scholarly journals A Hox code defines spinocerebellar neuron subtype regionalisation

2019 ◽  
Author(s):  
Eamon Coughlan ◽  
Victoria Garside ◽  
Siew Fen Lisa Wong ◽  
Huazheng Liang ◽  
Dominik Kraus ◽  
...  
Keyword(s):  
Body Position ◽  
Body Movement ◽  
Molecular Heterogeneity ◽  
Proprioceptive Information ◽  
Neuronal Tracing ◽  
Fluorescent Reporter ◽  
Protein Coding ◽  
Clarke's Column ◽  
Spinocerebellar Neurons

AbstractCoordinated body movement requires the integration of many sensory inputs. This includes proprioception, the sense of relative body position and force associated with movement. Proprioceptive information is relayed to the cerebellum via spinocerebellar neurons, located in the spinal cord within a number of major neuronal columns or as various scattered cell populations. Despite the importance of proprioception to fluid movement, a molecular understanding of spinocerebellar relay interneurons is only beginning to be explored, with limited knowledge of molecular heterogeneity within and between columns. Using fluorescent reporter knock-in mice, neuronal tracing and in situ hybridisation, we identify widespread expression of Hox cluster genes, including both protein-coding genes and microRNAs, within spinocerebellar neurons. We reveal a “Hox code” based on axial level and individual spinocerebellar column, which, at cervico-thoracic levels, is essential for subtype regionalisation. Specifically, we show that Hoxc9 function is required in most, but not all, cells of the major thoracic spinocerebellar column, Clarke’s column, revealing heterogeneity reliant on Hox signatures.

Abstract 13: Inhibition of Nudt6 Stabilizes Advanced Atherosclerotic Plaques

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Hong Jin ◽  
Yuhuang Li ◽  
Ekaterina Chernogubova ◽  
Alexandra Bäcklund ◽  
Stina Sellberg ◽  
...  
Keyword(s):  
Carotid Artery ◽  
Atherosclerotic Plaque ◽  
Plaque Rupture ◽  
Survival Rates ◽  
Atherosclerotic Plaques ◽  
Protein Coding ◽  
Fibrous Cap ◽  
Asymptomatic Patients ◽  
Rupture Model

Natural antisense transcripts (NATs), a non-coding RNA subclass, being transcribed in antisense direction to protein coding genes, are an intriguing novel class of targetable modulators, exerting crucial effects on gene expression. Aim of the current study was to investigate the contribution of NATs to atherosclerotic plaque vulnerability. Using laser capture micro-dissection, we isolated fibrous caps tissue of carotid artery plaques from 20 symptomatic patients with ruptured lesions vs. 20 samples from asymptomatic patients with stable lesions. A human transcriptome array (HTA; GeneChip 2.0 ) was used to profile the expression of all currently annotated RNA transcripts. Nucleoside diphosphate-linked moiety X motif 6 (NUDT6) was identified as one of the most significantly up-regulated transcripts in fibrous caps of ruptured lesions. Interestingly, NUDT6 is an established antisense RNA targeting the fibroblast growth factor 2 (FGF2). Of importance, FGF2 was among the most significantly down-regulated transcripts in ruptured lesions, corresponding to elevated NUDT6 expression. In situ hybridization in both, human and mouse carotid atherosclerotic plaques, confirmed substantially higher expression levels of NUDT6 in ruptured lesions compared to stable. In addition, in situ hybridization revealed a distinct co-localization with smooth muscle cells (SMCs) in advanced plaques. Overexpression of NUDT6 in cultured human carotid artery SMCs effectively limited FGF2 on the mRNA as well as protein level. Furthermore, reduction of NUDT6 via siRNA stimulated proliferation and blocked apoptosis in SMCs. In an inducible atherosclerotic plaque rupture model using incomplete ligation and cuff placement on common carotid arteries of male apoE -/- mice, NUDT6 inhibition with gapmeRs was able to significantly improve SMC survival rates, leading to thicker fibrous caps, and to reduce the plaque rupture rate compared to scramble-gapmeR control-treated mice (22% vs . 63%, p = 0.03). The present study presents NUDT6 as a novel crucial antisense regulator of fibrous cap stability through steering SMC survival via targeting its sense RNA transcript FGF2.

scholarly journals Cellular thermal shift analysis for interrogation of CRISPR-assisted proteomic changes

BioTechniques ◽  
2020 ◽  
Vol 68 (4) ◽  
pp. 180-184 ◽  
Author(s):  
Nam-Gu Her ◽  
Ivan Babic ◽  
Venkata M Yenugonda ◽  
Santosh Kesari ◽  
Elmar Nurmemmedov
Keyword(s):  
Protein Complexes ◽  
Physiological State ◽  
Protein Coding ◽  
Coding Sequences ◽  
Missing Link ◽  
Disease States ◽  
Shift Analysis ◽  
Versatile Tool ◽  
Thermal Shift

CRISPR–Cas9 has proven to be a versatile tool for the discovery of essential genetic elements involved in various disease states. CRISPR-assisted dense mutagenesis focused on therapeutically challenging protein complexes allows us to systematically perturb protein-coding sequences in situ and correlate them with functional readouts. Such perturbations can mimic targeting by therapeutics and serve as a foundation for the discovery of highly specific modulators. However, translation of such genomics data has been challenging due to the missing link for proteomics under the physiological state of the cell. We present a method based on cellular thermal shift assays to easily interrogate proteomic shifts generated by CRISPR-assisted dense mutagenesis, as well as a case focused on NuRD epigenetic complex.

scholarly journals Angiogenic patterning by STEEL, an endothelial-enriched long noncoding RNA

2018 ◽  
Vol 115 (10) ◽  
pp. 2401-2406 ◽  
Author(s):  
H. S. Jeffrey Man ◽  
Aravin N. Sukumar ◽  
Gabrielle C. Lam ◽  
Paul J. Turgeon ◽  
Matthew S. Yan ◽  
...  
Keyword(s):  
Noncoding Rna ◽  
De Novo ◽  
Feedback Inhibition ◽  
Body Position ◽  
In Vivo Model ◽  
Protein Coding ◽  
Angiogenic Potential ◽  
Hemodynamic Forces

Endothelial cell (EC)-enriched protein coding genes, such as endothelial nitric oxide synthase (eNOS), define quintessential EC-specific physiologic functions. It is not clear whether long noncoding RNAs (lncRNAs) also define cardiovascular cell type-specific phenotypes, especially in the vascular endothelium. Here, we report the existence of a set of EC-enriched lncRNAs and define a role for spliced-transcript endothelial-enriched lncRNA (STEEL) in angiogenic potential, macrovascular/microvascular identity, and shear stress responsiveness. STEEL is expressed from the terminus of the HOXD locus and is transcribed antisense to HOXD transcription factors. STEEL RNA increases the number and integrity of de novo perfused microvessels in an in vivo model and augments angiogenesis in vitro. The STEEL RNA is polyadenylated, nuclear enriched, and has microvascular predominance. Functionally, STEEL regulates a number of genes in diverse ECs. Of interest, STEEL up-regulates both eNOS and the transcription factor Kruppel-like factor 2 (KLF2), and is subject to feedback inhibition by both eNOS and shear-augmented KLF2. Mechanistically, STEEL up-regulation of eNOS and KLF2 is transcriptionally mediated, in part, via interaction of chromatin-associated STEEL with the poly-ADP ribosylase, PARP1. For instance, STEEL recruits PARP1 to the KLF2 promoter. This work identifies a role for EC-enriched lncRNAs in the phenotypic adaptation of ECs to both body position and hemodynamic forces and establishes a newer role for lncRNAs in the transcriptional regulation of EC identity.

Effect of body position on regional diaphragm function in dogs

1990 ◽  
Vol 69 (6) ◽  
pp. 2296-2302 ◽  
Author(s):  
J. Sprung ◽  
C. Deschamps ◽  
S. S. Margulies ◽  
R. D. Hubmayr ◽  
J. R. Rodarte
Keyword(s):  
Prone Position ◽  
Regional Differences ◽  
Body Position ◽  
Vertical Gradient ◽  
Transdiaphragmatic Pressure ◽  
Lung Capacity ◽  
Volume Relationship ◽  
Residual Capacity ◽  
Fractional Shortening

The in situ lengths of muscle bundles of the crural and three regions of the costal diaphragm between origin and insertion were determined with a video roentgenographic technique in dogs. At total lung capacity (TLC) in both the prone and supine positions, the length of the diaphragm is not significantly different from the unstressed excised length, suggesting that the diaphragm is not under tension at TLC and that there is a hydrostatic gradient of pleural pressure on the diaphragmatic surface. Except for the ventral region of the costal diaphragm, which does not change length at lung volumes greater than 70% TLC, all other regions are stretched during passive deflations from TLC. Therefore below TLC the diaphragm is under passive tension and supports a transdiaphragmatic pressure (Pdi). The length of the diaphragm relative to its unstressed length is not uniform at functional residual capacity (FRC) and does not follow a strict vertical gradient that reverses when the animal is changed from the supine to the prone position. By inference, the length of muscle bundles is determined by factors other than the vertical gradient of Pdi. During mechanical ventilation, regional shortening is identical to the passive deflation length-volume relationship near FRC. Prone and supine FRC is the same, but the diaphragm is slightly shorter in the prone position. In both positions, during spontaneous ventilation there are no consistent differences in regional fractional shortening, despite regional differences in initial length relative to unstressed length.

scholarly journals ARTIFICIAL NEURAL NETWORKS BASED SLEEP MOTION RECOGNITION USING NIGHT VISION CAMERAS

2004 ◽  
Vol 16 (02) ◽  
pp. 79-86 ◽  
Author(s):  
CHUNG-HSIEN KUO ◽  
FANG-CHUNG YANG ◽  
MING-YUAN TSAI ◽  
MING-YIH LEE
Keyword(s):  
Neural Networks ◽  
High Speed ◽  
Body Position ◽  
Body Movement ◽  
The Body ◽  
Night Vision ◽  
Ann Model ◽  
Motion Recognition ◽  
Video Frames ◽  
Artificial Neural

The body movement is one of the most important factors to evaluate the sleep quality. In general, the sleep motion is hardly investigated, and it must take a long time to observe the motion of the patient in terms of a pre-recoded video storage media with high speed playing. This paper proposes an image-based solution to recognize the sleep motions. We use the contact free and IR-based night vision camera to capture the video frames during the sleep of the patient. The video frames are used to recognize the body positions and the body directions such as the “body up”, “body down”, “body right”, and “body left”. In addition to the image processing, the proposed artificial neural network (ANN) sleep motion recognition solution is composed of two neural networks. These two neural networks are organized as in a cascade configuration. The first ANN model is used to identify the body position features from the images; and the follower ANN model is constructed based on the features that are identified by the first ANN model to recognize the body direction. Finally, the implementations and the practical results of this work are all illustrated in this paper.

scholarly journals Genome Sequence of Hydrogenovibrio sp. Strain SC-1, a Chemolithoautotrophic Sulfur and Iron Oxidizer

2018 ◽  
Vol 6 (5) ◽  
Author(s):  
Christopher Neely ◽  
Charbel Bou Khalil ◽  
Alex Cervantes ◽  
Raquel Diaz ◽  
Angelica Escobar ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Surface Sediment ◽  
Autotrophic Growth ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Marine Surface

ABSTRACT Hydrogenovibrio sp. strain SC-1 was isolated from pyrrhotite incubated in situ in the marine surface sediment of Catalina Island, CA. Strain SC-1 has demonstrated autotrophic growth through the oxidation of thiosulfate and iron. Here, we present the 2.45-Mb genome sequence of SC-1, which contains 2,262 protein-coding genes.

scholarly journals Evidence for genetically distinct direct and indirect spinocerebellar pathways mediating proprioception

2020 ◽  
Author(s):  
Iliodora V. Pop ◽  
Felipe Espinosa ◽  
Megan Goyal ◽  
Bishakha Mona ◽  
Mark A. Landy ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Granule Cells ◽  
Mossy Fiber ◽  
Cerebellar Nuclei ◽  
Reticular Nucleus ◽  
Proprioceptive Information ◽  
Lateral Reticular Nucleus ◽  
Axon Collaterals ◽  
Progenitor Domain ◽  
Clarke's Column

AbstractProprioception, the sense of limb and body position, generates a map of the body that is essential for proper motor control, yet we know little about precisely how neurons in proprioceptive pathways develop and are wired. Proprioceptive and cutaneous information from the periphery is sent to secondary neurons in the spinal cord that integrate and relay this information to the cerebellum either directly or indirectly through the medulla. Defining the anatomy of these direct and indirect pathways is fundamental to understanding how proprioceptive circuits function. Here, we use genetic tools in mice to define the developmental origins and unique anatomical trajectories of these pathways. Developmentally, we find that Clarke’s column (CC) neurons, a major contributor to the direct spinocerebellar pathway, derive from the Neurog1 progenitor domain. By contrast, we find that two of the indirect pathways, the spino-lateral reticular nucleus (spino-LRt) and spino-olivary pathways, are derived from the Atoh1 progenitor domain, despite previous evidence that Atoh1-lineage neurons form the direct pathway. Anatomically, we also find that the mossy fiber terminals of CC neurons diversify extensively with some axons terminating bilaterally in the cerebellar cortex. Intriguingly, we find that CC axons do not send axon collaterals to the medulla or cerebellar nuclei like other mossy fiber sources. Altogether, we conclude that the direct and indirect spinocerebellar pathways derive from distinct progenitor domains in the developing spinal cord and that the proprioceptive information from CC neurons is processed only at the level of granule cells in the cerebellum.Significance StatementWe find that a majority of direct spinocerebellar neurons in mice originate from Clarke’s column (CC), which derives from the Neurog1-lineage, while few originate from Atoh1-lineage neurons as previously thought. Instead, we find that spinal cord Atoh1-lineage neurons form mainly the indirect spino-lateral reticular nucleus and spino-olivary tracts. Moreover, we observe that mossy fiber axon terminals of CC neurons diversify proprioceptive information across granule cells in multiple lobules on both ipsilateral and contralateral sides without sending axon collaterals to the medulla or cerebellar nuclei. Altogether, we define the development and the anatomical projections of direct and indirect pathways to the cerebellum from the spinal cord.

Effects of body position and lung volume on in situ operating length of canine diaphragm

1990 ◽  
Vol 69 (5) ◽  
pp. 1702-1708 ◽  
Author(s):  
S. S. Margulies ◽  
G. A. Farkas ◽  
J. R. Rodarte
Keyword(s):  
Lung Volume ◽  
Body Position ◽  
Vertical Gradient ◽  
Postoperative Recovery ◽  
Optimal Force ◽  
Residual Capacity ◽  
Crural Diaphragm

The performance of the diaphragm is influenced by its in situ length relative to its optimal force-generating length (Lo). Lead markers were sutured to the abdominal surface of the diaphragm along bundles of the left ventral, middle, and dorsal regions of the costal diaphragm and the left crural diaphragm of six beagle dogs. After 2-3 wk postoperative recovery, the dogs were anesthetized, paralyzed, and scanned prone and supine in the Dynamic Spatial Reconstructor (DSR) at a total lung capacity (TLC), functional residual capacity (FRC), and residual volume (RV). The location of each marker was digitized from the reconstructed DSR images, and in situ lengths were determined. After an overdose of anesthetic had been administered to the dogs, each marked diaphragm bundle was removed, mounted in a 37 degrees C in vitro chamber, and adjusted to Lo (maximum tetanic force). The operating length of the diaphragm, or in situ length expressed as percent Lo, varied from region to region at the lung volumes studied; variability was least at RV and increased with increasing lung volume. At FRC, all regions of the diaphragm was shorter in the prone posture compared with the supine, but there was no clear gravity-dependent vertical gradient of in situ length in either posture. Because in vitro length-tension characteristics were similar for all diaphragm regions, regional in vivo length differences indicate that the diaphragm's potential to generate maximal force is nonuniform.

New Developments in Chronic Lymphocytic Leukaemia Diagnosis

2013 ◽  
Vol 09 (02) ◽  
pp. 114
Author(s):  
Julio Delgado ◽  
Rodrigo Santacruz ◽  
Tycho Baumann ◽  
Emili Montserrat ◽  
◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Next Generation Sequencing ◽  
Chronic Lymphocytic Leukaemia ◽  
Lymphocytic Leukaemia ◽  
Lymphoproliferative Disorders ◽  
Molecular Heterogeneity ◽  
New Developments ◽  
Developed World ◽  
Generation Sequencing

Chronic lymphocytic leukaemia (CLL) is the most prevalent leukaemia in the developed world, with a remarkable racial and sex diversity. The diagnosis of CLL is based on the presence in blood of more than 5,000 monoclonal B cells/μl, with a distinctive immunophenotype (CD5+, SmIgdim, CD20dim, CD19, CD23), which persists for more than 3 months. Newer monoclonal antibodies, such as anti-CD43, anti-CD200 or anti-ROR1, may provide further information in differentiating CLL from other chronic lymphoproliferative disorders. CLL lacks a specific genetic signature regarding chromosomic aberrations, but in cases of uncertain diagnosis molecular genetics including fluorescentin situhybridisation may be useful. Next-generation sequencing techniques are unfolding the molecular heterogeneity of CLL.

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