bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ohm’s Law for increasing fitness gene expression with selection pressure
Authors: Ciechonska Marta , Sturrock Marc , Grob Alice , Larrouy-Maumus Gerald , Shahrezaei Vahid , Isalan Mark 
Published: July 2019

AbstractNatural selection relies on genotypic and phenotypic adaptation in response to fluctuating environmental conditions and is the key to predicting and preventing drug resistance. Whereas classic persistence is all-or-nothing, here we show for the first time that an antibiotic resistance gene displays linear dose-responsive selection for increased expression in proportion to rising antibiotic concentration in E. coli. Furthermore, we observe the general nature of an instantaneous phenotypic selection process upon bactericidal and bacteriostatic antibiotic treatment, as well as an amino acid synthesis pathway enzyme under a range of auxotrophic conditions. To explain this phenomenon, we propose an analogy to Ohm’s law in electricity (V=IR) where fitness pressure acts similarly to voltage (V), gene expression to current (I), and resistance (R) to cellular machinery constraints. Lastly, mathematical modelling approaches reveal that the emergent gene expression mechanism requires variation in mRNA and protein production within an isogenic population, and cell ‘memory’ from positive feedbacks between growth and expression of any fitness-inducing gene.
Selective phosphorylation of AKT isoforms in response to dietary cues
Authors: Trautenberg Laura Christin , Prince Elodie , Maas Cornelia , Beier Nora , Honold Freya , Grzybek Michal , Brankatschk Marko 
Published: July 2019

AbstractA calorie-rich diet is one reason for the continuous spread of metabolic syndromes in western societies. Smart food design is one powerful tool to prevent metabolic stress, and the search for suitable bioactive additives is a continuous task. The nutrient-sensing insulin signaling pathway is an evolutionary conserved mechanism that plays an important role in metabolism, growth and development. Recently, lipid cues capable to stimulate insulin signaling were identified. However, the mechanistic base of their activity remains obscure to date. Here, we show that specific AKT/ Protein kinase B isoforms are responsive to dietary lipid extract compositions and potentiate cellular insulin signaling levels. Our data add a new dimension to existing models and position Drosophila as a powerful model to study the relation between dietary lipid cues and the insulin induced cellular signal cascade.
From injury to full repair: nerve regeneration and functional recovery in the common octopus,Octopus vulgaris
Authors: Imperadore Pamela , Parazzoli Dario , Oldani Amanda , Duebbert Michael , Büschges Ansgar , Fiorito Graziano 
Published: July 2019

AbstractSpontaneous nerve regeneration in cephalopod molluscs occurs in a relative short time after injury, achieving functional recovery of the lost capacities. In particular, transection of the pallial nerve in the common octopus (Octopus vulgaris) determines loss and subsequent restoring of two functions fundamental for survival, i.e. breathing and skin patterning, the latter involved in communication between animals and concealing. The phenomena occurring after lesion have been investigated in a series of previous studies, but a complete analysis of the changes occurring at the level of the axons and the effects on animals appearance during the whole regenerative process is still missing. Our goal is to determine the course of events following injury. Our goal is to determine the course of events following injury, from impairment to full recovery.We observed nerve regeneration, end-target re-innervation and functional reconnections between central brain and periphery, using the contralateral nerve in the same animal as internal control. The final architecture of the regenerated nervous tissue does not mirror the original structure, however functionality returns to match the phenotype of an intact octopus, and with no visible impact on the behaviour of the animal. This provides exceptional value to these findings for future studies.Summary statementHere we report events occurring after interruption of the peripheral neural circuitry inOctopus vulgaris, from the dramatic loss of normal functioning to full recovery.
A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in human
Authors: Casanova Miguel , Moscatelli Madeleine , Chauvière Louis Édouard , Huret Christophe , Samson Julia , Liyakat Ali Tharvesh Moideen , Rosspopoff Olga , Rougeulle Claire 
Published: July 2019

AbstractTransposable elements (TEs) have been of paramount importance in shaping genomic and epigenomic landscapes of their hosts and in driving the expansion of gene regulatory networks during mammalian evolution. They are found in nearly all long non-coding RNAs (lncRNAs) and have promoted their evolution and function, often in a species- and tissue-specific manner. X-chromosome inactivation (XCI) is an essential process that relies on several TE-enriched lncRNAs. While XCI is conserved across species, one striking difference between human and mouse is the existence of XACT (X active coating transcript), a human-specific lncRNA that coats active X chromosomes in pluripotent cells and may oppose X chromosome silencing in this context. Here, we explore how different families of TEs have contributed to shaping the XACT locus and how they couple its expression to pluripotency in humans. Through a combination of sequence analysis across primates, transcriptional interference and genome editing in human embryonic stem cells (hESCs), we identify a critical enhancer for the transcriptional regulation of the XACT locus that evolved from an ancestral group (LTR48B/ERV1) of mammalian endogenous retroviruses (ERVs), prior to the emergence of XACT. Furthermore, we show that this ancient ERV was hijacked by evolutionarily younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.
Direct Measurement of Light and Heavy Antibody Chains Using Differential Ion Mobility Spectrometry and Middle-Down Mass Spectrometry
Authors: Melani Rafael D , Srzentić Kristina , Gerbasi Vincent R , McGee John P , Huguet Romain , Fornelli Luca , Kelleher Neil L 
Published: July 2019

AbstractThe analysis of monoclonal antibodies (mAbs) by a middle-down approach is a growing field that attracts the attention of many researchers and biopharma companies. Usually, liquid fractionation techniques are used to separate mAbs polypeptides chains before mass spectrometry (MS) analysis. Gas-phase fractionation techniques such as high-field asymmetric waveform ion mobility spectrometry (FAIMS) can replace liquid-based separations and reduce both analysis time and cost. Here, we present a rapid FAIMS tandem MS method capable of characterizing the polypeptide sequence of mAbs light (Lc) and heavy (Hc) chains in an unprecedented, easy, and fast fashion. This new method uses commercially available instruments and takes ∼ 24 minutes —40-60% faster than regular LC-MS/MS analysis — to acquire fragmentation data using different dissociation methods.
Variations in terrestrial arthropod DNA metabarcoding methods recovers robust beta diversity but variable richness and site indicators based on exact sequence variants
Authors: Porter Teresita M. , Morris Dave M. , Basiliko Nathan , Hajibabaei Mehrdad , Doucet Daniel , Bowman Susan , Emilson Erik J.S. , Emilson Caroline E. , Chartrand Derek , Wainio-Keizer Kerrie , Séguin Armand , Venier Lisa 
Published: July 2019

AbstractTerrestrial arthropod fauna have been suggested as a key indicator of ecological integrity in forest systems. Because phenotypic identification is expert-limited, a shift towards DNA metabarcoding could improve scalability and democratize the use of forest floor arthropods for biomonitoring applications. The objective of this study was to establish the level of field sampling and DNA extraction replication needed for soil arthropod biodiversity assessments. Processing individually collected field samples recovered significantly higher richness (539-596 ESVs) than pooling the same number of field samples (126-154 ESVs), and we found no significant richness differences when using 1 or 3 pooled DNA extractions. Variations in the number of individual or composite samples or DNA extractions resulted in similar sample clustering based on community dissimilarities. Though our ability to identify taxa to species rank was limited, we were able to use arthropod COI metabarcodes from forest soil to assess richness, distinguish among sites, and recover site indicators based on unnamed exact sequence variants. Our results highlight the need to continue DNA barcoding of local taxa during COI metabarcoding studies to help build reference databases. All together, these sampling considerations support the use of soil arthropod COI metabarcoding as a scalable method for biomonitoring.
Complexity matching: brain signals mirror environment information patterns during music listening and reward
Authors: Carpentier Sarah M. , McCulloch Andrea R. , Brown Tanya M. , Ritter Petra , Wang Zhang , Salimpoor Valorie , Shen Kelly , McIntosh Anthony Randal 
Published: July 2019

AbstractUnderstanding how the human brain integrates information from the environment with ongoing, internal brain signals in order to produce individual perspective is an essential element of understanding the human mind. Brain signal complexity, measured with multiscale entropy, has been employed as a measure of information processing in the brain (Carpentier et al., 2016), and we propose that it can also be used to measure the information available from a stimulus. We can directly assess the correspondence, or functional isomorphism, between brain signal complexity and stimulus complexity as an indication of how well the brain reflects the content of the environment in an analysis that we termedcomplexity matching. Music makes an ideal stimulus input because it is a multidimensional, complex signal, and because of its emotion and reward-inducing potential. We found that electroencephalography (EEG) complexity was lower and more closely resembled the musical complexity when participants performed a perceptual task that required them to closely track the acoustics, compared to an emotional task that asked them to think about how the music made them feel. Music-derived reward scores on the Barcelona Music Reward Questionnaire (Mas-Herrero et al., 2013) correlated with worse complexity matching and higher EEG complexity. Compared to perceptual-level processing, emotional and reward responses are associated with additional internal information processes above and beyond those in the external stimulus.Significance StatementExperience of our world is combination of the input from the environment, our expectations, and individual responses. For example, the same piece of music can elict happiness in one person and sadness in another. We researched this by measuring the information in pieces of music and whether listener’s brain more closely followed that, or whether additional information was added by the brain. We noted when listener’s were reacting to how music made them feel, their brains added more information and the degree to which this occurred related to how much they find music rewarding. Thus, we were able to provide clues as to how the brain integrates incoming information, adding to it to provide a richer perceptual and emotional experience.
GEOlimma: Differential Expression Analysis and Feature Selection Using Pre-Existing Microarray Data
Authors: Lu Liangqun , Townsend Kevin A. , Daigle Bernie J. 
Published: July 2019

AbstractBackgroundDifferential expression and feature selection analyses are essential steps for the development of accurate diagnostic/prognostic classifiers of complicated human diseases using transcriptomics data. These steps are particularly challenging due to the curse of dimensionality and the presence of technical and biological noise. A promising strategy for overcoming these challenges is the incorporation of pre-existing transcriptomics data in the identification of differentially expressed (DE) genes. This approach has the potential to improve the quality of selected genes, increase classification performance, and enhance biological interpretability. While a number of methods have been developed that use pre-existing data for differential expression analysis, existing methods do not leverage the identities of experimental conditions to create a robust metric for identifying DE genes.ResultsIn this study, we propose a novel differential expression and feature selection method—GEOlimma—which combines pre-existing microarray data from the Gene Expression Omnibus (GEO) with the widely-applied Limma method for differential expression analysis. We first quantify differential gene expression across 2481 pairwise comparisons from 602 curated GEO Datasets, and we convert differential expression frequencies to DE prior probabilities. Genes with high DE prior probabilities show enrichment in cell growth and death, signal transduction, and cancer-related biological pathways, while genes with low prior probabilities were enriched in sensory system pathways. We then applied GEOlimma to four differential expression comparisons within two human disease datasets and performed differential expression, feature selection, and supervised classification analyses. Our results suggest that use of GEOlimma provides greater experimental power to detect DE genes compared to Limma, due to its increased effective sample size. Furthermore, in a supervised classification analysis using GEOlimma as a feature selection method, we observed similar or better classification performance than Limma given small, noisy subsets of an asthma dataset.ConclusionsOur results demonstrate that GEOlimma is a more effective method for differential gene expression and feature selection analyses compared to the standard Limma method. Due to its focus on gene-level differential expression, GEOlimma also has the potential to be applied to other high-throughput biological datasets.
ATP7B Variant c.1934T>G p.Met645Arg Causes Wilson Disease by Promoting Exon 6 Skipping
Authors: Merico Daniele , Spickett Carl , O’Hara Matthew , Kakaradov Boyko , Deshwar Amit G. , Fradkin Phil , Gandhi Shreshth , Gao Jiexin , Grant Solomon , Kron Ken , Schmitges Frank W. , Shalev Zvi , Sun Mark , Verby Marta , Cahill Matthew , Dowling James J. , Fransson Johan , Wienholds Erno , Frey Brendan J. 
Published: July 2019

ABSTRACTWilson Disease is a recessive genetic disorder caused by pathogenic loss-of-function variants in the ATP7B gene. It is characterized by disrupted copper homeostasis resulting in liver disease and/or neurological abnormalities. The variant NM_000053.3:c.1934T>G (Met645Arg) has been reported as compound heterozygous and is highly prevalent among Wilson Disease patients of Spanish descent. Accordingly, it is classified as pathogenic by leading molecular diagnostic centers. However, functional studies suggest that the amino acid change does not alter protein function, leading one ClinVar submitter to question its pathogenicity. Here we used a minigene system and gene-edited HepG2 cells to demonstrate that c.1934T>G causes approximately 70% skipping of exon 6. Exon 6 skipping results in frameshift and stop gain, which is expected to cause loss of ATP7B function. The elucidation of the mechanistic effect for this variant resolves any doubt about its pathogenicity and enables the development of genetic medicines for restoring correct splicing.
Electrical microstimulation evokes saccades in posterior parietal cortex of common marmosets
Authors: Ghahremani Maryam , Johnston Kevin D. , Ma Liya , Hayrynen Lauren K. , Everling Stefan 
Published: July 2019

AbstractThe common marmoset (Callithrix jacchus) is a small-bodied New World primate, increasing in prominence as a model animal for neuroscience research. The lissencephalic cortex of this primate species provides substantial advantages for the application of electrophysiological techniques such as high-density and laminar recordings, which have the capacity to advance our understanding of local and laminar cortical circuits and their roles in cognitive and motor functions. This is particularly the case with respect to the oculomotor system, as critical cortical areas of this network such as the frontal eye fields (FEF) and lateral intraparietal area (LIP) lie deep within sulci in macaques. Studies of cytoarchitecture and connectivity have established putative homologies between cortical oculomotor fields in marmoset and macaque, but physiological investigations of these areas, particularly in awake marmosets, have yet to be carried out. Here, we addressed this gap by probing the function of posterior parietal cortex (PPC) of the common marmoset using electrical microstimulation. We implanted two animals with 32-channel Utah arrays at the location of the putative area LIP and applied microstimulation while they viewed a video display and made untrained eye movements. Similar to previous studies in macaques, stimulation evoked fixed-vector and goal-directed saccades, staircase saccades, and eye blinks. These data demonstrate that area LIP of the marmoset plays a role in the regulation of eye movements, provide additional evidence that this area is homologous with that of the macaque, and further establish the marmoset as valuable model for neurophysiological investigations of oculomotor and cognitive control.New & NoteworthyThe macaque monkey has been the preeminent model for investigations of oculomotor control, but studies of cortical areas are limited as many of these areas are buried within sulci in this species. Here we applied electrical microstimulation to the putative area LIP of the lissencephalic cortex of awake marmosets. Similar to the macaque, microstimulation evoked contralateral saccades from this area, supporting the marmoset as a valuable model for studies of oculomotor control.
Customizable, engineered substrates for rapid screening of cellular cues
Authors: Huethorst Eline , Cutiongco Marie FA , Campbell Fraser A , Saeed Anwer , Love Rachel , Reynolds Paul M , Dalby Matthew J , Gadegaard Nikolaj 
Published: July 2019

AbstractBiophysical cues robustly direct cell responses and are thus important tools forin vitroand translational biomedical applications. High throughput platforms exploring substrates with varying physical properties are therefore valuable, however, currently existing platforms are limited in throughput, the biomaterials used, the capability to segregate between different cues and the assessment of dynamic cellular responses. Here we present a multiwell array (3×8) using a substrate engineered with patterns that present topography or rigidity cues welded to a bottomless plate with a 96-well format. Both the patterns on the engineered substrate and the well plate format can be easily customized, permitting systematic and efficient screening of biophysical cues. Here, we demonstrate three multiwell arrays patterned with a variety of topographical and mechanical cues (nano-grooves, soft pillars and nano pillars) tested with three different cell types. Using the multiwell array, we were able to measure cell functionality using analytical modalities such as live microscopy, qPCR and fluorescent immunochemistry. Cardiomyocytes cultured on 5µm grooves showed less variation in electrophysiology and contractile function. Nanopillars with 127 nm height, 100 nm diameter and 300 nm pitch showed improved chondrogenic maintenance from matrix deposition and chondrogenic gene expression. High aspect ratio pillars with an elastic shear modulus of 16 kPa mimicking the cortical bone altered cell adhesion, morphology, and increased expression of osteogenic genes. We have demonstrated the bespoke, controlled and high-throughput properties of the multiwell array that are currently unparalleled in the field today.
Oncoprotein GT198 Vaccination Delays Tumor Growth in MMTV-PyMT Mice
Authors: Achyut Bhagelu R. , Zhang Hao , Angara Kartik , Mivechi Nahid F. , Arbab Ali S. , Ko Lan 
Published: July 2019

ABSTRACTDifferent effects of anticancer drugs between mouse and human have caused increasing concerns. A better understanding of cancer initiation between the two species is needed. We have previously identified an oncoprotein GT198 (PSMC3IP) in human breast cancer. In this report, we investigated GT198 in MMTV-PyMT mouse mammary gland tumors and found a reconcilable mechanism in human and mouse. Specifically, distinct tumor initiating stimuli in human and mouse result in a common GT198-mediated tumorigenic pathway in both species. Here we show, similar to human breast cancer even before a tumor appears, GT198 has overexpressed in mouse tumor stroma including pericyte stem cells, descendent adipocytes, fibroblasts, and myoepithelial cells. Using recombinant GT198 protein as an antigen, we vaccinated MMTV-PyMT mice and found that the GT198 vaccine delayed mouse tumor growth and reduced lung metastasis. The antitumor effects in vaccinated mice were linearly correlated with serum titers of GT198 antibody, which can recognize cell surface GT198 protein on viable tumor cells confirmed by FACS. Furthermore, tumor cells isolated from MMTV-PyMT mice were re-implanted into normal FVB/N mice, GT198+tumor cells induced faster tumor growths than GT198-tumor cells. Together, this first study of GT198 vaccine in mouse showed its effectiveness in antitumor and anti-metastasis. The finding may accelerate future development of GT198 immunotherapy in human cancer. Our finding also indicates that even though distinct cancer-initiation stimuli exist between mouse and human, a common tumorigenic pathway mediated by oncoprotein GT198 is shared in both species.
The Impact on Estimations of Genetic Correlations of the Use, in Genome Wide Case-Control Studies, of Super-Normal, Unscreened and Family-History Screened Controls
Authors: Kendler Kenneth S. , Chatzinakos Chris , Bacanu Silviu-Alin 
Published: July 2019

ABSTRACTTraditionally, in normal case-control studies of disorder A, individuals with disorder A are screened-out of controls. However, in genome wide association (GWA) studies, controls are sometimes unscreened or screened for disorder A and disorder B, producing super-normal controls. Using simulations, we examine how the observed genetic correlations between two disorders (A and B) are influenced by the use of unscreened, normal, and super-normal controls. Normal controls produce unbiased estimates of the genetic correlation. However, unscreened and super-normal controls both bias upward the genetic correlations. The strength of the bias increases with increasing population prevalences for the two disorders. With super-normal controls, the magnitude of bias is stronger when the true genetic correlation is low. The opposite is seen with the use of unscreened controls. Adding screening of first-degree relatives of controls substantially increases the bias in genetic correlations with super-normal controls but has minimal impact when normal controls are used.