title: MKLP2 functions in early mitosis to ensure proper chromosome congression

abstract:
Mitotic kinesin-like protein 2 (MKLP2) is a motor protein with a well-established function in promoting cytokinesis. However, our results with siRNAs targeting MKLP2 and small molecule inhibitors of MKLP2 (MKLP2i) suggested a function earlier in mitosis, prior to anaphase. In this study we provide direct evidence that MKLP2 facilitates chromosome congression in prometaphase. We employed live imaging to observe HeLa cells with fluorescently tagged histones treated with MKLP2i and discovered a pronounced chromosome congression defect. We show that MKLP2 is essential for pole-based error correction as inhibited cells had a significant increase in unstable kinetochore-microtubule attachments due to impaired error correction of syntelic attachments. We propose that MKLP2 mediates kinetochore microtubule attachment stability by regulating Aurora Kinase activity and a downstream target, pHEC1 (Ser 55). Lastly, we show that MKLP2 inhibition results in aneuploidy, confirming that MKLP2 safeguards cells against chromosomal instability.

SummarySchrock et al. demonstrate that the mitotic kinesin, MKLP2, is required for congression of chromosomes located near the spindle poles. They show that MKLP2 inhibition causes elevated active Aurora Kinase A, unstable microtubule kinetochore attachments, and impaired syntelic error correction.


title: Transferrin receptor 1-mediated iron uptake regulates bone mass in mice via osteoclast mitochondria and cytoskeleton

abstract: Increased intracellular iron spurs mitochondrial biogenesis and respiration to satisfy high-energy demand during osteoclast differentiation and bone-resorbing activities. Transferrin receptor 1 (TFR1) mediates cellular iron uptake through endocytosis of iron-loaded transferrin and its expression increases during osteoclast differentiation. Nonetheless, the precise functions of TFR1 and TFR1-mediated iron uptake in osteoclast biology and skeletal homeostasis remain incompletely understood. To investigate the role of TFR1 in osteoclast lineage cells, we conditionally deleted Tfr1 gene in myeloid precursors or mature osteoclasts by crossing Tfr1- floxed mice with LysM-Cre and Ctsk-Cre mice, respectively. Skeletal phenotyping by {micro}CT and histology unveiled that loss of Tfr1 in osteoclast progenitor cells resulted in a three-fold increase in trabecular bone mass in the long bones of 10-week old female but not male mice. Although high trabecular bone volume in long bones was seen in both male and female mice with deletion of Tfr1 in mature osteoclasts, this phenotype was more pronounced in female knockout mice. Mechanistically, disruption of Tfr1 expression attenuated mitochondrial metabolism and cytoskeletal organization in mature osteoclasts, leading to decreased bone resorption with no impact on osteoclastogenesis. These results indicate that Tfr1-mediated iron uptake is specifically required for osteoclast function and is indispensable for bone remodeling.

category: cell biology


title: Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

abstract: AO_SCPLOWBSTRACTC_SCPLOWIn the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate {lambda} for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to [Formula] as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate  (where  < {lambda}), we also establish a similar result for birth-death trees, except that t/2 is replaced by t/2 {middle dot} (1 - /{lambda}). This  complete tree may contain subtrees that have died out before time t; for the  reduced tree that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.

category: evolutionary biology


title: Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation

abstract: The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here we examine a whitefish population introduced to northern Finnish Lake Tsahkal in late 1960s, where three divergent morphs (viz. littoral, pelagic and profundal feeders) were found ten generations after. Using demographic modelling based on genomic data we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid symmetric speciation scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping three quantitative trait loci associated with gonad weight variation, a proxy for sexual maturity and spawning time, were identified. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.


title: Intracellular force comparison of pathogenic KIF1A, KIF5, and dynein by fluctuation analysis

abstract:
In mammalian cells, there exist approximately 40 types of microtubule motor proteins that are assigned to specific cargo deliveries. For example, the kinesin-1 family motor KIF5 is the major motor responsible for anterograde mitochondrial transport, whereas the kinesin-3 family motor KIF1A is responsible for synaptic vesicle precursor transport. In contrast, cytoplasmic dynein is responsible for retrograde transport of nearly all cargos. The force and velocity of these microtubule motors have been investigated in in-vitro single-molecule experiments. In the present study, we compared the intracellular force and velocity of various types of motors in the mammalian neuronal axon obtained by non-invasive force measurement (fluctuation analysis) and extreme value analysis with those obtained by previous single-molecule experiments. As we found a high correlation between our results and the previous results, we next investigated synaptic vesicle precursor transport by hereditary spastic paraplegia-associated KIF1A variants (V8M, R350G, and A255V). KIF1A-V8M and KIF1A-A255V exhibited force and velocity impairment in mammalian neuronal axons, whereas the physical property of KIF1A-R350G was similar to that of the wild type. We believe that the development of new analytical techniques for investigating intracellular cargo transports is helpful to elucidate the molecular mechanism of KIF1A-associated neurological disorders.

Statement of SignificanceRecent in-vitro single-molecule experiments have clearly revealed that microtubule motors only fully exert their functions when fully equipped with the proteins associated with cargo vesicle transport. This emphasizes the significance of intracellular physical measurements, in which the motors should fully function. In addition to motor force and velocity, the number of motors transporting a single cargo together is an important physical quantity to characterize cargo transport, but is difficult to estimate using in-vitro single-molecule experiments. In this study, we aimed to extract physical information on microtubule motors in the intracellular environment.

category: biophysics


title: Dual-color Fluorescence Cross-Correlation Spectroscopy to study Protein-Protein Interaction and Protein Dynamics in Live Cells

abstract:
We present a protocol and workflow to perform live cell dual-color fluorescence crosscorrelation spectroscopy (FCCS) combined with Forster Resonance Energy transfer (FRET) to study membrane receptor dynamics in live cells using modern fluorescence labeling techniques. In dual-color FCCS, where the fluctuations in fluorescence intensity represents the dynamical "fingerprint" of the respective fluorescent biomolecule, we can probe co-diffusion or binding of the receptors. FRET, with its high sensitivity to molecular distances, serves as a well-known "nanoruler" to monitor intramolecular changes. Taken together, conformational changes and key parameters such as local receptor concentrations, and mobility constants become accessible in cellular settings.

Quantitative fluorescence approaches are challenging in cells due to high noise levels and the vulnerable sample itself. We will show how to perform the experiments including the calibration steps. We use dual-color labeled {beta}2-adrenergic receptor ({beta}2AR) labeled (eGFP and SNAPtag-TAMRA). We will guide you step-by-step through the data analysis procedure using open-source software and provide templates that are easy to customize.

Our guideline enables researchers to unravel molecular interactions of biomolecules in live cells in situ with high reliability despite the limited signal-to-noise levels in live cell experiments. The operational window of FRET and particularly FCCS at low concentrations allows quantitative analysis near-physiological conditions.

Link to accompanying video: https://tr240.uni-wuerzburg.de/vippclass/index.php/s/TL8aWmwE9RjGfLE


title: Condition Medium of Glioblastoma Cell Lines Decreases the Viability of Glioblastoma Cells by Modulating Gene Expression Profile

abstract:
Grade IV neoplasm of the central nervous system, GBM, is associated with poor prognosis and relatively short overall survival. Due to the current limitations in treatment methods, GBM is characterized as an incurable disease, and research to advance therapeutic options is required. Conditioned medium is commonly used in in-vitro studies complementary to animal experiments to simulate tumor microenvironment and has the potential to challenge and expand our current understanding of secretome effect on tumor characteristics. This study aimed to investigate the effects of conditioned mediums of GBM cell lines on each other. Conditioned mediums cellular and molecular effects were evaluated using commonly employed techniques such as MTT assay, colony formation assay, wound healing assay, EdU labeling-based flow cytometry, and qRT-PCR. Our study demonstrated that conditioned medium harvested from U87 or LN229 cells at 48th h exhibited an anti-growth activity on each other by changing the gene expression pattern. Furthermore, the conditioned medium of LN229 decreased the migration capacity of U87 cells, and the conditioned medium of U87 cells significantly suppressed the LN229 proliferation. We believe that this initial work provides new insights for a better understanding of GBM cell lines secretome roles and highlights the necessity of further studies to unveil the secretome content.

HighlightsO_LIConditioned medium harvested from GBM cells at different time points displayed various effects.
C_LIO_LIConditioned medium of GBM cell lines harvested at 48th h decreased the viability of each other.
C_LIO_LIThe expression level of anti-and pro-proliferative genes is altered upon condition medium treatment.
C_LI

category: cancer biology


title: SAMD1 Distribution Patterns in Mouse Atherosclerosis Models Suggest Roles in LDL Retention, Antigen Presentation, and Cell Phenotype Modulation

abstract: The theory that lesions formed by retention of circulating LDL can then progress to complicated atherosclerotic lesions has been a subject of debate, as has the mechanism of retention. In earlier work, we identified SAMD1, a protein expressed by intimal smooth muscle cells in human lesions that appears to irreversibly bind apoB-Lps in extracellular matrix near the lumen. We hypothesized this binding could contribute to the formation of lesions in mice, and that inhibiting binding could reduce lesion growth. In mouse models of atherosclerosis, we found that SAMD1 binds LDL; that SAMD1/apoB complex is ingested by intimal cells; and that recognizable epitopes of the SAMD1/apoB complex survive some degree of catabolism in foam cell. These data appear to support the SAMD1/LDL retention hypothesis of lesion growth. Despite apparently irreversible binding of human LDL to full-length human SAMD1, efficient anti-SAMD1-antibody inhibitors were created. In vivo lesion targeting of inhibitors was demonstrated by MRI, ultrasound, and ex vivo microscopy. However, only non-statistically significant reductions in spontaneous lesion size in apoE-/- mice were seen after 12 weeks of treatment with PEG-fab inhibitors of SAMD1/LDL binding. In contrast, these inhibitors substantially reduced LDL retention in carotid injury lesions in apoE-/- and LDLR-/- mice 7 days after injury. The most obvious difference between injury lesions and early spontaneous lesions is the presence of numerous smooth muscle cells and associated extracellular matrix in the injury lesions. Thus, SAMD1 may be involved in retention of apoB-Lps in mouse lesions, but not until smooth muscle cells have entered the intima. In addition, SAMD1 is seen throughout arteries in changing patterns that suggest broader and more complicated roles in atherosclerosis.

category: pathology


title: Ankfn1 vestibular defects in zebrafish require mutations in both ancestral and derived paralogs.

abstract: How and to what degree gene duplication events create regulatory innovation, redundancy, or neofunctionalization remain important questions in animal evolution and comparative genetics. Ankfn1 genes are single copy in most invertebrates, partially duplicated in jawed vertebrates, and only the derived copy retained in most mammals. Null mutations in the single mouse homolog have vestibular and neurological abnormalities. Null mutation of the single Drosophila homolog is typically lethal with severe sensorimotor deficits in rare survivors. The functions and potential redundancy of paralogs in species with two copies is not known. Here we define a vestibular role for Ankfn1 homologs in zebrafish based on simultaneous disruption of each locus. Zebrafish with both paralogs disrupted showed vestibular defects and early lethality from swim bladder inflation failure. One intact copy at either locus was sufficient to prevent major phenotypes. Our results show that vertebrate Ankfn1 genes are required for vestibular-related functions, with at least partial redundancy between ancestral and derived paralogs.

category: genetics


title: A high-quality de novo genome assembly based on nanopore sequencing of a wild-caught coconut rhinoceros beetle (Oryctes rhinoceros)

abstract:
BackgroundAn optimal starting point for relating genome function to organismal biology is a high-quality nuclear genome assembly, and long-read sequencing is revolutionizing the production of this genomic resource in insects. Despite this, nuclear genome assemblies have been under-represented for agricultural insect pests, particularly from the order Coleoptera. Here we present a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, Oryctes rhinoceros (Coleoptera: Scarabaeidae), based on Oxford Nanopore Technologies (ONT) long-read data generated from a wild-caught female, as well as the assembly process that also led to the recovery of the complete circular genome assemblies of the beetles mitochondrial genome and that of the biocontrol agent, Oryctes rhinoceros nudivirus (OrNV). As an invasive pest of palm trees, O. rhinoceros is undergoing an expansion in its range across the Pacific Islands, requiring new approaches to management that may include strategies facilitated by genome assembly and annotation.

ResultsHigh-quality DNA isolated from an adult female was used to create four ONT libraries that were sequenced using four MinION flow cells, producing a total of 27.2 Gb of high-quality long-read sequences. We employed an iterative assembly process and polishing with one lane of high-accuracy Illumina reads, obtaining a final size of the assembly of 377.36 Mb that had high contiguity (fragment N50 length = 12 Mb) and accuracy, as evidenced by the exceptionally high completeness of the benchmarked set of conserved single-copy orthologous genes (BUSCO completeness = 99.11%). These quality metrics place our assembly as the most complete of the published Coleopteran genomes. The structural annotation of the nuclear genome assembly contained a highly-accurate set of 16,371 protein-coding genes showing BUSCO completeness of 92.09%, as well as the expected number of non-coding RNAs and the number and structure of paralogous genes in a gene family like Sigma GST.

ConclusionsThe genomic resources produced in this study form a foundation for further functional genetic research and management programs that may inform the control and surveillance of O. rhinoceros populations, and we demonstrate the efficacy of de novo genome assembly using long-read ONT data from a single field-caught insect.

category: genomics


title: The Arabidopsis SAC9 Enzyme defines a cortical population of early endosomes and restricts PI(4,5)P2 to the Plasma Membrane

abstract:
Membranes lipids, and especially phosphoinositides, are differentially enriched within the eukaryotic endomembrane system. This generates a landmark code by modulating the properties of each membrane. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] specifically accumulates at the plasma membrane in yeast, animal and plant cells, where it regulates a wide range of cellular processes including endocytosis. However, the functional consequences of mispatterning PI(4,5)P2 in plants are unknown. Here, we functionally characterized the phosphoinositide phosphatase SUPPRESSOR OF ACTIN9 (SAC9) in Arabidopsis thaliana (Arabidopsis). We found that SAC9 depletion led to the ectopic localization of PI(4,5)P2 on cortical intracellular compartments, which depends on PI4P and PI(4,5)P2 production at the plasma membrane. SAC9 localizes to a subpopulation of trans-Golgi Network/early endosomes that are spatially restricted to a region close to the cell cortex and that are coated with clathrin. Furthermore, it interacts and colocalizes with the endocytic component Src Homology 3 Domain Protein 2 (SH3P2). In the absence of SAC9, SH3P2 localization is altered and the clathrin mediated endocytosis rate is significantly reduced. Thus, SAC9 is required to maintain efficient endocytic uptake, highlighting the importance of restricting the PI(4,5)P2 pool at the plasma membrane for the proper regulation of endocytosis in plants.

One-sentence summarySAC9 prevents the accumulation of PI(4,5)P2 along the endocytic pathway in plants and thereby contributes to the clathrin mediated endocytosis process at the plasma membrane via its interaction with SH3P2

category: plant biology


title: Full-length NLRP3 forms oligomeric cages to mediate NLRP3 sensing and activation

abstract: The nucleotide-binding domain and leucine-rich-repeat (LRR) containing protein 3 with a pyrin domain (NLRP3) is emerging to be a critical intracellular inflammasome sensor of membrane integrity and a highly important clinical target against chronic inflammation. Here we report that the endogenous, stimulus-responsive form of full-length NLRP3 is a 12-16 mer double ring cage held together by LRR-LRR interactions with the pyrin domains shielded within the assembly to avoid premature activation. Surprisingly, this NLRP3 form is predominantly membrane localized, which is consistent with previously noted localization of NLRP3 at various membrane organelles. Structure-guided mutagenesis reveals that trans-Golgi network dispersion into vesicles, an early event observed for all NLRP3 activating stimuli, requires the double ring cages of NLRP3. Double ring-defective NLRP3 mutants further abolish inflammasome punctum formation, caspase-1 processing and cell death. Thus, unlike other inflammasome sensors that are monomeric when inactive, our data uncover a unique NLRP3 oligomer on membrane that is poised to sense diverse signals to induce inflammasome activation.

category: immunology


title: The Drosophila TMEM184B ortholog Tmep ensures proper locomotion by restraining ectopic firing at the neuromuscular junction

abstract: TMEM184B is a putative seven-pass membrane protein that promotes axon degeneration after injury. TMEM184B mutation causes aberrant neuromuscular architecture and sensory and motor behavioral defects in mice. The mechanism through which TMEM184B causes neuromuscular defects is unknown. We employed Drosophila melanogaster to investigate the function of the TMEM184B ortholog, Tmep (CG12004) at the neuromuscular junction. We show that Tmep is required for full adult viability and efficient larval locomotion. Tmep mutant larvae have a reduced body contraction rate compared to controls, with stronger deficits in females. Surviving adult Tmep mutant females show "bang sensitivity," a phenotype associated with epileptic seizures. In recordings from body wall muscles, Tmep mutants show substantial hyperexcitability, with many post-synaptic potentials fired in response to a single stimulation, consistent with a role for Tmep in restraining synaptic excitability. Neuromuscular junctions in Tmep mutants show modest structural defects and satellite boutons, which could also contribute to poor locomotor performance. Tmep is expressed in endosomes and synaptic vesicles within motor neurons, suggesting a possible role in synaptic membrane trafficking. Using RNAi knockdown, we show that Tmep is required in motor neurons for proper larval locomotion and excitability. Locomotor defects can be rescued by presynaptic knock-down of endoplasmic reticulum calcium channels or by reducing evoked release probability, suggesting that excess synaptic activity drives behavioral deficiencies. Our work establishes a critical function for the TMEM184B ortholog Tmep in the regulation of synaptic transmission and locomotor behavior.

category: neuroscience


title: Post-encoding modulation of spatial memory by a GABAA-agonist

abstract:
We investigated the role of the post-encoding period for consolidation of self-centered (egocentric) and world-centered (allocentric) spatial memory in neurologically normal human subjects. We used the GABAA-ergic anesthetic propofol to transiently modulate neural activity during the early stage of spatial memory consolidation. A total of 52 patients undergoing minor surgery learned to navigate to a target in a five-armed maze derived from animal experiments immediately prior to injection of propofol (early group) or more than 60 minutes before injection (late group). Two hundred and forty minutes after anesthesia, subjects were tested for memory-guided navigation. Our results show a selective impairment of memory-guided navigation in the early group and near-normal performance in the late group. Both egocentric and allocentric navigation were affected, albeit with distinct error patterns. In the egocentric condition, early group patients navigated significantly more often to a wrong alley of the maze but showed normal navigation times, thus suggesting a deficit mainly for memory of sequences of path segments. By contrast, in the allocentric condition, early group patients mostly navigated to the correct alley of the maze but showed a significant increase in detours and prolonged navigation times, thus suggesting a weakened representation of the relationship between landmarks. We conclude that presumably hippocampus-dependent networks contribute to early consolidation of representations underlying both egocentric and allocentric memory-guided navigation. Distinct aspects of these representations are susceptible to GABAA-ergic modulation within a post-encoding time-window of less than 60 minutes, indicating a redistribution and reconfiguration of spatial memory networks early during consolidation.

Significance statementO_LIPropofol modulates consolidation of spatial representations underlying human spatial navigation.
C_LIO_LIFollowing administration of propofol, memory-guided navigation using self-centered (egocentric) and world-centered (allocentric) spatial information is impaired.
C_LIO_LIError patterns after administration of propofol suggest modulation of a post-encoding integration process relevant for ego- and allocentric memory representations.
C_LIO_LIThe transient susceptibility of this process to GABAA-ergic modulation is consistent with rapid reconfiguration of networks for spatial memory shortly after learning.
C_LIO_LIPropofol provides a pharmacological tool to investigate spatial memory consolidation in humans.
C_LI


title: Activation of the CaMKII-Sarm1-ASK1 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria

abstract: Mitochondrial defects are tightly linked to axon degeneration, yet the underlying cellular mechanisms remain poorly understood. In C. elegans, PVQ axons that lack mitochondria degenerate spontaneously with age. Using an unbiased genetic screen, we found that cell-specific activation of CaMKII/UNC-43 suppresses axon degeneration due to loss of mitochondria. Unexpectedly, CaMKII/UNC-43 protects against degeneration through the conserved Sarm1/TIR-1-ASK1/NSY-1 MAPK pathway. In addition, we show that disrupting a trafficking complex composed of calsyntenin/CASY-1, Mint/LIN-10, and kinesin suppresses axon degeneration. Further analysis indicates that disruption of this trafficking complex activates the CaMKII-Sarm1-MAPK pathway through L-type voltage-gated calcium channels. Our findings identify CaMKII as a pivot point between mitochondrial defects and axon degeneration, describe how it is regulated in this context, and uncover a surprising neuroprotective role for the Sarm1-ASK1 pathway.


title: Computation of the mitochondria age distribution along the axon length

abstract: We describe a compartmental model of mitochondrial transport in axons, which we apply to compute mitochondrial age at different distances from the soma. The model predicts that the average mitochondrial age at the tip of an axon with a length of 1 cm is approximately 22 hours. The mitochondria are youngest closest to the soma and their age scales approximately linearly with distance from the soma. To the best of the authors knowledge, this is the first attempt to predict the spatial distribution of mitochondrial age within an axon. A sensitivity study of the mean age of mitochondria to various model parameters is also presented.

category: bioengineering


title: Computation of the mitochondrial age distribution along the axon length


title: p57Kip2 regulates embryonic haematopoietic stem cell numbers by controlling the size of the sympathoadrenal progenitor pool

abstract: Haematopoietic stem cells (HSCs) are of major clinical importance, and finding methods for their in vitro generation is a prime research focus. We demonstrate that the cell cycle inhibitor p57Kip2/Cdkn1c limits HSC numbers by restricting the size of the sympathetic nervous system (SNS) and the amount of HSC-supportive catecholamines secreted by these cells, specifically in the aorta-gonads-mesonephros (AGM) region via {beta}2-adrenergic receptor signalling. This regulation occurs at the SNS progenitor level and is in contrast to the cell-intrinsic function of p57Kip2 in maintaining adult HSCs. Using single-cell RNA-Seq we dissect the differentiation pathway of neural crest cells into SNS cells in the AGM and reveal that they are able to take an alternative differentiation pathway, giving rise to a subset of mesenchymal cells expressing HSC-supportive factors. Neural crest cells thus appear to contribute to the AGM HSC niche via two different mechanisms: SNS-mediated catecholamine secretion and HSC-supportive mesenchymal cell production.

category: developmental biology


title: Fluctuation of cellular differentiation in limb regeneration is regulated by Pde4b in urodele amphibians

abstract: Urodele amphibians, Pleurodeles waltl and Ambystoma mexicanum, have organ-level regeneration capability, such as limb regeneration. Multipotent cells are induced by an endogenous mechanism in amphibian limb regeneration. It is well known that dermal fibroblasts receive regenerative signals and turn into multipotent cells, called blastema cells. However, the induction mechanism of the blastema cells from matured dermal cells was unknown. We previously found that BMP2, FGF2, and FGF8 (B2FF) could play sufficient roles in blastema induction in urodele amphibians. Here, we show that B2FF treatment can induce dermis-derived cells that can participate in multiple cell lineage in limb regeneration. We first established a newt dermis-derived cell line and confirmed that B2FF treatment on the newt cells provided plasticity in cellular differentiation in limb regeneration. Interspecies comparative analysis clarified that Pde4b upregulation by B2FF specifically took place in the newt cells. Blocking PDE4B signaling by Rolipram suppressed dermis-to-cartilage transformation and the mosaic knockout animals showed consistent results. Our results are a valuable insight into how dermal fibroblasts acquire multipotency during the early phase of limb regeneration via an endogenous program in amphibian limb regeneration.


title: Closed-Loop Control of Anesthetic State in Non-Human Primates

abstract: Continuous monitoring of electroencephalogram (EEG) recordings in humans under general anesthesia (GA) has demonstrated that changes in EEG dynamics induced by an anesthetic drug are reliably associated with the altered arousal states caused by the drug. This observation suggests that an intelligent, closed-loop anesthesia delivery (CLAD) system operating in real-time could track EEG dynamics and control the infusion rate of a programmable pump to precisely maintain unconsciousness. The United States FDA acknowledges the potential benefits of such automatic physiological closed-loop control devices for patient care. Bringing these devices into clinical practice requires establishing their feasibility in suitable animal models. Therefore, given the close neurophysiological proximity between human and non-human primates (NHPs), we address this problem by developing and validating a propofol CLAD system in rhesus macaques. Our CLAD system has three key components: (1) a data acquisition system that records cortical local field potentials (LFPs) from an NHP in real-time; (2) a computer executing our CLAD algorithm that takes in the LFP signals as input and outputs infusion rates; and (3) a computer-controlled infusion pump that administers intravenous propofol. Our CLAD system controls an empirically-determined LFP marker of unconsciousness (MOU) at a user-prescribed target value by updating every 20 seconds the propofol infusion rate based on real-time processing of the LFP signal. The MOU is the instantaneous power in the 20 to 30 Hz band of the LFP spectrogram. Every cycle (duration{approx} 20 sec), our CLAD algorithm updates the MOU estimate and uses a robust optimal control strategy to adjust the propofol infusion rate based on the instantaneous error. This error is computed as the difference between the current and the user-prescribed target MOU values. Using neural recordings from multiple NHP anesthesia sessions, we first established that our chosen MOU signal was strongly correlated with propofol-induced decreased spiking activity which itself has been shown earlier to be associated with the level of unconsciousness in NHPs. Then we designed robust optimal control strategies that used subject-specific pharmacokinetic-pharmacodynamic models describing the MOU dynamics due to propofol infusion rate changes. Finally, we achieved safe and efficient closed-loop control of level of unconsciousness in 9 CLAD experiments involving 2 NHPs and 2 different 125 min long target MOU profiles with three target MOU changes within a given experiment. Our CLAD system performs stably, accurately and robustly across a total of 1125 min of closed-loop control. The CLAD performance measures, represented as median (25th percentile, 75th percentile), are 3.13 % (2.62%, 3.53%) for inaccuracy, 0.54 %(-0.31%, 0.89%) for bias, -0.02%/min (-0.06%/min, 0.00%/min) for divergence, and 3% (2.49%, 3.59%) for wobble. These performance measures were comparable or superior to previously reported CLAD performance measures from clinical studies (conducted outside USA) as well as rodent-based studies. The key innovations here are: (1) a pre-clinical NHP model for CLAD development and testing, (2) a neuroscience-informed LFP-based MOU for CLAD, (3) parsimonious, pharmacology-informed models to describe MOU dynamics under propofol infusion in rhesus macaques, (4) a novel numerical testing framework for propofol CLAD that incorporates a principled optimal robust control strategy for titrating propofol, and finally (5) experimental findings demonstrating the feasibility of stable, accurate and robust CLAD in the NHP model. Our NHP-based CLAD framework provides a principled pre-clinical research platform that can form the foundation for future clinical studies.


title: Pleiotropy drives repeatability in the genetic basis of adaptation

abstract: Studies of trait-mapping and local adaptation often identify signatures of genetically parallel evolution, where different species evolve similar phenotypes using the same genes. Such patterns appear incongruent with current estimations of quantitative trait architecture. With hundreds or thousands or genes contributing to a trait, why would selection make repeated use of the same genes? Here, we use individual-based simulations to explore a two-patch model with quantitative, pleiotropic traits to understand the parameters which may lead to repeated use of a particular locus during independent bouts of adaptation. We find that repeatability can be driven by increased phenotypic effect size, a reduction in trait dimensionality and a reduction in mutational correlations at a particular locus relative to other loci in the genome, and that these patterns are magnified by increased migration between demes. These results suggest that evolutionary convergence can arise from multiple characteristics of a locus, and provide a framework for the interpretation of quantitative signatures of convergence in empirical studies.


title: Reciprocal differentiation via GABAergic components and ASD-related phenotypes in hES with 1q21.1 CNV

abstract: Copy number variations (CNVs) in the distal 1q21.1 region, both deletion (1q del) and duplication (1q dup), are associated with autism spectrum disorder, epilepsy and schizophrenia. Besides common phenotypes, 1q del and 1q dup manifest opposite clinical phenotypes--e.g., microcephaly in 1q del and macrocephaly in 1q dup. However, molecular and cellular mechanisms are still elusive. We generate isogenic human ES (hES) cell lines with reciprocal 1q21.1 CNVs using CRISPR/Cas9 system and differentiate them into 2-dimensional (2-D) neurons and 3-D cortical organoids. Our study recapitulates opposite organoid size and shows dosage-dependent differentiation changes i.e., more mature and GABAergic components in 1q del and more proliferative state in 1q dup. In contrast, both CNVs show hyperexcitability and altered expressions of glutamate system as common features. These results demonstrate that 1q21.1 CNVs dramatically affect cell fate in the early neurodevelopmental periods. This is the first isogenic model of hES CNVs and our findings provide new insights into the underlying mechanisms of neurodevelopmental disorders.


title: Therapeutic efficacy of an oral nucleoside analog of remdesivir against SARS-CoV-2 pathogenesis in mice.

abstract: The COVID-19 pandemic remains uncontrolled despite the rapid rollout of safe and effective SARS-CoV-2 vaccines, underscoring the need to develop highly effective antivirals. In the setting of waning immunity from infection and vaccination, breakthrough infections are becoming increasingly common and treatment options remain limited. Additionally, the emergence of SARS-CoV-2 variants of concern with their potential to escape therapeutic monoclonal antibodies emphasizes the need to develop second-generation oral antivirals targeting highly conserved viral proteins that can be rapidly deployed to outpatients. Here, we demonstrate the in vitro antiviral activity and in vivo therapeutic efficacy of GS-621763, an orally bioavailable prodrug of GS-441524, the parental nucleoside of remdesivir, which targets the highly conserved RNA-dependent RNA polymerase. GS-621763 exhibited significant antiviral activity in lung cell lines and two different human primary lung cell culture systems. The dose-proportional pharmacokinetic profile observed after oral administration of GS-621763 translated to dose-dependent antiviral activity in mice infected with SARS-CoV-2. Therapeutic GS-621763 significantly reduced viral load, lung pathology, and improved pulmonary function in COVID-19 mouse model. A direct comparison of GS-621763 with molnupiravir, an oral nucleoside analog antiviral currently in human clinical trial, proved both drugs to be similarly efficacious. These data demonstrate that therapy with oral prodrugs of remdesivir can significantly improve outcomes in SARS-CoV-2 infected mice. Thus, GS-621763 supports the exploration of GS-441524 oral prodrugs for the treatment of COVID-19 in humans.

category: microbiology


title: Elicitation of potent SARS-CoV-2 neutralizing antibody responses through immunization using a versatile adenovirus-inspired multimerization platform

abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown that vaccine preparedness is critical to anticipate a fast response to emergent pathogens with high infectivity. To rapidly reach herd immunity, an affordable, easy to store and versatile vaccine platform is thus desirable. We previously designed a non-infectious adenovirus-inspired nanoparticle (ADDomer), and in the present work, we efficiently decorated this original vaccine platform with glycosylated receptor binding domain (RBD) of SARS-CoV-2. Cryo-Electron Microscopy structure revealed that up to 60 copies of this antigenic domain were bound on a single ADDomer particle with the symmetrical arrangements of a dodecahedron. Mouse immunization with the RBD decorated particles showed as early as the first immunization a significant anti-coronavirus humoral response, which was boosted after a second immunization. Neutralization assays with spike pseudo-typed-virus demonstrated the elicitation of strong neutralization titers. Remarkably, the existence of pre-existing immunity against adenoviral-derived particles enhanced the humoral response against SARS-CoV-2. This plug and play vaccine platform revisits the way of using adenovirus to combat emergent pathogens while potentially taking advantage of the adenovirus pre-immunity.


title: Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods

abstract:
COVID-19 is a viral disease that has been a threat to the whole world since 2019. Although effective vaccines against the disease have been developed, there are still points to be clarified about the mechanism of SARS-CoV-2, which is the causative agent of COVID-19. In this study, we determined the binding energies and the bond types of complexes formed by open (6VYB) and closed (6VXX) forms of the Spike protein of SARS-CoV-2 and wild and mutant forms of IFITM1, IFITM2, and IFITM3 proteins using the molecular docking approach. First, all missense SNPs were found in the NCBI Single Nucleotide Polymorphism database (dbSNP) for IFITM1, IFITM2, and IFITM3 and analyzed with SIFT, PROVEAN, PolyPhen-2, SNAP2, Mutation Assessor, and PANTHER cSNP web-based tools to determine their pathogenicity. When at least four of these analysis tools showed that the SNP had a pathogenic effect on the protein product, this SNP was saved for further analysis. Delta delta G (DDG) and protein stability analysis for amino acid changes were performed in the web-based tools I-Mutant, MUpro, and SAAFEC-SEQ. The structural effect of amino acid change on the protein product was made using the HOPE web-based tool. HawkDock server was used for molecular docking and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and binding energies of all complexes were calculated. BIOVIA Discovery Studio program was utilized to visualize the complexes. Hydrogen bonds, salt bridges, and non-bonded contacts between Spike and IFITM protein chains in the complexes were detected with the PDBsum web-based tool. The best binding energy among the 6VYB-IFITM wild protein complexes belong to 6VYB-IFITM1 (-46.16 kcal/mol). Likewise, among the 6VXX-IFITM wild protein complexes, the most negative binding energy belongs to 6VXX-IFITM1 (-52.42 kcal/mol). An interesting result found in the study is the presence of hydrogen bonds between the cytoplasmic domain of the IFITM1 wild protein and the S2 domain of 6VYB. Among the Spike-IFITM mutant protein complexes, the best binding energy belongs to the 6VXX-IFITM2 N63S complex (-50.77 kcal/mol) and the worst binding energy belongs to the 6VXX-IFITM3 S50T complex (4.86 kcal/mol).

The study suggests that IFITM1 protein may act as a receptor for SARS-CoV-2 Spike protein. Assays must be advanced from in silico to in vitro for the determination of the receptor-ligand interactions between IFITM proteins and SARS-CoV-2.

category: bioinformatics


title: Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour.

abstract:
MotivationThe ongoing SARS-CoV-2 pandemic has demonstrated the utility of real-time analysis of sequencing data, with a wide range of databases and resources for analysis now available. Here we show how the real-time nature of Oxford Nanopore Technologies sequencers can accelerate consensus generation, lineage and variant status assignment. We exploit the fact that multiplexed viral sequencing libraries quickly generate sufficient data for the majority of samples, with diminishing returns on remaining samples as the sequencing run progresses. We demonstrate methods to determine when a sequencing run has passed this point in order to reduce the time required and cost of sequencing.

ResultsWe extended MinoTour, our real-time analysis and monitoring platform for nanopore sequencers, to provide SARS-CoV2 analysis using ARTIC network pipelines. We additionally developed an algorithm to predict which samples will achieve sufficient coverage, automatically running the ARTIC medaka informatics pipeline once specific coverage thresholds have been reached on these samples. After testing on run data, we find significant run time savings are possible, enabling flow cells to be used more efficiently and enabling higher throughput data analysis. The resultant consensus genomes are assigned both PANGO lineage and variant status as defined by Public Health England. Samples from within individual runs are used to generate phylogenetic trees incorporating optional background samples as well as summaries of individual SNPs. As minoTour uses ARTIC pipelines, new primer schemes and pathogens can be added to allow minoTour to aid in real-time analysis of pathogens in the future.

Availability and ImplementationSource code and documentation is available at https://github.com/LooseLab/minotourapp.

Supplementary informationSupplementary data are available from

https://github.com/LooseLab/artic_minotour_analyses.


title: Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants

abstract: The surge of COVID-19 infection cases is spurred by emerging SARS-CoV-2 variants such as B.1.617. Here we report 38 cryo-EM structures, corresponding to the spike protein of the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Kappa (B.1.617.1) variants in different functional states with and without its receptor, ACE2. Mutations on the N-terminal domain not only alter the conformation of the highly antigenic supersite of the Delta variant, but also remodel the glycan shield by deleting or adding N-glycans of the Delta and Gamma variants, respectively. Substantially enhanced ACE2 binding was observed for all variants, whose mutations on the receptor binding domain modulate the electrostatics of the binding interfaces. Despite their abilities to escape host immunity, all variants can be potently neutralized by three unique antibodies.


title: Competition Between Cell-Cell and Cell-Substrate Adhesion Determines Epithelial Monolayer Architecture in Culture

abstract: Organ surfaces are lined by epithelial monolayers - sheets of cells that are one-cell thick. This architecture underlies tissue function, and its loss is associated with disease, including cancer. Studies of in-plane epithelial cell behaviors show that a developing epithelium behaves as a fluid in respect to the tissue plane, and can therefore readily adapt to varying mechanical influences during morphogenesis. We asked the question of how monolayer architecture is achieved, and whether it demonstrates the same fluid behavior. To address this problem, we cultured MDCK (Madin-Darby Canine Kidney) cell layers at different densities and timepoints and analyzed their architectures using a novel tool, Automated Layer Analysis (ALAn), which we introduce here. Our experimental and theoretical results lead us to propose that epithelial monolayer architecture is governed by a balance of counteracting forces due to cell-cell and cell-substrate adhesion, and that this balance is influenced by cell density. MDCK cells do not undergo obvious rearrangement along the apical-basal axis; instead, cells that do not contact the substrate aggregate on top of the monolayer. Our findings therefore imply that monolayered architecture is under more rigid control than planar tissue shape in epithelia.


title: A liquid +TIP-network drives microtubule dynamics through tubulin condensation

abstract: Regulation of microtubule dynamics is essential for diverse cellular functions, and proteins that bind to dynamic microtubule ends can regulate network dynamics. Here we show, that two conserved microtubule end-binding proteins, CLIP-170 and EB3, undergo phase separation and form dense liquid-networks. When CLIP-170 and EB3 act together the multivalency of the network increases, which synergistically increases the amount of protein in the dense phase. In vitro and in cells these liquid networks can condense tubulin. In vitro in the presence of microtubules, EB3/CLIP-170 phase separation can co-condense tubulin all along the microtubule. At this condition microtubule growth speed increases up to two-fold and depolymerization events are strongly reduced, compared to conditions with phase separation deficient networks. Our data show that phase separated EB3/CLIP-170 networks impact microtubule growth dynamics beyond direct protein-microtubule interactions.


title: A liquid +TIP-network regulates microtubule dynamics through tubulin condensation


title: Phase separation of +TIP-networks regulates microtubule dynamics


title: Specificity and sensitivity of an RNA targeting type III CRISPR complex coupled with a NucC endonuclease effector

abstract: Type III CRISPR systems detect invading RNA, resulting in the activation of the enzymatic Cas10 subunit. The Cas10 cyclase domain generates cyclic oligoadenylate (cOA) second messenger molecules, activating a variety of effector nucleases that degrade nucleic acids to provide immunity. The prophage-encoded Vibrio metoecus type III-B (VmeCmr) locus is uncharacterised, lacks the HD nuclease domain in Cas10 and encodes a NucC DNA nuclease effector that is also found associated with Cyclic-oligonucleotide-based anti-phage signalling systems (CBASS). Here we demonstrate that VmeCmr is activated by target RNA binding, generating cyclic-triadenylate (cA3) to stimulate a robust NucC-mediated DNase activity. The specificity of VmeCmr is probed, revealing the importance of specific nucleotide positions in segment 1 of the RNA duplex and the protospacer flanking sequence (PFS). We harness this programmable system to demonstrate the potential for a highly specific and sensitive assay for detection of the SARS-CoV-2 virus RNA with a limit of detection (LoD) of 2 fM using a commercial plate reader without any extrinsic amplification step. The sensitivity is highly dependent on the guide RNA used, suggesting that target RNA secondary structure plays an important role that may also be relevant in vivo.

category: biochemistry


title: Ultrafast, one-step, and microwave heating-based synthesis of DNA/RNA-AuNP conjugates

abstract: DNA/RNA-gold nanoparticle (DNA/RNA-AuNP) nanoprobes have been widely employed for nanobiotechnology applications. Here we discovered that both thiolated and non-thiolated DNA/RNA can be efficiently attached to AuNPs to achieve high-stable spherical nucleic acid (SNA) within minutes under a domestic microwave (MW)-assisted heating-dry circumstance. Further studies showed that for non-thiolated DNA/RNA the conjugation is poly (T/U) tag dependent. Spectroscopy, test strip hybridization, and loading counting experiments indicate that low-affinity poly (T/U) tag mediates the formation of a standing-up conformation, which is distributed in the outer layer of such a SNA structure. In further applications study, CRISPR/Cas9-sgRNA (135 bp), RNA from Nucleocapsid (N) gene of SARS-CoV-2 (1279 bp), and rolling circle amplification (RCA) DNA products (over 1000 bp) could be successfully attached on AuNPs, which overcomes the routine methods in long-chain nucleic acid-AuNP conjugation, exhibiting great promise in novel biosensing and nucleic acids delivery strategy. This novel heating-dry strategy has improved the traditional DNA/RNA-AuNP conjugation methods in simplicity, rapidity, cost, and universality.


title: Acoustic frequency-dependent physical mechanism of sub-MHz ultrasound neurostimulation

abstract: Ultrasound is an innovative physical modality allowing non-invasive and reversible modulation of neural circuit activity in the brain with high spatial resolution. Despite growing interest in clinical applications, the safe and effective use of ultrasound neuromodulation has been limited by a lack of understanding of the physical mechanisms underlying its effects. Here, we demonstrate acoustic frequency-dependent physical effects that underlie ultrasound neuromodulation, where cavitation and radiation forces are the dominant sources of low- and high-frequency stimulation, respectively. We used 39.5 kHz and 500 kHz acoustic frequencies to stimulate cultured neural and glial cells, excised from rat cortex, to study acoustic frequency-dependent neural responses. We demonstrate increased evoked responses due to increased cavitation activity at the 39.5 kHz acoustic frequency. In contrast, notable cavitation activity was not detected at 500 kHz despite detection of evoked responses. Our work highlights the dependence of ultrasound neuromodulation on acoustic frequencies, with different physical effects underlying cell responses to low and high sub-MHz acoustic frequency ranges.


title: Infer disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data

abstract: The identification of disease-associated microbial biomarkers is crucial for disease diagnosis and therapy. However, the heterogeneity, high dimensionality, and large amounts of microbial data present tremendous challenges for the discovery of biomarkers. In this paper, we present IDAM, a novel method for disease-associated biomarker inference from metagenomic and metatranscriptomic data, which does not require prior metadata. This method integrates gene context conservation (uber-operon) and regulatory mechanisms (gene co-expression patterns), using a mathematical graph model. We demonstrated the excellent performance of IDAM in biomarker inference, through the datasets from inflammatory bowel disease, melanoma, type 1 diabetes mellitus, and irritable bowel syndrome. The software of IDAM is freely available at https://github.com/OSU-BMBL/IDAM.


title: Inference of disease-associated microbial biomarkers based on metagenomic and metatranscriptomic data


title: ProtAnno, an Automated Cell Type Annotation Tool for Single Cell Proteomics Data that Integrates Information from Multiple Reference Sources

abstract: Compared with sequencing-based global genomic profiling, cytometry labels targeted surface markers on millions of cells in parallel either by conjugated rare earth metal particles or Unique Molecular Identifier (UMI) barcodes. Correct annotation of these cells to specific cell types is a key step in the analysis of these data. However, there is no computational tool that automatically annotates single cell proteomics data for cell type inference. In this manuscript, we propose an automated single cell proteomics data annotation approach called ProtAnno to facilitate cell type assignments without laborious manual gating. ProtAnno is designed to incorporate information from annotated single cell RNA-seq (scRNA-seq), CITE-seq, and prior data knowledge (which can be imprecise) on biomarkers for different cell types. We have performed extensive simulations to demonstrate the accuracy and robustness of ProtAnno. For several single cell proteomics datasets that have been manually labeled, ProtAnno was able to correctly label most single cells. In summary, ProtAnno offers an accurate and robust tool to automate cell type annotations for large single cell proteomics datasets, and the analysis of such annotated cell types can offer valuable biological insights.


title: PhyloVision: Interactive Software for Integrated Analysis of Single-Cell Transcriptomic and PhylogeneticData

abstract: Recent advances in CRISPR-Cas9 engineering and single-cell assays have enabled the simultaneous measurement of single-cell transcriptomic and phylogenetic profiles. However, there are few computational tools enabling users to integrate and derive insight from a joint analysis of these two modalities. Here, we describe PhyloVision: an open source software for interactively exploring data from both modalities and for identifying and interpreting heritable gene modules whose concerted expression are associated with phylogenetic relationships. PhyloVision provides a feature-rich, interactive, and shareable web-based report for investigating these modules, while also supporting several other data and meta-data exploration capabilities. We demonstrate the utility of PhyloVision using a published dataset of metastatic lung adenocarcinoma cells, whose phylogeny was resolved using a CRISPR/Cas9-based lineage-tracing system. Together, we anticipate that PhyloVision and the methods it implements will be a useful resource for scalable and intuitive data exploration for any assay that simultaneously measures cell state and lineage.


title: Disrupting the CmP signaling network unveils novel biomarkers for triple negative breast cancer in Caucasian American women

abstract: Triple-negative breast cancer (TNBC) constitutes [~]15 percent of all diagnosed invasive breast cancer cases with limited options for treatment since immunotherapies that target the ER, PR and HER2 receptors are ineffective. Progesterone (PRG) is capable of inducing its effects through either classic, non-classic, or combined responses by binding to classic nuclear PRG receptors (nPRs) or non-classic membrane PRG receptors (mPRs). Under PRG-induced actions, we previously demonstrated that the CSC (CCM signaling complex) can couple both nPRs and mPRs into a CmPn signaling network which plays an important role in nPR(+) breast cancer tumorigeneses. We recently defined the novel CmP signaling network in TNBC cells, which overlapped with our previously defined CmPn network in nPR(+) breast cancer cells. In this study, we were able to demonstrate alterations to key tumorigenesis pathways in Caucasian American Women (CAW)-TNBC cells, under mPRs-specific steroid actions. These results suggest that even though TNBC diagnoses in AAW are associated with more aggressive forms of the disease, and experience a higher mortality rate, TNBC in CAW share similar altered signaling pathways, under mPRs-specific steroid actions, demonstrating the overall aggressive nature of TNBCs, regardless of racial differences. Furthermore, in this report, we have identified 21 new CAW-TNBC specific candidate biomarkers that reinforce the definitive role of the CmP signaling network in TNBC tumorigenesis, initially identified in our previous studies with AAW-TNBCs. This new set of potential prognostic biomarkers may revolutionize molecular mechanisms and currently known concepts of tumorigenesis in CAW-TNBCs, leading to hopeful new therapeutic strategies.


title: Layered Feedback Control Overcomes Performance Trade-off in Synthetic Biomolecular Networks

abstract:
Layered feedback is an optimization strategy in feedback control designs widely used in electrical and mechanical engineering. Layered control theory suggests that the performance of controllers is bound by the universal robustness-efficiency tradeoff limit, which could be overcome by layering two or more feedbacks together. In natural biological networks, genes are often regulated with redundancy and layering to adapt to environmental perturbations. Control theory hypothesizes that this layering architecture is also adopted by nature to overcome this performance trade-off. In this work, we validated this property of layered control with a synthetic network in living E. coli cells. We performed system analysis on a node-based design to confirm the tradeoff properties before proceeding to simulations with an effective mechanistic model, which guided us to the best performing design to engineer in cells. Finally, we interrogated its system dynamics experimentally with eight sets of perturbations on chemical signals, nutrient abundance, and growth temperature. For all cases, we consistently observed that the layered control overcomes the robustness-efficiency trade-off limit. This work experimentally confirmed that layered control could be adopted in synthetic biomolecular networks as a performance optimization strategy. It also provided insights in understanding genetic feedback control architectures in nature.

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category: synthetic biology


title: Decoding natural astrocyte rhythms: dynamic actin waves result from environmental sensing by primary rodent astrocytes

abstract:
Astrocytes are key regulators of brain homeostasis, which is essential for proper cognitive function. The role of cytoskeletal dynamics in this critical regulatory process is unknown. Here we find that actin is dynamic in certain subcellular regions, especially near the cell boundary. Our results further indicate that actin dynamics concentrates into "hotspot" regions that selectively respond to certain chemophysical stimuli, specifically the homeostatic challenges of ion or water concentration increases. Substrate topography makes actin dynamics more frequent yet weaker, and it also alters actin network structure. Superresolution images analyzed with a filament extraction algorithm demonstrate that surface topography is associated with a predominant perpendicular alignment of actin filaments near the cell boundary whereas flat substrates result in an actin cortex mainly parallel to the cell boundary. Thus, actin structure and dynamics together integrate information from different aspects of the environment that might steer the operation of neural cell networks.

TeaserAstrocytes display dynamic actin that is modulated by combinations of chemophysical stimuli and environmental topographies.


title: A non-bactericidal cathelicidin provides prophylactic efficacy against bacterial infection by driving phagocyte influx

abstract: The roles of bactericidal cathelicidins against bacterial infection have been extensively studied. However, the anti-bacterial property and mechanism of action of non-bactericidal cathelicidins are rarely known. Herein, a novel naturally occurring cathelicidin (PopuCATH) from tree frog (Polypedates puerensis) didnt show any direct anti-bacterial activity in vitro. Intriguingly, intraperitoneal injection of PopuCATH before bacterial inoculation significantly reduced the bacterial load in tree frogs and mice, and reduced the inflammatory response induced by bacterial inoculation in mice. PopuCATH pretreatment also increased the survival rates of septic mice induced by a lethal dose of bacterial inoculation or cecal ligation and puncture (CLP). Intraperitoneal injection of PopuCATH significantly drove the leukocyte influx in both frogs and mice. In mice, PopuCATH rapidly drove neutrophil, monocyte/macrophage influx in mouse abdominal cavity and peripheral blood with a negligible impact on T and B lymphocytes, and neutrophils, monocytes/macrophages, but not T and B lymphocytes, were required for the preventive efficacy of PopuCATH. PopuCATH did not directly act as chemoattractant for phagocytes, but PopuCATH obviously drove phagocyte migration when it was cultured with macrophages. PopuCATH significantly elicited chemokine/cytokine production in macrophages through activating p38/ERK mitogen-activated protein kinases (MAPKs) and NF-{kappa}B p65. PopuCATH markedly enhanced neutrophil phagocytosis via promoting the release of neutrophil extracellular traps (NETs). Additionally, PopuCATH showed low side effects both in vitro and in vivo. Collectively, PopuCATH acts as a host-based immune defense regulator that provides prophylactic efficacy against bacterial infection without direct antimicrobial effects. Our findings reveal a non-bactericidal cathelicidin which possesses unique anti-bacterial action, and highlight the potential of PopuCATH to prevent bacterial infection.


title: Chromodomain protein regulates the expression of a subset of RIFINs in P. falciparum

abstract: Plasmodium falciparum expresses clonally variant proteins on the surface of infected erythrocytes to evade the host immune system. The clonally variant multigenes include var, rifin, and stevor, which express EMP1, RIFIN, and STEVOR proteins, respectively. The rifins are the largest multigene family and are essentially involved in the RBC rosetting, the hallmark of severe malaria. The regulators that control the RIFINs expression in P. falciparum have not been reported so far. This study reports a chromodomain-containing protein (PfCDP) that binds to H3K9me3 modification on P. falciparum chromatin. The ChIP- sequencing analysis revealed that the PfCDP is majorly associated with clonally variant gene families, primarily rifins in P. falciparum. Conditional deletion of the chromodomain (CD) gene in P. falciparum leads to the up-regulation of a subset of virulence genes, including rifins, a few var, and stevor genes. Further, we show that Pf{Delta}CDP P. falciparum lines promote the RBC rosetting. This study provides evidence of an epigenetic regulator mediated control on a subset of RIFINs expression and RBC rosetting by P. falciparum.


title: Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as identified by sCRilecs-seq

abstract: Antibiotic resistance in the important opportunistic human pathogen Streptococcus pneumoniae is on the rise. This is particularly problematic in the case of the {beta}-lactam antibiotic amoxicillin, which is the first-line therapy. It is therefore crucial to uncover targets that would kill or resensitize amoxicillin-resistant pneumococci. To do so, we developed a genome-wide, single-cell based, gene silencing screen using CRISPR interference called sCRilecs-seq (subsets of CRISPR interference libraries extracted by fluorescence activated cell sorting coupled to next generation sequencing). Since amoxicillin affects growth and division, sCRilecs-seq was used to identify targets that are responsible for maintaining proper cell size. Our screen revealed that downregulation of the mevalonate pathway leads to extensive cell elongation. Further investigation into this phenotype indicates that it is caused by insufficient transport of cell wall precursors across the cell membrane due to a limitation in the production of undecaprenyl phosphate (Und-P), the lipid carrier responsible for this process. The data suggest that whereas peptidoglycan synthesis continues even with reduced Und-P levels, cell constriction is specifically halted. We successfully exploited this knowledge to create a combination treatment strategy where the FDA-approved drug clomiphene, an inhibitor of Und-P synthesis, is paired up with amoxicillin. Our results show that clomiphene potentiates the antimicrobial activity of amoxicillin and that combination therapy resensitizes amoxicillin-resistant S. pneumoniae. These findings could provide a starting point to develop a solution for the increasing amount of hard-to-treat amoxicillin-resistant pneumococcal infections.


title: Amoxicillin-resistant Streptococcus pneumoniae can be resensitized by targeting the mevalonate pathway as indicated by sCRilecs-seq


title: The model arbuscular mycorrhizal fungus Rhizophagus irregularis harbours endosymbiotic bacteria with a highly reduce genome

abstract: Arbuscular mycorrhizal fungi (AMF; Glomeromycotina) are symbionts of most plant species that are known to possess unique intracytoplasmic endosymbiotic bacteria with an enigmatic role. Candidatus Moeniiplasma glomeromycotorum (CaMg) was shown to be widespread along the AMF phylogeny and present in most AMF species and isolates of those species. The model AMF species, Rhizophagus irregularis, that can be cultivated in vitro and for which a lot of genomic information now exists, would be the ideal model to study the true nature of the CaMg-AMF symbiosis. However, R. irregularis was never found to host endobacteria. Here we show by DNA sequencing that R. irregularis can, indeed, host CaMg (Ri-CaMg). However, this appears rare as only one R. irregularis isolate out of 58 hosted CaMg. In that isolate, the endosymbiotic bacterial population was genetically homogenous. By sequencing the complete genome of the bacteria, we found that its genome is among the smallest of all known CaMg and Mycoplasma-like genomes, with a highly reduced gene repertoire, suggesting a strong adaptation to the intracellular life. We discuss our findings in the light of previous literature on CaMg and on the same AMF isolates and suggest that these endosymbionts are more likely parasites than non-obligatory mutualists.


title: Comprehensive comparative genomics analysis for the emerging human pathogen Streptococcus dysgalactiae subsp. equisimilis (SDSE): A case study and Pan-subspecies genomic analysis

abstract:
BackgroundStreptococcus dysgalactiae subsp. equisimilis (SDSE) is the causal agent of various diseases that include wound infection, erysipelas, cellulitis, life-threatening necrotizing fasciitis, and streptococcal toxic shock syndrome. It is capable of infecting both humans and animals. In this investigation, we present a comprehensive genomic analysis for the SDSE strain SCDR1 that belongs to Lancefield group G, emm type (stG6) and (MLST) sequence type (ST44) that is the first time to be documented in Saudi Arabia and the middle east. Besides, we present the most comprehensive comparative genomics analysis for the emerging human pathogen SDSE.

MethodologyWe utilized next-generation sequencing techniques (NGS), bioinformatics, phylogenetic analysis, and comparative pathogenomics to characterize SCDR1 and all publicly available SDES genomes.

ResultsWe found that SCDR1 consisted of a circular genome of 2179136 bp. Comparative analyses among bacterial genomes indicated that SCDR1 was most closely related to AC-2713 and GGS_124. Genome annotation of SCDR-1 strain showed that it contains many genes with homology to known virulence factors, including genes involved in cellular invasion, Antiphagocytosis, immune evasion, invasion of skin and soft tissue, host mortality and tissue damage, toxins, pore-forming proteins, cytotoxins, beta-hemolysis agents. Two CRISPR arrays were identified in SCDR1 that are consist of 35 CRISPR repeats and 33 CRISPR spacers. Two CAS systems were observed in the SCDR-1 genome, namely, CAS-TypeIIA and CAS-TypeIC. SDSE core Resistome is consisting of 22 genes, including folA, gyrA, gyrB, and FabK. SDSE core Virulome consisting of 38 genes including, fba, fbp54, gidA, and lsp.

ConclusionOur study confirmed that the SDSE strains possess different characteristics in producing virulence factors for pathogenicity to humans and based on its genome sequence and close relationship with GAS. Our study shed light on the proposed pathogenic mechanisms of SDSE and may form the basis of molecular epidemiological research on these highly virulent bacteria.


title: Genetic interaction mapping highlights key roles of the Tol-Pal complex

abstract: The conserved Tol-Pal trans-envelope complex is important for outer membrane (OM) stability and cell division in Gram-negative bacteria. It has been proposed to mediate OM constriction during cell division via tethering to the cell wall. Yet, recent studies suggest that the complex has additional roles in OM lipid homeostasis and septal cell wall separation. How the Tol-Pal complex functions to facilitate these many processes is unclear. To gain insights into its role(s), we applied transposon insertion sequencing, and report here a detailed network of genetic interactions with the tol-pal locus in Escherichia coli. We found one positive and >20 negative strong interactions based on fitness. Disruption of genes responsible for osmoregulated periplasmic glucan biosynthesis restores fitness and OM barrier function, but not cell division defects, in tol-pal mutants. In contrast, deletions of genes involved in OM homeostasis and cell wall remodelling give rise to synthetic growth defects in strains lacking Tol-Pal, especially exacerbating OM barrier and/or cell division defects. Notably, the {Delta}tolA mutant having additional defects in OM protein assembly ({Delta}bamB) exhibited severe division phenotypes, even under conditions where the single mutants divide normally; this highlights the possibility for OM phenotypes to indirectly influence the cell division process. Overall, our work provides insights into the intricate nature of Tol-Pal function, and reinforces the model that this complex plays crucial roles in cell wall-OM tethering, cell wall remodelling, and in particular, OM homeostasis.


title: CTCF and cohesin promote focal detachment of DNA from the nuclear lamina

abstract: Lamina associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina (NL). It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator protein CTCF is enriched at LAD borders, it was postulated that CTCF binding could position a subset of LAD boundaries, possibly through its function in stalling cohesin and hence preventing cohesin to invade into the LAD. To test this, we mapped genome - NL interactions in mouse embryonic stem cells after rapid depletion of CTCF and other perturbations of cohesin dynamics. CTCF and cohesin contribute to a sharp transition in NL interactions at LAD borders, whilst LADs are maintained after depletion of these proteins, also at borders marked by CTCF. CTCF and cohesin may thus reinforce LAD borders, but do not position these. CTCF binding sites within LADs are locally detached from the NL and enriched for accessible DNA and active histone modifications. Remarkably, even though NL positioning is strongly correlated with genome inactivity, this DNA remains accessible after the local detachment is lost following CTCF depletion. At a chromosomal scale, cohesin depletion and cohesin stabilization (depletion of the unloading factor WAPL) quantitatively affect NL interactions, indicative of perturbed chromosomal positioning in the nucleus. Finally, while H3K27me3 is locally enriched at CTCF-marked LAD borders, we find no evidence for an interplay between CTCF and H3K27me3 on NL interactions. Combined, these findings illustrate that CTCF and cohesin do not shape LAD patterns. Rather, these proteins mediate fine-tuning of NL interactions.

category: molecular biology


title: TRIM25 inhibits Influenza A infection by destabilising its mRNA and is redundant for the RIG-I pathway.

abstract: The E3 ubiquitin ligase TRIM25 is a key factor in the innate immune response to RNA viruses. TRIM25 has been shown to play a role in the retinoic-acid-inducible gene-1 (RIG-I) pathway, which triggers expression of type 1 interferons upon viral infection. We and others have recently shown that TRIM25 is an RNA-binding protein, however not much is known about the RNA-binding roles of TRIM25 in the innate immune response to RNA viruses. Here, we demonstrate that influenza A virus (IAV A/PR/8/34_NS1(R38K41A)) infection is inhibited by TRIM25. Surprisingly, host RNA-binding deficient mutant TRIM25{Delta}RBD and TRIM25{Delta}RING, which lack E3 ubiquitin ligase activity rescued IAV inhibition in TRIM25 knock-out cells. Furthermore, we show that in human cultured cells activation of the RIG-I/interferon type 1 pathway mediated by an IAV-derived 5-triphosphate RNA does not require TRIM25 activity. Additionally, knocking out TRIM25 does not affect the activity of the IAV polymerase. We present new evidence that TRIM25 restricts IAV by directly binding to and destabilising its mRNAs. Finally, we show that direct tethering of TRIM25 to RNA is sufficient to downregulate the targeted RNA. In summary, our results uncover a novel mechanism that TRIM25 uses to inhibit IAV infection and regulate RNA metabolism.


title: Alpha-Gal Syndrome: Involvement of Amblyomma americanum α-D-galactosidase and β-1,4 Galactosyltransferase enzymes in α-gal metabolism

abstract: Alpha-Gal Syndrome (AGS) is an IgE-mediated delayed-type hypersensitivity reaction to the oligosaccharide galactose--1,3-galactose (-gal) injected into humans from the lone star tick (Amblyomma americanum) bite. This study aims at the functional characterization of two tick enzymes, -D-galactosidase (ADGal) and -1,4 galactosyltransferase ({beta}-1,4GalT) in -gal metabolism. The ADGal enzyme cleaves terminal -galactose moieties from glycoproteins and glycolipids, whereas {beta}-1,4GalT transfers -galactose to a {beta}1,4 terminal linkage acceptor sugars: GlcNAc, Glc, and Xyl in various processes of glycoconjugate synthesis. An RNA interference approach was utilized to silence ADGal and {beta}-1,4GalT in Am. americanum to examine their functional role in -gal metabolism and AGS onset. Silencing of ADGal led to the significant down regulation of genes involved in galactose metabolism and transport in Am. americanum. Immunoblot and N-glycan analysis of the Am. americanum salivary glands showed a significant reduction in -gal levels in silenced tissues. However, there was no significant difference in the level of -gal in {beta}-1,4GalT silenced tick salivary glands. A basophil-activation test showed a decrease in the frequency of activated basophil by ADGal silenced salivary glands. These results provide an insight into the role of -D galactosidase & {beta}-1,4GalT in tick biology and the probable involvement in the onset of AGS.


title: Mimicking extracellular matrix-mediated mechano-activation by antibodies to control signaling of the adhesion G protein-coupled receptor GPR126/ADGRG6

abstract:
The adhesion G protein-coupled receptor (aGPCR) GPR126/ADGRG6 plays an important role in several physiological functions, such as myelination or peripheral nerve repair. This renders the receptor an attractive pharmacological target. GPR126 is a mechano-sensor that translates binding of extracellular matrix (ECM) molecules to its N terminus into a metabotropic intracellular signal. To date, the structural requirements and the character of the forces needed for this ECM-mediated receptor activation are largely unknown.

In this study we provide this information by combining classic second messenger detection with single cell atomic force microscopy. We establish a monoclonal antibody targeting the N terminus to stimulate GPR126 and compare it to the activation through its known ECM ligands collagen IV and laminin 211. As each ligand uses a distinct mode of action, the N terminus can be viewed as an allosteric module that can fine-tune receptor activation in a context-specific manner.


title: The N terminus of adhesion G protein-coupled receptor GPR126/ADGRG6 as allosteric force integrator


title: Mitochondrial dynamics regulate genome stability via control of caspase-dependent DNA damage

abstract: Mitochondrial dysfunction is interconnected with cancer. Nevertheless, how defective mitochondria promote cancer is poorly understood. We find that mitochondrial dysfunction promotes DNA damage under conditions of increased apoptotic priming. Underlying this process, we reveal a key role for mitochondrial dynamics in the regulation of DNA damage and genome instability. The ability of mitochondrial dynamics to regulate oncogenic DNA damage centres upon the control of minority MOMP, a process that enables non-lethal caspase activation leading to DNA damage. Mitochondrial fusion suppresses minority MOMP, and its associated DNA damage, by enabling homogenous mitochondrial expression of anti-apoptotic BCL-2 proteins. Finally, we find that mitochondrial dysfunction inhibits pro-apoptotic BAX retrotranslocation, causing BAX mitochondrial localization thereby promoting minority MOMP. Unexpectedly, these data reveal oncogenic effects of mitochondrial dysfunction that are mediated via mitochondrial dynamics and caspase-dependent DNA damage.

category: cell biology


title: Human iPSC-Based Model Reveals NOX4 as Therapeutic Target in Duchenne Cardiomyopathy

abstract:
Duchenne muscular dystrophy (DMD) is an X-linked progressive muscle disorder, caused by mutations in the Dystrophin gene. Cardiomyopathy is one of the major causes of early death. In this study, we used DMD patient-specific induced pluripotent stem cells (iPSCs) to model cardiomyopathic features in DMD and unravel novel pathological mechanistic insights. Cardiomyocytes (CMs) differentiated from DMD iPSCs showed enhanced premature cell death, due to significantly elevated intracellular reactive oxygen species (ROS) concentrations, as a result of depolarized mitochondria and high NADPH oxidase 4 (NOX4) protein levels. Genetic correction of Dystrophin through CRISPR/Cas9 editing restored normal ROS levels. Application of ROS reduction by N-acetyl-L-cysteine (NAC), partial Dystrophin re-expression by ataluren (PTC124) and enhancing mitochondrial electron transport chain function by idebenone improved cell survival of DMD iPSC-CMs. We show applications that could counteract the detrimental oxidative stress environment in DMD iPSC-CMs by stimulating adenosine triphosphate (ATP) production. ATP could bind to the ATP-binding domain in the NOX4 enzyme, and we demonstrate that ATP resulted in partial inhibition of the NADPH-dependent ROS production of NOX4.

Considering the complexity and the early cellular stress responses in DMD cardiomyopathy, we propose to target ROS production and prevent the detrimental effects of NOX4 on DMD CMs as a promising therapeutic strategy.

GRAPHICAL ABSTRACT

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/460090v1_ufig1.gif" ALT="Figure 1">
View larger version (28K):
org.highwire.dtl.DTLVardef@d3606borg.highwire.dtl.DTLVardef@15f1d88org.highwire.dtl.DTLVardef@18bfb9corg.highwire.dtl.DTLVardef@133c6bd_HPS_FORMAT_FIGEXP  M_FIG The use of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) from Duchenne muscular dystrophy (DMD) patients to model cardiomyopathic features in DMD and unravel novel pathological mechanistic insights.

DMD iPSC-CMs showed accelerated cell death, caused by increased intracellular reactive oxygen species (ROS) levels. By intervention at different target sites, beneficial effects on the mitochondrial membrane potential ({Delta}{Psi}m) and the expression and ROS-producing activity of the cardiac-specific NADPH-oxidase 4 isoform (NOX4) were observed, resulting in an increased cell survival and function of DMD iPSC-CMs.

C_FIG


title: How Dickkopf molecules and Wnt/beta-catenin interplay to self-organise the Hydra body axis

abstract: The antagonising interplay between canonical Wnt signalling and Dickkopf (Dkk) molecules has been identified in various processes involved in tissue organisation, such as stem cell differentiation and body-axis formation. Disruption of the interplay between these molecules is related to several diseases in humans. However, the detailed molecular mechanisms of the {beta}-catenin/Wnt-Dkk interplay leading to robust formation of the body axis remain elusive. Although the {beta}-catenin/Wnt signalling system has been shown in the pre-bilaterian model organism Hydra to interact with two ancestral Dkks (HyDkk1/2/4-A and -C) to self-organise and regenerate the body axis, the observed Dkk expression patterns do not match any current pattern-formation theory, such as the famous activator-inhibitor model. To explore the function of Dkk in Hydra patterning process, we propose a new mathematical model which accounts for the two Dkks in interplay with HyWnt3/{beta}-catenin. Using a systematic numerical study, we demonstrate that the chosen set of interactions is sufficient to explain de novo body-axis gradient formation in Hydra. The presented mutual inhibition model goes beyond the classical activator-inhibitor model and shows that a molecular mechanism based on mutual inhibition may replace the local activation/long-range inhibition loop. The new model is validated using a range of perturbation experiments. It resolves several contradictions between previous models and experimental data, and provides an explanation for the interplay between injury response and pattern formation.


title: Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish

abstract:
Pericytes reside in capillary beds where they share a basement membrane with endothelial cells and regulate their function. However, little is known about embryonic pericyte development, in part, due to lack of specific molecular markers and genetic tools. Here, we applied single cell RNA-sequencing (scRNA-seq) of platelet derived growth factor beta (pdgfrb)-positive cells to molecularly characterize pericytes in zebrafish larvae. scRNA-seq revealed zebrafish cells expressing mouse pericyte gene orthologs while comparison to bulk RNA-seq from wild type and pdgfrb mutant larvae further refined a pericyte geneset. Subsequent integration with mouse pericyte scRNA-seq profiles revealed a core set of conserved pericyte genes. Using transgenic reporter lines, we validated pericyte expression of two genes identified in our analysis: NDUFA4 mitochondrial complex associated like 2a (ndufa4l2a), and potassium voltage-gated channel, Isk-related family, member 4 (kcne4). Both reporter lines exhibited pericyte expression in multiple anatomical locations, while kcne4 was also detected in a subset of vascular smooth muscle cells. Thus, our integrated molecular analysis revealed a molecular profile for zebrafish pericytes and allowed us to develop new tools to observe these cells in vivo.

SUMMARY STATEMENTAn integrated molecular analysis in zebrafish identifies new molecular markers for pericytes.


title: Gsx2 but not Gsx1 is necessary for early forebrain patterning and long-term survival in zebrafish

abstract: Central nervous system (CNS) development is regulated by regionally expressed transcription factors that impart initial cell identity, connectivity, and function to neural circuits through complex molecular genetic cascades. genomic screen homeobox 1 and 2 (gsx1 and gsx2) encode homeobox transcription factors expressed in the developing CNS in multiple vertebrates examined to date. However, we have limited knowledge of the expression of these transcription factors and the gene networks that they regulate across developing brain regions in zebrafish. The objective of this study was to comprehensively examine gsx1 and gsx2 expression throughout neurodevelopment and characterize gsx1 and gsx2 mutants to study the essential roles of these closely related transcription factors. Using RT-PCR, whole-mount in situ hybridization (WISH), and fluorescence in situ hybridization, we examine gsx1 and gsx2 expression from early embryonic to late larval stages. gsx1 is expressed initially in the hindbrain and diencephalon and later in the optic tectum, pretectum, and cerebellar plate. Comparatively, gsx2 is expressed in the early telencephalon and later in the pallium and olfactory bulb. gsx1 and gsx2 are regionally co-expressed in the hypothalamus, preoptic area, and hindbrain, however rarely co-localize in the same cells. To identify forebrain target genes, we utilize mutants made with Transcription activator-like effector nucleases (TALEN). gsx1 mutant zebrafish exhibit stunted growth, however, they survive through adulthood and are fertile. gsx2 mutant zebrafish experience swim bladder inflation failure that prevents survival past larval stage. Using WISH and RT-qPCR we demonstrate altered expression of genes including, distal-less homeobox genes and forkhead box gene foxp2. This work provides novel tools with which other target genes and functions of Gsx1 and Gsx2 can be characterized across the CNS to better understand the unique and overlapping roles of these highly conserved transcription factors.


title: Genetic and functional odorant receptor variation in the Homo lineage

abstract:
Using ancient DNA sequences, we explored the function of olfactory receptor genes in the genus Homo. Humans, Neandertals, and Denisovans independently adapted to a wide range of geographic environments and the odours produced by their food. Variations in their odorant receptor protein sequence and structure resulted in variation in detection and perception. Studying thirty olfactory receptor genes, we found our relatives showed highly conserved receptor structures, but Homo sapiens did not. Variants led to changes in sensitivity to some odors, but no change in specificity, indicating a common olfactory repertoire in our genus. Diversity of geographic adaptations in H. sapiens may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity.

One-Sentence SummaryUsing ancient DNA we studied the sense of smell in our extinct ancestors and in our relatives, Denisovans and Neanderthals

category: evolutionary biology


title: Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources

abstract:
Many fungal species utilize hydroxyderivatives of benzene and benzoic acid as carbon sources. The yeast Candida parapsilosis metabolizes these compounds via the 3-oxoadipate and gentisate pathways, whose components are encoded by two metabolic gene clusters. In this study, we determine the chromosome level assembly of the C. parapsilosis strain CLIB214 and use it for transcriptomic and proteomic investigation of cells cultivated on hydroxyaromatic substrates. We demonstrate that the genes coding for enzymes and plasma membrane transporters involved in the 3-oxoadipate and gentisate pathways are highly upregulated and their expression is controlled in a substrate-specific manner. However, regulatory proteins involved in this process are not known. Using the knockout mutants, we show that putative transcriptional factors encoded by the genes OTF1 and GTF1 located within these gene clusters function as transcriptional activators of the 3-oxoadipate and gentisate pathway, respectively. We also show that the activation of both pathways is accompanied by upregulation of genes for the enzymes involved in {beta}-oxidation of fatty acids, glyoxylate cycle, amino acid metabolism, and peroxisome biogenesis. Transcriptome and proteome profiles of the cells grown on 4-hydroxybenzoate and 3-hydroxybenzoate, which are metabolized via the 3-oxoadipate and gentisate pathway, respectively, reflect their different connection to central metabolism. Yet we find that the expression profiles differ also in the cells assimilating 4-hydroxybenzoate and hydroquinone, which are both metabolized in the same pathway. This finding is consistent with the phenotype of the Otf1p-lacking mutant, which exhibits impaired growth on hydroxybenzoates, but still utilizes hydroxybenzenes, thus indicating that additional, yet unidentified transcription factor could be involved in the 3-oxoadipate pathway regulation. Moreover, we propose that bicarbonate ions resulting from decarboxylation of hydroxybenzoates also contribute to differences in the cell responses to hydroxybenzoates and hydroxybenzenes. Finally, our phylogenetic analysis highlights evolutionary paths leading to metabolic adaptations of yeast cells assimilating hydroxyaromatic substrates.

Author summaryBenzene and its derivatives are simple aromatic compounds representing key substances for the chemical industry. While benzene itself is toxic and carcinogenic, benzoic acid is commonly used in the food industry and some of its derivatives are used in pharmacology (aspirin) or cosmetics (parabens). The benzene ring of aromatic molecules is relatively stable, but many microorganisms including yeasts break it enzymatically and, in a series of biochemical reactions, utilize resulting metabolites as carbon sources. Understanding the genetic basis of corresponding metabolic pathways and their regulation opens a venue for applications in biotechnology and bioremediation of polluted environments. Here we investigate the yeast Candida parapsilosis which assimilates various hydroxybenzenes and hydroxybenzoates via the 3-oxoadipate and gentisate pathways. We show that the genes coding for the substrate transporters and enzymes involved in both pathways are co-expressed and regulated by the transcriptional activators Otf1p and Gtf1p, respectively. Our results also reveal the connections of both pathways to central metabolism and organelle biogenesis and provide an insight into evolution of metabolism of hydroxyaromatic compounds.


title: Quantitative prediction of variant effects on alternative splicing using endogenous pre-messenger RNA structure probing

abstract: Splicing is a highly regulated process that depends on numerous factors. It is particularly challenging to quantitatively predict how a mutation will affect precursor messenger RNA (mRNA) structure and the subsequent functional consequences. Here we use a novel Mutational Profiling (-MaP) methodology to obtain highly reproducible endogenous precursor and mature mRNA structural probing data in vivo. We use these data to estimate Boltzmann suboptimal ensembles, and predict the structural consequences of mutations on precursor mRNA structure. Together with a structural analysis of recent cryo-EM spliceosome structures at different stages of the splicing cycle, we determined that the footprint of the Bact complex on precursor mRNA is best able to predict splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene. However, structure alone only achieves 74% accuracy. We therefore developed a {beta}-regression weighting framework that incorporates splice site strength, structure and exonic/intronic splicing regulatory elements which together achieves 90% accuracy for 47 known and six newly discovered splice-altering variants. This combined experimental/computational framework represents a path forward for accurate prediction of splicing related disease-causing variants.


title: Thermoregulatory morphodynamics of honeybee clusters

abstract: During reproductive swarming, honeybees form clusters of more than 10,000 bees that hang from structures in the environment (e.g., tree branches) and are exposed to diurnal variations in ambient temperature for up to one week during the search for a new nesting site. Swarm clusters collectively modulate their morphology in response to these variations (i.e., expanding/contracting in response to heating/cooling) to maintain their internal temperature within a tolerable range and to avoid exhausting their honey stores prematurely. To understand the spatiotemporal aspects of thermoregulatory morphing, we measured the change in size and shape of swarm clusters over time and the internal temperature profiles in response to dynamic temperature ramp perturbations. We found that swarm clusters can achieve a twofold increase/decrease their volume/density when heated from 15{degrees}C to 30{degrees}C, but they do not reach an equilibrium size or shape when held at 30{degrees}C for 5 hours, long after the core temperature of the cluster has stabilized. Furthermore, the changes in cluster shape and size are hysteretic, contracting in response to cooling faster than expanding in response to heating. Although the contact diameter of the cluster increased continuously when the swarm is heated, the change in length of the swarm (base to tip) over time is non-monotonic. Consequently, the aspect ratio of the swarm fluctuated continuously even when held at a constant temperature. Taken together, our results quantify the hysteretic and anisotropic morphological responses of swarm clusters to ambient temperature variations while suggesting that both mechanical constraints and heat transfer govern the thermoregulatory morphing dynamics of swarm clusters.

category: animal behavior and cognition


title: Addressing Enzymatic-Independent Tumor-Promoting Function of NAMPT via PROTAC-Mediated Degradation

abstract: The rate-limiting enzyme of salvage pathway for NAD+ synthesis, NAMPT, is aberrantly overexpressed in a variety of tumor cells and is a poor prognosis factor for patient survival. NAMPT plays a major role in tumor cell proliferation, acting concurrently as an NAD+ synthase and unexpectedly, an extracellular ligand for several tumor-promoting signaling pathways. While previous efforts to modulate NAMPT activity were limited to enzymatic inhibitors with low success in clinical studies, protein degradation offers a possibility to simultaneously disrupt NAMPTs enzyme activity and ligand capabilities. Here, we report the development of two highly selective NAMPT-targeted proteolysis-targeting chimeras (PROTACs), which promoted rapid and potent NAMPT degradation in a cereblon-dependent manner in multiple tumor cell lines. Notably, both PROTAC degraders outperform a clinical candidate, FK866, in killing effect on hematological tumor cells. These results emphasize the importance and feasibility of applying PROTACs as a better strategy for targeting proteins like NAMPT with dual tumor-promoting functions, which are not easily achieved by conventional enzymatic inhibitors.


title: PAOX1 expression in mixed-substrate continuous cultures of Komagataella phaffii (Pichia pastoris) is completely determined by methanol uptake regardless of the secondary carbon source: a simplifying principle for predicting recombinant protein production.

abstract: The expression of recombinant proteins by the AOX1 promoter of Komagataella phaffii is typically induced by adding methanol to the cultivation medium. Since growth on methanol imposes a high oxygen demand, the medium is often supplemented with an additional "secondary" carbon source which serves to reduce the consumption of methanol, and hence, oxygen. Early research recommended the use of glycerol as the secondary carbon source, but more recent studies recommend the use of sorbitol because glycerol represses PAOX1 expression. To assess the validity of this recommendation, we measured the steady state concentrations of biomass, residual methanol, and AOX1 over a wide range of dilution rates (0.02-0.20 h-1) in continuous cultures of the Mut+ strain fed with methanol, methanol + glycerol, and methanol + sorbitol. We find that when the specific AOX1 expression and methanol uptake rates for each of the three feeds are plotted against each other, they collapse into a single hyperbolic curve. The specific AOX1 expression rate is therefore completely determined by the specific methanol uptake rate regardless of the existence (present/absent) and type (repressing/non-repressing) of the secondary carbon source. In particular, cultures fed with methanol + glycerol and methanol + sorbitol that consume methanol at equal rates also express the protein at equal rates and levels. Now, it turns out that the simple unstructured model developed by Egli and co-workers can predict the specific methanol uptake rates of single- and mixed-substrate cultures over a wide range of dilution rates and feed concentrations. By combining this model with our data, we derive simple formulas that predicts the protein expression rates and levels of single- and mixed-substrate cultures over a wide range of conditions.


title: A Statistical Framework for Data Purification with Application to Microbiome Data Analysis

abstract: Identification of disease-associated microbial species is of great biological and clinical interest. However, this investigation still remains challenges due to heterogeneity in microbial composition between individuals, data quality issues, and complex relationships among species. In this paper, we propose a novel data purification algorithm that allows elimination of noise observations, which leads to increased statistical power to detect disease-associated microbial species. We illustrate the proposed algorithm using the metagenomic data generated from colorectal cancer patients.