness against SARS-CoV-2 infection within the first 3-6 months after a completed series. Consequently, the main metric tracked by the CDC (percent “fully vaccinated,” with no adjustment for booster status) has become insufficiently informative.

METHODS

We analyzed CDC daily vaccination data to quantify COVID-19 immunization status for 4 mutually-exclusive groups: (1) not immunized; (2) partially immunized (people who received the 1st dose of a 2-dose series); (3) immunized with waning immunity (previously immunized people whose booster dose is overdue); and (4) optimally immunized (people who: (a) received the Janssen vaccine <2 months ago or completed an mRNA vaccine series <6 months ago, or (b) received the Janssen vaccine >2 months ago or completed an mRNA vaccine series >6 months ago and received a booster dose.)

RESULTS

The proportion of the total US population who were optimally immunized against COVID-19 fell from a high of 45.3% on July 17 to 29.4% on November 30. During November, the majority of states experienced a worsening trend in the percent of the total population who were overdue for a booster dose, including the 4 largest states, with percentage point increases of 3.5 in New York, 3.4 in California, 2.3 in Texas and 1.7 in Florida.

CONCLUSIONS

Our proposed classification scheme accounts for type-specific vaccine waning intervals, provides an accurate assessment of progress toward national immunization goals, and reveals the urgent need for additional public health mitigation strategies to successfully combat the COVID-19 pandemic in the United States.
Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults respectively, with both subclades exhibiting extensive genetic diversity
Authors: Howson-Wells Hannah C. , Tsoleridis Theocharis , Zainuddin Izzah , Tarr Alexander W. , Irving William L. , Ball Jonathan K. , Berry Louise , Clark Gemma , McClure C. Patrick
Published: December 2021

Enterovirus D68 (EV-D68) has been recently identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-D68 in 194 known EV positive samples from late 2018, UK. EV-D68 was detected in 83 (58%) of the 143 EV positive samples. Sequencing and phylogenetic analysis revealed an extensive genetic diversity, split between subclades B3 (n=50) and D1 (n=33), suggesting epidemiologically unrelated infections. B3 predominated in children and younger adults, and D1 in older adults and the elderly (p=0.0009). Clinical presentation indicated causation or exacerbation of respiratory distress in 91.4% of EV-D68-positive individuals, principally: cough (75.3%), shortness of breath (56.8%), coryza (48.1%), wheeze (46.9%), supplemental oxygen required (46.9%) and fever (38.9%). Clinical features were not distinguished by subclade. Two cases of AFM were observed, one with EV-D68 detectable in the cerebrospinal fluid, otherwise neurological symptoms were rarely reported (n=4).
First and Second Wave Dynamics of Emergency Department Utilization during the COVID-19 Pandemic: a retrospective study
Authors: Dijk Robi , Plaum Patricia , Tummers Stan , van Osch Frits H.M. , Barten Dennis G. , Latten Gideon H.P.
Published: December 2021

Background

Since the COVID-19 pandemic, there has been a decrease in emergency department(ED) utilization. Although this has been thoroughly characterized for the first wave(FW), studies during the second wave(SW) are limited. We examined the changes in ED utilization between the FW and SW, compared to 2019 reference periods.

Methods

We performed a retrospective analysis of ED utilization in 3 Dutch hospitals in 2020. The FW and SW (March-June and September–December, respectively) were compared to the reference periods in 2019. ED visits were labeled as (non-)COVID-suspected.

Findings

During the FW and SW ED visits decreased by 20.3% and 15.3%, respectively, when compared to reference periods in 2019. During both waves high urgency visits significantly increased with 3.1% and 2.1%, and admission rates (ARs) increased with 5.0% and 10.4%. Trauma related visits decreased by 5.2% and 3.4%. During the SW we observed less COVID-related visits compared to the FW (4,407 vs 3,102 patients). COVID-related visits were significantly more often in higher need of urgent care and ARs where at least 24.0% higher compared to non-COVID visits.

Interpretation

During both COVID-19 waves ED visits were significantly reduced, with the most distinct decline during the FW. ED patients were more often triaged as high urgent and the ARs were increased compared to the reference period in 2019, reflecting a high burden on ED resources. These findings indicate the need to gain more insight into motives of patients to delay or avoid emergency care during pandemics and prepare EDs for future pandemics.

Funding

None
A co-opted endogenous retroviral envelope promotes cell survival by controlling SLC31A1/CTR1-mediated copper transport and homeostasis
Authors: Tury Sandrine , Chauveau Lise , Courgnaud Valérie , Battini Jean-Luc
Published: December 2021

Copper is a critical element for eukaryotic life, involved in numerous cellular functions and in redox balance but it can be toxic in excess. Therefore, tight regulation of copper acquisition and homeostasis is essential for cell physiology and survival. Here, we identified a unique mechanism for cell survival involving the regulation of copper homeostasis by an endogenous retroviral (ERV) envelope glycoprotein called Refrex1. We show that extracellular copper sensing by cells increases Refrex1 expression, which in turn regulates copper acquisition through interaction with the main copper transporter SLC31A1/CTR1. Downmodulation of Refrex1 resulted in intracellular copper accumulation leading to ROS production and subsequent apoptosis, which could be reverted by copper chelator treatment. Our results demonstrate that Refrex1 has been co-opted for its ability to regulate copper entry through CTR1 interaction in order to limit copper excess for a proper redox balance, and suggests that other ERV may have similar metabolic functions among vertebrates.
Long read sequencing reveals sequential complex rearrangements driven by Hepatitis B virus integration
Authors: Wang Songbo , Lin Jiadong , Yang Xiaofei , Li Zihang , Tun Xu , Wang Tingjie , Wang Bo , Hu Liangshuo , Ye Kai
Published: December 2021

Integration of Hepatitis B virus (HBV) into human genome disrupts genetic structures and cellular functions. Here, we conducted multiplatform long read sequencing on two cell lines and five clinical samples of HBV-infected hepatocellular carcinomas (HCC). We resolved three types of viral integration-induced complex genome rearrangements (CGR) and proposed a model of ‘multi-hits and sequential-breaks’ to depict their formation process by differentiating inserted HBV copies with HiFi long reads. We deduced that all three complex types were initialized from focal replacement and fragile virus-human junctions triggered subsequent rearrangements. We further revealed that such rearrangements caused a prevalent loss-of-heterozygosity at chr4q, accounting for 19.5% of HCC samples in ICGC cohort and contributing to immune and metabolic dysfunction. Overall, our long read based analysis reveals novel sequential rearrangement processes initiated by HBV integration, hinting its structural and functional impact on HCC.
Accurate measurement of microsatellite length by disrupting its tandem repeat structure
Authors: Levy Dan , Wang Zihua , Moffitt Andrea B. , Wigler Michael
Published: December 2021

Replication of tandem repeats of simple sequence motifs, also known as microsatellites, is error prone and variable lengths frequently occur during population expansions. Therefore, microsatellite length variations could serve as markers for cancer. However, accurate error-free quantitation of microsatellite lengths is difficult with current methods because of a high error rate during amplification and sequencing. We have solved this problem by using partial mutagenesis to disrupt enough of the repeat structure so that it can replicate faithfully, yet not so much that the flanking regions cannot be reliably identified. In this work we use bisulfite mutagenesis to convert a C to a U, later read as T. Compared to untreated templates, we achieve three orders of magnitude reduction in the error rate per round of replication. By requiring two independent first copies of an initial template, we reach error rates below one in a million. We discuss potential clinical applications of this method.
Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga
Authors: Leung Christelle , Grulois Daphné , Chevin Luis-Miguel
Published: December 2021

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - but significant - effect of strain × environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.
Integration of visual motion and pursuit signals in areas V3A and V6+ across cortical depth using 9.4T fMRI
Authors: Molaei-Vaneghi Fatemeh , Zaretskaya Natalia , van Mourik Tim , Bause Jonas , Scheffler Klaus , Bartels Andreas
Published: December 2021

Neural mechanisms underlying a stable perception of the world during pursuit eye movements are not fully understood. Both, perceptual stability as well as perception of real (i.e. objective) motion are the product of integration between motion signals on the retina and efference copies of eye movements. Human areas V3A and V6 have previously been shown to have strong objective (‘real’) motion responses. Here we used high-resolution laminar fMRI at ultra-high magnetic field (9.4T) in human subjects to examine motion integration across cortical depths in these areas. We found an increased preference for objective motion in areas V3A and V6+ i.e. V6 and possibly V6A towards the upper layers. When laminar responses were detrended to remove the upper-layer bias present in all responses, we found a unique, condition-specific laminar profile in V6+, showing reduced mid-layer responses for retinal motion only. The results provide evidence for differential, motion-type dependent laminar processing in area V6+. Mechanistically, the mid-layer dip suggests a special contribution of retinal motion to integration, either in the form of a subtractive (inhibitory) mid-layer input, or in the form of feedback into extragranular or infragranular layers. The results show that differential laminar signals can be measured in high-level motion areas in the human occipitoparietal cortex, opening the prospect of new mechanistic insights using non-invasive brain imaging.

Significance Statement

Visual stability and our ability to differentiate between self-induced and real motion are central to our visual sense. Both require the integration of two signals – retinal motion and copies of muscle commands used for eye movements (efference copies). A reasonable assumption is that either the efference copy or the result of integration will be conveyed to high-level visual regions along with visual retinal input, possibly differentially across cortical depth as the input sources differ. Our ultra-high field recordings present the first laminar evidence of differential signal processing of retinal and objective motion signals in area V6+, and present a first window into a mechanistic understanding of visual high-level motion processing.
SARS-CoV-2 Omicron Spike Glycoprotein Receptor Binding Domain Exhibits Super-Binder Ability with ACE2 but not Convalescent Monoclonal Antibody
Authors: Omotuyi I. O. , Olubiyi O. , Nash O. , Afolabi E.O. , Oyinloye B.E. , Fatumo S. , Femi-Oyewo M. N. , Bogoro S.E.
Published: December 2021

Background

SARS-CoV-2, the causative virus for COVID-19 has now super-mutated into the Omicron (Om) variant. On its spike glycoprotein alone, more than 30 substitutions have been characterized with 15 within the receptor binding domain (RBD); It therefore calls to question the transmissibility and antibody escapability of Omicron. This study was setup to investigate the Omicron RBD’s interaction with ACE2 (host receptor) and a SARS-CoV-2 neutralizing monoclonal antibody (mAb).

Methods

In-silico mutagenesis was used to generate the Om-RBD in complex with ACE2 or mAb from the wildtype. All-atom molecular dynamics (MD) simulation trajectories were analyzed for interaction.

Results

MD trajectories showed that Omicron RBD has evolved into an efficient ACE2 binder, via pi-pi (Om-RBD-Y501/ACE2-Y41) and salt-bridge (Om-RBD-K493/ACE2-Y41) interactions. Conversely, in binding mAb, it has become less efficient (Center of mass distance of RBD from mAb complex, wildtype ≈ 30 Å, Omicron ≈ 41 Å). Disruption of Om-RBD/mAb complex resulted from loose interaction between Om-RBD and the light chain complementarity-determining region residues.

Conclusions

Omicron is expected to be better transmissible and less efficiently interacting with neutralizing convalescent mAbs.

General significance

Our results elucidate the mechanisms for higher transmissibility in Omicron variant.
Transcriptional response in a sepsis mouse model reflects transcriptional response in sepsis patients
Authors: Rosier Florian , Nuñez Nicolas Fernandez , Torres Magali , Loriod Béatrice , Rihet Pascal , Pradel Lydie C.
Published: December 2021

Mortality due to sepsis remains unacceptably high, especially for septic shock patients. Murine models have been used to better understand pathophysiology mechanisms. However, the mouse model is still under debate. Here we investigated the transcriptional response of mice injected with lipopolysaccharide (LPS) and compared it to either human cells stimulated in vitro with LPS or to blood cells of septic patients. We identified a molecular signature composed of 2331 genes with an FDR median of 0%. This molecular signature is highly enriched in regulated genes in peritoneal macrophages stimulated with LPS. There is a significant enrichment in several inflammatory signaling pathways, and in disease terms, such as pneumonia, sepsis, systemic inflammatory response syndrome, severe sepsis, an inflammatory disorder, immune suppression, and septic shock. A significant overlap between the genes up-regulated in mouse and human cells stimulated with LPS has been demonstrated. Finally, genes up-regulated in mouse cells stimulated with LPS are enriched in genes up-regulated in human cells stimulated in vitro and in septic patients, who are at high risk of death. Our results support the hypothesis of common molecular and cellular mechanisms between mouse and human sepsis.
Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma
Authors: Peña-Pérez Lucía , Frengen Nicolai , Hauenstein Julia , Gran Charlotte , Gustafsson Charlotte , Eisfeldt Jesper , Kierczak Marcin , Taborsak-Lines Fanny , Olsen Remi-André , Wallblom Ann , Krstic Aleksandra , Ewels Philip , Lindstrand Anna , Månsson Robert
Published: December 2021

Multiple myeloma (MM) is an incurable and aggressive plasma cell malignancy characterized by a complex karyotype with multiple structural variants (SVs) and copy number variations (CNVs). Linked-read whole-genome sequencing (lrWGS) allows for refined detection and reconstruction of SVs by providing long-range genetic information from standard short-read sequencing. This makes lrWGS an attractive solution for capturing the full genomic complexity of MM. Here we show that high-quality lrWGS data can be generated from low numbers of FACS sorted cells without DNA purification. Using this protocol, we analyzed FACS sorted MM cells from 37 MM patients with lrWGS. We found high concordance between lrWGS and FISH for the detection of recurrent translocations and CNVs. Outside of the regions investigated by FISH, we identified >150 additional SVs and CNVs across the cohort. Analysis of the lrWGS data allowed for resolving the structure of diverse SVs affecting the MYC and t(11;14) loci causing the duplication of genes and gene regulatory elements. In addition, we identified private SVs causing the dysregulation of genes recurrently involved in translocations with the IGH locus and show that these can alter the molecular classification of the MM. Overall, we conclude that lrWGS allows for the detection of aberrations critical for MM prognostics and provides a feasible route for providing comprehensive genetics. Implementing lrWGS could provide more accurate clinical prognostics, facilitate genomic medicine initiatives, and greatly improve the stratification of patients included in clinical trials.

KEY POINTS

- Linked-read WGS can be performed without DNA purification and allows for resolving the diverse structural variants found in multiple myeloma.

- Linked-read WGS can, as a stand-alone assay, provide comprehensive genetics in myeloma and other diseases with complex genomes.
Neurexins in serotonergic neurons regulate serotonin transmission and complex mouse behaviors
Authors: Cheung Amy , Konno Kohtarou , Kawasawa Yuka Imamura , Matsui Aya , Abe Manabu , Sakimura Kenji , Sasaoka Toshikuni , Uemura Takeshi , Watanabe Masahiko , Futai Kensuke
Published: December 2021

Extensive serotonin (5-HT) innervation throughout the brain corroborates 5-HT’s modulatory role in numerous cognitive activities. Volume transmission is the major mode for 5-HT transmission but mechanisms underlying 5-HT signaling are still largely unknown. Abnormal brain 5-HT levels and function have been implicated in autism spectrum disorder (ASD). Neurexin (Nrxn) genes encode presynaptic cell adhesion molecules important for the regulation of synaptic neurotransmitter release, notably glutamatergic and GABAergic transmission. Mutations in Nrxn genes are associated with neurodevelopmental disorders including ASD. However, the role of Nrxn genes in the 5-HT system is poorly understood. Here, we generated a mouse model with all three Nrxn genes disrupted specifically in 5-HT neurons to study how Nrxns affect 5-HT transmission. Loss of Nrxns in5-HT neurons reduced the number of serotonin neurons in the early postnatal stage, impaired 5-HT release, anddecreased 5-HT release sitesand serotonin transporter expression. Furthermore, 5-HT neuron-specific Nrxn knockout reduced sociability and increased depressive-like behavior. Our results highlight functional roles for Nrxns in 5-HT neurotransmission,5-HT neuron survival, and the execution of complex behaviors.
Seeing the future: predictive control in neural models of ocular accommodation
Authors: Read Jenny C. A. , Kaspiris-Rousellis Christos , Wood Toby , Wu Bing , Vlaskamp Björn N. S. , Schor Clifton M.
Published: December 2021

Ocular accommodation is the process of adjusting the eye's crystalline lens so as to bring the retinal image into sharp focus. The major stimulus to accommodation is therefore retinal defocus, and in essence, the job of accommodative control is to send a signal to the ciliary muscle which will minimise the magnitude of defocus. In this paper, we first provide a tutorial introduction to control theory to aid vision scientists without this background. We then present a unified model of accommodative control that explains properties of the accommodative response for a wide range of accommodative stimuli. Following previous work, we conclude that most aspects of accommodation are well explained by dual integral control, with a "fast" or "phasic" integrator enabling response to rapid changes in demand, which hands over control to a "slow" or "tonic" integrator which maintains the response to steady demand. Control is complicated by the sensorimotor latencies within the system, which delay both information about defocus and the accommodation changes made in response, and by the sluggish response of the motor plant. These can be overcome by incorporating a Smith predictor, whereby the system predicts the delayed sensory consequences of its own motor actions. For the first time, we show that critically-damped dual integral control with a Smith predictor accounts for adaptation effects as well as for the gain and phase for sinusoidal oscillations in demand. In addition, we propose a novel proportional-control signal to account for the power spectrum of accommodative microfluctuations during steady fixation, which may be important in hunting for optimal focus, and for the nonlinear resonance observed for low-amplitude, high-frequency input. Complete Matlab/Simulink code implementing the model is provided at https://doi.org/10.25405/data.ncl.14945550
Iron treatment induces defense responses and disease resistance against Magnaporthe oryzae in rice
Authors: Sánchez-Sanuy Ferran , Cuadra Roberto Mateluna , Okada Kazunori , Sacchi Gian Attilio , Campo Sonia , Segundo Blanca San
Published: December 2021

Background

Iron is an essential micronutrient required for plant growth and development. The impact of iron in plant-pathogen interactions is also well recognized. However, the molecular basis underlying the effect of plant iron status and immune function in plants is poorly understood. Here, we investigated the impact of treatment with high iron in rice immunity at the cellular and molecular level.

Results

We show that treatment with high iron confers resistance to infection by the blast fungus M. oryzae in rice. Histochemical staining of M. oryzae-infected leaves revealed that iron and Reactive Oxygen Species (ROS) accumulate at high levels in cells in the vicinity of the infection site. During pathogen infection, a stronger induction of defense-related genes occurs in leaves of iron-treated plants. Notably, a superinduction of phytoalexin biosynthetic genes, both diterpene phytoalexins and sakuranetin, is observed in iron-treated plants during pathogen infection. As a consequence, phytoalexin accumulation was higher in iron-treated plants compared with control plants. Transcriptional alterations of iron homeostasis-related genes and a reduction in apoplastic iron content were observed in leaves of Fe-treated rice plants.

Conclusions

These results illustrate that the iron status plays a key role in the response of rice plants to pathogen infection, while reinforcing the notion that iron signaling and defense signaling must operate in a coordinated manner in controlling disease resistance in plants. This information provides a basis to better understand the molecular mechanisms involved in rice immunity.
Drosulfakinin signaling modulates female sexual receptivity in Drosophila
Authors: Wang Tao , Jing Biyang , Deng Bowen , Shi Kai , Li Jing , Ma Baoxu , Wu Fengming , Zhou Chuan
Published: December 2021

Female sexual behavior as an innate behavior is of prominent biological importance for survival and reproduction. However, molecular and circuit mechanisms underlying female sexual behavior is not well understood. Here, we identify the Cholecystokinin-like peptide Drosulfakinin (DSK) promotes female sexual behavior in Drosophila. Manipulation both Dsk and DSK neuronal activity impact female sexual receptivity. In addition, we reveal that Dsk-expressing neurons receive input signal from R71G01GAL4 neurons to promote female sexual receptivity. Based on intersectional technique, we further found the regulation of female sexual behavior relies mainly on medial DSK neurons rather than lateral DSK neurons, and medial DSK neurons modulate female sexual behavior by acting on its receptor CCKLR-17D3. Thus, we characterized DSK/CCKLR-17D3 as R71G01GAL4 neurons downstream signaling to regulate female sexual behavior.
Phosphate-induced resistance to pathogen infection in Arabidopsis
Authors: Val-Torregrosa Beatriz , Bundó Mireia , Martín-Cardoso Héctor , Bach-Pages Marcel , Chiou Tzyy-Jen , Flors Victor , San Segundo Blanca
Published: December 2021

In nature, plants are concurrently exposed to a number of abiotic and biotic stresses. Our understanding of convergence points between responses to combined biotic/abiotic stress pathways remains, however, rudimentary. Here we show that MIR399 overexpression, loss-of-function of PHO2 (PHOSPHATE2), or treatment with high Pi, is accompanied by an increase in phosphate (Pi) content and accumulation of reactive oxygen species (ROS) in Arabidopsis thaliana. High Pi plants (e.g. miR399 overexpressor, pho2 mutant, and plants grown under high Pi supply) exhibited resistance to infection by necrotrophic and hemibiotrophic fungal pathogens. In the absence of pathogen infection, the expression level of genes in the salicylic acid (SA)- and jasmonic acid (JA)-dependent signaling pathways was higher in high Pi plants compared to wild type plants, which is consistent with increased levels of SA and JA in non-infected high Pi plants. During infection, an opposite regulation in the two branches of the JA pathway (ERF1/PDF1.2 and MYC2/VSP2) occurs in high Pi plants. Thus, while the ERF1-PDF1 branch positively responds to fungal infection, the MYC2/VSP2 branch is negatively regulated during pathogen infection in high Pi plants. This study supports that Pi accumulation promotes resistance to infection by fungal pathogens in Arabidopsis, while providing a basis to better understand crosstalk between Pi signaling and hormonal signalling pathways for modulation of plant immune responses.

Significance statement

This study highlights the importance of phosphate (Pi) in regulating immune responses, hence, disease resistance in Arabidopsis thaliana. Increasing Pi content either by MIR399 overexpression (or loss-of-function of PHOSPHATE2), as well as by Pi treatment enhances resistance to infection by necrotrophic and hemibiotrophic fungal pathogens through modulation of SA- and JA-dependent signaling pathways. These results also support that miR399 functions as a regulator of Arabidopsis immunity.
Stereotyped Behavioral Maturation and Rhythmic Quiescence in C. elegans Embryos
Authors: Ardiel Evan L. , Xu Stephen , Nurrish Stephen , Lauziere Andrew , Harvey Brandon J. , Kaplan Joshua M. , Shroff Hari
Published: December 2021

Abstract

Systematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here we apply this approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were built using a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom tracking software. Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping nor the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in diverse animals and may play an important role in promoting normal developmental outcomes.
Glucose dynamics during ozone exposure measured using radiotelemetry: Stress drivers
Authors: Henriquez Andres R. , Snow Samantha J. , Jackson Thomas W. , House John S. , Motsinger-Reif Alison A. , Ward-Caviness Cavin K. , Schladweiler Mette C. , Alewel Devin I. , Miller Colette N. , Farraj Aimen K. , Hazari Mehdi S , Grindstaff Rachel , Diaz-Sanchez David , Ghio Andrew J , Kodavanti Urmila P.
Published: December 2021

Background

Stress-related neurobehavioral and metabolic disorders are associated with altered circulating adrenal-derived hormones and hyperglycemia. Temporal assessment of glucose and these hormones is critical for insights on an individual’s health.

Objectives

Here we used implantable-telemetry in rats to assess real-time changes in circulating glucose during and after exposure to the air pollutant ozone, and link responses to circulating neuroendocrine stress and metabolic hormones. We also compared rodent glucose and corticosterone (cortisol in humans) responses to humans exposed to ozone.

Methods

First, using a cross-over design, we monitored glucose levels during single or repeated ozone exposures (0.0, 0.2, 0.4 and 0.8-ppm) and non-exposure periods in male Wistar-Kyoto-rats implanted with glucose-telemeters. A second cohort of un-implanted rats was exposed to ozone (0.0, 0.4 or 0.8-ppm) for 30-min, 1-hour, 2-hour, or 4-hour with hormones measured immediately after exposure. Then we assessed glucose metabolism in sham and adrenalectomized rats with or without pharmacological interventions of adrenergic and glucocorticoid receptors. Finally, we assessed glucose and cortisol in serum samples from a clinical study involving exposure of human volunteers to air or 0.3 ppm ozone.

Results

Ozone (0.8-ppm) caused hyperglycemia and hypothermia beginning 90-min into exposure, with reversal of effects 4-6 hours post-exposure. Glucose monitoring during four daily 4-hour ozone exposures revealed duration of hyperglycemia, adaptation, and diurnal variations. Ozone-induced hyperglycemia was preceded by increased adrenocorticotropic hormone, corticosterone, and epinephrine, but depletion of thyroid-stimulating, prolactin, and luteinizing hormones. Hyperglycemia was inhibited in rats that were adrenalectomized and/or treated with glucocorticoid inhibitor. The depletion of cortisol was dampened in humans exposed to ozone during intermittent exercise.

Discussion

We demonstrate for the first time the temporality of neuroendocrine-stress-mediated biological sequalae responsible for ozone-induced metabolic dysfunction as exposure occurs. Real-time glucose monitoring with stress hormones assessment may be useful in identifying interactions among pollutants and stress-related illnesses.
The SPEECHLESS-induced stomatal increase is required for the salt tolerance of oil palm
Authors: Song Zhuojun , Wang Le , Lai Chong Cheong , Yang Zituo , Lee May , Yue Gen Hua
Published: December 2021

Oil palm is the most productive oil producing plant. Salt stress leads to growth damage and decrease in yield of oil palm. However, the physiological responses of oil palm to salt stress and their underlying mechanisms are not clear. RNA-Seq for leaf samples from young palms challenged under three levels of salts (100, 250 and 500 mM NaCl) and control for 14 days was conducted. Diverse signalling pathways were involved in responses to different levels of salt stress. All the three levels of salt stress activated EgSPCH expression and induced stomatal density of oil palm, which was contrasting to that in Arabidopsis. Under strong salt stress group, oil palm removed excessive salt via stomata. Overexpression of EgSPCH in Arabidopsis increased the stomatal production but lowered the salt tolerance. These data suggest that in oil palm, salt activates EgSPCH to generate more stomata in response to salt stress. Our results shed a light on the cellular response to salt stress of oil palm and provide new insights into the mechanisms of different salt-induced stomatal development between halophytes and glycophytes.
Skopi: a simulation package for diffractive imaging of noncrystalline biomolecules
Authors: Peck Ariana , Chang Hsing-Yin , Dujardin Antoine , Ramalingam Deeban , Uervirojnangkoorn Monarin , Wang Zhaoyou , Mancuso Adrian , Poitevin Frédéric , Yoon Chun Hong
Published: December 2021

X-ray free electron lasers (XFEL) have the ability to produce ultra-bright femtosecond X-ray pulses for coherent diffraction imaging of biomolecules. While the development of methods and algorithms for macromolecular crystallography is now mature, XFEL experiments involving aerosolized or solvated biomolecular samples offer new challenges both in terms of experimental design and data processing. Skopi is a simulation package that can generate single-hit diffraction images for reconstruction algorithms, multi-hit diffraction images of aggregated particles for training machine learning classification tasks using labeled data, diffraction images of randomly distributed particles for fluctuation X-ray scattering (FXS) algorithms, and diffraction images of reference and target particles for holographic reconstruction algorithms. We envision skopi as a resource to aid the development of on-the-fly feedback during non-crystalline experiments at XFEL facilities, which will provide critical insights into biomolecular structure and function.
Fast in-vitro screening of FLT3-ITD inhibitors using silkworm-baculovirus protein expression system
Authors: Yamamoto Naoki , Kikuchi Jiro , Furukawa Yusuke , Shibayama Naoya
Published: December 2021

We report expression and purification of a FLT3 protein with ITD mutation (FLT3-ITD) with a steady tyrosine kinase activity using a silkworm-baculovirus system, and its application as a fast screening system of tyrosine kinase inhibitors. The FLT3-ITD protein was expressed in Bombyx mori L. pupae infected by gene-modified nucleopolyhedrovirus, and was purified as an active state. We performed an inhibition assay using 17 potential kinase inhibitors, and succeeded in identifying two potent inhibitors for FLT3-ITD. The result has paved the way for screening FLT3-ITD inhibitors in a fast and easy manner, and also for structural studies.
Whole genome resequencing and comparative genome analysis of threePuccinia striiformisf. sp.triticipathotypes prevalent in India
Authors: Yadav Inderjit Singh , Bhardwaj S. C. , Kaur Jaspal , Singla Deepak , Kaur Satinder , Kaur Harmandeep , Rawat Nidhi , Tiwari Vijay Kumar , Saunders Diane , Uauy Cristobal , Chhuneja Parveen
Published: December 2021

Stripe rust disease of wheat, caused byPuccinia striiformisf. sp.tritici,(Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome sequencing of three prevalent IndianPstpathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively. Pathotypes were found to be highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene family expansion was also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known US, European, African and Asian races. Diagnostic markers developed for the identification of different Pst pathotypes will help tracking of yellow rust at farmers’ field and strategizing resistance gene deployment.
Visual Interpretation of the Meaning of kcat/KM in Enzyme Kinetics
Authors: Park Chiwook
Published: December 2021

kcat and kcat/KM are the two fundamental kinetic parameters in enzyme kinetics. kcat is the first-order rate constant that determines the reaction rate when the enzyme is fully occupied at a saturating concentration of the substrate. kcat/KM is the second-order rate constant that determines the reaction rate when the enzyme is mostly free at a very low concentration of the substrate. Both parameters provide critical information on how the enzyme lowers the energy barriers along the reaction pathway for catalysis. However, it is surprising how often kcat/KM is used inappropriately as a composite parameter derived by dividing kcat with KM to assess both catalytic power and affinity to the substrate of the enzyme. The main challenge in explaining the true meaning of kcat/KM is the difficulty to demonstrate how the reaction energetics of enzyme catalysis determines kcat/KM in a simple way. Here, I report a step-by-step demonstration on how to visualize the meaning of kcat/KM on the reaction energy diagram. By using the reciprocal form of the expression of kcat/KM with the elementary rate constants in kinetic models, I show that kcat/KM is a harmonic sum of several kinetic terms that correspond to the heights of the transition states relative to the free enzyme. Then, I demonstrate that the height of the highest transition state has the dominant influence on kcat/KM, i. e. the step with the highest transition state is the limiting step for kcat/KM. The visualization of the meaning of kcat/KM on the reaction energy diagram offers an intuitive way to understand all the known properties of kcat/KM, including the Haldane relationship.
Engineering efficient termination of bacteriophage T7 RNA polymerase transcription
Authors: Calvopina-Chavez Diana G. , Gardner Mikaela A. , Griffitts Joel S.
Published: December 2021

The bacteriophage T7 expression system is one of the most prominent transcription systems used in biotechnology and molecular-level research. However, T7 RNA polymerase is prone to read-through transcription due to its high processivity. As a consequence, enforcing efficient transcriptional termination is difficult. The termination hairpin found natively in the T7 genome is adapted to be inefficient, exhibiting 62% termination efficiency in vivo and even lower efficiency in vitro. In this study, we engineered a series of sequences that outperform the efficiency of the native terminator hairpin. By embedding a previously discovered 8-nucleotide T7 polymerase pause sequence within a synthetic hairpin sequence, we observed in vivo termination efficiency of 91%; by joining two short sequences into a tandem 2-hairpin structure, termination efficiency was increased to 98% in vivo and 91% in vitro. This study also tests the ability of these engineered sequences to terminate transcription of theEscherichia coliRNA polymerase. Two out of three of the most successful T7 polymerase terminators also facilitated termination of the bacterial polymerase with around 99% efficiency.
The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence
Authors: Wilbert Steven A. , Newman Dianne K.
Published: December 2021

Microbial assemblages are omnipresent in the biosphere, forming communities on the surfaces of roots, rocks, and within living tissues. These communities can exhibit strikingly beautiful compositional structures, with certain members reproducibly occupying particular spatiotemporal microniches. Despite this reproducibility, we lack the ability to explain these spatial patterns. We hypothesize that certain spatial patterns in microbial communities may be explained by the exchange of redox-active metabolites whose biological function is sensitive to microenvironmental gradients. To test this, we developed a simple community consisting of synthetic Pseudomonas aeruginosa strains with a partitioned denitrification pathway: a strict consumer and strict producer of nitric oxide (NO), a key pathway intermediate. Because NO can be both toxic or beneficial depending on the amount of oxygen present, this system provided an opportunity to investigate whether dynamic oxygen gradients can tune metabolic cross-feeding and fitness outcomes in a predictable fashion. Using a combination of genetic analysis, controlled growth environments and imaging, we show that oxygen availability dictates whether NO cross-feeding is deleterious or mutually beneficial, and that this organizing principal maps to the microscale. More generally, this work underscores the importance of considering the contrasting and microenvironmentally tuned roles redox-active metabolites can play in shaping microbial communities.
Rec8 cohesin-mediated axis-loop chromatin architecture is required for meiotic recombination
Authors: Sakuno Takeshi , Tashiro Sanki , Tanizawa Hideki , Iwasaki Osamu , Ding Da-Qiao , Haraguchi Tokuko , Noma Ken-ichi , Hiraoka Yasushi
Published: December 2021

During meiotic prophase, cohesin-dependent axial structures are formed in the synaptonemal complex (SC). However, the functional correlation between these structures and cohesion remains elusive. Here, we examined the formation of cohesin-dependent axial structures in the fission yeastSchizosaccharomyces pombe. This organism forms atypical SCs composed of linear elements (LinEs) resembling the lateral elements of SC but lacking the transverse filaments. Hi-C analysis using a highly synchronous population of meioticS. pombecells revealed that the axis-loop chromatin structure formed in meiotic prophase was dependent on the Rec8 cohesin complex. In contrast, the Rec8-mediated formation of the axis-loop structure occurred in cells lacking components of LinEs. To dissect the functions of Rec8, we identified arec8-F204Smutant that lost the ability to assemble the axis-loop structure without losing cohesion of sister chromatids. This mutant showed defects in the formation of the axis-loop structure and LinE assembly and thus exhibited reduced meiotic recombination. Collectively, our results demonstrate that the Rec8-dependent axis-loop structure provides a structural platform essential for LinE assembly, facilitating meiotic recombination of homologous chromosomes, independently of its role in sister chromatid cohesion.
Expressional Diversity and Cancer-prone Phenotypes in Cigarette-smoking Lungs at Single Cell Resolution
Authors: Nakayama Jun , Yamamoto Yusuke
Published: December 2021

Single-cell RNA-seq (scRNA-seq) technologies have been broadly utilized to reveal molecular mechanisms of respiratory pathology and physiology at single-cell resolution. Here, we established single-cell meta-analysis (scMeta-analysis) by integrating data from 8 public datasets, including 104 lung scRNA-seq samples with clinicopathological information and designated a cigarette smoking lung atlas. The atlas revealed early carcinogenesis events and defined the alterations of single-cell transcriptomics, cell population, and fundamental properties of biological pathways induced by smoking. In addition, we developed two novel scMeta-analysis methods: VARIED (Visualized Algorithms of Relationships In Expressional Diversity) and AGED (Aging-related Gene Expressional Differences). VARIED analysis revealed expressional diversity associated with smoking carcinogenesis. AGED analysis revealed differences in gene expression related to both aging and smoking states. The scMeta-analysis pave the way to utilize publicly -available scRNA-seq data and provide new insights into the effects of smoking and into cellular diversity in human lungs, at single-cell resolution.