bluuebunny/crossref_metadata_2025_split huggingface dataset:
Slit/Robo signals prevent spinal motor neuron emigration by organizing the spinal cord basement membrane
Authors: Kim Minkyung , Lee Clare H , Barnum Sarah J , Watson Roland CJ , Li Jennifer , Mastick Grant S 
Published: July 2019

AbstractThe developing spinal cord builds a boundary between the CNS and the periphery, in the form of a basement membrane. The spinal cord basement membrane is a barrier that retains CNS neuron cell bodies, while being selectively permeable to specific axon types. Spinal motor neuron cell bodies are located in the ventral neural tube next to the floor plate and project their axons out through the basement membrane to peripheral targets. However, little is known about how spinal motor neuron cell bodies are retained inside the ventral neural tube, while their axons can exit. In previous work, we found that disruption of Slit/Robo signals caused motor neuron emigration outside the spinal cord. In the current study, we investigate how Slit/Robo signals are necessary to keep spinal motor neurons within the neural tube. Our findings show that when Slit/Robo signals were removed from motor neurons, they migrated outside the spinal cord. Furthermore, this emigration was associated with abnormal basement membrane protein expression in the ventral spinal cord. Using Robo2 and Slit2 conditional mutants, we found that motor neuron-derived Slit/Robo signals were required to set up a normal basement membrane in the spinal cord. Together, our results suggest that motor neurons produce Slit signals that are required for the basement membrane assembly to retain motor neuron cell bodies within the spinal cord.
A general strategy to develop cell permeable and fluorogenic probes for multi-colour nanoscopy
Authors: Wang Lu , Tran Mai , D’Este Elisa , Roberti Julia , Koch Birgit , Xue Lin , Johnsson Kai 
Published: July 2019

ABSTRACTLive-cell fluorescence nanoscopy is a powerful tool to study cellular biology on a molecular scale, yet its use is held back by the paucity of suitable fluorescent probes. Fluorescent probes based on regular fluorophores usually suffer from low cell permeability and unspecific background signal. We report a general strategy to transform regular fluorophores into fluorogenic probes with excellent cell permeability and low unspecific background signal. The strategy is based on the conversion of a carboxyl group found in rhodamines and related fluorophores into an electron-deficient amide. This conversion does not affect the spectroscopic properties of the fluorophore but permits it to exist in a dynamic equilibrium between two different forms: a fluorescent zwitterion and a non-fluorescent, cell permeable spirolactam. Probes based on such fluorophores generally are fluorogenic as the equilibrium shifts towards the fluorescent form when the probe binds to its cellular targets. The resulting increase in fluorescence can be up to 1000-fold. Using this simple design principle we created fluorogenic probes in various colours for different cellular targets for wash-free, multicolour, live-cell nanoscopy. The work establishes a general strategy to develop fluorogenic probes for live-cell bioimaging.
Ingestible Osmotic Pill for In-vivo Sampling of Gut Microbiome
Authors: Nejad Hojatollah Rezaei , Oliveira Bruno C. M. , Sadeqi Aydin , Dehkharghani Amin , Kondova Ivanela , Langermans Jan A.M. , Guasto Jeffrey S. , Tzipori Saul , Widmer Giovanni , Sonkusale Sameer R. 
Published: July 2019

AbstractTechnologies capable of non-invasively sampling different locations in the gut upstream of the colon will enable new insights into the role of organ-specific microbiota in human health. We present an ingestible, biocompatible, battery-less, 3D-printed micro-engineered pill with integrated osmotic sampler and microfluidic channels for in vivo sampling of the gut lumen and its microbiome upstream of the colon. The pill’s sampling performance was characterized using realistic in vitro models and validated in vivo in pigs and primates. Our results show that the bacterial populations recovered from the pills’ microfluidic channels closely resemble the bacterial population demographics of the microenvironment to which the pill was exposed. We believe such lab-on-a-pill devices will revolutionize our understanding of the spatial diversity of the gut microbiome and its response to medical conditions and treatments.
Decreased electrocortical temporal complexity distinguishes sleep from wakefulness
Authors: González Joaquín , Cavelli Matias , Mondino Alejandra , Pascovich Claudia , Castro-Zaballa Santiago , Torterolo Pablo , Rubido Nicolás 
Published: July 2019

ABSTRACTIn most mammals, the sleep-wake cycle is constituted by three behavioral states: wakefulness (W), non-NREM (NREM) sleep, and REM sleep. These states are associated with drastic changes in cognitive capacities, mostly determined by the function of the thalamo-cortical system. The intra-cranial electroencephalogram or electocorticogram (ECoG), is an important tool for measuring the changes in the thalamo-cortical activity during W and sleep. In the present study we analyzed broad-band ECoG recordings of the rat by means of a time-series complexity measure that is easy to implement and robust to noise: the Permutation Entropy (PeEn). We found that PeEn is maximal during W and decreases during sleep. These results bring to light the different thalamo-cortical dynamics emerging during sleep-wake states, which are associated with the well-known spectral changes that occur when passing from W to sleep. Moreover, the PeEn analysis allows to determine behavioral states independently of the electrodes’ cortical location, which points to an underlying global pattern in the signal that differs among the cycle states that is missed by classical methods. Consequently, our data suggest that PeEn analysis of a single EEG channel could allow for cheap, easy, and efficient sleep monitoring.
Human POT1 Unfolds G-Quadruplexes by Conformational Selection
Authors: Chaires Jonathan B. , Gray Robert D. , Dean William L. , Monsen Robert , DeLeeuw Lynn W. , Stribinskis Vilius , Trent John O. 
Published: July 2019

ABSTRACTThe reaction mechanism by which shelterin protein POT1 (ProtectionofTelomeres) unfolds human telomeric G-quadruplex structures is not fully understood. We report here kinetic, thermodynamic, hydrodynamic and computational studies that show that a conformational selection mechanism, in which POT1 binding is coupled to an obligatory unfolding reaction, is the most plausible mechanism. We show that binding of the single-strand oligonucleotide d[TTAGGGTTAG] to POT1 is fast, with an apparent relaxation time of 80.0 ± 0.4 ms, and strong, with a binding free energy of −10.1 ± 0.3 kcal mol−1. That favourable free energy arises from a large favourable enthalpy contribution of −38.2 ± 0.3 kcal mol−1. In sharp contrast, the binding of POT1 to an initially folded 24 nt G-quadruplex structure is slow, with an average relaxation time of 2000-3000 s. Fluorescence, circular dichroism and analytical ultracentrifugation studies show that POT1 binding is coupled to quadruplex unfolding with a final stoichiometry of 2 POT1 molecules bound per 24 nt DNA. The binding isotherm for the POT1-quadruplex binding interaction is sigmoidal, indicative of a complex reaction. A conformational selection model that includes equilibrium constants for both G-quadruplex unfolding and POT1 binding to the resultant single-strand provides an excellent quantitative fit to the experimental binding data. The overall favourable free energy of the POT1-quadruplex interaction is −7.1 kcal mol−1, which arises from a balance between unfavourable free energy of +3.4 kcal mol−1for quadruplex unfolding and a large, favorable free energy of −10.5 kcal mol−1for POT1 binding. We show that POT1 can unfold and bind to any conformational form of human telomeric G-quadruplex (antiparallel, hybrid or parallel), but will not interact with duplex DNA or with a parallel G-quadruplex structure formed by a c-myc promoter sequence. Finally, molecular dynamics simulations provide a detailed structural model of a 2:1 POT1:DNA complex that is fully consistent with experimental biophysical results.
Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation
Authors: Williams Leah M. , Inge Melissa M. , Mansfield Katelyn M. , Rasmussen Anna , Afghani Jamie , Agrba Mikhail , Albert Colleen , Andersson Cecilia , Babaei Milad , Babaei Mohammad , Bagdasaryants Abigail , Bonilla Arianna , Browne Amanda , Carpenter Sheldon , Chen Tiffany , Christie Blake , Cyr Andrew , Dam Katie , Dulock Nicholas , Erdene Galbadrakh , Esau Lindsie , Esonwune Stephanie , Hanchate Anvita , Huang Xinli , Jennings Timothy , Kasabwala Aarti , Kehoe Leanne , Kobayashi Ryan , Lee Migi , LeVan Andre , Liu Yuekun , Murphy Emily , Nambiar Avanti , Olive Meagan , Patel Devansh , Pavesi Flaminio , Petty Christopher A. , Samofalova Yelena , Sanchez Selma , Stejskal Camilla , Tang Yinian , Yapo Alia , Cleary John P. , Yunes Sarah A. , Siggers Trevor , Gilmore Thomas D. 
Published: July 2019

ABSTRACTBiological and biochemical functions of immunity transcription factor NF-κB in basal metazoans are largely unknown. Herein, we characterize transcription factor NF-κB from the demosponge Amphimedon queenslandica (Aq), in the phylum Porifera. Structurally and phylogenetically, the Aq-NF-κB protein is most similar to NF-κB p100 and p105 among vertebrate proteins, with an N-terminal DNA-binding/dimerization domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile more similar to human NF-κB proteins than Rel proteins. Aq-NF-κB also resembles the mammalian NF-κB protein p100 in that C-terminal truncation results in translocation of Aq-NF-κB to the nucleus and increases its transcriptional activation activity. Overexpression of a human or sea anemone IκB kinase (IKK) can induce C-terminal processing of Aq-NF-κB in vivo, and this processing requires C-terminal serine residues in Aq-NF-κB. Unlike human NF-κB p100, however, the C-terminal sequences of Aq-NF-κB do not effectively inhibit its DNA-binding activity when expressed in human cells. Tissue of another demosponge, a black encrusting sponge, contains NF-κB site DNA-binding activity and an NF-κB protein that appears mostly processed and in the nucleus of cells. NF-κB DNA-binding activity and processing is increased by treatment of sponge tissue with LPS. By transcriptomic analysis of A. queenslandica we identified likely homologs to many upstream NF-κB pathway components. These results present a functional characterization of the most ancient metazoan NF-κB protein to date, and show that many characteristics of mammalian NF-κB are conserved in sponge NF-κB, but the mechanism by which NF-κB functions and is regulated in the sponge may be somewhat different.
Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts
Authors: Lang Kevin S. , Merrikh Houra 
Published: July 2019

AbstractConflicts between the replication and transcription machineries have profound effects on chromosome duplication, genome organization, as well as evolution across species. Head-on conflicts (lagging strand genes) are significantly more detrimental than co-directional conflicts (leading strand genes). The source of this fundamental difference is unknown. Here, we report that topological stress underlies this difference. We find that head-on conflict resolution requires the relaxation of positive supercoils DNA gyrase and Topo IV. Interestingly, we find that after positive supercoil resolution, gyrase introduces excessive negative supercoils at head-on conflict regions, driving pervasive R-loop formation. The formation of these R-Loops through gyrase activity is most likely caused by the diffusion of negative supercoils through RNA polymerase spinning. Altogether, our results address a longstanding question regarding replication-transcription conflicts by revealing the fundamental mechanistic difference between the two types of encounters.
Salience network atrophy links neuron type-specific pathobiology to loss of empathy in frontotemporal dementia
Authors: Pasquini Lorenzo , Nana Alissa L. , Toller Gianina , Brown Jesse , Deng Jersey , Staffaroni Adam , Kim Eun-Joo , Hwang Ji-Hye L. , Li Libo , Park Youngsoon , Gaus Stephanie E. , Allen Isabel , Sturm Virginia E. , Spina Salvatore , Grinberg Lea T. , Rankin Katherine P. , Kramer Joel , Rosen Howard H. , Miller Bruce L. , Seeley William W. 
Published: July 2019

AbstractEach neurodegenerative syndrome reflects a stereotyped pattern of cellular, regional, and large-scale brain network degeneration. In behavioral variant frontotemporal dementia (bvFTD), a disorder of social-emotional function, von Economo neurons (VENs) and fork cells are among the initial neuronal targets. These large layer 5 projection neurons are concentrated in the anterior cingulate and frontoinsular (FI) cortices, regions that anchor the salience network, a large-scale system linked to social-emotional function. Here, we studied patients with bvFTD, amyotrophic lateral sclerosis (ALS), or both, given that these syndromes share common pathobiological and genetic factors. Our goal was to determine how neuron type-specific TAR DNA-binding protein of 43 kDa (TDP-43) pathobiology relates to atrophy in specific brain structures and to loss of emotional empathy, a cardinal feature of bvFTD. We combined questionnaire-based empathy assessments, in vivo structural MR imaging, and quantitative histopathological data from 16 patients across the bvFTD/ALS spectrum. We show that TDP-43 pathobiology within right FI VENs and fork cells is associated with salience network atrophy spanning insular, medial frontal, and thalamic regions. Gray matter degeneration within these structures mediated loss of emotional empathy, suggesting a chain of influence linking the cellular, regional/network, and behavioral levels in producing signature bvFTD clinical features.
Associations of waking cortisol with DHEA and testosterone across the pubertal transition: Effects of threat-related early life stress
Authors: King Lucy S. , Graber Madelaine G. , Colich Natalie L. , Gotlib Ian H. 
Published: July 2019

AbstractAtypical regulation of the hypothalamic-pituitary-adrenal (HPA) axis is a putative mechanism underlying the association between exposure to early life stress (ELS) and the subsequent development of mental and physical health difficulties. Recent research indicates that puberty is a period of HPA-axis plasticity during which the effects of exposure to ELS on cortisol regulation may change. In particular, increases in the sex hormones that drive pubertal maturation, including dehydroepiandrosterone (DHEA) and testosterone, may be implicated in pubertal recalibration of cortisol regulation. In the current study, we examined the associations among levels of objectively-rated threat-related ELS and salivary waking cortisol, DHEA, and testosterone in a sample of 178 adolescents (55% female) who were in early puberty at baseline (Tanner stages 1-3; mean Tanner stage[SD]=1.93[0.64]; mean age[SD]=11.42[1.04]) and were followed up approximately two years later (mean Tanner stage[SD]=3.46[0.86]; mean age[SD]=13.38[1.06]). Using multi-level modeling, we disaggregated the effects of between-individual levels and within-individual increases in pubertal stage and sex hormones on change in cortisol. Controlling for between-individual differences in average pubertal stage, the association between levels of cortisol and DHEA was more strongly positive among adolescents who evidenced greater within-individual increases in pubertal stage across time. Both higher average levels and greater within-individual increases in DHEA and testosterone were associated with increases in cortisol across time, indicating positive coupling of developmental changes in these hormones; however, coupling was attenuated in adolescents who were exposed to more severe threat-related ELS prior to puberty. These findings advance our understanding of the development of the HPA-axis and its association with childhood environmental risk during puberty.
A developmental gene regulatory network for invasive differentiation of theC. elegansanchor cell
Authors: Medwig-Kinney Taylor N. , Smith Jayson J. , Palmisano Nicholas J. , Tank Sujata , Zhang Wan , Matus David Q. 
Published: July 2019

ABSTRACTCellular invasion is a key part of development, immunity, and disease. Using thein vivomodel ofC. elegansanchor cell invasion, we characterize the gene regulatory network that promotes invasive differentiation. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conserved transcription factors,fos-1a(Fos),egl-43(EVI1/MEL),hlh-2(E/Daughterless) andnhr-67(NR2E1/TLX), that mediate anchor cell specification and/or invasive differentiation. Connections between these transcription factors and the underlying cell biology that they regulate is poorly understood. Here, using genome editing and RNA interference, we examine transcription factor interactions prior to and after anchor cell specification. During invasion we identify thategl-43,hlh-2, andnhr-67function together in a type I coherent feed-forward loop with positive feedback. Conversely, prior to specification, these transcription factors function independent of one another to regulate LIN-12 (Notch) activity. Together, these results demonstrate that, although the same transcription factors can function in fate specification and differentiated cell behavior, a gene regulatory network can be rapidly re-wired to reinforce a post-mitotic, pro-invasive state.SUMMARY STATEMENTBasement membrane invasion by theC. elegansanchor cell is coordinated by a dynamic gene regulatory network encompassing cell cycle dependent and independent sub-circuits.
Bacterial communities of herbivores and pollinators that have co-evolved Cucurbita spp
Authors: Shapiro Lori R. , Youngblom Madison , Scully Erin D. , Rocha Jorge , Paulson Joseph Nathaniel , Klepac-Ceraj Vanja , Cibrián-Jaramillo Angélica , López-Uribe Margarita M. 
Published: July 2019

AbstractInsects, like all animals, are exposed to diverse environmental microbes throughout their life cycle. Yet, we know little about variation in the microbial communities associated with the majority of wild, unmanaged insect species. Here, we use a 16S rRNA gene metabarcoding approach to characterize temporal and geographic variation in the gut bacterial communities of herbivores (Acalymma vittatum and A. trivittatum) and pollinators (Eucera (Peponapis) pruinosa) that have co-evolved with the plant genus Cucurbita (pumpkin, squash, zucchini and gourds). Overall, we find high variability in the composition of bacterial communities in squash bees and beetles collected from different geographic locations and different time points throughout a growing season. Still, many of the most common OTUs are shared in E. (P.) pruinosa, A. vittatum and A. trivittatum. This suggests these insects may be exposed to similar environmental microbial sources while foraging on the same genus of host plants, and that similar microbial taxa may aid in digestion of Cucurbita plant material. The striped cucumber beetle A. vittatum can also transmit Erwinia tracheiphila, the causal agent of bacterial wilt of cucurbits. We find that few field-collected A. vittatum individuals have detectable E. tracheiphila, and when this plant pathogen is detected, it comprises less than 1% of the gut bacterial community. Together, these results are consistent with previous studies showing that plant feeding insects have highly variable gut bacterial communities, and provides a first step towards understanding the spatiotemporal variation in the microbial communities associated with herbivores and pollinators that depend on Cucurbita host plants.
Photosynthetic conversion of CO2to hyaluronic acid by engineered cyanobacteria
Authors: Zhang Lifang , Selão Tiago Toscano , Nixon Peter J. , Norling Birgitta 
Published: July 2019

AbstractHyaluronic acid (HA), consisting of alternating N-acetylglucosamine and glucuronic acid units, is a natural polymer with diverse cosmetic and medical applications. Currently, HA is produced by overexpressing HA synthases from gram-negativePasteurella multocida(encoded bypmHAS) or gram-positiveStreptococcus equisimilis(encoded byseHasA) in various heterotrophic microbial production platforms. Here we introduced these two different types of HA synthase into the fast-growing cyanobacteriumSynechococcussp. PCC 7002 (Syn7002) to explore the capacity for producing HA in a photosynthetic system. Our results show that both HA synthases enable Syn7002 to produce HA photoautotrophically, but that overexpression of the soluble HA synthase (PmHAS) is less deleterious to cell growth and results in higher production. Genetic disruption of the competing cellulose biosynthetic pathway increased the HA titer by over 5-fold (from 14 mg/L to 80 mg/L) and the relative proportion of HA with molecular mass greater than 2 MDa. Introduction ofglmSandglmU, coding for enzymes involved in the biosynthesis of the precursor UDP-N-acetylglucosamine, in combination with partial glycogen depletion, allowed photosynthetic production of 112 mg/L of HA in 5 days, an 8-fold increase in comparison to the initial PmHAS expressing strain. Addition oftuaDandgtaB(coding for genes involved in UDP-glucuronic acid biosynthesis) also improved the HA yield, albeit to a lesser extent. Overall our results have shown that cyanobacteria hold promise for sustainable production of pharmaceutically important polysaccharides from sunlight and CO2.