bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumor MHCII immunity requires in situ antigen presentation by cancer-associated fibroblasts
Authors: Kerdidani Dimitra , Aerakis Emmanouil , Verrou Kleio-Maria , Stamoulis Petros , Goudevenou Katerina , Prados Alejandro , Tzaferis Christos , Vamvakaris Ioannis , Kaniaris Evangelos , Vachlas Konstantinos , Sepsas Evangelos , Potaris Konstantinos , Koutsopoulos Anastasios , Tsoumakidou Maria
Published: March 2020

A key unknown of the functional space in tumor immunity is whether physiologically relevant cancer antigen presentation occurs solely in draining lymph nodes versus tumors. Professional antigen presenting cells, i.e. the dendritic cells, are scarce and immature within tumors, greatly outnumbered by MHCII expressing non-hematopoietic cells, such as antigen-presenting cancer-associated fibroblasts (apCAFs). We hypothesized that after their exit from tumor-draining lymph nodes T cells depend on a second wave of antigen presentation provided in situ by structural cells. We show that dense apCAF regions in human lung tumors define hot immunological spots with increased numbers of CD4 T cells. The transcriptomic profile of human lung apCAFs aligned to that of pancreatic apCAFs across mice and humans and were both enriched for alveolar type II genes, suggesting an epithelial origin. Mechanistically, human apCAFs directly activated the TCRs of adjacent effector CD4 T cells and at the same time produced high levels of c1q, which acted on surface c1qbp on T cells to rescue them from apoptosis. Fibroblast-specific deletion of MHCII in mice impaired local MHCII immunity and accelerated tumor growth, while inducing c1qbp overexpression in adoptively transferred T cells expanded their numbers within tumors and reduced tumour burden. Collectively, our work shows that tumor T cell immunity post lymph node exit requires peripheral antigen presentation by a subset of CAFs and proposes a new conceptual framework upon which effective cancer immunotherapies can be built.
FSD1: a plastidial, nuclear and cytoplasmic enzyme relocalizing to the plasma membrane under salinity
Authors: Dvořák Petr , Krasylenko Yuliya , Ovečka Miroslav , Basheer Jasim , Zapletalová Veronika , Šamaj Jozef , Takáč Tomáš
Published: March 2020

Here, we aimed to resolve the developmental expression and subcellular localization ofArabidopsisiron superoxide dismutase FSD1, which belongs to the family of superoxide dismutases (SODs), prominent enzymes decomposing superoxide anion and determining abiotic stress tolerance. We found thatfsd1knockout mutants exhibit reduced lateral root number and that this phenotype was complemented byproFSD1::GFP:FSD1andproFSD1::FSD1:GFPconstructs. Light sheet fluorescence microscopy revealed a temporary accumulation of FSD1-GFP at the site of endosperm rupture during seed germination. In emerged roots, FSD1-GFP showed the highest abundance in cells of the lateral root cap, columella, and endodermis/cortex initials. The largest subcellular pool of FSD1-GFP was localized in the plastid stroma, while it was also located in the nuclei and cytoplasm. FSD1 is crucial for seed germination and salt stress tolerance, which is tightly coupled with FSD1-GFP subcellular relocation to the plasma membrane. FSD1 is most likely involved in superoxide decomposition in the periplasm. This study suggests a new osmoprotective function of SODs in plants.
Vocal convergence in a multi-level primate society: insights into the evolution of vocal learning
Authors: Fischer Julia , Wegdell Franziska , Trede Franziska , Pesco Federica Dal , Hammerschmidt Kurt
Published: March 2020

The extent to which nonhuman primate vocalizations are amenable to modification through experience is relevant for understanding the substrate from which human speech evolved. We examined the vocal behaviour of Guinea baboons,Papio papio, ranging in the Niokolo Koba National Park in Senegal. Guinea baboons live in a multi-level society, with units nested within parties nested within gangs. We investigated whether the acoustic structure of grunts of 27 male baboons of two gangs varied with party/gang membership and genetic relatedness. Males in this species are philopatric, resulting in increased male relatedness within gangs and parties. Grunts from members were more similar within than across social levels (N = 351 dyads for comparison within and between gangs, and N = 169 dyads within and between parties), but the effect sizes were small. Yet, acoustic similarity did not correlate with genetic relatedness, suggesting that higher amounts of social interactions rather than genetic relatedness promote the observed vocal convergence. We consider this convergence a result of sensory-motor integration and suggest this to be an implicit form of vocal learning shared with humans, in contrast to the goal-directed and intentional explicit form of vocal learning unique to human speech acquisition.
Evidence for a growth zone for deep subsurface microbial clades in near-surface anoxic sediments
Authors: Lloyd Karen G. , Bird Jordan T. , Buongiorno Joy , Deas Emily , Kevorkian Richard , Noordhoek Talor , Rosalsky Jacob , Roy Taylor
Published: March 2020

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily-metabolized organic compounds and total microbial cell abundance decrease steadily. However, it is unknown whether some microbial clades increase with depth, despite the overall trend of abundance decrease. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often anaerobic, uncultured, or common in deep marine sediments relative to those that decreased. Minimum turnover times (which are minimumin situdoubling times of growth rates) were estimated to be 2-25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the Fraction Read Abundance of 16S rRNA genes and total Cell counts (FRAxC). Turnover times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28 ± 19%). qPCR and FRAxC in WOR cores and FRAxC in CLB incubations produced similar turnover times for key deep subsurface uncultured cladesBathyarchaeota(8.7 ± 1.9 years) andThermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for natural selection of traits for long-term subsistence after resuspension events.

Significance statement

The current dogma is that the deeply-branching uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments – rather they exist in a sort of prolonged torpor for thousands of years. This is because no evidence has ever been found that these clades actually increase population sizes, or grow, as they are gradually buried. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This changes our dogma about marine sediments as a vast repository of non-growing microbes, to a vast repository of non-growing microbes with a thin and relatively rapid area of growth in the upper 10 centimeters.
Narrow oviposition preference of an insect herbivore risks survival under conditions of severe drought
Authors: Salgado Ana L. , DiLeo Michelle F. , Saastamoinen Marjo
Published: March 2020

Understanding species’ habitat preferences are crucial to predict organisms’ responses to the current climate crisis. In many insects, maternal habitat selection for oviposition essentially determines offspring performance. Whether changes in climatic conditions may pose future mismatches in oviposition preference and offspring performance when mothers continue to prefer microhabitats that now threaten offspring survival is an open question.

To address this, we tested if oviposition preferences put offspring at risk in the Glanville fritillary butterfly (Melitaea cinxia) under drought stress. Mainly, we focus on identifying the microhabitat determinants for oviposition and the variation of conditions experienced by the sessile offspring, using field observations from 12 populations collected over 2015-2018. These data are combined with ten years of larval nest and precipitation data to understand within-population patterns of habitat selection. We tested whether the preferred microhabitats maximized the extended larval performance (i.e. overwinter survival).

We found that females preferentially oviposited in microhabitats with higher host plant abundance and higher proportion of host plants with signs of drought stress. In most years, larval nests had higher survival in these drought-stressed microhabitats. However, in an extremely dry year, only two nests survived over the summer.

Our results highlight that a failure to shift habitat preference under extreme climate conditions may have drastic consequences for the survival of natural populations under changing climatic conditions.
Visualization of the initial fixed nitrogen transport in nodulated soybean plant using [13N]N2tracer gas in real-time
Authors: Nguyen Hung V. P. , Thi Hue Tong
Published: March 2020

The observation of initial transport of fixed nitrogen in intact soybean plants in real-time was conducted by using the positron-emitting tracer imaging system (PETIS). Soybean root nodules were fed with [13N]N2for 10 minutes, and the radioactivity of [13N]N tracer was recorded for 60 minutes. The serial images of nitrogen fixation activity and translocation of fixed nitrogen in the soybean plant were reconstructed to estimate the fixed-N transport to the upper shoot. As a result, the signal of nitrogen radiotracer moving upward through the intact stem was successfully observed. This is the first report that the translocation of fixed-N is visualized in real-time in soybean plant by a moving image. The signal of nitrogen radiotracer appeared at the base stem at about 20 minutes after the feeding of tracer gas and it took 40 minutes to reach the upper stem. The velocity of fixed nitrogen translocation was estimated approximately at 1.63 cm min-1. The autoradiography taken after PETIS experiment showed a clear picture of transport of fixed13N in the whole plant that the fixed-N moved not only via xylem system but also via the phloem system to the shoot after transferring from xylem to phloem in the stem although it has been generally considered that the fixed-N in nodule is transported dominantly via xylem by transpiration stream toward mature leaves. This result also suggests that the initial transport of fixed-N was mainly into the stem and subsequently translocated to young leaves and buds via the phloem system. These new findings in the initial transport of fixed nitrogen of soybean by PETIS observation will become the basis for future study of fixed-N transport in the whole legume plants.
High-content image-based drug screen identifies a clinical compound against cell transmission of adenovirus
Authors: Georgi Fanny , Kuttler Fabien , Murer Luca , Andriasyan Vardan , Witte Robert , Yakimovich Artur , Turcatti Gerardo , Greber Urs F
Published: March 2020

Human adenoviruses (HAdVs) are fatal to immuno-suppressed people, but no effective anti-HAdV therapy is available. Here, we present a novel image-based high-throughput screening (HTS) platform, which scores the full viral replication cycle from virus entry to dissemination of progeny. We analysed 1,280 small molecular weight compounds of the Prestwick Chemical Library (PCL) for interference with HAdV-C2 infection in a quadruplicate, blinded format, and included robust image analyses, and hit filtering. We present the entire set of the screening data including all the images, image analyses and data processing pipelines. The data are made available at the Image Data Repository (IDR)1, accession number idr0081. Our screen identified Nelfinavir mesylate as an inhibitor of HAdV-C2 multi-round plaque formation, but not single round infection. Nelfinavir has been FDA-approved for anti-retroviral therapy in humans. Our results underscore the power of image-based full cycle infection assays in identifying viral inhibitors with clinical potential.
No room to roam: King Cobras reduce movement in agriculture
Authors: Marshall Benjamin Michael , Crane Matt , Silva Inês , Strine Colin Thomas , Jones Max Dolton , Hodges Cameron Wesley , Suwanwaree Pongthep , Artchawakom Taksin , Waengsothorn Surachit , Goode Matt
Published: March 2020

Studying animal movement provides insights into how animals react to land-use changes, specifically how animals can change their behaviour in agricultural areas. Recent reviews show a tendency for species to reduce movements in response to increased human landscape modification, but the study of movement has not been extensively explored in reptiles. We examined movements of a large reptilian predator, the King Cobra (Ophiophagus hannah), in Northeast Thailand. We used a consistent regime of radio-telemetry tracking to document movements across protected forest and adjacent agricultural areas. We then adapted GPS-targeting analytic methods to examine the movement using metrics of site reuse and dynamic Brownian Bridge Movement Model derived motion variance. Examination of motion variance demonstrated that King Cobra movements increased in forested areas and tended to decrease in agricultural areas. Our Integrated Step-Selection Functions indicated that when moving in agricultural areas King Cobras restricted their movements, thereby remaining within vegetated semi-natural areas, often located along the banks of irrigation canals. Site reuse metrics of residency time and number of revisits remained unaffected by distance to landscape features. Neither motion variance nor reuse metrics were consistently affected by the presence of threatening landscape features (e.g. roads, human settlements); suggesting that King Cobras will remain in close proximity to threats, provided habitat patches are available. Although King Cobras displayed heterogeneity in their response to agricultural landscapes, the overall trend suggested a reduction in movements when faced with fragmented habitat patches embedded in an otherwise inhospitable land-use matrix. Reductions in movements are consistent with findings for mammals and forest specialist species.
Outer membrane-deprived cyanobacteria liberate periplasmic and thylakoid luminal components that support the growth of heterotrophs
Authors: Kojima Seiji , Okumura Yasuaki
Published: March 2020

Chloroplasts originate from endosymbiosis of a cyanobacterium within a heterotrophic host cell. Establishing endosymbiosis requires the translocation across its envelope of photosynthetic products generated inside the once free-living cyanobacterium to be exploited by host metabolism. However, the nature of this translocation event is unknown. We previously found that most cyanobacterial outer membrane components were eliminated during the primitive stage of chloroplast evolution, suggesting the importance of evolutionary changes of the outer membrane. Here, we removed the outer membrane fromSynechocystissp. PCC 6803 by disrupting the physical interaction with peptidoglycan, and characterized the effects on cell function. Outer membrane-deprived cells liberated diverse substances into the environment without significantly compromising photoautotrophic growth. The amount of liberated proteins increased to ~0.35 g/L within five days of culture. Proteomic analysis showed that most liberated proteins were periplasmic and thylakoid luminal components. Connectivity between the thylakoid lumen-extracellular space was confirmed by findings that an exogenous hydrophilic oxidant was reduced by photosynthetic electron transport chain on the thylakoid membrane. Metabolomic analysis detected the release of nucleotide-related metabolites at concentrations around 1 μM. The liberated materials supported the proliferation of heterotrophic bacteria. These findings show that breaching the outer membrane, without any manipulations to the cytoplasmic membrane, converts a cyanobacterium to a chloroplast-like organism that conducts photosynthesis and releases its biogenic materials. This conversion not only represents a potential explanation why the outer membrane markedly changed during the earliest stage of chloroplast evolution, but also provides the opportunity to harness cyanobacterial photosynthesis for biomanufacturing processes.

SIGNIFICANCE STATEMENT

Although it is well accepted that chloroplasts stem from endosymbiosis of a cyanobacterium within a heterotrophic host cell, the issue of how photosynthetic products generated inside a formerly free-living cyanobacterium are translocated across its envelope and exploited by host metabolism has been little addressed. Here we show that breaching the cyanobacterial outer membrane barrier converts a cyanobacterium to a chloroplast-like organism that conducts photosynthesis and releases its diverse biogenic materials into its external environment, which sustains the growth of heterotrophic organisms. This conversion represents a possible example of metabolic exploitation of cyanobacterial photosynthesis. Further, this “quasi-chloroplast” provides a potential opportunity for industrial application such as producing feedstock for biomanufacturing processes that harnesses heterotrophic bacteria.
Moving-average based index to timely evaluate the current epidemic situation after COVID-19 outbreak
Authors: Yun-ting He , Xiao-jin Wang , Hao He , Jing Zhai , Bing-shun Wang
Published: March 2020

[ABSTRACT]

A pneumonia outbreak caused by a novel coronavirus (COVID-19) occurred in Wuhan, China at the end of 2019 and then spread rapidly to the whole country. A total of 81,498 laboratory-confirmed cases, including 3,267 deaths (4.0%) had been reported in China by March 22, 2020, meanwhile, 210,644 laboratory-confirmed cases and 9,517 deaths (4.5%) were reported outside China. Common symptoms of COVID-19 pneumonia included fever, fatigue and dry cough. In face of such a sudden outbreak of emerging novel infectious diseases, we have no history to learn from and no evidence to count on. Traditional models often predict inconsistent results. There is an urgent need to establish a practical data-driven method to predict the evolutionary trend of the epidemic, track and prejudge the current epidemic situation after the COVID-19 outbreak. Here we propose a simple, directly and generally applicable index and we name it ‘epidemic evaluation index’ (EEI), which is constructed by 7-day moving average of the log-transformed daily new cases (LMA). EEI could be used to support the decision-making process and epidemic prevention and control strategies through the evaluation of the current epidemic situation. First, we used SARS epidemic data from Hong Kong in 2003 to verify the practicability of the new index, which shows that the index is acceptable. The EEI was then applied to the COVID-19 epidemic situation analysis. We found that the trend direction of different districts in China changed on different date during the epidemic. At the national level and at local Hubei Province level, the epidemic both peaked on February 9. While the peak occurred relatively earlier, i.e. on February 5 in other provinces. It demonstrated the effectiveness of decisive action and implementations of control measures made by Chinese governments. While local governments should adjust management measures based on local epidemic situation. Although the epidemic has eased since late February, continued efforts in epidemic control are still required to prevent transmission of imported cases in China. However, the global COVID-19 epidemic outside China continues to expand as indicated by the EEI we proposed. Currently, efforts have been made worldwide to combat the novel coronavirus pandemic. People all over the world should work together and governments of all countries should take efficient measures in the light of Chinas experience and according to national circumstances and local conditions.
One size does not fit all. Genomics differentiates among binge-eating disorder, bulimia nervosa, and anorexia nervosa
Authors: Hübel Christopher , Abdulkadir Mohamed , Herle Moritz , Loos Ruth J.F. , Breen Gerome , Bulik Cynthia M. , Micali Nadia
Published: March 2020

Objective

Genome-wide association studies have identified multiple genomic regions associated with anorexia nervosa. Relatively few or no genome-wide studies of other eating disorders, such as bulimia nervosa and binge-eating disorder, have been performed, despite their substantial heritability. Exploratively, we aimed to identify traits that are genetically associated with binge-type eating disorders.

Method

We calculated genome-wide polygenic scores for 269 trait and disease outcomes using PRSice v2.2 and their association with anorexia nervosa, bulimia nervosa, and binge-eating disorder in up to 640 cases and 17,050 controls from the UK Biobank. Significant associations were tested for replication in the Avon Longitudinal Study of Parents and Children (up to 217 cases and 3018 controls).

Results

Individuals with binge-type eating disorders had higher polygenic scores than controls for other psychiatric disorders, including depression, schizophrenia, and attention deficit hyperactivity disorder, and higher polygenic scores for body mass index.

Discussion

Our findings replicate some of the known comorbidities of eating disorders on a genomic level and motivate a deeper investigation of shared and unique genomic factors across the three primary eating disorders.
Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada
Authors: Tuite Ashleigh R. , Fisman David N. , Greer Amy L.
Published: March 2020

Background

We evaluated how non-pharmaceutical interventions could be used to control the COVID-19 pandemic and reduce the burden on the healthcare system.

Methods

Using an age-structured compartmental model of COVID-19 transmission in the population of Ontario, Canada, we compared a base case with limited testing, isolation, and quarantine to scenarios with: enhanced case finding; restrictive social distancing measures; or a combination of enhanced case finding and less restrictive social distancing. Interventions were either implemented for fixed durations or dynamically cycled on and off, based on projected ICU bed occupancy. We present median and credible intervals (CrI) from 100 replicates per scenario using a two-year time horizon.

Results

We estimated that 56% (95% CrI: 42-63%) of the Ontario population would be infected over the course of the epidemic in the base case. At the epidemic peak, we projected 107,000 (95% CrI: 60,760-149,000) cases in hospital and 55,500 (95% CrI: 32,700-75,200) cases in ICU. For fixed duration scenarios, all interventions were projected to delay and reduce the height of the epidemic peak relative to the base case, with restrictive social distancing estimated to have the greatest effect. Longer duration interventions were more effective. Dynamic interventions were projected to reduce the proportion of the population infected at the end of the two-year period. Dynamic social distancing interventions could reduce the median number of cases in ICU below current estimates of Ontario’s ICU capacity.

Interpretation

Without significant social distancing or a combination of moderate social distancing with enhanced case finding, we project that ICU resources would be overwhelmed. Dynamic social distancing could maintain health system capacity and also allow periodic psychological and economic respite for populations.
Prevalence of Malaria from Blood Smears Examination: A Three-Year Retrospective Study from Nakfa Hospital, Eritrea
Authors: Kesete Yafet , Mhretab Shewit , Tesfay Meron
Published: March 2020

Background

Malaria afflicts more than 90 countries in the tropical and subtropical region in which more than half of cases are present in sub-Saharan, Africa. It is one of the major health issues in Eritrea in which about 3.6 million (71%) of Eritrean population live in areas conducive for high transmission of malaria. Studying its prevalence is necessary to implement effective control measures. Therefore, this study was conducted to determine the three-year prevalence of malaria from peripheral blood smear examination.

Methods

A retrospective study was conducted at Nakfa Hospital from September 2016 to August 2019. All demographic details of subjects and positive malaria cases data were collected from laboratory registration book.

Results

The overall prevalence of smear positive malaria cases was 33.0% (1921 cases out of 5826). Males (58.19%) were more prone to have a positive malaria smear than females (41.8%). A higher prevalence of malaria was observed in the adult age group (35%) compared with children under 5 years old children (27%). The highest prevalence of malaria cases was found in the year 2016 in which correspond to 48.8%. A comparative incidence was also observed during the next year of 2017 with rate of 41% (1087 cases out of 2680) and decreased to low levels in recent couple of years. High slide positive rate was seen in summer (40%) and Autumn (39.52%) whereas Spring had the lowest frequency of cases (14.3%). Similarly, months of July (45%) and September (40.6%) had been noted to have the maximum number of cases.Plasmodium vivaxconstituted the most predominant malaria infections (78.06%), while markedly lowerp. falciparumwas also present (21.26 %). Almost around 70% of cases were reported from patients living in and at the peripheries of Nakfa town.

Conclusion

Eritrea is one of the few countries which has made a profound progress on decreasing transmission of common communicable diseases. However, vigilant surveillance is required especially during malaria transmission peaks from July to October which also overlap with harvesting seasons in Eritrea. Therefore, health planners need to organize intensive health education to increase community awareness via promotion of information and communication.
Enhanced mirroring upon mutual gaze: Multimodal evidence from TMS-assessed corticospinal excitability and the EEG mu rhythm
Authors: Prinsen Jellina , Alaerts Kaat
Published: March 2020

Eye-to-eye contact is a salient cue for regulating everyday social interaction and communication. Previous research has demonstrated that direct eye contact between actor and observer specifically enhances the ‘mirroring’ of others’ actions in the observer, as measured by transcranial magnetic stimulation (TMS)-induced motor evoked potentials (MEPs; an index of motor cortex excitability during action observation). However, it remains unknown whether other markers of mirror system activation, such as suppression of the EEG mu rhythm (i.e. attenuation of neural oscillations in the 8-13 Hz frequency band over the sensorimotor strip), are also susceptible to perceived eye contact. In the current study, a multimodal approach was adopted to assess both TMS-induced MEPs and EEG mu suppression (in separate sessions), while 32 participants (20 men; mean age: 24;8 years) observed a simple hand movement in combination with direct or averted gaze from the live stimulus person. Both indices of mirror system functioning were significantly modulated by perceived eye gaze; showing a significant increase in MEP amplitude and a significant attenuation of the mu rhythm when movement observation was accompanied with direct compared to averted gaze. Importantly, while inter-individual differences in absolute MEP and mu suppression scores were not significantly related, a significant association was identified between gaze-related changes in MEP responses and mu suppression. As such, it appears that while the neurophysiological substrates underlying mu suppression and TMS-induced MEP responses differ, both are similarly affected by the modulatory impact of gaze-related cues. In sum, our results suggest that both EEG mu rhythm and TMS-induced MEPs are sensitive to the social relevance of the observed actions, and that a similar neural substrate may drive gaze-related changes in these distinct markers of mirror system functioning.
Motor-evoked neural responses in auditory cortex are associated with improved sensitivity to self-generated sounds
Authors: Reznik Daniel , Hacohen Noa , Buaron Batel , Zion-Golumbic Elana , Mukamel Roy
Published: March 2020

Sensory perception is a product of complex interactions between the internal state of an organism and the physical attributes of a stimulus. One factor that modulates the internal state of the perceiving agent is voluntary movement. It has been shown across the animal kingdom that perception and sensory-evoked physiological responses are modulated depending on whether or not the stimulus is the consequence of voluntary actions. These phenomena are often attributed to motor signals sent to relevant sensory regions (efference copies), that convey information about expected upcoming sensory consequences. However, to date, there is nodirectevidence in humans for efferent signals underlying these motor-sensory interactions. In the current study we recorded neurophysiological (using Magnetoencephalography) and behavioral responses from 16 healthy subjects performing an auditory detection task of faint tones. Tones were either generated by subjects’ voluntary button presses or occurred predictably following a visual cue. By introducing a constant temporal delay between button press/cue and tone delivery and applying source-level analysis we decoupled motor-evoked and auditory-evoked activity in auditory cortex. We show motor-related evoked-responses in auditory cortex following sound-triggering actions and preceding sound onset. Such evoked-responses were not found for button-presses that were not coupled with expected sounds. Furthermore, the amplitude of these evoked-responses corresponded with subsequent sound detection, suggesting their functional relevance to auditory processing. Our results provide firstdirectevidence for efferent signals in sensory cortex that are evoked by voluntary actions coupled with sensory consequences.
Transcriptomic and proteomic dynamics during metamorphosis of Pacific oysterCrassostrea gigas
Authors: Xu Fei , Zhang Guofan
Published: March 2020

Many marine invertebrate phyla are characterized by indirect development. These animals transit from planktonic larvae to benthic adults via settlement and metamorphosis, which contributes to the adaption to the marine environment. Studying the biological process of metamorphosis is thus a key to understand the origin and evolution of indirect development. Numerous studies have been conducted on the relationships of metamorphosis with the marine environment, microorganisms, as well as the neurohormones, however, little is known on the gene regulation network (GRN) dynamics during metamorphosis. Metamorphosis competent pediveliger of Pacific oysterCrassostrea gigaswas assayed in this study. By identifying genes enriched in competent pediveliger and early spat, as well as pediveligers treated with epinephrine, the dynamics of genes and proteins was examined with transcriptomics and proteomics methods. The results indicated significantly different gene regulation networks before, during, and post metamorphosis. Genes encoding membrane integrated receptors and related to the remodeling of the nervous system were upregulated before the initiation of metamorphosis. Massive biogenesis, e.g., various enzymes and structural proteins, occurred during metamorphosis. Correspondingly, the protein synthesis system was comprehensively activated after epinephrine stimulation. Hierarchical downstream gene networks were also stimulated, where some transcription factors showed different temporal response patterns, including some important Homeobox, basic helix-loop-helix factors and nuclear receptors. Nuclear receptors, as well as their retinoic acid receptor partners, should play critical roles during the oyster metamorphosis, although they may not be responsible for the initiation process. Enriched genes in early spat were mainly related to environmental stress responses, indicating the GRN complexity of the transition stage during oyster metamorphosis.
Axenicin-vitrocultivation of nineteen peat-moss (SphagnumL.) species as a resource for basic biology, biotechnology and paludiculture
Authors: Heck Melanie A. , Lüth Volker M. , Krebs Matthias , Kohl Mira , Prager Anja , Joosten Hans , Decker Eva L. , Reski Ralf
Published: March 2020

The cultivation ofSphagnummosses reduces CO2emissions by rewetting drained peatlands and by substituting peat with renewable biomass. ‘Sphagnum farming’ requires large volumes of founder material, which can only be supplied sustainably by axenic cultivation in bioreactors.

We established axenicin-vitrocultures from sporophytes of 19Sphagnumspecies collected in Austria, Germany, Latvia, Netherlands, Russia and Sweden, namelyS. angustifolium, S. balticum, S. capillifolium, S. centrale, S. compactum, S. cuspidatum, S. fallax, S. fimbriatum, S. fuscum, S. lindbergii, S. medium/divinum, S. palustre, S. papillosum, S. rubellum, S. russowii, S. squarrosum, S. subnitens, S. subfulvum, andS. warnstorfii. These species cover five of the six EuropeanSphagnumsections, namelyAcutifolia, Cuspidata, Rigida, SphagnumandSquarrosa.

Their growth was measured in axenic suspension cultures, whereas their ploidy was determined by flow cytometry and compared with the genome size ofPhyscomitrella patens. We identified haploid and diploidSphagnumspecies, found that their cells are predominantly arrested in the G1-phase of the cell cycle, and did not find a correlation between plant productivity and ploidy.

With this collection, high-quality founder material for diverse large-scale applications but also for basicSphagnumresearch is available from the International Moss Stock Center (IMSC).
Physical confinement impacts cellular phenotype within living materials
Authors: Priks Hans , Butelmann Tobias , Illarionov Aleksandr , Johnston Trevor G. , Fellin Christopher , Tamm Tarmo , Nelson Alshakim , Kumar Rahul , Lahtvee Petri-Jaan
Published: March 2020

Additive manufacturing allows three-dimensional printing of polymeric materials together with cells, creating living materials for applications in biomedical research and biotechnology. However, understanding the cellular phenotype within living materials is lacking and a key limitation for their wider application. Herein, we present an approach to characterize the cellular phenotype within living materials. We immobilized the budding yeastSaccharomyces cerevisiaein three different photocross-linkable triblock polymeric hydrogels containing F127-bis-urethane methacrylate, F127-dimethacrylate, or poly(alkyl glycidyl ether)-dimethacrylate. Using optical and scanning electron microscopy, we showed that hydrogels based on these polymers were stable under physiological conditions, but yeast colonies showed differences in the interaction within the living materials. We found that the physical confinement, imparted by compositional and structural properties of the hydrogels, impacted the cellular phenotype by reducing the size of cells in living materials compared with suspension cells. These properties also contributed to the differences in immobilization patterns, growth of colonies, and colony coatings. We observed that a composition-dependent degradation of polymers was likely possible by cells residing in the living materials. In conclusion, our investigation highlights the need for a holistic understanding of the cellular response within hydrogels to facilitate the synthesis of application-specific polymers and the design of advanced living materials in the future.
Temporal resource continuity increases predator abundance in a metapopulation model: insights for conservation and biocontrol
Authors: Spiesman Brian J. , Iuliano Benjamin , Gratton Claudio
Published: March 2020

The amount of habitat in a landscape is an important metric for evaluating the effects of land cover and land use on biodiversity and ecosystem services, yet it fails to capture complex temporal dimensions of resource availability that could be consequential for species population dynamics. If ephemeral resources across multiple habitat patches are synchronously available, resource gaps could be detrimental to population growth. In contrast, asynchronously available resources create a mosaic of temporally complementary resources that mobile organisms can track across the landscape. Knowledge is especially lacking on the relevance of temporal complementation for tri-trophic interactions and biological pest control. Here we use a spatially-explicit predator-prey metapopulation model to test the effect of different spatiotemporal resource patterns on insect predators and their prey. We examined prey and predator responses in model landscapes that varied in both the amount and temporal variability of basal vegetation resources. Further, we examined cases where prey comprised either a single generalist species or two specialist species that use different resources available either early or late in the growing season. We found that predators and generalist prey benefitted from lower temporal variance of basal resources, which increased both of their landscape-scale abundances. However, increasing the amount of basal resources also increased the variability of generalist prey populations, resulting in a negative correlation between basal resource amount and predator abundance. Specialist prey, on the other hand, did not benefit from less temporally variable in basal resources, since they were restricted by habitat type while also suffering greater predation. Predators feeding on specialists achieved greater prey suppression in landscapes with less temporally variable resources. Our simulations demonstrate the joint importance of landscape-scale temporal dynamics of resources and resource amount in understanding how landscape heterogeneity influences biodiversity and ecosystem services such as the biological control of agricultural pests.
Ibrutinib blocks YAP1 activation and reverses BRAFi resistance in melanoma cells
Authors: Misek SA , Newbury PA , Chekalin E , Paithankar S , Doseff AI , Chen B , Gallo KA , Neubig RR
Published: March 2020

Most BRAF-mutant melanoma tumors respond initially to BRAFi/MEKi therapy, although few patients have durable long-term responses to these agents. The goal of this study was to utilize an unbiased computational approach to identify inhibitors which reverse an experimentally derived BRAFi resistance gene expression signature. Using this approach, we found that ibrutinib effectively reverses this signature and we demonstrate experimentally that ibrutinib re-sensitizes a subset of BRAFi-resistant melanoma cells to vemurafenib. Ibrutinib is used clinically as a BTK inhibitor; however, neither BTK deletion nor treatment with acalabrutinib, another BTK inhibitor with reduced off-target activity, re-sensitized cells to vemurafenib. These data suggest that ibrutinib acts through a BTK-independent mechanism in vemurafenib re-sensitization. To better understand this mechanism, we analyzed the transcriptional profile of ibrutinib-treated BRAFi-resistant melanoma cells and found that the transcriptional profile of ibrutinib was highly similar to that of multiple SRC kinase inhibitors. Since ibrutinib, but not acalabrutinib, has significant off-target activity against multiple SRC family kinases, it suggests that ibrutinib may be acting through this mechanism. Furthermore, genes either upregulated or downregulated by ibrutinib treatment are enriched in YAP1 target genes and we showed that ibrutinib, but not acalabrutinib, reduces YAP1 activity in BRAFi-resistant melanoma cells. Taken together, these data suggest that ibrutinib, or other SRC family kinase inhibitors, may be useful for treating some BRAFi/MEKi-refractory melanoma tumors.
MeSSII interplays the amylose and amylopectin biosynthesis by protein interactions in cassava storage root
Authors: He Shutao , Hao Xiaomeng , Wang Shanshan , Zhou Wenzhi , Ma Qiuxiang , Lu Xinlu , Chen Luonan , Zhang Peng
Published: March 2020

Starch is a glucose polymer synthesized by green plants for energy storage, and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis via forming protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII and MeISAII. TheMeSSII-RNAi cassava lines showed increased amylose content and reduced intermediate chain of amylopectin (B1 type) biosynthesis in their storage roots, leading to altered starch physico-chemical properties. Further gel permeation chromatography analysis of starch biosynthetic enzymes between the wild type andMeSSII-RNAi lines confirmed the key rule of MeSSII in the organization of heteromeric starch synthetic protein complexes, including the MeSSII-MeSSI-MeGBSSI and MeSBEII-MeSSI-MeSSII-MeISAII-MeISAI complexes. The lack of MeSSII in cassava also reduced the binding capacity of the MeSSI, MeSBEII, MeISAI, and MeISAII to starch granules. Our results show a close coordination between granule-bound starch synthase and amylopectin biosynthetic enzymes, which implies that the processes of amylose synthesis and amylopectin synthesis are directly interrelated. These findings shed light on the key components of the starch biosynthesis machinery in root crops.

One Sentence Summary

Here, by focusing on cassava SSII, we elucidated its function and the molecular mechanism by which it chaperones the starch synthase complex to regulate starch biosynthesis in cassava storage roots.
Sorting and cultivation ofFaecalibacterium prausnitziifrom fecal samples using flow cytometry in anaerobic conditions
Authors: Bellais Samuel , Nehlich Mélanie , Duquenoy Aurore , Ania Maryne , van den Engh Ger , Baijer Jan , Belotserkovsky Ilia , Thomas Vincent
Published: March 2020

Background

There is a growing interest in using gut commensal bacteria as ‘next generation’ probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was therefore to adapt flow cytometry and cell sorting to be able to detect, separate, isolate and cultivate new strains of Extremely Oxygen Sensitive (EOS) species from fecal material, focusing onFaecalibacterium prausnitziias a proof-of-concept.

Results

A BD Influx®cell sorter was equipped with a glovebox that covers the sorting area. This box is flushed with nitrogen to deplete oxygen in the enclosure. Several non-specific staining methods including Wheat Germ Agglutinin (WGA), Vancomycin BODIPY™ and LIVE/DEAD BacLight were evaluated with three different strains of the EOS speciesF. prausnitzii. In parallel, we generated polyclonal antibodies directed against this species by immunizing rabbits with heat-inactivated bacteria. Anaerobic conditions were maintained during the full process, resulting in only minor viability loss during sorting and culture of unstainedF. prausnitziireference strains. In addition, staining solutions did not severely impact bacterial viability while allowing discrimination between groups of strains. Efficient detection was achieved using polyclonal antibodies directed against heat-fixed bacteria. Finally, we were able to detect, isolate and cultivate a variety ofF. prausnitziistrains from healthy volunteer’s fecal samples using WGA staining and antibodies. These strains present markedly different phenotypes, thus confirming the heterogeneity of the species.

Conclusions

Cell-sorting in anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations and to sort strains of interest using specific antibodies, thus opening new avenues for targeted culturomics experiments.
Controlling minimal and maximal hook-length of the bacterial flagellum
Authors: Guse Alina , Rohde Manfred , Erhardt Marc
Published: March 2020

Hook-length control is a central checkpoint during assembly of the bacterial flagellum. During hook growth, a 405 amino acids (aa) protein, FliK, is intermittently secreted and thought to function as a molecular measuring tape that, in Salmonella, controls hook-length to 55 nm ± 6 nm. The underlying mechanism involves interactions of both the α-helical, N-terminal domain of FliK (FliKN) with the hook and hook cap, and of its C-terminal domain with a component of the export apparatus. However, various deletion mutants of FliKN display uncontrolled hook-length, which is not consistent with a ruler mechanism. Here, we carried out an extensive deletion analysis of FliKN to investigate its contribution in the hook-length control mechanism. We identified FliKN mutants deleted for up to 80 aa that retained wildtype motility. However, the short FliK variants did not produce shorter hook-lengths as expected from a physical ruler. Rather, the minimal length of the hook depends on the level of hook protein production and secretion. Our results thus support a model in which FliK functions as a hook growth terminator protein that limits the maximal length of the hook, and not as a molecular ruler that physically measures hook-length.
Sensing of endogenous nucleic acids by ZBP1 induces keratinocyte necroptosis and skin inflammation
Authors: Devos Michael , Tanghe Giel , Gilbert Barbara , Dierick Evelien , Verheirstraeten Maud , Nemegeer Josephine , de Reuver Richard , Lefebvre Sylvie , De Munck Jolien , Rehwinkel Jan , Vandenabeele Peter , Declercq Wim , Maelfait Jonathan
Published: March 2020

Aberrant detection of endogenous nucleic acids by the immune system can cause inflammatory disease. The scaffold function of the signalling kinase RIPK1 limits spontaneous activation of the nucleic acid sensor ZBP1. Consequently, loss of RIPK1 in keratinocytes induces ZBP1-dependent necroptosis and skin inflammation. Whether nucleic acid sensing is required to activate ZBP1 in RIPK1 deficient conditions and which immune pathways are associated with skin disease remained open questions. Using knock-in mice with disrupted ZBP1 nucleic acid binding activity, we report that sensing of endogenous nucleic acids by ZBP1 is critical in driving skin pathology characterised by antiviral and IL-17 immune responses. Inducing ZBP1 expression by interferons triggers necroptosis in RIPK1-deficient keratinocytes and epidermis-specific deletion of MLKL prevents disease, demonstrating that cell-intrinsic events cause inflammation. These findings indicate that dysregulated sensing of endogenous nucleic acid by ZBP1 can drive inflammation and may contribute to the pathogenesis of IL-17-driven inflammatory skin conditions such as psoriasis.

Devos, Tangheet al. find that the recognition of endogenous nucleic acids by the nucleic acid sensor ZBP1 causes necroptosis of RIPK1-deficient keratinocytes. This process drives the development of an inflammatory skin disease characterised by an IL-17 immune response.