title: Propranolol reduces sarcoma growth and enhances the response to anti-CTLA4 therapy by modulating the tumor microenvironment

abstract:
The nonselective beta blocker, propranolol, which for decades has been prescribed for treatment of cardiovascular conditions, has recently been used successfully to treat metastatic angiosarcoma. These results have led to an orphan drug designation by the European Medicines Agency for the treatment of soft tissue sarcomas. The anti-tumor effects of propranolol are suggested to involve the reduction of cancer cell proliferation as well as angiogenesis.

Here, we have investigated the anti-angiogenic properties of propranolol in the context of stimulating an anti-tumor immune response. We show that oral administration of propranolol delays tumor progression of MCA205 fibrosarcoma tumors and increases the survival rate of tumor bearing mice. Propranolol works by reducing tumor angiogenesis and facilitating an anti-tumoral microenvironment with increased T cell infiltration and reduced infiltration of myeloid-derived suppressor cells (MDSCs). Using T cell deficient mice, we demonstrate that the full anti-tumor effect of propranolol requires the presence of T cells. Flow cytometry-based analysis and RNA sequencing of FACS-sorted cells show that propranolol-treatment leads to an upregulation of PD-L1 on tumor-associated macrophages (TAMs) and changes in their chemokine expression profile. Lastly, we observe that the co-administration of propranolol significantly enhances the efficacy of anti-CTLA4 therapy.

Our results identify propranolol as an immune modulating agent, which can improve immune checkpoint inhibitor therapies in soft tissue sarcoma patients and potentially in other cancers.


title: The Interaction of Angiotensin II and Milk Fat Globule Epidermal Growth Factor VIII in Proinflammatory Arterial Remodeling

abstract:
BackgroundAngiotensin II (Ang II) and milk fat globule-epidermal growth factor VIII (MFG-E8) are involved in age-associated arterial remodeling; however, the inflammatory role of MFG-E8 in Ang II associated arterial remodeling with aging remains unknown.

Methods and ResultsIn this study, 30-week-old MFG-E8 knock out (KO) and age-matched wild-type (WT) mice were infused with Ang II or saline. After infusion the with Ang II, the aortic molecular, cellular, and structural remodeling were observed in mice and compared to those infused with saline, but these effects were dependent on the expression of MFG-E8: (1) In the WT mice, Ang II infusion substantially increased intimal-medial thickness, elastic lamina degradation, collagen deposition, and the proliferation of VSMCs; in contrast, in the KO mice, these effects were significantly reduced; (2) In the WT mice, Ang II treatment significantly increased the activation and expression of MMP2, TGF-{beta}1, and its downstream signaling molecule p-SMAD2, and collagen type I production, however, in the KO mice, these molecular effects were significantly reduced; (3) In the WT mice, Ang II treatment increased inflammatory p-NF-{kappa}B p65, MCP1, TNF-, ICAM1, and VCAM1 molecular expression, while conversely, in the KO mice, no significant inflammatory changes were found; (4) Importantly, compared to untreated control mice with a wide range of age from 4-96 weeks, Ang II infused "younger" mice produced an "older" arterial inflammatory phenotype, which was alleviated by MFG-E8 deficiency.

ConclusionsMFG-E8 mediates Ang II associated arterial inflammatory remodeling. Targeting MFG-E8 is a novel molecular approach to curb adverse arterial remodeling during aging and hypertension.

CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABS* Both Ang II and MFG-E8 increases are involved in proinflammatory arterial remodeling mediating the molecular, cellular and tissue events in aging and hypertension.
* MFG-E8 is essential for Ang II induced and age-associated adverse arterial remodeling via the increase of proinflammation, intimal medial thickening, elastin fragmentation, collagen deposition, and VSMC proliferation.

What Are the Clinical Implications?Since MFG-E8 mediates Ang II induced proinflammation in arterial wall remodeling in aging and hypertension, targeting MFG-E8 is a potential molecular approach to curb inflammatory arterial remodeling, maintaining the health of the vascular system during aging and hypertension.

category: pathology


title: The Inflammatory Role of Milk Fat Globule Epidermal Growth Factor VIII in Angiotensin II Induced Arterial Remodeling


title: Chronic exercise protects against the progression of renal cyst growth and dysfunction in rats with polycystic kidney disease

abstract:
IntroductionPolycystic kidney disease (PKD) is a genetic disorder characterized by the progressive enlargement of renal epithelial cysts and renal dysfunction. Previous studies have reported the beneficial effects of chronic exercise on chronic kidney disease. However, the effects of chronic exercise have not been fully examined in PKD patients or models. The effects of chronic exercise on the progression of PKD were investigated in a polycystic kidney (PCK) rat model.

MethodsSix-week-old male PCK rats were divided into a sedentary group and an exercise group. The exercise group underwent forced treadmill exercise for 12 weeks (28 m/min, 60 min/day, 5 days/week). After 12 weeks, kidney function and histology were examined, protein expressions were analyzed, and signaling cascades of PKD were examined.

ResultsChronic exercise reduced the excretion of urinary protein, liver-type fatty acid-binding protein, plasma creatinine, urea nitrogen, and increased plasma irisin and urinary arginine vasopressin (AVP) excretion. Chronic exercise also slowed renal cyst growth, glomerular damage, and interstitial fibrosis, and led to reduced Ki-67 expression. Chronic exercise had no effect on cAMP content but decreased the renal expression of B-Raf and reduced the phosphorylation of extracellular signal-regulated kinase (ERK), mammalian target of rapamycin (mTOR), and S6.

ConclusionChronic exercise slows renal cyst growth and damage in PCK rats, despite increasing AVP, with down-regulation of the cAMP/B-Raf/ERK and mTOR/S6 pathways in the kidney of PCK rats.

category: physiology


title: Value signals in orbitofrontal cortex predict economic decisions on a trial-to-trial basis

abstract: Neuroeconomics seeks to explain how neural activity contributes to decision behavior. For value-based decisions, the primate orbitofrontal cortex (OFC) is thought to have a key role; however, the mechanism by which single OFC cells contribute to choices is still unclear. Here, we show for the first time a trial-to-trial relationship between choices and population-level value representations in OFC, defined by the weighted sum of activity from many individual value-coding neurons.

category: neuroscience


title: A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing

abstract:
ObjectiveThe area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain.

MethodsUsing single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state.

ResultsOf these, 8910 are neurons that group into 30 clusters, with 4289 coming from mice fed ad libitum and 4621 from overnight fasted mice. 7124 nuclei are from non-neuronal cells, including oligodendrocytes, astrocytes and microglia. Interestingly, we identified that the oligodendrocyte population was particularly transcriptionally sensitive to an overnight fast. The receptors GLP1R, GIPR, GFRAL and CALCR, which bind GLP1, GIP, GDF15 and amylin respectively, are all expressed in the hindbrain and are major targets for anti-obesity therapeutics. We characterise the transcriptomes of these four populations and show that their gene expression profiles are not dramatically altered by an overnight fast. Notably, we find that roughly half of cells that express GIPR are oligodendrocytes. Additionally, we profile POMC expressing neurons within the hindbrain and demonstrate that 84% of POMC neurons express either PCSK1, PSCK2 or both, implying that melanocortin peptides are likely produced by these neurons.

ConclusionWe provide a detailed single-cell level characterisation of AP and NTS cells expressing receptors for key anti-obesity drugs that are either already approved for human use or are in clinical trials. This resource will help delineate the mechanisms underlying the effectiveness of these compounds, and also prove useful in the continued search for other novel therapeutic targets.


title: From synaptic activity to human in vivo quantification of neurotransmitter dynamics: a neural modelling approach

abstract:
Understanding the role of neurotransmitters glutamate and GABA during normal and abnormal brain function and under external stimulation in humans are critical neuroscientific and clinical goals. The recent development of functional 1H-Magnetic resonance spectroscopy (fMRS) has allowed us to study neuro-transmitter activity in vivo for the first time. However, the physiological basis of the observed fMRS signal remains unclear. It has been proposed that fMRS detects shifts in metabolite concentrations as they move from presynaptic vesicles, where they are largely invisible, to extracellular and cytosolic pools, where they are visible.

Here we bridge the gap between neural dynamics and fMRS by developing a mean-field model to link the neurotransmitter dynamics at the microscopic-level to the macroscopic-level imaging measurements. GABA and glutamate are described as cycling between three metabolic pools: in the vesicles; active in the cleft; or undergoing recycling in the astrocytic or neuronal cytosol. We interrogate the model by applying a current to manipulate the mean membrane potential and firing rate of the neural populations.

We find that by disregarding the contribution from the vesicular pool, our model predicts activity-dependent changes in the MRS signal, which are consistent with reported empirical findings. Further, we show that current magnitude and direction has a selective effect on the GABA/glutamate-MRS signal: inhibitory stimulation leads to reduction of both metabolites, whereas excitatory stimulation leads to increased glutamate and decreased GABA. In doing so, we link neural dynamics and fMRS and provide a mechanistic account for the activity-dependent change in the observed MRS signal.

Key Points SummaryO_LIThe recent development of functional 1H-Magnetic resonance spectroscopy (fMRS) has allowed us to study neurotransmitter activity in vivo for the first time in humans. However, the physiological basis of the observed fMRS signal is unclear.
C_LIO_LIIt has been proposed that fMRS detects shifts in metabolite concentrations as they move from presynaptic vesicles, where they are largely invisible to MRS, to extracellular and cytosolic pools, where they are visible to MRS.
C_LIO_LIWe test this hypothesis using a mean field model which links the neural dynamics of neurotransmitters at the microscopic-level to the macroscopic-level imaging measurements obtained in experimental studies.
C_LIO_LIBy disregarding activity in the vesicular pool, our model can generate activity-dependent changes in the MRS signal in response to stimulation which are consistent with experimental findings in the literature.
C_LIO_LIWe provide a mechanistic account for the activity-dependent change in observed neurotransmitter concentrations using MRS.
C_LI


title: Direct Extraction of Signal and Noise Correlations from Two-Photon Calcium Imaging of Ensemble Neuronal Activity

abstract: Neuronal activity correlations are key to understanding how populations of neurons collectively encode information. While two-photon calcium imaging has created a unique opportunity to record the activity of large populations of neurons, existing methods for inferring correlations from these data face several challenges. First, the observations of spiking activity produced by two-photon imaging are temporally blurred and noisy. Secondly, even if the spiking data were perfectly recovered via deconvolution, inferring network-level features from binary spiking data is a challenging task due to the non-linear relation of neuronal spiking to endogenous and exogenous inputs. In this work, we propose a methodology to explicitly model and directly estimate signal and noise correlations from two-photon fluorescence observations, without requiring intermediate spike deconvolution. We provide theoretical guarantees on the performance of the proposed estimator and demonstrate its utility through applications to simulated and experimentally recorded data from the mouse auditory cortex.


title: Profiling of cytokines, chemokines and growth factors in saliva and gingival crevicular fluid

abstract: In saliva and gingival crevicular fluid (GCF) soluble factors such as cytokines, chemokines and growth factors have shown a great potential serving as biomarkers for early detection and/or diagnosis of oral and systemic diseases. However, GCF and saliva, which one is a better source is still under debate. This study aimed to gain an overview of cytokines, chemokines and growth factors in saliva and GCF to pave the way for selecting suitable oral fluids for oral and systemic diseases. Multiplex cytokine assay was conducted to determine concentrations of cytokines, chemokines and growth factors in saliva and GCF samples from healthy subjects. The protocol for sample collection was carefully optimized. Stabilization, repeatability, and donor variation of the profiles were analyzed. We found that for different donors, cytokine and chemokine profiles showed unique patterns in saliva but similar patterns in GCF. In terms of growth factors, the profiles were individualized in saliva and GCF. All profiles stayed stable for the same healthy individual. In saliva, profiles of cytokines, chemokines and growth factors are individualized for different donors. In GCF, profiles of cytokines and chemokines are similar. Other factors, such as growth factors and T helper-related cytokines, are highly variable in donors. Profiles of soluble factors are not correlated in saliva and GCF. The comprehensive cytokine profiles in saliva and GCF reported in this work would serve as a good base for choosing promising cytokines for developing biomarkers in oral fluids.

category: immunology


title: Seronegative MSM at high-risk of HIV-1 acquisition show Immune quiescent profile with normal immune response against common antigens

abstract: HIV infection still represents a major public health problem worldwide, and a vaccine remains elusive. The study of HIV-exposed seronegative individuals (HESN) brings important information about the natural resistance to HIV, allows a better understanding of the infection and opens doors for new preventive and therapeutic strategies. Among HESN groups there are some men who have sex with men (MSM) with high-risk sexual behaviors, who represent an adequate cohort for the study of HESN because of their major exposure to HIV in the absence of infection. This study aimed to compare the immunological profile of Colombian seronegative MSM with different risk sexual behaviors. Sixty MSM at high-risk (n=16) and low-risk (n=44) of HIV-1 acquisition were included. No sex worker nor homozygous delta 32 mutation subjects were included. All the participants were negative for anti-HIV-1/2 antibodies and HIV-1 proviral DNA. The high-risk MSM presented a higher frequency of sexual partners in the last 3 months previous to the studys enrollment (Median 30 vs. 2), lifetime sexual partners (Median 1708 vs. 26), and unprotected anal intercourse (Median 12.5 vs. 2) than low-risk MSM. This group also showed a quiescent profile of T cells and NK cells, with a significantly lower percentage of CD4+CD38+, CD4+HLADR-CD38+, CD4+Ki67+ T cells, NKG2D+ NK cells (CD3-CD16+CD56+), a significantly higher percentage of CD4+HLADR-CD38- and a tendency to show a higher percentage of CD8+HLADR+CD38-T cells, than the low-risk group. Likewise, they showed higher mRNA levels of Serpin A1 from PBMCs. The results suggest that this cohort of MSM could be HESN individuals and their resistance would be explained by a quiescent profile of T cells and NK cells, and increased expression of Serpin A1. It is necessary to continue the study of MSM at high-risk of exposure to HIV-1 to better understand the natural resistance to HIV.


title: kinesin recruitment by adapter SKIP on melanosomes is dynamically controlled by LC3B phosphorylation

abstract:
Anterograde melanosome transport is essential for adaptive skin tanning response. However, the molecular components involved, their interplay and regulation by external cues in melanosome transport remain under-explored. Silencing of kinesin motors revealed that several members including the established KIF5B and a novel candidate KIF1B, mediate melanosome movement. The camouflage behaviour of zebrafish embryos induced by incident light or  -MSH requires kif1b, suggesting a conserved melanosome transport machinery across vertebrates. Interestingly, the peri-nuclear melanosome accumulation upon kinesin knockdown is recapitulated by the silencing of autophagy effector MAP1LC3B (LC3B). Pull-down assays identified KIF1B, but not KIF5B, to be the LC3B-associated kinesin. LC3B binds the adapter SKIP via its LIR docking region that is proximal to Thr12 residue, a site for phosphorylation by Protein Kinase A. We demonstrate that phosphorylation of LC3B at Thr12 is stimulated by -MSH, which potentiates the anterograde melanosome transport. Thereby, our study, identifies a novel kinesin motor KIF1B for melanosome movement and establishes LC3B as the key molecular component that facilitates -MSH responsive mobilization of melanosomes.

Key HighlightsO_LIKinesin screen reveals non-redundant use of KIF5B, KIF1B motors for melanosome transport
C_LIO_LIkif1b is required for camouflage response in zebrafish and melanosome movement in mammals
C_LIO_LIN-terminal region of LC3B interacts with adapter SKIP and couples kinesin KIF1B
C_LIO_LI-MSH activates PKA-mediated phosphorylation of LC3B to potentiate anterograde movement
C_LI

SignificanceMelanosomes are lysosome related organelles containing melanin pigment, that are synthesized in melanocytes and transferred to the recipient keratinocytes of skin. This involves long range melanosome movement within melanocytes to reach cell periphery for the transfer to follow. Physiologically, UV protection involves local secretion of melanocyte stimulating hormone (-MSH) that acts on melanocytes to promote skin tanning response. Herein, we investigate the components involved in this process and establish that the melanosome movement is dynamically controlled by -MSH through phosphorylation of LC3B. These findings establish the mechanism behind the rapid distribution of melanosomes during tanning response and provide opportunity to intervene for sun protection.

category: cell biology


title: Epigenetic switching outcompetes genetic mutations during adaptation to fluctuating environments

abstract: Epigenetic inheritance allows for the emergence of phenotypic plasticity in clonal populations and enables the rapid stochastic switching between distinct phenotypes. In natural environments, where stress conditions can recurrently fluctuate, clones with an epigenetic control of genes targeted by selection should be fitter than clones that rely solely on genetic mutation. To test this prediction, we engineered switcher and non-switcher yeast strains, where the uracil biosynthesis gene URA3 is under fluctuating selection. Competitions of clones with an epigenetically controlled URA3 with clones without switching ability (SIR3 knock-out), show that epigenetic switching dominates under rapidly changing stresses. We further show that this advantage depends both on the switching rate and the period of environmental fluctuations. Remarkably, epigenetic clones with a high, but not with a low, rate of switching can co-exist with non-switchers even under a constant selective pressure, consistent with different constraints on the evolution of the rate of epigenetic switching.

category: evolutionary biology


title: The pangenome of the fungal pathogen Neonectria neomacrospora

abstract:
The fungal plant pathogen Neonectria neomacrospora (C. Booth & Samuels) Mantiri & Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback in fir (Abies spp.). Although often described as a mild pathogen, foresty and phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada and one current within Northern Europe. We present key genome features of N. neomacrospora, to facilitate the research into the biology of this pathogen.

We present the first genome assembly of N. neomacrospora as well as the first pangenome within this genus. The reference genome for N. neomacrospora is a long-read sequenced Danish isolate, while the pangenome is pieced together using additional 60 short-read sequenced strains covering the known geographical distribution of the species, including Europe, North America, and China.

The gapless reference genome consist of twelve chromosomes sequenced telomere to telomere to a total length of 37.1 Mb. The mitochondrial genome was assembled and circularised with a length of 22 Kb.

The gapless nuclear genome contains a total of 11,291 annotated genes, where 642 only have a hypothetical function, and a 4.3 % repeat content. Two minor chromosomes are enriched in transposable elements, AT content, and effector candidates. Chromosome 12 segregates within the population, indicating an accessory nature. The pangenome compile 15,101 genes, 34% more genes than present in the single isolate reference genome of N. neomacrospora. These genes organise into 13,069 homologous clusters, of which 8,316 clusters are present in all analysed strains, 985 are private to single strains.

The British Columbian population branched out before the other populations and are characterized by comparatively larger genomes. The increased genome size can be explained by an expansion of repetitive elements.

The comparative analysis finds a higher number of genes with a signal peptide within N. neomacrospora and species within the genus compared to the closely related genera. A species-specific pattern is observed in the carbohydrate-active enzyme repertoire, with a reduced number of polysaccharide lyases, compared to other species within the genus. The CAZymes battery responsible for plant cell wall degradation is similar to that observed in necrotrophic and hemibiotrophic plant pathogenic fungi.

The genome size of N. neomacrospora is close to the median size for Ascomycota but is the smallest genome within the Neonectria genus. Comparative analysis revealed significant intraspecies genome size differences between populations explained by a difference in repeat content. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. Based on the field observations, we assume that N. neomacrospora is a hemibiotroph. Our analysis revealed a secretome consistent with a hemibiotrophic lifestyle.

category: genomics


title: Transmembrane Kinases are essential for plant development

abstract:
Transmembrane kinase family proteins (TMKs) have been implicated in regulating both auxin signaling and plant development. To obtain insights of the potential TMKs function in plant development, we regenerated new full sets of tmk mutants, and discovered many new phenotypes, such as defective organogenesis, smaller rosette leaves, fertility defects and selfing population defects in different combination of tmk mutants. Taken together, our results demonstrated that TMKs participated in multiple aspects of plant development, which provided a great reference for any future research.

One-sentence summaryMultiple tmk mutants analysis illustrated the key roles of TMKs in plant development.

category: plant biology


title: Extracellular matrix gene expression signatures as cell type and cell state identifiers

abstract:
Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome - that is, all genes coding for structural proteins of the extracellular matrix - for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate important aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.

HighlightsO_LICell types produce unique extracellular matrix compositions
C_LIO_LIDynamic extracellular matrix gene expression profiles hold predictive power for cell type and cell state identification
C_LI

category: systems biology


title: YAP1 Regulates the Self-organized Fate Patterning of hESCs-Derived Gastruloids

abstract: During gastrulation, the coordinated activity of BMP, WNT and NODAL signaling pathways guide the differentiation of the pluripotent epiblast into the three germinal layers. Recent studies underline the role of the Hippo-effector YAP1 regulating WNT and NODAL signaling pathways and repressing mesoendodermal differentiation in human embryonic stem cells (hESCs). However, the contribution of YAP1 to the cell-fate patterning decisions that transform the epiblast in a three-germ layer gastrula remains unknown. We address this question by analyzing micropatterned 2D-gastruloids derived from hESCs, in the presence and absence of YAP1. Our findings show that YAP1 is necessary for gastrulation. YAP1 KO-gastruloids display reduced ectoderm layer and enlarged mesoderm and endoderm layers, compared to WT. Furthermore, YAP1 regulates the self-organized patterning of the hESCs, as the discrete position of the three germ layers is altered in the YAP1 KO-gastruloids. Our epigenome (single-nuclei ATACseq) and transcriptome (RNA-seq) analysis revealed that YAP1 directly represses the chromatin accessibility and transcription of key genes in the NODAL pathway, including the NODAL and FOXH1 genes. In WT gastruloids, a gradient of NODAL: SMAD2.3 signaling from the periphery to the center of the colony regulates the exit of pluripotency toward endoderm, mesoderm and ectoderm, respectively. Hence, in the absence of YAP1, a hyperactive NODAL signaling retains SMAD2.3 in the nuclei impeding the self-organized differentiation of hESCs. Accordingly, the partial inhibition of NODAL signaling is sufficient to rescue the differentiation and pattern -defective phenotypes of the YAP1 KO gastruloids. Our work revealed that YAP1 is a master regulator of NODAL signaling, essential to instruct germ layer fate patterning in human gastruloids.

category: developmental biology


title: Cargo crowding, stationary clusters and dynamical reservoirs in axonal transport

abstract: Molecular motors drive the directed transport of presynaptic vesicles along the narrow axons of nerve cells. Stationary clusters of such vesicles are a prominent feature of axonal transport, but little is known about their physiological and functional relevance. Here, we develop a simulation model describing key features of axonal cargo transport with a view to addressing this question, benchmarking the model against our experiments in the touch neurons of C. elegans. Our simulations provide for multiple microtubule tracks and varied cargo motion states while also incorporating cargo-cargo interactions. Our model also incorporates obstacles to vesicle transport in the form of microtubule ends, stalled vesicles, and stationary mitochondria. We devise computational methodologies to simulate both axonal bleaching and axotomy, showing that our results reproduce the properties of both moving as well as stationary cargo in vivo. Increasing vesicle numbers leads to larger and more long-lived stationary clusters of vesicular cargo. Vesicle clusters are dynamically stable, explaining why they are ubiquitously seen. Modulating the rates of cargo motion-state switching allows cluster lifetimes and flux to be tuned both in simulations and experiments. We demonstrate, both in simulations and in an experimental system, that suppressing reversals leads to larger stationary vesicle clusters being formed while also reducing flux. Our simulation results support the view that the physiological significance of clusters is located in their role as dynamic reservoirs of cargo vesicles, capable of being released or sequestered on demand.

category: biophysics


title: Protocol-Dependence of Middle Cerebral Artery Dilation to Modest Hypercapnia

abstract: There is a need for improved understanding of how different cerebrovascular reactivity (CVR) protocols affect vascular cross-sectional area (CSA) when measures of vascular CSA are not feasible. In human participants, we delivered ~{+/-}4mmHg end-tidal partial pressure of CO2 (PETCO2) relative to baseline through controlled delivery, and measured changes in middle cerebral artery (MCA) cross-sectional area (CSA; magnetic resonance imaging (7 Tesla MRI)), blood velocity (transcranial Doppler and Phase contrast MRI), and calculated CVR based on steady-state versus a ramp protocol during two protocols: a 3-minute steady-state (+4mmHg PETCO2) and a ramp (delta of -3 to +4mmHg of PETCO2). We observed that 1) the MCA did not dilate during the ramp protocol, but did dilate during steady-state hypercapnia, and 2) MCA blood velocity CVR was similar between ramp and steady-state hypercapnia protocols, although calculated MCA blood flow CVR was greater during steady-state hypercapnia than during ramp, the discrepancy due to MCA CSA changes during steady-state hypercapnia. Due to the ability to achieve similar levels of MCA blood velocity CVR as steady-state hypercapnia, the lack of change in MCA cross-sectional area, and the minimal expected change in blood pressure, we propose that a ramp model, across a delta of ~-3 to +4mmHg PETCO2, may provide one alternative approach to collecting CVR measures in young adults with TCD when CSA measures are not feasible.


title: Neural Correlates of Reactivation and Vividness Reveal Separable Contributions to Objective and Subjective Measures of Episodic Memory

abstract: Episodic recollections vary in fidelity, sharpness, and strength--qualities that can be examined using both introspective judgements of mental states and objective measures of brain activity. Subjective and objective measures are both valid ways of "reading out" the content of someones internal mnemonic states, each with different strengths and weaknesses. St-Laurent and colleagues (2015) investigated the neural correlates of memory vividness ratings and neural reactivation during memory recall and found considerable overlap, suggesting common neural basis underlying these different markers of successful recollection. Here we extended this work with a much more extensive examination in which we used meta-analytic methods to pool four neuroimaging datasets in order to compare and contrast the neural substrates of neural reactivation and vividness judgements. While reactivation and vividness judgements correlated positively with one another and were associated with common univariate activity in the dorsal attention network and anterior hippocampus, some differences were also observed. Vividness judgments were tied to stronger activation in the striatum and dorsal attention network, together with suppression of default mode network nodes, and we also observed a trend for reactivation to be more closely associated with early visual cortex activity. A mediation analysis found support for the hypothesis that neural reactivation is necessary for vivid recollection, with activity in the anterior hippocampus associated with greater reactivation. Our results suggest that neural reactivation and vividness judgements reflect common recollective processing but differ in the extent to which they engage effortful, attentional processing. Additionally, the similarity between reactivation and vividness appears to arise, partly, through hippocampal processing during recollection.


title: Inhibitors of the Small Membrane (M) Protein Viroporin Prevent Zika Virus Infection

abstract:
Flaviviruses, including Zika virus (ZIKV), are a significant global health concern, yet no licensed antivirals exist to treat disease. The small M (Membrane) protein plays well-defined roles during viral egress, yet remains within virion membranes following release and maturation. However, it is unclear whether M plays a functional role in this setting. Here, we show that M forms oligomeric membrane-permeabilising channels in vitro, with increased activity at acidic pH and sensitivity to the prototypic channel-blocker, rimantadine. In turn, rimantadine blocked an early stage of ZIKV cell culture infection.

Molecular dynamics (MD) generated rationalised structure-based channel models, comprising hexameric arrangements of dual trans-membrane protomers. Interestingly, His28 protonation increased channel opening, consistent with activation within acidifying endosomes. Models contained a predicted lumenal binding site for rimantadine, as well as a second target region on the membrane-exposed periphery. In silico screening enriched for repurposed drugs/compounds predicted to bind to one or other site. Multiple hits displayed potency in vitro and in cell culture, supporting the relevance of channel models. Finally, rimantadine effectively blocked ZIKV viraemia in a preclinical model, supporting that M constitutes a physiologically relevant antiviral target, for either repurposing rimantadine, or the development of new ZIKV therapies.

category: microbiology


title: Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity

abstract:
New SARS-CoV-2 variants that have accumulated multiple mutations in the spike (S) glycoprotein enable increased transmission and resistance to neutralizing antibodies. Here, we study the antigenic and structural impacts of the S protein mutations from four variants, one that was involved in transmission between minks and humans, and three that rapidly spread in human populations and originated in the United Kingdom, Brazil or South Africa. All variants either retained or improved binding to the ACE2 receptor. The B.1.1.7 (UK) and B.1.1.28 (Brazil) spike variants showed reduced binding to neutralizing NTD and RBD antibodies, respectively, while the B.1.351 (SA) variant showed reduced binding to both NTD- and RBD-directed antibodies. Cryo-EM structural analyses revealed allosteric effects of the mutations on spike conformations and revealed mechanistic differences that either drive inter-species transmission or promotes viral escape from dominant neutralizing epitopes.

HighlightsO_LICryo-EM structures reveal changes in SARS-CoV-2 S protein during inter-species transmission or immune evasion.
C_LIO_LIAdaptation to mink resulted in increased ACE2 binding and spike destabilization.
C_LIO_LIB.1.1.7 S mutations reveal an intricate balance of stabilizing and destabilizing effects that impact receptor and antibody binding.
C_LIO_LIE484K mutation in B.1.351 and B.1.1.28 S proteins drives immune evasion by altering RBD conformation.
C_LIO_LIS protein uses different mechanisms to converge upon similar solutions for altering RBD up/down positioning.
C_LI


title: Surf4 Promotes Endoplasmic Reticulum Exit of the Lysosomal Prosaposin-Progranulin Complex

abstract: Progranulin is a lysosomal protein whose haploinsufficiency causes frontotemporal dementia while homozygous loss of progranulin causes neuronal ceroid lipofuscinosis, a lysosomal storage disease. The sensitivity of cells to progranulin deficiency raises important questions about how cells coordinate intracellular trafficking of progranulin to ensure its efficient delivery to lysosomes. In this study, we discover that progranulin interacts with prosaposin, another lysosomal protein, within the lumen of the endoplasmic reticulum (ER) and that prosaposin is required for the efficient ER exit of progranulin. Mechanistically, we identify an interaction between prosaposin and Surf4, a receptor that promotes loading of lumenal cargos into COPII coated vesicles, and establish that Surf4 is critical for the efficient export of progranulin and prosaposin from the ER. Collectively, this work demonstrates a network of interactions occurring early in the secretory pathway that promote the ER exit and subsequent lysosomal delivery of newly translated progranulin and prosaposin.


title: TNF Blockade Reduces Prostatic Hyperplasia and Inflammation while Limiting BPH Diagnosis in Patients with Autoimmune Disease

abstract:
Benign prostatic hyperplasia (BPH) is ostensibly linked to autoimmune (AI) diseases, but whether the prostate is a target of systemic inflammation associated with AI conditions is unknown. Prostatic inflammation is linked to fibrosis, hyperplasia, and reduced responses to BPH-related medical therapies. This study was conducted to determine if AI disease correlates with BPH diagnosis and whether systemic targeting of an inflammatory mediator limits prostatic inflammation and hyperplasia. Patient medical records (n=112,152) were evaluated to determine BPH prevalence among different AI diseases. Inflammatory cells from human BPH tissues were analyzed by single-cell (sc)RNA-seq and the tumor necrosis factor (TNF)-antagonist etanercept was tested in two murine models of prostatic enlargement. BPH prevalence was significantly higher among patients with AI disease compared to unaffected individuals. However, AI patients treated with TNF-antagonists had a significantly reduced incidence of BPH. Data from scRNA- seq identified macrophages as a dominant source of TNF and in vitro assays confirmed that TNF stimulates BPH-derived fibroblast proliferation. In the AI patient cohort and murine models, systemic treatment with TNF-antagonists decreased prostatic epithelial proliferation, macrophage infiltration, and epithelial NF{kappa}B activation compared to control tissues. These studies are the first to show that patients with AI diseases have a heightened susceptibility to BPH and that the TNF-signaling axis is important for BPH pathogenesis. Macrophage-secreted TNF may mechanistically drive BPH via chronic activation of the signaling axis and NF{kappa}B. TNF blockade appears to be a promising new pharmacological approach to target inflammation and suppress BPH.

One sentence summaryPatient data and mouse models suggest that repurposing tumor necrosis factor alpha blockade reduces inflammation-mediated prostatic hyperplasia.


title: Nonlinear averaging in 2D: intraspecific variation in two interacting species and consequences for population dynamics

abstract: Recent empirical and theoretical work shows that intraspecific trait variation (ITV) is prevalent and ecologically important, and should thus be taken into account in ecological models. What is lacking, however, is a comprehensive understanding of the joint effects of ITV in two interacting species (two-dimensional ITV). Here we address this gap for the cases where interspecific individual-by-individual interactions are affected by the trait values of both participants. Using nonlinear averaging in two dimensions, we show for several interaction functions how ITV affects average predation rates or competition coefficients. We develop an intuition for the direction and magnitude of this effect by using a Taylor approximation based on the local curvatures of the interaction function, the trait means, and the trait variances and covariances. We then incorporate the estimated average interaction parameters into simple competition and predator-prey models to derive the expected population-dynamic consequences. We show that two-dimensional ITV can have quantitative effects on abundances, as well as qualitative effects, such as stabilizing or destabilizing coexistence. Our approach can straightforwardly be applied to other interaction functions and dynamical systems and thus provides a valuable tool for understanding the joint effect of trait variation in two interacting species.

category: ecology


title: Intergenerational Effects of Early Life Starvation on Life-History, Consumption, and Transcriptomes of a Holometabolous Insect

abstract: Intergenerational effects, also known as parental effects in which the offspring phenotype is influenced by the parental phenotype, can occur in response to factors that occur not only in early but also in late parental life. However, little is known about how these parental life stage-specific environments interact with each other and with the offspring environment to influence offspring phenotype, particularly in organisms that realize distinct niches across ontogeny. We examined the effects of parental larval starvation and adult reproductive environment on offspring traits under matching or mismatching offspring larval starvation conditions using the holometabolous, haplo-diploid insect Athalia rosae (turnip sawfly). We show that the parental larval starvation treatment had trait-dependent intergenerational effects on both life-history and consumption traits of offspring larvae, partly in interaction with offspring conditions and sex, while there was no significant effect of parental adult reproductive environment. In addition, while offspring larval starvation led to numerous gene- and pathway-level expression differences, parental larval starvation impacted fewer genes and only the ribosomal pathway. Our findings reveal that parental starvation evokes complex intergenerational effects on offspring life-history traits, consumption patterns as well as gene expression, although the effects are less pronounced than those of offspring starvation.


title: Intergenerational Effects of Early Life Starvation on Life-History, Consumption, and Transcriptome of a Holometabolous Insect


title: Optimal immune specificity at the intersection of host life history and parasite epidemiology

abstract: Epidemiology and life history are commonly hypothesized to influence host immune strategy, and the pairwise relationships between immune strategy and each factor have been extensively investigated. But the interaction of these two is rarely considered, despite evidence that this interaction might produce emergent effects on optimal immune strategy. Here we investigate the confluence of epidemiology and life history as it affects immune strategy through a demographically-framed model of sensitivity and specificity in parasite recognition and response. We find that variation in several different life history traits associated with both reproduction and longevity alters optimal immune strategies - but the direction and magnitude of these effects depends on how epidemiological risks vary across life. Drawing on published life history data, we also find that our predictions apply across chordate taxa. Our results shed light on the complex interactions shaping immune strategy and may prove valuable in interpreting empirical results in ecoimmunology.


title: Understanding the Evolution of Nutritive Taste in Animals: Insights from Biological Stoichiometry and Nutritional Geometry

abstract: A major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na, Ca, P, N and C containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the phylogenetic distribution of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology and ecology.


title: Reevaluating claims of ecological speciation in Halichoeres bivittatus

abstract: Understanding the role of ecological processes in speciation has become one of the most active areas of research in marine population biology in recent decades. The traditional view was that allopatry was the primary driver of speciation in marine taxa, but the geography of the marine environment and the dispersal capabilities of many marine organisms render this view somewhat questionable. One of the earliest and most highly cited empirical examples of ecological speciation with gene flow in marine fishes is that of the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep north-south divergence in a single mitochondrial locus, combined with a finding that these two haplotypes were associated with different habitat types in the Florida Keys and Bermuda, where they overlap. Here we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study, and find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations. These results severely undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. We argue that future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.


title: Two distinct mechanisms underlie dosage sensitivity in Pumilio1-associated diseases

abstract: Mutations in the RNA-binding protein (RBP) Pumilio1 (PUM1) can cause dramatically different phenotypes. Mild mutations that reduce PUM1 levels by 25% lead to a mild, adult-onset ataxia, whereas more severe mutations that reduce PUM1 levels 40-60% produce an infantile syndrome involving multiple developmental delays and seizures. Why this difference in expression should cause such different phenotypes has been unclear; known PUM1 targets are de-repressed to equal degrees in both diseases. We therefore sought to identify PUM1s protein partners in the murine brain. We identified a number of putative interactors involved in different aspects of RNA metabolism such as silencing, alternative splicing, and polyadenylation. We find that PUM1 haploinsufficiency alters the stability of several interactors and disrupts the regulation of targets of those interactors, whereas mild PUM1 loss only de-represses PUM1-specific targets. We validated these phenomena in patient-derived cell lines and show that normalizing PUM1 levels rescues the levels of interactors and their targets. We therefore propose that dosage sensitivity does not necessarily reflect a linear change in levels but can involve distinct mechanisms. Studying the interactors of RBPs in vivo will be necessary to understand their functions in neurological diseases.

category: genetics


title: Dosage sensitivity in Pumilio1-associated diseases involves two distinct mechanisms


title: Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

abstract:
BackgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.

ResultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.

ConclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.


title: Deep learning from phylogenies to uncover the transmission dynamics of epidemics

abstract: Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep.

category: bioinformatics


title: Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks


title: Guidance for RNA-seq co-expression estimates: the importance of data normalization, batch effects, and correlation measures

abstract:
MotivationGene co-expression analysis is an attractive tool for leveraging enormous amounts of public RNA-seq datasets for the prediction of gene functions and regulatory mechanisms. However, the optimal data processing steps for the accurate prediction of gene co-expression from such large datasets remain unclear. Especially the importance of batch effect correction is understudied.

ResultsWe processed RNA-seq data of 68 human and 76 mouse cell types and tissues using 50 different workflows into 7,200 genome-wide gene co-expression networks. We then conducted a systematic analysis of the factors that result in high-quality co-expression predictions, focusing on normalization, batch effect correction, and measure of correlation. We confirmed the key importance of high sample counts for high-quality predictions. However, choosing a suitable normalization approach and applying batch effect correction can further improve the quality of co-expression estimates, equivalent to a >80% and >40% increase in samples. In larger datasets, batch effect removal was equivalent to a more than doubling of the sample size. Finally, Pearson correlation appears more suitable than Spearman correlation, except for smaller datasets.

ConclusionA key point for accurate prediction of gene co-expression is the collection of many samples. However, paying attention to data normalization, batch effects, and the measure of correlation can significantly improve the quality of co-expression estimates.


title: Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data


title: Refget: standardised access to reference sequences

abstract: Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself. We present four reference implementations across in-house and cloud infrastructure, a compliance suite and a web report used to ensure specification conformity across implementations. https://w3id.org/ga4gh/refget.


title: Relevance of Circulating Hybrid Cells as a Non-Invasive Biomarker for Myriad Solid Tumors

abstract:
AbstractMetastatic progression defines the final stages of tumor evolution and underlies the majority of cancer-related deaths. The heterogeneity in disseminated tumor cell populations capable of seeding and growing in distant organ sites contributes to the development of treatment resistant disease. We recently reported the identification of a novel tumor-derived cell population, circulating hybrid cells (CHCs), harboring attributes from both macrophages and neoplastic cells, including functional characteristics important to metastatic spread. These disseminated hybrids outnumber conventionally defined circulating tumor cells (CTCs) in cancer patients. It is unknown if CHCs represent a generalized cancer mechanism for cell dissemination, or if this population is relevant to the metastatic cascade. Herein, we detect CHCs in the peripheral blood of patients with cancer in myriad disease sites encompassing epithelial and non-epithelial malignancies. Further, we demonstrate that in vivo-derived hybrid cells harbor tumor-initiating capacity in murine cancer models and that CHCs from human breast cancer patients express stem cell antigens, features consistent with the ability to seed and grow at metastatic sites. Finally, we reveal heterogeneity of CHC phenotypes reflect key tumor features, including oncogenic mutations and functional protein expression. Importantly, this novel population of disseminated neoplastic cells opens a new area in cancer biology and renewed opportunity for battling metastatic disease.

Simple SummaryThere is an incomplete understanding of circulating neoplastic cell populations and the fundamental mechanisms that drive dissemination, immune evasion, and growth --all critical information to more effectively prevent and treat cancer progression. A novel disseminated tumor cell population, circulating hybrid cells, are detected across many cancer types and carry functional tumor-initiating properties. Additionally, circulating hybrid cells are found at significantly higher levels than conventionally defined circulating tumor cells. Our study demonstrates that neoplastic hybrid cells harbor phenotypic and genetic characteristics of tumor and immune cells, display stem features, and are a generalizable phenomenon in solid tumors. Circulating hybrid cells therefore have relevance as a novel biomarker and open a new field of study in malignancy.

category: cancer biology


title: Whole-organism 3D Quantitative Characterization of Zebrafish Melanin by Silver Deposition Micro-CT

abstract: Melanin-rich zebrafish melanophores are used to study pigment development, human skin color, and as a large-scale screening phenotype. To facilitate more detailed whole-body, computational analyses of melanin content and morphology, we have combined X-ray microtomography (micro-CT), a non-destructive, full-volume imaging modality, with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, for both dramatic and subtle phenotypes not previously described. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, three-dimensional computational phenomic analysis of a particular cell type at cellular resolution, with potential applications in other model organisms and human melanoma biopsies. Whole-organism, high-resolution phenotyping is a challenging ideal, but provides superior context for functional studies of mutations, diseases, and environmental influences.


title: Adipocyte Tribbles1 Regulates Plasma Adiponectin and Plasma Lipids in Mice

abstract: Multiple GWAS have identified SNPs in the 8q24 locus near the TRIB1 gene that significantly associate with plasma lipids and coronary artery disease. While subsequent studies have uncovered roles for hepatic and myeloid Trib1 in contributing to either plasma lipids or atherosclerosis, the causal tissue for these GWAS associations remains unclear. The same 8q24 SNPs significantly associate with plasma adiponectin levels in humans as well, suggesting a role for TRIB1 in adipose tissue. Here, we report that adipocyte-specific Trib1 knockout mice (Trib1_ASKO) have increased plasma adiponectin levels and decreased plasma cholesterol and triglycerides. We demonstrate that loss of Trib1 increases adipocyte production and secretion of adiponectin independent of the known TRIB1 function of regulating proteasomal degradation. RNA-seq analysis of adipocytes and livers from Trib1_ASKO mice suggests that alterations in adipocyte function underlie the plasma lipid changes observed in these mice. Secretomics and RNA-seq analysis revealed that Trib1_ASKO mice have increased production of Lpl and decreased production of Angptl4 in adipose tissue, and fluorescent substrate assays confirm an increase in adipose tissue Lpl activity, which likely underlies the observed triglyceride phenotype. In summary, we demonstrate here a novel role for adipocyte Trib1 in regulating plasma adiponectin, total cholesterol, and triglycerides in mice, confirming previous genetic associations observed in humans and providing a novel avenue through which Trib1 regulates plasma lipids and coronary artery disease.


title: Embryo development in Carica papaya Linn

abstract: Papaya (Carica papaya Linn.) is a tropical plant whose draft genome has been sequenced. Papaya produces large fruits rich in vitamins A and C and is an important cash crop in developing countries. Nonetheless, little is known about how the female gametophyte develops, how it is fertilized and how it develops into a mature seed containing an embryo and an endosperm. The Papaya female gametophyte displays a Polygonum-type architecture consisting of two synergid cells, an egg cell, a central cell, and three antipodal cells. Reports are available of the presumed existence of varieties in which cross fertilization is bypassed and autonomous development of embryos occurs (e.g., apomixis). In this study, we analyzed the development of female gametophytes in a commercial Hawaiian parental line and in the presumed apomictic Costa Rican line L1. Samples were collected before and after anthesis to compare the overall structure, size and transcriptional patterns of several genes that may be involved in egg and endosperm cell fate and proliferation. These genes were the putative papaya homologs of ARGONAUTE9 (AGO9), MEDEA (MEA), RETINOBLASTOMA RELATED-1 (RBR1), and SLOW WALKER-1 (SWA1). Our results suggest that its feasibly to identify structural features of Polygonum-type development, and that in bagged female flowers of line L1 we might have observed autonomous development of embryo-like structures. Possible downregulation of papaya homologs for AGO9, MEA, RBR1 and SWA1 was observed in embryo sacs from line L1 before and after anthesis, which may suggest a link between suspected apomixis and transcriptional downregulation of genes for RNA-directed DNA methylation, histone remodelers, and rRNA processing. Most notably, the large size of the papaya embryo sac suggests that it could be a cytological alternative to Arabidopsis thaliana for study. Significant variation in embryo sac size was observed between the varieties under study, suggesting wide differences in the genetic regulation of anatomical features.


title: Embryo development in Carica papaya Linn.


title: Effects of long-term high-temperature stress on reproductive growth and seed development in development in Brassica napus

abstract:
Brassica napus is the second most important oilseed crop worldwide. Increasing average temperatures and extreme weather have a severe impact on rapeseed yield. We determined the response of three cultivars to different temperature regimes (21/18 {degrees}C, 28/18 {degrees}C and 34/18 {degrees}C), focusing on the plant appearance, seed yield, seed quality, seed viability, and embryo development. Our microscopic observations identified that embryo development is affected by high temperatures. We noticed an acceleration of its development, in addition to pattern defects. Reduced fertilization rate, increased abortion rate, and preharvest sprouting would be responsible for the low seed yield at the high-temperature regime. Hormone profiling indicates that reduced auxin levels in young seeds may cause the observed embryo pattern defects. Moreover, reduced seed dormancy may result from low ABA and IAA levels in mature seeds. Glucosinolates and oil composition measurements suggest reduced seed quality. These identified cues help understand seed thermomorphogenesis and pave the way to the development of thermoresilient rapeseed plants.

HighlightBrassica napus flowering plants growth at high temperatures accelerates embryo development, causing a high seed abortion rate and reduced seed quality. Temperature-reduced ABA levels cause premature seed sprouting.


title: Examination of the contribution of Nav1.7 to axonal propagation in nociceptors

abstract:
Nav1.7 is a promising drug target for the treatment of pain because individuals with Nav1.7 loss-of-function mutations are insensitive to pain and do not have other serious neurological deficits. However, current peripherally restricted Nav1.7 inhibitors have not performed well in clinical pain trials, which may reflect a lack of understanding of the function of Nav1.7 in the transmission of nociceptive information. Although numerous studies have reported that Nav1.7 has a moderate role in peripheral transduction, the precise contribution of Nav1.7 to axonal propagation in nociceptors is not clearly defined, particularly for afferents innervating deep structures.

In this study, we examined the contribution of Nav1.7 to axonal propagation in nociceptors utilising sodium channel blockers in in vivo electrophysiological and calcium imaging recordings from L4 in the mouse. Using the sodium channel blocker TTX (1-10M) to inhibit Nav1.7 and other TTX-S sodium channels along the sciatic nerve, we first showed that around 2/3rds of nociceptive neurons innervating the skin, but a lower proportion innervating the muscle (45%), are blocked by TTX. In contrast, nearly all large-sized A-fibre cutaneous afferents (95-100%) were blocked by axonal TTX. Characterisation of TTX resistant cutaneous nociceptors revealed that many were polymodal (57%) and capsaicin sensitive (57%).

Next, we examined the role of Nav1.7 in axonal propagation in nociceptive neurons by applying the selective channel blocker PF-05198007 (300nM-1M) to the sciatic nerve between stimulating and recording sites. 100-300nM PF-05198007 blocked propagation in 63% of C-fibre sensory neurons, whereas similar concentrations did not affect propagation in rapidly conducting A-fibre neurons. We conclude that Nav1.7 has an essential contribution to axonal propagation in only around 2/3rds of nociceptive C-fibre neurons, and a lower proportion ([≤]45%) of nociceptive neurons innervating muscle.


title: PBN-PVT projection modulates negative emotions in mice

abstract: Long-lasting negative affections dampen enthusiasm for life, and dealing with negative affective states is essential for individual survival. The parabrachial nucleus (PBN) and the thalamic paraventricular nucleus (PVT) are critical for modulating affective states in mice. However, the functional role of the PBN-PVT projection in modulating affective states remains elusive. Here, we show that the PBN neurons send dense projection fibers to the PVT and form direct excitatory synapses with the PVT neurons. Activation of the PBN-PVT projection or PVT-projecting PBN neurons induces robust anxiety-like, aversion-like, and fear-like behaviors without affecting nociceptive behaviors. Inhibition of the PBN-PVT projection or PVT-projecting PBN neurons reduces fear-like and aversion-like behaviors. Furthermore, the PVT neurons innervated by the PBN are activated by aversive stimulation, and activation of PBN-PVT projection enhances the neuronal activity of PVT neurons in response to the aversive stimulus. Activation of these downstream PVT neurons induces anxiety-like behavior behaviors. Thus, our study indicates that the PBN-PVT projection modulates negative affective states in mice.


title: PBN-PVT projection modulates negative affective states in mice


title: A cell-ECM mechanism for connecting the ipsilateral eye to the brain

abstract:
Information about features in the visual world are parsed by circuits in the retina and are then transmitted to the brain by distinct subtypes of retinal ganglion cells (RGCs). Axons from RGC subtypes are stratified in retinorecipient brain nuclei, such as the superior colliculus (SC), to provide a segregated relay of parallel and feature-specific visual streams. Here, we sought to identify the molecular mechanisms that direct the stereotyped laminar targeting of these axons. We focused on ipsilateral-projecting subtypes of RGCs (ipsiRGCs) whose axons target a deep SC sublamina. We identified an extracellular glycoprotein, Nephronectin (NPNT), whose expression is restricted to this ipsiRGC-targeted sublamina. SC-derived NPNT and integrin receptors generated by ipsiRGCs are both required for the targeting of ipsiRGC axons to the deep sublamina of SC. Thus, a cell-extracellular matrix (ECM) recognition mechanism specifies precise laminar targeting of ipsiRGC axons and the assembly of eye-specific parallel visual pathways.

Significance StatementDistinct features of the visual world are transmitted from the retina to the brain through anatomically segregated circuits. Despite this being an organizing principle of visual pathways in mammals, we lack an understanding of the signaling mechanisms guiding axons of different types of retinal neurons into segregated layers of brain regions. We explore this question by identifying how axons from the ipsilateral retina innervate a specific lamina of the superior colliculus. Our studies reveal a unique cell-extracellular matrix (ECM) recognition mechanism that specifies precise targeting of these axons to the superior colliculus. Loss of this mechanism not only resulted in the absence of this eye-specific visual circuit, but it led to an impairment of innate predatory visual behavior as well.


title: Central tendency biases must be accounted for to consistently capture Bayesian cue combination in continuous response data

abstract: Observers in perceptual tasks are often reported to combine multiple sensory cues in a weighted average that improves precision - in some studies, approaching statistically-optimal (Bayesian) weighting, but in others departing from optimality, or not benefitting from combined cues at all. To correctly conclude which combination rules observers use, it is crucial to have accurate measures of their sensory precision and cue weighting. Here, we present a new approach for accurately recovering these parameters in perceptual tasks with continuous responses. Continuous responses have many advantages, but are susceptible to a central tendency bias, where responses are biased towards the central stimulus value. We show such biases lead to inaccuracies in estimating both precision gains and cue weightings, two key measures used to assess sensory cue combination. We introduce a method that estimates sensory precision by regressing continuous responses on targets and dividing the variance of the residuals by the squared slope of the regression line, "correcting-out" the error introduced by the central bias and increasing statistical power. We also suggest a complementary analysis that recovers the sensory cue weights. Using both simulations and empirical data, we show that the proposed methods can accurately estimate sensory precision and cue weightings in the presence of central tendency biases. We conclude that central tendency biases should be (and can easily be) accounted for to consistently capture Bayesian cue combination in continuous response data.


title: Nicotinamide riboside alleviates Parkinson's disease symptoms but downregulates dopamine metabolism upon lactacystin-induced proteostasis failure

abstract: Activation of mitochondrial metabolism and proteostasis with the NAD+ precursor nicotinamide riboside (NR) has emerged as a potential therapeutic approach for neurodegenerative disorders including Parkinsons disease (PD). However, despite recently started clinical trials, studies on NR in animal models of PD are scarce. In this study, we investigated the effect of NR in multiple models of PD. In transgenic C. elegans overexpressing -synuclein, a protein of which aggregation is believed to promote PD, NR rescued PD-like phenotypes including mitochondrial dysfunction and motility defects, decreased oxidative stress, and age-related dopamine (DA) neuron loss. We found that NR eased symptoms of disease by activating the mitochondrial unfolded protein response (UPRmt) via the transcription factor atfs-1. Similarly, in a proteasome inhibitor, lactacystin, -induced mouse model of PD, NR rescued mitochondrial dysfunction and behavioural deficits caused by lactacystin lesion. However, long-term NR supplementation, in conjunction with proteasome inhibition, resulted in decreased DA levels in both the lesioned and unlesioned sides of the substantia nigra with concomitant downregulation of key genes in DA metabolism. Our results suggest specific endpoints that should be monitored in ongoing NR clinical trials.


title: Baseline power of theta oscillations predicts mystical-type experiences induced by DMT

abstract: N,N-Dimethyltryptamine (DMT) is a classic psychedelic capable of inducing short-lasting but profound changes in consciousness. As with other psychedelics, the experience induced by DMT strongly depends upon contextual factors, yet the neurobiological determinants of this variability remain unknown. We combined wireless electroencephalography and source imaging to map changes in neural oscillations elicited by inhaled DMT. Furthermore, we found that the power of frontal and temporal theta oscillations was inversely correlated with scales indexing feelings of unity and transcendence, which are an integral part of the phenomenology of mystical-type experiences. Finally, we established the robustness of these results using a machine learning model for regression trained and tested following a cross-validation procedure. Our results are consistent with the observation that the state of mind prior to consuming a psychedelic drug influences the ensuing subjective experience of the user. We also suggest that priming subjects to reduce their theta power before administration of a serotonergic psychedelic could enhance the likelihood of inducing mystical-type experiences, leading to sustained positive effects in well-being and improving the outcome of therapeutic interventions.


title: When shared concept cells support associations: theory of overlapping memory engrams

abstract:
Assemblies of neurons, called concepts cells, encode acquired concepts in human Medial Temporal Lobe. Those concept cells that are shared between two assemblies have been hypothesized to encode associations between concepts. Here we test this hypothesis in a computational model of attractor neural networks. We find that for concepts encoded in sparse neural assemblies there is a minimal fraction cmin of neurons shared between assemblies below which associations cannot be reliably implemented; and a maximal fraction cmax of shared neurons above which single concepts can no longer be retrieved. In the presence of a periodically modulated background signal, such as hippocampal oscillations, recall takes the form of association chains reminiscent of those postulated by theories of free recall of words. Predictions of an iterative overlap-generating model match experimental data on the number of concepts to which a neuron responds.

Authors contributionsAll authors contributed to conception of the study and writing of the manuscript. CG and TS developed the theory. CG wrote the code for all figures. EDF and RQQ provided the experimental data. EDF and CG analyzed the data. WG and CG developed algorithms to fit the experimental data.


title: Impairing one sensory modality enhances another by reprogramming peptidergic circuits in Caenorhabditis elegans

abstract: Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. To probe these mechanisms, we perform a forward genetic screen for mutants with enhanced O2 perception in C. elegans. Multiple mutants exhibiting increased responsiveness to O2 concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL chemosensory neurons. We find that ADLs responsiveness to pre-synaptic input from O2- sensing neurons is heightened in qui-1 and other sensory defective mutants resulting in an enhanced neurosecretion. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling of ADL neurons indicates its acquired O2-evoked neurosecretion is the result of a transcriptional reprogramming that up-regulates neuropeptide signalling. We show that the conserved neuropeptide receptor NPR-22 is necessary and sufficient in ADL to enhance its neurosecretion levels. Sensory loss can thus confer cross-modal plasticity by re-wiring peptidergic circuits.


title: THINGSvision: a Python toolbox for streamlining the extraction of activations from deep neural networks

abstract: Over the past decade, deep neural network (DNN) models have received a lot of attention due to their near-human object classification performance and their excellent prediction of signals recorded from biological visual systems. To better understand the function of these networks and relate them to hypotheses about brain activity and behavior, researchers need to extract the activations to images across different DNN layers. The abundance of different DNN variants, however, can often be unwieldy, and the task of extracting DNN activations from different layers may be non-trivial and error-prone for someone without a strong computational background. Thus, researchers in the fields of cognitive science and computational neuroscience would benefit from a library or package that supports a user in the extraction task. THINGSvision is a new Python module that aims at closing this gap by providing a simple and unified tool for extracting layer activations for a wide range of pretrained and randomly-initialized neural network architectures, even for users with little to no programming experience. We demonstrate the general utility of THINGsvision by relating extracted DNN activations to a number of functional MRI and behavioral datasets using representational similarity analysis, which can be performed as an integral part of the toolbox. Together, THINGSvision enables researchers across diverse fields to extract features in a streamlined manner for their custom image dataset, thereby improving the ease of relating DNNs, brain activity, and behavior, and improving the reproducibility of findings in these research fields.


title: Egocentric Asymmetric Coding in Sensory Cortical Border Cells

abstract:
Both egocentric and allocentric representations of space are essential to spatial navigation. Although some studies of egocentric coding have been conducted within and around the hippocampal formation, externally anchored egocentric spatial representations have not yet been fully explored. Here we record and identify two subtypes of border cell in the rat primary somatosensory cortex (S1) and secondary visual cortex (V2). Subpopulations of S1 and V2 border cells exhibit rotation-selective asymmetric firing fields in an either clockwise (CW) or counterclockwise (CCW) manner. CW- and CCW-border cells increase their firing rates when animals move unidirectionally along environmental border(s). We demonstrate that both CW- and CCW-border cells fire in an egocentric reference frame relative to environmental borders, maintain preferred directional tunings in rotated, stretched, dark as well as novel arenas, and switch their directional firings in the presence of multi-layer concentric enclosures. These findings may provide rotation-selective egocentric reference frames within a larger spatial navigation system, and point to a common computational principle of spatial coding shared by multiple sensory cortical areas.

HighlightsO_LIEgocentric border cells are present in rat S1 and V2
C_LIO_LISubtypes of border cells display egocentric asymmetric coding
C_LIO_LIEgocentric and allocentric streams coexist in sensory cortices
C_LIO_LIRotation-selective asymmetric firing is robust with environmental manipulations
C_LI


title: Ras guanine nucleotide exchange factor RasGRP1 promotes acute inflammatory response and restricts inflammation-contributed cancer cell growth

abstract: Acute inflammatory response needs to be tightly regulated for promoting the elimination of pathogens and preveting the risk of tumorigenesis, but the mechanism has not been fully elucidated. Here, we report that Ras guanine nucleotide releasing protein 1 (RasGRP1) plays a bifunctional regulator that promotes acute inflammation and inhibits inflammation-associated cancer. At the mRNA level, RasGRP1 strengthens the inflammatory response by functioning as a competing endogenous RNA to specifically promote IL-6 expression by sponging let-7a. In vivo overexpression of the RasGRP1 3 untranslated region significantly aggravated lipopolysaccharide-induced systemic inflammation and dextran sulphate sodium-induced colitis in IL-6+/+ mice but not in IL-6-/- mice. At the protein level, RasGRP1 restricts the growth of inflammation-contributed cancer cells by impairing EGFR-SOS1-Ras-AKT signalling. Tumour patients with high RasGRP1 expression showed a better clinical outcome than those with low expression. Considering acute inflammation rarely leads to tumorigenesis, this work reveals that RasGRP1 is an essential bifunctional regulator for acute inflammatory response.


title: NCoR1 and SMRT fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling

abstract: Dendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT (NCoR2) enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4+ and CD8+ T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic and transcriptomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion represses mTOR-STAT3-IL10 signaling in cDC1 by downregulating NR4A1. Besides, Nfkbia and Socs3 were down-regulated in Ncor2 (Smrt) knockdown cDC1, supporting increased production of inflammatory cytokines. Moreover, studies in mice showed, adoptive transfer of SMRT knockdown cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8+ T-cell frequency, respectively. We also depicted decreased Ncor2 expression in Rheumatoid Arthritis, a Th1/Th17 disease.


title: Measurement of Volatile Compounds for Real-time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

abstract: Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.


title: The role of copper resistance in Mycobacterium tuberculosis pathogenesis

abstract:
Despite the development of new drugs and social interventions, tuberculosis remains a leading cause of mortality. This burden falls disproportionately on developing countries, particularly those where the incidence of HIV is high. In the Western Cape, South Africa, we have identified and isolated two Beijing family strains of Mycobacterium tuberculosis that, despite few differences at a genomic level, differ greatly in their severity of disease caused, providing an opportunity to study virulence in this organism. The aim of this study was to identify differences at a genomic and transcriptomic level that may identify the cause of the different virulence levels observed in the two isolates.

The isolates were compared at the transcriptome level under four different growth conditions including oxidative stress. In comparing the transcriptome of the two isolates, an operon containing genes involved in the production of molybdenum cofactor that showed consistently lower levels of expression in the hypervirulent isolate was identified. A copper sensing transcriptional regulator was identified as the most probable regulator, and we found that the Cso operon which it is known to regulate was similarly differentially expressed in the strains.

The production of molybdenum cofactor is effected in two ways by copper levels. Through the independent insertion of copper into molybdopterin (MPT), and destabilisation of Fe-S clusters. As MoaA3 contains a Fe-S cluster that is known to be destabilised by copper, and a number of copper sensitive genes are likewise found differentially expressed, it is likely that the strains differ in terms of their levels of resistance to copper.

It is therefore hypothesised that the differences in virulence are as a result of different levels of resistance to phagosome copper overload, and the mechanism by which copper levels are linked to the production of molybdenum cofactor is described.

Author summaryIn this article, we describe the differences in gene expression of two closely related strains of Mycobacterium tuberculosis isolated in the Western Cape of South Africa that differ in the severity of disease that they cause. We compared the strains at a genomic and transcriptomic level, and in doing so, we discovered a set of molybdenum cofactor genes regulated by a copper sensing transcription factor that came up in all datasets. Further genes linked to copper response were identified, providing greater evidence that the difference between the two strains was the manner in which they responded to copper stress. Phagocytes are known to exploit high levels of copper to kill intracellular bacteria, suggesting an important link between copper and disease. We conclude that resistance to copper toxicity is the most probable reason for the relative increase in virulence, and describe the regulatory relationship between copper levels and molybdenum cofactor synthesis.


title: Structure of human Mediator-RNA polymerase II transcription pre-initiation complex

abstract: Mediator is a conserved coactivator that enables regulated transcription initiation from eukaryotic protein-coding genes1-3. Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate RNA polymerase II (Pol II) phosphorylation and promoter escape1-6. Here we prepare a 20-subunit recombinant human Mediator, reconstitute a 50-subunit Mediator-PIC complex, and resolve the complex structure by cryo-EM at an overall resolution of 4.5 [A]. Mediator binds with its head module to the Pol II stalk and the general transcription factors TFIIB and TFIIE, resembling the Mediator-PIC interactions in the corresponding yeast complex7-9. One end of Mediator contains the metazoan-specific subunits MED27-MED30, which associate with exposed regions in MED14 and MED17 to form the proximal part of the tail module that binds activators. The opposite end of Mediator positions the flexibly linked CDK-activating kinase (CAK) of the general transcription factor TFIIH near the C-terminal repeat domain (CTD) of Pol II. The Mediator shoulder domain holds the CAK subunit CDK7, whereas the hook domain contacts a CDK7 element that flanks the kinase active site. The shoulder and hook reside in the Mediator head and middle modules, respectively, which can move relative to each other and may induce an active conformation of CDK7 to allosterically stimulate CTD phosphorylation and Pol II escape from the promoter.

category: molecular biology


title: Temperature and O2, but not CO2, interact to affect aerobic performance of European sea bass (Dicentrarchus labrax)

abstract: Climate change causes warming, decreased O2, and increased CO2 in marine systems and responses of organisms will depend on interactive effects between these factors. We provide the first experimental assessment of the interactive effects of warming (14 to 22{degrees}C), reduced O2 ([~]3 - 21 kPa O2), and increased CO2 ([~]400 or [~]1000 {micro}atm ambient CO2) on four indicators of aerobic performance (standard metabolic rate, SMR, maximum metabolic rate, MMR, aerobic scope, and hypoxia tolerance, O2crit), blood chemistry, and O2 transport (P50) of a marine fish, the European sea bass (Dicentrarchus labrax). Warming increased SMR and O2crit (i.e. reduced hypoxia tolerance) as well as MMR in normoxia but there was an interactive effect with O2 so that hypoxia caused larger reductions in MMR and aerobic scope at higher temperatures. Increasing CO2 had minimal effects on SMR, MMR and O2crit and did not show interactive effects with temperature or O2 for any measured variables. Aerobic performance was not linked to changes in blood chemistry or P50. Despite lack of effects of CO2 on aerobic performance, increased CO2 induced 30% mortality of fish exercised in low O2 at 22{degrees}C indicating important threshold effects independent of aerobic performance. Overall, our results show temperature and O2, but not CO2, interact to affect aerobic performance of sea bass, disagreeing with predictions of the oxygen- and capacity-limited thermal tolerance hypothesis.


title: Niche shifts and hybridization in two Amazona parrot sister-species introduced to Southern California

abstract: This paper has been withdrawn by the authors while evaluating reviewer concerns about interpretation of the genomic data and due to errors found by the authors in the scoring of photos. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.


title: Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes.

abstract:
O_LIWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes.
C_LIO_LIHere, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector.
C_LIO_LIWe identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation.
C_LIO_LIHere we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y.
C_LI


title: Evolutionary trajectories of three independent neo-sex chromosomes in Drosophila

abstract: Dosage compensation (DC) on the X chromosome is a mechanism to counteract the deleterious effects by gene loss from the Y chromosome. However, DC cannot work efficiently if the X chromosome also degenerates. This indeed occurs in the neo-sex chromosomes in Drosophila miranda, where neo-X as well as neo-Y chromosomes are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that independently emerged in D. albomicans and D. americana and compared their evolutionary processes with that in D. miranda. Comparative genomic and transcriptomic analyses revealed that the pseudogenization rate on neo-X is also accelerated in the two species (though lesser extent in D. americana). We also found that neo-X-linked genes whose neo-Y homologs are pseudogenized tend to be upregulated more stringently than those whose neo-Y homologs remain functional. Moreover, the genes under strong functional constraints and highly expressed in the testis tended to remain functional on neo-X and neo-Y, respectively. Focusing on the D. miranda and D. albomicans neo-sex chromosomes that independently emerged from the same autosome, we further found that the same genes tend to have been pseudogenized in parallel on neo-Y. Those genes include Idgf6 and JhI-26 whose functions seem to be unnecessary or could be even harmful for males. These results indicate that neo-sex chromosomes in Drosophila share a common evolutionary trajectory after their emergence, which may be applicable to other sex chromosomes in a variety of organisms to avoid being an evolutionary dead-end.


title: DNA Preparation In Vitis vinifera L. For Third Generation Sequencing

abstract:
BackgroundThere have been several attempts to sequence the genome of Vitis vinifera L. (grapevine), utilizing low-resolution second-generation platforms. Nevertheless, the characterization of the grapevine genetic resources and its adaptation to vulnerable conditions could be better addressed through extensive and high-resolution genome sequencing.

MinION is a third-generation sequencer preferred by many laboratories due to its relatively low cost, ease of use and small size. Even though this long-read technology has been rapidly improving, to reach its full potential requires high-quality DNA.

ResultsHere we establish a workflow for DNA extraction suitable for MinION sequencing long reads from grapevine. This protocol was tested with leaf samples from different positions on annual growing branches of grapevine, Purified nuclei from fresh young leaves that led to high quality, long DNA fragments, suitable for long-read sequencing were successfully generated. It is evident that longer reads in grapevine associate with both fresh tissue and adjusted conditions used for nuclei purification.

ConclusionsWe propose that this workflow presents a significant advancement for long-read quality DNA isolation for grapevine and likely other plant species.