bluuebunny/crossref_metadata_2025 huggingface dataset:
Precision Breast Cancer Screening with a Polygenic Risk Score
Authors: Tasa Tõnis , Puustusmaa Mikk , Tõnisson Neeme , Kolk Berit , Padrik Peeter
Published: August 2020

Breast cancer (BC) is the leading cause of cancer deaths in women in the world. Genome-wide association studies have identified numerous genetic variants (SNPs) independently associated with BC. The effects of such SNPs can be combined into a single polygenic risk score (PRS). Stratification of women according to PRS could be introduced to primary and secondary prevention. Our aim was to revalidate a PRS model and to develop a pipeline for individualizing breast cancer screening.

Previously published PRS models for predicting the risk of breast cancer were collected from the literature. Models were validated on the Estonian Biobank (EGC) dataset consisting of 32,548 quality-controlled genotypes with 315 prevalent and 365 incident BC cases and on 249,062 samples in the UK Biobank dataset consisting of 8637 prevalent and 6825 incident cases. The best performing model was selected based on the AUC in prevalent data and independently validated in both incident datasets. Using Estonian BC background information, we performed absolute risk simulations and developed individual risk-based recommendations for prevention.

The best-performing PRS included 2803 SNPs. The C-index of the Cox regression model associating BC status with PRS was 0.656 (SE = 0.05) with a hazard ratio of 1.66 (95% confidence interval 1.5 - 1.84) on the incident EGC dataset. The PRS is able to stratify individuals with more than a 3-fold risk increase. The observed 10-year risks of individuals in the 99th percentile exceeded the 1st percentile more than 10-fold.

PRS is a powerful predictor of breast cancer risk. Currently, PRS scores are not implemented in routine BC screening. We have developed PRS-based recommendations for personalized primary and secondary prevention and our approach is easily adaptable to other nationalities by using population-specific background data of other genetically similar populations.
The necessary cooperation between governments and public in the fight against COVID-19: why non-pharmaceutical interventions may be ineffective
Authors: Borges Christielly Mendonça , Coelho Marco Túlio Pacheco , Diniz-Filho José Alexandre Felizola , Rangel Thiago Fernando
Published: August 2020

The coronavirus disease (COVID-19) outbreak is the biggest public health challenge in the last 100 years. No successful pharmaceutical treatment is yet available, thus effective public health interventions to contain COVID-19 include social distancing, isolation and quarantine measures, however the efficiency of these containment measures varied among countries and even within states in the same country. Despite Brazil being deeply affected by coronavirus, the federal government never proposed a coordinated action to control COVID-19 and Brazilian states, which are autonomous, each imposed different containment measures. The state of Goiás declared strict social distancing measures in March 13, but gradually relaxed many of its first measures due specially to public pressure. Here we use a Susceptible-Infected-Recovered (SIR) model combined with Bayesian inference and a time-dependent spreading rate to assess how past state-level interventions affected the spread of COVID-19 in Goiás. The interventions succeeded in decreasing the transmission rate in the state, however, after the third intervention the rate remained positive and exponential. Thus, other stricter interventions were made necessary to avoid the growth of new cases and a collapse in the health system. Governmental interventions need to be taken seriously by the population in order for them have the proposed outcome. Our results reflect the population’s disregard with the measures imposed and the need for cooperation between governments and its citizens in the fight against COVID-19.
Suboptimal SARS-CoV-2-specific CD8+ T-cell response associated with the prominent HLA-A*02:01 phenotype
Authors: Habel Jennifer R , Nguyen Thi H O , van de Sandt Carolien E , Juno Jennifer A , Chaurasia Priyanka , Wragg Kathleen , Koutsakos Marios , Hensen Luca , Jia Xiaoxiao , Chua Brendon , Zhang Wuji , Tan Hyon-Xhi , Flanagan Katie L , Doolan Denise L , Torresi Joseph , Chen Weisan , Wakim Linda M , Cheng Allen C , Doherty Peter C , Petersen Jan , Rossjohn Jamie , Wheatley Adam K , Kent Stephen J , Rowntree Louise C , Kedzierska Katherine
Published: August 2020

An improved understanding of human T-cell-mediated immunity in COVID-19 is important if we are to optimize therapeutic and vaccine strategies. Experience with influenza shows that infection primes CD8+ T-cell memory to shared peptides presented by common HLA types like HLA-A2. Following re-infection, cross-reactive CD8+ T-cells enhance recovery and diminish clinical severity. Stimulating peripheral blood mononuclear cells from COVID-19 convalescent patients with overlapping peptides from SARS-CoV-2 Spike, Nucleocapsid and Membrane proteins led to the clonal expansion of SARS-CoV-2-specific CD8+ and CD4+ T-cells in vitro, with CD4+ sets being typically robust. For CD8+ T-cells taken directly ex vivo, we identified two HLA-A*02:01-restricted SARS-CoV-2 epitopes, A2/S269–277 and A2/Orf1ab3183–3191. Using peptide-HLA tetramer enrichment, direct ex vivo assessment of the A2/S269+CD8+ and A2/Orf1ab3183+CD8+ populations indicated that the more prominent A2/S269+CD8+ set was detected at comparable frequency (∼1.3×10−5) in acute and convalescent HLA-A*02:01+ patients. But, while the numbers were higher than those found in uninfected HLA-A*02:01+ donors (∼2.5×10−6), they were low when compared with frequencies for influenza-specific (A2/M158) and EBV-specific (A2/BMLF1280) (∼1.38×10−4) populations. Phenotypic analysis ex vivo of A2/S269+CD8+ T-cells from COVID-19 convalescents showed that A2/S269+CD8+ T-cells were predominantly negative for the CD38, HLA-DR, PD-1 and CD71 activation markers, although the majority of total CD8+ T-cells were granzyme and/or perforin-positive. Furthermore, the bias towards naïve, stem cell memory and central memory A2/S269+CD8+ T-cells rather than effector memory populations suggests that SARS-CoV2 infection may be compromising CD8+ T-cell activation. Priming with an appropriate vaccine may thus have great value for optimizing protective CD8+ T-cell immunity in COVID-19.
A Lymph Node Targeted Amphiphile Vaccine Induces Potent Cellular and Humoral Immunity to SARS-CoV-2
Authors: Steinbuck Martin P. , Seenappa Lochana M. , Jakubowski Aniela , McNeil Lisa K. , Haqq Christopher M. , DeMuth Peter C.
Published: August 2020

The SARS-CoV-2 pandemic has led to public health, economic, and social consequences that mandate urgent development of effective vaccines to contain or eradicate infection. To that end, we evaluated a novel amphiphile (AMP) vaccine adjuvant, AMP-CpG, composed of diacyl lipid-modified CpG, admixed with the SARS-CoV-2 Spike-2 receptor binding domain protein as a candidate vaccine (ELI-005) in mice. AMP immunogens are efficiently delivered to lymph nodes, where innate and adaptive immune responses are generated. Compared to alum, AMP immunization induced >25-fold higher antigen-specific T cells which produced multiple Th1 cytokines and trafficked into lung parenchyma and respiratory secretions. Antibody responses favored Th1 isotypes (IgG2bc, IgG3) and potently neutralized Spike-2-ACE2 receptor binding, with titers 265-fold higher than the natural immune response from convalescent COVID-19 patients; responses were maintained despite 10-fold dose-reduction in Spike antigen. Both cellular and humoral immune responses were preserved in aged mice. These advantages merit clinical translation to SARS-CoV-2 and other protein subunit vaccines.
Short duration splice promoting compound enables a tunable mouse model of spinal muscular atrophy
Authors: Rietz A , Hodgetts KJ , Lusic H , Quist KM , Osman EY , Lorson CL , Androphy EJ
Published: August 2020

Spinal muscular atrophy (SMA) is a motor neuron disease and the leading cause of infant mortality. SMA results from insufficient survival motor neuron protein (SMN) levels due to alternative splicing. Antisense oligonucleotides, gene therapy and splicing modifiers recently received FDA approval. However, early intervention is required for optimal outcomes, and even continuous treatment maybe insufficient to restore full motor function. Although severe SMA transgenic mouse models have been beneficial for testing therapeutic efficacy, models mimicking milder cases that manifest post-infancy have proven challenging to develop. We have established a titratable model of mild and moderate SMA using the splicing compound NVS-SM2. Administration for 30 days prevented development of the SMA phenotype in severe SMA mice, which typically show rapid weakness and succumb by postnatal day 11. Furthermore, administration at day eight resulted in phenotypic recovery. Remarkably, acute dosing limited to the first three days of life significantly enhanced survival in two severe SMA mice models, easing the burden on neonates and demonstrating the compound as suitable for evaluation of follow-on therapies without potential drug-drug interactions.
Potent neutralizing equine antibodies raised against recombinant SARS-CoV-2 spike protein for COVID-19 passive immunization therapy
Authors: Cunha Luis Eduardo R. , Stolet Adilson A. , Strauch Marcelo A. , Pereira Victor A. R. , Dumard Carlos H. , Gomes Andre M. O. , Souza Patrícia N. C. , Fonseca Juliana G. , Pontes Francisco E. , Meirelles Leonardo G. R. , Albuquerque José W. M. , Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Lima Tulio M. , Alvim Renata G. F. , Marsili Federico F. , Caldeira Marcella Moreira , Higa Luisa M. , Monteiro Fábio L. , Zingali Russolina B. , de Oliveira Guilherme A. P. , Souza Thiago M. L. , Tanuri Amilcar , Oliveira Andréa C. , Guedes Herbert L. M. , Castilho Leda R. , Silva Jerson L.
Published: August 2020

We used the trimeric spike (S) glycoprotein (residues 1-1208) in the prefusion conformation to immunize horses for production of hyperimmune globulins against SARS-CoV-2. Serum antibody titers measured by anti-spike ELISA were above 1:1,000,000, and neutralizing antibody titer was 1:14,604 (average PRNT90), which is 140-fold higher than the average neutralizing titer of plasma from three convalescent COVID-19 patients analyzed for comparison. Using the same technology routinely used for industrial production of other horse hyperimmune products, plasma from immunized animals was pepsin digested to remove the Fc portion and purified, yielding a F(ab’)2preparation with PRNT90titers 150-fold higher than the neutralizing titers in human convalescent plasma. Repeating the hyperimmunization in a second group of horses confirmed the very high neutralizing titers in serum and in a GMP clinical F(ab’)2lot. Virus-neutralizing activity in samples from mice that received the F(ab’)2preparation was detected even three days after injection, indicating an appropriate half-life for therapeutic intervention. These results supported the design of a clinical trial (identifierNCT04573855) to evaluate safety and efficacy of this horse F(ab’)2preparation.
Distinct roles of two RDL GABA-receptors in fipronil action in the diamondback moth (Plutella xylostella)
Authors: Li Benjie , Wang Kunkun , Chen Dongping , Yan Ying , Cai Xuling , Chen Huimin , Dong Ke , Lin Fei , Xu Hanhong
Published: August 2020

The phenylpyrazole insecticide, fipronil, blocks insect RDL γ-aminobutyric acid (GABA) receptors, thereby impairs inhibitory neurotransmission. Some insect species, such as the diamondback moth (Plutella xylostella), possess more than oneRdlgene. The involvement of multipleRdlsin fipronil toxicity and resistance remain largely unknown. In this study, we investigated the roles of twoRdlgenes,PxRdl1andPxRdl2, fromP. xylostellain the action of fipronil. Expressed inXenopusoocytes,PxRDL2 receptors were 40-times less sensitive to fipronil thanPxRDL1.PxRDL2 receptors were also less sensitive to GABA compared toPxRDL1. Knockout of the fipronil-sensitivePxRdl1gene reduced the potency of fipronil by 10 fold, whereas knockout of the fipronil-resistantPxRdl2gene enhanced the potency of fipronil by 4.4 fold. Furthermore, in two fipronil-resistant diamondback moth field populations, the expression ofPxRdl2was elevated by 3.7-fold and 4.1-fold, respectively compared to a susceptible strain, whereas the expression ofPxRdl1was comparable among the resistant and susceptible strains. Collectively, our results indicate antagonistic effects ofPxRDL1 andPxRDL2 on the fipronil actionin vivoand suggest enhanced expression of fipronil-resistantPxRdl2 potentially a new mechanism of fipronil resistance in insects.
A Newly Identified Role for IL-22 in Bladder Immunity
Authors: Honeycutt Jared , Le Loc , Hsieh Yi-Ju , Hsieh Michael H.
Published: August 2020

Bacterial and parasitic urinary tract infections(UTI) affect many, but our understanding of associated immunity remains poor. Prior work indicates interleukin-22(IL-22) is a key cytokine during infection of other epithelia. We hypothesized IL-22 is crucial during UTI.

IL-22-null(KO) and wild-type(wt) mice underwent bladder wall injection withS. haematobiumeggs or transurethral infection with uropathogenicE. coliUTI89.

IL-22 and its soluble binding protein, IL-22BP, were increased in the bladder afterS. haematobiumegg injection. Genes typically induced by IL-22(CXCL2, REG3G[antimicrobial defense protein]], S100A8, S100A9, and Areg) were expressed at higher levels followingS. haematobiumegg injection. IL-22 stimulation of bladder tissue induced REG3B expression. IL-22 receptor alpha-1 expression was detectable in the urothelium by immunofluorescence and qPCR.

Injection ofS. haematobiumeggs into IL-22-KO vs wt mice triggered differential expression of genes related to transferase activity(transferring alkyl or aryl groups) and epithelial cell development. Numerous uroplakin genes were downregulated in egg-injected, IL-22-KO mice versus their wt counterparts. These decreases in uroplakin expression suggest that, as in the gut, IL-22 is important for replenishing the epithelium during infection-related injury.

Following transurethral infection with UTI89, IL-22-KO mice had lower bacterial counts in their urine, bladder, and kidneys. Giving stabilized IL-22 cytokine (IL-22-Fc) to UTI89-infected mice led to higher kidney bacterial counts and increased morbidity.

Our data suggest that IL-22 is indeed important in urinary tract immunity, and may interfere with clearance of bacteria from the urinary tract, potentially through its role in maintenance of mature urothelium.
GATA4 regulates epithelial morphogenesis in the developing mouse stomach to promote establishment of a glandular columnar epithelium
Authors: DeLaForest Ann , Kohlnhofer Bridget M. , Franklin Olivia D. , Stavniichuk Roman , Thompson Cayla A. , Pulakanti Kirthi , Rao Sridhar , Battle Michele A.
Published: August 2020

The transcription factor GATA4 is broadly expressed in nascent foregut endoderm. As development progresses, GATA4 is lost in the domain giving rise to the stratified squamous epithelium of the esophagus and forestomach (FS), while it is maintained in the domain giving rise to the simple columnar epithelium of the hindstomach (HS). Differential GATA4 expression within these domains coincides with the onset of distinct tissue morphogenetic events, suggesting a role for GATA4 in diversifying foregut endoderm into discrete esophageal/FS and HS tissues. By eliminating GATA4 in the developing HS or maintaining GATA4 in the developing FS, we identified GATA4 as an essential, principal regulator of simple columnar epithelium morphogenesis within the developing HS. GATA4- deficient HS epithelium adopted FS-like fate, and conversely, GATA4- expressing FS epithelium adopted HS-like fate. Underlying structural changes in these epithelia were broad changes in gene expression networks attributable to GATA4 directly activating or repressing expression of HS or FS defining transcripts. Our data implicate GATA4 as having a primary role in suppressing an esophageal/FS transcription factor network during HS development to promote a columnar epithelium. Moreover, GATA4-dependent phenotypes in developmental mutants reflected changes associated with Barrett’s esophagus, suggesting that developmental biology can provide insight into human disease mechanisms.
A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
Authors: Juan Jiménez-Sánchez , Álvaro Martínez-Rubio , Anton Popov , Julián Pérez-Beteta , Youness Azimzade , David Molina-García , Juan Belmonte-Beitia , Gabriel F Calvo , Víctor M Pérez-García
Published: August 2020

Increasingly complex in-silico modeling approaches offer a way to simultaneously access cancerous processes at different spatio-temporal scales. High-level models, such as those based on partial differential equations, are computationally affordable and allow large tumor sizes and long temporal windows to be studied, but miss the discrete nature of many key underlying cellular processes. Individual-based approaches provide a much more detailed description of tumors, but have difficulties when trying to handle full-sized real cancers. Thus, there exists a trade-off between the integration of macroscopic and microscopic information, now widely available, and the ability to attain clinical tumor sizes. In this paper we put forward a stochastic mesoscopic simulation framework that incorporates key cellular processes during tumor progression while keeping computational costs to a minimum. Our framework captures a physical scale that allows both the incorporation of microscopic information, tracking the spatio-temporal emergence of tumor heterogeneity and the underlying evolutionary dynamics, and the reconstruction of clinically sized tumors from high-resolution medical imaging data, with the additional benefit of low computational cost. We illustrate the functionality of our modeling approach for the case of glioblastoma, a paradigm of tumor heterogeneity that remains extremely challenging in the clinical setting.

Author summary

Computer simulation based on mathematical models provides a way to improve the understanding of complex processes in oncology. In this paper we develop a stochastic mesoscopic simulation approach that incorporates key cellular processes while keeping computational costs to a minimum. Our methodology captures the development of tumor heterogeneity and the underlying evolutionary dynamics. The physical scale considered allows microscopic information to be included, tracking the spatio-temporal evolution of tumor heterogeneity and reconstructing clinically sized tumors from high-resolution medical imaging data, with a low computational cost. We illustrate the functionality of the modeling approach for the case of glioblastoma, an epitome of heterogeneity in tumors.
Ascorbate peroxidase neofunctionalization at the origin of APx-R and APx-L: evidences from basal Archaeplastida
Authors: Lazzarotto Fernanda , Menguer Paloma Koprovski , Del-Bem Luiz-Eduardo , Margis-Pinheiro Márcia
Published: August 2020

Ascorbate peroxidases (APx) are class I members of the non-animal peroxidases superfamily, a large group of evolutionarily related enzymes. Through mining in public databases, our group has previously identified two unusual subsets of APx homologs, disclosing the existence of two uncharacterized families of class I peroxidases, which were named ascorbate peroxidase-related (APx-R) and ascorbate peroxidase-like (APx-L). As APx, APx-R proteins possess all catalytic residues required for peroxidase activity. Nevertheless, these proteins do not contain residues known to be critical for ascorbate binding, implying that members of this family must use other substrates while reducing hydrogen peroxide. On the other hand, APx-L proteins not only lack ascorbate-binding residues, as do not contain any residue known to be essential for peroxidase activity, in contrast with every other member of the non-animal peroxidase superfamily, which is composed by over 10,000 proteins distributed among bacteria, archaea, fungi, algae, and plants. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, we now show the existence of hybrid proteins, which combine features of these three families. Analysis performed on public databases show that the prevalence of these proteins varies among distinct groups of organisms, accounting for up to 33% of total APx homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APx-R and APx-L, through a process characterized by the progressive deterioration of ascorbate-binding sites and catalytic sites towards neofunctionalization.
Loss of Fas-signaling in pro-fibrotic fibroblasts impairs homeostatic fibrosis resolution and promotes persistent pulmonary fibrosis
Authors: Redente Elizabeth F. , Chakraborty Sangeeta , Sajuthi Satria , Black Bart P. , Edelman Benjamin L. , Seibold Max A. , Riches David W.H.
Published: August 2020

Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible fibrotic disease of the distal lung alveoli that culminates in respiratory failure and reduced lifespan. Unlike normal lung repair in response to injury, IPF is associated with the accumulation and persistence of fibroblasts and myofibroblasts and continued production of collagen and other extracellular matrix (ECM) components. Prior in vitro studies have led to the hypothesis that the development of resistance to Fas-induced apoptosis by lung fibroblasts and myofibroblasts contibributes to their accumulation in the distal lung tissues of IPF patients. Here, we test this hypothesis in vivo in the resolving model of bleomycin-induced pulmonary fibrosis in mice. Using genetic loss-of-function approaches to inhibit Fas signaling in fibroblasts, novel flow cytometry strategies to quantify lung fibroblast subsets and transcriptional profiling of lung fibroblasts by bulk and single cell RNA-sequencing, we show that Fas is necessary for lung fibroblast apoptosis during homeostatic resolution of bleomycin-induced pulmonary fibrosis in vivo. Furthermore, we show that loss of Fas signaling leads to the persistence and continued pro-fibrotic functions of lung fibroblasts. Our studies provide novel insights into the mechanisms that contribute to fibroblast survival, persistence and continued ECM deposition in the context of IPF and how failure to undergo Fas-induced apoptosis prevents fibrosis resolution.
Detection of ‘relict’ western lineage of citrus tristeza virus virulent genotype in decliningArunachal Wakro orange
Authors: Datta Sibnarayan , Das Bidisha , Budhauliya Raghvendra , Gopalakrishnan Reji , Muaka Vanlalh , Meghvansi Mukesh K , Rahman Safior , Dwivedi Sanjai K , Veer Vijay
Published: August 2020

Eastern Himalayan foothills are known to have optimal agro-climatic conditions for production of quality citrus fruits including oranges. Among the citrus growing regions of eastern Himalayas, Wakro in the far eastern state of Arunachal Pradesh is known for its superior quality oranges, popular as theWakro orangeor theArunachal orange, which has been included in Geographical Indication Registry by the Government of India. However, during last few years, Arunachal orange orchards have been experiencing severe infestation of aphid associated with rapid decline disease, causing catastrophe to the farmers as well as state economy. Therefore, in 2015, an intensive survey of severely affected orange orchards was carried out to investigate the aetiological factors of citrus decline. RNA samples extracted from leaf and aphid specimens collected from Wakro orchards were subjected to CTV detection through 3’-UTR specific RT-PCR. Subsequently, ORF1 and CP genetic regions were amplified and clonal-sequencing was performed. Although, BLAST search showed close homology of the present sequences with other virulent genotype VT sequences, detailed phylogenetic analysis demonstrated affinity and clustering of present sequences with VT sequences belonging to the ‘western’ lineage. This finding is considerably distinct from CTV sequences reported from citrus growing orchards in India and other neighbouring countries. Additionally, low diversity of CP gene sequences, recombination patterns and presence of sequence segments identical to the present ones in other CTV genotypes was also revealed. Collectively, these observations indicate pristine and primeval nature of present CTV sequences, corroborating well with the proposed origin of CTV in this part of the globe. We here report our finding of western lineage of CTV virulent genotype VT, which is distinct from CTV molecular epidemiology in other parts of India and discuss the implications of these findings.
The relationship between hippocampal-dependent task performance and hippocampal grey matter myelination and iron content
Authors: Clark Ian A. , Callaghan Martina F. , Weiskopf Nikolaus , Maguire Eleanor A.
Published: August 2020

Individual differences in scene imagination, autobiographical memory recall, future thinking and spatial navigation have long been linked with hippocampal structure in healthy people, although evidence for such relationships is, in fact, mixed. Extant studies have predominantly concentrated on hippocampal volume. However, it is now possible to use quantitative neuroimaging techniques to model different properties of tissue microstructure in vivo such as myelination and iron. Previous work has linked such measures with cognitive task performance, particularly in older adults. Here we investigated whether performance on scene imagination, autobiographical memory, future thinking and spatial navigation tasks was associated with hippocampal grey matter myelination or iron content in young, healthy adult participants. MRI data were collected using a multi-parameter mapping protocol (0.8mm isotropic voxels) from a large sample of 217 people with widely-varying cognitive task scores. We found little evidence that hippocampal grey matter myelination or iron content was related to task performance. This was the case using different analysis methods (voxel-based quantification, partial correlations), when whole brain, hippocampal regions of interest, and posterior:anterior hippocampal ratios were examined, and across different participant sub-groups (divided by gender, task performance). Variations in hippocampal grey matter myelin and iron levels may not, therefore, help to explain individual differences in performance on hippocampal-dependent tasks, at least in young, healthy individuals.
Assessment of Structural Units Deletions in the Archaeal Oligosaccharyltransferase AglB
Authors: Pedebos Conrado , Verli Hugo
Published: August 2020

Oligosaccharyltransferases (OSTs) are enzymes that catalyze the transfer of a glycan chain to an acceptor protein. Their structure is composed by a transmembrane domain and a periplasmic / C-terminal domain, which can be divided into structural units. TheArchaeoglobus fulgidusOST, AfAglB, has unique structural units with unknown functions. Here, we evaluate the stability role proposed for AfAglB units by employing molecular modelling and molecular dynamics simulations, to examine the effect of single and double deletions in the enzyme structure. Our results show a strong effect on the dynamics of the C-terminal domain for the mutated systems with increased fluctuations near the deleted areas. Conformational profile and stability are deeply affected, mainly in the double unit deletion, modifying the enzyme behavior and binding interfaces. Coordination at the catalytic site was not disrupted, indicating that the mutated enzymes could retain activity at some level. Hotspots of variation were identified and rationalized with previous data. Our data shows that structural units may provide stabilization interactions, contributing for integrity of the wild-type enzyme at high temperatures. By correlating our findings to structural units mutagenesis experimental data available, it was observed that structural units deletion can interfere with OSTs stability and dynamics but it is not directly related to catalysis. Instead, they may influence the OST structural integrity, and, potentially, thermostability. This work offers a basis for future experiments involving OSTs structural and functional characterization, as well as for protein engineering.
Amino acids whose intracellular levels change most during aging alter chronological lifespan of fission yeast
Authors: Rallis Charalampos , Mülleder Michael , Smith Graeme , Au Yan Zi , Ralser Markus , Bähler Jürg
Published: August 2020

Amino acid deprivation or supplementation can affect cellular and organismal lifespan, but we know little about the role of concentration changes in free, intracellular amino acids during aging. Here, we determine free amino-acid levels during chronological aging of non-dividing fission yeast cells. We compare wild-type with long-lived mutant cells that lack the Pka1 protein of the protein kinase A signalling pathway. In wild-type cells, total amino-acid levels decrease during aging, but much less so inpka1mutants. Two amino acids strongly change as a function of age: glutamine decreases, especially in wild-type cells, while aspartate increases, especially inpka1mutants. Supplementation of glutamine is sufficient to extend the chronological lifespan of wild-type but not ofpka1Δcells. Supplementation of aspartate, on the other hand, shortens the lifespan ofpka1Δbut not of wild-type cells. Our results raise the possibility that certain amino acids are biomarkers of aging, and their concentrations during aging can promote or limit cellular lifespan.
Brain activity fluctuations propagate as waves traversing the cortical hierarchy
Authors: Gu Yameng , Sainburg Lucas E. , Kuang Sizhe , Han Feng , Williams Jack W. , Liu Yikang , Zhang Nanyin , Zhang Xiang , Leopold David A. , Liu Xiao
Published: August 2020

The brain exhibits highly organized patterns of spontaneous activity as measured by resting-state fMRI fluctuations that are being widely used to assess the brain’s functional connectivity. Some evidence suggests that spatiotemporally coherent waves are a core feature of spontaneous activity that shapes functional connectivity, though this has been difficult to establish using fMRI given the temporal constraints of the hemodynamic signal. Here we investigated the structure of spontaneous waves in human fMRI and monkey electrocorticography. In both species, we found clear, repeatable, and directionally constrained activity waves coursed along a spatial axis approximately representing cortical hierarchical organization. These cortical propagations were closely associated with activity changes in distinct subcortical structures, particularly those related to arousal regulation, and modulated across different states of vigilance. The findings demonstrate a neural origin of spatiotemporal fMRI wave propagation at rest and link it to the principal gradient of resting-state fMRI connectivity.
Distributed source modeling of intracranial stereoelectroencephalographic measurements
Authors: Lin Fa-Hsuan , Lee Hsin-Ju , Ahveninen Jyrki , Jääskeläinen Iiro P. , Yu Hsiang-Yu , Lee Cheng-Chia , Chou Chien-Chen , Kuo Wen-Jui
Published: August 2020

Intracranial stereoelectroencephalography (sEEG) provides unsurpassed sensitivity and specificity for human neurophysiology. However, sEEG group analyses are complicated because the electrode implantations differ greatly across individuals. Here, using an auditory experiment as the test case, we developed a distributed, anatomically realistic sEEG source-modeling approach for within- and between-subject analyses. In addition to intracranial event-related potentials (iERP), we also estimated the sources of high broadband gamma activity (HBBG), a putative correlate of local neural firing. The source models accounted for a significant portion of the variance of the sEEG measurements in leave-one-out cross-validation. After logarithmic transformations, the sensitivity and signal-to-noise ratio were linearly inversely related to the minimal distance between the brain location and electrode contacts (slope≈-3.6). The HGGB source estimates were remarkably consistent with analyses of intracranial-contact data. In conclusion, distributed sEEG source modeling provides a powerful neuroimaging tool, which facilitates anatomically-normalized group analyses of both iERP and HBBG.
Coronatine contributesPseudomonas cannabinapv.alisalensisvirulence by overcoming both stomatal and apoplastic defenses in dicot and monocot plants
Authors: Sakata Nanami , Ishiga Takako , Masuo Shunsuke , Hashimoto Yoshiteru , Ishiga Yasuhiro
Published: August 2020

P. cannabinapv.alisalensis(Pcal) is a causative agent of bacterial blight of crucifer including cabbage, radish, and broccoli. Importantly,Pcalcan infect not only a wide range of Brassicaceae, but also green manure crops such as oat. However,Pcalvirulence mechanisms have not been investigated and are not fully understood. We focused on coronatine (COR) function, which is one of the well-knownP. syringaepv. tomatoDC3000 virulence factors, inPcalinfection processes on both dicot and monocot plants. Cabbage and oat plants dip-inoculated with aPcalKB211 COR mutant (ΔcmaA) exhibited reduced virulence compared toPcalWT. Moreover, ΔcmaAfailed to reopen stomata on both cabbage and oat, suggesting that COR facilitatesPcalentry through stomata into both plants. Furthermore, cabbage and oat plants syringe-infiltrated with ΔcmaAalso showed reduced virulence, suggesting that COR is involved in overcoming not only stomatal-based defense, but also apoplastic defense. Indeed, defense related genes, includingPR1andPR2, were highly expressed in plants inoculated with ΔcmaAcompared toPcalWT, indicating that COR suppresses defense-related genes of both cabbage and oat. Additionally, SA accumulation increases after ΔcmaAinoculation compared toPcalWT. Taken together, COR contributes to cause disease by suppressing stomatal-based defense and apoplastic defense in both dicot and monocot plants. This is the first study to investigate COR functions in the interaction ofPcaland different host plants (dicot and monocot plants) using genetically and biochemically defined COR deletion mutants.

Author summary

Disease outbreaks caused by newPseudomonas syringaeisolates are problems worldwide.P. cannabinapv.alisalensis(Pcal) causes bacterial blight on a wide range of cruciferous plants and bacterial brown spot on oat plants. AlthoughP. syringaedeploys a variety of virulence factors,Pcalvirulence factors have not been investigated. We focused on coronatine (COR) function, which is one of the well-knownP. syringaevirulence factors. COR is a non-host-specific phytotoxin and contributes toP. syringaegrowth and lesion formation or expansion in several host plants. COR function has been mainly studied in the model pathogenP. syringaepv.tomatoDC3000 and model the plantArabidopsis thaliana. Thus, COR roles inPcalinfection especially on monocot plants have not been well studied. Therefore, we investigated COR role inPcalinteraction with both dicot and monocot plants. Here, we revealed that COR functions as a multifunctional suppressor to managePcalvirulence on both plants.
Low replication stress leads to specific replication timing advances associated to chromatin remodelling in cancer cells
Authors: Courtot Lilas , Bournique Elodie , Maric Chrystelle , Guitton-Sert Laure , Madrid-Mencía Miguel , Pancaldi Vera , Cadoret Jean-Charles , Hoffmann Jean-Sébastien , Bergoglio Valérie
Published: August 2020

DNA replication is well orchestrated in mammalian cells through a tight regulation of the temporal order of replication origin activation, named the replication timing, a robust and conserved process in each cell type. Upon low replication stress, the slowing of replication forks induces delayed replication of fragile regions leading to genetic instability. The impact of low replication stress on the replication timing in different cellular backgrounds has not been explored yet. Here we analysed the whole genome replication timing in a panel of 6 human cell lines under low replication stress. We first demonstrated that cancer cells were more impacted than non-tumour cells. Strikingly, we unveiled an enrichment of specific replication domains undergoing a switch from late to early replication in some cancer cells. We found that advances in replication timing correlate with heterochromatin regions poorly sensitive to DNA damage signalling while being subject to an increase of chromatin accessibility. Finally, our data indicate that, following release from replication stress conditions, replication timing advances can be inherited by the next cellular generation, suggesting a new mechanism by which cancer cells would adapt to cellular or environmental stress.
Nucleotide substitutions during speciation may explain substitution rate variation
Authors: Janzen Thijs , Bokma Folmer , Etienne Rampal S.
Published: August 2020

Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life.
Understanding metabolic behaviour in whole-cell model output
Authors: Landon Sophie , Chalkley Oliver , Breese Gus , Grierson Claire , Marucci Lucia
Published: August 2020

Whole-cell modelling is a newly expanding field that has many applications in lab experiment design and predictive drug testing. Although whole-cell model output contains a wealth of information, it is complex and high dimensional, thus hard to interpret. Here, we present an analysis pipeline that combines machine learning, dimensionality reduction and network analysis to interpret and visualise metabolic reaction fluxes from a set of single gene knockouts simulated in theMycoplasma genitaliumwhole-cell model. We found that the reaction behaviours show trends that correlate with phenotypic classes of the simulation output, highlighting particular cellular subsystems that malfunction after gene knockouts. From a graphical representation of the metabolic network, we saw that there is a set of reactions that can be used as markers of a phenotypic class, showing their importance within the network. Our analysis pipeline can support the understanding of the complexity ofin silicocells without detailed knowledge of the constituent parts, which can help to understand the effects of gene knockouts, and, as whole-cell models become more widely built and used, aid genome design.
Multigenerational downregulation of insulin/IGF-1 signalling in adulthood improves lineage survival, reproduction, and fitness inC. eleganssupporting the developmental theory of ageing
Authors: Duxbury Elizabeth ML , Carlsson Hanne , Sales Kris , Sultanova Zahida , Immler Simone , Chapman Tracey , Maklakov Alexei A
Published: August 2020

Adulthood-only downregulation of insulin/IGF-1 signalling (IIS), an evolutionarily conserved pathway regulating resource allocation between somatic maintenance and reproduction, increases lifespan without fecundity cost in the nematode,Caenorhabditis elegans. However, long-term multigenerational effects of reduced IIS remain unexplored and are proposed to carry costs for offspring quality. To test this hypothesis, we ran a mutation accumulation (MA) experiment and downregulated IIS in half of the 400 MA lines by silencingdaf-2gene expression using RNA interference (RNAi) across 40 generations. Contrary to the prediction, adulthood-onlydaf-2RNAi reduced extinction of MA lines both under UV-induced and spontaneous mutation accumulation. Fitness of the surviving UV-induced MA lines was higher underdaf-2RNAi. Reduced IIS increased intergenerational F1 offspring fitness under UV stress but had no quantifiable transgenerational effects. Functionalhrde-1was required for the benefits of multigenerationaldaf-2RNAi. Overall, we found net benefit to fitness from multigenerational reduction of IIS and the benefits became more apparent under stress. Because reduceddaf-2expression during development carries fitness costs, we suggest that our findings are best explained by the developmental theory of ageing, which maintains that the decline in the force of selection with age results in poorly regulated gene expression in adulthood.
Direct non-destructive total reflection X-ray fluorescence elemental determinations in zirconium alloy samples
Authors: Sanyal Kaushik , Kanrar Buddhadev , Dhara Sangita , Sibilia Mirta , Sengupta Arijit , Karydas Andreas Germanos , Mishra Nand Lal
Published: August 2020

The development of a direct non-destructive synchrotron-radiation-based total reflection X-ray fluorescence (TXRF) analytical methodology for elemental determinations in zirconium alloy samples is reported for the first time. Discs, of diameter 30 mm and about 1.6 mm thickness, of the zirconium alloys Zr-2.5%Nb and Zircalloy-4 were cut from plates of these alloys and mirror polished. These specimens were presented for TXRF measurements directly after polishing and cleaning. The TXRF measurements were made at the XRF beamline at Elettra synchrotron light source, Trieste, Italy, at two different excitation energies, 1.9 keV and 14 keV, for the determinations of low- and high-Z elements, respectively. The developed analytical methodology involves two complementary quantification schemes, i.e. using either the fundamental parameter method or relative sensitivity based method, allowing quantification of fifteen minor and trace elements with respect to Zr with very good precision and accuracy. In order to countercheck the TXRF analytical results, some samples were analyzed using the DC arc carrier distillation atomic emission spectrometry technique also, which shows an excellent agreement with the results of the TXRF-based methodology developed in this work. The present work resulted in a non-destructive TXRF elemental characterization methodology of metal and alloy samples avoiding the cumbersome dissolution and matrix separation which are normally required in other techniques and traditional methods of TXRF determination. In addition, the production of analytical waste could also be avoided to a large extent. Although the work was carried out for specific applications in the nuclear industry, it is equally suitable for other such samples in different industrial applications.
Neutron sub-micrometre tomography from scattering data
Authors: Heacock B. , Sarenac D. , Cory D. G. , Huber M. G. , MacLean J. P. W. , Miao H. , Wen H. , Pushin D. A.
Published: August 2020

Neutrons are valuable probes for various material samples across many areas of research. Neutron imaging typically has a spatial resolution of larger than 20 µm, whereas neutron scattering is sensitive to smaller features but does not provide a real-space image of the sample. A computed-tomography technique is demonstrated that uses neutron-scattering data to generate an image of a periodic sample with a spatial resolution of ∼300 nm. The achieved resolution is over an order of magnitude smaller than the resolution of other forms of neutron tomography. This method consists of measuring neutron diffraction using a double-crystal diffractometer as a function of sample rotation and then using a phase-retrieval algorithm followed by tomographic reconstruction to generate a map of the sample's scattering-length density. Topological features found in the reconstructions are confirmed with scanning electron micrographs. This technique should be applicable to any sample that generates clear neutron-diffraction patterns, including nanofabricated samples, biological membranes and magnetic materials, such as skyrmion lattices.
High-resolution structure of the alcohol dehydrogenase domain of the bifunctional bacterial enzyme AdhE
Authors: Azmi Liyana , Bragginton Eilis C. , Cadby Ian T. , Byron Olwyn , Roe Andrew J. , Lovering Andrew L. , Gabrielsen Mads
Published: August 2020

The bifunctional alcohol/aldehyde dehydrogenase (AdhE) comprises both an N-terminal aldehyde dehydrogenase (AldDH) and a C-terminal alcohol dehydrogenase (ADH). In vivo, full-length AdhE oligomerizes into long oligomers known as spirosomes. However, structural analysis of AdhE is challenging owing to the heterogeneity of the spirosomes. Therefore, the domains of AdhE are best characterized separately. Here, the structure of ADH from the pathogenic Escherichia coli O157:H7 was determined to 1.65 Å resolution. The dimeric crystal structure was confirmed in solution by small-angle X-ray scattering.
Pairwise running of automated crystallographic model-building pipelines
Authors: Alharbi Emad , Calinescu Radu , Cowtan Kevin
Published: August 2020

For the last two decades, researchers have worked independently to automate protein model building, and four widely used software pipelines have been developed for this purpose: ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE. Here, the usefulness of combining these pipelines to improve the built protein structures by running them in pairwise combinations is examined. The results show that integrating these pipelines can lead to significant improvements in structure completeness and R
free. In particular, running Phenix AutoBuild after Buccaneer improved structure completeness for 29% and 75% of the data sets that were examined at the original resolution and at a simulated lower resolution, respectively, compared with running Phenix AutoBuild on its own. In contrast, Phenix AutoBuild alone produced better structure completeness than the two pipelines combined for only 7% and 3% of these data sets.