title: Cell-to-cell and type-to-type heterogeneity of signaling networks: Insights from the crowd

abstract:
Recent technological developments allow us to measure the status of dozens of proteins in individual cells. This opens the way to understand the heterogeneity of complex multi-signaling networks across cells and cell-types, with important implications to understand and treat diseases such as cancer. These technologies are however limited to proteins for which antibodies are available and are fairly costly, making predictions of new markers and of existing markers under new conditions a valuable alternative. To assess our capacity to make such predictions and boost further methodological development, we organised the Single Cell Signaling in Breast Cancer DREAM challenge. We used a mass cytometry data set, covering 36 markers in over 4,000 conditions totalling 80 million single cells across 67 breast cancer cell lines. Through four increasingly difficult subchallenges, the participants predicted missing markers, new conditions, and the time course response of single cells to stimuli in the presence and absence of kinase inhibitors. The challenge results show that despite the stochastic nature of signal transduction in single cells, the signaling events are tightly controlled and machine learning methods can accurately predict new experimental data.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=58 SRC="FIGDIR/small/436603v2_ufig1.gif" ALT="Figure 1">
View larger version (24K):
org.highwire.dtl.DTLVardef@a95337org.highwire.dtl.DTLVardef@966d5aorg.highwire.dtl.DTLVardef@1e55b18org.highwire.dtl.DTLVardef@bfb5d7_HPS_FORMAT_FIGEXP  M_FIG C_FIG Key pointsO_LIOver 80 million single-cell multiplexed measurements across 67 cell lines, 54 conditions and 10 time points to benchmark predictive models of single cell signaling
C_LIO_LI73 approaches from 27 teams for predicting response to kinase inhibitors on single cell level, and dynamic response from unperturbed basal omics data
C_LIO_LIPredictions of single marker models correlate with measurements with a correlation coefficient of 0.76
C_LIO_LITop models of whole signaling response models perform almost as well as a biological replicate
C_LIO_LICell-line specific variation in dynamics can be predicted from basal omics
C_LI


title: VICTOR: A visual analytics web application for comparing cluster sets

abstract: Clustering is the process of grouping together different data objects based on similar properties. Clustering has applications in various case studies from several fields such as graph theory, image analysis, pattern recognition, statistics and others. Nowadays, there are numerous algorithms and tools able to generate clustering results. However, different algorithms or parameterization may result in very different clusters. This way, the user is often forced to manually filter and compare these results in order to decide which of them produce the ideal clusters. To automate this process, in this study, we present VICTOR, the first fully interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering algorithms. VICTOR can handle multiple clustering results simultaneously and compare them using ten different metrics. Clustering results can be filtered and compared to each other with the use of interactive heatmaps, bar plots, correlation networks, sankey and circos plots. We demonstrate VICTORs functionality using three examples. In the first case, we compare five different algorithms on a protein-protein interaction dataset whereas in the second example, we test four different parameters of the same clustering algorithm applied on the same dataset. Finally, as a third example, we compare four different meta-analyses with hierarchically clustered differentially expressed genes found to be involved in myocardial infarction. VICTOR is available at http://bib.fleming.gr:3838/VICTOR.

category: bioinformatics


title: Physical mechanisms of ESCRT-III-driven cell division in archaea

abstract: Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division.

category: biophysics


title: On-off transition and ultrafast decay of amino acid luminescence driven by modulation of supramolecular packing

abstract: It has been experimentally observed that various biomolecules exhibit clear luminescence in the visible upon aggregation, contrary their monomeric state. However, the physical basis for this phenomenon is still elusive. Here, we systematically examine all coded amino acids to provide non-biased insights into this phenomenon. Several amino acids, including non-aromatic, show intense visible luminescence. While lysine crystals display the highest signal, the very chemically similar non-coded ornithine does not, implying a role for molecular packing rather than the chemical characteristics of the molecule. Furthermore, cysteine show luminescence that is indeed crystal-packing-dependent as repeated rearrangements between two crystal structures result in a reversible on-off optical transition. In addition, ultrafast lifetime decay is experimentally validated, corroborating a recently raised hypothesis regarding the governing role of n{pi}* states in the emission formation. Collectively, our study supports the hypothesis that electronic interactions between molecules that are non-fluorescent and non-absorbing at the monomeric state may result in reversible optically-active states by the formation of supramolecular fluorophores.


title: A Multiscale Immuno-Oncology on-Chip System (MIOCS) establishes that collective T cell behaviors govern tumor regression

abstract: T cell-based tumor immunotherapies such as CAR T cells or immune checkpoint inhibitors harness the cytotoxic potential of T cells to promote tumor regression. However, patient response to immunotherapy remains heterogeneous, highlighting the need to better understand the rules governing a successful T cell attack. Here, we develop a microfluidic-based method to track the outcome of T cell activity on many individual cancer spheroids simultaneously, with a high spatiotemporal resolution. By combining these parallel measurements of T cell behaviors and tumor fate with probabilistic modeling, we establish that the first recruited T cells initiate a positive feedback loop leading to an accelerated effector accumulation on the spheroid. We also provide evidence that cooperation between T cells on the spheroid during the killing phase facilitates tumor destruction. We propose that tumor destruction does not simply reflect the sum of individual T cell activities but relies instead on collective behaviors promoting both T cell accumulation and function. The possibility to track many replicates of immune-tumor interactions with such a level of detail should help delineate the mechanisms and efficacy of various immunotherapeutic strategies.


title: PHAROH lncRNA regulates c-Myc translation in hepatocellular carcinoma via sequestering TIAR

abstract: Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, Gm19705, that is over-expressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA Pluripotency and Hepatocyte Associated RNA Overexpressed in HCC, or PHAROH. Depletion of PHAROH impacts cell proliferation and migration, which can be rescued by ectopic expression of PHAROH. RNA-seq analysis of PHAROH knockouts revealed that a large number of genes with decreased expression contain a c-Myc motif in their promoter. C-MYC is decreased at the protein level, but not the mRNA level. RNA-antisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within PHAROH, sequestration of which increases c-MYC translation. In summary, our data suggest that PHAROH regulates c-MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.

category: cancer biology


title: Within- and transgenerational plasticity of a temperate salmonid in response to thermal acclimation and acute temperature stress

abstract:
Environmental temperatures associated with climate change are rising too rapidly for many species to adapt, threatening the persistence of taxa with limited capacities for thermal acclimation. We investigated the capacity for within- and transgenerational responses to increasing environmental temperatures in brook trout (Salvelinus fontinalis), a cold-adapted salmonid. Adult fish were acclimated to temperatures within (10{square}) and above (21{square}) their thermal optimum for six months before spawning, then mated in a full factorial breeding design to produce offspring from cold- and warm-acclimated parents as well as bidirectional crosses between parents from both temperature treatments. Offspring families were subdivided and reared at two acclimation temperatures (15{square} and 19{square}) representing their current environment and a projected climate change scenario. Offspring thermal physiology was measured as the rate of oxygen consumption (MO2) during an acute change in temperature (+2{square} h-1) to observe their MO2-temperature relationship. We also recorded resting MO2, the highest achieved (peak) MO2, and critical thermal maximum (CTM) as performance metrics. Within-generation plasticity was greater than transgenerational plasticity, with offspring acclimation temperature having demonstrable effects on peak MO2 and CTM. Transgenerational plasticity was evident as an elevated resting MO2 and the MO2-temperature relationship in offspring from warm-acclimated parents. Both parents contributed to offspring thermal responses, although the paternal effect was stronger. Although brook trout exhibit both within- and transgenerational plasticity for thermal physiology, it is unlikely that these will be sufficient for coping with long-term changes to environmental temperatures resulting from climate change.

SummaryBrook trout (Salvelinus fontinalis) exhibit within-generation and transgenerational plasticity for thermal performance, although neither response appears sufficient to cope with long-term climate change effects.

category: physiology


title: The fern CYPome: Fern-specific cytochrome P450 family involved in convergent evolution of chemical defense.

abstract: Plant natural products encompass an enormous chemical diversity bearing witness to great molecular innovation that occured throughout land plant evolution. Cytochrome P450 monooxygenases (CYPs) catalyze a wide variety of monooxygenation reactions essential to the metabolic repertoire of plants natural products. Ferns constitute the second largest group of vascular plants and hold a significant phylogenetic position in land evolution, lying sister to seed plants. To date, CYP diversity has not been described for this taxon and pathway discovery in ferns in general is scarce, despite possessing a rich diversity of natural products. We analysed over 8000 available fern CYPs, classifing and characterizing the landscape of this super-enzyme group. Fern CYPs are dominated by fern-specific families ([~]60%), with the largest family - CYP981 - constituting approximately 15% of all predicted fern CYPs in the dataset. The abundancy and dynamics of the CYP981 family suggest a position equivalent to the CYP71 family present in seed plants, with potential roles in natural product biosynthesis. Ferns are the evolutionary oldest group to biosynthesize cyanogenic glycosides; amino acid-derived defense compounds. We show that CYP981F5 from the highly cyanogenic fern Phlebodium aureum catalyzes the conversion of phenylacetonitrile to mandelonitrile, an intermediate step in cyanogenic glycoside biosynthesis. The fern CYPome provides an important platform to further understand evolution of metabolite biosynthesis throughout the plant kingdom, and in ferns specifically.

category: plant biology


title: Reward boosts reinforcement-based motor learning

abstract: Besides relying heavily on sensory and reinforcement feedback, motor skill learning may also depend on the level of motivation experienced during training. Yet, how motivation by reward modulates motor learning remains unclear. In 90 healthy subjects, we investigated the net effect of motivation by reward on motor learning while controlling for the sensory and reinforcement feedback received by the participants. Reward improved motor skill learning beyond performance-based reinforcement feedback. Importantly, the beneficial effect of reward involved a specific potentiation of reinforcement-related adjustments in motor commands, which concerned primarily the most relevant motor component for task success and persisted on the following day in the absence of reward. We propose that the long-lasting effects of motivation on motor learning may entail a form of associative learning resulting from the repetitive pairing of the reinforcement feedback and reward during training, a mechanism that may be exploited in future rehabilitation protocols.

category: neuroscience


title: Sensitivity and resolution improvement for in-vivo magnetic resonance current density imaging (MRCDI) of the human brain

abstract:
PurposeMagnetic resonance current density imaging (MRCDI) combines MR brain imaging with the injection of time-varying weak currents (1-2 mA) to assess the current flow pattern in the brain. However, the utility of MRCDI is still hampered by low measurement sensitivity and poor image quality.

MethodsWe recently introduced a multi-gradient-echo-based MRCDI approach that has the hitherto best documented efficiency. We now advanced our MRCDI approach in three directions and performed phantom and in-vivo human brain experiments for validation: First, we verified the importance of enhanced spoiling and optimize it for imaging of the human brain. Second, we improved the sensitivity and spatial resolution by using acquisition weighting. Third, we added navigators as a quality control measure for tracking physiological noise. Combining these advancements, we tested our optimized MRCDI method by using 1 mA transcranial electrical stimulation (TES) currents injected via two different electrode montages in five subjects.

ResultsFor a session duration of 4:20 min, the new MRCDI method was able to detect magnetic field changes caused by the TES current flow at a sensitivity level of 84 pT, representing in a twofold increase relative to our original method. Comparing both methods to current flow simulations based on personalized head models demonstrated a consistent increase in the coefficient of determination of {Delta}R2=0.12 for the current-induced magnetic fields and {Delta}R2=0.22 for the current flow reconstructions. Interestingly, some of the simulations still clearly deviated from the measurements despite of the strongly improved measurement quality. This suggests that MRCDI can reveal useful information for the improvement of head models used for current flow simulations.

ConclusionThe advanced method strongly improves the sensitivity and robustness of MRCDI and is an important step from proof-of-concept studies towards a broader application of MRCDI in clinical and basic neuroscience research.


title: Biophysical demonstration of co-packaging of glutamate and GABA in individual synaptic vesicles in the central nervous system

abstract: Many mammalian neurons release multiple neurotransmitters to activate diverse classes of ionotropic receptors on their postsynaptic targets. Entopeduncular nucleus somatostatin (EP Sst+) neurons that project to the lateral habenula (LHb) release both glutamate and GABA, but it is unclear if these are packaged into the same or segregated pools of synaptic vesicles. Here we describe a novel method combining electrophysiology, spatially-patterned optogenetics, and computational modeling designed to analyze the mechanism of glutamate/GABA corelease. We find that the properties of PSCs elicited in LHb neurons by optogenetic activation of EP Sst+ terminals are only consistent with co-packaging of glutamate and GABA into individual vesicles. Furthermore, serotonin, which acts presynaptically to weaken EP Sst+ to LHb synapses, does so by altering the release probability of vesicles containing both transmitters. Our approach is broadly applicable to the study of multi-transmitter neurons throughout the brain and our results constrain mechanisms of neuromodulation in LHb.


title: Brain kernel: a new spatial covariance function for fMRI data

abstract: A key problem in functional magnetic resonance imaging (fMRI) is to estimate spatial activity patterns from noisy high-dimensional signals. Spatial smoothing provides one approach to regularizing such estimates. However, standard smoothing methods ignore the fact that correlations in neural activity may fall off at different rates in different brain areas, or exhibit discontinuities across anatomical or functional boundaries. Moreover, such methods do not exploit the fact that widely separated brain regions may exhibit strong correlations due to bilateral symmetry or the network organization of brain regions. To capture this non-stationary spatial correlation structure, we introduce the brain kernel, a continuous covariance function for whole-brain activity patterns. We define the brain kernel in terms of a continuous nonlinear mapping from 3D brain coordinates to a latent embedding space, parametrized with a Gaussian process (GP). The brain kernel specifies the prior covariance between voxels as a function of the distance between their locations in embedding space. The GP mapping warps the brain nonlinearly so that highly correlated voxels are close together in latent space, and uncorrelated voxels are far apart. We estimate the brain kernel using resting-state fMRI data, and we develop an exact, scalable inference method based on block coordinate descent to overcome the challenges of high dimensionality (10-100K voxels). Finally, we illustrate the brain kernels usefulness with applications to brain decoding and factor analysis with multiple task-based fMRI datasets.


title: Temporal filtering of luminance and chromaticity in macaque visual cortex

abstract: The visibility of a periodic light modulation depends on its temporal frequency and spectral properties. Contrast sensitivity is highest at 8-10 Hz for modulations of luminance but is substantially lower for modulations between equiluminant lights. This difference between luminance and chromatic contrast sensitivity is rooted in retinal filtering, but additional filtering occurs in the cerebral cortex. To measure the cortical contributions to luminance and chromatic temporal contrast sensitivity, signals in the lateral geniculate nucleus (LGN) were compared to the behavioral contrast sensitivity of macaque monkeys. Long wavelength-sensitive (L) and medium wavelength-sensitive (M) cones were modulated in phase, to produce a luminance modulation (L+M), or in counterphase, to produce a chromatic modulation (L-M). The sensitivity of LGN neurons was well matched to behavioral sensitivity at low temporal frequencies but was approximately 7 times greater at high temporal frequencies. Similar results were obtained for L+M and L-M modulations. These results show that differences in the shapes of the luminance and chromatic temporal contrast sensitivity functions are due almost entirely to pre-cortical mechanisms. Simulations of cone photoreceptor currents show that temporal information loss in the retina and at the retinogeniculate synapse exceeds cortical information loss under most of the conditions tested.


title: Financial incentives facilitate the neural computation of prosocial decisions stronger in low empathic individuals

abstract: Financial incentives are commonly used to motivate behaviours. There is also evidence that incentives can decline the behaviour they are supposed to foster, for example, documented by a decrease in blood donations if a financial incentive is offered. Based on these findings, previous studies assumed that prosocial motivation is shaped by incentives. However, so far, there is no direct evidence showing an interaction between financial incentives and a specific prosocial motive. Combining drift-diffusion modelling and fMRI, we investigated the effect of financial incentives on empathy, i.e., one of the key motives driving prosocial decisions. In the empathy-alone condition, participants made prosocial decisions based on empathy, in the empathy-bonus condition, they were offered a financial bonus for prosocial decisions, in addition to empathy induction. On average, the bonus enhanced the information accumulation in empathy-based decision. On the neural level, this enhancement was related to the anterior insula, the same region that also correlated with empathy ratings. Moreover, the effect of the financial incentive on anterior insula activation was stronger the lower a person scored on empathy. These findings show that financial incentives enhance prosocial motivation in the absence of empathy but have little effect on high empathic individuals.


title: The oxygen sensor Prolyl hydroxylase domain 2 regulates the in vivo suppressive capacity of regulatory T cells

abstract: The oxygen sensor PHD2 (prolyl hydroxylase domain 2) plays an important role in cell hypoxia adaptation by regulating the stability of HIF proteins (HIF1 and HIF2) in numerous cell types including T lymphocytes. The role of oxygen sensor on immune cells, in particular on regulatory T cell (Treg) function, has not been fully elucidated. The purpose of our study was to evaluate the role of PHD2 in the regulation of Treg phenotype and function. We demonstrate herein that selective ablation of PHD2 expression in Treg (PHD2{Delta}Treg mice) leads to a spontaneous systemic inflammatory syndrome, as evidenced by weight loss, development of a rectal prolapse, splenomegaly, shortening of the colon and elevated expression of IFN-{gamma} in the mesenteric lymph nodes, intestine and spleen. PHD2 deficiency in Tregs led to an increased number of activated CD4 conventional T cells expressing a Th1-like effector phenotype. Concomitantly, the expression of innate-type cytokines such as Il1b, Il12a, Il12b and Tnfa was found to be elevated in peripheral (gut) tissues and spleen. PHD2{Delta}Treg mice also displayed an enhanced sensitivity to DSS-induced colitis and to toxoplasmosis, suggesting that PHD2-deficient Tregs did not efficiently control inflammatory response in vivo, in particular those characterized by IFN-{gamma} production. Further analysis revealed that Treg dysregulation was largely prevented in PHD2-HIF2 (PHD2-HIF2{Delta}Treg mice), but not in PHD2-HIF1 (PHD2-HIF1{Delta}Treg mice) double KOs, suggesting an important and possibly selective role of the PHD2-HIF2 axis in the control of Treg function. Finally, the transcriptomic analysis of PHD2-deficient Tregs identified the STAT1 pathway as a target of the PHD2-HIF2 axis in regulatory T cell phenotype and in vivo function.

category: immunology


title: Aggregated Mycobacterium tuberculosis enhances the inflammatory response

abstract: Mycobacterium tuberculosis (Mtb) readily aggregates in culture and Mtb aggregates in the lung were observed in experimental Mtb infection. However, the physiological consequences of Mtb aggregation are incompletely understood. Here we examined the human macrophage transcriptional response to aggregated Mtb relative to infection with non-aggregated single or multiple bacilli per host cell. Infection with aggregated Mtb led to an early upregulation of pro-inflammatory associated genes and enhanced TNF signaling via the NF{kappa}B pathway. Both these pathways were significantly upregulated relative to infection with single bacilli, and TNF signaling was also significantly elevated relative to infection with multiple non-aggregated Mtb. Secretion of TNF and downstream cytokines were also enhanced. On a longer timescale, aggregate infection led to overall increased acidification per macrophage and a high proportion of death in these cells after aggregate phagocytosis. Host cell death did not occur when Mtb aggregates were heat killed despite such clumps being readily picked up. To validate that Mtb aggregates do occur in the human lung, we document Mtb aggregates surrounding a cavity in a human TB lesion. Aggregates may therefore be present in some lesions and elicit a stronger inflammatory response resulting in recruitment of additional phagocytes and their subsequent death, potentially leading to necrosis and transmission.

category: microbiology


title: Should deep-sequenced amplicons become the new gold-standard for analysing malaria drug clinical trials?

abstract:
BackgroundRegulatory clinical trials are required to ensure the continued supply and deployment of effective antimalarial drugs. Patient follow-up in such trials typically lasts several weeks as the drugs have long half-lives and new infections often occur during this period. "Molecular correction" is therefore used to distinguish drug failures from new infections. The current WHO-recommend method for molecular correction uses length-polymorphic alleles at highly diverse loci but is inherently poor at detecting low density clones in polyclonal infections. This likely leads to substantial underestimates of failure rates, delaying the replacement of failing drugs with potentially lethal consequences. Deep sequenced amplicons (AmpSeq) substantially increase the detectability of low-density clones and may offer a new "gold standard" for molecular correction.

MethodsPharmacological simulation of clinical trials was used to evaluate the suitability of AmpSeq for molecular correction. We investigated the impact of factors such as the number of amplicon loci analysed, the informatics criteria used to distinguish genotyping  noise from real low density signals, the local epidemiology of malaria transmission, and the potential impact of genetic signals from gametocytes.

ResultsAmpSeq greatly improved molecular correction and provided accurate drug failure rate estimates. The use of 3 to 5 amplicons was sufficient, and simple, non-statistical, criteria could be used to classify recurrent infections as drug failures or new infections.

ConclusionsThese results strongly endorse the deployment of AmpSeq as the standard for molecular correction in regulatory trials, with its potential extension into routine surveillance once the requisite technical support becomes established.


title: A novel type of IRES having variable numbers of eIF4E-binding site and synergistic effect in RNA2 of WYMV isolates

abstract: Some viral proteins were translated in cap-independent manner via internal ribosome entry site (IRES), which ever maintained conservative characteristic among different isolates of same species of virus. However, IRES activity presented 7-fold of variance in RNA2 of wheat yellow mosaic virus (WYMV) HC and LYJN isolates. Based on RNA structure probing and mutagenesis assay, the loosened middle stem of H1 and hepta-nucleotide top loop of H2 in LYJN isolate synergistically ensured the higher IRES activity than that in HC isolate. In addition, the conserved top loop of H1 ensured basic IRES activity in HC and LYJN isolates. RNA2 5'-UTR specifically interacted with the wheat eIF4E, which was accomplished by the top loop of H1 in HC isolate or the top loop of H1 and H2 in LYJN isolate. Different IRES activity of WYMV RNA2 was regulated by different numbers of eIF4E-binding site and their synergistic effect, which was accomplished by the proximity of H1 and H2 due to the flexibility of middle stem in H1. It is represented a novel evolution pattern of IRES.


title: Serotonin and dopamine modulate aging in response to food perception and availability

abstract: An organisms ability to perceive and respond to changes in its environment is crucial for its health and survival. Here we reveal how the most well-studied longevity intervention, dietary restriction (DR), acts in-part through a cell non-autonomous signaling pathway that is inhibited by the perception of attractive smells. Using an intestinal reporter for a key gene induced by DR but suppressed by attractive smells, we identify three compounds that block food perception in C. elegans, thereby increasing longevity as DR mimetics. These compounds clearly implicate serotonin and dopamine in limiting lifespan in response to food perception. We further identify an enteric neuron in this pathway that signals through the serotonin receptor 5-HT1A/ser-4 and dopamine receptor DRD2/dop-3. Aspects of this pathway are conserved in D. melanogaster and mammalian cells. Thus, blocking food perception through antagonism of serotonin or dopamine receptors is a plausible approach to mimic the benefits of dietary restriction.

category: molecular biology


title: Genome-wide decoupling of H2Aub and H3K27me3 in early mouse development

abstract: Polycomb group (PcG) proteins are crucial chromatin regulators during development. H2Aub and H3K27me3 are catalyzed by Polycomb-repressive Complex 1 and 2 (PRC1/2) respectively, and largely overlap in the genome due to mutual recruitment of the two complexes. However, whether PRC1/H2Aub and PRC2/H3K27me3 can function independently remains obscure. Here we uncovered a genome-wide decoupling of H2Aub and H3K27me3 in preimplantation mouse embryos, at both canonical PcG targets and broad distal domains. H2Aub represses future bivalent genes without H3K27me3 but does not contribute to maintenance of H3K27me3-dependent non-canonical imprinting. Our study thus revealed their distinct and independent functions in early mammalian development.


title: The architecture of Cidec-mediated interfaces between lipid droplets

abstract: Lipid droplets (LDs) are intracellular organelles responsible for storing surplus energy as neutral lipids. Their size and number vary enormously (1). In white adipocytes, they reach up to 100 {micro}m in size, occupying >90% of the cell. Cidec, which is strictly required for the formation of such large LDs, is concentrated at interfaces between adjacent LDs and facilitates the directional flux of neutral lipids from the smaller to the larger LD (2-7). However, the mechanism of lipid transfer is unclear, in part because the architecture of interfaces between LDs has remained elusive. Here we visualised interfaces between LDs by electron cryo-tomography (cryo-ET) and analysed the kinetics of lipid transfer by quantitative live fluorescence microscopy (FM). We show that transfer occurs through closely apposed intact monolayers, is slowed down by increasing the distance between the monolayers and follows exponential kinetics suggesting a pressure-driven mechanism. We thus propose that unique architectural features of LD-LD interfaces are mechanistic determinants of neutral lipid transfer.

category: cell biology


title: Single cell transcriptome analysis of decidua macrophages in normal and recurrent spontaneous abortion patients

abstract: Due to the heterogeneity and different polarization state of decidual macrophages (dM{Phi}), they play an important role during the pregnancy, but their definition and exact function remain elusive. We isolated CD14+CD45+ dM{Phi} from the normal or RSA decidua by flow cytometry, followed by single cell RNA sequencing (scRNA-seq). In total, 23,062 single-cell transcriptomes of macrophage were profiled (12,470 Normal and 10,592 RSA), which were divided into 13 major clusters via T-distributed stochastic neighbor embedding (t-SNE) visualization. We observed that there is higher percentage composition of M1 cells (70.6%) in the normal decidua, and higher percentage composition of M2 cells (68.3%) in the RSA decidua. We identified new markers (M1: S100A8, S100A9, M2: SELENOP, FOLR2, RNASE1) and secreted cytokines (M1: IL1{beta}, TNFSF13B and MMP9; M2: CCL3, CCL4) of the dM{Phi}. We found that cluster 10 as the specific cluster of dM{Phi} highly expressing BAG3 in normal group and cluster 7 specific highly expressing CXCL9/10/11 chemokine. After pseudo-time trajectory analysis, we found that the dM{Phi} formed a continuous "V-shaped" trajectory, with M1 and M2 type cells mainly occupying the two heads. We found that NF{kappa}B1, MYC and TCF12 acted as the key transcription factors of dM{Phi}. Our study redefined the polarization state and physiological characteristic of dM{Phi} in early normal and RSA pregnancy, which suggests a novel view and therapeutic target for spontaneous abortion prevention.


title: Mycena species can be opportunist-generalist plant root invaders

abstract:
Recently, several saprotrophic genera have been found to invade/interact with plant roots in laboratory growth experiments, and this coincides with reports of abundant saprotrophic fungal sequences in plant roots. However, it is uncertain if this reflects field phenomena, and if reports on coincidentally amplified saprotrophs are simply coincidental.

We investigated root invasion by presumed saprotrophic fungi by focusing on the large genus Mycena in 1) a systematic analysis of the occurrence of saprotrophic fungi in new and previously published ITS1/ITS2 datasets generated from roots of 10 mycorrhizal plant species, and 2) we analysed natural abundances of 13C/15N stable isotope signatures of fungal/plant communities from five comparable field locations to examine the trophic status of Mycena species.

Mycena was the only saprotrophic genus consistently found in 9 of 10 plant host roots, with high within-host variation in Mycena sequence proportions (0-80%) recovered. Mycena carpophores displayed isotopic signatures consistent with published 13C/15N profiles of both saprotrophic or mutualistic lifestyles, with considerable intraspecific variation, resembling the patterns seen in growth experiments. These results indicate that multiple Mycena species opportunistically invade the roots of a range of plant species, possibly forming a spectrum of interactions. This potentially challenges our general understanding of fungal ecology.

Originality significance statementThis is the first study to apply a dual approach of systematic metabarcoding of plant roots and stable isotope signatures on dried field material to the large and common saprotrophic fungal genus Mycena. This is significant as it shows that members of this genus, normally not expected to be found inside plant roots at all, are in fact associated eith multiple plant hosts. The study furthermore shows that species in this genus may occupy different ecological roles in the field besides being saprotrophic. That a large and common fungal genus known to be a quantitatively important litter decayer can be an opportunistic root invader and interact with host plants is of interest to all mycologists and ecologists working on plant-fungus/microb symbiosis.

category: ecology


title: Shining a light on Laurentian Great Lakes cisco (Coregonus artedi): how ice coverage may impact embryonic development

abstract: Changes in winter conditions, such as decreased ice coverage and duration, have been observed in the Laurentian Great Lakes for more than 20 years. Such changes have been hypothesized to be linked to low Coregonus spp. survival to age-1 as most cisco (Coregonus artedi) populations are autumn spawners whose embryos incubate under ice throughout the winter. The quantity of light during winter is regulated by ice coverage, and light affects embryo survival and development in some teleosts. We experimentally evaluated how cisco embryos from lakes Superior and Ontario respond to three light treatments that represented day-light intensity under 0-10, 40-60, and 90-100% ice coverage. Embryonic response measures included two developmental factors (embryo survival and incubation period) and two morphological traits (length-at-hatch and yolk-sac volume). Embryo survival was highest at the medium light treatment and decreased at high and low treatments for both populations, suggesting cisco may be adapted to withstand some light exposure from inter-annual variability in ice coverage. Light intensity had no overall effect on length of incubation. Increasing light intensity decreased length-at-hatch in Lake Superior but had no effect in Lake Ontario. Yolk-sac volume was positively correlated with increasing light in Lake Superior and negatively correlated in Lake Ontario. Contrasting responses in embryo development between lakes suggests differences in populations response to light is flexible. Our results provide a step towards better understanding the high variability observed in coregonine recruitment and may help predict what the future of this species may look like under current climate trends.


title: Salted roads lead to edema and reduced locomotor function in wood frogs

abstract: Human activities have caused massive losses of natural populations across the globe. Like many groups, amphibians have experienced substantial declines worldwide, driven by environmental changes such as habitat conversion, pollution, and disease emergence. Each of these drivers is often found in close association with the presence of roads. Here we report a novel consequence of roads affecting an amphibian native to much of North America, the wood frog (Rana sylvatica). Across 38 populations distributed from southern to central New England, we found that adult wood frogs living adjacent to roads had higher incidence and severity of edema (bloating caused by fluid accumulation) during the breeding season than frogs living away from the influence of roads. This effect was best explained by increased conductivity of breeding ponds, caused by runoff pollution from road salt used for de-icing. Edema severity was negatively correlated with locomotor performance in more northerly populations. Interestingly, northern populations experience more intense winters, which tends to result in more de-icing salt runoff and increased energetic demands associated with overwintering cryoprotection needs. Thus, this emerging consequence of roads appears to impose potential fitness costs associated with locomotion, and these effects might be most impactful on populations living in regions where de-icing is most intense.


title: Linking habitat and population dynamics to inform conservation benchmarks for data-limited salmon stocks

abstract: Management of data-limited populations is a key challenge to the sustainability of fisheries around the world. For example, sockeye salmon (Oncorhynchus nerka) spawn and rear in many remote coastal watersheds of British Columbia (BC), Canada, making population assessment a challenge. Estimating conservation and management targets for these populations is particularly relevant given their importance to First Nations and commercial fisheries. Most sockeye salmon have obligate lake-rearing as juveniles, and total abundance is typically limited by production in rearing lakes. Although methods have been developed to estimate population capacity based on nursery lake photosynthetic rate (PR) and lake area or volume, they have not yet been widely incorporated into stock-recruit analyses. We tested the value of combining lake-based capacity estimates with traditional stock-recruit based approaches to assess population status using a hierarchical-Bayesian stock-recruit model for 70 populations across coastal BC. This analysis revealed regional variation in sockeye population productivity (Ricker ), with coastal stocks exhibiting lower mean productivity than those in interior watersheds. Using moderately-informative PR estimates of capacity as priors reduced model uncertainty, with a more than five-fold reduction in credible interval width for estimates of conservation benchmarks (e.g. SMAX - spawner abundance at carrying capacity). We estimated that almost half of these remote sockeye stocks are below one commonly applied conservation benchmarks (SMSY), despite substantial reductions in fishing pressure in recent decades. Thus, habitat-based capacity estimates can dramatically reduce scientific uncertainty in model estimates of management targets that underpin sustainable sockeye fisheries. More generally, our analysis reveals opportunities to integrate spatial analyses of habitat characteristics with population models to inform conservation and management of exploited species where population data are limited.


title: Immune stimulation alters chemical profiles of Tribolium castaneum

abstract: I.Rapid recognition of disease cues is essential for preventing pathogenic infections and for disease management in group-living animals. Healthy individuals across taxa can detect illness in other conspecifics and adjust their responses to limit further infections of themselves and the group. However, little is known about potential changes in chemical phenotypes due to disease, which may mediate these responses. We here asked whether individual immune experience resulting from wounding or the injection of heat-killed bacteria of Bacillus thuringiensis (i.e., immune priming) leads to changes in the chemical profiles of adult red flour beetles (Tribolium castaneum). This group-living insect species is a well-studied example for both immune priming as a form of innate immune memory and niche construction via  external immunity, i.e., the secretion of quinone-containing antimicrobials into the flour. Upon interaction with wounded conspecifics, naive beetles were previously found to not only up-regulate immunity, but moreover reduce gene expression of the evolutionary capacitor HSP90, an effect that has the potential to enhance adaptability. We here used gas chromatography-flame-ionisation detection (GC-FID) to study the composition of stink gland secretions and cuticular hydrocarbons (CHCs) of immune-primed and wounded beetles compared to controls. The overall profiles as well as target compounds of the stink gland secretions showed transient, slight changes after these treatments, particularly in wounded females. Priming and wounding led to pronounced changes in CHC profiles with increases in the proportion of methyl-branched alkanes. Furthermore, we found sex-specific differences, that were particularly pronounced in the CHCs, although the changes due to immune stimulation were overall similar in both sexes. We suggest that CHCs are potential candidates for the transfer of information related to individual immunological experience into the group.

category: evolutionary biology


title: Sexual selection affects the evolution of physiological and life history traits

abstract: Sexual selection and sexual conflict are expected to affect all aspects of the phenotype, not only traits that are directly involved in reproduction. Here, we show coordinated evolution of multiple physiological and life history traits in response to long-term experimental manipulation of the mating system in populations of Drosophila pseudoobscura. Development time was extended under polyandry relative to monogamy in both sexes, potentially due to higher investment in traits linked to sexual selection and sexual conflict. Individuals (especially males) evolving under polyandry had higher metabolic rates and locomotor activity than those evolving under monogamy. Polyandry individuals also invested more in metabolites associated with increased endurance capacity and efficient energy metabolism and regulation, namely lipid and glycogen. Finally, polyandry males were less desiccation- and starvation-resistant than monogamy males, suggesting trade-offs between resistance and sexually selected traits. Our results provide experimental evidence that mating systems can impose selection that influences the evolution of non-sexual phenotypes such as development, activity, metabolism, and nutrient homeostasis.


title: Experimental sexual selection affects the evolution of physiological and life history traits


title: PRIMATE LIMB CONFORMATION: IMPLICATIONS FOR MECHANICAL ENERGY CONSERVATION

abstract: In order to understand the energy implications of primate limb conformation, the biomechanics of swing phase and the vertical movements of limb center of gravity were examined in the arboreal rhesus macaque (Macaca mulatta) and the semi-terrestrial long-tailed macaque (Macaca fascicularis). The objective was to better understand the potential variation in locomotor adaptations in these two macaque species within different ecological environments. In particular, the objective of this study was to identify the implications that these movements have on the internal energy costs of locomotion. I show that the biomechanics of swing phase for these two species have important effects on their limb center of gravity, although they may have similar limb segment mass distributions. This study suggests that mechanical energy conservation during swing phase is important in mammalian locomotion.


title: Evaluation and Optimization of High-Field Asymmetric Waveform Ion Mobility Spectrometry for Multiplexed Quantitative Site-specific N-glycoproteomics

abstract:
The heterogeneity and complexity of glycosylation hinder the depth of site-specific glycoproteomics analysis. High-field asymmetric-waveform ion-mobility spectrometry (FAIMS) has shown to improve the scope of bottom-up proteomics. The benefits of FAIMS for quantitative N-glycoproteomics have not been investigated yet. In this work, we optimized FAIMS settings for N-glycopeptide identification, with or without the tandem mass tag (TMT) label. The optimized FAIMS approach significantly increased the identification of site-specific N-glycopeptides derived from the purified IgM protein or human lymphoma cells. We explored in detail the changes in FAIMS mobility caused by N-glycopeptides with different characteristics, including TMT labeling, charge state, glycan type, peptide sequence, glycan size and precursor m/z. Importantly, FAIMS also improved multiplexed N-glycopeptide quantification, both with the standard MS2 acquisition method and with our recently developed Glyco-SPS-MS3 method. The combination of FAIMS and Glyco-SPS-MS3 provided the highest quantitative accuracy and precision. Our results demonstrate the advantages of FAIMS for improved mass-spectrometry-based qualitative and quantitative N-glycoproteomics.

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category: biochemistry


title: Brain solute transport is more rapid in periarterial than perivenous spaces

abstract:
BackgroundPerivascular fluid flow, of cerebrospinal or interstitial fluid in spaces surrounding brain blood vessels, is recognized as a key component underlying brain transport and clearance. An important open question is how and to what extent differences in vessel type or geometry affect perivascular fluid flow and transport.

MethodsUsing computational modelling in both idealized and image-based geometries, we study and compare fluid flow and solute transport in pial (surface) periarterial and perivenous spaces.

ResultsOur findings demonstrate that differences in geometry between arterial and venous pial perivascular spaces (PVSs) lead to higher net CSF flow, more rapid tracer transport and earlier arrival times of injected tracers in periarterial spaces compared to perivenous spaces.

ConclusionsThese findings can explain the experimentally observed rapid appearance of tracers around arteries, and the delayed appearance around veins without the need of a circulation through the parenchyma, but rather by direct transport along the PVSs.

category: bioengineering


title: The unraveling of balanced complexes in metabolic networks

abstract:
Balanced complexes in biochemical networks are at core of several theoretical and computational approaches that make statements about the properties of the steady states supported by the network. Recent computational approaches have employed balanced complexes to reduce metabolic networks, while ensuring preservation of particular steady-state properties; however, the underlying factors leading to the formation of balanced complexes have not been studied, yet. Here, we present a number of factorizations providing insights in mechanisms that lead to the origins of the corresponding balanced complexes. The proposed factorizations enable us to categorize balanced complexes into four distinct classes, each with specific origins and characteristics. They also provide the means to efficiently determine if a balanced complex in large-scale networks belongs to a particular class from the categorization. The results are obtained under very general conditions and irrespective of the network kinetics, rendering them broadly applicable across variety of network models. Application of the categorization shows that all classes of balanced complexes are present in large-scale metabolic models across all kingdoms of life, therefore paving the way to study their relevance with respect to different properties of steady states supported by these networks.

HighlightsO_LIBalanced complexes are ubiquitous in real-world networks, and facilitate insights in steady state flux phenotypes in large-scale metabolic networks.
C_LIO_LINovel factorizations are proposed that explain the formation of balanced complexes and enable their categorization.
C_LIO_LIThe results also provide a computationally-efficient tool for the identification of balanced complexes in large-scale networks.
C_LIO_LIExamination of metabolic network models across all kingdoms of life shows that all categories naturally arise in this type of networks.
C_LI


title: Pan-genomic Matching Statistics for Targeted Nanopore Sequencing

abstract: Nanopore sequencing is an increasingly powerful tool for genomics. Recently, computational advances have allowed nanopores to sequence in a targeted fashion; as the sequencer emits data, software can analyze the data in real time and signal the sequencer to eject "non-target" DNA molecules. We present a novel method called SPUMONI, which enables rapid and accurate targeted sequencing with the help of efficient pangenome indexes. SPUMONI uses a compressed index to rapidly generate exact or approximate matching statistics (half-maximal exact matches) in a streaming fashion. When used to target a specific strain in a mock community, SPUMONI has similar accuracy as minimap2 when both are run against an index containing many strains per species. However SPUMONI is 12 times faster than minimap2. SPUMONIs index and peak memory footprint are also 15 to 4 times smaller than minimap2, respectively. These improvements become even more pronounced with even larger reference databases; SPUMONIs index size scales sublinearly with the number of reference genomes included. This could enable accurate targeted sequencing even in the case where the targeted strains have not necessarily been sequenced or assembled previously. SPUMONI is open source software available from https://github.com/oma219/spumoni.


title: Comparative genome analysis using sample-specific string detection in accurate long reads

abstract:
MotivationComparative genome analysis of two or more whole-genome sequenced (WGS) samples is at the core of most applications in genomics. These include discovery of genomic differences segregating in population, case-control analysis in common diseases, and rare disorders. With the current progress of accurate long-read sequencing technologies (e.g., circular consensus sequencing from PacBio sequencers) we can dive into studying repeat regions of genome (e.g., segmental duplications) and hard-to-detect variants (e.g., complex structural variants).

ResultsWe propose a novel framework for addressing the comparative genome analysis by discovery of strings that are specific to one genome ("samples-specific" strings). We have developed an accurate and efficient novel method for discovery of samples-specific strings between two groups of WGS samples. The proposed approach will give us the ability to perform comparative genome analysis without the need to map the reads and is not hindered by shortcomings of the reference genome. We show that the proposed approach is capable of accurately finding samples-specific strings representing nearly all variation (> 98%) reported across pairs or trios of WGS samples using accurate long reads (e.g., PacBio HiFi data).

AvailabilityThe proposed tool is publicly available at https://github.com/Parsoa/PingPong.


title: SPECT/CT imaging, biodistribution and radiation dosimetry of a 177Lu-DOTA-integrin αvβ6 cystine knot peptide in a pancreatic cancer xenograft model

abstract:
IntroductionPancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignant neoplasms, as many cases go undetected until they reach an advanced stage. Integrin v{beta}6 is a cell surface receptor overexpressed in PDAC. Consequently, it may serve as a target for the development of probes for imaging diagnosis and radioligand therapy. Engineered cystine knottin peptides specific for integrin v{beta}6 have recently been developed showing high affinity and stability. This study aimed to evaluate an integrin v{beta}6-specific knottin molecular probe containing the therapeutic radionuclide 177Lu for targeting of PDAC.

MethodsThe expression of integrin v{beta}6 in PDAC cell lines BxPC3 and Capan2 was analyzed using RT-qPCR and immunofluorescence. In vitro competition and saturation radioligand binding assays were performed to calculate the binding affinity of the DOTA-coupled tracer loaded with and without lutetium to BxPC3 and Capan2 cell lines. To evaluate tracer accumulation in the tumor and organs, SPECT/CT, biodistribution and dosimetry projections were carried out using a Capan2 xenograft tumor mouse model.

ResultsRT-qPCR and immunofluorescence results showed high expression of integrin v{beta}6 in BxPC3 and Capan2 cells. A competition binding assay revealed high affinity of the tracer with IC50 values of 1.69 nM and 9.46 nM for BxPC3 and Capan2, respectively. SPECT/CT and biodistribution analysis of the conjugate 177Lu-DOTA-integrin v{beta}6 knottin demonstrated accumulation in Capan2 xenograft tumors (3.13 {+/-} 0.63 %IA/g at day 1 post injection) with kidney uptake at 19.2 {+/-} 2.5 %IA/g, declining much more rapidly than in tumors.

Conclusion177Lu-DOTA-integrin v{beta}6 knottin was found to be a high-affinity tracer for PDAC tumors with considerable tumor accumulation and moderate, rapidly declining kidney uptake. These promising results warrant a preclinical treatment study to establish therapeutic efficacy.


title: A short ERK5 isoform modulates nucleocytoplasmic shuttling of active ERK5 and associates with poor survival in breast cancer

abstract:
BackgroundThe nucleocytoplasmic shuttling of ERK5 has gained recent attention as a regulator of its diverse roles in cancer progression but the exact mechanisms for this shuttling are still under investigation.

MethodsUsing in vitro, in vivo and in silico studies, we investigated the roles of shorter ERK5 isoforms in regulating the nucleocytoplasmic shuttling of active phosphorylated-ERK5 (pERK5). Retrospective cohorts of primary and metastatic breast cancer cases were used to evaluate the association of the subcellular localization of pERK5 with clinicopathological features.

ResultsExtranuclear localization of pERK5 was observed during cell migration in vitro and at the invasive fronts of metastatic tumors in vivo. The nuclear and extranuclear cell fractions contained different isoforms of pERK5, which are encoded by splice variants expressed in breast and other cancers in the TCGA data. One isoform, isoform-3, lacks the C-terminal transcriptional domain and the nuclear localization signal. The co-expression of isoform-3 and full-length ERK5 associated with high epithelial-to-mesenchymal transition (EMT) and poor patient survival. Experimentally, expressing isoform-3 with full-length ERK5 in breast cancer cells increased cell migration, drove EMT and led to tamoxifen resistance. In breast cancer patient samples, pERK5 showed variable subcellular localizations where its extranuclear localization associated with aggressive clinicopathological features, metastasis, and poor survival.

ConclusionOur studies support a model of ERK5 nucleocytoplasmic shuttling driven by splice variants in an interplay between mesenchymal and epithelial states during metastasis. Using ERK5 as a biomarker and a therapeutic target should account for its splicing and context-dependent biological functions.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/436061v1_ufig1.gif" ALT="Figure 1">
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org.highwire.dtl.DTLVardef@1491ed5org.highwire.dtl.DTLVardef@1875fbeorg.highwire.dtl.DTLVardef@9edbbcorg.highwire.dtl.DTLVardef@16c34c8_HPS_FORMAT_FIGEXP  M_FIG C_FIG ERK5 isoform-3 expression deploys active ERK5 (pERK5) outside the nucleus to facilitate EMT and cell migration. In cells dominantly expressing isoform-1, pERK5 shuttles to the nucleus to drive cell expansion.


title: Moonlighting adenylyl cyclases in plants: an Arabidopsis thaliana 9-cis-epoxycarotenoid dioxygenase as point in case

abstract:
Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of plant responses. AC domains are intrinsic components of complex molecules with multiple functions, some of which are co-regulated by cAMP. Here we used an amino acid search motif based on annotated ACs in organisms across species to identify 12 unique Arabidopsis thaliana candidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3, At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally for activity. We show that an NCED3 AC fragment can complement an AC deficient E. coli mutant and this rescue is nullified when key amino acids in the AC motif are mutated. AC activity was also confirmed by tandem liquid chromatography mass spectrometry (LC-MS/MS). Our results are consistent with a moonlighting role for mononucleotide cyclases in multi-domain proteins that have at least one other distinct molecular function such as catalysis or ion channel activation and promise to yield new insights into tuning mechanisms of ABA dependent plant responses. Finally, our search method can also be applied to discover ACs in other species including Homo sapiens.

HighlightsO_LIAn adenylyl cyclase (AC) catalytic center motif identifies novel ACs in plants
C_LIO_LIACs can moonlight in complex proteins with other enzymatic domains
C_LIO_LIA 9-cis-epoxycarotenoid dioxygenase essential for abscisic acid synthesis contains an AC
C_LIO_LIThis finding implicates cAMP in abscisic acid synthesis and signaling
C_LI


title: Measuring splash-dispersal of a major wheat pathogen in the field

abstract:
Capacity for dispersal is a fundamental fitness component of plant pathogens. Empirical characterization of plant pathogen dispersal is of prime importance for understanding how plant pathogen populations change in time and space. We measured dispersal of Zymoseptoria tritici in natural environment. Primary disease gradients were produced by rain-splash driven dispersal and subsequent transmission via asexual pycnidiospores from infected source. To achieve this, we inoculated field plots of wheat (Triticum aestivum) with two distinct Z. tritici strains and a 50/50 mixture of the two strains. We measured effective dispersal of the Z. tritici population based on pycnidia counts using automated image analysis. The data were analyzed using a spatially-explicit mathematical model that takes into account the spatial extent of the source. We employed robust bootstrapping methods for statistical testing and adopted a two-dimensional hypotheses test based on the kernel density estimation of the bootstrap distribution of parameter values. Genotyping of re-isolated pathogen strains with strain-specific PCR-reaction further confirmed the conclusions drawn from the phenotypic data. The methodology presented here can be applied to other plant pathosystems.

We achieved the first estimates of the dispersal kernel of the pathogen in field conditions. The characteristic spatial scale of dispersal is tens of centimeters - consistent with previous studies in controlled conditions. Our estimation of the dispersal kernel can be used to parameterize epidemiological models that describe spatial-temporal disease dynamics within individual wheat fields. The results have the potential to inform spatially targeted control of crop diseases in the context of precision agriculture.


title: Decoding brain states on the intrinsic manifold of human brain dynamics across wakefulness and sleep

abstract: Current state-of-the-art functional magnetic resonance imaging (fMRI) offers remarkable imaging quality and resolution, yet, the intrinsic dimensionality of brain dynamics in different states (wakefulness, light and deep sleep) remains unknown. Here we present a novel method to reveal the low dimensional intrinsic manifold underlying human brain dynamics, which is invariant of the high dimensional spatio-temporal representation of the neuroimaging technology. By applying this novel intrinsic manifold framework to fMRI data acquired in wakefulness and sleep, we reveal the nonlinear differences between wakefulness and three different sleep stages, and successfully decode these different brain states with an average accuracy of 96%. Remarkably, a further group analysis shows that the intrinsic manifolds of all participants share a common topology. Overall, our results reveal the intrinsic manifold underlying the spatiotemporal dynamics of brain activity and demonstrate how this manifold enables the decoding of different brain states such as wakefulness and various sleep stages.


title: Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

abstract: This study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the  1% paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.


title: Antibacterial activity of Balanites aegyptiaca Oil Extract on Staphylococcus aureus and Escherichia coli

abstract: Africa is very rich with biodiversity resources, vegetation and it is estimated about 40,000- 45,000 species of different flora. A very large number of plant species are medicinally used for the treatment of various diseases. Balanites aegyptiaca also called "desert date" indeed a plant with amazing benefits for human, Balanites aegyptiaca was popularly known to have added value and hope for person who went to pursue it for health. In Nigeria, there are evidences of serious bacterial infections with Gram-positive and Gram-negative Staphylococcus aureus and Escherichia coli respectively. Balanites aegyptica is used to treat so many illnesses including laxative, diarrhea, hemorrhoid, stomach aches, jaundice, yellow fever, syphilis and epilepsy. The Balanite aegyptica sample was sun dried for easy removal of the seed from the shell; it was washed to remove un-wanted particles and was dried off then pounded fine powder using mortar and pestle. Antibacterial activity of the Balanites aegyptica oil at different concentrations on staphylococcus aureus and Escherichia coli bacteria and different meters in diameter of the zones was observed.The results shows significant effect of Balanites oil on bacteria by observing the presence of clear spaces known as the zone of inhibitions in the experiments.


title: Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear byproducts

abstract: In RNA field, the demarcation between coding and non-coding has been negotiated by the recent discovery of occasionally translated circular RNAs (circRNAs). Although absent of 5 cap structure, circRNAs can be translated cap-independently. Complementary intron-mediated overexpression is one of the most utilized methodologies for circRNA research but not without bearing echoing skepticism for its poorly defined mechanism and latent coexistent side products. In this study, leveraging such circRNA overexpression system, we have interrogated the protein-coding potential of 30 human circRNAs containing infinite open reading frames in HEK293T cells. Surprisingly, pervasive translation signals are detected by immunoblotting. However, intensive mutagenesis reveals that numerous translation signals are generated independently of circRNA synthesis. We have developed a dual tag strategy to isolate translation noise and directly demonstrate that the fallacious translation signals originate from cryptically spliced linear transcripts. The concomitant linear RNA byproducts, presumably concatemers, can be translated to allow pseudo rolling circle translation signals, and can involve backsplicing junction (BSJ) to disqualify the BSJ-based evidence for circRNA translation. We also find non-AUG start codons may engage in the translation initiation of circRNAs. Taken together, our systematic evaluation sheds light on heterogeneous translational outputs from circRNA overexpression vector and comes with a caveat that ectopic overexpression technique necessitates extremely rigorous control setup in circRNA translation and functional investigation.


title: Overexpression-based detection of translatable circular RNAs is vulnerable to coexistent linear RNA byproducts


title: Perturbation of ribosomal subunits dynamics by inhibitors of tRNA translocation

abstract: Many antibiotics that bind to the ribosome inhibit translation by blocking the movement of tRNAs and mRNA or interfering with ribosome dynamics, which impairs the formation of essential translocation intermediates. Here we show how translocation inhibitors viomycin (Vio), neomycin (Neo), paromomycin (Par), kanamycin (Kan), spectinomycin (Spc), hygromycin B (HygB), and streptomycin (Str, an antibiotic that does not inhibit tRNA translocation), affect principal motions of the small ribosomal subunits (SSU) during EF-G-promoted translocation. Using ensemble kinetics, we studied the SSU body domain rotation and SSU head domain swiveling in real time. We show that although antibiotics binding to the ribosome can favor a particular ribosome conformation in the absence of EF-G, EF-G-induced transition to the rotated/swiveled state of the SSU is hardly affected. The major effect of the antibiotics is observed at the stage when the SSU body and the head domain move backward. Vio, Spc and high concentrations of Neo completely inhibit the backward movements of the SSU body and head domain. Kan, Par, HygB and low concentrations of Neo slow down both movements, but their sequence and coordination are retained. Finally, Str has very little effect on the backward rotation of the SSU body domain, but retards the SSU head movement. The data underscore the importance of ribosome dynamics for tRNA-mRNA translocation and provide new insights into the mechanism of antibiotic action.


title: DNA replication during acute MEK inhibition drives acquisition of resistance through amplification of the BRAF oncogene

abstract: Mutations and gene amplifications that confer drug resistance emerge frequently during chemotherapy, but their mechanism and timing is poorly understood. Here, we investigate BRAFV600E amplification events that underlie resistance to the MEK inhibitor selumetinib (AZD6244/ARRY-142886) in COLO205 cells, a well-characterised model for reproducible emergence of drug resistance, and show that de novo amplification of BRAF is the primary path to resistance irrespective of pre-existing amplifications. Selumetinib causes long-term G1 arrest accompanied by reduced expression of DNA replication and repair genes, but cells stochastically re-enter the cell cycle during treatment despite continued repression of pERK1/2. Most DNA replication and repair genes are re-expressed as cells enter S and G2, however, mRNAs encoding a subset of factors important for error-free replication and chromosome segregation including TIPIN, PLK2 and PLK3 remain at low abundance. This suggests that DNA replication in drug is more error prone and provides an explanation for the DNA damage observed under long-term RAF-MEK-ERK1/2 pathway inhibition. To test the hypothesis that DNA replication in drug promotes de novo BRAF amplification, we exploited the combination of palbociclib and selumetinib. Combined treatment with selumetinib and a dose of palbociclib sufficient to reinforce G1 arrest in selumetinib-sensitive cells, but not to impair proliferation of resistant cells, delays the emergence of resistant colonies, meaning that escape from G1 arrest is critical in the formation of resistant clones. Our findings demonstrate that acquisition of MEK inhibitor resistance often occurs through de novo gene amplification and can be suppressed by impeding cell cycle entry in drug.


title: Two promoters integrate multiple enhancer inputs to drive wild-type knirps expression in the D. melanogaster embryo

abstract: Proper development depends on precise spatiotemporal gene expression patterns. Most genes are regulated by multiple enhancers and often by multiple core promoters that generate similar transcripts. We hypothesize that these multiple promoters may be required either because enhancers prefer a specific promoter or because multiple promoters serve as a redundancy mechanism. To test these hypotheses, we studied the expression of the knirps locus in the early Drosophila melanogaster embryo, which is mediated by multiple enhancers and core promoters. We found that one of these promoters resembles a typical "sharp" developmental promoter, while the other resembles a "broad" promoter usually associated with housekeeping genes. Using synthetic reporter constructs, we found that some, but not all, enhancers in the locus show a preference for one promoter. By analyzing the dynamics of these reporters, we identified specific burst properties during the transcription process, namely burst size and frequency, that are most strongly tuned by the specific combination of promoter and enhancer. Using locus-sized reporters, we discovered that even enhancers that show no promoter preference in a synthetic setting have a preference in the locus context. Our results suggest that the presence of multiple promoters in a locus is both due to enhancer preference and a need for redundancy and that "broad" promoters with dispersed transcription start sites are common among developmental genes. Our results also imply that it can be difficult to extrapolate expression measurements from synthetic reporters to the locus context, where many variables shape a genes overall expression pattern.

category: developmental biology


title: A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

abstract: Shotgun metagenomic sequencing is a powerful approach to study microbiomes in an unbiased manner and of increasing relevance for identifying novel enzymatic functions. However, the potential of metagenomics to relate from microbiome composition to function has thus far been underutilized. Here, we introduce the Metagenomics Genome-Phenome Association (MetaGPA) study framework, which allows to link genetic information in metagenomes with a dedicated functional phenotype. We applied MetaGPA to identify enzymes associated with cytosine modifications in environmental samples. From the 2365 genes that met our significance criteria, we confirm known pathways for cytosine modifications and proposed novel cytosine-modifying mechanisms. Specifically, we characterized and identified a novel nucleic acid modifying enzyme, 5-hydroxymethylcytosine carbamoyltransferase, that catalyzes the formation of a previously unknown cytosine modification, 5-carbamoyloxymethylcytosine, in DNA and RNA. Our work introduces MetaGPA as a novel and versatile tool for advancing functional metagenomics.

category: genomics


title: In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei

abstract: AbstractThe chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila nuclei tagged with GFP expressed under Gal4/UAS control. Using this protocol, we profiled chromatin accessibility using Omni-ATAC, and examined the distribution of histone marks using ChIP-seq and CUT&Tag in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.


title: Bioinformatic analysis deciphers the molecular toolbox in the endophytic/pathogenic behaviour in F. oxysporum f. sp. vanillae - V. planifolia Jacks interaction

abstract:
BackgroundF. oxysporum as a species complex (FOSC) possesses the capacity to specialize into host-specific pathogens known as formae speciales. This with the help of horizontal gene transfer (HGT) between pathogenic and endophytic individuals of FOSC. From these pathogenic forma specialis, F. oxysporum f. sp. vanillae (Fov) is the causal agent of fusarium wilt producing root and stem rot (RSR) and is positioned as the main phytosanitary problem in vanilla plantations worldwide. Nonetheless, the origin of this forma speciales and the behavioral genetics dictating the endophytic/pathogenic Fusarium lifestyles still unknown. To elucidate the underlying molecular mechanisms that establish these behaviors we analyzed the RNA-seq libraries of two-times frames of vanilla-Fov interactions.

ResultsOur analyses identified the sets of transcripts corresponding to Fov pathogenic strain JAGH3 during the two-times frames of the infection as the sets of the transcripts belonging to endophytic Fox in vanilla. Functional predictions of de novo annotated transcripts as the enriched GO terms with the overrepresented metabolic pathways, allowed us to identify the processes that establish the pathogenic lifestyle in Fov being virulence, hypervirulence, sporulation, conidiation, necrosis and fusaric acid related genes with the carbohydrates, amino acids, proteins, glycerophospholipids and autophagy metabolic pathways that are key regulators of spores germination and pathogenicity establishment as the underlying mechanisms behind this behavior. As the absence of these were found in the vanilla endophytic Fox.

ConclusionsThis work reveals the main players of the behavioral genetics in pathogenic Fov/endophytic Fox in V. planifolia Jacks. Its pathogenic strategy allows Fov to infect in a SIX genes-independent manner. As the other pathogenic elements found in this study could be explained by the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes in Fov. These play a central role as carriers of genes involved with pathogenic activity and could be obtained through HGT.


title: Additive manufactured scaffolds for bone tissue engineering: physical characterization of thermoplastic composites with functional fillers

abstract: Thermoplastic polymer - filler composites are excellent materials for bone tissue engineering (TE) scaffolds, combining the functionality of fillers with suitable load bearing ability, biodegradability, and additive manufacturing (AM) compatibility of the polymer. Two key determinants of their utility are their rheological behavior in the molten state, determining AM processability, and their mechanical load-bearing properties. We report here the characterization of both these physical properties for four bone TE relevant composite formulations with poly(ethylene oxide terephthalate) / poly(butylene terephthalate (PEOT/PBT) as a base polymer, which is often used to fabricate TE scaffolds. The fillers used were reduced graphene oxide (rGO), hydroxyapatite (HA), gentamycin intercalated in zirconium phosphate (ZrP-GTM) and ciprofloxacin intercalated in MgAl layered double hydroxide (MgAl-CFX). The rheological assessment showed that generally the viscous behavior dominated the elastic behavior (G > G) for the studied composites, at empirically determined extrusion temperatures. Coupled rheological-thermal characterization of ZrP-GTM and HA composites showed that the fillers increased the solidification temperatures of the polymer melts during cooling. Both these findings have implications for the required extrusion temperatures and bonding between layers. Mechanical tests showed that the fillers generally made the polymer stiffer but more brittle in proportion to the filler fractions. Furthermore, the elastic moduli of scaffolds did not directly correlate with the corresponding bulk material properties, implying composite-specific AM processing effects on the mechanical properties. Lastly, we show computational models to predict multi-material scaffold elastic moduli using measured single material scaffold and bulk moduli. The reported characterizations are essential for assessing the AM processability and ultimately the suitability of the manufactured scaffolds for the envisioned bone regeneration application.


title: A comparison of approaches to scaffolding multiple regions along the 16S rRNA gene for improved resolution

abstract:
MotivationFull length, high resolution 16s rRNA marker gene sequencing has been challenging historically. Short amplicons provide high accuracy reads with widely available equipment, at the cost of taxonomic resolution. One recent proposal has been to reconstruct multiple amplicons along the full-length marker gene, however no barcode-free computationally tractable approach for this is available. To address this gap, we present Sidle (SMURF Implementation Done to acceLerate Efficiency), an implementation of the Short MUltiple Reads Framework algorithm with a novel tree building approach to reconstruct rRNA genes from individually amplified regions.

ResultsUsing simulated and real data, we compared Sidle to two other approaches of leveraging multiple gene region data. We found that Sidle had the least bias in non-phylogenetic alpha diversity, feature-based measures of beta diversity, and the reconstruction of individual clades. With a curated database, Sidle also provided the most precise species-level resolution.

Availability and ImplementationSidle is available under a BSD 3 license from https://github.com/jwdebelius/q2-sidle


title: Neutralization of European, South African, and United States SARS-CoV-2 mutants by a human antibody and antibody domains

abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission with several emerging variants remain uncontrolled in many countries, indicating the pandemic remains severe. Recent studies showed reduction of neutralization against these emerging SARS-CoV-2 variants by vaccine-elicited antibodies. Among those emerging SARS-CoV-2 variants, a panel of amino acid mutations was characterized including those in the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. In the present study, we evaluated our previously identified antibody and antibody domains for binding to these RBD variants with the emerging mutations, and neutralization of pseudo typed viruses carrying spike proteins with such mutations. Our results showed that one previously identified antibody domain, ab6, can bind 32 out of 35 RBD mutants tested in an ELISA assay. All three antibodies and antibody domains can neutralize pseudo typed B.1.1.7 (UK variant), but only the antibody domain ab6 can neutralize the pseudo typed virus with the triple mutation (K417N, E484K, N501Y). This domain and its improvements have potential for therapy of infections caused by SARS-CoV-2 mutants.


title: Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers

abstract: As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here we leverage our expertise in computational antibody engineering to rationally design/optimize three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R, and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS. Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody induced virus activation or enhancement, we applied NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.


title: Neurite growth kinetics regulation through hydrostatic pressure in a novel triangle-shaped neurofluidic system

abstract: Microfluidic neuro-engineering design rules have been widely explored to create in vitro neural networks with the objective to replicate physiologically relevant structures of the brain. Several neurofluidic strategies have been reported to study the connectivity of neurons, either within a population or between two separated populations, through the control of the directionality of their neuronal projections. Yet, the in vitro regulation of the growth kinetics of those projections remains challenging. Here, we describe a new neurofluidic chip with a triangular design that allows the accurate monitoring of neurite growth kinetics in a neuronal culture. This device permits to measure the maximum achievable length of projecting neurites over time and to report variations in neurite length under several conditions. Our results show that, by applying positive or negative hydrostatic pressure to primary rat hippocampal neurons, neurite growth kinetics can be tuned. This work presents a pioneering approach for the precise characterization of neurite length dynamics within an in vitro minimalistic environment.


title: fMRIflows: a consortium of fully automatic univariate and multivariate fMRI processing pipelines

abstract: How functional MRI (fMRI) data are analyzed depends on the researcher and the toolbox used. It is not uncommon that the processing pipeline is rewritten for each new dataset. Consequently, code transparency, quality control and objective analysis pipelines are important for improving reproducibility in neuroimaging studies. Toolboxes, such as Nipype and fMRIPrep, have documented the need for and interest in automated analysis pipelines. Here, we introduce fMRIflows: a consortium of fully automatic neuroimaging pipelines for fMRI analysis, which performs standard preprocessing, as well as 1st- and 2nd-level univariate and multivariate analysis. In addition to the standardized processing pipelines, fMRIflows also provides flexible temporal and spatial filtering to account for datasets with increasingly high temporal resolution and to help appropriately prepare data for multivariate analysis and improve signal decoding accuracy. This paper first describes fMRIflows structure and functionality, then explains its infrastructure and access, and lastly validates the toolbox by comparing it to other neuroimaging processing pipelines such as fMRIPrep, FSL and SPM. This validation was performed on three datasets with varying temporal resolution to ensure flexibility and robustness, as well as to showcase the improved capability of fMRIflows. The outcome of the validation analysis shows that fMRIflows preprocessing pipeline performs comparably to the ones obtained from other toolboxes. Importantly, fMRIflows flexible temporal filtering approach leads to improved signal-to-noise-ratio after preprocessing and increased statistical sensitivity, particularly in datasets with high temporal resolution. fMRIflows is a fully automatic fMRI processing pipeline which uniquely offers univariate and multivariate single-subject and group analyses as well as preprocessing. It offers flexible spatial and temporal filtering and thereby leads to more pronounced results for datasets with temporal resolutions at or below 1000ms.


title: Identification, crystallization and epitope determination of public TCR shared and expanded in COVID-19 patients

abstract: T cells play pivotal roles in protective immunity against SARS-CoV-2 infection. Follicular helper T (Tfh) cells mediate the production of antigen-specific antibodies; however, T cell receptor (TCR) clonotypes used by SARS-CoV-2-specific Tfh cells have not been well characterized. Here, we first identified and crystallized public TCR of Tfh clonotypes that are shared and expanded in unhospitalized COVID-19-recovered patients. These clonotypes preferentially recognized SARS-CoV-2 spike (S) protein epitopes which are conserved among emerging SARS-CoV-2 variants. These clonotypes did not react with S proteins derived from common cold human coronaviruses, but cross-reacted with symbiotic bacteria, which might confer the publicity. Among SARS-CoV-2 S epitopes, S864-882, presented by frequent HLA-DR alleles, could activate multiple public Tfh clonotypes in COVID-19-recovered patients. Furthermore, S864-882-loaded HLA tetramer preferentially bound to CD4+ T cells expressing CXCR5. In this study, we identified and crystallized public TCR for SARS-CoV-2 that may contribute to the prevention of COVID-19 aggravation.


title: Clonal dissection of immunodominance and cross-reactivity of the CD4+ T cell response to SARS-CoV-2

abstract: The identification of CD4+ T cell epitopes is essential for the design of effective vaccines capable of inducing neutralizing antibodies and long-term immunity. Here we demonstrate in COVID-19 patients a robust CD4+ T cell response to naturally processed SARS-CoV-2 Spike and Nucleoprotein, including effector, helper and memory T cells. By characterizing 2,943 Spike-reactive T cell clones, we found that 34% of the clones and 93% of the patients recognized a conserved immunodominant region encompassing residues S346-365 in the RBD and comprising three nested HLA-DR and HLA-DP restricted epitopes. By using pre- and post-COVID-19 samples and Spike proteins from alpha and beta coronaviruses, we provide in vivo evidence of cross-reactive T cell responses targeting multiple sites in the SARS-CoV-2 Spike protein. The possibility of leveraging immunodominant and cross-reactive T helper epitopes is instrumental for vaccination strategies that can be rapidly adapted to counteract emerging SARS-CoV-2 variants.


title: FECAL MICROBIOME OF CHILDREN WITH NOROVIRUS GASTROENTERITIS

abstract: The human fecal microbiome is composed of endogenous bacteria, eukaryotic viruses, bacteriophages and retroviruses. Several pathological conditions, including gastroenteritis, may be characterized by imbalance of gastrointestinal functions, with alteration in the diversity and composition of the fecal microbiota. Were analyzed twenty-seven fecal microbiome in children hospitalized with gastroenteritis (norovirus positive) from northern region of Brazil. After sequencing, was verified the presence of the domains Bacteria (95%) and Eukaryota (3.1%), the viruses represented 1.9%. Among the pathogenic viruses were found in addition to noroviruses the picornaviruses, enterovirus and parechovirus. The bacteriophages detected were of Caudovirales order, families Siphoviridae, Podoviridae and Myoviridae. In 22.2% (6/27) of the samples was observed co-infection between norovirus, enterovirus B and echovirus. As for the others components of the microbiome, we can highlight the presence of the taxonomic groups: Terrabacteria (50.2%), composed mainly of Actinobacteria and Firmicutes; Proteobacteria (34.5%) represented by the Enterobacteriaceae family; and FCB group (22%) whose most abundant microorganisms were those of the phylum Bacterioidetes. We performed a metagenomic approach to analyze the fecal microbiota of children with viral gastroenteritis, it was observed that the bacterias (Enterobacteriaceae) deserve attention in a possible association with noroviruses, as they were found in large quantities in infections. In addition, other enteric viruses were observed, such as enteroviruses.


title: Beta-arrestin-mediated Angiotensin II type 1 Receptor Activation Promotes Pulmonary Vascular Remodeling in Pulmonary Hypertension

abstract:
ObjectivesThe goal of this study was to test whether a {beta}-arrestin-biased agonist of the angiotensin II (AngII) type 1 receptor (AT1R), which acts as a vasodilator while not blocking cellular proliferation, would have positive effects compared to a balanced agonist, angiotensin II (AngII), or an antagonist, losartan, in pulmonary arterial hypertension (PAH).

BackgroundPAH is a disease of abnormal pulmonary vascular remodeling whose treatment has focused on targeting vasoactive substances, such as inhibiting endothelin signaling and promoting prostacyclin signaling. PAH medical therapies are thought to primarily act as vasodilators, although they may also have effects on pulmonary vascular remodeling. There are a number of reports that blocking AT1R signaling can be beneficial in preclinical models of PAH. The AT1R is a G protein-coupled receptor (GPCR) that promotes vasoconstriction through heterotrimeric G proteins but also signals via {beta}-arrestins, which promote cardioprotective effects and vasodilation.

MethodsWe compared the effects of a {beta}-arrestin-biased AT1R agonist, TRV120023 (TRV023), to a balanced agonist (AngII) and an antagonist (losartan) in preclinical PAH models.

ResultsIn acute infusion studies, AngII increased right ventricular (RV) pressures while TRV023 did not. However, with chronic infusion in monocrotaline (MCT) PAH rats, TRV023 failed to improve hemodynamics or survival compared to AngII, while losartan significantly improved survival. Both TRV023 and AngII enhanced proliferation and migration of pulmonary artery smooth muscle cells (PASMCs) from PAH patients, which was associated with the promotion of proliferative MAP kinase signaling.

Conclusions{beta}-arrestin-mediated AT1R signaling promotes vascular remodeling and worsens PAH, and suggests that the primary benefit of current PAH therapies is through pulmonary vascular reverse remodeling and not vasodilation.


title: Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues

abstract:
1.Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a "transient fraction" of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids.

SynopsisThis study explores the interaction of rhizosphere carbon, minerals, and microbial influence on the fate of soil carbon.

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title: Crotamine as a vehicle for non-viral gene delivery for Pompe disease

abstract: Genetic deficiency of lysosomal acid alpha glucosidase or acid maltase (GAA) results in Pompe disease (PD), encompassing at least five clinical subtypes of varying severity. The current approved enzyme replacement therapy (ERT) for PD is via IV infusion every 2 weeks of a recombinant human GAA (rhGAA) secreted by Chinese hamster ovary (CHO) cells (alglucosidase alfa/Myozyme, Sanofi/Genzyme). Although alglucosidase alfa has proven to be efficient in rescuing cardiac abnormalities and extending the life span of the infantile form, the response in skeletal muscle is variable. ERT usually begins when the patients are symptomatic and secondary problems are already present which are compounded by low alglucosidase alfa uptake, transient nature (every 2 weeks with a rapid return to defect levels), variable glycogen reduction, autophagic accumulation, immune response and high cost. A consensus at a recent US Acid Maltase Deficiency (AMD) conference suggested that a multi-pronged approach including gene therapy, diet, exercise, etc. must be evaluated for a successful treatment of PD. Compared to replication defective viruses, non-viral gene transfer offers fewer safety concerns and, if recent studies are validated, has a wider range of cells. In order for gene therapy (GT) to succeed, the gene of interest must be delivered into the affected cell and expressed to overcome the inherited deficiency. Cell penetrating peptides (CPPs) enter eukaryotic cells through an energy-independent mechanism and efficiently carry biologically active and therapeutic molecules into cells and localize in the cytoplasm or nucleus. CPPs are usually covalently linked to the cargo, including peptides and DNA. Crotamine (Cro) from the South American rattlesnake-Crotalus durrissus terrificus venom, can bind electrostatically to plasmid DNA to deliver into cells, including muscle. We have assembled a bacterial expression vector for Cro and purified the recombinant Cro (rCro). Transient transfection in AMD fibroblasts and ex vivo in whole blood from an adult Pompe patient with rCro complexed with the pcDNA3 x hGAA cDNA demonstrated increased GAA activity. In GAA knockout (KO) mice receiving a single injection of rCro complexed to pcDNA3 x hGAA cDNA intraperitoneally (IP), we found increased GAA activity in tissues after 48 hr. After 8 treatments-IP over 55 days, we found increased vertical hang-time activity, reduced glycogen deposition, increased GAA activity/hGAA plasmid in tissues and minimal immune-reaction to rCro. A subsequent study of 5 administrations every 2 to 3 weeks showed reverse of the clinical phenotypes by running wheel activity, Rotarod, grip-strength meter, open field mobility and T-maze. Tissue culture experiments in PD fibroblast, lymphoid and skeletal muscle cell lines showed increased GAA activity after rCro transient gene delivery.

category: genetics