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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Multiple signaling pathways converge onto the regulation of HAD-like phosphatases to modulate cellular resistance to the metabolic inhibitor 2-deoxyglucose

Cancer cells display an altered metabolism with an increased glycolysis and glucose uptake. Anti-cancer strategies targeting glycolysis through metabolic inhibitors have been considered. Particularly, the glucose analogue 2-deoxyglucose (2DG) is imported into cells and phosphorylated into 2DG-6-phosphate, a toxic by-product that inhibits glycolysis. Recent data suggest that 2DG has additional effects in the cell, and resistance to 2DG has also been observed. Using yeast as a model, we engaged an unbiased, mass-spectrometry-based approach to probe the cellular effects of 2DG on the proteome and study resistance mechanisms. This revealed that two 2DG-6-phosphate phosphatases, Dog1 and Dog2, are induced upon exposure to 2DG and participate in 2DG detoxication. 2DG induces Dog2 by upregulating several signaling pathways, such as the MAPK (Hog1/p38)-based stress-responsive pathway, the Unfolded Protein Response (UPR) triggered by 2DG-induced ER stress, and the MAPK (Slt2)-based Cell Wall Integrity pathway. Thus, 2DG-induced interference with cellular signaling rewires the expression of these endogenous phosphatases to promote 2DG resistance. Consequently, loss of the UPR or CWI pathways leads to hypersensitivity to 2DG. In contrast, DOG2 is transcriptionally repressed by glucose availability in a Snf1/AMPK-dependent manner, and mutants impaired in this pathway are 2DG-resistant. The characterization and genome resequencing of spontaneous 2DG-resistant mutants revealed that DOG2 overexpression is a common strategy to achieve 2DG resistance. The human Dog2 orthologue, HDHD1, also displays 2DG-6-phosphate phosphatase activity in vitro, and its overexpression confers 2DG resistance in HeLa cells, which has important implications for potential future chemotherapies involving 2DG.

genetics↗

bioRxiv2018

Diagnostic high-throughput sequencing of 2,390 patients with bleeding, thrombotic and platelet disorders

A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multi-disciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2,390 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbour variants associated with rare bleeding, thrombotic or platelet disorders (BPD). The diagnostic rate was determined by the clinical phenotype, with an overall rate of 50.4% for all thrombotic, coagulation, platelet count and function disorder patients and a rate of 6.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 756 unique variants, including copy number and intronic variants, as Pathogenic, Likely Pathogenic or Variants of Uncertain Significance. Almost half (49.7%) of these variants are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BPD. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 897 index patients providing evidence that introducing a HTS genetic test for BPD patients is meeting an important unmet clinical need.\n\nKey pointsO_LIHigh-throughput sequencing (HTS) test reveals a molecular diagnosis for 38% of 2,390 patients with bleeding, thrombotic and platelet disorders.\nC_LIO_LIThromboGenomics HTS test validates recent gene discoveries and detects copy number and intronic variants.\nC_LI

genetics↗

bioRxiv2018

Challenging the function of motor inhibition: Does it really assist action selection?

By applying transcranial magnetic stimulation (TMS) over the primary motor cortex (M1) to elicit motor-evoked potentials (MEPs) in muscles of the contralateral hand during reaction time (RT) tasks, many studies have reported a strong suppression of MEPs during action preparation, a phenomenon called preparatory inhibition. Several hypotheses have been put forward regarding the role of this inhibition, with the predominant view suggesting that it would help action selection. However, this assumption is still a matter of debate. Here, we aimed at directly addressing this idea by comparing MEPs in a task that required subjects to select a finger response within a set of predefined options (choice RT task: left or right index finger abduction) or when subjects simply had to provide the same finger response on every trial, in the absence of choice (simple RT task). Moreover, we minimized any effect that could be associated with other forms of inhibition. In both versions of the task, TMS was applied on both M1 (double-coil protocol) at several time points between the go signal and the left or right index finger response, eliciting MEPs bilaterally in the prime mover (index finger agonist) and in an irrelevant muscle (pinky agonist). Overall, MEP suppression was moderate in this study; it was only found for the irrelevant muscle. As such, MEPs in the index agonist were facilitated when elicited in a responding hand (e.g. left MEPs preceding left responses) and remained mostly unchanged in a non-responding hand (e.g. left MEPs preceding right responses). In contrast, MEPs were almost always suppressed in the pinky muscle when elicited in the non-responding hand and sometimes also in the responding hand. Importantly, this effect was more consistent in the choice than in the simple RT task, supporting the view that preparatory inhibition may assist action selection. Moreover, the fact that it sometimes concerned the responding hand is coherent with the idea of a global process, suppressing broadly the motor system.\n\nHighlightsO_LIAddressed the debated idea that preparatory inhibition assists action selection\nC_LIO_LICompared MEPs in simple and choice RT tasks (no catch, no delay)\nC_LIO_LIDetected preparatory suppression of MEPs, although weaker than usual\nC_LIO_LIObserved a more consistent suppression of MEPs in the choice than simple setting\nC_LIO_LIProvided support for action selection hypothesis, with traces of broad inhibition\nC_LI

neuroscience↗

bioRxiv2018

Embedding the Skin Conductance Response into the Brain Connectivity Framework: Monoaminergic Signaling Visible Through the Lenses of Computational Modeling

Relying on evidence for the functional, neurochemical, and spectral parallelism between the late event-related potentials, delta oscillatory brain responses, and the skin conductance response (SCR) system the hypotheses about the existence of the SCR-related brain oscillations and their connectivity with the SCR system have been here suggested. In contrast to classical approach to event-related oscillations which relies on either stimulus- or response-locked time reference, an approach assigned as "oscillatory process-related oscillations" has been introduced. The method enables us to overcome the variability of latency period of the SCR. The hypothesis about the existence of the SCR-related brain oscillations and their delta nature has been confirmed through the grand averaging method. An unexpected finding was the complex nature of the SCR-related oscillations: in addition to the two second EEG segment which was correlated with the SCR system signals they also comprised an initial 200 ms segment uncorrelated with the SCR. The hypothesis about the connectivity between the SCR system and the respective delta brain oscillatory response has been operationalized through a multiple time series regression model. The predictor set consists of the SCR, its first three derivatives, and their mutual interactions. The Monte Carlo test of the causal link between the SCR system signals and the related delta EEG signal demonstrated significance in more than half of the participants. The findings have been considered from the standpoints of the segmental structure of the EEG, monoaminergic signaling and recently emerged the "brain-body dynamic syncytium" hypothesis.

neuroscience↗

bioRxiv2018

Population-wide copy number variation calling using variant call format files from 6,898 individuals

MotivationCopy number variants (CNVs) are large deletions or duplications at least 50 to 200 base pairs long. They play an important role in multiple disorders, but accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process.\n\nResultsWe use a regression tree-based approach to call CNVs from whole-genome sequencing (WGS, > 18x) variant call-sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. 61.8% of detected events have been previously reported in the Database of Genomic Variants. 23% of high-quality deletions affect entire genes, and we recapitulate known events such as the GSTM1 and RHD gene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe the LD structure and copy number variation underlying the association between levels of the CCL3 protein and a complex structural variant (MAF = 0.15, p = 3.6x10-12) affecting CCL3L3, a paralog of the CCL3 gene. We also identify a cis- association between a low-frequency NOMO1 deletion and the protein product of this gene (MAF = 0.02, p = 2.2x10-7), for which no cis- or trans- single nucleotide variant-driven protein quantitative trait locus (pQTL) has been documented to date. This work demonstrates that existing population-wide WGS call-sets can be mined for CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.\n\nAvailabilityThe regression tree based approach, UN-CNVc, is available as an R and bash executable on GitHub at https://github.com/agilly/un-cnvc.\n\nContacteleftheria.zeggini@helmholtz-muenchen.de; arthur.gilly@helmholtz-muenchen.de\n\nSupplementary InformationSupplementary information is appended.

bioinformatics↗

bioRxiv2018

An event-based paradigm for analyzing fluorescent astrocyte activity uncovers novel single-cell and population-level physiology

Recent work examining astrocytic physiology centers on fluorescence imaging approaches, due to development of sensitive fluorescent indicators and observation of spatiotemporally complex calcium and glutamate activity. However, the field remains hindered in fully characterizing these dynamics, both within single cells and at the population-level, because of the insufficiency of current region-of-interest-based approaches to describe activity that is often spatially unfixed, size-varying, and propagative. Here, we present a paradigm-shifting analytical framework that releases astrocyte biologists from ROI-based tools. Astrocyte Quantitative Analysis (AQuA) software enables users to take an event-based approach to accurately capture and quantify the irregular activity observed in astrocyte imaging datasets. We apply AQuA to a range of ex vivo and in vivo imaging data, and uncover previously undescribed physiological phenomena in each. Since AQuA is data-driven and based on machine learning principles, it can be applied across model organisms, fluorescent indicators, experimental modes, and imaging resolutions and speeds, enabling researchers to elucidate fundamental astrocyte physiology.

neuroscience↗

bioRxiv2018

Microglial activation in an amyotrophic lateral sclerosis-like model caused by Ranbp2 lossand nucleocytoplasmic transport impairment in retinal ganglion neurons

Nucleocytoplasmic transport is dysregulated in sporadic and familial amyotrophic lateral sclerosis (ALS) and retinal ganglion neurons (RGNs) are purportedly involved in ALS. The Ran-binding protein 2 (Ranbp2) controls rate-limiting steps of nucleocytoplasmic transport. Mice with Ranbp2 loss in Thy1+-motoneurons develop cardinal ALS-like traits, but the impairments in RGNs and the degree of dysfunctional consonance between RGNs and motoneurons caused by Ranbp2 loss are unknown. This understanding will facilitate to discern the role of nucleocytoplasmic transport in the differential vulnerability of neurons to ALS and to develop therapeutic approaches and biomarkers in ALS. Here, we ascertain Ranbp2s function and endophenotypes in RGNs of an ALS-like mouse model lacking Ranbp2 in motoneurons and RGNs. Thy1+-RGNs lacking Ranbp2 shared with motoneurons the dysregulation of nucleocytoplasmic transport. RGN abnormalities were comprised morphologically by soma hypertrophy and optic nerve axonopathy and physiologically by a delay of the visual pathways evoked potentials. Whole-transcriptome analysis showed restricted transcriptional changes in optic nerves that were distinct from those found in sciatic nerves. Specifically, the level and nucleocytoplasmic partition of the anti-apoptotic and novel substrate of Ranbp2, Pttg1/securin, were dysregulated. Further, acetyl-CoA carboxylase 1, which modulates de novo synthesis of fatty acids and T-cell immunity, showed the highest up-regulation (35-fold). This effect was reflected by the activation of ramified Cd11b+ and CD45+-microglia, increase of F4\\80+-microglia and a shift from pseudopodial/lamellipodial to amoeboidal F4\\80+-microglia intermingled between RGNs of naive mice. This immunogenic phenotype was accompanied by the intracellular sequestration in RGNs of metalloproteinase-28, which regulates macrophage recruitment and polarization in inflammation. Ranbp2 genetic insults in RGNs and motoneurons trigger distinct paracrine signaling likely by the dysregulation of nucleocytoplasmic transport of neural-type selective substrates. Metabolic and immune-modulators underpinning RGN-to-microglial signaling are regulated by Ranbp2, and this neuroglial system manifests endophenotypes that are likely useful in the prognosis and diagnosis of ALS.

neuroscience↗

bioRxiv2018

Dual-color volumetric imaging of neural activity of cortical columns

To capture the emergent properties of neural circuits, high-speed volumetric imaging of neural activity at cellular resolution is desirable. But while conventional two-photon calcium imaging is a powerful tool to study population activity in vivo, it is restrained to two-dimensional planes. Expanding it to 3D while maintaining high spatiotemporal resolution appears necessary. Here, we developed a two-photon microscope with dual-color laser excitation that can image neural activity in a 3D volume. We imaged the neuronal activity of primary visual cortex from awake mice, spanning from L2 to L5 with 10 planes, at a rate of 10 vol/sec, and demonstrated volumetric imaging of L1 long-range PFC projections and L2/3 somatas. Using this method, we map visually-evoked neuronal ensembles in 3D, finding a lack of columnar structure in orientation responses and revealing functional correlations between cortical layers which differ from trial to trial and are missed in sequential imaging. We also reveal functional interactions between presynaptic L1 axons and postsynaptic L2/3 neurons. Volumetric two-photon imaging appears an ideal method for functional connectomics of neural circuits.

neuroscience↗

bioRxiv2018

The Bayesian Superorganism III: externalised memories facilitate distributed sampling

A key challenge for any animal (or sampling technique) is to avoid wasting time by searching for resources (information) in places already found to be unprofitable. In biology, this challenge is particularly strong when the organism is a central place forager - returning to a nest between foraging bouts - because it is destined repeatedly to cover much the same ground. This problem will be particularly acute if many individuals forage from the same central place, as in social insects such as the ants. Foraging (sampling) performance may be greatly enhanced by coordinating movement trajectories such that each ant ( walker) visits separate parts of the surrounding (unknown) space. We find experimental evidence for an externalised spatial memory in Temnothorax albipennis ants: chemical markers (either pheromones or cues such as cuticular hydrocarbon footprints) that are used by nestmates to mark explored space. We show these markers could be used by the ants to scout the space surrounding their nest more efficiently through indirect coordination. We also develop a simple model of this marking behaviour that can be applied in the context of Markov chain Monte Carlo methods (Baddeley et al. 2019). This substantially enhances the performance of standard methods like the Metropolis-Hastings algorithm in sampling from sparse probability distributions (such as those confronted by the ants) with little additional computational cost. Our Bayesian framework for superorganismal behaviour motivates the evolution of exploratory mechanisms such as trail marking in terms of enhanced collective information processing.

animal behavior and cognition↗

bioRxiv2018

A role for gut microbiota in m6A epitranscriptomic mRNA modifications in different host tissues

The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. A recently discovered layer of gene expression regulation is N6-methyladenosine (m6A) modification of mRNA. To unveil if this epitranscriptomic mark in part mediates the impact of the gut microbiota on the host, we analyzed m6A-modifications in transcripts of mice displaying either a conventional, or a modified, or no gut flora. We discovered that the microbiota has a strong influence on m6A-modifications in the cecum, and also, albeit to a lesser extent, in the liver. We furthermore show that a single commensal bacterium, Akkermansia muciniphila, can affect specific m6A modifications. Together, we report here epitranscriptomic modifications as an unexpected level of interaction in the complex interplay between commensal bacteria and their host.

molecular biology↗

bioRxiv2018

Sensorimotor conflicts alter perceptual and action monitoring

Bodily self-consciousness is defined as a set of prereflective representations of integrated bodily signals giving rise to self-identification, self-location and first-person perspective. While bodily self-consciousness is known to modulate perception, little is known about its influence on higher-level cognitive processes. Here, we manipulated bodily self-consciousness by applying sensorimotor conflicts while participants performed a perceptual task followed by confidence judgments. Results showed that sensorimotor conflicts altered perceptual monitoring by decreasing metacognitive performance. In a second experiment, we replicated this finding and extended our results by showing that sensorimotor conflicts also altered action monitoring, as measured implicitly through intentional binding. In a third experiment, we showed that effects on perceptual monitoring were induced specifically by sensorimotor conflicts related to the trunk and not to the hand. Taken together, our results suggest that bodily self-consciousness may serve as a scaffold for perceptual and action monitoring.

neuroscience↗

bioRxiv2018

PSI controls tim splicing and circadian period in Drosophila

The Drosophila circadian pacemaker consists of transcriptional feedback loops subjected to both post-transcriptional and post-translational regulation. While post-translational regulatory mechanisms have been studied in detail, much less is known about circadian post-transcriptional control. To have a better understanding of the role and mechanisms of circadian post-transcriptional regulation, we targeted 364 RNA binding and RNA associated proteins with RNA interference. Among the 43 genes we identified was the alternative splicing regulator P-element somatic inhibitor (PSI). PSI downregulation shortens the period of circadian rhythms both in the brain and in peripheral tissues. Interestingly, we found that PSI regulates the thermosensitive alternative splicing of timeless (tim), promoting splicing events favored at warm temperature over those increased at cold temperature. Moreover, the period of circadian behavior was insensitive to PSI downregulation when flies could produce functional TIM proteins only from a transgene that cannot form the thermosensitive splicing isoforms. Therefore, we conclude that PSI regulates the period of Drosophila circadian rhythms through its modulation of the tim splicing pattern.

neuroscience↗

bioRxiv2018

Convergent Allostery in Ribonucleotide Reductase

Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a new and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible, active tetramer and two novel, inhibited filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

biochemistry↗

bioRxiv2018

Reduced central and peripheral inflammatory responses and increased mitochondrial activity contribute to diet-induced obesity resistance in WSB/EiJ mice.

ObjectivesEnergy balance disruption due to excess of calorie-rich food is considered to be one of the major players in the current worldwide obesity pandemic. In rodents, a high fat diet (HFD) induces not only obesity, but also inflammation and mitochondrial dysfunctions. To identify factors underlying diet-induced obesity (DIO) resistance we compared the wild-derived mouse strain WSB/EiJ, characterized by a striking resistance to DIO, with the more DIO-sensitive C57BL/6J strain.\n\nMethodsWe analysed circulating levels of lipids, cytokines and adipokines as well as hypothalamic markers of inflammatory status and mitochondrial activity in both strains exposed to HFD for three days (3d) or eight weeks (8wk). To identify hypothalamic genes potentially involved in these differential regulations, we selected 86 genes related to inflammation and mitochondrial pathways. We analysed their expression levels by high throughput microfluidic qPCR on RNA extracted from laser micro-dissected arcuate (ARC) and paraventricular (PVN) hypothalamic nuclei of the two strains of mice, under the different HFD treatments.\n\nResultsAfter 3d and 8wk HFD, C57BL/6J mice, in contrast to WSB/EiJ, displayed significantly increased body weight gain, and also increased circulating levels of leptin, cholesterol, HDL and LDL. WSB/EiJ mice displayed a lower inflammatory status, both peripherally (lower levels of circulating cytokines) and centrally (less activated microglia in the hypothalamus) as well as more reactive mitochondria in the hypothalamus. Principal Component Analysis and gene ontology analysis of gene expression data showed, first, that datasets segregated as a function of strain and second, allowed to identify the metabolic pathways involved. These results were reinforced by the identification of strain-specific differential expression of several individual hypothalamic genes as well as differential effects of HFD between strains.\n\nConclusionsAdaptation to metabolic stress in the DIO-resistant WSB/EiJ strain implicates enhanced lipid metabolism, lower peripheral and hypothalamic inflammatory status and higher mitochondrial activity than in the C57BL/6J strain. These results point to the implication of the hypothalamic inflammatory and mitochondrial pathways as key factors in the control of energy homeostasis and the resistance to DIO.\n\nDeclarations of interest: none\n\nHighlightsO_LIDiet-induced-obesity resistance of WSB/EiJ implicates enhanced lipid metabolism\nC_LIO_LIWSB/EiJ mice are protected from HFD-induced peripheral and central inflammation\nC_LIO_LIEnhanced hypothalamic transport and signalling of endocrine molecules in WSB/EiJ\nC_LIO_LIWSB/EiJ hypothalamic mitochondria dynamics differ from C57BL/6J\nC_LIO_LIDifferential regulation of hypothalamic inflammatory/mitochondria genes in WSB/EiJ\nC_LI

physiology↗

bioRxiv2018

Coordination of trait responses to above and belowground resource limitation in cultivated sunflower (Helianthus annuus L.)

O_LIIn the face of resource limitations, plants show plasticity in multiple trait categories, including biomass allocation, morphology and anatomy, yet inevitably also grow less. The extent to which passive mass-scaling plays a role in trait responses that contribute to increased potential for resource acquisition are poorly understood. Here we assessed the role of mass-scaling on the direction, magnitude and coordination of trait plasticity to light and/or nutrient limitation in cultivated sunflower (Helianthus annuus). C_LIO_LIWe grew seedlings of ten sunflower genotypes for three weeks in a factorial of light (50% shade) and nutrient (10% supply) limitation in the greenhouse and measured a suite of allocational, morphological and anatomical traits for leaves, stems, fine roots, and tap roots. C_LIO_LIUnder resource limitation, plants were smaller and more biomass was allocated to the organ capturing the most limiting resource, as expected. Traits varied in the magnitude of plasticity and the extent to which the observed response was passive (scaled with plant mass) and/or had an additional active component. None of the allocational responses were primarily passive. Plastic changes to specific leaf area and specific root length were primarily active, and adjusted towards more acquisitive trait values under light and nutrient limitation, respectively. For many traits, the observed response was a mixture of active and passive components, and for some traits the active adjustment was antagonistic to the direction of passive adjustment, e.g. stem height, and tap root and stem theoretical hydraulic conductance. Passive scaling with size played a major role in the coordinated response to light, but correcting for mass clarified that the active responses to both limitations were more similar in magnitude, although still resource and organ specific. C_LIO_LIOur results demonstrate that both passive plasticity and active plasticity can contribute to increased uptake capacity for limiting resources in a manner that is resource, organ and trait specific. Indeed, passive adjustments (scaling with mass) of traits due to resource stress extends well beyond just mass allocation traits. For a full understanding of plants response to environmental stress both passive and active plasticity needs to be taken into account. C_LI

plant biology↗

bioRxiv2018

Differential dominance of an allele of the Drosophila tbetah gene defies standard genetic techniques

The biogenic amine octopamine (OA) and its precursor tyramine (TA) are involved in controlling a plethora of different physiological and behavioral processes. The tyramine-{beta}-hydroxylase (t{beta}h) gene encodes the enzyme catalyzing the last synthesis step from TA to OA. Here, we report differential dominance (from recessive to overdominant) of the putative null t{beta}hnM18 allele in two behavioral measures in Buridans paradigm (walking speed and stripe deviation) and a proboscis extension assay in the fruit fly Drosophila melanogaster. The behavioral analysis of transgenic t{beta}h expression experiments in mutant and wild type flies as well as of OA- and TA-receptor mutants revealed a complex interaction of both aminergic systems. Our analysis suggests that the different neuronal networks responsible for the three phenotypes show differential sensitivity to t{beta}h gene expression levels. The evidence suggests that this sensitivity is brought about by a TA/OA opponent system modulating the involved neuronal circuits. This conclusion entails important implications for standard transgenic techniques, commonly used in functional genetics.

genetics↗

bioRxiv2018

Amyloid Precursor Protein (APP) controls excitatory/inhibitory synaptic inputs by regulating the transcriptional activator Neuronal PAS Domain Protein 4 (NPAS4)

Sequential proteolysis of the amyloid precursor protein (APP) and amyloid-{beta} peptide (A{beta}) release is an upstream event in Alzheimers disease (AD) pathogenesis. The function of APP in neuronal physiology is still, however, poorly understood. Along with its paralog APP-like Proteins 1 and 2 (APLP1-2), APP is involved in neurite formation and synaptic function by mechanisms that are not elucidated. APP is a single-pass transmembrane protein expressed at high levels in the brain that resembles a cell adhesion molecule or a membrane receptor, suggesting that its function relies on cell interaction processes and/or activation of intracellular pathways of signal transduction. Along this line, the APP intracellular domain (AICD) was reported to act as a transcriptional factor for targeted gene activation that mediates physiological APP functions. Here, we used an unbiased transcriptome-based approach to identify the genes transcriptionally regulated by APP in the rodent embryonic cortex and upon maturation of primary cortical neurons. The transcriptome analysis did not detect any significant differences in expression of previously proposed AICD target genes. The overall transcriptional changes were subtle, but we found that genes clustered in neuronal-activity dependent pathways are dysregulated in the absence of APP. Among these genes, we found the activity-dependent Neuronal PAS domain protein 4 (NPAS4) Immediate Early Gene to be downregulated in the absence of APP. Down-regulation of NPAS4 in APP knock-out (KO) neurons is not related to AICD but to the APP ectodomain. We studied the effect of APP deficiency on GABAergic and glutamatergic transmission, and found an increased production of the inhibitory neurotransmitter GABA in APP KO neurons, along with a reduced expression of the GABA(A) receptors alpha1, suggesting an impaired GABAergic neurotransmission in the absence of APP. CRISPR-Cas-mediated silencing of NPAS4 in neurons led to similar observations. Altogether, our results point out a new role for APP in the regulation of excitatory/inhibitory neurotransmission through the regulation of the activity-dependent NPAS4 gene.

neuroscience↗

bioRxiv2018

Structural and Biochemical Studies of Dihydrofolate Reductase from Streptococcus pyogenes as a Target for Antifolate Antibiotics

Streptococcus pyogenes, a beta-hemolytic bacterium, causes a wide spectrum of infections in human including pharyngitis, tonsillitis, scarlet fever, rheumatic fever, and necrotizing fasciitis. Streptococcal infections can also exist as co-infection with methicillin resistant Staphylococcus aureus (MRSA). Trimethoprim-sulfamethoxazole (TMP-SMX) combination has been used for treatment of S. pyogenes and MRSA co-infection. However, resistance to TMP, an inhibitor of dihydrofolate reductase enzyme (DHFR), has challenged the efficacy of TMP-SMX combination. We explored the activity of a series of novel DHFR inhibitors against S. pyogenes. This study identified potent inhibitors of DHFR enzyme from S. pyogenes with excellent inhibitory activity against the growth of the live bacteria. We determined, for the first time, the crystal structure of S. pyogenes DHFR which provides structural insights into design and development of antifolate agents against this global pathogen.

microbiology↗