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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,693 records · Page 94Linked to original sources
bioRxiv2018

Vitamin D3 regulates estrogen’s action and affects mammary epithelial organization in 3D cultures

Vitamin D3 (vitD3) and its active metabolite, calcitriol (1,25-(OH)2D3), affect multiple tissue types by interacting with the vitamin D receptor (VDR). Although vitD3 deficiency has been correlated with increased incidence of breast cancer and less favorable outcomes across ethnic groups and latitudes, randomized human clinical trials have yet to provide conclusive evidence on the efficacy of vitD3 in treating and/or preventing breast cancer. When considering that carcinogenesis is \"development gone awry\", it becomes imperative to understand the role of vitD3 during breast development. Mammary gland development in VDR KO mice is altered by increased ductal elongation and lateral branching during puberty, precocious and increased alveologenesis at pregnancy and delayed post-lactational involution. These developmental processes are largely influenced by mammotropic hormones, i.e., ductal elongation by estrogen, branching by progesterone and alveologenesis by prolactin. However, research on vitD3s effects on mammary gland morphogenesis focused on cell proliferation and apoptosis in 2D culture models and utilized supra-physiological doses of vitD3, conditions that spare the microenvironment in which morphogenesis takes place. Here, using two 3D culture models, we investigated the role of vitD3 in mammary epithelial morphogenesis. We found that vitD3 interferes with estrogens actions on T47D human breast cancer cells in 3D differently at different doses, and recapitulates what is observed in vivo. Also, vitD3 can act autonomously and affect the organization of MCF10A cells in 3D collagen matrix by influencing collagen fiber organization. Thus, we uncovered how vitD3 modulates mammary tissue organization independent of its already known effects on cell proliferation.

developmental biology↗
bioRxiv2018

Fast, volumetric live-cell imaging using high-resolution light-field microscopy

Visualizing diverse anatomical and functional traits that span many spatial scales with high spatio-temporal resolution provides insights into the fundamentals of living organisms. Light-field microscopy (LFM) has recently emerged as a scanning-free, scalable method that allows for high-speed, volumetric functional brain imaging. Given those promising applications at the tissue level, at its other extreme, this highly-scalable approach holds great potential for observing structures and dynamics in single-cell specimens. However, the challenge remains for current LFM to achieve subcellular level, near-diffraction-limited 3D spatial resolution. Here, we report high-resolution LFM (HR-LFM) for live-cell imaging with a resolution of 300-700 nm in all three dimensions, an imaging depth of several micrometers, and a volume acquisition time of milliseconds. We demonstrate the technique by imaging various cellular dynamics and structures and tracking single particles. The method may advance LFM as a particularly useful tool for understanding biological systems at multiple spatio-temporal levels.

bioengineering↗
bioRxiv2018

Lateral Asymmetry in Weekly Reproducibility of Resting State Amygdala Functional Connectivity

Abnormal functional connectivity of the amygdala with several other brain regions has been observed in patients with higher anxiety or post-traumatic stress disorder, both in a resting state and threatening conditions. However, findings on the specific connections of the amygdala might be varied due to temporal and individual fluctuations in the resting state functional connectivity (rsFC) of the amygdala and its lateral asymmetry, as well as possible variability in anxiety among healthy subjects. We studied reproducibility of rsFC data for the right and left amygdala, obtained by functional magnetic resonance imaging twice in a one-week interval in 20 healthy volunteers with low to moderate anxiety. We found resting-state amygdala network, which included not only areas involved in the emotion circuit, but regions of the default mode network (DMN) associated with memory and other brain areas involved in motor inhibition and emotion suppression. The amygdala network was stable in time and within subjects, but between-session reproducibility was asymmetrical for the right and left amygdala rsFC. The right amygdala had more significant connections with DMN regions and the right ventrolateral prefrontal cortex. The rsFC values of the right amygdala were more sustained across the week than the left amygdala rsFC. Our results support a hypothesis of functional lateralization of the amygdala. The left amygdala is more responsible for the conscious processing of threats, which may produce more variable rsFC; the right amygdala rsFC is more stable due to its greater engagement in continuous automatic evaluation of stimuli.\n\nHighlightsO_LIAmygdala resting state network included areas of emotion circuit and motor control\nC_LIO_LIDuring rest amygdala was functionally connected with areas of default mode network\nC_LIO_LIFunctional connectivity of the right amygdala was more sustained across the week\nC_LIO_LIFunctional connections of amygdala network were more stable in the right hemisphere\nC_LI

neuroscience↗
bioRxiv2018

AMPK Signaling Regulates Expression of Urea Cycle Enzymes in Response to Changes in Dietary Protein Intake

Abundance of urea cycle enzymes in the liver is regulated by the dietary protein intake. Although urea cycle enzyme levels rise in response to a high protein diet, signaling networks that sense dietary protein intake and trigger changes in expression of urea cycle genes have not been identified. The aim of this study was to identify signaling pathway(s) that respond to changes in protein intake and regulate expression of urea cycle genes in mice and human hepatocytes. Mice were adapted to either control or high (HP) protein diets followed by isolation of liver protein and mRNA and integrated analysis of the proteomic and transcriptome profiles. HP diet led to increased expression of mRNA and enzymes in amino acid degradation pathways, and decreased expression of mRNA and enzymes in carbohydrate and fat metabolism, which implicated AMPK as a possible regulator. Primary human hepatocytes, treated with AICAR an activator of AMPK, were used to test whether AMPK regulates expression of urea cycle genes. The abundance of CPS1 and OTC mRNA increased in hepatocytes treated with AICAR, which supports a role for AMPK signaling in regulation of the urea cycle. Because AMPK is either a target of drugs used to treat type-2 diabetes, these drugs might increase the expression of urea cycle enzymes in patients with urea cycle disorders, which could be the basis of a new therapeutic approach.\n\nAuthor summaryIntegrated analysis of transcriptional and proteomic profiles of the liver tissue from mice fed different protein content diets revealed that AMPK signaling pathway regulates expression of urea cycle enzymes.

molecular biology↗
bioRxiv2018

MTHFD1 is a genetic interactor of BRD4 and links folate metabolism to transcriptional regulation

The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for genetic and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression, and pharmacologic inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin-associated suggests a direct role for nuclear metabolism in the control of gene expression.

cancer biology↗
bioRxiv2018

The Influence of Molecular Reach and Diffusivity on the Efficacy of Membrane-Confined Reactions

Signalling by surface receptors often relies on tethered reactions whereby an enzyme bound to the cytoplasmic tail f a receptor catalyses reactions on substrates within reach. The overall length and stiffness of the receptor tail, the enzyme, and the substrate determine a biophysical parameter termed the molecular reach of the reaction. This parameter determines the probability that the receptor-tethered-enzyme will contact the substrate, in the volume proximal to the membrane, when separated by different distances within the membrane plane. Here, we develop particle-based stochastic reaction-diffusion models to study the interplay between molecular reach and diffusion. We find that increasing the molecular reach can increase reaction efficacy when diffusion is slow, but when diffusion is fast, increasing molecular reach reduces reaction efficacy. This switching is lost if reactions are forced to take place within the 2D plasma membrane instead of the 3D volume proximal to it, or if molecules diffuse in 3D. We show results in the context of immune receptors (PD-1 dephosphorylating CD28), a standard opposing kinase-phosphatase reaction, and a minimal two-particle model. The work highlights the 3D nature of many 2D membrane-confined interactions, illustrating a role for molecular reach in controlling biochemical reactions.

biophysics↗
bioRxiv2018

Overlapping and unique neural circuits support perceptual decision making and confidence

The period of making a perceptual decision is often followed by a period of confidence generation where one rates the likely accuracy of the initial decision. However, it remains unclear whether the same or different neural circuits are engaged during periods of perceptual decision making and confidence generation. To address this question, we conducted two functional MRI experiments in which we dissociated the periods related to perceptual decision making and confidence report by either separating their respective regressors or asking for confidence ratings only in the second half of the experiment. We found that perceptual decision making and confidence reports gave rise to activations in large and mostly overlapping brain circuits including frontal, parietal, posterior, and cingulate regions with the results being remarkably consistent across the two experiments. Further, the confidence report period activated a number of unique regions, whereas there was no evidence for the decision period activating unique regions not involved in the confidence period. We discuss the possible reasons for this overlap and explore their implications about theories of perceptual decision making and confidence generation.

neuroscience↗
bioRxiv2018

Demonstration of End-to-End Automation of DNA Data Storage

We developed a complete end-to-end DNA data storage device. The device enables the encoding of data, which is then written to a DNA oligonucleotide using a custom DNA synthesizer, pooled for liquid storage, and read using a nanopore sequencer and a novel, minimal preparation protocol. We demonstrate an automated 5-byte write, store, and read cycle with the ability to expand as new technology is available.

synthetic biology↗
bioRxiv2018

Alternative stable states in a model of microbial community limited by multiple essential nutrients

Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To better understand the mechanisms and origins of multistability in microbial communities, we introduce and study a model of a microbial ecosystem colonized by multiple specialist species selected from a fixed pool. Growth of each species can be limited by essential nutrients of two types, e.g. carbon and nitrogen, each represented in the environment by multiple metabolites. We demonstrate that our model has an exponentially large number of potential stable states realized for different environmental parameters. Using game theoretical methods adapted from the stable marriage problem we predict all of these states based only on ranked lists of competitive abilities of species for each of the nutrients. We show that for every set of nutrient influxes, several mutually uninvadable stable states are generally feasible and we distinguish them based upon their dynamic stability. We further explore an intricate network of discontinuous transitions (regime shifts) between these alternative states both in the course of community assembly, or upon changes of nutrient influxes.

ecology↗
bioRxiv2018

PSMA Expression in the Hi-Myc Model; Extended Utility of a Representative Model of Prostate Cancer for Biological Insight and as a Drug Discovery Tool

Prostate specific membrane antigen (PSMA), also known as glutamate carboxypeptidase II (GCPII), is highly overexpressed in primary and metastatic prostate cancer (PCa). This has led to the development of radiopharmaceuticals for targeted imaging and therapy under current clinical evaluation. Despite this progress, the exact biological role of the protein in prostate cancer development and progression has not been fully elucidated. This is in part because the human PSMA and mouse PSMA (mPSMA) have different patterns of anatomical expression which confound study in the most widely utilized model organisms. Most notably, mPSMA is not expressed in the healthy murine prostate. Here, we reveal that mPSMA is highly upregulated in the prostate and prostate adenocarcinoma in the spontaneous Hi-Myc mouse model, a highly accurate and well characterized mouse model of prostate cancer development. Antibody detection and molecular imaging tools are used to confirm that mPSMA is expressed from early prostatic intraepithelial neoplasia (PIN) through adenocarcinoma.

cancer biology↗
bioRxiv2018

Mcidas mutant mice reveal a two-step process for the specification and differentiation of multiciliated cells in mammals

Motile cilia on multiciliated cells (MCCs) function in fluid clearance over epithelia. Studies with Xenopus embryos and patients with the congenital respiratory disorder reduced generation of multiple motile cilia, have implicated the nuclear protein MCIDAS (MCI), in the transcriptional regulation of MCC specification and differentiation. Recently, a paralogous protein, GMNC, was also shown to be required for MCC formation. Surprisingly, and in contrast to the presently held view, we find that Mci mutant mice can specify MCC precursors. However, these precursors cannot produce multiple basal bodies, and mature into single ciliated cells. We show that MCI is required specifically to induce deuterosome pathway components for the production of multiple basal bodies. Moreover, GMNC and MCI associate differentially with the cell-cycle regulators E2F4 and E2F5, which enables them to activate distinct sets of target genes (ciliary transcription factor genes versus genes for basal body generation). Our data establish a previously unrecognized two-step model for MCC development: GMNC functions in the initial step for MCC precursor specification. GMNC induces Mci expression, which then drives the second step of basal body production for multiciliation.\n\nSUMMARY STATEMENTWe show how two GEMININ family proteins function in mammalian multiciliated cell development: GMNC regulates precursor specification and MCIDAS induces multiple basal body formation for multiciliation.

developmental biology↗
bioRxiv2018

Left planum temporale growth predicts language development in newborns with congenital heart disease

Congenital heart diseases (CHD) are the most common congenital anomalies, accounting for a third of all congenital anomaly cases. While surgical correction dramatically improved survival rates, the lag behind normal neurodevelopment appears to persist. Deficits of higher cognitive functions are particularly common, including developmental delay in communication and oral-motor apraxia. It remains unclear whether the varying degree of cognitive developmental delay is reflected in variability in brain growth patterns. To answer this question, we aimed to investigate whether the rate of regional brain growth is correlated with later life neurodevelopment. 44 newborns were included in our study, out of whom 33 were diagnosed with dextro-transposition of the great arteries (d-TGA) and 11 with other forms of severe CHD. During the first month of life, neonates underwent corrective or palliative cardiovascular bypass surgery, pre- and postoperative cerebral MRI were performed 18.7 {+/-} 7.03 days apart. MRI was performed in natural sleep on a 3.0T scanner using an 8-channel head coil, fast spin-echo T2-weighted anatomical sequences were acquired in three planes. Based on the principles of deformation based morphometry, we calculated brain growth rate maps that reflected the rate of non-linear deformation that occurs between pre- and post-operative brain images. An explorative, whole-brain, threshold-free cluster enhancement analysis revealed strong correlation between the growth rate of the left planum temporale and the posterior operculum of the left frontal lobe and language score at 12 months of age, corrected for demographic variables (p=0.018, t=5.656). No significant correlation was found between brain growth rates and motor or cognitive scores. Post hoc analysis showed that the length of hospitalization interacts with this correlation with longer hospitalization stay results in faster enlargement of the internal cerebro-spinal fluid spaces. Our study provides evidence to the early importance of left-dominant perisylvian regions in language development even before the direct postnatatal exposure to native language. In CHD patients, the perioperative period results in a critical variability of brain growth rate in this region, which is a reliable neural correlate of language development at one year of age.

neuroscience↗
bioRxiv2018

Thalamic state influences timing and feature selectivity in the thalamocortical circuit

Sensory signals from the outside world are transduced at the periphery, passing through thalamus before reaching cortex, ultimately giving rise to the sensory representations that enable us to perceive the world. The thalamocortical circuit is particularly sensitive to the temporal precision of thalamic spiking due to highly convergent synaptic connectivity. Thalamic neurons can exhibit burst and tonic modes of firing that strongly influence timing within the thalamus. The impact of these changes in thalamic state on sensory encoding in the cortex, however, remains unclear. Here, we investigated the role of thalamic state on timing in the thalamocortical circuit of the vibrissa pathway in the anesthetized rat. We optogenetically hyperpolarized thalamus while recording single unit activity in both thalamus and cortex. Tonic spike triggered analysis revealed temporally precise thalamic spiking that was locked to weak white-noise sensory stimuli, while thalamic burst spiking was associated with a loss in stimulus-locked temporal precision. These thalamic state dependent changes propagated to cortex such that the cortical timing precision was diminished during the hyperpolarized (burst biased) thalamic state. While still sensory driven, the cortical neurons became significantly less precisely locked to the weak white-noise stimulus. The results here suggests a state dependent differential regulation of spike timing precision in the thalamus that could gate what signals are ultimately propagated to cortex.

neuroscience↗
bioRxiv2018

Novel use of Diffusion Tensor Imaging to Delineate the Rat Basolateral Amygdala

The amygdaloid complex, including the basolateral nucleus (BLA) contributes crucially to emotional and cognitive brain functions, and is thus a major target of research in both humans and rodents. However, delineating structural amygdala plasticity in both normal and disease-related contexts using neuroimaging has been hampered by the difficulty of unequivocally identifying the boundaries of the BLA. This challenge is a result of poor contrast between BLA and the surrounding gray matter, including other amygdala nuclei. Here we describe a novel DTI approach to enhance contrast, enabling optimal identification of BLA in rodent brain from MR images. We employed this methodology together with a slice-shifting approach to measure BLA volume. We then validated the results by direct comparison to both histological and cellular-identity (parvalbumin)-based conventional techniques for defining BLA in the same brains used for MRI. We also confirmed the BLA region using DTI based tractography. The novel approach used here enables accurate and reliable delineation of BLA. Because this nucleus is involved in, and is changed by, developmental, degenerative and adaptive processes, the instruments provided here should be highly useful to a broad range of neuroimaging studies. Finally, the principles used here are readily applicable to numerous brain regions and across species.\n\nSummary StatementUse of MRI directionally encoded diffusion tensor imaging (DTI) can delineate the basolateral amygdala (BLA) and volumes derived from DTI were found to match those obtained using histological methods. Our approach can be used to identify the BLA.

neuroscience↗
bioRxiv2018

Muller’s ratchet as a mechanism of frailty and multimorbidity

Mutation accumulation has been proposed as a cause of senescence. In this process, both constitutional and recurrent mutations accumulate gradually and differentially among differentiating cells, tissues and organs, in relation to stage and age, analogous to Mullers ratchet in asexually reproducing organisms. Latent and cascading deleterious effects of mutations might initiate steady \"accumulation of deficits\" in cells, leading to cellular senescence, and functional decline of tissues and organs, and ultimately manifest as frailties and disease. We investigated a few of these aspects in cell populations through modeling and simulation using the Moran birth-death process, under varied scenarios of mutation accumulation. Our results agree with the principle of Mullers ratchet. The ratchet speed in a given tissue depends on the population size of cells, mutation rate, and selection coefficient. Additionally, deleterious mutations seem to rapidly accumulate particularly early in the life-course, during which the rate of cell division is high, thereby exerting a greater effect on cellular senescence. The speed of the ratchet afterward varies greatly between cells nested in tissues and tissues within organs due to heterogeneity in the life span and turnover rate of specific cell types. Importantly, the ratchet accelerates with age, resulting in a synergistic fitness decay in cell populations. We extend Fishers average excess concept and rank order scale to interpret differential phenotypic effects of mutation load in a given tissue. We conclude that classical evolutionary genetic models could explain partially, the origins of frailty, subclinical conditions, morbidity and health consequences of senescence.\n\nSignificanceFrailty is defined as physiological and functional decline of organs and organ systems, due to deficit accumulation from stochastic damages within the organism with advanced age. Equivalently, with age, both constitutional and somatic mutations accumulate gradually and differentially among cells, cell lineages, tissues, and organs. Since most mutations are deleterious, accumulation of random and recurrent mutations could create a \"load,\" on the genome and contextually express in the epigenome and phenotype spaces. Here we extend Mullers ratchet principle to explain frailty and multi-morbidity using the Moran model and simulations. Our results agree with the Mullers ratchet principle. We emphasize the need for considering cumulative effects of the entire spectrum of mutations for explaining the origin of frailty, sub-clinical conditions, and morbidity.

genetics↗
bioRxiv2018

Diminished pre-stimulus alpha-lateralization suggests compromised self-initiated attentional control of auditory processing in old age

Older adults experience difficulties in daily situations that require flexible information selection in the presence of multiple competing sensory inputs, like for instance multi-talker situations. Modulations of rhythmic neural activity in the alpha-beta (8-30 Hz) frequency range in posterior brain areas have been established as a cross-modal neural correlate of selective attention. However, research linking compromised auditory selective attention to changes in rhythmic neural activity in aging is sparse.\n\nWe tested younger (n = 25; 22-35 years) and older adults (n = 26; 63-76 years) in an attention modulated dichotic listening task. In this, two streams of highly similar auditory input were simultaneously presented to participants' both ears (i.e., dichotically) while attention had to be focused on the input to only one ear (i.e. target) and the other, distracting information had to be ignored.\n\nWe here demonstrate a link between severely compromised auditory selective attention in aging and a partial reorganization of attention-related rhythmic neural responses. In particular, in old age we observed a shift from a self-initiated, preparatory modulation of alpha rhythmic activity to an externally driven, response in the alpha-beta range. Critically, moment-to-moment fluctuations in the age-specific patterns of self-initiated and externally driven lateralized rhythmic activity were tied to selective attention. We conclude that adult age difference in spatial selective attention likely derive from a functional reorganization of rhythmic neural activity within the aging brain.

neuroscience↗
bioRxiv2018

Interactions of medial and lateral prefrontal cortex in hierarchical predictive coding

Cognitive control and decision-making relies on the interplay of medial and lateral prefrontal cortex (mPFC/LPFC), particularly for circumstances in which correct behavior requires integrating and selecting among multiple sources of interrelated information. While the interaction between mPFC and LPFC is generally acknowledged as a crucial circuit in adaptive behavior, the nature of this interaction remains open to debate, with various proposals suggesting complementary roles in (i) signaling the need for and implementing control, (ii) identifying and selecting appropriate behavioral policies from a candidate set, and (iii) constructing behavioral schemata for performance of structured tasks. Although these proposed roles capture salient aspects of conjoint mPFC/LPFC function, none are sufficiently well-specified to provide a detailed account of the continuous interaction of the two regions during ongoing behavior. A recent computational model of mPFC and LPFC, the Hierarchical Error Representation (HER) model, places the regions within the framework of hierarchical predictive coding, and suggests how they interact during behavioral periods preceding and following salient events. In this manuscript, we extend the HER model to incorporate real-time temporal dynamics and demonstrate how the extended model is able to capture single-unit neurophysiological, behavioral, and network effects previously reported in the literature. Our results add to the wide range of results that can be accounted for by the HER model, and provide further evidence for predictive coding as a unifying framework for understanding PFC function and organization.

neuroscience↗
bioRxiv2018

A cellular anatomy of the normal adult human prostate and prostatic urethra

A cellular anatomy of normal human organs is essential for solving the cellular origins of disease. We report the first comprehensive cellular atlas of the young adult human prostate and prostatic urethra using an iterative process of single cell RNA sequencing and flow cytometry on ~98,000 cells taken from different anatomical regions. Two previously unrecognized epithelial cell types were identified by KRT13 and SCGB1A1 expression and found to be highly similar to hillock and club cells of the proximal lung. It was demonstrated by immunohistochemistry that prostate club and hillock cells are similarly concentrated in the proximal prostate. We also optimized a new flow cytometry antibody panel to improve cell type-specific purification based on newly established cellular markers. The molecular classification, anatomical distribution, and purification methods for each cell type in the human prostate create a powerful new resource for experimental design in human prostate disease.

cell biology↗