title: Dynamics of Aedes albopictus invasion. Insights from a spatio-temporal model

abstract: France displays a latitudinal range for the expansion of Aedes albopictus invasive populations that is not yet completely colonized providing a critical opportunity to address key invasion processes. We propose a spatio-temporal model (DISTIGRI) to describe and predict current and future expansion at both intra- and inter-annual scales of A. albopictus. This process-based model integrates mechanistic descriptions of the developmental cycle and the dispersal process of A. albopictus within a reaction-diffusion framework, depending on climatic suitability and photoperiod with a high spatio-temporal resolution. Using this model coupled with a climatic database, we propose several maps describing the current intra-annual distribution of A. albopictus, including the date of first emergence and the length of the period with significant adult presence. We also compute its future distribution over the next 10 years under several climatic scenarios, which shows a range expansion with a strong dependence on the climatic scenario. The outputs of the model may constitute a valuable asset for designing control and avoidance strategies, and to anticipate the biting nuisance with a high spatio-temporal resolution. These outputs also emphasize the importance of taking both dispersal and life cycle into account to obtain accurate descriptions of out-of-equilibrium processes such as ongoing invasions.


title: A report on a characteristic vocalization in Corvus macrorhynchos osai with an indication of vocal learning

abstract: In the process of vocal learning, animals give immature vocalization, such as babbling and subsong. Here I report a characteristic vocalization given by a subspecies of large-billed crow, Corvus macrorhynchos osai, that live in Kuroshima Island, Okinawa, Japan. This vocalization (type-K) is characterized by very rapid bill movements (ca. 13 times/sec). The type-K was heard throughout the island, indicating that the population of the Kuroshima Island share this call type. In addition, a juvenile crow was observed giving immature type-K repeatedly. This observation suggests that this call type is not innate but acquired through vocal learning.

category: animal behavior and cognition


title: Functional Communication between IP3R and STIM2 at sub-threshold stimuli is a critical checkpoint for initiation of SOCE

abstract:
Stromal interaction molecules, STIM1 and STIM2, sense decreases in the endoplasmic reticulum (ER) [Ca2+] ([Ca2+]ER) and cluster in ER-plasma membrane (ER-PM) junctions where they recruit and activate Orai1. While STIM1 responds when [Ca2+]ER is relatively low, STIM2 displays constitutive clustering in the junctions and is suggested to regulate basal Ca2+ entry. The cellular cues that determine STIM2 clustering under basal conditions is not known. By using gene editing to fluorescently tag endogenous STIM2, we report that endogenous STIM2 is constitutively localized in mobile and immobile clusters. The latter associate with ER-PM junctions and recruit Orai1 under basal conditions. Agonist stimulation increases immobile STIM2 clusters which co- ordinate recruitment of Orai1 and STIM1 to the junctions. Extended synaptotagmin (E-Syt)2/3 are required for forming the ER-PM junctions, but are not sufficient for STIM2 clustering. Importantly, inositol 1,4,5-triphosphate receptor (IP3R) function and local [Ca2+]ER are the main drivers of immobile STIM2 clusters. Enhancing, or decreasing, IP3R function at ambient [IP3] causes corresponding increase, or attenuation, of immobile STIM2 clusters. We show that immobile STIM2 clusters denote decreases in local [Ca2+]ER mediated by IP3R that is sensed by the STIM2-N terminus. Finally, under basal conditions, ambient PIP2-PLC activity of the cell determines IP3R function, immobilization of STIM2, and basal Ca2+ entry while agonist stimulation augments these processes. Together, our findings reveal that immobilization of STIM2 clusters within ER-PM junctions, a first response to ER-Ca2+ store depletion, is facilitated by the juxtaposition of IP3R and marks a checkpoint for initiation of Ca2+ entry.

SignificanceSTIM proteins sense decreases in [Ca2+]ER and cluster in endoplasmic reticulum (ER)-plasma membrane (PM) junctions where they recruit and activate Orai1. While STIM1 clustering requires substantial [Ca2+]ER decrease, STIM2 displays pre-clustering under resting conditions and regulates basal Ca2+ entry. The mechanism(s) underlying constitutive clustering of STIM2 is not known. We show herein that endogenous STIM2 assembles as mobile and immobile clusters and that Orai1 is recruited to the latter. Anchoring of STIM2 clusters is triggered by decreases in local [Ca2+]ER that is mediated by ambient activity of IP3R and sensed by the STIM2 N-terminus. This functional link between IP3R and STIM2 governs constitutive STIM2 clustering and ensures coupling of [Ca2+]ER decrease at sub-threshold stimuli with activation of Ca2+ entry.

category: physiology


title: Disynaptic Effect of Hilar Cells on Pattern Separation in A Spiking Neural Network of Hippocampal Dentate Gyrus

abstract: We investigate the disynaptic effect of the hilar cells on pattern separation in a spiking neural network of the hippocampal dentate gyrus (DG). The principal granule cells (GCs) in the DG perform pattern separation, transforming similar input patterns into less-similar output patterns. In our DG network, the hilus consists of excitatory mossy cells (MCs) and inhibitory HIPP (hilar perforant path-associated) cells. Here, we consider the disynaptic effects of the MCs and the HIPP cells on the GCs, mediated by the inhibitory basket cells (BCs) in the granular layer; MC [->] BC [->] GC and HIPP [->] BC [->] GC. Disynaptic inhibition from the MCs tends to decrease the firing activity of the GCs. On the other hand, the HIPP cells disinhibit the intermediate BCs, which leads to increasing the activity of the GCs. By changing the synaptic strength K(BC,X) [from the presynaptic X (= MC or HIPP) to the postsynaptic BC] from the default value K(BC,X)*, we study the change in the pattern separation degree [S]d. When decreasing K(BC,MC) or independently increasing K(BC,HIPP) from their default values, [S]d is found to decrease (i.e., pattern separation is reduced). On the other hand, as K(BC,MC) is increased or independently K(BC,HIPP) is decreased from their default values, pattern separation becomes enhanced (i.e., [S]d increases). In this way, the disynaptic effects of the MCs and the HIPP cells on the pattern separation are opposite ones. Thus, when simultaneously varying both K(BC,MC) and K(BC,HIPP), as a result of balance between the two competing disynaptic effects of the MCs and the HIPP cells, [S]d forms a bell-shaped curve with an optimal maximum at their default values. Moreover, we also investigate population and individual behaviors of the sparsely synchronized rhythm of the GCs, and find that the amplitude measure [M]a (representing population synchronization degree) and the random-phase-locking degree [L]d (denoting individual activity degree) are strongly correlated with the pattern separation degree [S]d. Consequently, the larger the synchronization and the random phase-locking degrees of the sparsely synchronized rhythm is, the more the pattern separation becomes enhanced.

category: neuroscience


title: Knowledge-driven perceptual organization reshapes information sampling via eye movements

abstract: Humans constantly move their eyes to explore the environment and obtain information. Competing theories of gaze guidance consider the factors driving eye movements within a dichotomy between low-level visual features and high-level object representations. However, recent developments in object perception indicate a complex and intricate relationship between features and objects. Specifically, image-independent object-knowledge can generate objecthood by dynamically reconfiguring how feature space is carved up by the visual system. Here, we adopt this emerging perspective of object perception, moving away from the simplifying dichotomy between features and objects in explanations of gaze guidance. We recorded eye movements in response to stimuli that appear as meaningless patches on initial viewing but are experienced as coherent objects once relevant object-knowledge has been acquired. We demonstrate that gaze guidance differs substantially depending on whether observers experienced the same stimuli as meaningless patches or organized them into object representations. In particular, fixations on identical images became object-centred, less dispersed, and more consistent across observers once exposed to relevant prior object-knowledge. Observers gaze behaviour also indicated a shift from exploratory information-sampling to a strategy of extracting information mainly from selected, object-related image areas. These effects were evident from the first fixations on the image. Importantly, however, eye-movements were not fully determined by object representations but were best explained by a simple model that integrates image-computable features and high-level, knowledge-dependent object representations. Overall, the results show how information sampling via eye-movements in humans is guided by a dynamic interaction between image-computable features and knowledge-driven perceptual organization.


title: UCHL1 inhibited by A1 astrocytes facilitates aggregates clearance to promote neural stem cells activation after spinal cord injury

abstract:
Spinal cord injury (SCI) is a devastating central nervous system (CNS) disease with no satisfying therapies available. Mobilizing endogenous neural stem cells (NSCs) to trigger intrinsic regeneration exhibits promising potentials for SCI repair. However, neurogenesis from endogenous NSCs is extremely restricted in the non-neurogenic spinal cord after SCI. Accumulation of protein aggregates has been shown to impede quiescent NSCs activation and the subsequent neurogenesis. Here, we found that ubiquitin c-terminal hydrolase l-1 (UCHL1), a deubiquitinating enzyme, functioned to regulate NSCs activation and neurogenesis by reducing protein aggregations through ubiquitin-proteasome pathway (UPP) in vitro. Upregulation of UCHL1 in spinal cord NSCs of rats with complete transection SCI efficiently enhanced NSCs proliferation and neurogenesis, leading to significantly improved functional outcomes. Based on protein microarray analysis of cerebrospinal fluid (CSF), our results revealed that A1 reactive astrocytes acted to restrict NSCs neurogenesis by negatively regulating UCHL1-depentdent protein aggregates removal via the C3/Nrf2 signaling. Indeed, blockade of A1 astrocytes using neutralizing antibodies after SCI also led to NSCs activation, increased neurogenesis and remarkably enhanced motor function recovery. This study not only revealed a novel mechanism regulating NSCs-medicated neurogenesis in the spinal cord, but also provided new molecular targets for neural repair strategies after SCI.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/461600v1_ufig1.gif" ALT="Figure 1">
View larger version (78K):
org.highwire.dtl.DTLVardef@1aca62eorg.highwire.dtl.DTLVardef@1d23083org.highwire.dtl.DTLVardef@6eee85org.highwire.dtl.DTLVardef@ed683d_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIUCHL1 facilitates NSCs activation by clearing intracellular protein aggregates through ubiquitin-proteasome approach
C_LIO_LIA1 reactive astrocytes result in down-regulation of UCHL1 to inhibit spinal NSCs activation by C3 after SCI
C_LIO_LIOverexpression of UCHL1 or blockade of A1 astrocytes lead to NSCs activation and neurons formation to promote SCI repair via UCHL1-proteasome pathway
C_LI


title: Alpha oscillations link action to cognition: An oculomotor account of the brain's dominant rhythm

abstract: Power modulations in alpha oscillations (8-14Hz) have been associated with most human cognitive functions and psychopathological conditions studied. These reports are often inconsistent with the prevailing view of a specific relationship of alpha oscillations to attention and working memory (WM). We propose that conceptualizing the role of alpha oscillations in oculomotor control resolves this inconsistency. This proposition is based on a review of results across species (human Npooled=295, one non-human primate, honey bee N=5), experimental conditions (rest, attention, and working memory), and recording techniques (EEG, ECOG, eye-tracking, and MEG) that encourage the following relationships between alpha oscillations and eye-movement control: (i) saccade initiation prompts power decrease in brain circuits associated with saccadic control; (ii) the direction of a saccade is consistent with alpha lateralization, both during task and resting conditions; (iii) the phase of alpha activity informs saccade occurrence and biases miniature eye movements during fixation (e.g. fixational tremor); and (iv) oculomotor action differentiates WM load. A new theory on how alpha oscillations link oculomotor action to cognition is proposed. Generalizing across tasks and species: low oculomotor activity is associated with high alpha power and vice versa. Alpha oscillations regulate how long to look at a given target and how fast to saccade to a next. By ensuring steady gaze position, any potential input outside foveal vision is "suppressed".


title: Mice With Monoallelic GNAO1 Loss Exhibit Reduced Inhibitory Synaptic Input To Cerebellar Purkinje Cells

abstract:
GNAO1 encodes Go, a heterotrimeric G protein alpha subunit in the Gi/o family. In this report, we used a Gnao1 mouse model "G203R" previously described as a "gain-of-function" Gnao1 mutant with movement abnormalities and enhanced seizure susceptibility. Here, we report an unexpected second mutation resulting in a loss-of-function Go protein and describe alterations in central synaptic transmission.

Whole cell patch clamp recordings from Purkinje cells (PCs) in acute cerebellar slices from Gnao1 mutant mice showed significantly lower frequencies of spontaneous and miniature inhibitory postsynaptic currents (sIPSCs and mIPSCs) compared to WT mice. There was no significant change in sEPSCs or mEPSCs. Whereas mIPSC frequency was reduced, mIPSC amplitudes were not affected, suggesting a presynaptic mechanism of action. A modest decrease in the number of molecular layer interneurons was insufficient to explain the magnitude of IPSC suppression. Paradoxically, Gi/o inhibitors (pertussis toxin), enhanced the mutant-suppressed mIPSC frequency and eliminated the difference between WT and Gnao1 mice. While GABAB receptor regulates mIPSCs, neither agonists nor antagonists of this receptor altered function in the mutant mouse PCs. This study is the first electrophysiological investigation of the role of Gi/o protein in cerebellar synaptic transmission using an animal model with a loss-of-function Gi/o protein.

Significance StatementThis is the first report on the electrophysiological mechanisms of a movement disorder animal model with monoallelic Gnao1 loss. This study illustrates the role of Go protein in regulating GABA release in mouse cerebellum. This study could also facilitate the discovery of new drugs or drug repurposing for GNAO1-associated disorders. Moreover, since GNAO1 shares pathways with other genes related to movement disorders, developing drugs for the treatment of GNAO1-associated movement disorders could further the pharmacological intervention for other monogenic movement disorders.


title: Model-based dynamic off-resonance correction for improved accelerated fMRI in awake behaving non-human primates

abstract:
PurposeTo estimate dynamic off-resonance due to vigorous body motion in accelerated fMRI of awake behaving non-human primates (NHPs) using the standard EPI 3-line navigator, in order to attenuate the effects of time-varying off-resonance on the reconstruction.

MethodsIn NHP fMRI the animals head is usually head-posted, and the dynamic off-resonance is mainly caused by motion in body parts that are distant from the brain and have low spatial frequency. Hence, off-resonance at each frame can be approximated as a spatially linear perturbation of the off-resonance at a reference frame, and is manifested as a relative linear shift in k-space. Using GRAPPA operators, we estimated these shifts by comparing the 3-line navigator at each time frame with that at the reference frame. Estimated shifts were then used to correct the data at each frame. The proposed method was evaluated in phantom scans, simulations, and in vivo data.

ResultsThe proposed method is shown to successfully estimate low-spatial order dynamic off-resonance perturbations, including induced linear off-resonance perturbations in phantoms, and is able to correct retrospectively corrupted data in simulations. Finally, it is shown to reduce ghosting artifacts and geometric distortions by up to 20% in simultaneous multi-slice in vivo acquisitions in awake-behaving NHPs.

ConclusionA method is proposed that does not need any sequence modification or extra acquisitions and makes accelerated awake behaving NHP imaging more robust and reliable, reducing the gap between what is possible with NHP protocols and state-of-the-art human imaging.


title: Mechanics Of Ultrasonic Neuromodulation In A Mouse Subject

abstract: Ultrasound neuromodulation (UNM), where a region in the brain is targeted by focused ultrasound (FUS), which, in turn, causes excitation or inhibition of neural activity, has recently received considerable attention as a promising tool for neuroscience. Despite its great potential, several aspects of UNM are still unknown. An important question pertains to the off-target sensory effects of UNM and their dependence on stimulation frequency. To understand these effects, we have developed a finite-element model of a mouse, including elasticity and viscoelasticity, and used it to interrogate the response of mouse models to focused ultrasound (FUS). We find that, while some degree of focusing and magnification of the signal is achieved within the brain, the induced pressure-wave pattern is complex and delocalized. In addition, we find that the brain is largely insulated, or  cloaked, from shear waves by the cranium and that the shear waves are largely carried away from the skull by the vertebral column, which acts as a waveguide. We find that, as expected, this waveguide mechanism is strongly frequency dependent, which may contribute to the frequency dependence of UNM effects. Our calculations further suggest that off-target skin locations experience displacements and stresses at levels that, while greatly attenuated from the source, could nevertheless induce sensory responses in the subject.


title: Rapamycin attenuated zinc-induced tau phosphorylation and oxidative stress in animal model: Involvement of dual mTOR/p70S6K and Nrf2/HO-1 pathways

abstract: Alzheimers disease is pathologically featured by abnormal accumulation of amyloid-beta plaque, neurofibrillary tangles, oxidative stress, neuroinflammation, and neurodegeneration. Metal dysregulation including excessive zinc released by presynaptic neurons plays an important role in tau pathology and oxidase activation. The activities of mammalian target of rapamycin (mTOR)/ ribosomal S6 protein kinase (p70S6K) are elevated in the brains of patients with Alzheimers disease. Zinc induces tau hyperphosphorylation via mTOR/P70S6K activation in vitro. However, the involvement of mTOR/P70S6K pathway in zinc-induced oxidative stress, tau degeneration, synaptic and cognitive impairment, has not been fully elucidated in vivo. Here we assessed in the effect of pathological concentration of zinc in SH-SY5Y cells by using biochemical assays and immunofluorescence staining. Rats (n = 18, male) were lateral ventricularly-injected with zinc and treated with rapamycin (intraperitoneal injection) for one week and assessed using Morris water maze. Evaluation of the oxidative stress, tau phorsphylation and synaptic impairment were performed using the hippocampus tissue of the rats by biochemical assays and immunofluorescence staining. Results from Morris water maze showed that the capacity of spatial memory is impaired in zinc-treated rats. Zinc sulfate significantly increased the levels of P-mTOR Ser2448, P-p70S6K Thr389, and P-tau Ser356, and decreased levels of Nrf2 and HO{square}1 in SH-SY5Y cells and in zinc-treated rats compared with control groups. Increased expressions of reactive oxygen species were observed in zinc sulfate-induced SH-SY5Y cells as well as in the hippocampus of zinc-injected rats. Rapamycin, an inhibitor of mTOR, rescued the zinc-induced increases in mTOR/p70S6K activations, tau phosphorylation and oxidative stress, as well as Nrf2/HO{square}1 inactivation, cognitive impairment and synaptic impairment reduced the expression of synapse-related proteins in zinc-injected rats. In conclusion, our findings imply that rapamycin prevents zinc-induced cognitive impairment and protects neurons from tau pathology, oxidative stress and synaptic impairment, by decreasing mTOR/p70S6K hyperactivity and increasing Nrf2/HO {square} 1 activity.


title: Learning of biased representations in LIP through interactions between recurrent connectivity and Hebbian plasticity

abstract: When monkeys learn to group visual stimuli into arbitrary categories, lateral intraparietal area (LIP) neurons become category-selective. Surprisingly, the representations of learned categories are overwhelmingly biased: nearly all LIP neurons in a given animal prefer the same category over other behaviorally equivalent categories. We propose a model where such biased representations develop through the interplay between Hebbian plasticity and the recurrent connectivity of LIP. In this model, two separable processes of positive feedback unfold in parallel: in one, category selectivity emerges from competition between prefrontal inputs; in the other, bias develops due to lateral interactions among LIP neurons. This model reproduces the levels of category selectivity and bias observed under a variety of conditions, as well as the redevelopment of bias after monkeys learn redefined categories. It predicts that LIP receptive fields would spatially cluster by preferred category, which we experimentally confirm. In summary, our model reveals a mechanism by which LIP learns abstract representations and assigns meaning to sensory inputs.


title: Self-Administration of entactogen psychostimulants dysregulates GABA and Kappa Opioid Receptor signaling in the central nucleus of the amygdala of female Wistar rats

abstract: Male rats escalate intravenous self-administration of entactogen psychostimulants, 3,4-methylenedioxymethcathinone (methylone) and 3,4-methylenedioxymethamphetamine (MDMA) under extended access conditions, as with typical psychostimulants. Here, we investigated whether female rats escalate self-administration of methylone, 3,4-methylenedioxypentedrone (pentylone), and MDMA and then studied consequences of MDMA and pentylone self-administration on GABAA receptor and kappa opioid receptor (KOR) signaling in the central nucleus of the amygdala (CeA), a brain area critically dysregulated by extended access self-administration of alcohol or cocaine. Adult female Wistar rats were trained to self-administer methylone, pentylone, MDMA (0.5 mg/kg/infusion), or saline-vehicle using a fixed-ratio 1 response contingency in 6-hour sessions (long-access: LgA) followed by progressive ratio (PR) dose-response testing. The effects of pentylone-LgA, MDMA-LgA and saline on basal GABAergic transmission (miniature postsynaptic inhibitory currents, mIPSCs) and the modulatory role of KOR at CeA GABAergic synapses were determined in acute brain slices using whole-cell patch-clamp. Methylone-LgA and pentylone-LgA rats similarly escalated their drug intake (both obtained more infusions compared to MDMA-LgA rats) however, pentylone-LgA rats reached higher breakpoints in PR tests. At the cellular level, baseline CeA GABA transmission was markedly elevated in pentylone-LgA and MDMA-LgA rats compared to saline-vehicle. Specifically, pentylone-LgA was associated with increased CeA mIPSC frequency (GABA release) and amplitude (postsynaptic GABAA receptor function), while mIPSC amplitudes (but not frequency) was larger in MDMA-LgA rats compared to saline rats. In addition, pentylone-LgA and MDMA-LgA profoundly disrupted CeA KOR signaling such as both KOR agonism (1mM U50488) and KOR antagonism (200nM nor-binaltorphimine) decreased mIPSC frequency suggesting recruitment of non-canonical KOR signaling pathways. This study confirms escalated self-administration of entactogen psychostimulants under LgA conditions in female rats which is accompanied by increased CeA GABAergic inhibition and altered KOR signaling. Collectively, our study suggests that CeA GABA and KOR mechanisms play a critical role in entactogen self-administration like those observed with escalation of alcohol or cocaine self-administration.


title: Unrestricted eye movements strengthen causal connectivity from hippocampal to oculomotor regions during scene construction

abstract: Scene construction is a key component of memory recall, navigation, and future imagining, and relies on the medial temporal lobes (MTL). A parallel body of work suggests that eye movements may enable the imagination and construction of scenes, even in the absence of external visual input. There are vast structural and functional connections between regions of the MTL and those of the oculomotor system. However, the directionality of connections between the MTL and oculomotor control regions, and how it relates to scene construction, has not been studied directly in human neuroimaging. In the current study, we used dynamic causal modeling (DCM) to investigate this relationship at a mechanistic level using a scene construction task in which participants eye movements were either restricted (fixed-viewing) or unrestricted (free-viewing). By omitting external visual input, and by contrasting free-versus fixed-viewing, the directionality of neural connectivity during scene construction could be determined. As opposed to when eye movements were restricted, allowing free viewing during construction of scenes strengthened top-down connections from the MTL to the frontal eye fields, and to lower-level cortical visual processing regions, suppressed bottom-up connections along the visual stream, and enhanced vividness of the constructed scenes. Taken together, these findings provide novel, non-invasive evidence for the causal architecture between the MTL memory system and oculomotor system associated with constructing vivid mental representations of scenes.


title: High-throughput super-resolution analysis of influenza virus pleomorphism reveals insights into viral spatial organization

abstract: Many viruses form highly pleomorphic particles; in influenza, these particles range from spheres of ~ 100 nm in diameter to filaments of several microns in length. Virion structure is of interest, not only in the context of virus assembly, but also because pleomorphic variations may correlate with infectivity and pathogenicity. We have used fluorescence super-resolution microscopy combined with a rapid automated analysis pipeline to image many thousands of individual influenza virions, gaining information on their size, morphology and the distribution of membrane-embedded and internal proteins. We observed broad phenotypic variability in filament size, and Fourier transform analysis of super resolution images demonstrated no generalized common spatial frequency patterning of HA or NA on the virion surface, suggesting a model of virus particle assembly where the release of progeny filaments from cells occurs in a stochastic way. Finally, we showed that in long filaments, viral RNP complexes are located preferentially within Archetti bodies, suggesting that these structures may play a role in virus transmission. Our approach therefore offers exciting new insights into influenza virus morphology and represents a powerful technique that is easily extendable to the study of pleomorphism in other pathogenic viruses.

category: microbiology


title: Firmicutes and Bacteroidetes explain mass gain variation in an obligate hibernator

abstract:
O_LIBody condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival.
C_LIO_LIIt is well documented that symbiotic microorganisms play a vital role in animal physiology and behaviour. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity; Firmicutes is consistently associated with obesity while Bacteroidetes is associated with leanness both in humans and other animals.
C_LIO_LIThe focus of most microbiome studies has been on human health or involved lab reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife.
C_LIO_LIHere we test whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes are associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by quantifying microbial abundance over five years of fecal samples (2015 - 2019) collected during their summer active season.
C_LIO_LIResults show that marmots with higher mass gain rates have a greater abundance of Firmicutes. In contrast, higher abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates, and similarly in harsher environments.
C_LIO_LIAlthough correlative, these results highlight the importance of symbiotic gut microbiota to mass gain in the wild, a trait associated with survival and fitness in many taxonomic groups.
C_LI


title: The retromer complex regulates C. elegans development and mammalian ciliogenesis

abstract: The mammalian retromer is comprised of subunits VPS26, VPS29 and VPS35, and a more loosely-associated sorting nexin (SNX) heterodimer. Despite known roles for the retromer in multiple trafficking events in yeast and mammalian cells, its role in development is poorly understood, and its potential function in primary ciliogenesis remains unknown. Using CRISPR-Cas9 editing, we demonstrated that vps-26 homozygous knockout C. elegans have reduced brood sizes and impaired vulval development, as well as decreased body length which has been linked to defects in primary ciliogenesis. Since many endocytic proteins are implicated in the generation of primary cilia, we addressed whether the retromer regulates ciliogenesis in mammalian cells. We observed VPS35 localized to the primary cilium, and depletion of VPS26, VPS35 or SNX1/SNX5 led to decreased ciliogenesis. Retromer also coimmunoprecipitated with the capping protein, CP110, and was required for its removal from the mother centriole. Herein, we characterize new roles for the retromer in C. elegans development and in the regulation of ciliogenesis in mammalian cells, and suggest a novel role for the retromer in CP110 removal from the mother centriole.

category: cell biology


title: A Drosophila Su(H) Model of Adams-Oliver Syndrome Reveals Notch Cofactor Titration as a Mechanism Underlying Developmental Defects

abstract: Notch signaling is a conserved pathway that converts extracellular receptor-ligand interactions into changes in gene expression via a single transcription factor (CBF1/RBPJ in mammals; Su(H) in Drosophila). In humans, RBPJ variants have been linked to Adams-Oliver syndrome (AOS), a rare autosomal dominant disorder characterized by scalp, cranium, and limb defects. Here, we found that a previously described Drosophila Su(H) allele encodes a missense mutation that alters an analogous residue found in an AOS-associated RBPJ variant. Importantly, genetic studies support a model that Drosophila with a single copy of the AOS-like Su(H) allele behave in an opposing manner as flies with a Su(H) null allele due to a dominant activity of sequestering either the Notch co-activator or the antagonistic Hairless co-repressor. Consistent with this model, AOS-like Su(H) and Rbpj variants decrease DNA binding activity compared to wild type proteins, but these variants do not significantly alter protein binding to the Notch co-activator or the fly and mammalian co-repressors, respectively. Taken together, these data suggest a cofactor sequestration mechanism underlies AOS phenotypes associated with RBPJ variants, whereby a single RBPJ allele encodes a protein with compromised DNA binding activity that retains cofactor binding, resulting in Notch target gene dysregulation.

category: genetics


title: Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication by targeting its major protease in a non-competitive way

abstract: Anticoagulants are associated with clinical benefit against the 2019 coronavirus disease (COVID-19), preventing COVID-19 associated coagulopathy. Blood coagulation factor Xa (FXa) and SARS-CoV-2 major protease (Mpro) share over 80% homology at the three-dimensional protein level. Thus, it is worth interrogating whether there is crosstalk between inhibitors and substrates between these enzymes. Here, we found that the clinically-approved FXa inhibitor apixaban targets SARS-CoV-2 Mpro with a 21-fold higher potency than boceprevir (GC376). Apixaban displayed a non-competitive mechanism of inhibition towards Mpro, since it targets the enzyme/substrate complex and the allosteric site onto the viral protease. Enzymatic assays were further validated in infected Calu-3 cells, which reveal that apixaban decreases the production of infectious viral particles in a dose-dependent manner, with an inhibitory potency in the micromolar range. Our results are in line with the proposed early use of anticoagulants, including FXa inhibitors, to improve clinical outcome of COVID-19 patients. In this context, apixaban may display a dual mechanism of action by targeting FXa to prevent coagulopathy and, at some level, SARS-CoV-2 Mpro.


title: White matter hyperintensities may be an early marker for age-related cognitive decline in the ADNI cohort

abstract:
BackgroundResearch suggests that cerebral small vessel disease (CSVD), amyloid, and pTau contribute to age-related cognitive decline. It remains unknown how these factors relate to one another, nor how they jointly contribute to cognitive decline in normal aging. This project examines the association between these pathologies and their relationship to cognitive decline in cognitively normal older adults without subjective cognitive decline.

MethodsA total of 230 subjects with CSF A{beta}42, CSF pTau181, white matter hyperintensities (WMHs) used as a proxy of CSVD and cognitive scores from the Alzheimers Disease Neuroimaging Initiative were included. Associations between each pathology and cognitive score were investigated using regression models. Furthermore, relationships between the three pathologies were also examined using regression models.

ResultsAt baseline, there was an inverse association between WMH load and A{beta}42 (t=-4.20, p<.001). There was no association between WMH load and pTau (t=0.32, p=0.75), nor with A{beta}42 and pTau (t=0.51, p=.61). Correcting for age, sex and education, baseline WMH load was associated with baseline ADAS-13 scores (t=2.59, p=.01) and lower follow-up executive functioning (t= -2.84, p=.005). Baseline A{beta}42 was associated with executive function at baseline (t=3.58, p<.004) but not at follow-up (t=1.05, p=0.30), nor with ADAS-13 at baseline (t=-0.24, p0.81) or follow-up (t=0.09, p=0.93). Finally, baseline pTau was not associated with any cognitive measure at baseline or follow-up.

ConclusionBoth baseline A{beta}42 and WMH load are associated with some baseline cognition scores, but only baseline WMH load is associated with follow-up executive functioning, indicating that it may be one of the earliest pathologies that contributes to future cognitive decline, in cognitively healthy older adults. Given that healthy older adults with WMH pathology exhibit declines in cognitive functioning, they may be less resilient to future pathology increasing their risk for cognitive impairment due to dementia than those without WMHs.


title: SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo.

abstract:
Cell-cell interactions govern differentiation and cell competition in pluripotent cells during early development, but the investigation of such processes is hindered by a lack of efficient analysis tools. Here we introduce SyNPL: clonal pluripotent stem cell lines which employ optimised Synthetic Notch (SynNotch) technology to report cell-cell interactions between engineered "sender" and "receiver" cells in cultured pluripotent cells and chimaeric mouse embryos. A modular design makes it straightforward to adapt the system for programming differentiation decisions non-cell-autonomously in receiver cells in response to direct contact with sender cells. We demonstrate the utility of this system by enforcing neuronal differentiation at the boundary between two cell populations. In summary, we provide a new tool which could be used to identify cell interactions and to profile changes in gene or protein expression that result from direct cell-cell contact with defined cell populations in culture and in early embryos, and which can be adapted to generate synthetic patterning of cell fate decisions.

SUMMARY STATEMENTOptimised Synthetic Notch circuitry in mouse pluripotent stem cells provides a modular tool to monitor cell-cell interactions and program synthetic patterning of cell fates in culture and in embryos.

category: developmental biology


title: Transoceanic voyages of drywood termites (Isoptera: Kalotermitidae) inferred from extant and extinct species

abstract: Termites are major decomposers of organic matter in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae, the second-largest termite family, are widely distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes and nuclear ribosomal RNA genes of [~]120 species, about 27% of kalotermitid diversity, including representatives of 22 of the 23 kalotermitid genera. We found that extant kalotermitids shared a common ancestor 81 Mya (72-91 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the [~]40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying that the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for a critical taxonomic revision of the family and for future comparative analyses of Kalotermitidae.

category: evolutionary biology


title: Neutron crystallography reveals novel mechanisms used by Pseudomonas aeruginosa for host-cell binding

abstract: The opportunistic pathogen Pseudomonas aeruginosa, a major cause of nosocomial infections, uses carbohydrate-binding proteins (lectins) as part of its binding to host cells. The fucose-binding lectin, LecB, displays a unique carbohydrate-binding site that incorporates two closely located calcium ions bridging between the ligand and protein, providing specificity and unusually high affinity. Here, we investigate the mechanisms involved in binding based on neutron crystallography studies of a fully deuterated LecB/fucose/calcium complex. The neutron structure, which includes the positions of all the hydrogen atoms, reveals that the high affinity of binding may be related to the occurrence of a low barrier hydrogen bond induced by the proximity of the two calcium ions, the presence of coordination rings between the sugar, calcium and LecB, and the dynamic behaviour of bridging water molecules at room temperature. These key structural details may assist in the design of anti-adhesive compounds to combat multi-resistance bacterial infections.

category: biochemistry


title: Reconstitution and use of highly active human CDK1:Cyclin-B:CKS1 complexes

abstract: As dividing cells transition into mitosis, hundreds of proteins are phosphorylated by a complex of cyclin-dependent kinase 1 (CDK1) and Cyclin-B, often at multiple sites. CDK1:Cyclin-B phosphorylation patterns alter conformations, interaction partners, and enzymatic activities and need to be recapitulated in vitro for the structural and functional characterization of the mitotic protein machinery. This requires a pure and active recombinant kinase complex. The kinase activity of CDK1 critically depends on the phosphorylation of a Threonine residue in its activation loop by a CDK1 activating kinase (CAK). We developed protocols to activate CDK1:Cyclin-B either in vitro with purified CDK1 activating kinases (CAK) or in insect cells through CDK-CAK co-expression. To boost kinase processivity, we reconstituted a tripartite complex consisting of CDK1, Cyclin-B, and CKS1. In this work, we provide and compare detailed protocols to obtain and use highly active CDK1:Cyclin-B (CC) and CDK1:Cyclin-B:CKS1 (CCC).


title: Systemic impact of the expression of the mitochondrial alternative oxidase on Drosophila development

abstract: Despite the beneficial effects of xenotopically expressing the mitochondrial alternative oxidase AOX from Ciona intestinalis in mammalian and insect models, important detrimental outcomes have also been reported, raising concerns regarding its potential deployment as a therapeutic enzyme for human mitochondrial diseases. Because of its non-protonmotive terminal oxidase activity, AOX can bypass the cytochrome segment of the respiratory chain whilst not contributing to mitochondrial ATP synthesis. We have previously shown that pupal lethality occurs when AOX-expressing Drosophila larvae are cultured on a low-nutrient diet, indicating that AOX can perturb normal metabolism during development. Here, combined omics analyses revealed multiple correlates of this diet-dependent lethality, including a general alteration of larval amino acid and lipid metabolism, functional and morphological changes to the larval digestive tract, and a drastic decrease in larval biomass accumulation. Pupae at the pre-lethality stage presented a general downregulation of mitochondrial metabolism and a signature of starvation and deregulated signaling. AOX-induced lethality was partially rescued when the low-nutrient diet was supplemented with tryptophan and/or methionine, but not with proline and/or glutamate, strongly suggesting perturbation of one-carbon metabolism. The developmental dependence on tryptophan and/or methionine, associated with elevated levels of lactate dehydrogenase, 2-hydroxyglutarate, choline-containing metabolites and breakdown products of membrane phospholipids, indicates that AOX expression promotes tissue proliferation and larval growth, but this is ultimately limited by energy dissipation due to partial mitochondrial uncoupling. We speculate that the combination of dietary interventions and AOX expression might, nevertheless, be useful for the metabolic regulation of proliferative tissues, such as tumors.


title: Effects of arm swing amplitude and lower limb asymmetry on motor variability patterns during treadmill gait

abstract:
Motor variability is a fundamental feature of gait. Altered arm swing and lower limb asymmetry (LLA) may be contributing factors having been shown to affect the magnitude and dynamics of variability in spatiotemporal and trunk motion. However, the effects on lower limb joints remain unclear.

Full-body kinematics of 15 healthy young adults were recorded during treadmill walking using the Computer-Assisted Rehabilitation Environment system. Participants completed six trials, combining three arm swing (AS) amplitude (normal, active, held) and two LLA (symmetrical, asymmetrical) conditions. The mean standard deviation (meanSD), maximum Lyapunov exponent ({lambda}max), detrended fluctuation analysis scaling exponent of range of motion (DFA), and sample entropy (SaEn) were computed for tridimensional trunk, pelvis, and lower limb joint angles, and compared using repeated-measures ANOVAs.

Relative to normal AS, active AS increased meanSD of all joint angles, {lambda}max of frontal plane hip and ankle angles, and SaEn of sagittal plane ankle angles. Active AS, however, did not affect {lambda}max or SaEn of trunk or pelvis angles. LLA increased meanSD of sagittal plane joint angles, {lambda}max of Euclidean norm trunk angle and of lower limb joint angles, and SaEn of ankle dorsiflexion/ plantarflexion, but decreased SaEn of tridimensional trunk angles and hip rotation in the slower moving leg.

Alterations in lower limb variability with active AS and LLA suggest that young adults actively exploit their lower limb redundancies to maintain gait. This appears to preserve trunk stability and regularity during active AS but not during LLA.

category: bioengineering


title: Fabrication and delivery of mechano-activedmicrocapsules containing osteogenic factors in alarge animal model of osteochondral injury

abstract: Chondral and osteochondral repair strategies are limited by adverse bony changes that occur after injury. Bone resorption can cause entire scaffolds, engineered tissues, or even endogenous repair tissues to subside below the cartilage surface. To address this translational issue, we fabricated poly(D,L-lactide-co-glycolide) (PLGA) microcapsules containing the pro-osteogenic agents triiodothyronine and {beta}-glycerophosphate, and delivered these microcapsules in a large animal model of osteochondral injury to preserve bone structure. We demonstrate that developed microcapsules ruptured in vitro under increasing mechanical loads, and readily sink within a liquid solution, allowing for gravity-based positioning onto the osteochondral surface. In a large animal, these mechano-active microcapsules (MAMCs) were assessed through two different delivery strategies. Intra-articular injection of control MAMCs enabled fluorescent quantification of MAMC rupture and cargo release in a synovial joint setting over time in vivo. This joint-wide injection also confirmed that the MAMCs do not elicit an inflammatory response. In the contralateral hindlimbs, chondral defects were created, MAMCs were locally administered, and nanofracture (Nfx), a clinically utilized method to promote cartilage repair, was performed. The NFx holes enabled marrow-derived stromal cells to enter the defect area and served as repeatable bone injury sites to monitor over time. Animals were evaluated 1 and 2 weeks after injection and surgery. Analysis of injected MAMCs showed that bioactive cargo was released in a controlled fashion over 2 weeks. A bone fluorochrome label injected at the time of surgery displayed maintenance of mineral labeling in the therapeutic group, but resorption in both control groups. Alkaline phosphatase (AP) staining at the osteochondral interface revealed higher AP activity in defects treated with therapeutic MAMCs. Overall, this study establishes a new micro-fluidically generated delivery platform that releases therapeutic factors in an articulating joint, and reduces this to practice in the delivery of therapeutics that preserve bone structure after osteochondral injury.


title: Overcoming microenvironment-mediated chemoprotection through stromal Galectin-3 inhibition in acute lymphoblastic leukemia

abstract: Environmentally-mediated drug resistance in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) significantly contributes to relapse. Stromal cells in the bone marrow environment protect leukemia cells by secretion of chemokines as cues for BCP-ALL migration towards, and adhesion to, stroma. Stromal cells and BCP-ALL cells communicate through stromal galectin-3. Here, we investigated the significance of stromal galectin-3 to BCP-ALL cells. We used CRISPR/Cas9 genome editing to ablate galectin-3 in stromal cells and found that galectin-3 is dispensable for steady-state BCP-ALL proliferation and viability. However, efficient leukemia migration and adhesion to stromal cells are significantly dependent on stromal galectin-3. Importantly, loss of stromal galectin-3 production sensitized BCP-ALL cells to conventional chemotherapy. We therefore tested novel carbohydrate-based small molecule compounds (Cpd14 and Cpd17) with high specificity for galectin-3. Consistent with results obtained using galectin-3-knockout stromal cells, treatment of stromal-BCP-ALL co-cultures inhibited BCP-ALL migration and adhesion. Moreover, these compounds induced anti-leukemic responses in BCP-ALL cells including a dose-dependent reduction of viability and proliferation, induction of apoptosis and, importantly, inhibition of drug resistance. Collectively, these findings indicate galectin-3 regulates BCP-ALL cell responses to chemotherapy through the interactions between leukemia cells and the stroma, and show that a combination of galectin-3 inhibition with conventional drugs can sensitize the leukemia cells to chemotherapy.

category: cancer biology


title: Pericyte-mediated constriction of renal capillaries evokes no-reflow and kidney injury following ischemia

abstract: Acute kidney injury is common, with [~]13 million cases and 1.7 million deaths/year worldwide. A major cause is renal ischemia, typically following cardiac surgery, renal transplant or severe hemorrhage. We examined the cause of the sustained reduction in renal blood flow ("no-reflow"), which exacerbates kidney injury even after an initial cause of compromised blood supply is removed. After 60 min kidney ischemia and 30-60 min reperfusion, renal blood flow remained reduced, especially in the medulla, and kidney tubule damage was detected as Kim-1 expression. Constriction of the medullary descending vasa recta and cortical peritubular capillaries occurred near pericyte somata, and led to capillary blockages, yet glomerular arterioles and perfusion were unaffected, implying that the long-lasting decrease of renal blood flow contributing to kidney damage was generated by pericytes. Blocking Rho kinase to decrease pericyte contractility from the start of reperfusion increased the post-ischemic diameter of the descending vasa recta capillaries at pericytes, reduced the percentage of capillaries that remained blocked, increased medullary blood flow and reduced kidney injury. Thus, post-ischemic renal no-reflow, contributing to acute kidney injury, reflects pericytes constricting the descending vasa recta and peritubular capillaries. Pericytes are therefore an important therapeutic target for treating acute kidney injury.

category: pathology


title: Artificial neural networks enable genome-scale simulations of intracellular signaling

abstract: Mammalian cells adapt their functional state in response to external signals in form of ligands that bind receptors on the cell-surface. Mechanistically, this involves signal-processing through a complex network of molecular interactions that govern transcription factor (TF) activity patterns. Computer simulations of the information flow through this network could help predict cellular responses in health and disease. Here we develop a recurrent neural network constrained by prior knowledge of the signaling network with ligand concentrations as input, TF activity as output and signaling molecules as hidden nodes. Simulations are assumed to reach steady state, and we regularize the parameters to enforce this. Using synthetic data, we train models that generalize to unseen data and predict the effects of gene knockouts. We also fit models to a small experimental data set from literature and confirm the predictions using cross validation. This demonstrates the feasibility of simulating intracellular signaling at the genome-scale.

category: systems biology


title: A neurocomputational model of the basal ganglia for the analysis of motor deficits after dopaminergic loss in Parkinson's disease

abstract:
The basal ganglia (BG) are part of a basic feedback circuit, regulating cortical function, such as voluntary movement control, via their influence on thalamocortical projections. BG disorders, namely Parkinsons disease (PD), characterized by the loss of neurons in the substantia nigra (SN), involve the progressive loss of motor functions. The process that leads to these neural alterations is still unknown. At the present, PD cannot be cured, but an early diagnosis (ED) could allow to better manage its symptoms and evolution. A branch of neuroscience research is currently investigating the possibility of using motor alterations, e.g. handwriting, caused by the disease as diagnostic signs in the early stage of the disease, expression of small entity of SN lesion.

In the present work, we propose a neurocomputational model to investigate the behaviour of the simulated neural system after several degrees of lesion, with the aim of evaluating, if possible, which is the smallest lesion compromising motor learning. The performance of the network in learning a novel motor task has been analyzed, in physiological and pathological conditions. The proposed neural network proves that there may exist abnormalities of motor learning process, due to alterations in the BG, which do not yet involve the presence of symptoms typical of the confirmed diagnosis, since the network shows having some difficulties in motor learning already with 20% DA depletion.


title: Phostensin Enables Lymphocyte Integrin Activation and Population of Peripheral Lymphoid Organs

abstract:
Rap1 GTPase drives assembly of the Mig-10/RIAM/lamellipodin-Integrin-Talin (MIT) complex that enables integrin-dependent lymphocyte functions. Here we used tandem affinity tag-based proteomics to isolate and analyze the MIT complex and reveal that Phostensin (PTSN), a regulatory subunit of protein phosphatase 1, is a component of the complex. PTSN mediates de-phosphorylation of Rap1 thereby preserving the activity and membrane localization of Rap1 to stabilize the MIT complex. CRISPR/Cas9-induced deletion of PPP1R18, which encodes PTSN, markedly suppresses integrin activation in Jurkat human T cells. We generated apparently healthy Ppp1r18-/- mice that manifest lymphocytosis and reduced population of peripheral lymphoid tissues ascribable to defective activation of integrins L{beta}2 and 4{beta}7. Ppp1r18-/- T cells exhibit reduced capacity to induce colitis in a murine adoptive transfer model. Thus, PTSN enables lymphocyte integrin-mediated functions by dephosphorylating Rap1 to stabilize the MIT complex. As a consequence, loss of PTSN ameliorates T cell-mediated colitis.

SUMMARYPhostensin, a protein phosphatase 1 regulatory subunit, supports lymphocyte integrin-dependent functions by mediating dephosphorylation of Rap1 to stabilize the MIT complex thereby enabling the population of peripheral lymphoid organs and T cell-mediated colitis.

category: immunology


title: Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp.

abstract:
Campylobacter is the most common cause of bacterial gastroenteritis worldwide and diarrheal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries (LMICs). Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we characterised the genetic diversity and accessory genome content of a collection of Campylobacter isolates from Cairo, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24) and patients (n=57) suffering from gastroenteritis. Among the most common sequence types (STs) we identified were the globally disseminated, host generalist ST-21 clonal complex (CC21) and the poultry specialist CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented with a total absence of CC61. Comparative genomics were used to quantify core and accessory genome sharing among isolates from the same country compared to sharing between countries. Lineage-specific accessory genome sharing was significantly higher among isolates from the same country, particularly CC21 which demonstrated greater local geographical clustering. In contrast, no geographic clustering was noted in either the core or accessory genomes of the CC828, suggesting a highly admixed population. A greater proportion of C. coli isolates were multidrug resistant (MDR) compared to C. jejuni. This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies in the Egyptian market to combat such a threat.

Impact statementCampylobacter is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- and middle-income countries, where infection can be fatal, culture-based isolation is rare and the genotypes responsible for disease are seldom identified. Here, we sequenced the genomes of a collection of isolates from clinical cases and potential infection reservoirs from Cairo in Egypt and characterised their genetic diversity. Among the most common genotypes we identified were globally disseminated lineages implicated in human disease worldwide, including the host generalist ST-21 clonal complex (CC21) and the poultry specialist genotypes CC206, CC464 and CC48. Notably however, some other globally common genotypes were under-represented or entirely absent from our collection, including those from cattle-specialist lineages, CC42 and CC61. By focussing on specific lineages, we demonstrate that there is increased accessory genome sharing in specific clonal complexes. This increased local sharing of genes may have contributed to a greater proportion of C. coli isolates possessing antimicrobial resistance determinants that suggest they could be multidrug resistant (MDR). This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies.

Data summaryShort read data are available on the NCBI Sequence Read Archive, associated with BioProject PRJNA576513 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA576513). Assembled genomes, supplementary material and additional analysis files are available from FigShare: https://doi.org/10.6084/m9.figshare.9956597. Phylogenetic trees can be visualised and manipulated on Microreact for C. jejuni (https://next.microreact.org/project/Cjejuni_Egypt) and C. coli (https://next.microreact.org/project/Ccoli_Egypt) separately, or combined Cairo and Oxford data with additional PopPunk network clustering (https://microreact.org/project/Campy-Egypt).


title: Hemodynamic evaluation of chemical mediators of sepsis during systemic inflammatory response in an experimental animal model

abstract: The early diagnosis of sepsis increases the chances of its successful treatment. Biomarkers are able to distinguish between systemic inflammatory response syndrome and sepsis and are used to monitor pro- and anti-inflammatory changes associated with the host response to pathogens. A total of 11 rats underwent sepsis induction and measured systolic, diastolic and mean arterial blood pressure. Leukocyte counts, procalcitonin, and nitric oxide also were measured 0, 2, and 4 hours after the induction of sepsis using the cecal ligation and puncture method. The animals were divided into two groups: control (SHAM) and induced. Procalcitonin levels remained within the normal range for an inflammatory response throughout the experiment. There was a statistically insignificant increase in nitric oxide levels. All animals showed increased diastolic arterial blood pressure; however, the increase in the induced animals was even more pronounced. Procalcitonin and nitric oxide levels can increase due to surgical manipulation, while arterial blood pressure was not a good predictor for the onset of sepsis during the time period studied here.


title: Glycosylation-on-a-chip: a flow-based microfluidic system for cell-free glycoprotein biosynthesis

abstract: In recent years, cell-free synthetic glycobiology technologies have emerged that enable production and remodeling of glycoproteins outside the confines of the cell. However, many of these systems combine multiple synthesis steps into one pot where there can be competing reactions and side products that ultimately lead to low yield of the desired product. In this work, we describe a microfluidic platform that integrates cell-free protein synthesis, glycosylation, and purification of a model glycoprotein in separate compartments where each step can be individually optimized. Microfluidics offer advantages such as reaction compartmentalization, tunable residence time, the ability to tether enzymes for reuse, and the potential for continuous manufacturing. Moreover, it affords an opportunity for spatiotemporal control of glycosylation reactions that is difficult to achieve with existing cell-based and cell-free glycosylation systems. In this work, we demonstrate a flow-based glycoprotein synthesis system that promotes enhanced cell-free protein synthesis, efficient protein glycosylation with an immobilized oligosaccharyltransferase, and enrichment of the protein product from cell-free lysate. Overall, this work represents a first-in-kind glycosylation-on-a-chip prototype that could find use as a laboratory tool for mechanistic dissection of the protein glycosylation process as well as a biomanufacturing platform for small batch, decentralized glycoprotein production.

category: synthetic biology


title: Complete sequences of epidermin and nukacin encoding plasmids from oral-derived Staphylococcus epidermidis and their antibacterial activity

abstract: Staphylococcus epidermidis is a commensal bacterium in humans. To persist in the bacterial flora of the host, some bacteria produce antibacterial factors such as the antimicrobial peptides known as bacteriocins. In this study, we tried to isolate bacteriocin-producing S. epidermidis strains. Among 150 S. epidermidis isolates from the oral cavities of 287 volunteers, we detected two bacteriocin-producing strains, KSE56 and KSE650. Complete genome sequences of the two strains confirmed that they carried the epidermin-harbouring plasmid pEpi56 and the nukacin IVK45-like- harbouring plasmid pNuk650. The amino acid sequence of epidermin from KSE56 was identical to the previously reported sequence, but the epidermin synthesis-related genes were partially different. The prepeptide amino acid sequences of nukacin KSE650 and nukacin IVK45 showed one mismatch, but both mature peptides were entirely similar. pNuk650 was larger and had an additional seven ORFs compared to pIVK45. We then investigated the antibacterial activity of the two strains against several skin and oral bacteria and found their different activity patterns. In conclusion, we report the complete sequences of 2 plasmids coding for bacteriocins from S. epidermidis, which were partially different from those previously reported. Furthermore, this is the first report to show the complete sequence of an epidermin-carrying plasmid, pEpi56.


title: Mammals adjust diel activity across gradients of urbanization

abstract: Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator-prey dynamics. Yet, changes in animal behavior within the shorter 24-hour light-dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of eight mammal species across ten U.S. cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hour cycle to reduce risk, adapt, and therefore persist in human-dominated ecosystems.

category: ecology


title: Maturyoshka: a maturase inside a maturase, and other peculiarities of the novel chloroplast genomes of marine euglenophytes

abstract: Organellar genomes often carry group II introns, which occasionally encode proteins called maturases that are important for splicing. The number of introns varies substantially among various organellar genomes, and bursts of introns have been observed in multiple eukaryotic lineages, including euglenophytes, with more than 100 introns in their plastid genomes. To examine the evolutionary diversity and history of maturases, an essential gene family among euglenophytes, we searched for their homologs in newly sequenced and published plastid genomes representing all major euglenophytes lineages. We found that maturase content in plastid genomes has a patchy distribution, with a maximum of eight of them present in Eutreptiella eupharyngea. The most basal lineages of euglenophytes, Eutreptiales, share the highest number of maturases, but the lowest number of introns. We also identified a peculiar convoluted structure of a gene located in an intron, in a gene within an intron, within yet another gene, present in some Eutreptiales. Further investigation of functional domains of identified maturases shown that most of them lost at least one of the functional domains, which implies that the patchy maturase distribution is due to frequent inactivation and eventual loss over time. Finally, we identified the diversified evolutionary origin of analysed maturases, which were acquired along with the green algal plastid or horizontally transferred. These findings indicate that euglenophytes plastid maturases have experienced a surprisingly dynamic history due to gains from diversified donors, their retention, and loss.


title: Gene identification and genome annotation in Caenorhabditis briggsae by high throughput 5' RNA end determination

abstract: The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin C. elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the Trans-spliced Exon Coupled RNA End Determination (TEC-RED) technique. In addition to identifying the 5 ends of expressed genes, we have discovered operons and paralogs. In summary, our analysis yielded 10,243 unique 5 end sequence tags with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. These genes included 14 that are exclusively trans-spliced in C. briggsae when compared with C. elegans orthologs. A major contribution of this study is the identification of 493 operons, of which two-thirds are fully supported by tags. In addition, two SL1-type operons were discovered. Interestingly, comparisons with C. elegans showed that only 40% of operons are conserved. Of the remaining operons, 73 are novel, including 12 that entirely lack orthologs in C. elegans. Further analysis revealed that four of the 12 novel operons are conserved in C. nigoni. Altogether, the work described here has significantly advanced our understanding of the C. briggsae system and serves as a rich resource to aid biological studies involving this species.


title: Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons


title: Cell-adaptable dynamic hydrogel reinforced with stem cells improves the functional repair of spinal cord injury by alleviating neuroinflammation

abstract: Spinal cord injury (SCI) is one of the most challenging clinical issues. It is characterized by the disruption of neural circuitry and connectivity, resulting in neurological disability. Adipose-derived stem cells (ADSCs) serve as a promising source of therapeutic cells for SCI treatment. However, the therapeutic outcomes of direct ADSCs transplantation are limited in the presence of an inflammatory microenvironment. Herein, a cell-adaptable neurogenic (CaNeu) hydrogel was developed as a delivery vehicle for ADSCs to promote neuronal regeneration after SCI. The dynamic network of CaNeu hydrogel loaded with ADSCs provides a cell-infiltratable matrix that enhances axonal growth and eventually leads to improved motor evoked potential, hindlimb strength, and coordination of complete spinal cord transection in rats. Furthermore, the CaNeu hydrogel also establishes an anti-inflammatory microenvironment by inducing a shift in the polarization of the recruited macrophages toward the pro-regeneration (M2) phenotype. Our study showed that the CaNeu-hydrogel-mediated ADSCs delivery resulted in significantly suppressed neuroinflammation and apoptosis, and that this phenomenon involved the PI3K/Akt signaling pathway. Our findings indicate that the CaNeu hydrogel is a valuable delivery vehicle to assist stem cell therapy for SCI, providing a promising strategy for central nervous system diseases.


title: The coordination of hip, knee and ankle joint angles during gait in soccer players and controls

abstract:
BackgroundClinical researchers are trying to unravel the impact of different training interventions on the kinematics of human gait. However, the effects of long-term training experience on the kinematics of a healthy gait pattern remains unclear. Here we assess the effect of long-term training experience on joint angle variability during walking.

MethodsHip, knee, and ankle joint angles from fourteen soccer players and sixteen controls were acquired during treadmill and overground walking. Hip-knee coupling, knee-ankle coupling and coupling angle variability (CAV) of the right leg in the sagittal plane were assessed using a vector coding technique.

ResultsSoccer players showed reduced hip-knee CAV during the mid-stance and terminal-stance phases and reduced knee-ankle CAV during the pre-swing phase of gait compared to the control group. In addition, soccer players less often used an ankle coordination pattern, in which only the ankle joint but not the knee joint rotates.

InterpretationThese findings show that soccer players had more stability in the ankle joint during the stance phase of the gait compared to the control group. Future studies can test whether these differences in the coordination of the ankle joint reflect the effects of long-term training on normal gait by comparing knee-ankle coupling and variability before and after exercise training interventions.


title: Deep-learning based retinal fluid segmentation in optical coherence tomography images using a cascade of ENets

abstract: Optical coherence tomography (OCT) is a non-invasive, painless and reproducible examination which allows ophthalmologists to visualize retinal layers. This imaging modality is useful to detect diseases such as diabetic macular edema (DME) or age related macular degeneration (AMD), which are associated with fluid accumulations. In this paper, a cascade of deep convolutional neural networks is proposed using ENets for the segmentation of fluid accumulations in OCT B-Scans. After denoising the B-Scans, a first ENet extracts the region of interest (ROI) between the inner limiting membrane (ILM) and the Bruchs membrane (BM), whereas the second ENet segments the fluid in the ROI. A random forest classifier was applied on the segmented fluid regions to reject false positive. Our framework was trained on three different datasets with several diseases such as diabetic retinopathy (DR) and AMD. Our method achieves an average Dice Score for fluid segmentation of 0.80, 0.83 and 0.83 on the UMN DME, UMN AMD and Kermany datasets respectively.

category: bioinformatics


title: Coding sequence-independent homology search identifies highly divergent homopteran putative effector gene family

abstract: Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors. Sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall- forming aphid, Tetraneura ulmi, and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of Hormaphis cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.


title: Gene structure-based homology search identifies highly divergent putative effector gene family


title: Endothelial PHD2 Deficiency Induces Nitrative Stress via Suppression of Caveolin-1 in Pulmonary Arterial Hypertension

abstract: Nitrative stress is a characteristic feature of the pathology of human pulmonary arterial hypertension (PAH). However, the role of nitrative stress in the pathogenesis of obliterative vascular remolding and severe PAH remains largely unclear. Our recent studies identified a novel mouse model (Egln1Tie2Cre, Egln1 encoding prolyl hydroxylase 2 [PHD2]) with obliterative vascular remodeling and right heart failure, which provides us an excellent model to study the role of nitrative stress in obliterative vascular remodeling. Here we show that nitrative stress was markedly elevated whereas endothelial Caveolin-1 (Cav1) expression was suppressed in the lungs of Egln1Tie2Cre mice. Treatment with a superoxide dismutase mimetic, manganese (III) tetrakis (1-methyl-4-pyridyl) porphyrin pentachloride (MnTmPyP, also known as a peroxynitrite scavenger) treatment inhibited obliterative pulmonary vascular remodeling and attenuated severe PAH in Egln1Tie2Cre mice. Genetic restoration of endothelial Cav1 expression in Egln1Tie2Cre mice normalized nitrative stress, reduced PAH and improved right heart function. These data suggest that suppression of endothelial Cav1 expression secondary to PHD2 deficiency augments nitrative stress, which contributes to obliterative vascular remodeling and severe PAH. Thus, reactive oxygen/nitrogen species scavenger might have great therapeutic potential for the inhibition of obliterative vascular remodeling and severe PAH.


title: Endotaxis: A Universal Algorithm for Mapping, Goal-Learning, and Navigation

abstract: An animal entering a new environment typically faces three challenges: explore the space for resources, memorize their locations, and navigate towards those targets as needed. Experimental work on exploration, mapping, and navigation has mostly focused on simple environments - such as an open arena, a pond [1], or a desert [2] - and much has been learned about neural signals in diverse brain areas under these conditions [3, 4]. However, many natural environments are highly constrained, such as a system of burrows, or of paths through the underbrush. More generally, many cognitive tasks are equally constrained, allowing only a small set of actions at any given stage in the process. Here we propose an algorithm that learns the structure of an arbitrary environment, discovers useful targets during exploration, and navigates back to those targets by the shortest path. It makes use of a behavioral module common to all motile animals, namely the ability to follow an odor to its source [5]. We show how the brain can learn to generate internal "virtual odors" that guide the animal to any location of interest. This endotaxis algorithm can be implemented with a simple 3-layer neural circuit using only biologically realistic structures and learning rules. Several neural components of this scheme are found in brains from insects to humans. Nature may have evolved a general mechanism for search and navigation on the ancient backbone of chemotaxis.


title: Topological insights into the neural basis of flexible behavior

abstract: 1It is widely accepted that there is an inextricable link between neural computations, biological mechanisms, and behavior, but there exists no framework that can simultaneously explain all three. Here, we show that topological data analysis (TDA) provides that necessary bridge. We demonstrate that cognitive processes change the topological description of the shared activity of populations of visual neurons. These topological changes provide uniquely strong constraints on a mechanistic model, explain behavior, and, via a link with network control theory, reveal a tradeoff between improving sensitivity to subtle visual stimulus changes and increasing the chance that the subject will stray off task. These discoveries provide a blueprint for using TDA to uncover the biological and computational mechanisms by which cognition affects behavior in health and disease.


title: Global composition of the bacteriophage community in honeybees

abstract: The microbial communities in animal digestive systems are critical to host development and health. These assemblages of primarily viruses, bacteria, and fungi stimulate the immune system during development, synthesize important chemical compounds like hormones, aid in digestion, competitively exclude pathogens, etc. The bacteriophages in animal microbiomes are harder to characterize than the bacterial or fungal components of the microbiome and thus we know comparatively little about the temporal and spatial dynamics of bacteriophage communities in animal digestive systems. Recently, the bacteriophages of the honeybee gut were characterized in two European bee populations. Most of the bacteriophages described in these two reports were novel, encoded many metabolic genes in their genomes, and had a community structure that suggests coevolution with their bacterial hosts. To describe the conservation of bacteriophages in bees and begin to understand their role in the bee microbiome, we sequenced the virome of Apis mellifera from Austin, Texas and compared bacteriophage composition between three locations around the world. We found that the majority of bacteriophages from Austin are novel, sharing no sequence similarity to anything in public repositories. However, many bacteriophages are shared among the three bee viromes, indicating specialization of bacteriophages in the bee gut. Our study along with the two previous bee virome studies shows that the bee gut bacteriophage community is simple compared to that of many animals, consisting of several hundred types of bacteriophages that primarily infect four of the dominant bacterial phylotypes in the bee gut.


title: A lack of repeatability creates the illusion of a trade-off between basal and plastic cold tolerance.

abstract: The thermotolerance-plasticity trade-off hypothesis predicts that ectotherms with greater basal thermal tolerance have a lower acclimation capacity. This hypothesis has been tested at both high and low temperatures but the results often conflict. If basal tolerance constrains plasticity (e.g. through shared mechanisms that create physiological constraints), it should be evident at the level of the individual, provided the trait measured is repeatable. Here, we used chill-coma onset temperature and chill-coma recovery time (CCO and CCRT; non-lethal thermal limits) to quantify cold tolerance of Drosophila melanogaster across two trials (pre- and post-acclimation). Cold acclimation improved cold tolerance, as expected, but individual measurements of CCO and CCRT in non-acclimated flies were not (or only slightly) repeatable. Surprisingly, however, there was still a strong correlation between basal tolerance and plasticity in cold-acclimated flies. We argue that this relationship is a statistical artefact (specifically, a manifestation of regression to the mean; RTM) and does not reflect a true trade-off or physiological constraint. Thermal tolerance trade-off patterns in previous studies that used similar methodology are thus likely to be impacted by RTM. Moving forward, controlling and/or correcting for RTM effects is critical to determining whether such a trade-off or physiological constraint truly exists.


title: Conserved structural elements specialize ATAD1 as a membrane protein extraction machine

abstract: The mitochondrial AAA protein ATAD1 (in humans; Msp1 in yeast) removes mislocalized membrane proteins, as well as stuck import substrates from the mitochondrial outer membrane, facilitating their re-insertion into their cognate organelles and maintaining mitochondrias protein import capacity. In doing so, it helps to maintain proteostasis in mitochondria. How ATAD1 tackles the energetic challenge to extract hydrophobic membrane proteins from the lipid bilayer and what structural features adapt ATAD1 for its particular function has remained a mystery. Previously, we determined the structure of Msp1 in complex with a peptide substrate (Wang et al., 2020). The structure showed that Msp1s mechanism follows the general principle established for AAA proteins while adopting several structural features that specialize it for its function. We used the yeast growth assay to test the function of key amino acids within these structural elements. In this work, we determined the cryo-EM structures of the human ATAD1 in complex with a peptide substrate at near atomic resolution. The structures show that phylogenetically conserved structural elements adapt ATAD1 for its function while generally adopting a conserved mechanism shared by many AAA proteins. ATAD1s distinguishing features include an abundance of aromatic amino acids that line the central pore proposed to give ATAD1 a firm grip on its substrate and a short -helix at the C-terminus that strongly facilitates ATAD1s oligomerization. We also developed a microscopy-based assay reporting on protein mislocalization, with which we directly assessed ATAD1s activity in live cells.


title: Insight into mammary gland development and tumor prevention in a newly developed metastatic mouse model of breast cancer

abstract: The development of breast cancer has been observed due to altered regulation of mammary gland developmental processes. Thus, a better understand of the normal mammary gland development can reveal possible mechanism in how normal cells are re-programmed to become malignant cells. E2F1-4 are part of the E2F transcription factor family with varied roles in mammary development. However, little is known about the role of E2F5 in mammary gland development. A combination of scRNAseq and predictive signature tools demonstrate the presence of E2F5 in the mammary gland and showed altered activity during the various phases of mammary gland development and function. Testing the hypothesis that E2F5 regulates mammary function, we generated a mammary-specific E2F5 knockout mouse model, resulting in modest mammary gland development changes. However, after a prolonged latency the E2F5 conditional knockout mice developed highly metastatic mammary tumors with metastases in both the lung and liver. Transplantation of the tumors revealed metastases to lymph nodes that was enriched through serial transplantation. Through whole genome sequencing and RNAseq analysis we identified, and then confirmed in vivo, that Cyclin D1 was dysregulated in E2F5 conditional knockout mammary glands and tumors. Based on these findings, we propose that loss of E2F5 leads altered regulation of Cyclin D1, which facilitates the development of mammary tumors.


title: KEAP1 mutation in lung adenocarcinoma promotes immune evasion and immunotherapy resistance

abstract:
Lung cancer treatment has benefited greatly from the development of effective immune-based therapies. However, these strategies still fail in a large subset of patients. Tumor-intrinsic mutations can drive immune evasion via recruiting immunosuppressive populations or suppressing anti-tumor immune responses. KEAP1 is one of the most frequently mutated genes in lung adenocarcinoma patients and is associated with poor prognosis and inferior response to all therapies, including checkpoint blockade. Here, we established a novel antigenic lung cancer model and showed that Keap1-mutant tumors promote dramatic remodeling of the tumor immune microenvironment. Combining single-cell technology and depletion studies, we demonstrate that Keap1-mutant tumors diminish dendritic cell and T cell responses driving immunotherapy resistance. Importantly, analysis of KEAP1 mutant patient tumors revealed analogous decrease in dendritic cell and T cell infiltration. Our study provides new insight into the role of KEAP1 mutations in promoting immune evasion and suggests a path to novel immune-based therapeutic strategies for KEAP1 mutant lung cancer.

Statement of significanceThis study establishes that tumor-intrinsic KEAP1 mutations contribute to immune evasion through suppression of dendritic cell and T cell responses, explaining the observed resistance to immunotherapy of KEAP1 mutant tumors. These results highlight the importance of stratifying patients based on KEAP1 status and paves the way for novel therapeutic strategies.


title: Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and drought

abstract: Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of their levels is of great relevance for plant performance. Cellular IAA concentration depends on the combined result of its transport, biosynthesis and various redundant pathways to inactivate IAA, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high level of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock-out the group II GH3 pathway. The gh3oct plants had an improved root architecture, were more tolerant to osmotic stresses due to locally increased IAA levels and were more drought tolerant. IAA metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that oxIAA production depends, at least partly, on the GH3 pathway. Targeted stress-hormone analysis further suggested an involvement of ABA in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.

category: plant biology


title: Aging reduces calreticulin expression and alters spontaneous calcium signals in astrocytic endfeet of the mouse dorsolateral striatum

abstract:
Aging-related impairment of the blood brain barrier (BBB) and neurovascular unit (NVU) increases risk for neurodegeneration. Among the various cells participating in BBB and NVU function, spontaneous Ca2+ signals in astrocytic endfeet are crucial for maintaining BBB and NVU integrity. To assess if aging is associated with changes in spontaneous Ca2+ signals within astrocytic endfeet of the dorsolateral striatum (DLS), we expressed a genetically encoded Ca2+ indicator, Lck-GCaMP6f in DLS astrocytes of young (3-4 month) and aging (20-24 month) mice. Compared to young mice, endfeet in the DLS of aging mice demonstrated a decrease in calreticulin (CALR) expression, and dramatic alterations in the dynamics of endfoot membrane-associated and mitochondrial Ca2+ signals. While young mice required both extracellular and endoplasmic reticulum (ER) Ca2+ sources for generating endfoot Ca2+ signals, aging mice showed exclusive dependence on ER Ca2+. These data suggest that aging is associated with significant changes in Ca2+ buffers and Ca2+ signals within astrocytic endfeet, which has important implications for understanding mechanisms involved in aging-related impairment of the BBB and NVU.

Graphical abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/461710v1_ufig1.gif" ALT="Figure 1">
View larger version (30K):
org.highwire.dtl.DTLVardef@1d61571org.highwire.dtl.DTLVardef@19e2f9org.highwire.dtl.DTLVardef@18455cborg.highwire.dtl.DTLVardef@11ca928_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LIAging mice show reduced calreticulin expression in astrocytic endfeet
C_LIO_LIAging astrocytic endfeet show dramatic changes in spontaneous Ca2+ activity
C_LIO_LICa2+ signals in aging endfeet depend exclusively on endoplasmic reticulum Ca2+
C_LI


title: Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

abstract: Cohesin organizes the genome by forming intra-chromosomal loops and inter-sister chromatid linkages. During gamete formation by meiosis, chromosomes are reshaped to support crossover recombination and two consecutive rounds of chromosome segregation. Here we show that Eco1 acetyltransferase positions both chromatin loops and sister chromatid cohesion to organize meiotic chromosomes into functional domains in budding yeast. Eco1 acetylates the Smc3 cohesin subunit in meiotic S phase to establish chromatin boundaries, independently of DNA replication. Boundary formation by Eco1 is critical for prophase exit and for the maintenance of cohesion until meiosis II, but is independent of the ability of Eco1 to antagonize the cohesin-release factor, Wpl1. Conversely, prevention of cohesin release by Wpl1 is essential for centromeric cohesion, kinetochore monoorientation and co-segregation of sister chromatids in meiosis I. Our findings establish Eco1 as a key determinant of chromatin boundaries and cohesion positioning, revealing how local chromosome structuring directs genome transmission into gametes.


title: Regulation of membrane homeostasis by TMC1 mechanoelectrical transduction channelsis essential for hearing

abstract: The mechanoelectrical transduction (MET) channel complex of auditory hair cells converts sound into electrical signals, allowing us to hear. After decades of research, the transmembrane-like channel 1 and 2 (TMC1 and TMC2) have been recently identified as pore-forming subunits of the MET channels, but the molecular peculiarity that differentiates these two proteins and makes TMC1 essential for hearing remains elusive. Here, we show that TMC1, but not TMC2, is essential for membrane remodeling triggered by a decrease in intracellular calcium concentration. We demonstrate that inhibition of MET channels or buffering of intracellular calcium lead to pronounced phosphatidylserine externalization, membrane blebbing and ectosome release at the hair cell sensory organelle, culminating in the loss of TMC1 protein. Moreover, three TMC1 deafness-causing mutations cause constitutive phosphatidylserine externalization that correlates with the deafness phenotype, suggesting that the mechanisms of hearing loss involve alterations in membrane homeostasis.


title: RNA helicase DDX6 in P-bodies is essential for the assembly of stress granules

abstract:
Two prominent cytoplasmic RNA granules, ubiquitous RNA-processing bodies (PB) and inducible stress granules (SG), regulate storage of translationally arrested mRNAs and are intimately related. In this study, we found the dependence of SG formation on PB in the cells under arsenite (ARS) stress, but not the other way around. GW182, 4E-T and DDX6 essential for PB formation differentially affect SG formation in the cells under ARS stress, with DDX6 being the most prominent. The cells with DDX6 deficiency display irregular shape of SG which could be rescued by ectopic wt DDX6, but not its helicase mutant E247A DDX6, which induces SG in the cells without stress, indicating that DDX6 helicase activity is essential for PB, but suppressive for SG. DDX6s dual roles are independent of DDX6 interactors EDC3, CNOT1, and PAT1B. This study provides a conceptual advance of how DDX6 involves in the biogenesis of PB and SG.

HighlightsO_LIPB act as the seeds for SG nucleation
C_LIO_LIPB components colocalize with SG
C_LIO_LIDDX6 plays a critical role in biogenesis of both PB and SG
C_LIO_LIDDX6 helicase activity prevents SG formation in normal cells
C_LI


title: Structure insights of the human peroxisomal ABC transporter ALDP

abstract: Adrenoleukodystrophy protein (ALDP) is responsible for the transport of free very-long-chain fatty acids (VLCFAs) and corresponding CoA-esters across the peroxisomal membrane. ALDP belongs to the ATP-binding cassette sub-family D, which is also named as ABCD1. Dysfunction of ALDP leads to peroxisomal metabolic disorder exemplified by X-linked adrenoleukodystrophy (ALD). Hundreds of ALD-causing mutations are identified on ALDP. However, the pathogenic mechanisms of these mutations are restricted to clinical description due to limited structural information. Furthermore, ALDP plays a role in myelin maintenance, which is tightly associated with axon regeneration. Here we report the cryo-electron microscopy (cryo-EM) structure of human ALDP with nominal resolution of 3.4 [A] in nucleotide free state. The structure of ALDP exhibits a typical assembly of ABC transporters. The nucleotide binding domains (NBDs) displays a ligand free state. ALDP exhibits an inward-open conformation to the cytosol. A short helix is located at the peroxisomal side, which is different from other three members of ABCD transporters. The two transmembrane domains (TMDs) of ALDP form a cavity, in which two lipid-like densities can be recognized as the head group of an coenzyme-A ester of a lipid. This structure provides a framework for understanding the working mechanism of ALDP and classification of the disease-causing mutations.


title: Age of diabetes onset in the mutant proinsulin syndrome correlates with mutational impairment of protein foldability and stability

abstract: Diverse heterozygous mutations in the human insulin gene cause a monogenic diabetes mellitus (DM) syndrome due to toxic misfolding of the variant proinsulin. Whereas mutations that add or remove cysteines (thereby leading to an odd number of thiol groups) generally lead to neonatal-onset DM, non-Cys-related mutations can be associated with a broad range of ages of onset. Here, we compare two mutations at a conserved position in the central B-chain -helix: one neonatal in DM onset (ValB18[->]Gly) and the other with onset delayed until adolescence (AlaB18). The substitutions were introduced within a 49-residue single-chain insulin precursor optimized for folding efficiency (Zaykov, A., et al. ACS Chem. Biol. 9, 683-91 (2014)). Although mutations are each unfavorable, GlyB18 (a) more markedly perturbs DesDi folding efficiency in vitro than does AlaB18 and (b) more severely induces endoplasmic reticulum (ER) stress in cell-based studies of the respective proinsulin variants. In corresponding two-chain hormone analogs, GlyB18 more markedly perturbs structure, function and thermodynamic stability than does AlaB18. Indeed, the GlyB18-insulin analog forms a molten globule with attenuated -helix content whereas the AlaA18 analog retains a nativelike cooperative structure with reduced free energy of unfolding ({Delta}{Delta}Gu 1.2({+/-}0.2) kcal/mole relative to ValB18 parent). We propose that mutations at B18 variably impede nascent pairing of CysB19 and CysA20 to an extent correlated with perturbed core packing once native disulfide pairing is achieved. Differences in age of disease onset (neonatal or adolescent) reflect relative biophysical perturbations (severe or mild) of an obligatory on-pathway protein folding intermediate.