title: Territory-level temperature influences settlement decisions, breeding phenology and productivity in three forest passerine birds

abstract: Temperature plays an important role in determining breeding phenology of temperate birds, with higher spring temperatures associated with earlier breeding. However, the effect of localised territory-scale temperature variations is poorly understood, with relationships between temperature and breeding phenology mostly studied using coarse-grained climatic indices. Here, we interpolate spring temperatures recorded at 150 m2 grid intersections encompassing 417 ha of forest to examine the influence of territory-scale temperature, and its interaction with mean annual temperature, on territory selection, breeding phenology, clutch size and fledgling success for three co-occurring single-brooded passerine birds using data from 672 nests over four years. All species exhibited significant trends in reproductive traits associated with territory-scale temperature. Pied flycatchers Ficedula hypoleuca settled in cooler territories first, where they raised more fledglings. Blue tits Cyanistes caeruleus laid larger clutches in warmer territories in warm years and always laid earlier at warmer territories irrespective of annual temperature variation. Contrastingly, pied flycatcher and wood warbler Phylloscopus sibilatrix breeding phenology was earlier at warmer territories in cool years and cooler territories in warm years, with wood warbler clutch size responding similarly to this interaction. Greater previous breeding experience and increased higher rates of historical territory occupancy (territory quality) also predicted earlier breeding phenology and higher fledging success for pied flycatchers. We suggest that the migratory pied flycatcher and wood warbler are best synchronised with their prey availability in cooler years at a local population level while resident blue tits match local phenology across all years, which is potentially advantageous under warmer predicted climate change scenarios. We conclude that temperature at the territory scale can be an important driver of settlement and breeding phenology and influence reproductive traits.

category: ecology


title: Territory-level temperature influences breeding phenology and reproductive output in three forest passerine birds


title: Host PDZ-containing proteins targeted by SARS-Cov-2

abstract: Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins E, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E, 3A and N showing significant interactions with dissociation constants values ranging from 3 M to 82 M. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS-CoV while three (NHERF1, MAST2, RADIL) are specific to SARS-CoV-2 E protein. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti-coronaviral agents for therapeutic purposes.

category: biochemistry


title: Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

abstract: The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). During the 2020 CASP14 experiment, we developed and tested several EMA predictors that used deep learning with the new features based on inter-residue distance/contact predictions as well as the existing model quality features. The average global distance test (GDT-TS) score loss of ranking CASP14 structural models by three multi-model MULTICOM EMA predictors (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) is 0.073, 0.079, and 0.081, respectively, which are ranked first, second, and third places out of 68 CASP14 EMA predictors. The single-model EMA predictor (MULTICOM-DEEP) is ranked 10th place among all the single-model EMA methods in terms of GDT_TS score loss. The results show that deep learning and contact/distance predictions are useful in ranking and selecting protein structural models.

category: bioinformatics


title: The secreted peptide IRP functions as a DAMP in rice immunity

abstract: Small signaling peptides play important roles in various plant processes, but information regarding their involvement in plant immunity is limited. We previously identified a novel small secreted protein in rice, named immune response peptide (IRP) by the integrated multi-omics analyses. Here, we studied IRP functions in rice immunity. Rice plants overexpressing IRP enhanced resistance to the blast fungus. Application of the IRP peptide to rice suspension cells triggered the expression of IRP itself and defense gene PAL1. RNA-seq results revealed that 84% of genes upregulated by IRP peptide were also induced by chitin, including 13 OsWRKY transcription factors, indicating that IRP and chitin share the similar signaling pathway. Co-treatment with chitin and IRP elevated the expression level of PAL1 and OsWRKYs in an additive manner. When results of IRP and PAL1 expression and MAPK activation by IRP were compared with those by chitin, IRP had a stronger effect on MAPK activation rather than IRP and PAL1 expression. Collectively, our findings indicate that IRP functions as a damage-associated molecular pattern (DAMP) in rice immunity, regulating MAPKs and OsWRKYs to amplify chitin signaling, and provide new insights into how PAMPs and DAMPs cooperatively regulate rice immunity.

category: plant biology


title: The Giardia lamellipodium-like ventrolateral flange supports attachment and rapid cytokinesis

abstract:
Attachment to the intestinal epithelium is critical to the lifestyle of the ubiquitous parasite Giardia lamblia. The microtubule cytoskeleton plays a well characterized role in attachment via the ventral adhesive disc, whereas the role of the unconventional actin cytoskeleton is controversial. We identified a novel actin associated protein with putative WH2-like actin binding domains we named Flangin. Flangin complexes with Giardia actin and is enriched in the ventrolateral flange (VLF), a lamellipodium-like membrane protrusion at the interface between parasites and attached surfaces. Live imaging revealed that the VLF grows to ~1 m in width after cytokinesis, then remains size-uniform in interphase, grows during mitosis, and is resorbed during cytokinesis. A Flangin truncation mutant stabilizes the VLF and blocks cytokinesis, indicating that the VLF is a membrane reservoir supporting rapid myosin-independent cytokinesis in Giardia. Rho family GTPases are important regulators of membrane protrusions, GlRac, the sole Rho family GTPase in Giardia, was localized to the VLF. Knockdown of Flangin, actin, and GlRac result in VLF formation defects indicating a conserved role for GlRac and actin in forming membrane protrusions, despite the absence of canonical actin binding proteins that link Rho GTPase signaling to lamellipodia formation. Flangin-depleted parasites challenged with fluid shear force in flow chambers had a reduced ability to remain attached, indicating a role for the VLF in attachment. This secondary attachment mechanism complements the microtubule based adhesive ventral disc, a feature that is particularly important during mitosis when the parental ventral disc begins disassembly in preparation for cytokinesis.

ImportanceThe ventrolateral flange (VLF) is a lamellipodium-like structure found at the host-parasite interface that has long been thought to be involved in parasite attachment. The proteins responsible for building the VLF have remained unidentified precluding manipulation of the VLF to determine its role in Giardia biology. We identified Flangin, a novel actin associated protein that localizes to the VLF, implicating Giardia actin in VLF formation. We demonstrate that: 1.) Flangin, actin, and GlRac are required for VLF formation, 2.) the VLF serves as a membrane reservoir to support Giardias incredibly fast cytokinesis, and 3) the VLF augments attachment, which is critical to parasitism. The microtubule-based adhesive ventral disc and the actin-based ventrolateral flange represent redundant means of maintaining attachment, the presence of redundant systems illustrate the importance of attachment to the lifestyle of this ubiquitous parasite.

category: cell biology


title: Early, color-specific neural responses to object color knowledge

abstract: Some familiar objects are associated with specific colors, e.g., rubber ducks with yellow. Whether and at what stage neural responses occur to these color associations remain open questions. We tested for frequency-tagged electroencephalogram (EEG) responses to periodic presentations of yellow-associated objects, shown among sequences of non-periodic blue-, red-, and green-associated objects. Both color and grayscale versions of the objects elicited yellow-specific responses, indicating an automatic activation of color knowledge from object shape. Follow-up experiments replicated these effects with green-specific responses, and demonstrated modulated responses for incongruent color-object associations. Importantly, the onset of color-specific responses was as early to grayscale as actually colored stimuli (before 100 ms), the latter additionally eliciting a conventional later response (approximately 140-230 ms) to actual stimulus color. This suggests that the neural representation of familiar objects includes both diagnostic shape and color properties, such that shape can elicit associated color-specific responses before actual color-specific responses occur.

category: neuroscience


title: Structural analysis of viral ExoN domains reveals polyphyletic hijacking events

abstract: Nidoviruses and arenaviruses are the only known RNA viruses encoding a 3-5 exonuclease domain (ExoN). The proofreading activity of the ExoN domain has played a key role in the growth of nidoviral genomes, while in arenaviruses this domain partakes in the suppression of the host innate immune signaling. Sequence and structural homology analyses suggest that these proteins have been hijacked from cellular hosts many times. Analysis of the available nidoviral ExoN sequences reveals a high conservation level comparable to that of the viral RNA-dependent RNA polymerases (RdRp), which are the most conserved viral proteins. Two highly preserved zinc fingers are present in all nidoviral exonucleases, while in the arenaviral protein only one zinc finger can be identified. This is in sharp contrast with the reported lack of zinc fingers in cellular ExoNs, and opens the possibility of therapeutic strategies in the struggle against COVID-19.

category: evolutionary biology


title: A functional bacterial-derived restriction modification system in the mitochondrion of a heterotrophic protist

abstract: The overarching trend in mitochondrial evolution is functional streamlining coupled with gene loss; therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in organellar genomes, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification system originating from a horizontal gene transfer event involving bacteria related to flavobacteria. This restriction modification system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase. We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that toxin-antitoxin selfish elements, such as restriction modification systems, could be co-opted by eukaryotic genomes to drive uniparental organellar inheritance.


title: Verapamil/Curcumin treatment attenuates the behavioral alterations observed in Williams Syndrome mice by regulation of MAPK pathway and Microglia overexpression

abstract: Williams-Beuren syndrome (WBS) is a rare neurodevelopmental disorder characterized by a distinctive cognitive phenotype for which there currently are not any effective treatments. We investigated the progression of behavioral deficits present in CD (complete deletion) mice, a rodent model of WBS, after chronic treatment with curcumin, verapamil and a combination of both. These compounds have been proven to have beneficial effects over different cognitive aspects of various murine models and thus, may have neuroprotective effects in WBS. Treatment was administered orally dissolved in drinking water. A set of behavioral tests demonstrated the efficiency of combinatorial treatment. Some histological and molecular analyses were performed to analyze the effects of treatment and its underlying mechanism in CD mice. Behavioral improvement correlates with the molecular recovery of several affected pathways regarding MAPK signaling, in tight relation with the control of synaptic transmission. Moreover, CD mice showed an increased activated microglia density in different brain regions, which was prevented by treatment. Therefore, results show that treatment prevented behavioral deficits by recovering altered gene expression in cortex of CD mice, reducing activated microglia and normalizing Bdnf expression levels. These findings unravel the mechanisms underlying the beneficial effects of this novel treatment on behavioral deficits observed in CD mice, and suggest that the combination of curcumin and verapamil could be a potential candidate to treat the cognitive impairments in WBS patients.

category: animal behavior and cognition


title: Development and validation of a cellular host response test as an early diagnostic for sepsis

abstract: Sepsis must be diagnosed quickly to avoid morbidity and mortality. However, the clinical manifestations of sepsis are highly variable and emergency department (ED) clinicians often must make rapid, impactful decisions before laboratory results are known. We previously developed a technique that allows the measurement of the biophysical properties of white blood cells as they are stretched through a microfluidic channel. In this study we describe and validate the resultant output as a model and score - the IntelliSep Index (ISI) - that aids in the diagnosis of sepsis in patients with suspected or confirmed infection from a single blood draw performed at the time of ED presentation. By applying this technique to a high acuity cohort with a 23.5% sepsis incidence (n=307), we defined specific metrics - the aspect ratio and visco-elastic inertial response - that are more sensitive than cell size or cell count in predicting disease severity. The final model was trained and cross-validated on the high acuity cohort, and the performance and generalizability of the model was evaluated on a separate low acuity cohort with a 6.4% sepsis incidence (n=94) and healthy donors (n=72). For easier clinical interpretation, the ISI is divided into three interpretation bands of Green, Yellow, and Red that correspond to increasing disease severity. The ISI agreed with the diagnosis established by retrospective physician adjudication, and accurately identified subjects with severe illness as measured by SOFA, APACHE-II, hospital-free days, and intensive care unit admission. Measured using routinely collected blood samples, with a short run-time and no requirement for patient or laboratory information, the ISI is well suited to aid ED clinicians in rapidly diagnosing sepsis.

category: bioengineering


title: Sablefish (Anoplopoma fimbria) plasma biochemistry and hematology reference intervals including blood cell morphology

abstract: Plasma biochemistry and hematology reference intervals are integral health assessment tools in all medical fields, including aquatic animal health. As sablefish (Anoplopoma fimbria) are becoming aquaculturally and economically more important, this manuscript provides essential reference intervals (RI) for their plasma biochemistry and hematology along with reference photomicrographs of blood cells in healthy, fasted sablefish. Blood cell morphology can differ between fish species. In addition, blood cell counts and blood chemistry can vary between fish species, demographics, water conditions, seasons, diets, and culture systems, which precludes the use of RIs from other fish species. For this study, blood was collected for plasma biochemistry and hematology analysis between June 20 and July 18, 2019, from healthy, yearling sablefish, hatched and reared in captivity on a commercial diet. Overnight fast of 16-18 hours did not sufficiently reduce lipids in the blood, which led to visible lipemia and frequent rupture of blood cells during analysis. Therefore, sablefish should be fasted for 24 to 36 hours before blood is collected to reduce hematology artifacts or possible reagent interference in plasma biochemistry analysis. Lymphocytes were the most dominant leukocytes (98%), while eosinophils were rare, and basophils were not detected in sablefish. Neutrophils were very large cells with Dohle bodies. In mammals and avian species, Dohle bodies are usually signs of toxic change from inflammation, but no such association was found in these fish. In conclusion, lipemia can interfere with sablefish blood analysis, and available removal methods should be evaluated as fasting for up to 36 h might not always be feasible. Also, more studies are required to establish RI for different developmental stages and rearing conditions.

category: zoology


title: Sablefish (Anoplopoma fimbria Pallas, 1814) plasma biochemistry and hematology reference intervals including blood cell morphology


title: Input-independent homeostasis of developing thalamocortical activity

abstract: The isocortex of all mammals studied to date shows a progressive increase in the amount and continuity of background activity during early development. In humans the transition from a discontinuous (mostly silent, intermittently bursting) cortex to one that is continuously active is complete soon after birth and is a critical prognostic indicator in newborns. In the visual cortex of rodents this switch from discontinuous to continuous background activity occurs rapidly during the two days before eye-opening, driven by activity changes in relay thalamus. The factors that regulate the timing of continuity development, which enables mature visual processing, are unknown. Here we test the role of the retina, the primary input, in the development of continuous spontaneous activity in the visual system of mice using depth electrode recordings of cortical activity from enucleated mice in vivo. Bilateral enucleation at postnatal day (P)6, one week prior to the onset of continuous activity, acutely silences cortex, yet firing rates and early oscillations return to normal within two days and show a normal developmental trajectory through P12. Enucleated animals showed differences in silent period duration and continuity on P13 that resolved on P16, and an increase in low frequency power that did not. Our results show that the timing of cortical activity development is not determined by the major driving input to the system. Rather, homeostatic mechanisms in thalamocortex regulate firing rates and continuity even across periods of rapid maturation.


title: Geometry of neural computation unifies working memory and planning

abstract: Real-world tasks require coordination of working memory, decision making, and planning, yet these cognitive functions have disproportionately been studied as independent modular processes in the brain. Here we propose that contingency representations, defined as mappings for how future behaviors depend on upcoming events, can unify working memory and planning computations. We designed a task capable of disambiguating distinct types of representations. Our experiments revealed that human behavior is consistent with contingency representations, and not with traditional sensory models of working memory. In task-optimized recurrent neural networks we investigated possible circuit mechanisms for contingency representations and found that these representations can explain neurophysiological observations from prefrontal cortex during working memory tasks. Finally, we generated falsifiable predictions for neural data to identify contingency representations in neural data and to dissociate different models of working memory. Our findings characterize a neural representational strategy that can unify working memory, planning, and context-dependent decision making.


title: Hierarchical modelling of functional brain networks in population and individuals from big fMRI data

abstract:
A major goal of large-scale brain imaging datasets is to provide resources for investigating heterogeneous populations. Characterisation of functional brain networks for individual subjects from these datasets will have an enormous potential for prediction of cognitive or clinical traits. We propose for the first time a technique, Stochastic Probabilistic Functional Modes (sPROFUMO), that is scalable to UK Biobank (UKB) with expected 100,000 participants, and hierarchically estimates functional brain networks in individuals and the population, while allowing for bidirectional flow of information between the two. Using simulations, we show the models utility, especially in scenarios that involve significant cross-subject variability, or require delineation of fine-grained differences between the networks. Subsequently, by applying the model to resting-state fMRI from 4999 UKB subjects, we mapped resting state networks (RSNs) in single subjects with greater detail than has been possible previously in UKB (>100 RSNs), and demonstrate that these RSNs can predict a range of sensorimotor and higher-level cognitive functions. Furthermore, we demonstrate several advantages of the model over independent component analysis combined with dual-regression (ICA-DR), particularly with respect to the estimation of the spatial configuration of the RSNs and the predictive power for cognitive traits. The proposed model and results can open a new door for future investigations into individualised profiles of brain function from big data.

HighlightsO_LIWe introduce stochastic PROFUMO (sPROFUMO) for inferring functional brain networks from big data
C_LIO_LIsPROFUMO hierarchically estimates fMRI networks for the population and every individual
C_LIO_LIWe characterised high dimensional resting state fMRI networks from UK Biobank
C_LIO_LIModel outperforms ICA and dual regression for estimation of individual-specific network topography
C_LIO_LIWe demonstrate the models utility for predicting cognitive traits, and capturing subject variability in network topographies versus connectivity
C_LI


title: Non-Canonical Projections from Ventral CA1 and Subicular Complex to CA3 Augments the Feedforward Hippocampal Trisynaptic Pathway

abstract: The hippocampal formation is well documented as having a feedforward, unidirectional circuit organization termed the trisynaptic pathway. This circuit organization exists along the septotemporal axis of the hippocampal formation, but the circuit connectivity across septal to temporal regions is less well described. The emergence of viral-genetic mapping techniques enhances our ability to determine the detailed complexity of hippocampal formation circuitry. In earlier work, we mapped a subiculum back-projection to CA1 prompted by the discovery of theta wave back-propagation from the subiculum to CA1 and CA3. We reason that this circuitry may represent multiple extended non-canonical pathways involving the subicular complex and hippocampal subregions CA1 and CA3. In the present study, multiple retrograde viral tracing approaches produced robust mapping results, which supports this prediction. We find significant non-canonical synaptic inputs to dorsal hippocampal CA3 from ventral CA1, perirhinal cortex, and the subicular complex. Thus, CA1 inputs to CA3 run opposite the trisynaptic pathway and in a temporal to septal direction. Our retrograde viral tracing results are confirmed by anterograde-directed viral mapping of projections from input mapped regions to hippocampal dorsal CA3. Together, our data provide a circuit foundation to explore novel functional roles contributed by these non-canonical hippocampal circuit connections to hippocampal dynamics and behavior.


title: Protein SUMOylation is crucial for phagocytosis in Entamoeba histolytica trophozoites

abstract:
During phagocytosis, a key event in the virulence of the protozoan Entamoeba histolytica, several molecules in concert contact the target, generate pseudopodia, and internalize and digest the ingested prey. Posttranslational modifications provide proteins the timing and signaling to intervene in these processes. SUMOylation is a posttranslational modification that in several systems grants a fine tuning for protein functions, protein interactions and cellular location, but it has not been studied in E. histolytica. In this paper, we characterized the E. histolytica SUMO gene and its product (EhSUMO) and elucidated the EhSUMO 3D-structure. Furthermore, here we studied the relevance of SUMOylation in phagocytosis, particularly in its association with EhADH (an ALIX family protein) and EhVps32 (a protein of the ESCRT-III complex), both involved in phagocytosis. Our results indicated that EhSUMO has an extended N-terminus that differentiates other SUMO from ubiquitin. It also presents the GG residues at the C-terminus and the {Psi}KXE/D binding motif, both involved in target protein contact. Additionally, E. histolytica genome possesses the enzymes belonging to the SUMOylation-deSUMOylation machineries. Confocal microscopy assays, using -EhSUMO antibodies disclosed a remarkable membrane activity with convoluted and changing structures in trophozoites during erythrophagocytosis. SUMOylated proteins appeared in pseudopodia, phagocytic channels, and around the adhered and ingested erythrocytes. Docking analysis predicted interaction of EhSUMO with EhADH, and immunoprecipitation and immunofluorescence assays revealed that the EhADH-EhSUMO association increased during phagocytosis, whereas the EhVps32-EhSUMO interaction appeared stronger since basal conditions. In EhSUMO knocked down trophozoites, the bizarre membranous structures disappeared, and EhSUMO interaction with EhADH and EhVps32 diminished. Our results evidenced the presence of a SUMO gene in E. histolytica and the SUMOylation relevance during phagocytosis.

Authors AbstractPhagocytosis is one of the main functions that Entamoeba histolyitica trophozoites carry out during the invasion to the host. Many proteins are involved in this fascinating event, in which the plasmatic membrane undergoes to multiple and speedy changes. Posttraductional modifications activate proteins in the precise time that they must get involved. SUMOylation, that consists in the non-covalent binding of SUMO protein with target molecules, is one of the main changes suffered by proteins in order to enable them to participate in cellular functions. SUMOylation had not been studied in E. histolytica nor in phagocytosis, and our working hypothesis is that this event is deeply engaged in the ingestion of target molecules and cells. The results of this paper prove the presence of an intronless bona fide EhSUMO gene encoding for a predicted 12.6 kDa protein that is actively involved in phagocytosis. Silencing of the EhSUMO gene affected the rate of phagocytosis and interfered with the EhADH and EhVps32 function, two proteins involved in phagocytosis, strongly supporting the importance of SUMOylation in this event.

category: microbiology


title: Energy content of anchovy and sardine using surrogate calorimetry methods

abstract: European anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) are crucial species for the marine ecosystem of the Northwestern Mediterranean Sea. They account for a high percentage of fish landings and they represent an important economic income. Concerns over their stock status are rising in recent years as biomass, growth, reproductive capacity and body condition of both species are declining. Therefore, there is an urgent need for a continuous and fast body condition monitoring scheme. Energy storage variability has important implications for both fish recruitment and population structure. Direct condition indices, such as bomb calorimetry, are highly reliable for measuring the energy content, but extremely time-consuming. Alternatively, fatmeter analysis and relative condition index (Kn) have been proposed as effective indirect methods. The aim of this study is to test the application of fatmeter as a surrogate of bomb calorimetry to infer the energy content of both small pelagic fishes. For the validation, fatmeter values were compared with both energy density (ED; via bomb calorimetry) and Kn values. Individuals of both species were sampled monthly in Barcelona harbor for a year in order to assess seasonal variations in energy content. Our results highlight that fatmeter measurements are strongly correlated with calorimetry for sardine, while a weaker but significant correlation was found for anchovy. The observed differences between the two species are related to their breeding strategies. Based on this study, fatmeter analysis appears to be a faster and suitable method to evaluate the energy content of both species routinely., In addition, we provide a linear model to infer ED from fatmeter values of both small pelagic fish. Eventually, these findings could allow for the avoidance of bomb calorimetry and could be used to implement body condition monitoring protocols, and to boost continuous large-scale monitoring.

category: physiology


title: In-land long-term culture of colonial ascidians

abstract:
Tunicates are highly diverse marine invertebrate filter-feeders that are vertebrates closest relatives. These organisms, despite a drastically different body plan during their adulthood, have a tissue complexity related to that of vertebrates. Ascidians, which compose most of the Tunicata, are benthic sessile hermaphrodites that reproduce sexually through a motile tadpole larval stage. Over half of the known ascidians species are able to reproduce asexually by budding, typically leading to the formation of colonies where animals, called zooids, are interconnected through an external vascular system. In addition, colonial ascidians are established models for important biological processes including allorecognition, immunobiology, aging, angiogenesis and whole-body regeneration. However, the current paucity in breeding infrastructures limits the study of these animals to coastal regions.

To promote a wider scientific spreading and popularity of colonial ascidians, we have developed a flexible recirculating husbandry setup for their long-term in-lab culture. Our system is inspired both by the flow-through aquariums used by coastal ascidian labs, as well as by the recirculating in-lab systems used for zebrafish research. Our hybrid system thus combines colony breeding, water filtering and food culturing in a semi-automated system where specimens develop on hanging microscopy glass slides. Temperature, light/dark cycles, flow speed and feeding rates can be controlled independently in four different breeding environments to provide room for species-specific optimization as well as for running experiments. This setup is complemented with a quarantine for the acclimatization of wild isolates.

Herein we present our success in breeding Botrylloides diegensis, a species of colonial ascidians, for more than 3 years in recirculating artificial seawater over 600 km away from their natural habitat. We show that colonies adapt well to in-lab culturing provided that a suitable marine microbiome is present, and that a specific strain can be isolated, propagated and efficiently used for research over prolonged periods of time. The flexible and modular structure of our system can be scaled and adapted to the needs of specific species, such as Botryllus schlosseri, as well as of particular laboratory spaces. Overall, we show that Botrylloides diegensis can be proficiently bred in-land and suggest that our results can be extended to other species of colonial ascidians to promote research on these fascinating animals.

HighlightsO_LIFirst artificial seawater based recirculating aquaculture for colonial ascidians
C_LIO_LIOver 3 years of continuous breeding
C_LIO_LISemi-automated setup with minimized maintenance
C_LIO_LIGood biomass production for strain propagation
C_LIO_LI4 different culture conditions for optimized breeding for species of interest
C_LI


title: Artificial seawater based long-term culture of colonial ascidians


title: Task-specific elevation of motor learning by conjunctive transcranial direct current stimulation

abstract: The optimal protocol for neuromodulation by transcranial direct current stimulation (tDCS) remains unclear. Using rotarod paradigm, we found that mouse motor learning was enhanced by anodal tDCS (3.2 mA/cm2) during but not before or after task performance. Dual-task experiments showed that motor learning enhancement was specific to the task accompanied by concurrent anodal tDCS. Studies using stroke model mice induced by middle cerebral artery occlusion (MCAO) showed that concurrent anodal tDCS restored motor learning capability in a task-specific manner. Transcranial in vivo calcium imaging further showed that anodal and cathodal tDCS elevated and suppressed neuronal activity in the primary motor cortex (M1), respectively. Anodal tDCS specifically promoted the activity of task-related M1 neurons during task performance, suggesting that elevated Hebbian synaptic potentiation in task-activated circuits accounts for motor learning enhancement. Thus, application of tDCS concurrent with the targeted behavioral dysfunction could represent a more effective approach for treating brain disorders.


title: Neural mechanism underlying task-specific enhancement of motor learning by concurrent transcranial direct current stimulation


title: Identification of Pectobacterium species isolated from the soft rot of tetecho (Neobuxbaumia tetetzo), a columnar cactus, and associated metagenomics

abstract: Neobuxbaumia tetetzo, commonly known as tetecho, is a columnar cactus endemic to Mexico. In the last 15 years, damage has been observed in young and adult plants of N. tetetzo, ranging from chlorotic spots with a wet appearance in early stages to tissue necrosis in advanced stages and finally the death of the plant; Pectobacterium brasiliense is the causal agent of the damages. Disease progression may be delayed or accelerated by the involvement of other bacteria, either pathogenic or endophytic, at the site of infection. Our goal was to confirm the presence of Pectobacterium brasiliense, in the soft rot of N. tetetzo and to determine the presence of other bacteria associated with the rot. We isolated three bacterial strains (A1, A3 and A8) from diseased tissue from three separate N. tetetzo plants, and compare them using biochemical and molecular techniques, such as whole-genome sequencing of strains A1 and A3. Phylogenetic analyzes confirmed that A1 corresponded to P. brasiliense, whereas A3 was more misimlar to P. polaris. Additionally, sequencing of 16S rRNA gene from metagenomic DNA isolated from healthy and diseased tissue of N. tetetzo indicated the presence of four operational taxonomic units (OTUs) at the order level, unique to the diseased tissue: Actinomycetales, Burkholderiales, Caulobacterales, and Sphingomonadales, with probable participation in the soft rot process.


title: TRIM71 deficiency causes germ cell loss during mouse embryogenesis and promotes human male infertility

abstract: Mutations affecting the germline can result in infertility or the generation of germ cell tumors (GCT), highlighting the need to identify and characterize the genes controlling the complex molecular network orchestrating germ cell development. TRIM71 is a stem cell-specific factor essential for embryogenesis, and its expression has been reported in GCT and adult mouse testes. To investigate the role of TRIM71 in mammalian germ cell embryonic development, we generated a germline-specific conditional Trim71 knockout mouse (cKO) using the early primordial germ cell (PGC) marker Nanos3 as a Cre-recombinase driver. cKO mice are infertile, with male mice displaying a Sertoli cell-only (SCO) phenotype, which in humans is defined as a specific subtype of non-obstructive azoospermia characterized by the absence of developing germ cells in the testes seminiferous tubules. Infertility originates during embryogenesis, as the SCO phenotype was already apparent in neonatal mice. The in vitro differentiation of mouse embryonic stem cells (ESCs) into PGC-like cells (PGCLCs) revealed reduced numbers of PGCLCs in Trim71-deficient cells. Furthermore, in vitro growth competition assays with wild type and CRISPR/Cas9-generated TRIM71 mutant NCCIT cells, a human GCT-derived cell line which we used as a surrogate model for proliferating PGCs, showed that TRIM71 promotes NCCIT cell proliferation and survival. Our data collectively suggest that germ cell loss in cKO mice results from combined defects during the specification and maintenance of PGCs prior to their sex determination in the genital ridges. Last, via exome sequencing analysis, we identified several TRIM71 variants in a cohort of infertile men, including a loss-of-function variant in a patient with SCO phenotype. Our work reveals for the first time an association of TRIM71 variants with human male infertility, and uncovers further developmental roles for TRIM71 in the generation and maintenance of germ cells during mouse embryogenesis.

category: developmental biology


title: Genomic Considerations for FHIR; eMERGE Implementation Lessons

abstract: Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Networks Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7 FHIR), to represent clinical genomics results. These new standards improve the utility of HL7 FHIR as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.

category: genomics


title: MDA5 autoimmune disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA

abstract: Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoimmune disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more tightly to synthetic Alu:Alu dsRNA. CryoEM structures MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 side-chain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle-RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via a novel allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides new insights on how MDA5 recognizes dsRNA in health and disease.


title: Molecular basis for two stereoselective Diels-Alderases that produce decalin skeletons

abstract: Molecular chirality, discovered by Louis Pasteur in the middle of the 19th century1, is found in most primary and secondary metabolites. Particularly, the so-called natural products are rich in chiral centres2. The stereochemistry of natural products is strictly recognized in living organisms, and is thus closely related to their biological functions. The Diels-Alder (DA) reaction, which forms a six-membered ring with up to four chiral centres, is a fundamental practical reaction for C-C bond formation in synthetic chemistry3. Nature has also adopted this reaction to elaborate the complex structures of natural products using enzymes derived from various progenitor proteins4-7. Although enzymes catalysing the DA reaction, Diels-Alderases (DAases), have attracted increasing attention, little is known about the molecular mechanism by which they control the stereochemistry and perform catalysis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyse intramolecular DA reactions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin8,9. Based on the crystal structures, docking simulations followed by all-atom molecular dynamics simulations provided dynamic binding models demonstrating the folding of linear polyenoyl tetramic acid substrates in the binding pocket of these enzymes, explaining the stereoselectivity in the construction of decalin scaffolds. Site-directed mutagenesis studies verified the binding models and, in combination with density functional theory calculations, clarified how hydrophilic amino acid residues in the Phm7 pocket regulate and catalyse the stereoselective DA reaction. This study highlights the distinct molecular mechanisms of the enzymatic DA reaction and its stereoselectivity experimentally and computationally. We anticipate that clarified molecular mechanism herein provides not only the basic understanding how these important enzymes work but also the guiding principle to create artificial enzymes that produce designer bioactive molecules.


title: Meta-Analysis of Oxidative Transcriptomes in Insects

abstract: Data accumulation in public databases has resulted in extensive use of meta-analysis, a statistical analysis that combines the results of multiple studies. Oxidative stress occurs when there is an imbalance between free radical activity and antioxidant activity, which can be studied in insects by transcriptome analysis. This study aimed to apply a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data. We collected oxidative stress response-related RNA sequencing (RNA-seq) data for a wide variety of insect species, mainly from public gene expression databases, by manual curation. Only RNA-seq data of Drosophila melanogaster were found and were systematically analyzed using a newly developed RNA-seq analysis workflow for species without a reference genome sequence. The results were evaluated by two metric methods to construct a reference dataset for oxidative stress response studies. Many genes were found to be downregulated under oxidative stress and related to organ system process (GO:0003008) and adherens junction organization (GO:0034332) by gene enrichment analysis. A cross-species analysis was also performed. RNA-seq data of Caenorhabditis elegans were curated, since no RNA-seq data of insect species are currently available in public databases. This method, including the workflow developed, represents a powerful tool for deciphering conserved networks in oxidative stress response.


title: Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences

abstract: Telomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and designing therapies. However, molecular factors triggering selective activation of either the telomerase dependent (TEL) or the alternative lengthening of telomeres (ALT) pathway are poorly understood. In addition, more accurate and easy-to-use methodologies are required for TMM phenotyping. In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs. Gene expression data were used for computational assessment of TMM pathway activities and compared with experimental assays for TEL and ALT. Explicit consideration of pathway topology makes bioinformatics analysis more informative compared to computational methods based on simple summary measures of gene expression. Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation. Our approach offers a novel option for systematic investigation of TMM activation patterns across cancers and healthy tissues for dissecting pathway-based molecular markers with diagnostic impact.


title: DRDOCK: A Drug Repurposing platform integrating automated docking, simulations and a log-odds-based drug ranking scheme

abstract:
MotivationDrug repurposing, where drugs originally approved to treat a disease are reused to treat other diseases, has received escalating attention especially in pandemic years. Structure-based drug design, integrating small molecular docking, molecular dynamic (MD) simulations and AI, has demonstrated its evidenced importance in streamlining new drug development as well as drug repurposing. To perform a sophisticated and fully automated drug screening using all the FDA drugs, intricate programming, accurate drug ranking methods and friendly user interface are very much needed.

ResultsHere we introduce a new web server, DRDOCK, Drug Repurposing DOcking with Conformation-sampling and pose re-ranKing - refined by MD and statistical models, which integrates small molecular docking and molecular dynamic (MD) simulations for automatic drug screening of 2016 FDA-approved drugs over a user-submitted single-chained target protein. The drugs are ranked by a novel drug-ranking scheme using log-odds (LOD) scores, derived from feature distributions of true binders and decoys. Users can submit a selection of LOD-ranked poses for further MD-based binding affinity evaluation. We demonstrated that our platform can indeed recover one of the substrates for nsp16, a cap ribose 2'-O methyltransferase, and recommends that fluralaner, tegaserod and fenoterol could be repurposed for the COVID19 treatment with the latter two being confirmed in SARS-CoV2 suppression experiments. All the sampled docking poses and trajectories can be 3D-viewed and played via our web interface. This platform shall be easy-to-use for general scientists and medicinal researchers to carry out drug repurposing within a couple of days which should add value to our timely responses to, particularly, emergent disease outbreaks.

Availability and implementationDRDOCK can be freely accessed from https://dyn.life.nthu.edu.tw/drdock/. (Due to the hardware upgrade, the service is NOT available before 7/18, 2021)


title: OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data

abstract:
MotivationThe increasing amount of data produced by omics technologies has significantly improved the understanding of how biological information is transferred across different omics layers and to which extent it is involved in the manifestation of a given phenotype. Besides data-driven analysis strategies, interactive visualization tools have been developed to make the analysis in the multi-omics field more transparent. However, most state-of-the-art tools do not reconstruct the impact of a given omics layer on the final integration result. In general, the amount of omics data analyses strategies and the fields of applications lack a clearer classification of the different approaches.

ResultsWe developed a classification for omics data focusing on different aspects of multi-omics data sets, such as data type and experimental design. Based on this classification we developed the Omics Trend-comparing Interactive Data Explorer (OmicsTIDE), an interactive visualization tool developed to address the limitations of current visualization approaches in the multi-omics field. The tool consists of an automated part that clusters omics data to determine trends and an interactive visualization. The trends are visualized as profile plots and are connected by a Sankey diagram that allows an interactive pairwise trend comparison to discover concordant and discordant trends. Moreover, large-scale omics data sets are broken down into small subsets of concordant and discordant regulatory trends within few analysis steps. We demonstrate the interactive analysis using OmicsTIDE with two case studies focusing on different types of experimental designs.

AvailabilityOmicsTIDE is a web tool and available via http://tuevis.informatik.uni-tuebingen.de/

Contactkay.nieselt@uni-tuebingen.de


title: Associations of weather fronts with pig reproduction and mortality

abstract: Farmers and practising veterinarians have long suspected the impact of weather fronts on production and animal health. A common impression is that sows will farrow earlier in connection with a cold front. There might be a correlation between daily mortality and the occurrence of a strong atmospheric front. Population-based quantitative studies on weather fronts effects on animal health and production are very sparse in the scientific literature. In this study, the associations between the weather fronts and daily farrowing incidence, the pregnancy length and the daily death incidence were analysed. The results show that cold front increased the odds of more than daily six farrowings on the day of the front (with at least 3{degrees}C cooling OR: 4.79, 95%CI: 1.08-21.21, p=0.039). On the day of the front, with at least 3{degrees}C temperature change both the cold and the warm front increased the odds of the farrowing on the day [≥] 118th day of the gestation (OR: 3.10, 95%CI: 1.04-9.30, p=0.43 and OR: 4.39, 95%CI: 1.73-11.15, p=0.002, respectively). On the day after the day of front, the odds of farrowing on the [≤] 113th day of gestation are increased, if the temperature decrease was at least 2{degrees}C the OR: 2.30 (95%CI: 1.04-5.06, p=0.039). On the day after the warm front with at least 1{degrees}C temperature increase the odds of more than daily three deaths is increased (OR: 5.44, 95%CI: 1.23-24.05, p=0.025).

category: biophysics


title: Machine learning based cellular contractile force detection: a new approach to predict cell mechanics by images

abstract:
Combining experiments with artificial intelligence algorithms, we propose a new machine learning based approach to extract the cellular force distributions from the microscope images. The full process can be divided into three steps. First, we culture the cells on a special substrate allowing to measure both the cellular traction force on the substrate and the corresponding substrate wrinkles simultaneously. The cellular forces are obtained using the traction force microscopy (TFM), at the same time that cell-generated contractile forces wrinkle their underlying substrate. Second, the wrinkle positions are extracted from the microscope images. Third, we train the machine learning system with GAN (generative adversarial network) by using sets of corresponding two images, the traction field and the input images (raw microscope images or extracted wrinkle images), as the training data. The network understands the way to convert the input images of the substrate wrinkles to the traction distribution from the training. After sufficient training, the network is utilized to predict the cellular forces just from the input images. Our system provides a powerful tool to evaluate the cellular forces efficiently because the forces can be predicted just by observing the cells under the microscope, which is a way simpler method compared to the TFM experiment. Additionally, the machine learning based approach presented here has the profound potential for being applied to diverse cellular assays for studying mechanobiology of cells.

Significance StatementCell-generated forces are indispensable determinants of fundamental cell functions such as motility and cell division. As such, quantifying how the forces change upon perturbations to the cells such as gene mutations and drug administration is of profound importance. Here we present a novel machine learning based system that allows for efficient estimations of the forces that are determined only by "observing" microscope images. Given that the cellular traction forces are regulated downstream of diverse signaling pathways, our system - that helps significantly improve the throughput of the measurements - presents a new, high throughput platform for real time analysis of the effects of a massive number of genetic and molecular perturbations on the forces and resulting cell mechanics.


title: Wrinkle force microscopy: a new machine learning based approach to predict cell mechanics from images


title: Targeted therapy for LIMD1-deficient non-small cell lung cancer subtypes.

abstract:
An early event in lung oncogenesis is loss of the tumour suppressor gene LIMD1 (LIM domains containing 1); this encodes a scaffold protein, which suppresses tumourigenesis via a number of different mechanisms. Approximately 45% of non-small cell lung cancers (NSCLC) are deficient in LIMD11, yet this subtype of NSCLC has been overlooked in preclinical and clinical investigations. Defining therapeutic targets in these LIMD1 loss-of-function patients is difficult due to a lack of  druggable targets, thus alternative approaches are required. To this end, we performed the first drug repurposing screen to identify compounds that confer synthetic lethality with LIMD1 loss in NSCLC cells. PF-477736 was shown to selectively target LIMD1 deficient cells in vitro through inhibition of multiple kinases, inducing cell death via apoptosis. Furthermore, PF-477736 was effective in treating LIMD1-/- tumors in subcutaneous xenograft models, with no significant effect in LIMD1+/+ cells. We have identified a novel drug tool with significant preclinical characterization that serves as an excellent candidate to explore and define LIMD1-deficient cancers as a new therapeutic subgroup of critical unmet need.

Significance StatementHere we provide the first proof-of-concept data validating the scope for development of a targeted therapy against the non-small cell lung cancers (NSCLC) subtypes deficient in expression of the LIMD1 tumor suppressor gene. Approximately 45% of NSCLC are deficient in LIMD11 representing at least 1.2 million lung cancer patients worldwide; yet this subtype has been ignored in preclinical and clinical investigations with no targeted therapies available. This seminal study applied synthetic lethality drug screening to target the loss/reduction of LIMD1 in lung cancer and normal cell lines, identifying and validating the multi-kinase inhibitor PF-477736 as a selectively cytotoxic compound towards LIMD1 deficient cells. This study provides rationale for further investigation into targeting LIMD1 loss in lung cancer, thereby addressing a critical unmet need for therapeutic approached to targeting LIMD1-deficent cancer subtypes.

category: cancer biology


title: Catechin complexed with lysine has potent antitumor activities in human breast cancer xenograft model

abstract: bioRxiv has withdrawn this preprint as it was posted without proper authorization therefore violating confidentiality agreements between involved parties.


title: The Prognostic Value of Tumor-Infiltrating Immune Cells in Gynecologic Cancers

abstract: Immunotherapy has changed the standard of treatment for many cancers. However, only a small number of gynecologic cancer patients benefit from immunotherapy. The intra-tumoral immune landscapes are suggested as a predictor of the response to immunotherapies, but there are no studies that provide a comprehensive immune characterization for gynecologic cancers. To characterize cellular compositions of the immune infiltrates and investigate if the immune landscape is a predictor for patient prognosis in gynecologic cancers, we analyzed tumor immune infiltrates of ovarian cancer, cervical cancer, and uterine cancer from The Cancer Genome Atlas Program (TCGA) using QuanTIseq and EPIC. Ovarian cancer had the highest percentage of total immune cells. Cervical cancer and uterine corpus endometrial carcinoma have lower percentages of immune cells with 17% and 16%, respectively. Furthermore, ovarian cancer had a significantly higher monocyte and M2-liked macrophage percentage, but a lower percentage for CD8 T cells and neutrophils compared to cervical cancer and uterine cancer. Cervical cancer had the highest percentage for M1-liked macrophages and the lowest for CD4 T cells. Uterine cancer had the highest percentage of dendritic cells. In cervical cancer, higher cell infiltration of CD8 T-Cells and M2-liked macrophages was associated with a better prognosis. In uterine cancer, patients with a higher number of dendritic cells and CD8 T-Cells had significantly better clinical outcomes. However, higher CD4 T-cell infiltration was associated with a poor prognosis in uterine cancer. Interestingly, the patient survival was not affected by the infiltration of any individual immune cells which we analyzed in ovarian cancer. We identified and validated four immune subtypes associated with distinct immune cell infiltration in gynecologic cancers. Cervical and uterine cancer patients from an immune-desert subtype that had the least amount of lymphocyte infiltration and a high level of monocyte had the worst prognosis. By contrast, cervical and uterine cancer patients from an immune-warm subtype that had higher infiltration of CD8 T-cell, natural killer (NK) cells, and dendritic cells (DCs) had the best prognosis. However, the survival rate of ovarian cancer patients is similar among the four different subtypes. Our study provides a conceptual framework to understand the tumor immune microenvironment of different gynecologic cancers.


title: Modelling TGFβR and Hh pathway regulation of prognostic matrisome molecules in ovarian cancer

abstract: In a multi-level  deconstruction of omental metastases, we previously identified a prognostic matrisome gene expression signature in high-grade serous ovarian cancer (HGSOC) and twelve other malignancies. Here, our aim was to understand how six of these extracellular matrix, ECM, molecules, COL11A1, COMP, FN1, VCAN, CTSB and COL1A1, are up-regulated in cancer. Using biopsies, we identified significant associations between TGF{beta}R activity, Hedgehog signalling and these ECM molecules and then studied the associations in mono-, co- and tri-culture. Activated omental fibroblasts produced more matrix than malignant cells, directed by TGF{beta}R and Hedgehog signalling crosstalk. We  reconstructed omental metastases in tri-culture of HGSOC cells, omental fibroblasts and adipocytes. This combination was sufficient to generate all six ECM proteins and the matrisome expression signature. TGF{beta}R and Hedgehog inhibitor combinations attenuated fibroblast activation, gel remodelling and ECM remodelling in these models. The tri-culture model reproduces key features of omental metastases and allows study of diseased-associated ECM.


title: Cannabinoids is a "No-Go" While a Cancer Patient is on Immunotherapy; but is It Safe to Use Psychedelics During Cancer Immunotherapy?

abstract:
The use of Psychedelics by patients with cancer to relieve anxiety and depression has increased in the past few years. Since Psychedelics have immunomodulatory effects, their consumption among cancer patients should be carefully considered due to their potential negative effects on the tumor immune stroma, especially in view of the increase in the utilization of therapeutic approaches that are based on immune activation such as treatment with immune checkpoint inhibitors (ICIs). Preclinical data provided in this report indicate a potentially negative impact on tumor growth as a result of Psychedelics consumption during treatment with ICIs. Furthermore, our research suggests that the use of psychedelic agents (Lysergic acid diethylamide [LSD] or Psylocibin) might diminish the beneficial therapeutic benefits of ICIs.

It might be necessary to expend this line of research in order to validate these findings, in view of the increase use of cannabinoids and psychedelics among cancer patients, some of them being treated with immune-based modalities.


title: Metabolomic profiling of pancreatic adenocarcinoma reveals fundamental clinical features

abstract:
In this study, we perform the metabolomics profiling of 77 PDAC patient-derived tumor xenografts (PDTX) to investigate the relationship of metabolic profiles with overall survival (OS) in PDAC patients, tumor phenotypes and resistance to five anticancer drugs (gemcitabine, oxaliplatin, docetaxel, SN-38 and 5-Fluorouracil). We identified a metabolic signature that was able to predict the clinical outcome of PDAC patients (p < 0.001, HR=2.68 [95% CI: 1.5-4.9]). The correlation analysis showed that this metabolomic signature was significantly correlated with the PDAC molecular gradient (PAMG) (R = 0.44 and p < 0.001) indicating significant association to the transcriptomic phenotypes of tumors. Resistance score established, based on growth rate inhibition metrics using 35 PDTX-derived primary cells, allowed to identify several metabolites related to drug resistance which was globally accompanied by accumulation of several diacy-phospholipids and decrease in lysophospholipids. Interestingly, targeting glycerophospholipid synthesis improved sensitivity to the three tested cytotoxic drugs indicating that interfering with metabolism could be a promising therapeutic strategy to overcome the challenging resistance of PDAC.

Short abstractTargeting metabolism of cancer cells gives a precious opportunity to overcome challenges related to the high mortality and chemoresistance in PDAC.

Metabolic profiling of PDAC patient-derived tumor xenografts used in this study allowed highlighting the strong link between metabolism and both clinical outcome of the patients and chemoresistance.

Metabolic signature was able to discriminate between good and bad prognosis groups of patients based on their level of key metabolites.

Identification of key metabolic markers associated to chemoresistance allowed to improve sensitivity to anticancer drugs.

These results provide new insights to help to predict patient survival and elaborate new combinatory therapies against chemoresistance in PDAC patients attesting of the important clinical value of this work.


title: Differential activation of parathyroid and renal Ca2+-sensing receptors underlies the renal phenotype in autosomal dominant hypocalcemia 1

abstract:
BackgroundParathyroid Ca2+-sensing receptor (CaSR) activation inhibits parathyroid hormone (PTH) release, while activation of CaSRs in kidneys and intestine attenuates local transepithelial Ca2+ transport. In patients with autosomal dominant hypocalcemia 1 (ADH1) due to activating CASR mutations, treatment of symptomatic hypocalcemia can be complicated by treatment-induced hypercalciuria, resulting in nephrocalcinosis and renal insufficiency. Although CaSRs throughout the body are activated by increased extracellular Ca2+ concentrations, it is not understood why some ADH1 patients have reduced PTH, but not hypercalciuria at presentation, despite CaSR expression in both kidney and parathyroid.

MethodsActivation of the CaSR was studied in mouse models and a ADH1 patient. In vitro CaSR activation was studied in HEK293 cells.

ResultsMice with a gain-of-function mutation in Casr are hypocalcemic with reduced plasma PTH levels. However, renal CaSRs are not activated as indicated by normal urinary calcium handling and unaltered renal Cldn14 expression. Activation of renal CaSRs only occurred after increasing plasma Ca2+ levels. Similarly, calcimimetic administration to wildtype mice induced hypocalcemia without activating renal CaSRs. Moreover, significant hypercalciuria was not observed in an ADH1 patient until blood Ca2+ was normalized. In vitro experiments suggest that increased CaSR levels in the parathyroid relative to the kidney contribute tissue-specific CaSR activation thresholds.

ConclusionHere we delineate tissue-specific CaSR activation thresholds, where parathyroid CaSR overactivity can reduce plasma Ca2+ to levels insufficient to activate renal CaSRs, even with overactivating mutations. These findings may aid in the management of ADH1 patients.


title: Evidence for efficient non-evaporative leaf-to-air heat dissipation in a pine forest under drought conditions

abstract:
O_LIDrier climates predicted for many regions can result in reduced evaporative cooling leading to leaf heat stress and enhanced mortality. To what extent non-evaporative cooling can contribute to plant resilience to the increasingly stressful conditions is poorly known at present.
C_LIO_LIUsing a novel, high accuracy infrared system for continuous measurements of leaf temperature in mature trees under field conditions, we assessed leaf-to-air temperature differences {Delta}Tleaf-air of pine needles during drought.
C_LIO_LIOn mid-summer days, {Delta}Tleaf-air remained <1.5 {degrees}C, both in trees exposed to summer drought, and in those provided with a supplement irrigation having a 10x higher transpiration rate. The non-evaporative cooling in the drought-exposed trees must be facilitated by low resistance to heat transfer generating large H. {Delta}Tleaf-air was weakly related to variations in the radiation load and mean wind speed in the lower part of the canopy, but highly dependent on canopy structure and within-canopy turbulence that enhanced the sensible heat flux H.
C_LIO_LINon-evaporative cooling is demonstrated as an effective cooling mechanism in needle-leaf trees, which can be a critical factor in forest resistance to drying climates. The generation of a large H at the leaf scale provides a basis for the development of the previously identified canopy-scale  convector effect.
C_LI


title: Motor cortex activity across movement speeds is predicted by network-level strategies for generating muscle activity

abstract: Learned movements can be skillfully performed at different paces. What neural strategies produce this flexibility? Can they be predicted and understood by network modeling? We trained monkeys to perform a cycling task at different speeds, and trained artificial recurrent networks to generate the empirical muscle-activity patterns. Network solutions reflected the principle that smooth well-behaved dynamics require low trajectory tangling. Network solutions had a consistent form, which yielded quantitative and qualitative predictions. To evaluate predictions, we analyzed motor cortex activity recorded during the same task. Responses supported the hypothesis that the dominant neural signals reflect not muscle activity, but network-level strategies for generating muscle activity. Single-neuron responses were better accounted for by network activity than by muscle activity. Similarly, neural population trajectories shared their organization not with muscle trajectories, but with network solutions. Thus, cortical activity could be understood based on the need to generate muscle activity via dynamics that allow smooth, robust control over movement speed.


title: Transcriptomics-informed large-scale cortical model captures topography of pharmacological neuroimaging effects of LSD

abstract: Psychoactive drugs can transiently perturb brain physiology while preserving brain structure. The role of physiological state in shaping neural function can therefore be investigated through neuroimaging of pharmacologically-induced effects. This paradigm has revealed that neural and experiential effects of lysergic acid diethylamide (LSD) are attributable to its agonist activity at the serotonin-2A receptor. Here, we integrate brainwide transcriptomics with biophysically-based large-scale circuit modeling to simulate acute neuromodulatory effects of LSD on human cortical dynamics. Our model captures the topographic effects of LSD-induced changes in cortical BOLD functional connectivity. These findings suggest that serotonin-2A-mediated modulation of pyramidal cell gain is the circuit mechanism through which LSD alters cortical functional topography. Individual-subject fitting reveals that the model captures patterns of individual neural differences in drug response that predict altered states of consciousness. This work establishes a framework for linking molecular-level manipulations to salient changes in brain function, with implications for precision medicine.


title: Properties of multi-vesicular release from rod photoreceptors support transmission of single photon responses

abstract: Vision under starlight requires rod photoreceptors to transduce and transmit single photon responses to the visual system. This remarkable sensitivity depends on a small voltage change reliably reducing glutamate release such that post-synaptic rod bipolar cells can robustly detect the signal. To transmit this small signal, we have found that rod vesicle release deviates strongly from a Poisson process under conditions that mimic darkness. Specifically, at their resting membrane potential in darkness, rods exhibit coordinated and regularly timed multivesicular release events. Each release event consisted of [~]17 vesicles and occurred 2-3 times more regularly than expected from a Poisson process. Hyperpolarizing rods to mimic the voltage change produced by a single photon response abruptly reduced the probability of multivesicular release nearly to zero with a rebound increase in release probability at stimulus offset. Simulations of these release dynamics indicate that this regularly timed, multivesicular release promotes transmission of single photon responses to post-synaptic neurons. Furthermore, the mechanism is efficient, requiring fewer vesicles to be released per second than uniquantal release governed by Poisson statistics.


title: Increasing age is independently associated with higher free water in non-active MS brain - A multi-compartment analysis using FAST-T2

abstract:
PurposeTo explore the relationship between the cerebral cortical perivascular space (PVS) and aging in non-active MS subjects by using the multi-echo T2 relaxometry based cerebrospinal fluid fraction (CSFF) map.

MethodsMulti-echo spiral T2 data from 111 subjects with non-active multiple sclerosis (MS) were retrospectively investigated by fitting the T2 data into a three-compartment model, the three water compartments including myelin water, intra-extracellular water, and cerebrospinal fluid. Segmentation of T1w image was performed to get the region of interest (ROI) in cerebral cortical regions. The white matter lesion segmentation was conducted using a convolutional neural network (CNN) based segmentation tool. The CSFF in the ROIs were correlated with age by controlling the gender, white matter hyperintensity lesion burden, and MS disease duration. Multiple linear models were created for the analysis of aging effect on the CSFF.

ResultsThe ROI analysis shows that the CSFF in the cerebral cortical regions (temporal, occipital, parietal, front, hippo, and mtl) are significantly linear increasing with age (p<0.01). The intra-extracellular water fraction (IEWF) in the ROIs are significantly linear decreasing (p<0.01).

ConclusionThe multi-echo T2 based three-compartment model can be used to quantify the CSFF. The linear increase of CSF water contents in the cerebral cortical regions indicates increased perivascular space load in cortex with aging. The quantification of CSFF may provide a way to understand the glymphatic clearance function in aging and neurodegenerations.

HighlightsO_LIMR T2 relaxometry is a valid method to quantify the cerebrospinal fluid fraction (CSFF) in cerebral cortical regions
C_LIO_LIThe CSFF in the cerebral cortical regions are positively correlated with age by controlling the white matter lesion load in non-active MS subjects.
C_LIO_LIQuantification of cerebral CSFF may reflect the perivascular space load in cortex and better interpret the disease progression in neurodegenerative disease, such as MS.
C_LI


title: Preparatory activity links frontal eye field activity with small amplitude motor unit recruitment of neck muscles during gaze planning

abstract:
A hallmark of intelligent behavior is that we can separate intention from action. To understand the mechanism that gates the flow of information between motor planning and execution, we compared the activity of frontal eye field neurons with motor unit activity from neck muscles in the presence of an intervening delay period in which spatial information regarding the target was available to plan a response. Whereas we could infer spatially-specific delayed period activity from the activity of frontal eye field neurons, neck motor unit activity during the delay period could not be used to infer the direction of an upcoming movement, Nonetheless, motor unit activity was correlated with the time it took to initiate saccades. Interestingly, we observed a heterogeneity of responses amongst motor units, such that only units with smaller amplitudes showed a clear modulation during the delay period. These small amplitude motor units also had higher spontaneous activity compared to the units which showed modulation only during the movement epoch. Taken together, our results suggest that the temporal information is visible in the periphery amongst smaller motor units during eye movement planning and explains how the delay period primes muscle activity leading to faster reaction times.

Significance statementThis study shows that the temporal aspects of a motor plan in the oculomotor circuitry can be accessed by peripheral neck muscles hundreds of milliseconds prior to the instruction to initiate a saccadic eye movement. The coupling between central and peripheral processes during the delay time is mediated by the recruitment pattern of motor units with smaller amplitude in the periphery. Besides giving insight into how information processed in cortical areas is read out by the muscles, these findings could be useful to decode intentional signals from the periphery to control brain machine interface devices.


title: The beta component of gamma-band auditory steady-state responses in patients with schizophrenia

abstract: The mechanisms underlying circuit dysfunctions in schizophrenia (SCZ) remain poorly understood. Auditory steady-state responses (ASSRs), especially in the gamma and beta band, have been suggested as a potential biomarker for SCZ. While the reduction of 40Hz power for 40Hz drive has been well established and replicated in SCZ patients, studies are inconclusive when it comes to an increase in 20Hz power during 40Hz drive. There might be several factors explaining the inconsistencies, including differences in the sensitivity of the recording modality (EEG vs MEG), differences in stimuli (click-trains vs amplitude-modulated tones) and large differences in the amplitude of the stimuli. Here, we used a computational model of ASSR deficits in SCZ and explored the effect of three SCZ-associated microcircuit alterations: reduced GABA activity, increased GABA decay times and NMDA receptor hypofunction. We investigated the effect of input strength on gamma (40 Hz) and beta (20 Hz) band power during gamma ASSR stimulation and saw that the pronounced increase in beta power during gamma stimulation seen experimentally could only be reproduced in the model when GABA decay times were increased and only for a specific range of input strengths. More specifically, when the input was in this specific range, the rhythmic drive at 40Hz produced a strong 40Hz rhythm in the control network; however, in the  SCZ-like network, the prolonged inhibition led to a so-called  beat-skipping, where the network would only strongly respond to every other input. This mechanism was responsible for the emergence of the pronounced 20Hz beta peak in the power spectrum. The other two microcircuit alterations were not able to produce a substantial 20 Hz component but they further narrowed the input strength range for which the network produced a beta component when combined with increased GABAergic decay times. Our finding that the beta component only existed for a specific range of input strengths might explain the seemingly inconsistent reporting in experimental studies and suggests that future ASSR studies should systematically explore different amplitudes of their stimuli. Furthermore, we provide a mechanistic link between a microcircuit alterations and an electrophysiological marker in schizophrenia and argue that more complex ASSR stimuli are needed to disentangle the nonlinear interactions of microcircuit alterations. The computational modelling approach put forward here is ideally suited to facilitate the development of such stimuli in a theory-based fashion.


title: Quality control strategies for brain MRI segmentation and parcellation: practical approaches and recommendations - insights from The Maastricht Study

abstract:
BackgroundQuality control of brain segmentation is a fundamental step to ensure data quality. Manual quality control is the current gold standard, despite unfeasible in large neuroimaging samples. Several options for automated quality control have been proposed, providing potential time efficient and reproducible alternatives. However, those have never been compared side to side, which prevents to reach consensus in the appropriate QC strategy to use. This study aims to elucidate the changes manual editing of brain segmentations produce in morphological estimates, and to analyze and compare the effects of different quality control strategies in the reduction of the measurement error.

MethodsWe used structural MR images from 259 participants of The Maastricht Study. Morphological estimates were automatically extracted using FreeSurfer 6.0. A subsample of the brain segmentations with inaccuracies was manually edited, and morphological estimates were compared before and after editing. In parallel, 11 quality control strategies were applied to the full sample. Those included: a manual strategy, manual-QC, in which images were visually inspected and manually edited; five automated strategies where outliers were excluded based on the tools MRIQC and Qoala-T, and the metrics morphological global measures, Euler numbers and Contrast-to-Noise ratio; and five semi-automated strategies, were the outliers detected through the mentioned tools and metrics were not excluded, but visually inspected and manually edited. We used a regression of morphological brain measures against age as a test case to compare the changes in relative unexplained variance that each quality control strategy produces, using the reduction of relative unexplained variance as a measure of increase in quality.

ResultsManually editing brain surfaces produced changes particularly high in subcortical brain volumes and moderate in cortical surface area, thickness and hippocampal volumes. The exclusion of outliers based on Euler numbers yielded a larger reduction of relative unexplained variance for measurements of cortical area, subcortical volumes and hippocampal subfields, while manual editing of brain segmentations performed best for cortical thickness. MRIQC produced a lower, but consistent for all types of measures, reduction in relative unexplained variance. Unexpectedly, the exclusion of outliers based on global morphological measures produced an increase of relative unexplained variance, potentially removing more morphological information than noise from the sample.

ConclusionOverall, the automatic exclusion of outliers based on Euler numbers or MRIQC are reliable and time efficient quality control strategies that can be applied in large neuroimaging cohorts.


title: Itaconate and fumarate derivatives exert a dual inhibitory effect on canonical NLRP3 activation in macrophages and microglia

abstract:
The NLRP3 inflammasome is a multi-protein complex that regulates the protease caspase-1 and subsequent interleukin (IL)-1{beta} release from cells of the innate immune system, or microglia in the brain, in response to infection or injury. Derivatives of the metabolites itaconate and fumarate, dimethyl itaconate (DMI), 4-octyl itaconate (4OI) and dimethyl fumarate (DMF), limit both expression of IL-1{beta}, and IL-1{beta} release following NLRP3 inflammasome activation. However, the direct effects of these metabolite derivatives on NLRP3 inflammasome responses in macrophages and microglia require further investigation. Using murine bone marrow-derived macrophages, mixed glia and organotypic hippocampal slice cultures (OHSCs), we demonstrate that DMI and 4OI pre-treatment limited IL-1{beta}, IL-6 and tumor necrosis factor production in response to lipopolysaccharide (LPS) priming, as well as inhibiting subsequent NLRP3 inflammasome activation. DMI, 4OI, DMF and monomethyl fumarate (MMF), another fumarate derivative, also directly inhibited biochemical markers of NLRP3 activation in LPS-primed macrophages, mixed glia and OHSCs, including ASC speck formation, caspase-1 activation, gasdermin D cleavage and IL-1{beta} release. Finally, DMF, an approved treatment for multiple sclerosis, as well as DMI, 4OI and MMF, inhibited NLRP3 activation in macrophages in response to the phospholipid lysophosphatidylcholine, which is used to induce demyelination, suggesting a possible mechanism of action for DMF in multiple sclerosis through NLRP3 inhibition. Together, these findings reveal the importance of immunometabolic regulation for both the priming and activation steps of NLRP3 activation in macrophages and microglia. Furthermore, we highlight itaconate and fumarate derivatives as a potential therapeutic option in NLRP3-driven diseases, including in the brain.

Summary statementWe show that itaconate and fumarate derivatives inhibit both the priming and activation steps of NLRP3 inflammasome responses in macrophages and microglia, revealing the importance of immunometabolic NLRP3 regulation.

category: immunology


title: Heliorhodopsin evolution is driven by photosensory promiscuity in monoderms

abstract: The ability to harness Suns electromagnetic radiation by channeling it into high-energy phosphate bonds empowered microorganisms to tap into a cheap and inexhaustible source of energy. Lifes billion-years history of metabolic innovations led to the emergence of only two biological complexes capable of harvesting light: one based on rhodopsins and the other on (bacterio)chlorophyll. Rhodopsins encompass the most diverse and abundant photoactive proteins on Earth and were until recently canonically split between type-1 (microbial rhodopsins) and type-2 (animal rhodopsins) families. Unexpectedly, the long-lived type-1/type-2 dichotomy was recently amended through the discovery of heliorhodopsins (HeRs) (Pushkarev et al. 2018), a novel and exotic family of rhodopsins (i.e. type-3) that evaded recognition in our current homology-driven scrutiny of lifes genomic milieu. Here, we bring to resolution the debated monoderm/diderm occurrence patterns by conclusively showing that HeR distribution is restricted to monoderms. Furthermore, through investigating protein domain fusions, contextual genomic information, and gene co-expression data we show that HeRs likely function as generalised light-dependent switches involved in the mitigation of light-induced oxidative stress and metabolic circuitry regulation. We reason that HeRs ability to function as sensory rhodopsins is corroborated by their photocycle dynamics (Pushkarev et al. 2018) and that their presence and function in monoderms is likely connected to the increased sensitivity to light-induced damage of these organisms (Maclean et al. 2009).


title: LncRNA XIST knockdown suppresses cell proliferation and promotes apoptosis in diabetic cataract via miR-34a/SMAD2 axis

abstract: Emerging evidence has manifested that long non-coding RNAs (lncRNAs) played critical roles in diabetes. The present research aimed to investigate the role and mechanism of XIST on proliferation, migration and apoptosis in diabetic cataract (DC). In the present study, lens epithelial cells (SRA01/04) were treated by high glucose (HG). The levels of XIST, miR-34a and SMAD2 were examined by RT-qPCR. MTT, transwell, wound healing and TUNEL assays were employed to examine cell proliferation, invasion, migration and apoptosis. The interaction between miR-34a and XIST or SMAD2 was verified by luciferase reporter assay. It was found that XIST expression was increased and miR-34a level was decreased in DC tissues and HG-induced SRA01/04 cells. XIST knockdown or miR-34a addition attenuated cell proliferation and migration, and induced apoptosis in SRA01/04 cells under HG. XIST targeted miR-34a and regulated DC progression via miR-34a. SMAD2 was a target gene of miR-34a and was positively modulated by XIST. SMAD2 addition accelerated cell proliferation, migration and inhibited the apoptosis in HG-stimulated SRA01/04 cells, which were abrogated by XIST depletion. In conclusion, XIST facilitated the proliferation, migration and invasion, and inhibited the apoptosis via miR-34a/SMAD2 axis in DC.


title: Synapomorphic variations in the THAP domains of the human THAP protein family and its homologs

abstract: The THAP (Thanatos-associated protein) domain is a DNA-binding domain which binds DNA via a zinc coordinating C2CH motif. Although THAP domains share a conserved structural fold, they bind different DNA sequences in different THAP proteins which in turn perform distinct cellular functions. In this study, we investigate (using multiple sequence alignment, in silico motif and secondary structure prediction) THAP domain conservation within the homologs of the human THAP (hTHAP) protein family. We report that there is significant variation in sequence and predicted secondary structure elements across hTHAP homologs. Interestingly, we report that the THAP domain can be either longer or shorter than the conventional 90 residues and the amino terminal C2CH motif within the THAP domain serves as a hotspot for insertion or deletion. Our results lay the foundation for future studies which will further our understanding of the evolution of THAP domain and regulation of its function.

category: molecular biology


title: Molecular mechanism behind the involvement of apple flavonoid glycosyltransferase gene MdGT1 in the color of apple leaves

abstract: Nowadays, the plant family 1 UDP-glycosyltransferases (UGTs) are more and more investigated owing to their contribution to the plant secondary metabolism and diverse biological roles. Apple (Malus domestica) is one of the most widely cultivated fruit trees with great economical importance. However, poor knowledge is known about the apple UGTs. In this study, we identified 229 members of family 1 through a genome-wide analysis of the apple UGTs, which were clustered into 18 groups, from A to R. We also performed detailed analysis to 34 apple UGTs with quantitavive RT-PCR, and discovered a number of stress-regulated UGTs. Among them, we characterized the role of MD09G1064900, also named as MdUGT83L3, which is significantly induced by salt and cold. In vivo analysis showed that it has high activity towards cyanidin, and moderate activity towards quercetin and keampferol. The transgenic callus and regenerated apple plants overexpressing MdUGT83L3 showed enhanced tolerance to salt and cold treatments. Overexpression of MdUGT83L3 also increased anthocyanin accumulation in the callus tissues and enhanced ROS clearing upon exposed to salt and cold stresses. Futhermore, via yeast-two-hybrid assay, EMSA and CHIP analysis, we also found that MdUGT83L3 could be directly regualted by MdMYB88. Our study indicated that MdUGT83L3, under the regulation of MdMYB88, plays important roles in salt and cold stress adaptation via modulating flavonoid metabolism in apple.


title: Genome-wide analysis of the apple family 1 glycosyltransferases identified a flavonoid-modifying UGT, MdUGT83L3, which is targeted by MdMYB88 and contributes to stress adaptation


title: EMC is required for biogenesis and membrane insertion of Xport-A, an essential chaperone of rhodopsin-1 and the TRP channel

abstract: Insertion of hydrophobic transmembrane domains (TMDs) into the endoplasmic reticulum (ER) lipid bilayer is an essential step during eukaryotic membrane protein biogenesis. The ER membrane complex (EMC) functions as an insertase for TMDs of low hydrophobicity and is required for the biogenesis of a subset of tail-anchored (TA) and polytopic membrane proteins, including rhodopsin-1 (Rh1) and the TRP channel. To better understand the physiological implications of membrane protein biogenesis dependent on the EMC, we performed a bioinformatic analysis to predict TA proteins present in the Drosophila proteome. From 254 predicted TA proteins, subsequent genetic screening in Drosophila larval eye discs led to the identification of 2 proteins that require EMC for their biogenesis: farinelli (fan) and Xport-A. Fan is required for sperm individualization and male fertility in Drosophila and we now show that EMC is also required for these important biological processes. Interestingly, Xport-A is essential for the biogenesis of both Rh1 and TRP, raising the possibility that disruption of Rh1 and TRP biogenesis in EMC loss of function mutations is secondary to the Xport-A defect. We show that EMC is required for Xport-A TMD membrane insertion and increasing the hydrophobicity of Xport-A TMD rendered its membrane insertion to become EMC-independent. Moreover, these EMC-independent Xport-A mutants rescued Rh1 and TRP biogenesis in EMC mutants. Our data establish that EMC can impact the biogenesis of polytopic membrane proteins indirectly, by controlling the biogenesis and membrane insertion of an essential protein co-factor.


title: Mouse oocytes do not contain a conventional Balbiani body

abstract:
Oocytes spend the majority of their lifetime in a primordial, dormant state. Unlike many somatic cell types and mature oocytes, the cellular and molecular biology of primordial oocytes is largely unexplored. Yet, studying their cellular biology is necessary to understand the mechanisms through which oocytes maintain cellular fitness for decades, and why they eventually fail with age.

A hallmark of primordial oocytes in many species is the Balbiani body, a non-membrane bound compartment that contains the majority of mitochondria in the oocyte cytoplasm. The Balbiani body has been proposed to be essential for maintaining mitochondria in a healthy state during long-lasting dormancy, however, the architecture and function of the mammalian Balbiani body remains unknown.

Here, we develop enabling methods for live-imaging based comparative characterization of Xenopus, mouse and human primordial oocytes. We show that primordial oocytes in all three vertebrate species contain active mitochondria, Golgi apparatus and lysosomes. We further demonstrate that human and Xenopus oocytes have a Balbiani body characterized by a dense accumulation of mitochondria in their cytoplasm. However, despite previous reports, we did not find a Balbiani body in mouse oocytes. Instead, we demonstrate what was previously used as a marker for the Balbiani body in mouse primordial oocytes is in fact a ring-shaped Golgi apparatus that is not functionally associated with oocyte dormancy. Our work provides the first insights into the organisation of the cytoplasm in mammalian primordial oocytes, and clarifies relative advantages and limitations of choosing different model organisms for studying oocyte dormancy.


title: Mouse oocytes do not contain a Balbiani body


title: Long noncoding RNA VENTHEART is required for cardiomyocyte specification and function

abstract:
RationaleLong noncoding RNAs (lncRNAs) control cardiac gene expression during heart development and disease. It is accordingly plausible for the same lncRNA to regulate both cardiac development, as well as play a role in adult heart disease progression. lncRNA regulators of early cardiomyocyte (CM) lineage commitment have been identified and characterised, however those controlling later CM specification remain unknown.

ObjectivesIn this study we identified a novel lncRNA required for CM specification, maturation and function, and also discovered its suggested relevance to heart disease.

Methods and ResultsWe performed single cell RNA-seq on human embryonic stem cell derived cardiomyocytes at 2, 6 and 12 weeks of differentiation. Weighted correlation network analysis (WGCNA) identified core gene modules, including lncRNAs highly abundant and uniquely expressed in the human heart. A lncRNA (we call VENTHEART, VHRT) co-expressed with cardiac maturation and ventricular-specific genes MYL2 and MYH7, as well as in adult human ventricular tissue. CRISPR-mediated excision of VHRT led to impaired CM sarcomere formation, and loss of the CM specification gene program. VHRT knockdown (KD) in hESC-CMs confirmed its regulatory role for key cardiac contraction, calcium hemostasis and heart development genes, including MYH6 and RYR2. Functional evaluation after VHRT KD using impedance-based technology and action potential recordings, proved reduced contraction amplitude and loss of the ventricular-like action potential in CM, respectively. Through an integrative analysis of genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) and gene co-expression network, we found VHRT to be co-regulated with core cardiac contractile genes, and the likely source of a heart failure genetic association signal overlapping the VHRT gene locus. Finally, VHRT KD and human failing heart transcriptome comparison validates the consistent downregulation again of cardiac contractile and calcium regulatory genes (P<0.05).

ConclusionWe conclude that VHRT lncRNA is required for proper CM specification and function. Furthermore, reduced VHRT may contribute to the development or progression of human heart disease.


title: MESOMELIC DYSPLASIAS ASSOCIATED WITH THE HOXD LOCUS ARE CAUSED BY REGULATORY REALLOCATIONS

abstract: Some human families display severe shortening and bending of the radius and ulna, a condition referred to as mesomelic dysplasia. Many of these families contain chromosomal rearrangements at 2q31, where the human HOXD locus maps. In mice, the dominant X-ray-induced Ulnaless inversion of the HoxD gene cluster produces a similar phenotype suggesting that the same mechanism is responsible for this pathology in humans and mice. Amongst the proposed explanations, the various alterations to the genomic structure of HOXD could expose Hoxd13 to proximal limb enhancers, leading to its deleterious gain-of-expression in the embryonic forelimb. To assess this hypothesis, we used an engineered 1Mb large inversion including the HoxD gene cluster, in order to position Hoxd13 within a chromatin domain rich in proximal limb enhancers. We show that these enhancers contact and activate Hoxd13 in proximal cells, concomitant to the formation of a mesomelic dysplasia phenotype. A secondary mutation in the coding frame of the HOXD13 protein in-cis with the inversion completely rescued the limb alterations, demonstrating that ectopic HOXD13 is indeed the unique cause of this bone anomaly. Single cell expression analysis and evaluation of HOXD13 binding sites in cells from this ectopic expression domain suggests that the phenotype arises primarily by acting through genes normally controlled by HOXD13 in distal limb cells. Altogether, these results provide a conceptual and mechanistic framework to understand and unify the molecular origins of human mesomelic dysplasia associated with 2q31.


title: The carbon footprint of meat and dairy proteins: a practical perspective to guide low carbon footprint dietary choices

abstract: Meat and dairy products in the food industry represent a significant portion of anthropogenic green house gas emissions. To meet the Intergovernemental Panel on Climate Change recommendations to limit global warming, these emissions should be reduced. Meat and dairy products are also responsible for the majority of our daily, vital, protein intake. Yet, meat and dairy products contain very different amounts of proteins, making it difficult in general to rationalize which protein source has the lowest carbon footprint. Here we present a practical and pedagogical review, comparing the carbon footprint of a variety of meat and dairy products with respect to their protein content. We investigate the carbon footprint of different dietary choices for several countries, by keeping the total number of meat and dairy proteins constant. Interestingly, we find that dairy-only diets are in general only a little less carbon intensive than current diets. However, 50% carbon footprint reduction may be obtained, throughout the world, with a "low CO2"-tailored diet including only small poultry, eggs and yogurt. Such a dietary pattern suggests easy to follow consumer guidelines for reduced carbon footprint. We report further on a number of consumer oriented questions (local or imported? organic or not? cow or goat milk? hard or soft cheese?). Our methodology may be applied to broader questions, such as the carbon footprint of proteins in general (including fish and plant proteins). We hope our work will drive more studies focusing on consumer-oriented questions.

category: ecology