title: rTg(TauP301L)4510 mice exhibit increased VGLUT1 in hippocampal presynaptic glutamatergic vesicles and increased extracellular glutamate release

abstract: The molecular pathways that contribute to the onset of symptoms in tauopathy models, including Alzheimers Disease (AD), are difficult to distinguish because multiple changes can happen simultaneously at different stages of disease progression. Understanding early synaptic alterations and their supporting molecular pathways is essential in order to develop better pharmacological targets to treat AD. Here we focus on an early onset rTg(TauP301L)4510 tauopathy mouse model that exhibits hyperexcitability in hippocampal neurons of adult mice that is correlated with presynaptic changes and increased extracellular glutamate levels. However, it is not clear if increased extracellular glutamate is caused by presynaptic changes alone, or if presynaptic changes are a contributing factor among other factors. To determine whether pathogenic tau alters presynaptic function and glutamate release, we studied cultured hippocampal neurons at 14-18 DIV from animals of both sexes to measure presynaptic changes in tauP301L positive mice. We observed that presynaptic vesicles exhibit increased vesicular glutamate transporter 1 (VGLUT1) using immunohistochemistry of fixed cells and an established pH-sensitive green fluorescent protein approach. We show that tauP301L positive neurons exhibit a 40% increase in VGLUT1 per vesicle compared to tauP301L negative littermates. Further, we use the extracellular glutamate reporter iGluSnFR to show that increased VGLUT1 per vesicle directly translates into a 40% increase in extracellular glutamate. Together, these results show that increased extracellular glutamate levels observed in tauP301L mice are not caused by increased vesicle exocytosis probability but rather are directly related to increased VGLUT1 transporters per synaptic vesicle.


title: Synaptotagmin 7 docks synaptic vesicles for Doc2α-triggered asynchronous neurotransmitter release

abstract: The molecular basis of asynchronous neurotransmitter release remains enigmatic despite decades of intense study. Synaptotagmin (syt) 7 and Doc2 have both been proposed as Ca2+ sensors that trigger this mode of exocytosis, but conflicting findings have led to controversy. Here, we demonstrate that at excitatory mouse hippocampal synapses, Doc2 is the major Ca2+ sensor for asynchronous release, while syt7 supports this process through activity-dependent docking of synaptic vesicles. In synapses lacking Doc2, asynchronous release after single action potentials is strongly reduced, while deleting syt7 has no effect. However, in the absence of syt7, docked vesicles cannot recover on millisecond timescales. Consequently, both synchronous and asynchronous release depress from the second pulse on during repetitive activity. By contrast, synapses lacking Doc2 have normal activity-dependent docking, but continue to exhibit decreased asynchronous release after multiple stimuli. Moreover, disruption of both Ca2+ sensors is non-additive. These findings result in a new model whereby syt7 drives activity-dependent docking, thus  feeding synaptic vesicles to Doc2 for asynchronous release during on-going transmission.

category: neuroscience


title: Birth and Death in Terminal Complement Pathway

abstract: The cytolytic activity of the membrane attack complex (MAC) has a crucial role in the complement-mediated elimination of pathogens. Terminal complement pathway (TCP) genes encode the proteins that form the MAC. Although the TCP genes are well conserved within most vertebrate species, the early evolution of the TCP genes is poorly understood. Based on the comparative genomic analysis of the early evolutionary history of the TCP homologs, we evaluated four possible scenarios that could have given rise to the vertebrate TCP. Currently available genomic data support a scheme of complex sequential protein domain gains that may be responsible for the birth of the vertebrate C6 gene. The subsequent duplication and divergence of this vertebrate C6 gene formed the C7, C8, C8{beta}, and C9 genes. Compared to the widespread conservation of TCP components within vertebrates, we discovered that C9 has disintegrated in the genomes of galliform birds. Publicly available genome and transcriptome sequencing datasets of chicken from Illumina short read, PacBio long read, and Optical mapping technologies support the validity of the genome assembly at the C9 locus. In this study, we have generated a >120X coverage whole-genome Chromium 10x linked-read sequencing dataset for the chicken and used it to verify the loss of the C9 gene in the chicken. We find multiple CR1 (chicken repeat 1) element insertions within and near the remnant exons of C9 in several galliform bird genomes. The reconstructed chronology of events shows that the CR1 insertions occurred after C9 gene loss in an early galliform ancestor. Our study of C6 gene birth in an early vertebrate ancestor and C9 gene death in galliform birds provides insights into the evolution of the TCP.

category: immunology


title: Drosophila immunity: The Drosocin gene encodes two host defence peptides with pathogen-specific roles

abstract: 1.1Antimicrobial peptides (AMPs) are key players in innate defence against infection in plants and animals. In Drosophila, many host defence peptides are produced downstream of the Toll and Imd NF-{kappa}B pathways. Use of single and compound AMP mutations in Drosophila has revealed that AMPs can additively or synergistically contribute to combat pathogens in vivo. However, these studies also revealed a high degree of specificity, wherein just one AMP can play a major role in combatting a specific pathogen. We recently uncovered a specific importance of the antibacterial peptide Drosocin for defence against Enterobacter cloacae. Here, we show that the Drosocin locus (CG10816) is more complex than previously described. In addition to its namesake peptide "Drosocin", it encodes a second peptide generated from a precursor via furin cleavage. We name this peptide "Buletin", and show that it corresponds to the uncharacterized "Immune-induced Molecule 7" previously identified by MALDI-TOF. The existence of a naturally occurring polymorphism (Thr52Ala) in the CG10816 precursor protein masked the identification of this peptide previously. Using mutations differently affecting the production of these two CG10816 gene products, we show that Drosocin, but not Buletin, contributes to the CG10816-mediated defence against E. cloacae. Strikingly, we observed that Buletin, but not Drosocin, contributes to the CG10816-mediated defence against Providencia burhodogranariea. Moreover, the Thr52Ala polymorphism in Buletin affects survival to P. burhodogranariea, wherein the Alanine allele confers better defence than the Threonine allele. However, we found no activity of Buletin against either P. burhodogranariea or E. coli in vitro. Collectively, our study reveals that CG10816 encodes not one but two prominent host defence peptides with different specificity against different pathogens. This finding emphasizes the complexity of the Drosophila humoral response consisting of multiple host defence peptides with specific activities, and demonstrates how natural polymorphisms found in Drosophila populations can affect host susceptibility.


title: Yield Stress and Creep Control Depot Formation and Persistence of Injectable Hydrogels Following Subcutaneous Administration

abstract: Hydrogels that can be injected into the body using standard needles or catheters enable a minimally invasive strategy to prolong local delivery of therapeutic drug and cellular cargo. In particular, physically crosslinked hydrogels exhibit shear-thinning and self-healing behaviors enabling facile injectability and depot formation upon administration. While prior efforts to characterize these systems have focused on injectability and cargo release behaviors, prediction of cargo release in the body often assumes the materials form a depot rather than spreading out upon administration. Here, we evaluate how hydrogel rheology correlates with depot formation and persistence following subcutaneous administration in mice with two physicochemically-distinct, physically crosslinked hydrogel systems. We evaluate calcium-alginate and polymer-nanoparticle hydrogel systems exhibiting variable mechanical behaviors across several rheological properties (stiffness, viscoelasticity, yield stress, and creep). By relating measured rheological properties to depot formation and persistence time following subcutaneous administration, we identify that yield stress is predictive of initial depot formation while creep is predictive of depot persistence. Indeed, only materials with yield stresses greater than 25 Pa form robust depots and reduced creep correlates with longer depot persistence. These findings provide predictive insights into design considerations for hydrogel technologies capable of extended controlled release of therapeutic cargo.

category: bioengineering


title: Low temperature induced quiescence in parasitoids Trichogramma evanescens Westwood and Trichogramma chilonis Ishii reared on Plodia interpunctella (Hübner): Its utilization as quality control for mass rearing

abstract: Egg parasitoid, Trichogramma spp. is an important potential biological control agent for wide range of lepidopteran pests. Cold storage of host eggs has been proposed as a valuable technique for ensuring the release of sufficient parasitoid numbers whenever it is needed. Thus, the impact of low temperatures to induce quiescence in Trichogramma evanescens and Trichogramma chilonis was studied using eggs of Plodia interpunctella as hosts. Prepupae of the parasitoids Trichogramma evanescens and T.chilonis were stored for 15, 30, 45, 60 and 75 d at 4{degrees}C, following a 7 d period of acclimation at 10{degrees}C. Both parasitoid species seem to survive unfavorable temperature conditions by entering a state of quiescence. Parasitism, adult emergence, female proportion relative to male and F1 adult emergence were not affected by cold storage in either parasitoid for up to 30 d of storage. Parasitized host eggs of P. interpunctella can be stored for up to 60 d at 4{degrees}C for both parasitoids, but there was no emergence at 75 d. Results clearly show that there are specific intervals of cold storage during which the parasitoids can remain unaffected for relatively long periods of time. Although we observed some adverse effect in longevity and parasitism rates, the technique described here can be further utilized in mass rearing strategies of egg parasitoids for relatively long periods that will allow shipment and application in biological control programs.

category: zoology


title: Neuromuscular denervation and deafferentation but not motor neuron death are disease features in the Smn 2B/- mouse model of SMA

abstract: Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by loss of motor neurons and skeletal muscle atrophy which is caused by ubiquitous deficiency in the survival motor neuron (SMN) protein. Several cellular defects contribute to sensory-motor circuit pathology in SMA mice, but the underlying mechanisms have often been studied in one mouse model without validation in other available models. Here, we used Smn2B/- mice to investigate specific behavioral, morphological, and functional aspects of SMA pathology that we previously characterized in the SMN{Delta}7 model. Smn2B/- SMA mice on a pure FVB/N background display deficits in body weight gain and muscle strength with onset in the second postnatal week and median survival of 19 days. Morphological analysis revealed severe loss of proprioceptive synapses on the soma of motor neurons and prominent denervation of neuromuscular junctions (NMJs) in axial but not distal muscles. In contrast, no evidence of cell death emerged from analysis of several distinct pools of lumbar motor neurons known to be lost in the disease. Moreover, SMA motor neurons from Smn2B/- mice showed robust nuclear accumulation of p53 but lack of phosphorylation of serine 18 at its amino-terminal, which selectively marks degenerating motor neurons in the SMN{Delta}7 mouse model. These results indicate that NMJ denervation and deafferentation, but not motor neuron death, are conserved features of SMA pathology in Smn2B/- mice.


title: Asymmetric dysregulation of glutamate dynamics across the synaptic cleft in a mouse model of Alzheimer disease

abstract: Most research on glutamate spillover focuses on the deleterious consequences of postsynaptic glutamate receptor overactivation. However, two decades ago, it was noted that the glial coverage of hippocampal synapses is asymmetric: astrocytic coverage of postsynaptic sites exceeds coverage of presynaptic sites by a factor of four. The fundamental relevance of this glial asymmetry remains poorly understood. Here, we used the glutamate biosensor iGluSnFR, and restricted its expression to either CA3 or CA1 neurons to visualize glutamate dynamics at pre- and postsynaptic microenvironments, respectively. We demonstrate that inhibition of the primarily astrocytic glutamate transporter-1 (GLT-1) slows glutamate clearance to a greater extent at presynaptic compared to postsynaptic membranes. GLT-1 expression was reduced early in a mouse model of AD, resulting in slower glutamate clearance rates at presynaptic but not postsynaptic membranes that opposed presynaptic short-term plasticity. Overall, our data demonstrate that the presynapse is particularly vulnerable to GLT-1 dysfunction and may have implications for presynaptic impairments in a variety of brain diseases.


title: Breakpoint models shown no evidence of thresholds in recreational response to increasing wildfire smoke in the American West

abstract: Ambient wildfire smoke in the American West has worsened considerably in recent decades, while the number of individuals recreating outdoors has simultaneously surged. Wildfire smoke poses a serious risk to human health, especially during long periods of exposure and during exercise. Here we aggregate data on black carbon, a major component of wildfire smoke, and recreational visitation in 32 U.S. national parks from 1980 - 2019 to examine how visitors respond to wildfire smoke. We hypothesize that visitor response may exhibit a threshold effect where ambient smoke reduces visitation after a critical level, but not before. We develop a series of breakpoint models to test this hypothesis. Overall, these models show little to no effect of ambient smoke on visitation to the 32 parks tested, even when allowing for critical thresholds at the extreme upper ranges of the smoke data. This suggests that wildfire smoke does not significantly alter behavior of park attendance. This finding has implications for the management of recreation areas, public health, and climate change adaptation broadly.

category: ecology


title: Private and sub-family specific mutations of founder haplotypes in the BXD family reveal phenotypic consequences relevant to health and disease

abstract:
The BXD recombinant inbred (RI) mouse strains are the largest and most deeply phenotyped inbred panel of vertebrate organisms. RIs allow phenotyping of isogenic individuals across virtually any environment or treatment. We performed whole genome sequencing and generated a compendium of SNPs, indels, short tandem repeats, and structural variants in these strains and used them to analyze phenomic data accumulated over the past 50 years.

We show that BXDs segregate >6 million variants with high minor allele which are dervied from the C57BL/6J and DBA/2J founders and use this dense variant set to define  infinite marker maps and a novel family-level pangenome. We additionally characterize rates and spectra de novo variants which have accumulated over 20-200 generations of inbreeding, and have largely been ignored previously. Overall, the uniquely rich phenome when linked with WGS enables a new type of integrative modeling of genotype-to-phenotype relations.

category: genomics


title: Improving the assessment of deep learning models in the context of drug-target interaction prediction

abstract: AO_SCPLOWBSTRACTC_SCPLOWMachine Learning techniques have been widely adopted to predict drug-target interactions, a central area of research in early drug discovery. These techniques have shown promising results on various benchmarks although they tend to suffer from poor generalization. This is typically related to very sparse and nonuniform datasets available, which limits the applicability domain of machine learning techniques. Moreover, widespread approaches to split datasets (into training and test sets) treat a drug-target interaction as an independent entities, when in reality the drug and target involved may take part in other interactions, breaking apart the assumption of independence. We observe that this leads to overly optimistic test results and poor generalization of out-of-distribution samples for various state-of-the-art sequence-based machine learning models for drug-target prediction. We show that previous approaches to reduce bias in binding datasets focus on drug or target information only and, thus, lead to similar pitfalls. Finally, we propose a minimum viable solution to evaluate the generalization capability of a machine learning model based on the systematic separation of test samples with respect to drugs and targets in the training set, thus discerning the three out-of-distribution scenarios seen at test time: (1) drug or (2) target present in the training set, or (3) neither.

category: bioinformatics


title: Comparative transcriptomics and metabolomics reveal specialized metabolite drought stress responses in switchgrass (Panicum virgatum L.)

abstract:
O_LISwitchgrass (Panicum virgatum) is a bioenergy model crop valued for its energy efficiency and drought tolerance resilience. The related monocot species rice (Oryza sativa) and maize (Zea mays) deploy species-specific, specialized metabolites as core stress defenses. By contrast, specialized chemical defenses in switchgrass are largely unknown.
C_LIO_LITo investigate specialized metabolic drought responses in switchgrass, we integrated tissue-specific transcriptome and metabolite analyses of the genotypes Alamo and Cave-in-Rock that feature different drought tolerance.
C_LIO_LIThe more drought-susceptible Cave-in-Rock featured an earlier onset of transcriptomic changes and significantly more differentially expressed genes in response to drought compared to Alamo. Specialized pathways showed moderate differential expression compared to pronounced transcriptomic alterations in carbohydrate and amino acid metabolism. However, diterpenoid-biosynthetic genes showed drought-inducible expression in Alamo roots, contrasting largely unaltered triterpenoid and phenylpropanoid pathways. Metabolomic analyses identified common and genotype-specific flavonoids and terpenoids. Consistent with transcriptomic alterations, several root diterpenoids showed significant drought-induced accumulation, whereas triterpenoid abundance remained predominantly unchanged. Structural analysis of drought-responsive root diterpenoids verified these metabolites as oxygenated furanoditerpenoids.
C_LIO_LIDrought-dependent transcriptome and metabolite profiles provide the foundation to understand the molecular mechanisms underlying switchgrass environmental resilience. Accumulation of specialized root diterpenoids and corresponding pathway transcripts supports a role in drought stress tolerance for these compounds.
C_LI

Significance statementWith an increasing demand for renewable energy opposed by rising climate-driven crop losses, understanding, and leveraging plant natural defenses can enable the development of sustainable crop production systems. Here, we integrated comparative transcriptomics and metabolomics analyses to gain a detailed understanding of the diversity and physiological relevance of specialized metabolites in upland and lowland switchgrass ecotypes and provide resources for future investigations of drought response mechanisms in switchgrass.

category: plant biology


title: Microbiota-induced active translocation of peptidoglycan across the intestinal barrier dictates its within-host dissemination

abstract: Peptidoglycan, the major structural polymer forming the cell wall of bacteria, is an important mediator of physiological and behavioral effects in mammalian hosts. These effects are frequently linked to its translocation from the intestinal lumen to host tissues. However, the modality and regulation of this translocation across the gut barrier has not been precisely addressed. In this study, we characterized the absorption of peptidoglycan across the intestine and its systemic dissemination. We report that peptidoglycan has a distinct tropism for host organs when absorbed via the gut, most notably by favoring access to the brain. We demonstrate that intestinal translocation of peptidoglycan occurs through a microbiota-induced active process. This process is regulated by the parasympathetic pathway via the muscarinic acetylcholine receptors. Together, this study reveals fundamental parameters concerning the uptake of a major microbiota molecular signal from the steady-state gut.

category: microbiology


title: McaA and McaB control the dynamic positioning of a bacterial magnetic organelle

abstract: Magnetotactic bacteria (MTB) are a diverse group of microorganisms that use intracellular chains of ferrimagnetic nanocrystals, produced within their magnetosome organelles, to align and navigate along the geomagnetic field. The cell biological and biochemical properties of magnetosomes make them a powerful model for studying the molecular mechanisms of biomineralization and compartmentalization in bacteria. While several conserved magnetosome formation genes have been described, the evolutionary strategies for their species-specific diversification remain unknown. Here, we demonstrate that the fragmented nature of magnetosome chains in Magnetospirillum magneticum AMB-1 is controlled by two genes named mcaA and mcaB. McaA recognizes the positive curvature of the inner cell membrane while McaB localises to magnetosomes. Along with the MamK actin-like cytoskeleton, they create space for addition of new magnetosomes in between pre-existing magnetosomes. Phylogenetic analyses suggest that McaAB homologs are widespread and may represent an ancient strategy for organelle positioning in MTB.


title: Diversity of Secretion System Apparatus in Tomato Wilt Causing Ralstonia solanacearum Strains: a Comparative Analysis Using in-silico Approach

abstract: Ralstonia solanacearum (Rs) species is the leading cause of bacterial wilt disease in a wide range of host plants worldwide. In the present study, secretion system analysis of five tomato pathogenic Rs strains was carried out in-silico. This paper describes a new protocol to identify the secretion system components i.e. SSCs (T1SS-T6SS, Flg, T4P, and Tad-Tat). A total of 865 SSCs were identified using the new protocol. Contributions of SSCs into core-secretion system apparatus (i.e. SSA) were also studied. Synteny was discovered among the secretion system apparatus (SSA) where relative frequency of SSCs to core-SSA is high (>20%) which includes T1SS, T2SS, T5SS, T4P, and Tad-Tat, but excludes T3SS, T4SS, and Flg. To the best of our knowledge, this is the first report indicating that during the evolution of Rs, most of the secretion system apparatus (T1SS, T2SS, T5SS, T4P, and Tad-Tat) were highly conserved and came from a single ancestor, while T3SS and T6SS may have arrived later, probably from horizontal gene transfer.


title: Improved assessments of milk microbiota composition via sample preparation and DNA extraction methods

abstract: Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is now a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine milk, we assembled a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. Variations to the following methods were examined: BCMC enumeration method (colony enumeration or microscopy), sample volume (200 l to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was shown to be more accurate for quantification of the BCMC contents. We found that least 10 mL ([≥] 104 cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. These approaches were confirmed to provide similar results in commercial milk samples. Overall, variations in cell lysis methods conferred the greatest changes to milk microbiota composition and therefore should be optimized for sample type.


title: Transient developmental increase in cortical projections to amygdala GABAergic neurons contribute to circuit dysfunction following early life stress

abstract: Early life stress (ELS) results in enduring dysfunction of the cortico-limbic circuitry, underlying emotional and social behavior. However, the neurobiological mechanisms by which ELS affects development of the circuitry remain elusive. Here, we have combined viral tracing and electrophysiological techniques to study the effects of maternal separation (MS) on fronto-limbic connectivity and function in young (P14-21) rats. We report that aberrant prefrontal (mPFC) inputs to basolateral amygdala (BLA) GABAergic interneurons transiently increase the strength of feedforward inhibition in the BLA, which raises LTP induction threshold in MS treated male rats. The enhanced GABAergic activity after MS exposure associates with lower functional synchronization within prefrontal-amygdala networks in vivo. Intriguingly, no differences in these parameters were detected in females, which were also resistant to MS dependent changes in anxiety-like behaviors. Impaired plasticity and synchronization during the sensitive period of circuit refinement may contribute to long-lasting functional changes in the prefrontal-amygdaloid circuitry that predispose to neuropsychiatric conditions later on in life.


title: Cerebral activity in monkeys Papio anubis during the perception of conspecific and heterospecific agonistic vocalizations: A functional Near Infrared Spectroscopy study

abstract: Are conspecific emotional vocalizations special? Although often investigated in non-human primates using functional magnetic resonance imaging or positron emission tomography, it remains unclear whether the listening of conspecific vocal emotions leads to similar or different cerebral activations when compared to heterospecific calls (i.e. expressed by another primate species). Using a neuroimaging technique rarely employed in monkeys so far, functional Near Infrared Spectroscopy (fNIRS), the present study investigated cortical temporal activities during exposure to both conspecific and heterospecific calls in three female adult baboons (Papio anubis). The three subjects were lightly anesthetized and passively exposed to agonistic baboon and chimpanzee (Pan troglodytes) vocalizations, as well as energy matched white noises in order to control for this low-level acoustic feature. Despite inter-individual variabilities, permutation test analyses on the extracted OxyHemoglobin signal revealed for two subjects out of three significant differences between the passive listening of baboon versus chimpanzee stimuli. Additionally, in one subject, a modulation of the left temporal cortex activity was found for the perception of baboon calls contrasted to chimpanzee vocalizations as well as for the passive listening of baboon white noises compared to chimpanzee ones. Although the lack of generalization of those findings in all three subjects prevents us to drawn any conclusion and that more subjects would be needed, the hypothesis that baboons cortical temporal regions may be more sensitive to the processing of conspecific sounds compared to heterospecific stimuli is not excluded. Our study highlights that fNIRS may be a promising alternative to further investigate the auditory mechanisms at play in the right and left baboons temporal cortices for the processing of emotional vocalizations.


title: Molecular-enriched functional connectivity in the human brain using multiband multi-echo simultaneous ASL/BOLD fMRI

abstract:
Receptor-Enriched Analysis of functional Connectivity by Targets (REACT) is a novel analytical strategy that enriches functional connectivity (FC) information from functional MRI (fMRI) with molecular information on the neurotransmitter distribution density in the human brain, providing a biological basis to the FC analysis. So far, this integrative approach has been used in blood oxygen level-dependent (BOLD) fMRI studies only, providing new insights into the brain mechanisms underlying specific disorders and its response to pharmacological challenges. In this study, we demonstrate that the application of REACT can be further extended to arterial spin labelling (ASL) fMRI. Some of the advantages of this extension include the combination of neurotransmitter specific information provided by molecular imaging with a quantitative marker of neuronal activity, the suitability of ASL for pharmacological MRI (phMRI) studies assessing drug effects on baseline brain function, and the possibility to acquire images that are not affected by susceptibility artifacts in the regions linked to major neurotransmitter systems.

In this work, we tested the feasibility of applying REACT to resting state ASL fMRI and compared the molecular-enriched FC maps derived from ASL data with those derived from BOLD data. We applied REACT to high-resolution, whole-brain simultaneous ASL/BOLD resting-state fMRI data of 29 healthy subjects and estimated the ASL- and BOLD-based FC maps related to six molecular systems, including the transporters of dopamine, noradrenaline, serotonin and vesicular acetylcholine, and the GABA-A and mGlu5 receptors. We then compared the ASL and BOLD FC maps in terms of spatial similarity, using the Dice Similarity Index and the voxel-wise spatial correlation. On a data subsample (N=19) we also evaluated the test-retest reproducibility of each modality using the regional intraclass correlation coefficient, and compared the two modalities.

Our results showed robust spatial patterns of molecular-enriched functional connectivity for both modalities, moderate to high similarity between BOLD- and ASL-derived FC maps and mixed results in terms of reproducibility (i.e., none of the modalities outperformed the other). Overall, our findings show that the ASL signal is as informative as BOLD in detecting functional circuits associated with specific molecular pathways, and that the two modalities may provide complementary information related to these circuits.

Considering the more direct link of ASL imaging with neuronal acrivity compared to BOLD and its suitability for phMRI studies, this new integrative approach could become a valuable asset in clinical studies investigating functional alterations in patients with brain disorders, or in pharmacological studies investigating the effects of new or existing compounds on the brain.


title: Pallidal neuromodulation of the explore/exploit trade-off in decision-making

abstract: Every decision that we make involves a conflict between exploiting our current knowledge of an actions value or exploring alternative courses of action that might lead to a better, or worse outcome. The sub-cortical nuclei that make up the basal ganglia have been proposed as a neural circuit that may contribute to resolving this explore-exploit  dilemma. To test this hypothesis, we examined the effects of neuromodulating the basal ganglias output nucleus, the globus pallidus interna, in patients who had undergone deep brain stimulation (DBS) for isolated dystonia. Neuromodulation enhanced the number of exploratory choices to the lower value option in a 2-armed bandit probabilistic reversal-learning task. Enhanced exploration was explained by a reduction in both rate of evidence accumulation (drift rate) and by the amount of evidence needed to decide (boundary separation) in a reinforcement learning drift diffusion model. We estimated the functional connectivity profile between the stimulating DBS electrode and the rest of the brain using a normative functional connectome derived from heathy controls. Variation in the extent of neuromodulation induced exploration between patients was predicted by the degree of functional connectivity between the stimulating electrode and prefrontal and sensorimotor cortices. We conclude that the basal ganglias output nucleus, the globus pallidus interna, can adaptively modify decision choice when faced with the dilemma to explore or exploit.


title: Architecture and Assembly Mechanism of Human LACTB

abstract: Mitochondria are complex organelles that play a central role in metabolism. Dynamic membrane-associated processes regulate mitochondrial morphology and biogenesis in response to cellular demand. In tumor cells, metabolic reprogramming requires active mitochondrial metabolism for providing key metabolites and building blocks for tumor growth and rapid proliferation. To counter this, the mitochondrial serine beta-lactamase-like protein (LACTB) alters mitochondrial lipid metabolism and potently inhibits the proliferation of a variety of tumor cells. Mammalian LACTB is localized in the mitochondrial intermembrane space, where it assembles into filaments to regulate mitochondrial membrane organization and the efficiency of essential metabolic processes. However, the structural basis of LACTB polymerization and regulation remains incompletely understood. Here, we describe how human LACTB self-assembles into micron-scale filaments that increase their catalytic activity. The electron cryo-microscopy (cryoEM) structure defines the mechanism of assembly and reveals how highly ordered filament bundles stabilize the active state of the enzyme. We identify and characterize residues that are located at the filament-forming interface, and further show that mutations that disrupt filamentation reduce enzyme activity. Furthermore, our results provide evidence that LACTB filaments can bind lipid membranes. These data reveal the detailed molecular organization and polymerization-based regulation of human LACTB and provide new insights into the mechanism of mitochondrial membrane organization that modulates tumor suppression.

category: biophysics


title: Apurinic/apyrimidinic nuclease 1 drives genomic evolution contributing to chemoresistance and tumorigenesis in solid tumor

abstract: Genomic instability fuels genomic alterations that befit cancer cells with necessary adaptations to keep proliferating and overcome the impact of host anti-tumor immunity and cytotoxic therapy. Since DNA breaks are required for genomic rearrangements to take place, we hypothesized that dysregulated nuclease activity mediates genomic instability in cancer. Using an integrated genomics protocol, we identified a four gene deoxyribonuclease signature correlating with genomic instability in six human cancers which included adenocarcinomas of esophagus (EAC), lung, prostate, stomach, pancreas and triple negative breast cancer. Functional screens confirmed the role of these nucleases in genomic instability and growth of cancer cells. Apurinic/apyrimidinic nuclease 1 (APE1), identified as top nuclease in functional screen, was further investigated in five cell lines representing four solid tumors (EAC, lung, prostate and breast cancer). We demonstrate that chemical as well as transgenic suppression of APE1 impaired growth/colony formation and increased cytotoxicity of chemotherapeutic agent, whereas inhibited spontaneous as well as chemotherapy-induced DNA breaks, homologous recombination (HR) activity and genomic instability in all cancer cell types tested. Treatment with APE1 inhibitor also impaired tumor growth and significantly increased efficacy of a chemotherapeutic agent in a subcutaneous mouse model of EAC. Overexpression of APE1 in normal esophageal epithelial cells increased DNA breaks and HR activity, leading to massive mutational, copy number as well as karyotypic instability. Evaluation of by whole genome sequencing identified HR as the top mutational process activated by APE1. Normal cells overexpressing APE1 grew as tumors in mice and tumors removed from mice displayed additional karyotypic changes, providing evidence of genomic instability in vivo. Overall, our data demonstrate that elevated APE1 dysregulates HR activity, G2/M checkpoint and genome stability thus contributing to tumorigenesis and chemoresistance in cancer. Therefore, inhibitors of APE1 have potential to inhibit growth and increase cytotoxicity of chemotherapeutic agents while minimizing spontaneous as well as chemotherapy-induced genomic damage and instability in EAC and other solid tumors.

category: cancer biology


title: The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila

abstract: Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag.

category: genetics


title: Bridging scales from spiking activity to the local field potential through latent dynamics

abstract:
During wakefulness, cortical networks exhibit diverse states of activity arising from fluctuations in modulatory inputs, any of which may shape the recorded neural activity across a range of scales, from local field potential (LFP) to the spiking of individual neurons. Multiple studies have uncovered state-dependent changes in single neuron activity specific to cell type. These changes are heterogeneous across cell types, suggesting that there is a link between changes in states of wakefulness and the dynamic patterns of spiking activity across the population, yet this is currently not well understood. Here, we use an unsupervised statistical modeling framework to link fluctuations in the state of the LFP to the dynamics of spiking activity of populations of neurons in the whisker area of primary somatosensory cortex of awake male mice. By identifying latent states from population spiking activity, we show that these spiking states are more informative of states of the LFP than a direct readout of the spiking activity of single neurons or of the population. Further, we find that the latent spiking states predict trial-by-trial variability in sensory responses as well as one aspect of behavior, whisking activity. Taken together, our approach captures the latent variables that underlie the dynamics of the spiking activity of cortical neuronal populations, providing a framework to relate cortical activity across different scales.

Significance statementDuring wakefulness, variability in cortical activity can arise from shifts in arousal or behavior. We analyze the dynamics of two measures of cortical activity, the spiking activity of local populations of neurons and the local field potential (LFP), typically used to track overall levels of arousal. We show that the latent states that capture variability in population spiking activity are highly predictive of LFP state changes, even more so than spiking activity directly. By linking latent states of spiking activity to changes in the LFP, our novel approach bridges fine-scale microcircuits ensemble activity and the meso-scale LFP. Our latent-state framework opens new avenues for extracting information from the LFP as well as identification of subject-level sources of variability.


title: A three-photon head-mounted microscope for imaging all layers of visual cortex in freely moving mice.

abstract: Recent advances in head-mounted microscopes have enabled imaging of neuronal activity using genetic-tools in freely moving mice but these microscopes are restricted to recording in minimally lit arenas and imaging upper cortical layers. Here we built a 2 gram, three-photon excitation-based microscope, containing a z-drive that enabled access to all cortical layers while mice freely behaved in a fully lit environment. We show that neuronal population activity in cortical layer-4 and layer-6 was differentially modulated by lit and dark conditions during free exploration.


title: Neural resources shift under Methylphenidate: a computational approach to examine anxiety-cognition interplay

abstract: The reciprocal interplay between anxiety and cognition is well documented. Anxiety negatively impacts cognition, while cognitive engagement can down-regulate anxiety. The brain mechanisms and dynamics underlying such interplay are not fully understood. To study this question, we experimentally and orthogonally manipulated anxiety (using a threat of shock paradigm) and cognition (using methylphenidate; MPH). The effects of these manipulations on the brain and behavior were evaluated in 50 healthy participants (25 MPH, 25 placebo), using an n-back working memory fMRI task (with low and high load conditions). Behaviorally, improved response accuracy was observed as a main effect of the drug across all conditions. We employed two approaches to understand the neural mechanisms underlying MPH-based cognitive enhancement in safe and threat conditions. First, we performed a hypothesis-driven computational analysis using a mathematical framework to examine how MPH putatively affects cognitive enhancement in the face of induced anxiety across two levels of cognitive load. Second, we performed an exploratory data analysis using Topological Data Analysis (TDA)-based Mapper to examine changes in spatiotemporal brain activity across the entire cortex. Both approaches provided converging evidence that MPH facilitated greater differential engagement of neural resources (brain activity) across low and high working memory load conditions. Furthermore, load-based differential management of neural resources reflects enhanced efficiency that is most powerful during higher load and induced anxiety conditions. Overall, our results provide novel insights regarding brain mechanisms that facilitate cognitive enhancement under MPH and, in future research, may be used to help mitigate anxiety-related cognitive underperformance.


title: Upregulated Ca2+ release from the endoplasmic reticulum leads to impaired presynaptic function in Alzheimer's disease

abstract: Neurotransmitter release from presynaptic terminals is primarily regulated by rapid Ca2+ influx through membrane-resident voltage-gated Ca2+ channels (VGCCs). Also, accumulating evidence indicates that the endoplasmic reticulum (ER) is extensively present in axonal terminals of neurons and plays a modulatory role in synaptic transmission by regulating Ca2+ levels. Alzheimers disease (AD) is marked by enhanced Ca2+ release from the ER and downregulation of Ca2+ buffering proteins. However, the precise consequence of impaired Ca2+ signalling within the vicinity of VGCCs (active zone (AZ)) on exocytosis is poorly understood. Here, we perform in-silico experiments of intracellular Ca2+ signalling and exocytosis in a detailed biophysical model of hippocampal synapses to investigate the effect of aberrant Ca2+ signalling on neurotransmitter release in AD. Our model predicts that enhanced Ca2+ release from the ER increases the probability of neurotransmitter release in AD. Moreover, over very short timescales (30-60 msec), the model exhibits activity-dependent and enhanced short-term plasticity in AD, indicating neuronal hyperactivity--a hallmark of the disease. Similar to previous observations in AD animal models, our model reveals that during prolonged stimulation (~450 msec), pathological Ca2+ signalling increases depression and desynchronization with stimulus, causing affected synapses to operate unreliably. Overall, our work provides direct evidence in support of a crucial role played by altered Ca2+ homeostasis mediated by intracellular stores in AD.


title: Mind the gap: decoding decreases in tonic firing in populations of spiking neurons

abstract: A stimulus can be encoded in a population of spiking neurons through any change in the statistics of their spike patterns. Thus, the baseline spike statistics in the absence of a stimulus can impact the populations encoding capacity. Some neurons maintain a baseline firing pattern and can decrease their spike rate in response to a stimulus. Not only do baseline firing rates vary widely among different types of neurons, but so do their higher-order statistics, like the degree to which they tend to group their spikes together into bursts and how those bursts are grouped across the population. We investigated how higher-order statistics of baseline spike patterns impact how much information a neural population can transmit about a stimulus that drives a gap in firing using a novel information-theoretic decoding mechanism which we call an "information train." We discover that there is an optimal level of burstiness for gap detection that is robust to other parameters of the neural population like its size, mean firing rate, and level of correlation. We consider this theoretical result in the context of experimental data from different types of retinal ganglion cells with different baseline spike statistics and determine that the spike statistics of bursty suppressed-by-contrast (bSbC) retinal ganglion cells support nearly optimal detection of both the onset and strength of a contrast step.


title: Atlantic cod as an indicator of rapid climate change

abstract:
Atlantic cod (Gadus morhua) in the northwest Atlantic has become the textbook example of overfishing. However, this narrative has blinded us from the larger environmental context of this decline. Cod prefer cold and shallow habitats, environments that are also the most susceptible to rapid climate change. Cod habitat deterioration was evident well before their numerical decline, and as such, cod was a harbinger of rapid climate change. Recovery requires their habitat quality to first improve and stabilize. Calls for a cull of seals, the consensus actor causing the lack of recovery of cod, may therefore be unwise. Recovery will only occur once the variability associated with rapid climate change subsides and habitat quality improves. The timeline for this is of course unknown.

One-Sentence SummaryWas the decline of cod a harbinger of rapid climate change in the northwest Atlantic?


title: Macroecological variation in movement profiles: body size does not explain it all

abstract: Animals couple habitats by three types of movement: dispersal, migration, and foraging, which dynamically link populations, communities, and ecosystems. Spatial distances of movement tend to correlate with each other, reflecting shared allometric scaling with body size, but may diverge due to biomechanical, phylogenetic, and ecological constraints. While these constraints have been investigated within specific taxa, the macroecological and macroevolutionary constraints on movement distances, and causes of those constraints, are still unknown. Here, we synthesized distances of all three movement types across 300+ vertebrate species, and investigated how the relationships between movement types and body size were modified by movement medium, taxonomy, and trophic guild (carnivore, herbivore, etc.). We found that the strength of relationships between movement types and body size varied among environments, taxa, and trophic guilds. Movement profiles interacted with physiological, taxonomic, and ecological traits to depart from expected body mass scaling. Overall, we find that there are systematic patterns to movement distances, and that movement types with very distinct ecological consequences (foraging, migration) can be correlated and subject to similar constraints. This implies that the scales of population dynamics in ecological communities are not entirely determined by the environment and likely reflect general biomechanical, evolutionary and metabolic constraints.


title: Mitigating pseudoreplication and bias in resource selection functions with autocorrelation-informed weighting

abstract: Resource selection functions are among the most commonly used statistical tools in both basic and applied animal ecology. They are typically parameterized using animal tracking data, and advances in animal tracking technology have led to increasing levels of autocorrelation between locations in such data sets. Because resource selection functions assume that data are independent and identically distributed, such autocorrelation can cause misleadingly narrow confidence intervals and biased parameter estimates. Data thinning, generalized estimating equations, and step selection functions have been suggested as techniques for mitigating the statistical problems posed by autocorrelation, but these approaches have notable limitations that include statistical inefficiency, unclear or arbitrary targets for adequate levels of statistical independence, constraints in input data, and (in the case of step selection functions) scale-dependent inference. To remedy these problems, we introduce a method for likelihood weighting of animal locations to mitigate the negative consequences of autocorrelation on resource selection functions. This method weights each observed location in an animals movement track according to its level of autocorrelation, expanding confidence intervals to match an objective target (i.e., the effective sample size for Autocorrelated Gaussian Density Estimation) and accounting for bias that can arise when there are gaps in the movement track. In this study, we describe the mathematical principles underlying our method, demonstrate its practical advantages versus conventional approaches using simulations and empirical data on a water mongoose (Atilax paludinosus), a caracal (Caracal caracal), and a serval (Leptailurus serval), and discuss pathways for further development of our method. We also provide a complete, annotated analytical workflow to help new users apply our method to their own animal tracking data using the ctmm R package.


title: Seasonal movement of royal chambers: where are the kings and queens of temperate termites in winter?

abstract: Overwintering is a critical part of the annual cycle for species that live in temperate, polar, and alpine regions. As a result, low-temperature biology is a key determinant of temperate species distribution. Termites distribute predominantly in tropical regions, and only a few species are found in the temperate zone. As with other social insects, termites are characterized by the division of labor between reproductive and non-reproductive castes in which the survival of reproductives is crucial to maintaining their society. Here, in the termite Reticulitermes speratus, we report the discovery of an underground royal chamber that kings and queens use to survive the winter, which is separate from the one they use during the warmer breeding season. Our investigation of field colonies indicates that in the spring the royals are localized in decayed logs on the ground, then move to their underground royal chamber located in the roots of stumps in the fall. The winter minimum temperature measured in the royal chamber was higher than the ground surface temperature. In overwintering termites, the kings and queens had higher cold tolerance than workers and soldiers. The kings and queens were at risk of mortality from -8 {degrees}C, compared to the workers and soldiers at -4 {degrees}C. Air temperatures dropped below this critical temperature of -8 {degrees}C multiple times, as evidenced from the past 140 years of weather records in Kyoto. This suggests that the underground movement of the royal chamber may contribute to avoiding the risk of overwintering mortality. These results demonstrate the social strategies implemented to overcome the environment met while living at the latitudinal limits. This study sheds light on one of the most important aspects of the biology of termites in terms of predicting their geographic distribution and spread by climate change. This work also helps further the understanding of the termites social system, seasonal phenology, long-term survivorship, and life cycle, and contributes to the development of pest control strategies.


title: Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother's curse hypothesis

abstract: Strict maternal inheritance of mitochondria favors the evolutionary accumulation of sex-biased fitness effects, as mitochondrial evolution occurs exclusively in female lineages. The "mothers curse" hypothesis proposes that male-harming mutations should accumulate in mitochondrial genomes when they have neutral or beneficial effects on female fitness. Rigorous empirical tests have largely focused on Drosophila, where support for the predictions of mothers curse has been mixed. We investigated the impact of mothers curse mutations in Tigriopus californicus, a minute crustacean. Using nonrecombinant backcrosses, we introgressed four divergent mitochondrial haplotypes into two nuclear backgrounds and recorded measures of fertility and longevity. We found that the phenotypic effects of mitochondrial mutations were context-dependent, being influenced by the nuclear-background in which they were expressed, as well as the sex of the individual and rearing temperature. Mitochondrial haplotype effects were greater for fertility than longevity, and temperature effects were greater for longevity. However, in opposition to mothers curse expectations, females had a higher level of mitochondrial genetic variance than males for both fertility and longevity, and there was no evidence for mitochondrial mutations favoring female performance at the cost of male performance. These results indicate that selection has not resulted in the accumulation of male mutation load in Tigriopus californicus.

category: evolutionary biology


title: A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies

abstract: The success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods or scalability for advanced CRISPR applications. Here, we present a new ecosystem of R packages that enables efficient gRNA design and annotation for a multitude of CRISPR technologies, including CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interference (CRISPRi) and CRISPR base editing (CRISPRbe). The core package, crisprDesign, offers a comprehensive, user-friendly, and unified interface to add on- and off-target annotations via several alignment methods, rich gene and SNP annotations, and a dozen on- and off-target activity scores. These functionalities are enabled for any RNA- or DNA-targeting nucleases, including Cas9, Cas12, and Cas13. We illustrate the general applicability of our tools by designing optimal gRNAs for three case studies: tiling CRISPRbe library for BRCA1 using the base editor BE4max, tiling RNA-targeting libraries for CD46 and CD55 using CasRx, and activation of MMP7 using CRISPRa. Our suite of R packages is open-source and deployed through the Bioconductor project to facilitate their use by the CRISPR community.


title: Xlink Mapping and AnalySis (XMAS) - Smooth Integrative Modeling in ChimeraX

abstract: Crosslinking mass spectrometry (XL-MS) adds tremendous value to structural biology investigations. Its main strength lies in uncovering structural information in the form of distance constraints between neighboring amino acids of proteins, protein regions and complex samples, which are difficult to assess by other analytical techniques. However, although several approaches have been proposed, interpreting XL-MS data in a structural context has been cumbersome. ChimeraX has gained momentum as a flexible and widely used software package for the visualization of structural data, but is currently lacking functionalities for integration of experimental XL-MS data. Here, we introduce XMAS, a bundle that allows users to load results from several XL-MS search engines directly into ChimeraX and map the information onto protein structures. Besides automatically locating distance constraints on protein structures, XMAS offers the possibility to work with replicate experiments and/or different crosslinkers, and filter this data based on how many replicates for which a given distance constraint was detected, thereby increasing the data quality. Additionally, we introduce the concept of self-links, which allows easy modeling of homo-dimeric interactions. Its core functionality is extended by the implementation of seamless connections to the HADDOCK suite to streamline otherwise time-consuming tasks in structural modeling pipelines. We then demonstrate these key elements of the XMAS bundle by modeling crosslinking data obtained from human fibrin clots. This software is freely available from the ChimeraX toolshed, with an extensive user manual and example datasets.


title: DrugRepo: A novel approach to repurpose a huge collection of compounds based on chemical and genomic features

abstract: Drug development process consumes 9-12 years and approximately one billion US dollars in terms of costs. Due to high finances and time costs required by the traditional drug discovery paradigm, repurposing of the old drugs to treat cancer as well as rare diseases is becoming popular. Computational approaches are mainly data-driven and involve a systematic analysis of different data types leading to the formulation of repurposing hypotheses. In this study, we present a novel scoring algorithm based on chemical and genomic data types to repurpose a huge collection of compounds for 674 cancer types and other diseases. The data types used to design the scoring algorithm are chemical structures, drug-target interactions (DTI), pathways, and disease-gene associations. The repurpose scoring algorithm is strengthened by integrating the most comprehensive manually curated datasets for each data type. More than 100 of our repurposed compounds can be matched with ongoing studies at clinical trial (https://clinicaltrials.gov/). Our analysis is supported by a web tool available at: http://drugrepo.org/.


title: Detecting intragenic trans-splicing events with hybrid transcriptome sequencing in cancer cells

abstract: Trans-splicing can generate non-co-linear (NCL) transcripts that consist of exons in an order topologically inconsistent with the corresponding DNA template. Detecting trans-spliced RNAs (ts-RNAs) may be interfered by false positives from experimental artifacts, circular RNAs (circRNAs), and genetic rearrangements. Particularly, intragenic ts-RNAs, which are derived from separate precursor mRNA molecules of the same genes, are often mistaken for circRNAs through analyses of high-throughput transcriptome sequencing (RNA-seq) data. In addition, the biogenesis and function of ts-RNAs remain elusive. Here we developed a bioinformatics pipeline, NCLscan-hybrid, with the integration of long and short RNA-seq reads to minimize false positives and identify intragenic ts-RNAs. We utilized two features of long reads, out-of-circle and rolling circle, to distinguish intragenic ts-RNAs from circRNAs. We also designed multiple experimental validation steps to examine each type of false positives and successfully confirmed an intragenic ts-RNA (ts-ARFGEF1) in breast cancer cells. On the basis of ectopic expression and CRISPR-based endogenous genome modification experiments, we confirmed that ts-ARFGEF1 formation was significantly dependent on the reverse complementary sequences in the flanking introns of the NCL junction. Subsequent in vitro and in vivo experiments demonstrated that ts-ARFGEF1 silencing can significantly inhibit tumor cell growth. We further showed the regulatory role of ts-ARFGEF1 in p53-mediated apoptosis through affecting the PERK/eIF2a/ATF4/CHOP signaling pathway in breast cancer cells. This study thus described both bioinformatics procedures and experimental validation steps for rigorous characterization of transcriptionally non-co-linear RNAs, expanding the discovery of this important but understudied class of RNAs.


title: Modelling eNvironment for Isoforms (MoNvIso): A general platform to predict structural determinants of protein isoforms in genetic diseases

abstract: The seamless integration of human disease-related mutation data into protein structures is an essential component of any attempt to correctly assess the impact of the mutation. The key step preliminary to any structural modelling is the identification of the correct isoform onto which mutations should be mapped because there are several functionally different protein isoforms from the same gene. To handle large sets of data coming from omics techniques, this challenging task should be automatized. Here we present our code MoNvIso (Modelling eNvironment for Isoforms), which pinpoints the correct isoform associated with the mutation of interest and builds a structural model of both the wild type isoform and the related variants starting from the name of the gene and the list of mutations of interest.


title: In silico identification of novel peptides as potential modulators of Aβ42 Amyloidogenesis

abstract: Alzheimers Disease is a neurodegenerative disease for which no cure is available at present. The presence of amyloid plaques in the extracellular space of neural cells is the key feature of this fatal disease. Amyloid-Beta (A{beta}) is a 40-42 amino acid peptide and the main component of amyloid plaques. This peptide is produced by the proteolysis of Amyloid Precursor Protein by presenilin. Deposition of 42 residual A{beta} peptides forms fibrils structure, leading to disruption of neuron synaptic transmission, inducing neural cell toxicity, ultimately leading to neuron death. To modulate the amyloidosis of A{beta} peptides, various novel peptides have been investigated via molecular docking and molecular dynamic simulation studies. The sequence-based peptides were designed and investigated for their interaction with A{beta}42 monomer and fibril using the molecular docking method, and their influence on the structural stability of target proteins was studied using molecular simulations. According to the docking results, amongst all the synthetic peptides, the peptide YRIGY (P6) has the highest binding affinity with A{beta}42 fibril, and the peptide DKAPFF (P12) shows better binding with A{beta}42 monomer. Moreover, simulation results also suggest that the higher the binding affinity, the better the inhibitory action. From these findings, it is suggested that both the peptides can modulate the amyloidogenesis, but peptide (P6) has better potential for the disaggregation of the fibrils, whereas peptide P12 stabilizes the native structure of the A{beta}42 monomer more effectively and hence can serve as a potential amyloid inhibitor. Thus, these peptides can be explored as therapeutic agents against Alzheimers Disease.


title: Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis

abstract: HOTAIR is a 2.2 kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities during the process of epithelial-to-mesenchymal transition (EMT). However, the oncogenic transformation determined by HOTAIR in vivo and its impact on chromatin dynamics are incompletely understood. Here we generate a transgenic mouse model with doxycycline-inducible expression of human HOTAIR in the context of the MMTV-PyMT breast cancer-prone background to systematically interrogate the cellular mechanisms by which human HOTAIR lncRNA acts to promote breast cancer progression. We show that sustained high levels of HOTAIR over time increased breast metastatic capacity and invasiveness in breast cancer cells, promoting migration and subsequent metastasis to the lung. Subsequent withdrawal of HOTAIR overexpression reverted the metastatic phenotype, indicating oncogenic lncRNA addiction. Furthermore, HOTAIR overexpression altered both the cellular transcriptome and chromatin accessibility landscape of multiple metastasis-associated genes and promoted epithelial to mesenchymal transition. These alterations are abrogated within several cell cycles after HOTAIR expression is reverted to basal levels, indicating an erasable lncRNA-associated epigenetic memory. These results suggest that a continual role for HOTAIR in programming a metastatic gene regulatory program. Targeting HOTAIR lncRNA may potentially serve as a therapeutic strategy to ameliorate breast cancer progression.


title: Motor pattern generation is robust to neural network anatomical imbalance favoring inhibition but not excitation

abstract:
Animals display rich and coordinated motor patterns during walking and running. Previous modelling as well as experimental results suggest that the balance between excitation and inhibition in neural networks may be critical for generating such structured motor patterns. However, biological neural networks have an anatomical imbalance between excitatory and inhibitory neural populations. We explore the influence of such an anatomical imbalance on the ability of a reservoir computing artificial neural network to learn human locomotor patterns for slow walking, fast walking and running. We varied the numbers of neurons, connections percentages and connection strengths of excitatory and inhibitory populations. We showed that performance depended on the network anatomy. First, it deteriorated when the total number of neurons was too small or the total connection strength was too large. Second, performance was critically dependent on the balance between excitation and inhibition. Imbalance towards excitation caused a reduction in the richness of internal network dynamics, leading to a stereotypical motor output and poor overall performance. In contrast, rich internal dynamics and good overall performance were found when the network anatomy was either balanced or imbalanced towards inhibition. This suggests that motor pattern generation may be robust to increased inhibition but not increased excitation in neural networks.

1 Author summaryHow does the anatomy of the nervous system allow the generation of the complex motor patterns observed during the movements of humans and other animals? We explore this question in a model of the spinal cord in which we vary the neural anatomy. We find that movement generation requires the neural network to have rich internal dynamics. Such rich internal dynamics emerge from the interaction between the excitatory and inhibitory neurons in the network. Strong inhibition causes fluctuations in the neural activity which allow rich motor patterns to be produced. However, strong excitation quenches these fluctuations and causes a reduction in the variability of motor patterns. When both excitation and inhibition are strong, the neural activity becomes chaotic, and dysfunctional, highly variable motor patterns are produced. We therefore predict that diseases of the nervous system which affect inhibitory and excitatory neurons differently will have a different signature in terms of motor patterns. Diseases causing increased excitation in neural circuits should lead to stereotypical motor behaviors, whereas diseases causing increased excitation and inhibition should lead to unstable motor patterns.


title: Tbx3 is required for mammalian retinal angiogenesis.

abstract:
Neural tissue formation requires coordinated, interwoven development of both neural and vascular cells. Spatially distinct regions of the central nervous system (CNS) express factors that are predicted to affect vasculature in one area but not another, yet an example of this idea has not been found. Due to its accessibility, the eye is an excellent tissue to study this question. The factor TBX3 is required for frog eye development, yet its role in mammalian eye formation was not known. To determine how Tbx3 loss-of-function affected eye formation, we crossed the validated Tbx3-floxed mice with the optic cup-Cre recombinase driver, BAC-Dkk3-CRE. We confirmed earlier expression studies of Tbx3 RNA and protein in the embryonic dorsal optic vesicle and, postnatally, in sporadic clusters of cells of the inner nuclear layer. Surprisingly, we also found TBX3 in astrocyte precursors at P0. With Tbx3 loss, blood vessels were malformed throughout the retina, but with more severe effects seen in the dorsal retina. Astrocyte precursors were reduced in number and failed to form a lattice at the dorsal edge. We next examined retinal ganglion cells, as they have been shown to play a critical role in retinal angiogenesis. We found that a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) were missing melanopsin in the dorsal half of the retina. In previous studies, loss of melanopsin has been linked to hyaloid artery persistence, which we also observed in the Tbx3 cKO retina. Together, these results show that TBX3 is required for retinal angiogenesis.

Summary StatementTBX3 is a multifunctional protein important for frog eye development. This is the first study showing that TBX3 is critical for mammalian eye formation, controlling the function of key cells required for angiogenesis.


title: Differential regulation of gene expression pathways with dexamethasone and ACTH after early life seizures

abstract: Early-life seizures (ELS) are associated with persistent cognitive deficits such as ADHD and memory impairment. These co-morbidities have a dramatic negative impact on the quality of life of patients. Therapies that improve cognitive outcomes have enormous potential to improve patients quality of life. Our previous work in a rat flurothyl-induction model showed that administration of adrenocorticotropic hormone (ACTH) at time of seizure induction led to improved learning and memory in the animals despite no effect on seizure latency or duration. Administration of dexamethasone (Dex), a corticosteroid, did not have the same positive effect on learning and memory and has even been shown to exacerbate injury in a rat model of temporal lobe epilepsy. We hypothesized that ACTH exerted positive effects on cognitive outcomes through beneficial changes to gene expression and proposed that administration of ACTH at seizure induction would return gene-expression in the brain towards the normal pattern of expression in the Control animals whereas Dex would not. Twenty-six Sprague-Dawley rats were randomized into vehicle- Control, and ACTH-, Dex-, and vehicle-ELS. Rat pups were subjected to 60 flurothyl seizures from P5 to P15. After seizure induction, brains were removed and the hippocampus and PFC were dissected, RNA was extracted and sequenced, and differential expression analysis was performed using generalized estimating equations. Differential expression analysis showed that ACTH pushes gene expression in the brain back to a more normal state of expression through enrichment of pathways involved in supporting homeostatic balance and down-regulating pathways that might contribute to excitotoxic cell-damage post-ELS.


title: Combining Stem Cell Rejuvenation and Senescence Targeting to Synergistically Extend Lifespan

abstract: Why biological age is a major risk factor for many of the most important human diseases remains mysterious. We know that as organisms age, stem cell pools are exhausted while senescent cells progressively accumulate. Independently, induction of pluripotency via expression of Yamanaka factors (Oct4, Klf4, Sox2, c-Myc; OKSM) and clearance of senescent cells have each been shown to ameliorate cellular and physiological aspects of aging, suggesting that both processes are drivers of organismal aging. However, stem cell exhaustion and cellular senescence likely interact in the etiology and progression of age-dependent diseases because both undermine tissue and organ homeostasis in different if not complementary ways. Here, we combine transient cellular reprogramming (stem cell rejuvenation) with targeted removal of senescent cells to test the hypothesis that simultaneously targeting both cell-fate based aging mechanisms will maximize life and health span benefits. We show that these interventions protect the intestinal stem cell pool, lower inflammation, activate pro-stem cell signaling pathways, and synergistically improve health and lifespan. Our findings suggest that a combination therapy, simultaneously replacing lost stem cells and removing senescent cells, shows synergistic potential for anti-aging treatments. Our finding that transient expression of both is the most effective suggests that drug-based treatments in non-genetically tractable organisms will likely be the most translatable.

category: developmental biology


title: Fluid manipulations uncover mechanosensation for zebrafish left-right establishment during one-hour time interval

abstract:
Humans and other vertebrates define body axis left-right asymmetry in the early stages of embryo development. The mechanism behind left-right establishment is not fully understood. Although it is known that the symmetry break occurs in a dedicated organ called the left-right organizer (LRO) and involves motile cilia generating fluid flow therein, it has been a matter of debate whether the process of symmetry breaking relies on a chemosensory or a mechanosensory mechanism. Novel tailored manipulations for LRO fluid extraction in living zebrafish embryos allowed us to pinpoint a decisive developmental period for breaking left-right symmetry during development. This critical time-window was narrowed to one hour and is characterized by a mild counterclockwise flow. The experimental challenge in our approach consisted of emptying the LRO of any potential fluid, abrogating simultaneously flow force and chemical determinants. Our findings revealed an unprecedented recovery capacity of the embryo to re-inflate and re-circulate the fluid inside the LRO exposing unknown properties of this transient organ. Live extraction and replacement of LRO fluid while changing dilution or viscosity demonstrated that early left-right patterning depends on fluid flow mechanics rather than on the nature of the fluid content. Our results advocate for a mechanosensory mechanism ruling left-right early development.

TeaserZebrafish uses mechanosensation during one-hour time-window to initiate left-right development


title: Why the architecture of environmental fluctuation matters for fitness

abstract: The physical environment represents the very stage upon which the eco-evolutionary play unfolds. How fluctuations in the environment affect fitness is thus central to demographic projections, selection predictions, life history analyses, and conservation of populations. Here we systematically compare and explain why different  architectures of fluctuations--both in how they are generated in nature and constructed theoretically--alter fitness. Modelling efforts have mostly characterized variable environments with stochasticity. However, stochasticity refers to a random process. Many fluctuating environments in nature are non-random, driven by geophysical forces that create feedbacks or cyclicality: for example, seasons, tides, day/night, and disturbances such as floods, fires, and hurricanes. We show that evolutionary fitness log{lambda}s of a simple structured population is sensitive to the nature of fluctuations, even if different fluctuations appear indistinguishable in long-run statistical distributions. Importantly, we uncover two mathematical explanations of why fitness depends on the architecture of environmental fluctuations-- consecutiveness of deviations from the environmental mean, and Jensens Inequality acting on nonlinear biological parameters--both arguably relevant features in virtually all populations inhabiting variable environments. The fitness divergence we demonstrate and explain is a useful step towards developing evolutionary demographic theory for the prevalent categories of non-random environments.


title: Landscape change and alien invasions drive shifts in native lady beetle communities over a century

abstract:
AimUnderstanding drivers of insect population declines is essential for the development of successful conservation plans, but data limitations restrict assessment across spatial and temporal scales. Museum records represent a unique source of historical data that can be leveraged to investigate temporal trends in insect communities. Native lady beetle decline has been attributed to competition with established alien species and landscape change, but the relative importance of these drivers is difficult to measure with short-term field-based studies. Here we assessed distribution patterns for native lady beetle species over 12 decades using museum records and evaluated the relative importance of alien species and landscape change as long-term drivers contributing to changes in lady beetle communities.

LocationOhio, USA.

MethodsWe compiled occurrence records for 28 lady beetle species collected in Ohio, USA from 1900-2018. Incidence-based measures of taxonomic beta-diversity were used to evaluate changes in lady beetle community composition over time. To evaluate the relative influence of temporal, spatial, landscape, and community drivers on the captures of native lady beetles, we constructed negative binomial generalized additive models.

ResultsWe report evidence of declines in captures for several native species, including Adalia bipunctata, Coccinella novemnotata, Hippodamia convergens, and Coleomegilla maculata. Importantly, the timing, severity, and drivers of these documented declines were species-specific. Changes in lady beetle species composition began in the 1980s, when processes of species loss/gain and turnover shifted communities towards dominance by a few alien lady beetle species. Land cover change also was associated with declines in captures, particularly for C. novemnotata which declined prior to the arrival of alien species in the state.

Main conclusionsOur study documented shifts in Ohios lady beetle communities beginning in the 1980s as alien species supplanted natives. Drivers of declines in captures of native lady beetle species were highly species-specific, emphasizing that mechanisms driving population losses cannot be generalized even among closely related species. These findings also indicate the importance of museum holdings and the analysis of species-level data when studying temporal trends in insect populations.


title: Rising Temperature Drives Tipping Points in Mutualistic Networks

abstract: The effect of climate warming on species physiological parameters, including growth rate, mortality rate, and handling time, is well established from empirical data. However, with an alarming rise in global temperature more than ever, predicting the interactive influence of these changes on mutualistic communities remains uncertain. Using 139 real plant-pollinator networks sampled across the globe and a modelling approach, we study the impact of species individual thermal responses on mutualistic communities. We show that at low mutualistic strength plant-pollinator networks are at potential risk of rapid transitions at higher temperatures. Evidently, generalist species plays a critical role in guiding tipping points in mutualistic networks. Further, we derive stability criteria for the networks in a range of temperatures using a two-dimensional reduced model. We identify network structures that can ascertain the delay of a community collapse. Until the end of this century, many real mutualistic networks can be under the threat of sudden collapse, and we frame strategies to mitigate them. Together, our results indicate that knowing individual species thermal responses and network structure can improve predictions for communities facing rapid transitions.


title: Evaluating risk-taking behaviors in Lycosidae: are the nutritional benefits of sugar water worth the risk of predation?

abstract: The risk-taking tendencies and addiction in small vertebrates are often used to understand the processes of larger vertebrates, such as humans. We set out to find whether certain risk-taking behaviors characteristic of addiction remain consistent between vertebrates and invertebrates. Different animals will gorge on sugar water, and addiction-like tendencies are often associated with the overconsumption of sucrose. The goal of my study was to evaluate those risk-taking behaviors and compare invertebrate risk-taking behaviors to vertebrate risk-taking behaviors. The risk-taking behavior we observed was the process of relieving cravings while the risk of predation was present. Through this study we document evidence of wolf spiders feeding on a 25% sucrose solution and explain the wolf spiders preference to a sugar water solution over filtered tap water. To evaluate if wolf spiders exhibit addiction like behaviors associated with sucrose, we placed a green-colored, sugar water-soaked cotton ball on the silk of a large, predatory Tigrosa helluo wolf spider and a regular, filtered water-soaked cotton ball on the "safe" side of a plastic trial arena and then evaluated the behaviors of the prey spiders. We used a mixture of Pardosa milvina and Rabidosa rabida as test spiders, with one group given a sugar-water treatment beforehand and the other group was given a green colored control cotton ball with filtered tap water (n=14 for both the sugar water treatment and control groups). The wolf spiders who were predisposed to the sugar water treatment were more likely to cross through their predators silk in order to gain access to the sugar water cotton ball than their counterparts who were not given a sugar water treatment prior. These results suggest the risk for predation of the wolf spider is not worth the benefits of the sugar water, unless a wolf spider has been allowed unlimited access to sugar water in advance. When a wolf spider who was allowed unlimited access to sugar water beforehand is presented with a risky situation, they will increase their risk-taking behaviors via crossing through a predators silk in order indulge in the sugar water. These results suggest the addictive properties of sugar spans across vertebrates and invertebrates, and potentially opens the door for a cost-efficient and ethically acceptable invertebrate model-organism for examining the risk-taking behaviors associated with addiction.

category: animal behavior and cognition


title: UMINT: Unsupervised Neural Network For Single Cell Multi-Omics Integration

abstract: AO_SCPLOWBSTRACTC_SCPLOWMulti-omics studies have enabled us to understand the mechanistic drivers behind complex disease states and progressions, thereby providing novel and actionable biological insights into health status. However, integrating data from multiple modalities is challenging due to the high dimensionality of data and noise associated with each platform. Non-overlapping features and technical batch effects in the data make the task of learning more complicated. Conventional machine learning (ML) tools are not quite effective against such data integration hazards. In addition, existing methods for single cell multi-omics integration are computationally expensive. This has encouraged the development of a novel architecture that produces a robust model for integration of high-dimensional multi-omics data, which would be capable of learning meaningful features for further downstream analysis. In this work, we have introduced a novel Unsupervised neural network for single cell Multi-omics INTegration (UMINT). UMINT serves as a promising model for integrating variable number of single cell omics layers with high dimensions, and provides substantial reduction in the number of parameters. It is capable of learning a latent low-dimensional embedding that can capture useful data characteristics. The effectiveness of UMINT has been evaluated on benchmark CITE-seq (paired RNA and surface proteins) datasets. It has outperformed existing state-of-the-art methods for multi-omics integration.


title: Systems-level identification of key transcription factors in immune cell specification

abstract: Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.

category: systems biology


title: GABAergic regulation of cell proliferation within the adult mouse spinal cord

abstract: Manipulation of neural stem cell proliferation and differentiation in the postnatal CNS is receiving significant attention due to therapeutic potential. In the spinal cord, such manipulations may promote repair in conditions such as multiple sclerosis or spinal cord injury, but may also limit excessive cell proliferation contributing to tumours such as ependymomas. Here we show that when ambient GABA is increased in vigabatrin-treated or decreased in glutamic acid decarboxylase67-green fluorescent protein (GAD67-GFP) mice, the numbers of proliferating cells respectively decreased or increased. Thus, intrinsic spinal cord GABA levels are correlated with the extent of cell proliferation, providing important evidence for the possibility of manipulating these levels. Diazepam binding inhibitor, an endogenous protein that interacts with GABA receptors and its breakdown product, octadecaneuropeptide, which preferentially activates central benzodiazepine (CBR) sites, were highly expressed in the spinal cord, especially in ependymal cells surrounding the central canal. Furthermore, animals with reduced CBR activation via treatment with flumazenil or Ro15-4513, or with a G2F77I mutation in the CBR binding site had greater numbers of Ethynyl-2-deoxyuridine positive cells compared to control, which maintained their stem cell status since the proportion of newly proliferated cells becoming oligodendrocytes or astrocytes was significantly lower. Altering endogenous GABA levels or modulating GABAergic signaling through specific sites on the GABA receptors therefore influences NSC proliferation in the adult spinal cord. These findings provide a basis for further study into how GABAergic signaling could be manipulated to enable spinal cord self-regeneration and recovery or limit pathological proliferative activity.


title: Dissection of a sensorimotor circuit that regulates aversion to odors and pathogenic bacteria in C. elegans by whole-brain simulation

abstract: Altering behavior to reduce pathogen exposure is a key line of defense against pathogen attack for nearly all animals. The use of Caenorhabditis elegans bacterial infection models have allowed for many insights into the molecular mechanisms of behavioral immunity. However, the neural circuitry between chemosensory neurons that sense pathogenic bacterial cues and the motor neurons responsible for avoidance-associated locomotion remains unknown. We found that backward locomotion was a component of learned pathogen avoidance, as animals pre-exposed to Pseudomonas aeruginosa or Enterococcus faecalis showed reflexive aversion to drops of the bacteria, requiring ASI, AWB, and AWC neurons and ASE, AWB, and AWC neurons, respectively. This response also involved intestinal distention and, for E. faecalis, required expression of TRPM channels in the intestine and excretory system. Using whole-brain simulation and functional assays, we uncovered a sensorimotor circuit governing learned reflexive aversion. This behavior is controlled by a four-layer neural circuit composed of olfactory neurons, interneurons, and motor neurons that control backward locomotion crucial for learned reflexive aversion to pathogenic bacteria, learned avoidance, and a repulsive odor. The discovery of a complete sensorimotor circuit for reflexive aversion demonstrates the utility of using the C. elegans connectome and computational modeling in uncovering new neuronal regulators of behavior.


title: A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors

abstract: Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3 Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.


title: Divergent acute versus prolonged in vivo GLP-1R responses in β-arrestin 2-deleted primary beta cells

abstract: The glucagon-like peptide-1 receptor (GLP-1R) is a GPCR from the glucagon receptor family with important roles in the regulation of beta cell function and feeding behaviours. After ligand-stimulated G protein binding, active GLP-1Rs are rapidly desensitised by GRKs, followed by recruitment of {beta}-arrestins, scaffolding proteins that terminate G protein interaction through steric hindrance but also act as independent signalling mediators. GLP-1R agonists (GLP-1RAs) are well-established therapeutics in type 2 diabetes and obesity that are nevertheless associated with dose-related gastrointestinal side effects affecting [~]50% of patients. Exploiting the power of ligand-directed signalling bias with modified {beta}-arrestin engagement is a promising approach to favour therapeutically beneficial over harmful GLP-1RA effects. Although GLP-1R interacts with both {beta}-arrestin isoforms 1 and 2 with similar affinities, expression of the latter is greatly enhanced in beta cells, making this the most functionally relevant isoform. To increase our understanding of the effect of {beta}-arrestin 2 activity in beta cell GLP-1R function, we have assessed in vivo glycaemic responses to the pharmacological GLP-1RA exendin-4 in an adult beta cell-selective {beta}-arrestin 2 KO mouse model. Lean female KO mice and mice of both sexes fed a high-fat high-glucose diet displayed worse acute exendin-4 responses versus control littermates, an effect that was reversed 6 hours post-agonist injection, mirrored by differences in plasma insulin levels and ex vivo calcium and insulin secretion responses. Similar effects were observed for semaglutide and tirzepatide, two clinically relevant GLP-1RAs, but not for the less {beta}-arrestin 2-reliant biased agonist exendin-phe1. Acute exendin-4-induced cAMP was impaired, but cAMP responses to GLP-1 following overnight exendin-4 exposure tended to improve in KO versus control islets. Acute signalling defects were attributed to the concerted effect of phosphodiesterase PDE4 and {beta}-arrestin 1, as beta cell {beta}-arrestin 2 KO islets regained cAMP responsivity with either {beta}-arrestin 1 knockdown or PDE4 inhibition. Cell-cell connectivity was prolonged in beta cell {beta}-arrestin 2 KO compared with control islets imaged in vivo following implantation in mouse eyes. While islet GLP-1R internalisation was not affected by {beta}-arrestin 2 deletion, both recycling and lysosomal targeting were significantly impaired, with active receptors redirected instead to the trans-Golgi network (TGN). Results were replicated in INS-1 832/3 {beta}-arrestin 2 knockdown cells, where we also measured increased levels of exendin-4-induced TGN signalling as well as reduced GLP-1R ubiquitination and recruitment of the E3 ubiquitin ligase NEDD4, suggesting a role for this post-translational modification in {beta}-arrestin 2-dependent GLP-1R trafficking. The present study represents the first in-depth in vivo and ex vivo analysis of the effects of beta cell {beta}-arrestin 2 gene ablation on acute versus sustained pharmacological GLP-1R responses.

category: cell biology


title: Population genomics of the island thrush elucidates one of earth's great archipelagic radiations

abstract: Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range, and is arguably the worlds most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea and New Guinea to Polynesia. The island thrushs success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.


title: A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World

abstract: Principal component analysis (PCA) is a widely used dimensionality reduction technique in machine learning and multivariate statistics. To improve the interpretability of PCA, various approaches to obtain sparse principal direction loadings have been proposed, which are termed Sparse Principal Component Analysis (SPCA). In this paper, we present ThreSPCA1, a provably accurate algorithm based on thresholding the Singular Value Decomposition for the SPCA problem, without imposing any restrictive assumptions on the input covariance matrix. Our thresholding algorithm is conceptually simple; much faster than current state-of-the-art; and performs well in practice. When applied to genotype data from the 1000 Genomes Project, ThreSPCA is faster than previous benchmarks, at least as accurate, and leads to a set of interpretable biomarkers, revealing genetic diversity across the world.