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https://www.readbyqxmd.com/read/29684640/three-invariant-hi-c-interaction-patterns-applications-to-genome-assembly
#1
Sivan Oddes, Aviv Zelig, Noam Kaplan
Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness...
April 20, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29680436/distal-muscle-activity-alterations-during-the-stance-phase-of-gait-in-restless-leg-syndrome-rls-patients
#2
Chloe Dafkin, Andrew Green, Benita Olivier, Warrick McKinon, Samantha Kerr
OBJECTIVE: To assess if there is a circadian variation in electromyographical (EMG) muscle activity during gait in restless legs syndrome (RLS) patients and healthy control participants. METHODS: Gait assessment was done in 14 RLS patients and 13 healthy control participants in the evening (PM) and the morning (AM). Muscle activity was recorded bilaterally from the tibialis anterior (TA), lateral gastrocnemius (GL), rectus femoris (RF) and biceps femoris (BF) muscles...
May 2018: Sleep Medicine
https://www.readbyqxmd.com/read/29677477/systems-immunology-learning-the-rules-of-the-immune-system
#3
Alexandra-Chloé Villani, Siranush Sarkizova, Nir Hacohen
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29667927/biophysics-of-object-segmentation-in-a-collision-detecting-neuron
#4
Richard Burkett Dewell, Fabrizio Gabbiani
Collision avoidance is critical for survival, including in humans, and many species possess visual neurons exquisitely sensitive to objects approaching on a collision course. Here, we demonstrate that a collision-detecting neuron can detect the spatial coherence of a simulated impending object, thereby carrying out a computation akin to object segmentation critical for proper escape behavior. At the cellular level, object segmentation relies on a precise selection of the spatiotemporal pattern of synaptic inputs by dendritic membrane potential-activated channels...
April 18, 2018: ELife
https://www.readbyqxmd.com/read/29663708/the-postmigratory-alar-topography-of-visceral-cranial-nerve-efferents-challenges-the-classical-model-of-hindbrain-columns
#5
Luis Puelles, Petr Tvrdik, Margaret Martínez-de-la-Torre
The classic columnar model of cranial nerve central representation assumes that all motor and sensory hindbrain neurons develop within four radial migration domains, held to be separated by a sulcal alar-basal boundary (sulcus limitans). This essay reviews a number of developmental data that challenge these concepts. These results are interpreted within the framework of present day neuromeric conception of the brainstem (the prosomeric model). Advances in dorsoventral patterning of the spinal cord and hindbrain now show that there exist up to eight alar microzones and five basal microzones (molecularly and histogenetically distinct longitudinal progenitor domains)...
April 16, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29663667/a-novel-splice-site-variant-in-itpr1-gene-underlying-recessive-gillespie-syndrome
#6
Leda Paganini, Chiara Pesenti, Donatella Milani, Laura Fontana, Silvia Motta, Silvia Maria Sirchia, Giulietta Scuvera, Paola Marchisio, Susanna Esposito, Claudia Maria Cinnante, Silvia Maria Tabano, Monica Rosa Miozzo
Gillespie syndrome (GLSP) is a rare congenital disorder characterized by partial aniridia, hypotonia, progressive cerebellar hypoplasia, nonprogressive ataxia, and intellectual disability. All causative variants to date affect the central or the 3'-terminal domains of ITPR1 gene and exhibit autosomal recessive or dominant inheritance pattern. We investigated by exome sequencing the molecular cause of GLSP in a family composed by consanguineous healthy parents, two affected siblings and one healthy son. We found the novel splice site variant c...
April 16, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29655930/circadian-signaling-in-homarus-americanus-region-specific-de-novo-assembled-transcriptomes-show-that-both-the-brain-and-eyestalk-ganglia-possess-the-molecular-components-of-a-putative-clock-system
#7
Andrew E Christie, Andy Yu, Micah G Pascual, Vittoria Roncalli, Matthew C Cieslak, Amanda N Warner, Tess J Lameyer, Meredith E Stanhope, Patsy S Dickinson, J Joe Hull
Essentially all organisms exhibit recurring patterns of physiology/behavior that oscillate with a period of ~24-h and are synchronized to the solar day. Crustaceans are no exception, with robust circadian rhythms having been documented in many members of this arthropod subphylum. However, little is known about the molecular underpinnings of their circadian rhythmicity. Moreover, the location of the crustacean central clock has not been firmly established, although both the brain and eyestalk ganglia have been hypothesized as loci...
April 11, 2018: Marine Genomics
https://www.readbyqxmd.com/read/29652824/full-genome-characterization-and-genetic-evolution-of-west-african-isolates-of-bagaza-virus
#8
Martin Faye, Oumar Faye, Moussa Moise Diagne, Gamou Fall, Manfred Weidmann, Mbacke Sembene, Amadou Alpha Sall, Ousmane Faye
Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014...
April 13, 2018: Viruses
https://www.readbyqxmd.com/read/29650062/fish-sperm-motility-analysis-the-central-role-of-the-flagellum
#9
Sergii Boryshpolets, Vitaliy Kholodnyy, Jacky Cosson, Borys Dzyuba
Motility analysis of spermatozoa relies on the investigation of either head trajectories or flagellum characteristics. Those two sets of parameters are far from being independent, the flagellum playing the role of motor, whereas the head plays a passive role of cargo. Therefore, quantitative descriptions of head trajectories represent a simplification of the complex pattern of whole sperm cell motion, resulting from the waves developed by the flagellum. The flagellum itself responds to a large variety of signals that precisely control its axoneme to allow activation, acceleration, slowing down or reorientation of the whole spermatozoon...
April 13, 2018: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/29649928/noninvasive-activation-of-cervical-spinal-networks-after-severe-paralysis
#10
Parag Gad, Sujin Lee, Nicholas Terrafranca, Hui Zhong, Amanda Turner, Yury Gerasimenko, Victor Reggie Edgerton
Paralysis of the upper extremities following cervical spinal cord injury (SCI) significantly impairs one's ability to live independently. While regaining hand function or grasping ability is considered one of the most desired functions in tetraplegics, limited therapeutic development in this direction has been demonstrated to date in humans with a high, severe cervical injury. The underlying hypothesis is after severe cervical SCI, nonfunctional sensory-motor networks within the cervical spinal cord can be transcutaneously neuromodulated to physiological states which enables and amplifies voluntary control of the hand...
April 13, 2018: Journal of Neurotrauma
https://www.readbyqxmd.com/read/29629945/clonal-evolution-in-primary-diffuse-large-b-cell-lymphoma-of-the-central-nervous-system
#11
Julia Garcia-Reyero, Nerea Martinez Magunacelaya, Ainara Gonzalez Pereña, Sara Marcos Gonzalez, Nuria Teran-Villagra, Ainara Azueta, Ana Batlle, Sonia Gonzalez de Villambrosia, Jose Revert Arce, Santiago Montes-Moreno
Primary diffuse large B-cell lymphoma (DLBCL) of the central nervous system (CNS) is an aggressive subtype of DLBCL with characteristic clinicopathologic features. Relapse outside the CNS involving extranodal locations has been found in a fraction of cases (16%). Here we describe a case of DLBCL arising in the CNS that relapsed 18 months after the initial diagnosis in the testis and bilateral adrenal glands. Both tumors showed equivalent morphology, phenotype, cytogenetic features, and clonal relationship. Somatic mutation analysis by next generation sequencing demonstrated MYD88L265P mutation in both tumors and de novo CD79B Y196S mutation exclusive to the relapse...
April 7, 2018: Applied Immunohistochemistry & Molecular Morphology: AIMM
https://www.readbyqxmd.com/read/29618802/integrative-analysis-of-multiple-sclerosis-using-a-systems-biology-approach
#12
Karla Cervantes-Gracia, Holger Husi
Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by inflammatory-demyelinating events in the central nervous system. Despite more than 40 years of MS research its aetiology remains unknown. This study aims to identify the most frequently reported and consistently regulated molecules in MS in order to generate molecular interaction networks and thereby leading to the identification of deregulated processes and pathways which could give an insight of the underlying molecular mechanisms of MS...
April 4, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29618590/wingless-signaling-a-genetic-journey-from-morphogenesis-to-metastasis
#13
Amy Bejsovec
This FlyBook chapter summarizes the history and the current state of our understanding of the Wingless signaling pathway. Wingless, the fly homolog of the mammalian Wnt oncoproteins, plays a central role in pattern generation during development. Much of what we know about the pathway was learned from genetic and molecular experiments in Drosophila melanogaster , and the core pathway works the same way in vertebrates. Like most growth factor pathways, extracellular Wingless/Wnt binds to a cell surface complex to transduce signal across the plasma membrane, triggering a series of intracellular events that lead to transcriptional changes in the nucleus...
April 2018: Genetics
https://www.readbyqxmd.com/read/29615562/moving-the-shh-source-over-time-what-impact-on-neural-cell-diversification-in-the-developing-spinal-cord
#14
REVIEW
Cathy Danesin, Cathy Soula
A substantial amount of data has highlighted the crucial influence of Shh signalling on the generation of diverse classes of neurons and glial cells throughout the developing central nervous system. A critical step leading to this diversity is the establishment of distinct neural progenitor cell domains during the process of pattern formation. The forming spinal cord, in particular, has served as an excellent model to unravel how progenitor cells respond to Shh to produce the appropriate pattern. In recent years, considerable advances have been made in our understanding of important parameters that control the temporal and spatial interpretation of the morphogen signal at the level of Shh-receiving progenitor cells...
April 12, 2017: Journal of Developmental Biology
https://www.readbyqxmd.com/read/29595306/sensory-substitution-using-a-vibrotactile-device-to-orient-and-walk-to-targets
#15
Lorena Lobo, David Travieso, David M Jacobs, Matthew Rodger, Cathy M Craig
This study investigates how active exploration helps users of sensory substitution devices (SSDs) to detect action-relevant information. A vibrotactile SSD was developed that generates stimulation that is contingent on the users' movements. Target direction was specified by the location of the vibratory stimulation, and target distance by the size and intensity of the pattern of stimulation. A series of experiments was performed with blindfolded participants. In Experiments 1a to 1c, participants used the SSD to align their central body axis with prespecified targets...
March 2018: Journal of Experimental Psychology. Applied
https://www.readbyqxmd.com/read/29593729/genomic-effects-of-the-vitamin-d-receptor-potentially-the-link-between-vitamin-d-immune-cells-and-multiple-sclerosis
#16
REVIEW
Ming Lu, Bruce V Taylor, Heinrich Körner
Vitamin D has a plethora of functions that are important for the maintenance of general health and in particular, the functional integrity of the immune system, such as promoting an anti-inflammatory cytokine profile and reducing the Treg/Th17 ratio. Multiple sclerosis (MS) is a chronic, inflammatory, and neurodegenerative central nervous system (CNS) disorder of probable autoimmune origin. MS is characterized by recurring or progressive demyelination and degeneration of the CNS due in part to a misguided immune response to as yet undefined (CNS) antigens, potentially including myelin basic protein and proteolipid protein...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29589906/long-range-capture-and-delivery-of-water-dispersed-nano-objects-by-microbubbles-generated-on-3d-plasmonic-surfaces
#17
Francesco Tantussi, Gabriele C Messina, Rosario Capozza, Michele Dipalo, Laura Lovato, Francesco De Angelis
The possibility of investigating small amounts of molecules, moieties or nano-objects dispersed in solution constitutes a central step for various application areas in which high sensitivity is necessary. Here, we show that the rapid expansion of a water bubble can act as a fast-moving net for molecules or nano-objects, collecting the floating objects in the surrounding medium in a range up to 100 µm. Thanks to an engineered 3D patterning of the substrate, the collapse of the bubble could be guided toward a designed area of the surface with micrometric precision...
March 28, 2018: ACS Nano
https://www.readbyqxmd.com/read/29589252/the-role-of-phase-shifts-of-sensory-inputs-in-walking-revealed-by-means-of-phase-reduction
#18
Azamat Yeldesbay, Tibor Tóth, Silvia Daun
Detailed neural network models of animal locomotion are important means to understand the underlying mechanisms that control the coordinated movement of individual limbs. Daun-Gruhn and Tóth, Journal of Computational Neuroscience 31(2), 43-60 (2011) constructed an inter-segmental network model of stick insect locomotion consisting of three interconnected central pattern generators (CPGs) that are associated with the protraction-retraction movements of the front, middle and hind leg. This model could reproduce the basic locomotion coordination patterns, such as tri- and tetrapod, and the transitions between them...
March 27, 2018: Journal of Computational Neuroscience
https://www.readbyqxmd.com/read/29587626/diversity-and-distribution-of-wolbachia-in-relation-to-geography-host-plant-affiliation-and-life-cycle-of-a-heterogonic-gall-wasp
#19
Hannes Schuler, Scott P Egan, Glen R Hood, Robert W Busbee, Amanda L Driscoe, James R Ott
BACKGROUND: The maternally inherited endosymbiont Wolbachia is widespread in arthropods and nematodes and can play an important role in the ecology and evolution of its host through reproductive manipulation. Here, we survey Wolbachia in Belonocnema treatae, a widely distributed North American cynipid gall forming wasp that exhibits regional host specialization on three species of oaks and alternation of sexually and asexually reproducing generations. We investigated whether patterns of Wolbachia infection and diversity in B...
March 27, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29579953/effects-of-the-gastric-juice-injection-pattern-and-contraction-frequency-on-the-digestibility-of-casein-powder-suspensions-in-an-in-vitro-dynamic-rat-stomach-made-with-a-3d-printed-model
#20
Xiaoai Zhang, Zhenkai Liao, Peng Wu, Liding Chen, Xiao Dong Chen
Previously, we have prepared a version of the dynamic in vitro rat stomach system (DIVRS-II or Biomimic Rat II). It was constructed and tested by showing similar digestive behaviors with those occurred in vivo. In the present work, a 3D-printed plastic mold was employed to create highly repeatable silicone rat stomach model. It has been seen to have shortened the time to handcraft a model like that used in DIVRS-II. The maximum mechanical force of the current stomach model generated by rolling extrusion is found to be more stable probably due to the more uniform wall thickness of the new model...
April 2018: Food Research International
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