Worthwhile goal, because with accurate genome reassembly, one can move beyond

Worthwhile goal, because with accurate genome Epigenetics reassembly, one can move beyond metagenomic gene inventories and conduct Autophagy comparative genomics of uncultivated viruses. There are other methods for more efficiently assembling viral genomes from complex assemblages, such as the use of large-insert clone libraries [42,43] or single-virus amplifications [44]. These methods are also fractionations, but rely on fractionation to the level of single genomes or virions. Bulk fractionation offers significant, complementary advantages. By fractionating populations of intact viruses en masse, it is possible to enrich for even rare populations of interest by screening with specific primers at each stage of the separation. Further, by narrowing the target populations while maintaining sufficient numbers of intact virions, it also becomes possible to more clearly link viral genomes with proteomes and with the physical properties of the virions (buoyant density, surface charge, morphology). Thus, we propose that an effective way to advance our understanding of uncultivated viralpopulations will be to combine the advantages of bulk fractionation with other methods that allow the assembly of discrete genomes. Initial bulk physical fractionation of a community will allow targeted separation and phenotypic characterization of populations, and subsequent single-virus genomics (whether by amplification, large-insert cloning, or direct sequencing) performed on a portion of the fractionated populations will allow accurate genome assemblies of the phenotypically characterized populations.AcknowledgmentsWe thank J. Cesar Ignacio-Espinoza for construction of the phylogenetic tree and Tina Carvalho of the University of Hawaii Biological Electron Microscope Facility for her assistance with TEM.Author ContributionsConceived and designed the experiments: JRB AIC GFS. Performed the experiments: JRB. Analyzed the data: JRB GFS. Contributed reagents/ materials/analysis tools: AIC GFS. Wrote the paper: JRB GFS.Assembly of a Viral Metagenome after Fractionation
Obesity increases the risk of a number of health conditions including cardiovascular disease, type 2 diabetes, and several cancers [1]. While obesity results from prolonged positive energy balance (i.e. energy intake exceeding energy expenditure), the cause of excessive positive energy balance in obesity has not been clearly defined. Key regulatory components reside in the hypothalamus (for reviews see [2?]). Amongst hypothalamic nuclei, the dorsomedial nucleus of the hypothalamus (DMH) is a critical structure for the regulation of a wide range of physiological processes, ranging from reproduction, thermogenesis, stress response, food intake, and circadian rhythms ([5?] and for reviews see [9?1]). Recent studies have demonstrated the existence of various neurotransmitters and signaling proteins that affect and/or are affected with altered food intake in the DMH. These include leptin-responsive GABAergic neurons [8,12], brain-derived neurotrophic factor (BDNF) [13], neuropeptide Y (NPY) [5], endocannabinoids, and nitric oxide (NO) [14]. Leptin receptorexpressing neurons in the DMH contribute to the regulation ofsympathetic brown adipose tissue outputs, implying that these neurons represent a subset of thermoregulatory circuits [8]. Deletion of BDNF or NPY in the DMH induces opposing effects on food intake [5,13]. Endocannabinoids and NO that are coreleased from DMH neurons differentially regulate GABAergic inhibitory ton.Worthwhile goal, because with accurate genome reassembly, one can move beyond metagenomic gene inventories and conduct comparative genomics of uncultivated viruses. There are other methods for more efficiently assembling viral genomes from complex assemblages, such as the use of large-insert clone libraries [42,43] or single-virus amplifications [44]. These methods are also fractionations, but rely on fractionation to the level of single genomes or virions. Bulk fractionation offers significant, complementary advantages. By fractionating populations of intact viruses en masse, it is possible to enrich for even rare populations of interest by screening with specific primers at each stage of the separation. Further, by narrowing the target populations while maintaining sufficient numbers of intact virions, it also becomes possible to more clearly link viral genomes with proteomes and with the physical properties of the virions (buoyant density, surface charge, morphology). Thus, we propose that an effective way to advance our understanding of uncultivated viralpopulations will be to combine the advantages of bulk fractionation with other methods that allow the assembly of discrete genomes. Initial bulk physical fractionation of a community will allow targeted separation and phenotypic characterization of populations, and subsequent single-virus genomics (whether by amplification, large-insert cloning, or direct sequencing) performed on a portion of the fractionated populations will allow accurate genome assemblies of the phenotypically characterized populations.AcknowledgmentsWe thank J. Cesar Ignacio-Espinoza for construction of the phylogenetic tree and Tina Carvalho of the University of Hawaii Biological Electron Microscope Facility for her assistance with TEM.Author ContributionsConceived and designed the experiments: JRB AIC GFS. Performed the experiments: JRB. Analyzed the data: JRB GFS. Contributed reagents/ materials/analysis tools: AIC GFS. Wrote the paper: JRB GFS.Assembly of a Viral Metagenome after Fractionation
Obesity increases the risk of a number of health conditions including cardiovascular disease, type 2 diabetes, and several cancers [1]. While obesity results from prolonged positive energy balance (i.e. energy intake exceeding energy expenditure), the cause of excessive positive energy balance in obesity has not been clearly defined. Key regulatory components reside in the hypothalamus (for reviews see [2?]). Amongst hypothalamic nuclei, the dorsomedial nucleus of the hypothalamus (DMH) is a critical structure for the regulation of a wide range of physiological processes, ranging from reproduction, thermogenesis, stress response, food intake, and circadian rhythms ([5?] and for reviews see [9?1]). Recent studies have demonstrated the existence of various neurotransmitters and signaling proteins that affect and/or are affected with altered food intake in the DMH. These include leptin-responsive GABAergic neurons [8,12], brain-derived neurotrophic factor (BDNF) [13], neuropeptide Y (NPY) [5], endocannabinoids, and nitric oxide (NO) [14]. Leptin receptorexpressing neurons in the DMH contribute to the regulation ofsympathetic brown adipose tissue outputs, implying that these neurons represent a subset of thermoregulatory circuits [8]. Deletion of BDNF or NPY in the DMH induces opposing effects on food intake [5,13]. Endocannabinoids and NO that are coreleased from DMH neurons differentially regulate GABAergic inhibitory ton.