bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement
Authors: Heo Lim , Feig Michael
Published: March 2020

Protein structures are crucial for understanding their biological activities. Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need to understand the biological behavior of the virus and provide a basis for developing effective therapies. Since the proteome of the virus was determined, some of the protein structures could be determined experimentally, and others were predicted via template-based modeling approaches. However, tertiary structures for several proteins are still not available from experiment nor they could be accurately predicted by template-based modeling because of lack of close homolog structures. Previous efforts to predict structures for these proteins include efforts by DeepMind and the Zhang group via machine learning-based structure prediction methods, i.e. AlphaFold and C-I-TASSER. However, the predicted models vary greatly and have not yet been subjected to refinement. Here, we are reporting new predictions from our in-house structure prediction pipeline. The pipeline takes advantage of inter-residue contact predictions from trRosetta, a machine learning-based method. The predicted models were further improved by applying molecular dynamics simulation-based refinement. We also took the AlphaFold models and refined them by applying the same refinement method. Models based on our structure prediction pipeline and the refined AlphaFold models were analyzed and compared with the C-I-TASSER models. All of our models are available athttps://github.com/feiglab/sars-cov-2-proteins.
Structure-Based Design, Synthesis and Biological Evaluation of Peptidomimetic Aldehydes as a Novel Series of Antiviral Drug Candidates Targeting the SARS-CoV-2 Main Protease
Authors: Dai Wenhao , Zhang Bing , Jiang Xia-Ming , Su Haixia , Li Jian , Zhao Yao , Xie Xiong , Jin Zhenming , Peng Jingjing , Liu Fengjiang , Li Chunpu , Li You , Bai Fang , Wang Haofeng , Chen Xi , Cen Xiaobo , Hu Shulei , Yang Xiuna , Wang Jiang , Liu Xiang , Xiao Gengfu , Jiang Hualiang , Rao Zihe , Zhang Lei-Ke , Xu Yechun , Yang Haitao , Liu Hong
Published: March 2020

SARS-CoV-2 is the etiological agent responsible for the COVID-19 outbreak in Wuhan. Specific antiviral drug are urgently needed to treat COVID-19 infections. The main protease (Mpro) of SARS-CoV-2 is a key CoV enzyme that plays a pivotal role in mediating viral replication and transcription, which makes it an attractive drug target. In an effort to rapidly discover lead compounds targeting Mpro, two compounds (11aand11b) were designed and synthesized, both of which exhibited excellent inhibitory activity with an IC50 value of 0.05 μM and 0.04 μM respectively. Significantly, both compounds exhibited potent anti-SARS-CoV-2 infection activity in a cell-based assay with an EC50 value of 0.42 μM and 0.33 μM, respectively. The X-ray crystal structures of SARS-CoV-2 Mproin complex with11aand11bwere determined at 1.5 Å resolution, respectively. The crystal structures showed that11aand11bare covalent inhibitors, the aldehyde groups of which are bound covalently to Cys145 of Mpro. Both compounds showed good PK properties invivo, and11aalso exhibited low toxicity which is promising drug leads with clinical potential that merits further studies.
Molecular and functional diversity of distinct subpopulations of extracellular vesicles from stressed pancreatic beta cells: implications for autoimmunity
Authors: Giri Khem Raj , de Beaurepaire Laurence , Jegou Dominique , Lavy Margot , Mosser Mathilde , Dupont Aurelien , Fleurisson Romain , Dubreil Laurence , Collot Mayeul , Van Endert Peter , Bach Jean-Marie , Mignot Gregoire , Bosch Steffi
Published: March 2020

Beta cell failure and apoptosis following islet inflammation have been associated with autoimmune type 1 diabetes pathogenesis. As conveyors of biological active material, extracellular vesicles (EV) act as mediators in communication with immune effectors fostering the idea that EV from inflamed beta cells may contribute to autoimmunity. Evidence accumulates that beta exosomes promote diabetogenic responses, but relative contributions of larger vesicles as well as variations in the composition of the beta cell’s vesiculome due to environmental changes have not been explored yet. Here, we made side-by-side comparisons of the phenotype and function of apoptotic bodies (AB), microvesicles (MV) and small EV (sEV) isolated from an equal amount of MIN6 beta cells exposed to inflammatory, hypoxic or genotoxic stressors. Under normal conditions, large vesicles represent 93% of the volume, but only 2% of the number of the vesicles. Our data reveal a consistently higher release of AB and sEV and to a lesser extent of MV, exclusively under inflammatory conditions commensurate with a 4-fold increase in the total volume of the vesiculome and enhanced export of immune-stimulatory material including the autoantigen insulin, microRNA, and cytokines. Whilst inflammation does not change the concentration of insulin inside the EV, specific Toll-like receptor-binding microRNA sequences preferentially partition into sEV. Exposure to inflammatory stress engenders drastic increases in the expression of monocyte chemoattractant protein 1 in all EV and of interleukin-27 solely in AB suggesting selective sorting towards EV subspecies. Functional in vitro assays in mouse dendritic cells and macrophages reveal further differences in the aptitude of EV to modulate expression of cytokines and maturation markers. These findings highlight the different quantitative and qualitative imprints of environmental changes in subpopulations of beta EV that may contribute to the spread of inflammation and sustained immune cell recruitment at the inception of the (auto-) immune response.

Graphical Abstract

Inflammation stimulates release of a heterogeneous population of beta EV with differential expression of immunogenic substances involved in immune cell recruitment and activation.

Highlights

Stress engenders an up to four-fold increase in the volume of the vesiculome and enhanced auto-antigen release

Cytokines are selectively sorted into EV subspecies

TLR-binding microRNAs are enriched in sEV

EV from stressed beta cells promote dendritic and macrophage cell activation
Sensorimotor conflicts induce somatic passivity and louden quiet voices in healthy listeners
Authors: Orepic Pavo , Rognini Giulio , Kannape Oliver Alan , Faivre Nathan , Blanke Olaf
Published: March 2020

Sensorimotor conflicts are known to alter the perception of accompanying sensory signals and deficits in sensory attenuation have been observed in schizophrenia. In the auditory domain, self-generated tones or voices (compared to tones or voices presented passively or with sensorimotor delays) have been associated with changes in loudness perception and attenuated neural responses. It has been argued that for sensory signals to be attenuated, predicted and sensory consequences must have a consistent spatiotemporal relationship, between button presses and reafferent tactile signals, via predictive sensory signaling, a process altered in schizophrenia. Here, we investigated auditory sensory attenuation for a series of morphed voices while healthy participants applied sensorimotor stimulations that had no spatiotemporal relationship to the voice stimuli and that have been shown to induce mild psychosis-like phenomena. In two independent groups of participants, we report a loudening of silent voices and found this effect only during maximal sensorimotor conflicts (versus several control conditions). Importantly, conflicting sensorimotor stimulation also induced a mild psychosis-like state in the form of somatic passivity and participants who experienced stronger passivity lacked the sensorimotor loudening effect. We argue that this conflict-related sensorimotor loudness amplification may represent a reduction of auditory self-attenuation that is lacking in participants experiencing a concomitant mild psychosis-like state. We interpret our results within the framework of the comparator model of sensorimotor control, and discuss the implications of our findings regarding passivity experiences and hallucinations in schizophrenia.
Mps1 expression is critical for chromosome orientation and segregation in yeast with high ploidy
Authors: Sartin Ashlea , Gish Madeline , Harsha Jillian , Haworth Dawson , LaVictoire Rebecca , Meyer Régis E
Published: March 2020

In aneuploid cancer cells, the chromosome segregation apparatus is sensitive to increased chromosome number. The conserved protein kinase, Mps1, is a critical actor of this machinery, orienting the chromosomes properly on the spindle. Abnormally high levels of this kinase have been found in tumors with elevated chromosome number. However, it remains unclear, mechanistically, if and how cells with higher ploidy become dependent upon increased Mps1 levels. To answer these questions, we explored Mps1 dependence in yeast cells with increased sets of chromosomes. We discovered that having more chromosomes affects the ability of cells to orient chromosomes properly. The cells with increased numbers of chromosomes are particularly sensitive to the reduction of Mps1 activity. Inmps1loss of function mutants, cells display an extended prometaphase with a longer spindle and a delay in orienting properly the chromosomes. Altogether, our results suggest that increased numbers of chromosomes render cells more dependent on Mps1 for orienting chromosomes on the spindle. The phenomenon described here may be relevant in understanding why hyperdiploid cancer cells become excessively reliant on high Mps1 expression for successful chromosome segregation.

Author summary

Most cells in solid tumors usually carry far more chromosomes than normal cells. Losing or gaining chromosomes during cell division can lead to aneuploidy (an abnormal number of chromosomes), cancer, and other diseases. Mps1 is a master regulator of cell division that is critical to keep the correct number chromosomes in each daughter cell. This master regulator has been shown to target and affect the function of various actors involved in cell division. Abnormally high levels of this master regulator are found in tumors with elevated chromosome numbers. The high levels of this regulator appear to be protecting these tumor cells. To answer if and how cells with higher ploidy become so dependent of Mps1, we generated yeast cells with increased set of chromosomes. Here, we report that cells with elevated chromosome number are particularly sensitive to the reduction of Mps1 level. In cells with higher ploidy and reduced level of Mps1, the progression during cell division is delayed. In the mutant cells, their ability to properly orient and segregate their chromosomes on the spindle is greatly reduced.
Behavioral, physiological, and neural signatures of surprise during naturalistic sports viewing
Authors: Antony James W. , Hartshorne Thomas H. , Pomeroy Ken , Gureckis Todd M. , Hasson Uri , McDougle Samuel D. , Norman Kenneth A.
Published: March 2020

Surprise signals a discrepancy between past and current beliefs. It is theorized to be linked to affective experiences, the creation of particularly resilient memories, and segmentation of the flow of experience into discrete perceived events. However, the ability to precisely measure naturalistic surprise has remained elusive. We used advanced basketball analytics to derive a quantitative measure of surprise and characterized its behavioral, physiological, and neural correlates in human subjects observing basketball games. We found that surprise was associated with segmentation of ongoing experiences, as reflected by subjectively perceived event boundaries and shifts in neocortical patterns underlying belief states. Interestingly, these effects differed by whether surprising moments contradicted or bolstered current predominant beliefs. Surprise also positively correlated with pupil dilation, activation in subcortical regions associated with dopamine, game enjoyment, and long-term memory. These investigations support key predictions from event segmentation theory and extend theoretical conceptualizations of surprise to real-world contexts.
Ultrasensitive small molecule fluorogenic probe for human heparanase
Authors: Liu Jun , Schleyer Kelton A. , Bryan Tyrel L. , Xie Changjian , Seabra Gustavo , Xu Yongmei , Kafle Arjun , Cui Chao , Wang Ying , Yin Kunlun , Fetrow Benjamin , Henderson Paul K. P. , Fatland Peter Z. , Liu Jian , Li Chenglong , Guo Hua , Cui Lina
Published: March 2020

Heparanase is a critical enzyme involved in the remodeling of the extracellular matrix (ECM), and its elevated expression has been linked with diseases such as cancer and inflammation. The detection of heparanase enzymatic activity holds tremendous value in the study of the cellular microenvironment, and search of molecular therapeutics targeting heparanase, however, assays developed for this enzyme so far have suffered prohibitive drawbacks. Here we present an ultrasensitive fluorogenic small-molecule probe for heparanase enzymatic activity. The probe exhibits a 756-fold fluorescence turn-on response in the presence of human heparanase, allowing one-step detection of heparanase activity in real-time with a picomolar detection limit. The high sensitivity and robustness of the probe are exemplified in a high-throughput screening assay for heparanase inhibitors.
Brain capillary pericytes exert a substantial but slow influence on blood flow
Authors: Hartmann David A. , Berthiaume Andrée-Anne , Grant Roger I. , Harrill Sarah A. , Noonan Tegan , Costello Jordan , Tieu Taryn , McDowell Konnor , Faino Anna , Kelly Abigail , Shih Andy Y.
Published: March 2020

The majority of the brain’s vasculature is comprised of intricate capillary networks lined by capillary pericytes. However, it remains unclear whether capillary pericytes contribute to blood flow control. Using two-photon microscopy to observe and manipulate single capillary pericytesin vivo, we find their optogenetic stimulation decreases lumen diameter and blood flow, but with slower kinetics than mural cells of upstream pial and pre-capillary arterioles. This slow, optogenetically-induced vasoconstriction was inhibited by the clinically-used vasodilator fasudil, a Rho kinase inhibitor that blocks contractile machinery. Capillary pericytes were also slower to constrict back to baseline following hypercapnia-induced dilation, and relax towards baseline following optogenetically-induced vasoconstriction. In a complementary approach, optical ablation of single capillary pericytes led to sustained local dilation and a doubling of blood cell flux in capillaries lacking pericyte contact. Altogether these data indicate that capillary pericytes contribute to basal blood flow resistance and slow modulation of blood flow throughout the capillary bed.
Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity
Authors: Zhu Yuanmei , Yu Danwei , Yan Hongxia , Chong Huihui , He Yuxian
Published: March 2020

The coronavirus disease COVID-19, caused by emerging SARS-CoV-2, has posed serious threats to global public health, economic and social stabilities, calling for the prompt development of therapeutics and prophylactics. In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Comparing to that of SARS-CoV, the heptad repeat 1 (HR1) sequence in the S2 fusion protein of SARS-CoV-2 possesses markedly increased α-helicity and thermostability, as well as a higher binding affinity with its corresponding heptad repeat 2 (HR1) site. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. IPB02 also inhibited the SARS-CoV pseudovirus efficiently. Moreover, the strcuture and activity relationship (SAR) of IPB02 were characterzized with a panel of truncated lipopeptides, revealing the amino acid motifs critical for its binding and antiviral capacities. Therefore, the presented results have provided important information for understanding the entry pathway of SARS-CoV-2 and the design of antivirals that target the membrane fusion step.
The roles of online and offline replay in planning
Authors: Eldar Eran , Lièvre Gaëlle , Dayan Peter , Dolan Raymond J.
Published: March 2020

Animals and humans replay neural patterns encoding trajectories through their environment, both whilst they solve decision-making tasks and during rest. Both on-task and off-task replay are believed to contribute to flexible decision making, though how their relative contributions differ remains unclear. We investigated this question by using magnetoencephalography to study human subjects while they performed a decision-making task that was designed to reveal the decision algorithms employed. We characterized subjects in terms of how flexibly each adjusted their choices to changes in temporal, spatial and reward structure. The more flexible a subject, the more they replayed trajectories during task performance, and this replay was coupled with re-planning of the encoded trajectories. The less flexible a subject, the more they replayed previously and subsequently preferred trajectories during rest periods between task epochs. The data suggest that online and offline replay both participate in planning but support distinct decision strategies.
Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis
Authors: Keller Andreas , Fehlmann Tobias , Backes Christina , Kern Fabian , Gislefoss Randi , Langseth Hilde , Rounge Trine B. , Ludwig Nicole , Meese Eckart
Published: March 2020

Small non-coding RNAs such as microRNAs are master regulators of gene expression. One of the most promising applications of miRNAs is the use as liquid biopsy. Especially early diagnosis is an effective means to increase patients’ overall survival. E.g. in oncology a tumor is detected at best prior to its clinical manifestation. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analyzed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom later developed cancer. We selected 210 serum samples of patients with lung, colon or breast cancer at three time points prior to diagnosis, after cancer diagnosis and controls. The controls were matched with regard to age of the blood donor and to the time points of blood drawing, which were 27, 32, or 38 years prior to diagnosis. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 had adjusted p-values<10−10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p<0.05). Unsupervised competitive learning by self-organized maps indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. Self-organized maps also highlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Our results indicate that tumors may be indicated by serum miRNAs decades prior the clinical manifestation.
Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response
Authors: Ortea Ignacio , Bock Jens-Ole
Published: March 2020

The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.
Evaluating Human Autosomal Loci for Sexually Antagonistic Viability Selection in Two Large Biobanks
Authors: Kasimatis Katja R. , Abraham Abin , Ralph Peter L. , Kern Andrew D. , Capra John A. , Phillips Patrick C.
Published: March 2020

Sex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very extreme in order to produce and maintain reported levels of between-sex allelic differentiation. We address this paradox between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n=438,427) along with a second large, independent cohort (BioVU, n=93,864). We performed association tests between genetically ascertained sex and genotypes. Although we found dozens of genome-wide significant associations, none replicated across samples. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well-powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.
A novel setup for simultaneous two-photon functional imaging and precise spectral and spatial visual stimulation inDrosophila
Authors: Feord R. C. , Wardill T. J.
Published: March 2020

Motion vision has been extensively characterised inDrosophila melanogaster, but substantially less is known about how flies process colour, or how spectral information affects other visual modalities. To accurately dissect the components of the early visual system responsible for processing colour, we developed a versatile visual stimulation setup to probe combined spatial, temporal and spectral response properties. Using flies expressing neural activity indicators, we tracked visual responses in the medulla to a projected colour stimulus. The introduction of custom bandpass optical filters enables simultaneous two-photon imaging and visual stimulation over a large range of wavelengths without compromising the temporal stimulation rate. With monochromator-produced light, any spectral bandwidth and centre wavelength from 390 to 730 nm can be selected to produce a narrow spectral hue. A specialised screen material scatters each band of light across the visible spectrum equally at all locations of the screen, thus enabling presentation of spatially structured stimuli. We show layer-specific shifts of spectral response properties in the medulla correlating with projection regions of photoreceptor terminals.
CRISPR/Cas9 mediated mutations as a new tool for studying taste in honeybees
Authors: Değirmenci Laura , Geiger Dietmar , Rogé Ferreira Fábio Luiz , Keller Alexander , Krischke Beate , Beye Martin , Steffan-Dewenter Ingolf , Scheiner Ricarda
Published: March 2020

Background

Honeybees rely on nectar as their main source of carbohydrates [1]. Sucrose, glucose and fructose are the main components of plant nectars [2] [3]. Intriguingly, honeybees express only three putative sugar receptors (AmGr1, AmGr2 and AmGr3) [4], which is in stark contrast to many other insects and vertebrates. The sugar receptors are only partially characterized [5] [6]. AmGr1 detects different sugars including sucrose and glucose. AmGr2 is assumed to act as a co-receptor only, while AmGr3 is assumedly a fructose receptor.

Results

We show that honeybee gustatory receptor AmGr3 is highly specialized for fructose perception when expressed inXenopusoocytes. When we introduced nonsense mutations to the respectiveAmGr3gene using CRISPR/Cas9 in eggs of female workers, the resulting mutants displayed almost a complete loss of responsiveness to fructose. In contrast, responses to sucrose were normal. Nonsense mutations introduced by CRISPR/Cas9 in honeybees can thus induce a measurable behavioural change and serve to characterize the function of taste receptorsin vivo.

Conclusion

CRISPR/Cas9 is an excellent novel tool for characterizing honeybee taste receptorsin vivo. Biophysical receptor characterisation inXenopusoocytes and nonsense mutation ofAmGr3in honeybees unequivocally demonstrate that this receptor is highly specific for fructose.

Graphical Abstract

Figure 0
Thiol efflux mediated by an ABCC-like transporter participates forTrypanosoma cruziadaptation to environmental and chemotherapeutic stresses
Authors: da Costa Kelli Monteiro , Salustiano Eduardo J. , do Carmo Valente Raphael , Freire-de-Lima Leonardo , Mendonça-Previato Lucia , Previato José Osvaldo
Published: March 2020

The protozoanTrypanosoma cruziis the etiologic agent for Chagas disease, which affects 6-7 million people worldwide. The parasite presents high biological diversity, reflecting on the inefficiency of benznidazole in chronic or older patients. ABC superfamily proteins contain active transporters involved in the xenobiotic and endobiotic efflux and overexpressed in MDR cells. An ABCC-like transport was identified in theT. cruziY strain, being able to extrude thiol-conjugated compounds. As non-protein thiols represent prime line of defense towards reactive species, ABCC-like activity could participate in the regulation of mediators implicated in responses to cellular stress arising from a variety of stimuli, as environmental or chemotherapeutic. This study shows thatT. cruziABCC-like protein transports GSH, GSSG and ceramides, all implicated in cellular stress. Hemin, representative from the hematophagous feeding of the vector, was transported as well, suggesting a role for ABCC as a metal-thiol transporter. In addition, all strains evaluated showed ABCC-like activity, while no ABCB1-like activity was detected. Also, results suggest that ABCC-like does not associate to natural resistance to benznidazole, considering that the sensitive strains CL Brener and Berenice showed higher ABCC-like activity than the resistant strains Y and Colombiana. Instead, ABCC-like efflux increased after continuous exposure of Y strain to benznidazole. Moreover, ABCC does not perform direct efflux of drug and its participation in the machinery of protection against stress depends on the efflux of metabolites in conjugation to or in cotransport with thiol.
Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL
Authors: Sloan Jeremy , Hakenjos Jana P. , Gebert Michael , Ermakova Olga , Gumiero Andrea , Stier Gunter , Wild Klemens , Sinning Irmgard , Lohmann Jan U.
Published: March 2020

Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.
Differential Effects of Value and Salience on Saccade Latencies
Authors: Shams-Ahmar Mohammad , Thier Peter
Published: March 2020

Express saccades, a mode of visually guided saccades that are distinguished from regular saccades by extremely short reaction times, are triggered by inserting a temporal gap between the fixation dot and the saccade target. It is usually assumed that they are produced by a specific pathway in which the superior colliculus plays a key role. Whether and how this pathway deals with information on the subjective value of a saccade target is unknown. Therefore, we studied the influence of varying reward expectancies and compared it with the impact of the presence and absence of a temporal gap between the disappearance of the fixation dot and the appearance of the target on the visually guided saccades of two rhesus macaques (Macaca mulatta). We observed that the introduction of a gap shifted the entire saccadic reaction time distribution to shorter latencies while increasing the probability of express saccades. On the other hand, promoting the monkey's reward expectancy shortened reaction times and increased peak velocities of regular saccades, and increased the probability of express saccades. Importantly, we observed that the reaction time and peak velocity of express saccades were not sensitive to the value of the saccade target, suggesting that the express pathway does not have access to information on value. We propose a new model on express saccades that treats the salience of visual objects in the scene differently from the subjective value assigned to them.
Developmental atlas of white lupin cluster roots
Authors: Gallardo Cécilia , Hufnagel Bárbara , Soriano Alexandre , Divol Fanchon , Marquès Laurence , Doumas Patrick , Péret Benjamin
Published: March 2020

During the course of evolution, plants have developed various strategies to improve micronutrient acquisition, such as cluster roots. These spectacular structures are dedicated to efficient phosphate remobilization and acquisition. When exposed to Pi-limitation, white lupin forms cluster roots made of dense clusters of short specialized roots, called rootlets. Although the physiological activity of rootlets has been well studied, their development remains poorly described. Here, we provide a developmental atlas of white lupin early rootlet development, using molecular markers derived from the model plant Arabidopsis. We first focused on cell division patterns to determine which cells contribute to the rootlet primordium. Then, we identified homologs of previously described tissue specific genes based on protein sequence analysis and also using detailed transcriptomic data covering rootlet development. This study provides a comprehensive description of the developmental phases of rootlet formation, highlighting that rootlet primordium arises from divisions in pericycle, endodermis and cortex. We describe that rootlet primordium patterning follows eight stages during which tissue differentiation is established progressively.

Highlight

White lupin cluster roots consist in the formation of numerous rootlets whose development can be divided in 8 stages and involves divisions in the pericycle, endodermis and cortex.
Non-invasive surveys of mammalian viruses using environmental DNA
Authors: Alfano Niccolò , Dayaram Anisha , Axtner Jan , Tsangaras Kyriakos , Kampmann Marie-Louise , Mohamed Azlan , Wong Seth T. , Gilbert M. Thomas P. , Wilting Andreas , Greenwood Alex D.
Published: March 2020

Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.

To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.

We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.

Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.
Anticipatory responses along motion trajectories in awake monkey area V1
Authors: Benvenuti Giacomo , Chemla Sandrine , Boonman Arjan , Perrinet Laurent , Masson Guillaume S , Chavane Frédéric
Published: March 2020

What are the neural mechanisms underlying motion integration of translating objects? Visual motion integration is generally conceived of as a feedforward, hierarchical, information processing. However, feedforward models fail to account for many contextual effects revealed using natural moving stimuli. In particular, a translating object evokes a sequence of transient feedforward responses in the primary visual cortex but also propagations of activity through horizontal and feedback pathways. We investigated how these pathways shape the representation of a translating bar in monkey V1. We show that, for long trajectories, spiking activity builds-up hundreds of milliseconds before the bar enters the neurons’ receptive fields. Using VSDI and LFP recordings guided by a phenomenological model of propagation dynamics, we demonstrate that this anticipatory response arises from the interplay between horizontal and feedback networks driving V1 neurons well ahead of their feedforward inputs. This mechanism could subtend several perceptual contextual effects observed with translating objects.

Highlights

Our hypothesis is that lateral propagation of activity in V1 contributes to the integration of translating stimuli

Consistent with this hypothesis, we find that a translating bar induces anticipatory spiking activity in V1 neurons.

A V1 model describes how this anticipation can arise from inter and intra-cortical lateral propagation of activity.

The dynamic of VSDi and LFP signals in V1 is consistent with the predictions made by the model.

The intra-cortical origin is further confirmed by the fact that a bar moving from the ipsilateral hemifield does not evoke anticipation.

Horizontal and feedback input are not only modulatory but can also drive spiking responses in specific contexts.
FLOWERING LOCUS T4 (HvFT4)delays flowering and decreases floret fertility in barley
Authors: Pieper Rebecca , Tomé Filipa , von Korff Maria
Published: March 2020

FLOWERING LOCUS T-like genes (FT-like) control the photoperiodic regulation of flowering in many angiosperm plants. The family ofFT-like genes is characterised by extensive gene duplication and subsequent diversification ofFTfunctions which occurred independently in modern angiosperm lineages. In barley, there are 12 knownFT-like genes (HvFT) but the function of most of them remains uncharacterised. This study aimed to characterise the role of HvFT4 in flowering time control and development in barley. The overexpression ofHvFT4in the spring cultivar Golden Promise delayed flowering time under long-day conditions. Microscopic dissection of the shoot apical meristem (SAM) revealed that overexpression ofHvFT4specifically delayed spikelet initiation and reduced the number of spikelet primordia and grains per spike. Furthermore, ectopic overexpression ofHvFT4was associated with floret abortion and with the downregulation of the barley MADS-box genesVRN-H1, HvBM3andHvBM8which promote floral development. This suggests that HvFT4 functions as a repressor of reproductive development in barley. Unraveling the genetic basis ofFT-like genes can contribute to the identification of novel breeding targets to modify reproductive development and thereby spike morphology and grain yield.

Highlight

We identify theFLOWERING LOCUS T(FT)-like geneHvFT4as a negative regulator of reproductive development, spikelet initiation, floret fertility and grain number in barley.
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-domain Camelid Antibodies
Authors: Wrapp Daniel , De Vlieger Dorien , Corbett Kizzmekia S. , Torres Gretel M. , Van Breedam Wander , Roose Kenny , van Schie Loes ,   VIB-CMB COVID-19 Response Team, Hoffmann Markus , Pöhlmann Stefan , Graham Barney S. , Callewaert Nico , Schepens Bert , Saelens Xavier , McLellan Jason S.
Published: March 2020

The pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV-1) and COVID-19 coronavirus (SARS-CoV-2) have all emerged into the human population with devastating consequences. These viruses make use of a large envelope protein called spike (S) to engage host cell receptors and catalyze membrane fusion. Because of the vital role that these S proteins play, they represent a vulnerable target for the development of therapeutics to combat these highly pathogenic coronaviruses. Here, we describe the isolation and characterization of single-domain antibodies (VHHs) from a llama immunized with prefusion-stabilized coronavirus spikes. These VHHs are capable of potently neutralizing MERS-CoV or SARS-CoV-1 S pseudotyped viruses. The crystal structures of these VHHs bound to their respective viral targets reveal two distinct epitopes, but both VHHs block receptor binding. We also show cross-reactivity between the SARS-CoV-1 S-directed VHH and SARS-CoV-2 S, and demonstrate that this cross-reactive VHH is capable of neutralizing SARS-CoV-2 S pseudotyped viruses as a bivalent human IgG Fc-fusion. These data provide a molecular basis for the neutralization of pathogenic betacoronaviruses by VHHs and suggest that these molecules may serve as useful therapeutics during coronavirus outbreaks.
Ppd-H1integrates drought stress signals to control spike development and flowering time in barley
Authors: Gol Leonard , Haraldsson Einar B. , von Korff Maria
Published: March 2020

Drought impairs growth and spike development and is therefore a major cause of yield losses in the temperate cereals barley and wheat. Here, we show that the photoperiod response genePHOTOPERIOD-H1(Ppd-H1) interacts with drought stress signals to modulate spike development. We tested the effects of a continuous mild and a transient severe drought stress on developmental timing and spike development in spring barley cultivars with a natural mutation inppd-H1and derived introgression lines carrying the wild-typePpd-H1allele from wild barley. Mild drought reduced the spikelet number and delayed floral development in spring cultivars but not the introgression lines with a wild-typePpd-H1allele. Similarly, drought-triggered reductions in plant height, tiller and spike number were more pronounced in the parental lines compared to the introgression lines. Transient severe stress halted growth and floral development, upon rewatering introgression lines, but not the spring cultivars, accelerated development so that control and stressed plants flowered almost simultaneously. These genetic differences in development were correlated with a differential downregulation of the flowering promotorsFLOWERING LOCUS T1and the BARLEY MADS-box genesBM3andBM8.Our findings, therefore, demonstrate thatPpd-H1affects developmental plasticity in response to drought in barley.

Highlight

We show thatPpd-H1integrates photoperiod and drought stress signals viaFLOWERING LOCUS T1 (FT1)and the downstream MADS-box genesBM3andBM8to modulate reproductive development, and shoot and spike morphology in barley.
Shared and distinct patterns of atypical cortical morphometry in children with autism and anxiety
Authors: Yin Shelly , Hong Seok-Jun , Di Martino Adriana , Milham Michael P. , Park Bo-Yong , Benkarim Oualid , Bethlehem Richard A.I. , Bernhardt Boris C. , Paquola Casey
Published: March 2020

Autism spectrum disorder (ASD) and anxiety disorders (ANX) are common neurodevelopmental conditions with several overlapping symptoms. Notably, many children and adolescents with ASD also have an ANX diagnosis, suggesting shared pathological mechanisms. Here, we leveraged structural imaging and phenotypic data from 82 closely matched children (28 ASD, 28 ANX, 26 typically developing controls). Our neuroimaging paradigm assessed cortical thickness and studied inter-regional structural covariance networks. Both ASD and ANX presented with atypical structural network organization relative to controls. Specifically, ASD presented with increased thickness in temporal and parietal midline cortices, while ANX was associated with increased cortical thickness in the left inferior frontal and precentral gyri. Despite the overall difference in the spatial distributions these clusters, unconstrained spin permutation testing showed that statistical maps from the ANX-vs-controls and ASD-vs-controls analyses were significantly correlated. The two diagnostic groups also presented with common decreases in structural covariance patterns, collectively pointing to decreased structural coupling between lateral frontal, lateral temporal, and temporo-parietal regions. Dimensional analysis of trait anxiety and social responsiveness partially recapitulated diagnosis-based findings. Collectively, our findings provide evidence for both shared as well as distinct effects of ASD and ANX on on regional and inter-regional structural network organization.
Site-specific analysis of the SARS-CoV-2 glycan shield
Authors: Watanabe Yasunori , Allen Joel D. , Wrapp Daniel , McLellan Jason S. , Crispin Max
Published: March 2020

The emergence of the betacoronavirus, SARS-CoV-2 that causes COVID-19, represents a significant threat to global human health. Vaccine development is focused on the principal target of the humoral immune response, the spike (S) glycoprotein, that mediates cell entry and membrane fusion. SARS-CoV-2 S gene encodes 22 N-linked glycan sequons per protomer, which likely play a role in immune evasion and occluding immunogenic protein epitopes. Here, using a site-specific mass spectrometric approach, we reveal the glycan structures on a recombinant SARS-CoV-2 S immunogen. This analysis enables mapping of the glycan-processing states across the trimeric viral spike. We show how SARS-CoV-2 S glycans differ from typical host glycan processing, which may have implications in viral pathobiology and vaccine design.
Testing theoretical minimal genomes using whole-cell models
Authors: Rees-Garbutt Joshua , Rightmyer Jake , Chalkley Oliver , Marucci Lucia , Grierson Claire
Published: March 2020

The minimal gene set for life has often been theorised, with at least ten produced forMycoplasma genitalium(M. genitalium). Due to the difficulty of usingM. genitaliumin the lab, combined with its long replication time of 12 - 15 hours, none of these theoretical minimal genomes have been tested, even with modern techniques. The publication of theM. genitaliumwhole-cell model provided the first opportunity to test them, simulating the genome editsin-silico. We simulated eight minimal gene sets from the literature, finding that they producedin-silicocells that did not divide. Using knowledge from previous research, we reintroduced specific essential and low essential genesin-silico; enabling cellular division. This reinforces the need to identify species-specific low essential genes and their interactions. Any genome designs created using the currently incomplete and fragmented gene essentiality information, will very likely requirein-vivoreintroductions to correct issues and produce dividing cells.
A Chlorophyte alga utilizes alternative electron transport for primary photoprotection
Authors: Ware Maxwell A. , Hunstiger Darcy , Cantrell Michael , Peers Graham
Published: March 2020

Desmodesmus armatusis an emerging biofuel platform producing high amount of lipids and biomass in mass culture. We observedD. armatusin light-limiting, excess light and sinusoidal light environments to investigate its photoacclimation behaviors and the mechanisms by which it dissipates excess energy. Chlorophylla:bratios and the functional absorption cross section of photosystem II (PSII) suggested a constitutively small light harvesting antenna size relative to other green algae.In situandex situmeasurements of photo-physiology revealed that nonphotochemical quenching (NPQ) is not a significant contributor to photoprotection, but cells do not suffer substantial photoinhibition despite its near absence. We performed membrane inlet mass spectrometry analysis to show thatD. armatushas a very high capacity for alternative electron transport (AET) measured as light dependent oxygen consumption. Up to 90% of electrons generated at PSII can be dissipated by AET in a water-water cycle during growth in rapidly fluctuating light environments like those found in industrial scale photobioreactors. This work highlights the diversity of photoprotective mechanisms shown in algal systems, that NPQ is not necessarily required for effective photoprotection in some algae and suggests that engineering AET may be an attractive target for increasing biomass productivity of some strains.

One-sentence summary

Constitutive small antennae, alternative electron transport and an efficient photosystem II turnover capacity enableD. armatusto photosynthesize efficiently.