title: Respiratory coupling between prefrontal cortex and hippocampus of rats anesthetized with urethane in theta and non-theta states

abstract: Respiratory modulation of forebrain activity, long considered hard to reliably separate from breathing artifacts, has been firmly established in recent years using a variety of advanced techniques. Respiratory related oscillation (RRO) is derived from rhythmic nasal airflow in the olfactory bulb (OB) and is conveyed to higher order brain networks, including the prefrontal cortex (PFC) and hippocampus (HC), where it may potentially contribute to communication between these structures by synchronizing their activities at the respiratory rate. RRO was shown to change with sleep-wake states, it is strongest in quiet waking, somewhat less in active waking, characterized with theta activity in the HC, and absent in sleep. The goal of this study was to test RRO synchronization between PFC and HC under urethane anesthesia where theta and non-theta states spontaneously alternate. We found that in theta states, PFC-HC coherences significantly correlated with OB-HC but not with OB-PFC, even though RRO was stronger in PFC than in HC. In non-theta states, PFC-HC synchrony correlated with coherences connecting OB to either PFC or HC. Thus, similar to freely behaving rats, PFC-HC synchrony at RRO was primarily dependent on the response of HC to the common rhythmic drive, but only in theta state. The findings help outlining the value and the limits of applications in which urethane-anesthetized rats can be used for modeling the neural mechanisms of RRO in behaving animals.


title: Microglia complement signaling promotes neuronal elimination and normal brain functional connectivity

abstract: Complement signaling is thought to serve as an opsonization signal to promote the phagocytosis of synapses by microglia. However, while its role in synaptic remodeling has been demonstrated in the retino-thalamic system, it remains unclear whether complement signaling mediates synaptic pruning in the brain more generally. Here we show that mice lacking the complement 3 receptor (C3r), the major microglia complement receptor, fail to show a deficit in either synaptic pruning or axon elimination in the developing mouse cortex. Instead, mice lacking C3r show a deficit in the perinatal elimination of neurons, both in the retina as well as in the cortex, a deficit that is associated with increased cortical thickness and enhanced functional connectivity in these regions in adulthood. These data demonstrate a preferential role for complement in promoting neuronal elimination in the developing brain and argue for a reconsideration of the role of complement in synaptic pruning.

category: neuroscience


title: Transmission of Candidatus Anaplasma camelii to laboratory animals by camel-specific keds, Hippobosca camelina

abstract:
Anaplasmosis, caused by infection with bacteria of the genus Anaplasma is an important veterinary and zoonotic disease. The characterization of transmission has concentrated on ticks and little is known about non-tick vectors of livestock anaplasmosis. This study investigated the presence of Anaplasma spp. in camels in northern Kenya and whether the hematophagous camel ked, Hippobosca camelina, acts as a vector. Camels (n = 976) and > 10,000 keds were sampled over a three-year study period and the presence of Anaplasma species was determined by PCR-based assays targeting the Anaplasmataceae 16S rRNA gene. Camels were infected by  Candidatus Anaplasma camelii occurring from 63 - 78% during the dry (September 2017), wet (June-July 2018), and late wet seasons (July-August 2019). 10 - 29% of camel keds harbored  Ca. Anaplasma camelii acquired from infected camels during blood feeding. We determined whether Anaplasma positive camel keds could transmit  Ca. Anaplasma camelii to small laboratory animals via blood-feeding. We show competence in pathogen transmission and subsequent infection in mice and rabbits by both direct detection in blood smears and subsequent molecular identification by PCR. Transmission of  Ca. Anaplasma camelii to mice (8 - 47%) and rabbits (25%) occurred readily after ked bites. Hence, we demonstrate, for the first time, the potential of H. camelina as a vector of anaplasmosis. This key finding provides the basis for establishing ked control programmes for improvement of livestock and human health.

Author summaryHematophagous flies such as Tabanids and Stomoxys, among other biting flies, are mechanical transmitters of various pathogens such as African trypanosomes and Anaplasma species. However, little is known about the role of common camel-specific biting keds (also known as camel flies or louse flies, genus Hippobosca) in pathogen transmission. Keds inflict painful bites to access host blood, and in the process may transmit bacterial hemopathogens frequently detected in both camels and their keds. We confirmed by experimental blood-feeding, gene amplification, and amplicon sequencing that camel keds can transmit "Candidatus Anaplasma camelii" from naturally-infected camels to healthy mice and rabbits. The high prevalence of camel anaplasmosis throughout the year in northern Kenya could be explained by the infestation camel-specific H. camelina, whose capacity as efficient fliers, unlike ticks, promotes disease transmission and maintenance within and among camel herds. Although this study focused on the transmission of Anaplasma sp. by camel keds, it is possible that other hemopathogens could also be transmitted by these flies through a similar mechanism. Notably, in the absence of their preferred hosts, keds occasionally bite humans and other vertebrates they come across in order to acquire bloodmeals, and in the process could transmit zoonotic pathogens.

category: microbiology


title: A meta-analysis of Microarray Data is Effective for Identifying Gravity-Sensitive Genes

abstract: Gravity affects the function and maintenance of organs, such as bones, muscles, and the heart. Several studies have used DNA microarrays to identify genes with altered expressions in response to gravity. However, it is technically challenging to combine the results from various microarray datasets because of their different data structures. We hypothesized it is possible to identify common changes in gene expression from the DNA microarray datasets obtained under various conditions and methods. In this study, we grouped homologous genes to perform a meta-analysis of multiple vascular endothelial cell and skeletal muscle datasets. According to the t-distributed stochastic neighbor embedding (t-SNE) analysis, the changes in the gene expression pattern in vascular endothelial cells formed specific clusters. We also identified candidate genes in endothelial cells that responded to gravity. Further, we exposed human umbilical vein endothelial cells to simulated microgravity using a clinostat and measured the expression levels of the candidate genes. Gene expression analysis using qRT-PCR revealed that the expression level of the prostaglandin transporter gene SLCO2A1 decreased in response to microgravity, consistent with the meta-analysis of microarray datasets. Furthermore, the direction of gravity affected the expression level of SLCO2A1, buttressing the finding that its expression was affected by gravity. These results suggest that a meta-analysis of DNA microarray datasets may help identify new target genes previously overlooked in individual microarray analyses.

category: cell biology


title: Endosomal recycling to the surface mediated by Gpa1 and PI3-Kinase is inhibited by glucose starvation

abstract: Cell surface protein trafficking is regulated in response to nutrient availability, with multiple pathways directing surface membrane proteins to the lysosome for degradation in response to suboptimal extracellular nutrients. Internalised protein and lipid cargoes recycle back to the surface efficiently in glucose replete conditions, but this trafficking is attenuated following glucose starvation. We find cells with either reduced or hyperactive phosphatidylinositol 3-kinase (PI3K) activity are defective for recycling. Furthermore, we find the yeast G subunit Gpa1, an endosomal PI3K effector, is required for surface recycling of cargoes. Following glucose starvation, mRNA and protein levels of a distinct G subunit Gpa2 are elevated following nuclear translocation of Mig1, which inhibits recycling of various cargoes. As Gpa1 and Gpa2 interact at the surface where Gpa2 concentrates during glucose starvation, we propose this disrupts PI3K activity required for recycling, potentially diverting Gpa1 to the surface and interfering with its endosomal role in recycling. In support of this model, glucose starvation and over-expression of Gpa2 alters PI3K endosomal phosphoinositide production. Glucose deprivation therefore triggers a survival mechanism to increase retention of surface cargoes in endosomes and promote their lysosomal degradation.


title: Endosomal cargo recycling mediated by Gpa1 and Phosphatidylinositol-3-Kinase is inhibited by glucose starvation


title: Eco-evolutionary dynamics lead to functionally robust and redundant communities

abstract: Microbial communities are functionally stable and taxonomically variable: species abundances fluctuate over time and space, while the functional composition is robust and reproducible. These observations imply functional redundancy: the same function is performed by many species, so that one may assemble communities with different species but the same functional composition. The clarity of this observation does not parallel with a theoretical understanding of its origin. Here we study the eco-evolutionary dynamics of communities interacting through competition and cross-feeding. We show that the eco-evolutionary trajectories rapidly converge to a "functional attractor", characterized by a functional composition uniquely determined by environmental conditions. The taxonomic composition instead follows non-reproducible dynamics, constrained by the conservation of the functional composition. Our framework provides a deep theoretical foundation to the empirical observations of functional robustness and redundancy.

category: ecology


title: Staying in touch: how highly specialised moth pollinators track host plant phenology in unpredictable climates

abstract: For pollinating insects that visit just a single flowering species, the co-occurrence of flowers and insects in time is likely to have critical implications for both plant and pollinator. Insects often utilise diapause to persist through periods in which resources are unavailable, timing their re-emergence by responding to the same environmental cues as their host plants. The obligate pollination mutualisms (OPMs) between Epicephala moths (Gracillariidae) and their leaf flower host plants are some of the most specialised interactions between plants and insects. However, to date there have been very few studies of Epicephala moth lifecycles and none of how they synchronise their activity with the flowering of their host plants. Breynia oblongifolia (Phyllanthaceae) is known to be exclusively pollinated by two highly specific species of Epicephala moth (Gracillariidae). We surveyed populations of both the host plant and its pollinators over multiple years to determine their annual phenology and then modelled the climatic factors that drive their activity. Using our newly gained knowledge of moth and host plant phenology, we then looked for evidence of diapause at both the egg and pre-pupal stages. Our phenology surveys showed that although female flowers were present throughout the entire year, the abundance of flowers and fruits was highly variable between sites and strongly associated with local rainfall and photoperiod. Fruit abundance, but not flower abundance, was a significant predictor of adult Epicephala activity, suggesting that eggs or early instar larvae diapause within dormant flowers and emerge as fruits mature. Searches of overwintering flowers confirmed this, with many containing evidence of pollen and diapausing pollinators. We also observed the behaviour of adult Epicephala prior to pupation and found that ~10% of the Autumn emerging Epicephala enter diapause, eclosing to adulthood after 38-56 weeks. The remaining 90% of autumn emerging adults pupate directly with no diapause, suggesting a bet hedging strategy for adult emergence. As such, Epicephala moths appear to utilise diapause at multiple stages in their lifecycle, and possibly bet hedging, in order to deal with variable flowering phenology and climatic unpredictability.


title: Expanding Asgard members in the domain of Archaea shed new light on the origin of eukaryotes

abstract: The hypothesis that eukaryotes originated from within the domain Archaea has been strongly supported by recent phylogenomic analyses placing Heimdallarchaeota from the Asgard superphylum as the closest known archaeal sister-group to eukaryotes. At present, only six phyla are described in the Asgard superphylum, which limits our understanding of the relationship between eukaryotes and archaea, as well as the evolution and ecological functions of the Asgard archaea. Here, we describe five previously unknown phylum-level Asgard archaeal lineages, tentatively named Tyr-, Sigyn-, Freyr-, Njord- and Balderarchaeota. Comprehensive phylogenomic analyses further supported the origin of eukaryotes within Archaea and a new Asgard lineage Njordarchaeota was supposed as the known closest branch with the eukaryotic nuclear host lineage. Metabolic reconstruction suggests that the Asgard archaea described here have potential to fix inorganic carbon via the Wood-Ljungdahl pathway and degrade organic matters except Njordarchaeota, which may possess a heterotrophic lifestyle with capability of peptides and amino acids utilization. Additionally, the Ack/Pta pathway for homoacetogenesis and de novo anaerobic cobalamin biosynthesis pathway were found in Balderarchaeota and Tyrarchaeota, respectively. This study largely expands the Asgard superphylum, provides additional evidences to support the 2-domain life tree and sheds new light on the evolution of eukaryotes.

category: evolutionary biology


title: Chromatin interaction aware gene regulatory modeling with graph attention networks

abstract: Linking distal enhancers to genes and modeling their impact on target gene expression are longstanding unresolved problems in regulatory genomics and critical for interpreting non-coding genetic variation. Here we present a new deep learning approach called GraphReg that exploits 3D interactions from chromosome conformation capture assays in order to predict gene expression from 1D epigenomic data or genomic DNA sequence. By using graph attention networks to exploit the connectivity of distal elements up to 2Mb away in the genome, GraphReg more faithfully models gene regulation and more accurately predicts gene expression levels than state-of-the-art deep learning methods for this task. Feature attribution used with GraphReg accurately identifies functional enhancers of genes, as validated by CRISPRi-FlowFISH and TAP-seq assays, outperforming both CNNs and the recently proposed Activity-by-Contact model. Sequence-based GraphReg also accurately predicts direct transcription factor (TF) targets as validated by CRISPRi TF knockout experiments via in silico ablation of TF binding motifs. GraphReg therefore represents an important advance in modeling the regulatory impact of epigenomic and sequence elements.

category: genomics


title: Structural heterogeneity in biliverdin modulates spectral properties of Sandercyanin fluorescent protein

abstract:
Sandercyanin, a blue homo-tetrameric lipocalin protein purified from Canadian walleye (Stizostedion vitreus), is the first far-red fluorescent protein reported in vertebrates(1-3). Sandercyanin binds non-covalently to biliverdin IX (BLA) and fluoresces at 675nm on excitation at 375nm and 635nm(1). Sandercyanin fluorescence can be harnessed for many in vivo applications when engineered into a stable monomeric form. Here, we report the spectral properties and crystal structures of engineered monomeric Sandercyanin-BLA complexes. Compared to wild-type protein, monomeric Sandercyanin ([~]18kDa) binds BLA with similar affinities and show a broad red-shifted absorbance spectra but possess reduced quantum efficiency. Crystal structures reveal D-ring pyrrole of BLA rotated around the C14-C15 bond, which is stabilized by neighboring aromatic residues and increased water-mediated polar contacts in the BLA-binding pocket. A tetrameric Sandercyanin variant (Tyr-142-Ala) co-displaying red- and far-red absorbing states, and reduced fluorescence shows similar conformational changes in BLA binding pocket. Our results suggest that D-ring flexibility of BLA and its rearrangement reduces the fluorescence quantum-yield of monomeric Sandercyanin. Structures of monomeric Sandercyanin could be utilized as prototypes to generate bright BLA-inducible fluorescent proteins. Further, our study postulates a mechanism for modulating photo-states in BLA-bound lipocalins, known only in phytochromes till date.

Significance StatementSandercyanin is a tetrameric red fluorescent protein from a blue variant of walleye (Stizostedion vitreum) that binds to biliverdin IX (BLA). Its biophysical properties and structures have been published earlier(1). A bright and stable monomeric Sandercyanin could be utilized as a fusion protein for fluorescence-based applications. Here we report the first structures and spectral properties of fluorescent monomeric Sandercyanin-BLA complexes and describe the molecular basis of modulated spectral properties due to rotated D-ring pyrrole around C14-C15 bond and re-shuffling of BLA-binding pocket. BLA-bound monomeric Sandercyanin could be engineered into brighter variants for in-vivo applications. Our study also reveals an unfamiliar mechanism in BLA-binding lipocalins that regulates red- and far-red absorbance states.

category: bioengineering


title: Benchmarking scRNA-seq imputation tools with respect to network inference highlights deficits in performance at high levels of sparsity

abstract:
Gene correlation network inference from single-cell transcriptomics data potentially allows to gain unprecendented insights into cell type-specific regulatory programs. ScRNA-seq data is severely affected by dropout, which significantly hampers and restrains current downstream analysis. Although newly developed tools are capable to deal with sparse data, no appropriate single-cell network inference workflow has been established. A potential way to end this deadlock is the application of data imputation methods, which already proofed to be useful in specific contexts of single-cell data analysis, e.g., recovering cell clusters. In order to infer cell-type specific networks, two prerequisites must be met: the identification of cluster-specific cell-types and the network inference itself.

Here, we propose a benchmarking framework to investigate both objections. By using suitable reference data with inherent correlation structure, six representative imputation tools and appropriate evaluation measures, we were able to systematically infer the impact of data imputation on network inference. Major network structures were found to be preserved in low dropout data sets. For moderately sparse data sets, DCA was able to recover gene correlation structures, although systematically introducing higher correlation values. No imputation tool was able to recover true signals from high dropout data. However, by using an additional biological data set we could show that cell-cell correlation by means of specific marker gene expression was not compromised through data imputation.

Our analysis showed that network inference is feasible for low and moderately sparse data sets by using the unimputed and DCA-prepared data, respectively. High sparsity data, on the other side, still pose a major problem since current imputation techniques are not able to facilitate network inference. The annotation of cluster-specific cell-types as a prerequisite is not hampered by data imputation but their power to restore the deeply hidden correlation structures is still not sufficient enough.

category: bioinformatics


title: A β-secretase modulator decreases Tau pathology and preserves short-term memory in a mouse model of neurofibrillary degeneration

abstract: A structure-activity relationship has enabled us to identify two molecules, MAGS02-14 and PEL24-199, sharing a {beta}-secretase modulatory effect but having or not a lysosomotropic activity, respectively. More importantly, MAGS02-14 and PEL24-199 only differ from each other by a single nitrogen atom. However, which of the lysosomotropic and/or {beta}-secretase modulating activities is necessary for the pharmacological effect in vivo remains ill-defined. To address this question, the THY-Tau22 transgenic model of NFD was treated for 6 weeks in a curative paradigm and short-term memory, Tau burden, and inflammatory processes were studied. PEL24-199, possessing only the {beta}-secretase modulatory activity, was shown to restore the short-term memory and to reduce NFD. This effect was associated with reduced phosphorylation of Tau, increased phosphatase expression, and a decrease of astrogliosis. Our results therefore suggest that the lysosomotropic activity may be dispensable for the effect on both A{beta} and Tau pathologies.

category: pharmacology and toxicology


title: Hydrogels improve plant growth in Mars analog conditions

abstract: The development of sustainable human presence in a Martian settlement will require in situ resource utilization (ISRU), the collect and utilization of Mars-based resources, including notably water and a substrate for food production. Plants will be fundamental components of future human missions to Mars, and the question as to whether Mars soils can support plant growth is still open. Moreover, plant cultivation will probably suffer from the lack of in situ liquid water, which might constitute one of the biggest challenges for ISRU-based food production on Mars. Enhancing the crop yield with less water input and improving water utilization by plants are thus chief concern for sustainable ISRU food production. Hydrogels are polymers able to absorb large quantity of water and have been shown to increase water retention in the soil, thus increasing plant establishment and growth. This work reports on the short-term assessment of plant growth in Mars soil analogs supplemented with hydrogels, in the constrained environment of a simulated life-on-Mars mission. Soil analogs consisted of sand and clay-rich material, with low amount organic matter and alkaline pH. Soils were supplemented with 10% (w/w) potting medium and were sampled in Utah desert, in the vicinity of the Mars Desert Research Station, a Mars analog facility surrounded by soils sharing similarities in mineralogical and chemical composition to Martian soils. Heights and dry biomass of Mentha spicata and seed germination of Raphanus sativus were monitored under various irrigation frequencies. Results indicate that the soil analogs, together with the limited irrigation regime, were less capable of supporting plant growth as a comparison to potting medium. The effects of hydrogel supplementation were significative under limited irrigation and led to growth increased by 3% and 6% in clay- and sand-containing soils, respectively. Similarly, hydrogel supplementation resulted in plant masses increased by 110% in clay-containing soils and 78% in sand-containing soils. Additionally, while seeds of Raphanus sativus failed to germinate, hydrogel supplementation allows for the germination of 27% of seeds, indicating that hydrogels might help loosening dense media with low water retention. Collectively, the results suggest that supplementation with hydrogel and traditional plant growth substrate could help plant cope with limited irrigation and poor alkaline Mars soil analogs, and are discussed in the context of strategies to develop ISRU for off-world colonization.

category: plant biology


title: Tuning Cell-free Composition Controls the Time-delay, Dynamics, and Productivity of TX-TL Expression

abstract: The composition of TX-TL cell-free expression systems are adjusted by adding macromolecular crowding agents and salts. However, the effects of these cosolutes on the dynamics of individual gene expression processes have not been systematically quantified. Here, we carry out kinetic mRNA and protein level measurements on libraries of genetic constructs using the common cosolutes PEG-8000, Ficoll-400, and magnesium glutamate. By combining these measurements with biophysical modeling, we show that cosolutes have differing effects on transcription initiation, translation initiation, and translation elongation rates with trade-offs between time-delays, expression tunability, and maximum expression productivity. We also confirm that biophysical models can predict translation initiation rates in TX-TL using E. coli lysate. We discuss how cosolute composition can be tuned to maximize performance across different cell-free applications, including biosensing, diagnostics, and biomanufacturing.

category: synthetic biology


title: The interplay between growth rate and nutrient quality defines gene expression capacity

abstract: The gene expression capacity of bacterial cells depends on the interplay between growth and the availability of the transcriptional and translational machinery. Growth rate is widely accepted as the global physiological parameter controlling the allocation of cell resources. This allocation has an impact on the ability of the cell to produce both host and heterologous proteins required for synthetic circuits and pathways. Understanding the relationship between growth and resources is key for the efficient design of artificial genetic constructs, however, it is obscured by the mutual dependence of growth and gene expression on each other. In this work, we investigate the individual contributions of molecular factors, growth rate and metabolism to gene expression by investigating the behaviour of bacterial cells growing in chemostats in growth-limited conditions. We develop a model of the whole cell that captures trade-offs in gene expression arising from the individual contributions of different factors, and validate it by analysing gene couplings which emerge from competition for the gene expression machinery. Our results show that while growth rate and molecular factors, such as the number of rRNA operons, set the abundance of transcriptional and translational machinery available, it is metabolism that governs the usage of those resources by tuning elongation rates. We show that synthetic gene expression capacity can be maximised by using low growth in a high-quality medium. These findings provide valuable insights into fundamental trade-offs in microbial physiology that will inform future strain and bioprocesses optimisation.


title: A single-cell resolved cell-cell communication model explains lineage commitment in hematopoiesis

abstract: Cells do not function in isolation. Arguably, every cell fate decision occurs in response to environmental signals. In many cases cell-cell communication alters the dynamics of a cells internal gene regulatory network to initiate cell fate transitions, yet models rarely take this into account. Here we develop a multiscale perspective to study the granulocyte-monocyte vs. megakaryocyte-erythrocyte fate decisions. This transition is dictated by the GATA1-PU.1 network, a classical example of a bistable cell fate system. We show that, for a wide range of cell communication topologies, even subtle changes in signaling can have pronounced effects on cell fate decisions. We go on to show how cell-cell coupling through signaling can spontaneously break the symmetry of a homogenous cell population. Noise, both intrinsic and extrinsic, shapes the decision landscape profoundly, and affects the transcriptional dynamics underlying this important hematopoietic cell fate decision-making system.

category: systems biology


title: Spontaneous Neural Activity Changes after Bariatric Surgery: a resting-state fMRI study

abstract:
1.BackgroundMetabolic disorders associated with obesity could lead to alterations in brain structure and function. Whether these changes can be reversed after weight loss is unclear. Bariatric surgery provides a unique opportunity to address these questions because it induces marked weight loss and metabolic improvements which in turn may impact the brain in a longitudinal fashion. Previous studies found widespread changes in grey matter (GM) and white matter (WM) after bariatric surgery. However, findings regarding changes in spontaneous neural activity following surgery, as assessed with the fractional amplitude of low frequency fluctuations (fALFF) and regional homogeneity of neural activity (ReHo), are scarce and heterogenous. In this study, we used a longitudinal design to examine the changes in spontaneous neural activity after bariatric surgery (comparing pre- to post-surgery), and to determine whether these changes are related to cardiometabolic variables.

MethodsThe study included 57 participants with severe obesity (mean BMI=43.1{+/-}4.3kg/m2) who underwent sleeve gastrectomy (SG), biliopancreatic diversion with duodenal switch (BPD), or Roux-en-Y gastric bypass (RYGB), scanned prior to bariatric surgery and at follow-up visits of 4 months (N=36), 12 months (N=29), and 24 months (N=14) after surgery. We examined fALFF and ReHo measures across 1022 cortical and subcortical regions (based on combined Schaeffer-Xiao parcellations) using a linear mixed effect model. Voxel-based morphometry (VBM) based on T1-weighted images was also used to measure GM density in the same regions. We also used an independent sample from the Human Connectome Project (HCP) to assess regional differences between individuals who had normal-weight (N=46) or severe obesity (N=46).

ResultsWe found a global increase in the fALFF signal with greater increase within dorsolateral prefrontal cortex, precuneus, inferior temporal gyrus, and visual cortex. This effect was more significant 4 months after surgery. The increase within dorsolateral prefrontal cortex, temporal gyrus, and visual cortex was more limited after 12 months and only present in the visual cortex after 24 months. These increases in neural activity measured by fALFF were also significantly associated with the increase in GM density following surgery. Furthermore, the increase in neural activity was significantly related to post-surgery weight loss and improvement in cardiometabolic variables, such as insulin resistance index and blood pressure. In the independent HCP sample, normal-weight participants had higher global and regional fALFF signals, mainly in dorsolateral/medial frontal cortex, precuneus and middle/inferior temporal gyrus compared to the obese participants. These BMI-related differences in fALFF were associated with the increase in fALFF 4 months post-surgery especially in regions involved in control, default mode and dorsal attention networks.

ConclusionsBariatric surgery-induced weight loss and improvement in metabolic factors are associated with widespread global and regional increases in neural activity, as measured by fALFF signal. These findings alongside the higher fALFF signal in normal-weight participants compared to participants with severe obesity in an independent dataset suggest an early recovery in the neural activity signal level after the surgery.


title: Dynamic functional connectivity links with treatment response of electroconvulsive therapy in major depressive disorder

abstract:
BackgroundElectroconvulsive Therapy (ECT) is one of the most effective treatments for major depressive disorder (DEP). There is recently increasing attention to evaluate ECTs effect on resting-state functional magnetic resonance imaging (rs-fMRI). This study aims to compare rs-fMRI of DEP patients with healthy participants, investigate whether dynamic functional network connectivity network (dFNC) estimated from rs-fMRI predicts the ECT outcome, and explore the effect of ECT on brain network states.

MethodResting-state fMRI data were collected from 119 patients with depression or DEP (76 females), and 61 Healthy (HC) participants (34 females) with an age mean of 52.25 (N=180) years old. The pre-ECT and post-ECT Hamilton Depression Rating Scale (HDRS) were 25.59{+/-}6.14 and 11.48{+/-}9.07, respectively. Twenty-four independent components from default mode (DMN) and cognitive control network (CCN) were extracted using group-independent component analysis from pre-ECT and post-ECT rs-fMRI. Then, the sliding window approach was used to estimate the pre-and post-ECT dFNC of each participant. Next, k-means clustering was separately applied to pre-ECT dFNC and post-ECT dFNC to assess three distinct states from each participant. We calculated the amount of time each individual spends in each state, called occupancy rate or OCR. Next, we compared OCR values between HC and DEP participants. We also calculated the partial correlation between pre-ECT OCRs and HDRS change while controlling for age, gender, number of treatment, and site. Finally, we evaluated the effectiveness of ECT by comparing pre-and post-ECT OCR of DEP and HC participants.

ResultsThe main findings include: 1) DEP patients had significantly lower OCR values than the HC group in a state, where connectivity between CCN and DMN was relatively higher than other states (corrected p= 0.015), 2) Pre-ECT OCR of state, with more negative connectivity between CCN and DMN components, predicted the HDRS changes (R=0.23 corrected p=0.03). This means that those DEP patients who spend less time in this state showed more HDRS change, and 3) The post-ECT OCR analysis suggested that ECT increased the amount of time DEP patients spend in state 2 (corrected p=0.03). Finally, we found ECT increases the total traveled distance in DEP.

ConclusionOur finding suggests that dFNC features, estimated from CCN and DMN, show promise as a predictive biomarker of the ECT outcome of DEP patients. Also, this study identified a possible underlying mechanism associated with the ECT effect in DEP patients.


title: An experimental prediction: granule cells can perform linearly non-separable computations

abstract: Multiple studies show how dendrites might extend some neurons computational capacity. Past works most often focus on pyramidal cells which have an extended dendritic tree where voltage can vary independently; pyramidal neurons dendrites emit local spikes turning dendritic branches into local non-linear subunits. However, these studies leave a large fraction of the nervous system unexplored. Here, we study a neuron with a modest dendritic and non-spiking dendrites. Granule cells dendrites do not spike and these cells membrane voltage remain constant over the neuron. This study uses a conjunction of Boolean algebra and biophysical modelling to predict that Granule cells can perform linearly non-separable computations. In a previous study, we found a linearly non-separable Boolean function possible to implement without dendritic spikes, we coined this computation the feature binding problem. In the present work, we use the intrinsic saturation of synaptic conductance to implement this computation in a biophysical model. An integrate and fire, cannot perform such type of computations. Confirming our prediction would change how we understand the nervous system.


title: A prediction: granule cells can perform linearly non-separable computations


title: Choosing between cocaine and sucrose under the influence: testing the effect of cocaine tolerance

abstract: Cocaine use not only depends on the reinforcing properties of the drug, but also on its intoxicating effects on alternative nondrug activities. In animal models investigating choice between cocaine and alternative sweet rewards, the latter influence can have a dramatic impact on choice outcomes. When cocaine intoxication at the moment of choice is prevented by imposing sufficiently long intervals between choice trials, animals typically prefer the sweet reward. However, when choosing under the drug influence is permitted, animals shift their preference in favor of cocaine. We previously hypothesized that this preference shift is mainly due to a direct suppression of responding for sweet reward by cocaine intoxication. Here we tested this hypothesis by making rats tolerant to this drug-induced behavioral suppression. Contrary to our expectation, tolerance did not prevent rats from shifting their preference to cocaine when choosing under the influence. Thus, other mechanisms must be invoked to explain the influence of cocaine intoxication on choice outcomes.


title: Single-Cell Multiomics Reveals Distinct Cell States at the Top of Human Hematopoietic Hierarchy

abstract: The advent of single cell (Sc) genomics has challenged the dogma of haematopoiesis as a tree-like structure of stepwise lineage commitment through distinct and increasingly restricted progenitor populations. Instead, analysis of ScRNA-seq has proposed that the earliest events in human hematopoietic stem cell (HSC) differentiation are characterized by only subtle molecular changes, with hematopoietic stem and progenitor cells (HSPCs) existing as a continuum of low-primed cell-states that gradually transition into a specific lineage (CLOUD-HSPCs). Here, we combine ScRNA-seq, ScATAC-seq and cell surface proteomics to dissect the heterogeneity of CLOUD-HSPCs at different stages of human life. Within CLOUD-HSPCs, pseudotime ordering of both mRNA and chromatin data revealed a bifurcation of megakaryocyte/erythroid and lympho/myeloid trajectories immediately downstream a subpopulation with an HSC-specific enhancer signature. Importantly, both HSCs and lineage-restricted progenitor populations could be prospectively isolated based on correlation of their molecular signatures with CD35 and CD11A expression, respectively. Moreover, we describe the changes that occur in this heterogeneity as hematopoiesis develops from neonatal to aged bone marrow, including an increase of HSCs and depletion of lympho-myeloid biased MPPs. Thus, this study dissects the heterogeneity of human CLOUD-HSPCs revealing distinct HSPC-states of relevance in homeostatic settings such as ageing.


title: Single-Cell Multiomics Reveals Distinct Cell States at the Top of the Human Hematopoietic Hierarchy


title: Novel zebrafish mutants reveal new roles for Apolipoprotein B during embryonic development and pathological conditions

abstract:
Apolipoprotein B (ApoB) is the primary protein of chylomicrons, VLDLs and LDLs and is essential for their assembly. Defects in ApoB synthesis and secretion result in several human diseases, including abetalipoproteinemia and familial hypobetalipoproteinemia. Conversely, high levels of APOB in plasma are associated with increased risk for coronary heart disease and atherosclerosis.

The involvement of APOB in lipid metabolism and atherogenesis prompted the generation of several mutant mice. However, as APOB is required for supplying nutrients to the developing embryo, ApoB null mice are embryonic lethal, thereby precluding the study of the roles of this protein during development.

Here, we established novel zebrafish mutants for two apoB genes: apoBa and apoBb.1. Double-mutant embryos display clear hallmarks of human hypolipidemia-related diseases, including intestinal defects and fatty liver, as well as profound vascular defects. We further use these models to identify the domains within ApoB responsible for its functions. By assessing the ability of different truncated forms of human APOB to rescue the mutant phenotypes, we demonstrate the benefits of this model for prospective therapeutic screens. Overall, our novel zebrafish models uncover new functions of ApoB in organ development and morphogenesis and shed new light on the mechanisms underlying hypolipidemia-related diseases.

category: developmental biology


title: Constrained flexibility of parental cooperation limits evolutionary responses to harsh conditions

abstract: Parental care is predicted to evolve to mitigate harsh environments, thus adaptive plasticity of care may be an important response to climate change. In biparental species, fitness costs may be reduced with plasticity of behavior among partners. We investigated this prediction with the burying beetle, Nicrophorus orbicollis, by exposing them to contrasting benign and harsh thermal environments. We found strong fitness costs under the harsh environment, but rather than select for more care, visualized selection was stabilizing. Examining different components of care revealed positive directional selection gradients for direct care and strong stabilizing selection gradients for indirect care, resulting in constrained evolutionary responses. Further, because males and females did not coordinate their investments, the potential for adaptive plasticity was not enhanced under biparental care. Females cared at capacity with or without male partners, while males with partners reduced direct care but maintained indirect care levels. Decision rules were not altered in different environments, suggesting no shift from sexual conflict to cooperation. We suggest that the potential for parenting to ameliorate the effects of our climate crisis may depend on the sex-specific evolutionary drivers of parental care, and that this may be best reflected in components of care.


title: Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes

abstract:
Root-knot nematodes are the major contributor to the crop losses caused by nematodes. Root-knot nematodes secrete effectors into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effectors. The details of how root-knot nematodes regulate transcription remain sparse.

Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands: providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus and termed it Mel-DOG.

Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode, and identify a new set of candidate effector genes that will guide future functional analyses.


title: The prostate cancer therapy enzalutamide compared with abirateroneacetate/prednisone impacts motivation for exploration, spatial learning andalters dopaminergic transmission in aged castrated mice

abstract: Cognitive side effects after cancer treatment, threatening quality of life (QoL) and adherence to treatments, now constitute a major challenge in oncology. Abiraterone acetate plus prednisone (AAP) and enzalutamide (ENZ) are next generation therapy (NGT) administered with androgen deprivation therapy to metastatic castration-resistant prostate cancer (mCRPC) patients. NGT significantly improved mCRPC overall survival but neurological side effects such as fatigue and cognitive impairment have been recently reported. We developed a behavioral 17 months-aged and castrated mouse model receiving per os AAP or ENZ during 5 days per week for six consecutive weeks. After behavioral tests, brain and plasma were collected for immunohistochemical studies. The objective was to elucidate the impact of NGT on spontaneous activity, cognitive functions and emotional reactivity, as well as neurobiological functions. ENZ exposure reduced spontaneous activity and exploratory behavior associated with a decreased tyrosine hydroxylase (TH)-dopaminergic activity in the substantia nigra pars compacta and the ventral tegmental area. A decrease in TH+-DA afferent fibers and Phospho-DARPP32-related dopaminergic neuronal activities in the striatum and the ventral hippocampus, highlighted ENZ-induced dopaminergic regulation whithin the nigrostriatal and mesolimbocortical pathways. ENZ and AAP treatments did not substantially modify spatial learning and memory or behavioral flexibility performances, but ENZ led to a thygmotaxis behavior impacting the cognitive score, and reduced c-fos-related activity of NeuN+-neurons in the dorsal hippocampus. These results establish the consequences of the mCRPC treatment ENZ in aged castrated mouse motivation to exploration and cognition, of particular importance for future management of patients elderly postrate cancer patients and their QoL.

category: animal behavior and cognition


title: A SIMPLI (Single-cell Identification from MultiPLexed Images) approach for spatially resolved tissue phenotypingat single-cell resolution.

abstract:
Multiplexed imaging technologies enable the study of biological tissues at single-cell resolution while preserving spatial information. Currently, high-dimension imaging data analysis is technology-specific and requires multiple tools, restricting analytical scalability and result reproducibility. Here we present SIMPLI (Single-cell Identification from MultiPlexed Images), a novel, flexible and technology-agnostic software that unifies all steps of multiplexed imaging data analysis. After raw image processing, SIMPLI performs a spatially resolved, single-cell analysis of the tissue slide as wells as cell-independent quantifications of marker expression to investigate features undetectable at the cell level. SIMPLI is highly customisable and can run on desktop computers as well as high-performance computing environments, enabling workflow parallelisation for large datasets. SIMPLI produces multiple tabular and graphical outputs at each step of the analysis. Its containerised implementation and minimum configuration requirements make SIMPLI a portable and reproducible solution for multiplexed imaging data analysis.

SIMPLI is available at: https://github.com/ciccalab/SIMPLI.


title: Physical observables to determine the nature of membrane-less cellular sub-compartments

abstract: The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of contexts, but the mechanism of their formation is not fully understood. Several competing mechanisms exist that are difficult to distinguish empirically, including liquid-liquid phase separation, and the trapping of molecules by multiple binding sites. Here we propose a theoretical framework and outline observables to differentiate between these scenarios from single molecule tracking experiments. In the binding site model, we derive relations between the distribution of proteins, their diffusion properties, and their radial displacement. We predict that protein search times can be reduced for targets inside a liquid droplet, but not in an aggregate of slowly moving binding sites. These results are applicable to future experiments and suggest different biological roles for liquid droplet and binding site foci.

category: biophysics


title: Mechanism of transcription modulation by the transcription-repair coupling factor

abstract: Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes distressed RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.


title: IDENTIFICATION OF BIOCHEMICAL AND MOLECULAR MARKERS OF EARLY AGING IN CHILDHOOD CANCER SURVIVORS

abstract:
PurposeSurvival rates of Childhood Cancer Patients have improved tremendously over the past four decades. However, cancer treatments are associated with an increased risk of developing an anticipated onset of chronic diseases typical of aging. Thus, we aimed to identify molecular/metabolic cellular alterations responsible for early aging in Childhood Cancer Survivors (CCS).

Patients and MethodsBiochemical, proteomic and molecular biology analyses were conducted on mononuclear cells (MNCs) isolated from peripheral blood of 196 CCS, comparing the results with those obtained on MNCs of 154 healthy subjects.

ResultsData demonstrate that CCS-MNCs show: i) inefficient oxidative phosphorylation associated with low energy status and a metabolic switch to lactate fermentation compared with age-matched normal controls; ii) increment of lipid peroxidation due to an unbalance among the oxidative stress production and the activation of the antioxidant defenses; (iii) significantly lower expression of genes and proteins involved in mitochondrial biogenesis and metabolism regulation, such as CLUH, PGC1-, and SIRT6 in CCS, not observed in the age-matched healthy or elderly subjects. The application of a mathematical model based on biochemical parameters predicts that CCS have a biological age significantly increased by decades compared to the chronological age. Overall, the results show that the impact of chemo/chemoradiotherapy on mitochondria efficiency in 196 CCS was rather homogeneous, irrespective of cancer type, treatment protocols, and time elapsed from the end of the curative period.

ConclusionsOur study identifies some biochemical and molecular alterations possibly contributing to the pathophysiology of anticipated aging and metabolic deficiency described in CCS. These results may be useful in identifying approaches to restore the mitochondrial function, slowing down the aging and the associated pathological conditions in CCS.

category: cancer biology


title: Chemotherapy-induced collagen IV drives cancer cell invasion through activation of Src/FAK signaling

abstract:
Triple-negative breast cancer (TNBC) is the most aggressive and deadly subtype of breast cancer, accounting for 30,000 cases annually in the US. While there are several clinical trials ongoing to identify new agents to treat TNBC, the majority of TNBC patients are treated with anthracycline- or taxane-based chemotherapies in the neoadjuvant setting, followed by surgical resection and adjuvant chemotherapy. While many patients respond well to this approach, as many as 25% will suffer local or metastatic recurrence within five years. Understanding the mechanisms that drive recurrence after chemotherapy treatment is critical to improving survival for patients with TNBC. It is well-established that the extracellular matrix, which provides structure and support to tissues, is a major driver of tumor growth, local invasion and dissemination of cancer cells to distant metastatic sites. In the present study, we show that decellularized extracellular matrix (dECM) obtained from chemotherapy-treated mice increases invasion of treatment-naive breast cancer cells compared to vehicle-treated dECM. Using tandem-mass-tag proteomics, we further demonstrate that anthracycline- and taxane-based chemotherapies induce drug-specific changes in tumor ECM composition. We identify the basement membrane protein collagen IV as significantly upregulated in the ECM of chemotherapy-treated mice and patients treated with neoadjuvant chemotherapy. We show that collagen IV drives invasion via Src/FAK signaling and that inhibiting collagen IV-driven signaling decreases invasion in chemotherapy-treated dECM. These studies provide a novel mechanism by which chemotherapy may induce metastasis via effects on ECM composition.

One Sentence SummaryChemotherapy alters the extracellular matrix of breast tumors leading to increased invasion of residual cancer cells.


title: Both transient and sustained MPK3/6 activities positively control expression of NLR genes in PTI and ETI.

abstract: Arabidopsis thaliana Mitogen Activated Protein Kinases 3 and 6 (MPK3/6) are known to be activated transiently in PAMP-Triggered Immunity (PTI) and durably in Effector-Triggered Immunity (ETI). However the functional differences between these two kinds of activation kinetics and how they allow coordination of the two layers of plant immunity remain poorly understood. Here, by analysing suppressors of the phenotype caused by a constitutively active form of MPK3, we demonstrate that ETI-mediating nucleotide-binding domain leucine-rich repeat receptors (NLRs) and NLR signaling can act downstream of MPK3 activities. Moreover we provide evidence that both sustained and transient MPK3/6 activities positively control the expression of at least two NLR genes, AT3G04220 and AT4G1110. We further show that the ETI regulators NDR1 and EDS1 also contribute to the upregulations of these two NLRs not only in an ETI context but also in a PTI context. Remarkably, while in ETI, MPK3/6 activities are dependent on NDR1 and EDS1, they are not in PTI, suggesting that if the same actors are involved in the two layers of immunity, the way they are interconnected is different. Finally we demonstrate that expression of the NLR AT3G04220 is sufficient to induce expression of defense genes from the SA branch. Overall this study enlarges our knowledge of MPK3/6 functions during immunity and gives a new insight into the intrication of PTI and ETI.


title: Root meristem shaping via brassinosteroid-controlled cell geometry

abstract: Growth extent and direction determine cell and whole-organ architecture. How they are spatiotemporally modulated to control size and shape? Here we tackled this question by studying the effect of brassinosteroid (BR) signaling on the structure of the root meristem. Quantification of the 3D geometry of thousands of individual meristematic cells across different tissue types showed that modulation of BR signaling yields distinct changes in growth rate and anisotropy, which affects the time cells spend in the meristem and has a strong impact on final root form. By contrast, the hormone effect on cell volume was minor, establishing cell volume as invariant to the effect of BR. Thus, BR has highest effect on cell shape and growth anisotropy, regulating overall radial growth of the meristem, while maintaining a coherent distribution of cell sizes. Moving from single-cell quantification to the whole organ, we developed a computational model of radial growth that demonstrates how differential growth regulation by BR between the inner and outer tissues shapes the meristem. The model explains the unintuitive outcomes of tissue-specific perturbation of BR signaling and suggests that the inner and outer tissues have independent but coordinated roles in growth regulation.


title: The monitoring system is attuned to others' actions during dyadic motor interactions

abstract:
Successful interpersonal motor interactions necessitate the simultaneous monitoring of our own and our partners actions. To characterize the dynamics of the action monitoring system for tracking self and other behaviors during dyadic synchronous interactions, we combined EEG recordings and immersive Virtual Reality in two tasks where participants were asked to coordinate their actions with those of a Virtual Partner (VP). The two tasks differed in the features to be monitored: the Goal task required participants to predict and monitor the VPs reaching goal; the Spatial task required participants to predict and monitor the VPs reaching trajectory. In both tasks, the VP performed unexpected movement corrections to which the participant needed to adapt. By comparing the neural activity locked to the detection of unexpected changes in the VP action (other-monitoring) or to the participants action-replanning (self-monitoring), we show that during interpersonal interactions the monitoring system is more attuned to others than to ones own actions. Additionally, distinctive neural responses to VPs unexpected goals and trajectory corrections were found: goal corrections were reflected both in early fronto-central and later posterior neural responses while trajectory deviations from the expected movement were reflected only in later and posterior responses. Since these responses were locked to the partners behavior and not to ones own, our results indicate that during interpersonal interactions the action monitoring system is dedicated to evaluating the partners movements. Hence, our results reveal an eminently social role of the monitoring system during motor interactions.

Significance StatementNon-verbal synchronous interpersonal interactions require the monitoring of both our actions and those of our partners. Understanding the neural underpinnings of this ability with a focus on the dynamics between self- and other-monitoring is fundamental to the comprehension of social coordination. By combining EEG and immersive Virtual Reality we demonstrate that the monitoring system is more attuned to others actions than to our own. In two tasks, we show that the neural activity associated with unexpected corrections in the goal or the trajectory of an action are locked to the partners actions rather than to the participants subsequent adaptation. This pattern of results highlights a social mode adopted by the monitoring system to handle motor interactions.


title: Validity and cultural generalisability of a 5-minute AI-based, computerised cognitive assessment in Mild Cognitive Impairment and Alzheimer's Dementia

abstract:
INTRODUCTIONEarly detection and monitoring of mild cognitive impairment (MCI) and Alzheimers Disease (AD) patients are key to tackling dementia and providing benefits to patients, caregivers, healthcare providers and society. We developed the Integrated Cognitive Assessment (ICA); a 5-minute, language independent computerised cognitive test that employs an Artificial Intelligence (AI) model to improve its accuracy in detecting cognitive impairment. In this study, we aimed to evaluate the generalisability of the ICA in detecting cognitive impairment in MCI and mild AD patients.

METHODSWe studied the ICA in a total of 230 participants. 95 healthy volunteers, 80 MCI, and 55 participants with mild AD completed the ICA, the Montreal Cognitive Assessment (MoCA) and Addenbrookes Cognitive Examination (ACE) cognitive tests.

RESULTSThe ICA demonstrated convergent validity with MoCA (Pearson r = 0.58, p<0.0001) and ACE (r = 0.62, p<0.0001). The ICA AI model was able to detect cognitive impairment with an AUC of 81% for MCI patients, and 88% for mild AD patients. The AI model demonstrated improved performance with increased training data and showed generalisability in performance from one population to another. The ICA correlation of 0.17 (p=0.01) with education years is considerably smaller than that of MoCA (r=0.34, p<0.0001) and ACE (r=0.41, p<0.0001) which displayed significant correlations. In a separate study the ICA demonstrated no significant practice effect observed over the duration of the study.

DISCUSSIONThe ICA can support clinicians by aiding accurate diagnosis of MCI and AD and is appropriate for large-scale screening of cognitive impairment. The ICA is unbiased by differences in language, culture and education.


title: Comparative anatomy of leaf petioles in temperate trees and shrubs

abstract: Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting leaf ability as well as transport of water, nutrient and biochemical signals. Despite petioles high diversity in size, shape and anatomical settings, little information is available about their structural adaptations across evolutionary lineages and environmental conditions. To fill our knowledge gap, we investigated the variation of petiole morphology and anatomy in 95 European woody plant species using phylogenetic comparative models. Two major axes of variation were related to leaf area (from large and soft to small and tough leaves), and plant size (from cold-adapted shrubs to warm-adapted tall trees). Larger and softer leaves are found in taller trees of more productive habitats. Their petioles are longer, with a circular outline, thin cuticles without trichomes, and are anatomically characterised by the predominance of sclerenchyma, larger vessels, interfascicular areas with fibers, indistinct phloem rays, and the occurrence of prismatic crystals and druses. In contrast, smaller and tougher leaves are found in shorter trees and shrubs of colder or drier habitats. Their petioles are characterized by teret outline, thick cuticle, simple and non-glandular trichomes, epidermal cells smaller than cortex cells, phloem composed of small cells and radially arranged vessels, fiberless xylem, lamellar collenchyma, acicular crystals and secretory elements. Individual anatomical traits were linked to different internal and external drivers. The petiole length and vessel conduit size increase, while cuticle thickness decreases, with increasing leaf blade area. Epidermis cell walls are thicker in leaves with higher specific leaf area. Collenchyma becomes absent with increasing temperature, epidermis cell size increases with plant height and temperature, and petiole outline becomes polygonal with increasing precipitation. We conclude that species temperature and precipitation optima, plant height, leaf area and thickness exerted a significant control on petiole anatomical and morphological structures not confounded by phylogenetic inertia. Unrelated species with different evolutionary histories but similar thermal and hydrological requirements have converged to similar petiole anatomical structures. Our findings contribute to improving current knowledge about the functional morphoanatomy of the petiole as the key organ that plays a crucial role in the hydraulic pathways in plants.


title: Noradrenergic alpha-2A receptor activation suppresses courtship vocalization in male Japanese quail.

abstract: Male Japanese quail produce high-frequency crow vocalizations to attract females during the breeding season. The nucleus of intercollicularis (ICo) is the midbrain vocal center in birds and electrical stimulation of the ICo produces calls that include crowing. Noradrenaline plays a significant role in sexual behavior but the contribution of noradrenaline in the control of courtship vocalizations in quail has not been well established. Using dose-dependent intracerebroventricular injection of clonidine, an 2-adrenergic receptor- specific agonist, crowing vocalization was immediately suppressed. At the same time as crow suppression by clonidine there was a reduction of immediate early gene, zenk mRNA, in the ICo; no zenk mRNA expression was detected in the dorsomedial division of the nucleus. Using histochemistry, we determined that the ICo receives noradrenergic innervation and expresses 2A-adrenergic receptor mRNA. Taken together, these data suggest that noradrenaline regulates courtship vocalization in quail, possibly via the alpha2A- adrenergic receptor expressed on ICo neurons.


title: ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

abstract: Regulatory elements control gene expression through transcription initiation (promoters) and by enhancing transcription at distant regions (enhancers). Accurate identification of regulatory elements is fundamental for annotating genomes and understanding gene expression patterns. While there are many attempts to develop computational promoter and enhancer identification methods, reliable tools to analyze long genomic sequences are still lacking. Prediction methods often perform poorly on the genome-wide scale because the number of negatives is much higher than that in the training sets. To address this issue, we propose a dynamic negative set updating scheme with a two-model approach, using one model for scanning the genome and the other one for testing candidate positions. The developed method achieves good genome-level performance and maintains robust performance when applied to other species, without re-training. Moreover, the unannotated predicted regulatory regions made on the human genome are enriched for disease-associated variants, suggesting them to be potentially true regulatory elements rather than false positives. We validated high scoring "false positive" predictions using reporter assay and all tested candidates were successfully validated, demonstrating the ability of our method to discover novel human regulatory regions.


title: Induction of Dopaminergic Neurons for Neuronal Subtype-Specific Modeling of Psychiatric Disease Risk

abstract: Dopaminergic neurons are critical to movement, mood, addiction, and stress. Current techniques for generating dopaminergic neurons from human induced pluripotent stem cells (hiPSCs) yield heterogenous cell populations with variable purity and inconsistent reproducibility between donors, hiPSC clones, and experiments. Here, we report the rapid (5 weeks) and efficient (~90%) induction of induced dopaminergic neurons (iDANs) through transient overexpression of lineage-promoting transcription factors combined with stringent selection across five donors. We observe maturation-dependent increase in dopamine synthesis, together with electrophysiological properties consistent with midbrain dopaminergic neuron identity, such as slow-rising after hyperpolarization potentials, an action potential duration of ~3ms, tonic sub-threshold oscillatory activity, and spontaneous burst firing at frequency of ~1.0-1.75 Hz. Transcriptome analysis reveals robust expression of genes involved in fetal midbrain dopaminergic neuron identity. Specifically expressed genes in iDANs, relative to their isogenic glutamatergic and GABAergic counterparts, were linked to the genetic risk architecture of a broad range of psychiatric traits, with iDANs showing particularly strong enrichment in loci conferring heritability for cannabis use disorder, schizophrenia, and bipolar disorder. Therefore, iDANs provide a critical tool for modeling midbrain dopaminergic neuron development and dysfunction in psychiatric disease.


title: Dorsomedial striatal activity tracks completion of behavioral sequences

abstract: For proper execution of goal-directed behaviors, individuals require both a general representation of the goal and an ability to monitor their own progress toward that goal. Here, we examine how dorsomedial striatum (DMS), a region pivotal for forming associations among stimuli, actions, and outcomes, encodes the execution of goal-directed action sequences that require self-monitoring of behavior. We trained rats to complete a sequence of at least 5 consecutive lever presses (without visiting the reward port) to obtain a reward and recorded the activity of individual cells in DMS while rats performed the task. We found that the pattern of DMS activity gradually changed during the execution of the sequence, permitting accurate decoding of sequence progress from neural activity at a population level. Moreover, this sequence-related activity was blunted on trials where rats did not complete a sufficient number of presses. Overall, these data suggest a link between DMS activity and the execution of behavioral sequences that require monitoring of ongoing behavior.


title: MiR-137 and miR-122, two outer subventricular zone-enriched non-coding RNAs, regulate basal progenitor expansion and neuronal differentiation

abstract: Cortical expansion in the primate brain relies on the presence and the spatial enlargement of multiple germinal zones during development and on a prolonged developmental period. In contrast to other mammals, which have two cortical germinal zones, the ventricular zone (VZ) and subventricular zone (SVZ), gyrencephalic species display an additional germinal zone, the outer subventricular zone (OSVZ), which role is to increase the number and types of neurons generated during corticogenesis. How the OSVZ emerged during evolution is poorly understood but recent studies suggest a role for non-coding RNAs, which allow tight regulations of transcriptional programs in time and space during development (Dehay et al. 2015; Arcila et al., 2014). Here, using in vivo functional genetics, single-cell RNA sequencing, live imaging and electrophysiology to assess progenitor and neuronal properties in mice, we identify two ferret and human OSVZ-enriched microRNAs (miR), miR-137 and miR-122, which regulate key cellular features associated with cortical expansion. MiR-137 promotes basal progenitor self-replication and superficial layer neuron fate, while miR-122 slows down neuronal differentiation pace. Together, these findings support a cell-type specific role for miR-mediated transcriptional regulation in cortical expansion.


title: Genome-wide association study reveals candidate genes for flowering time in cowpea (Vigna unguiculata  Walp)

abstract: Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 367 accessions from a cowpea minicore collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.

category: genetics


title: Kinetics of RNA and RNA:DNA hybrid strand displacement

abstract: In dynamic nucleic acids nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand which binds to a toehold, a single-stranded region on the duplex. With proper design and kinetic control, strand displacement is used to perform logic operations on molecular level to trigger the conformational change in nanostructures, initiate cascaded reactions, or even for in vivo diagnostics and treatments. While systematic experimental studies have been carried out to probe the kinetics of strand displacement in DNA, there has not been a comparable systematic work done for RNA or RNA-DNA hybrid systems. Here, we experimentally study how toehold length, toehold location (5' or 3' end of the strand) and mismatches influence the strand displacement kinetics. Through comparing the reaction rates, combined with previous theoretical studies, we observed reaction acceleration with increasing toehold length and placement of toehold at 5'end of the substrate. We find that mismatches closer to the interface of toehold and duplex slow down the reaction more than remote mismatches. Comparison of RNA displacement and DNA displacement with hybrid displacement (RNA invading DNA or DNA invading RNA) is in part explainable by the thermodynamic stabilities of the respective toehold regions, but also suggest that the rearrangement from B-form to A-form helix in case of RNA invading DNA might play a role in the kinetics. The measured kinetics of toehold-mediated strand displacement will be important in understanding and construction of more complex dynamic nucleic acid systems.


title: A realistic touch-transfer method reveals low risk of transmission for SARS-CoV-2 by contaminated coins and bank notes

abstract: The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created a significant threat to global health. While respiratory aerosols or droplets are considered as the main route of human-to-human transmission, secretions expelled by infected individuals can also contaminate surfaces and objects, potentially creating the risk of fomite-based transmission. Consequently, frequently touched objects such as paper currency and coins have been suspected as a potential transmission vehicle. To assess the risk of SARS-CoV-2 transmission by banknotes and coins, we examined the stability of SARS-CoV-2 and bovine coronavirus (BCoV), as surrogate with lower biosafety restrictions, on these different means of payment and developed a touch transfer method to examine transfer efficiency from contaminated surfaces to skin. Although we observed prolonged virus stability, our results, including a novel touch transfer method, indicate that the transmission of SARS-CoV-2 via contaminated coins and banknotes is unlikely and requires high viral loads and a timely order of specific events.


title: One dose of COVID-19 nanoparticle vaccine REVC-128 provides protection against SARS-CoV-2 challenge at two weeks post immunization

abstract: A COVID-19 vaccine with capability to induce early protection is needed to efficiently eliminate viral spread. Here, we demonstrate the development of a nanoparticle vaccine candidate, REVC-128, in which multiple trimeric spike ectodomain subunits with glycine (G) at position 614 were multimerized onto a nanoparticle. In-vitro characterization of this vaccine confirms its structural and antigenic integrity. In-vivo immunogenicity evaluation in mice indicates that a single dose of this vaccine induces potent serum neutralizing antibody titer at two weeks post immunization, which is significantly higher than titer induced by trimeric spike protein without nanoparticle presentation. The comparison of serum binding to spike subunits between animals immunized by spike with and without nanoparticle presentation indicates that nanoparticle prefers the display of spike RBD (Receptor-Binding Domain) over S2 subunit, likely resulting in a more neutralizing but less cross-reactive antibody response. Moreover, a Syrian golden hamster in-vivo model for SARS-CoV-2 virus challenge was implemented at two weeks post a single dose of REVC-128 immunization. The results show that vaccination protects hamsters against SARS-CoV-2 virus challenge with evidence of steady body weight, suppressed viral loads and alleviation of tissue damage (lung and nares) for protected animals, compared with ~10% weight loss, higher viral loads and tissue damage in unprotected animals. Furthermore, the data show that vaccine REVC-128 is thermostable at up to 37{degrees}C for at least 4 weeks. These findings, along with a long history of safety for protein vaccines, suggest that the REVC-128 is a safe, stable and efficacious single-shot vaccine candidate to induce the earliest protection against SARS-CoV-2 infection.


title: A high-throughput fluorescence polarization assay to discover inhibitors of arenavirus and coronavirus exoribonucleases

abstract:
Viral exoribonucleases are uncommon in the world of RNA viruses. To date, this activity has been identified only in the Arenaviridae and the Coronaviridae families. These exoribonucleases play important but different roles in both families: for mammarenaviruses the exoribonuclease is involved in the suppression of the host immune response whereas for coronaviruses, exoribonuclease is both involved in a proofreading mechanism ensuring the genetic stability of viral genomes and participating to evasion of the host innate immunity. Because of their key roles, they constitute attractive targets for drug development. Here we present a high-throughput assay using fluorescence polarization to assess the viral exoribonuclease activity and its inhibition. We validate the assay using three different viral enzymes from SARS-CoV-2, lymphocytic choriomeningitis and Machupo viruses. The method is sensitive, robust, amenable to miniaturization (384 well plates) and allowed us to validate the proof-of-concept of the assay by screening a small focused compounds library (23 metal chelators). We also determined the IC50 of one inhibitor common to the three viruses.

HighlightsO_LIArenaviridae and Coronaviridae viral families share an exoribonuclease activity of common evolutionary origin
C_LIO_LIArenaviridae and Coronaviridae exoribonuclease is an attractive target for drug development
C_LIO_LIWe present a high-throughput assay in 384 well-plates for the screening of inhibitors using fluorescence polarization
C_LIO_LIWe validated the assay by screening of a focused library of 23 metal chelators against SARS-CoV-2, Lymphocytic Choriomeningitis virus and Machupo virus exoribonucleases
C_LIO_LIWe determined the IC50 by fluorescence polarization of one inhibitor common to the three viruses.
C_LI

category: biochemistry


title: Interacting synapses stabilise both learning and neuronal dynamics in biological networks

abstract: Distinct synapses influence one another when they undergo changes, with unclear consequences for neuronal dynamics and function. Here we show that synapses can interact such that excitatory currents are naturally normalised and balanced by inhibitory inputs. This happens when classical spike-timing dependent synaptic plasticity rules are extended by additional mechanisms that incorporate the influence of neighbouring synaptic currents and regulate the amplitude of their efficacy changes accordingly. The resulting control of excitatory plasticity by inhibitory activation, and vice versa, gives rise to quick and long-lasting memories as seen experimentally in receptive field plasticity paradigms. In models with additional dendritic structure, we observe experimentally reported clustering of co-active synapses that depends on initial connectivity and morphology. Finally, in recurrent neuronal networks, rich and stable dynamics with high input sensitivity emerge, providing transient activity that resembles recordings from motor cortex. Our model provides a general framework for codependent plasticity that frames individual synaptic modifications in the context of population-wide changes, allowing us to connect micro-level physiology with network-wide phenomena.

category: neuroscience


title: Altered action potential waveform and shorter axonal initial segment in hiPSC-derived motor neurons with mutations in VRK1

abstract:
We recently described new pathogenic variants in VRK1, in patients affected with distal Hereditary Motor Neuropathy associated with upper motor neurons signs. Specifically, we provided evidences that hiPSC-derived Motor Neurons (hiPSC-MN) from these patients display Cajal bodies (CBs) disassembly and defects in neurite outgrowth and branching.

We here focused on the Axonal Initial Segment (AIS) and the related firing properties of hiPSC-MNs from these patients. We found that the patients Action Potential (AP) was smaller in amplitude, larger in duration, and displayed a more depolarized threshold while the firing patterns were not altered. These alterations were accompanied by a decrease in the AIS length measured in patients hiPSC-MNs. These data indicate that mutations in VRK1 impact the AP waveform and the AIS organization in MNs and may ultimately lead to the related motor neuron disease.

HighlightsO_LIhiPSC-MNs are functional and sustain firing patterns, typical of spinal MNs
C_LIO_LIhiPSC-MNs from patients with VRK1 mutations have altered Action Potential
C_LIO_LIAxonal Initial Segment is shorter in hiPSC-MNs from patients with mutated VRK1
C_LIO_LIhiPSC-MNs are a useful platform to study Motor Inherited Peripheral Neuropathies
C_LI

eTOC BlurbIn human spinal Motor Neurons derived from induced Pluripotent Stem Cells from patients with VRK1 -related distal Hereditary Motor Neuropathy, Bos, Rihan et al. show that the mutations in VRK1 affect the electrical properties of these neurons: they display defects in the initiation of the Action Potential due to a shortening of the Axonal Initial Segment.


title: Predicted Utility Modulates Working Memory Fidelity in the Brain

abstract: The predicted utility of information stored in working memory (WM) is hypothesized to influence the strategic allocation of WM resources. Prior work has shown that when information is prioritized, it is remembered with greater precision relative to other remembered items. However, these paradigms often complicate interpretation of the effects of predicted utility on item fidelity due to a concurrent memory load. Likewise, no fMRI studies have examined whether the predicted utility of an item modulates fidelity in the neural representation of items during the memory delay without a concurrent load. In the current study, we used fMRI to investigate whether predicted utility influences fidelity of WM representations in the brain. Using a generative model multivoxel analysis approach to estimate the quality of remembered representations across predicted utility conditions, we observed that items with greater predicted utility are maintained in memory with greater fidelity, even when they are the only item being maintained. Further, we found that this pattern follows a parametric relationship where more predicted utility corresponded to greater fidelity. These precision differences could not be accounted for based on a redistribution of resources among already-remembered items. Rather, we interpret these results in terms of a gating mechanism that allows for pre-allocation of resources based on predicted value alone. This evidence supports a theoretical distinction between resource allocation that occurs as a result of load and resource pre-allocation that occurs as a result of predicted utility.


title: Regimes and mechanisms of transient amplification in abstract and biological networks

abstract: We use upper triangular matrices as abstract representations of neuronal networks and directly manipulate their eigenspectra and non-normality to explore different regimes of transient amplification. Counter-intuitively, manipulating the imaginary distribution can lead to highly amplifying regimes. This is noteworthy, because biological networks are constrained by Dales law and the non-existence of neuronal self-loops, limiting the range of manipulations in the real dimension. Within these constraints we can further manipulate transient amplification by controlling global inhibition.


title: Establishing a Role of the Semantic Control Network in Social Cognitive Processing: A Meta-analysis of Functional Neuroimaging Studies

abstract: Most leading models of socio-cognitive processing devote little discussion to the nature and neuroanatomical correlates of cognitive control mechanisms. Recently, it has been proposed that the regulation of social behaviours could rely on brain regions specialised in the controlled retrieval of semantic information, namely the anterior inferior frontal gyrus (IFG) and posterior middle temporal gyrus. Accordingly, we set out to investigate whether the neural activation commonly found in social functional neuroimaging studies extends to these  semantic control regions. We conducted five coordinate-based meta-analyses to combine results of over 500 fMRI/PET experiments and identified the brain regions consistently involved in semantic control, as well as four social abilities: theory of mind, trait inference, empathy and moral reasoning. This allowed an unprecedented parallel review of the neural networks associated with each of these cognitive domains. The results confirmed that the anterior left IFG region involved in semantic control is reliably engaged in all four social domains. This suggests that social cognition could be partly regulated by the neurocognitive system underpinning semantic control.


title: A meta-analysis of areas of structural variation in grey matter in individuals with Autism Spectrum Disorder (ASD) in relation to gene expression of candidate ASD genes

abstract: Autism Spectrum Disorder (ASD) is a set of developmental pathologies with a strong genetic basis and high heritability. Although neuroimaging studies have indicated anatomical changes in grey matter (GM) morphometry, their associations with gene expression remain elusive. In the present study, we aim to understand how gene expression correlates with structural brain aberration in ASD and how it distributes in a functional network perspective. First, we performed an activation likelihood estimation (ALE) meta-analysis to determine GM alteration in the brain, then we selected genes from the SHANK, NRXN, NLGN family and MECP2, which have been implicated with ASD, particularly in regards to altered synaptic transmission. Gene expression maps were built. We then assessed the correlation between the gene expression maps and the GM alteration maps. We found that the default mode network regions were the most significantly correlated with gene expression of selected genes in both areas of GM decrease and increase. The dorsal attention and the cerebellar network regions are significantly correlated with ASD genes. Different networks, namely somatomotor, limbic and basal ganglia/thalamus network - were found in the increase; for each of these networks, however, only a few genes were significant. Our approach allowed to combine the well beaten path of genetic and brain imaging in a novel way, to specifically investigate the relation between gene expression and brain with structural damage, and individuate genes of interest for further investigation in specific functional networks.


title: Nutrient cycling is an important mechanism for homeostasis in plant cells

abstract:
Homeostasis in living cells refers to the steady state of internal, physical, and chemical conditions. It is maintained by self-regulation of the dynamic cellular system. In order to gain insight into homeostatic mechanisms that keep cytosolic nutrient concentrations in plant cells within a homeostatic range, I performed computational cell biology experiments. Systems of membrane transporters were modelled mathematically followed by the simulation of their dynamics. The detailed analyses of  what-if scenarios demonstrate that a single transporter type for a nutrient, irrespective whether it is a channel or a co-transporter, is not sufficient to set a desired cytosolic concentration. A cell cannot flexibly react on different external conditions. At least two different transporter types for the same nutrient are required, which are energized differently. The gain of flexibility in adjusting the nutrient concentration was accompanied by the establishment of energy-consuming nutrient cycles at the membrane suggesting that these sometimes called  futile cycles are not as futile as they appear. This understanding may help in future to design new strategies for increasing nutrient use efficiency of crop plants taking into account the complex interplay of transporter networks at the cellular level.

One sentence summaryFirst principles of membrane transport explain why the maintenance of a constant cytosolic nutrient concentration is often accompanied by the  futile cycling of the nutrient across the membrane.


title: Teacher Perceptions of Using Robots to Teach Neuroscience in Secondary School

abstract: The use of robots to help teachers to engage students in STEM subjects has been increasing in recent years, and much progress has been made in K12 schools to incorporate robots in the pedagogy. Recent studies indicate that robots can play a significant role to engage students in neuroscience subjects, but little is known about teachers perceptions of using robots to teach neuroscience. In this paper, we present a study based on a survey questionnaire conducted with 84 teachers across multiple high schools in the United States to understand their perceptions about the usefulness of using robots to teach neuroscience. To situate teachers with an example of how robots can be used in neuroscience classrooms, we describe an educational tool called the SpikerBot. Our preliminary results indicate that there is an opportunity for neuroscience-oriented robots in secondary education, provided sufficient on-boarding and training videos.

category: scientific communication and education


title: Weevil borers affect the spatio-temporal dynamics of banana Fusarium wilt

abstract: Dispersal of propagules of a pathogen has remarkable effects on the development of epidemics. Previous studies suggested that insect pests play a role in the development of Fusarium wilt (FW) epidemics in banana fields. We provided complementary evidence for the involvement of two insect pests of banana, the weevil borer (Cosmopolites sordidus L. - WB) and the false weevil borer (Metamasius hemipterus L. - FWB), in the dispersal of Fusarium oxysporum f. sp. cubense (Foc) using a comparative epidemiology approach under field conditions. Two banana plots located in a field with historical records of FW epidemics were used, one was managed with Beauveria bassiana to reduce the population of weevils, and the other was left without B. bassiana applications. The number of WB and FWB was monitored biweekly and the FW incidence was quantified bimonthly during two years. The population of WB and the incidence (6.7%) of FW in the plot managed with B. bassiana were lower than in the plot left unmanaged (13%). The monomolecular model best fitted the FW disease progress data and, as expected, the average estimated disease progress rate was lower in the plot managed with the entomopathogenic fungus (r = 0.0024) compared to the unmanaged plot (r = 0.0056). Aggregation of FW was higher in the field with WB management. WB affected the spatial and temporal dynamics of FW epidemics under field conditions and brought evidence that managing the insects may reduce FW of bananas intensity.


title: Reservoir of decision strategies in the mouse brain

abstract: In any given situation, the environment can be parsed in different ways to define useful decision variables (DVs) for any task, but the way in which this manifold of potential decision strategies is processed to shape behavioral policies is not known. We recorded neural ensembles in the frontal cortex of mice performing a foraging task admitting multiple DVs. Optogenetic manipulations revealed that the secondary motor cortex (M2) is needed for mice to use the different DVs in the task. Surprisingly, we found that, regardless of the DV best explaining the behavior of each mouse, M2 activity reflected a full basis set of computations spanning a repertoire of DVs extending beyond those useful for the present task. Random DVs with similar temporal structure were not represented in M2, suggesting that its representational capacity is vast, but not universal. This form of multiplexing may confer considerable advantages for learning and adaptive behavior.


title: A repertoire of foraging decision variables in the mouse brain


title: A new High-Throughput-Screening-assay for Photoantimicrobials Based on EUCAST Revealed Unknown Photoantimicrobials in Cortinariaceae

abstract: A spark of light might unravel antimicrobial activity of colored compounds, which otherwise would have been classified as inactive. While many mushrooms contain such colorful pigments but lack antimicrobial activity, we wondered if a controlled irradiation is needed to unleash their effect. To explore such photoantimicrobial actions in the Kingdom Fungi, an efficient high-throughput-screening (HTS) assay is needed. Here we report on the establishment of a reliable photoantimicrobial assay based on the EUCAST recommendations, which was validated with known photosensitzers (i.e., curcumin, phenalenone, rose bengal, an hypericum extract, and methylene blue). Furthermore, an improved LED-irradiation setup enabling with only 24 LEDs a homogenous irradiation of a 96-well plate is presented. The established HTS-assay was utilized to screen six colorful Cortinarius extracts unrevealing C. xanthophyllus and C. rufo-olivaceus as promising sources for new photoantimicrobials.

category: microbiology


title: Dissection of the ATPase active site of McdA reveals the sequential steps essential for carboxysome distribution

abstract: Carboxysomes, the most prevalent and well-studied anabolic bacterial microcompartment, play a central role in efficient carbon fixation by cyanobacteria and proteobacteria. In previous studies, we identified the two-component system called McdAB that spatially distributes carboxysomes across the bacterial nucleoid. McdA, a ParA-like ATPase, forms a dynamic oscillating gradient on the nucleoid in response to carboxysome-localized McdB. As McdB stimulates McdA ATPase activity, McdA is removed from the nucleoid in the vicinity of carboxysomes, propelling these proteinaceous cargos toward regions of highest McdA concentration via a Brownian-ratchet mechanism. However, how the ATPase cycle of McdA governs its in vivo dynamics and carboxysome positioning remains unresolved. Here, by strategically introducing amino acid substitutions in the ATP-binding region of McdA, we sequentially trap McdA at specific steps in its ATP cycle. We map out critical events in the ATPase cycle of McdA that allows the protein to bind ATP, dimerize, change its conformation into a DNA-binding state, interact with McdB-bound carboxysomes, hydrolyze ATP and release from the nucleoid. We also find that McdA is a member of a previously unstudied subset of ParA family ATPases, harboring unique interactions with ATP and the nucleoid for trafficking their cognate intracellular cargos.


title: SARS-CoV-2 B.1.1.7 infection of Syrian hamster does not cause more severe disease and is protected by naturally acquired immunity

abstract: Epidemiological studies have revealed the emergence of multiple SARS-CoV-2 variants of concern (VOC), including the lineage B.1.1.7 that is rapidly replacing old variants. The B.1.1.7 variant has been linked to increased morbidity rates, transmissibility, and potentially mortality (1). To assess viral fitness in vivo and to address whether the B.1.1.7 variant is capable of immune escape, we conducted infection and re-infection studies in naive and convalescent Syrian hamsters (>10 months old). Hamsters infected by either a B.1.1.7 variant or a B.1 (G614) variant exhibited comparable viral loads and pathology. Convalescent hamsters that were previously infected by the original D614 variant were protected from disease following B.1.1.7 challenge with no observable clinical signs or lung pathology. Altogether, our study did not find that the B.1.1.7 variant significantly differs from the B.1 variant in pathogenicity in hamsters and that natural infection-induced immunity confers protection against a secondary challenge by the B1.1.7 variant.


title: Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils

abstract: Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n= 49) and control (n= 51) compounds during baseline (pre-intervention) and after 24 months (post-intervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 20 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated target in 91% (163/179) of soils and a median of 3 (IQR=1.5, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of [≥]1 pathogen detected by 15% (adjusted prevalence ratio, aPR=0.85; 95% CI: 0.70, 1.0) and the total number of pathogens detected by 35% (aPR =0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24-months following the introduction of new latrines.

category: molecular biology


title: The Exon Junction Complex Core Represses Caner-specific Mature mRNA Re-splicing: A Potential Key Role in Terminating Splicing

abstract: Using the TSG101 pre-mRNA, we previously discovered cancer-specific resplicing of mature mRNA that generates aberrant transcripts/proteins. The fact that mRNA is aberrantly re-spliced in various cancer cells implies there must be an important mechanism to prevent deleterious re-splicing on the spliced mRNA in normal cells. We thus postulated that the mRNA re-splicing is controlled by specific repressors, and we searched for repressor candidates by siRNA-based screening for mRNA re-splicing activity. We found that knockdown of EIF4A3, which is a core component of the exon junction complex (EJC), significantly promoted mRNA re-splicing. Remarkably, we could recapitulate cancer-specific mRNA resplicing in normal cells by knock-down of any of the core EJC proteins, EIF4A3, MAGOH or RBM8A (Y14), implicating the EJC core as the repressor of mRNA re-splicing often observed in cancer cells. We propose that the EJC core is a critical mRNA quality control factor to prevent over-splicing of mature mRNA.