HOW AGN JETS HEAT the INTRACLUSTER MEDIUM - INSIGHTS from HYDRODYNAMIC SIMULATIONS

© 2016. The American Astronomical Society. All rights reserved. Feedback from active galactic nuclei (AGNs) is believed to prevent catastrophic cooling in galaxy clusters. However, how the feedback energy is transformed into heat, and how the AGN jets heat the intracluster medium (ICM) isotropically, still remain elusive. In this work, we gain insights into the relative importance of different heating mechanisms using three-dimensional hydrodynamic simulations including cold gas accretion and momentum-driven jet feedback, which are the most successful models to date in terms of reproducing the properties of cool cores. We find that there is net heating within two "jet cones" (within ∼30° from the axis of jet precession) where the ICM gains entropy by shock heating and mixing with the hot thermal gas within bubbles. Outside the jet cones, the ambient gas is heated by weak shocks, but not enough to overcome radiative cooling, therefore, forming a "reduced" cooling flow. Consequently, the cluster core is in a process of "gentle circulation" over billions of years. Within the jet cones, there is significant adiabatic cooling as the gas is uplifted by buoyantly rising bubbles; outside the cones, energy is supplied by the inflow of already-heated gas from the jet cones as well as adiabatic compression as the gas moves toward the center. In other words, the fluid dynamics self-adjusts such that it compensates and transports the heat provided by the AGN, and hence no fine-tuning of the heating profile of any process is necessary. Throughout the cluster evolution, turbulent energy is only at the percent level compared to gas thermal energy, and thus turbulent heating is not the main source of heating in our simulation

In Situ Monitoring of Intracellular Glucose and Glutamine in CHO Cell Culture

The development of processes to produce biopharmaceuticals industrially is still largely empirical and relies on optimizing both medium formulation and cell line in a product-specific manner. Current small-scale (well plate-based) process development methods cannot provide sufficient sample volume for analysis, to obtain information on nutrient utilization which can be problematic when processes are scaled to industrial fermenters. We envision a platform where essential metabolites can be monitored non-invasively and in real time in an ultra-low volume assay in order to provide additional information on cellular metabolism in high throughput screens. Towards this end, we have developed a model system of Chinese Hamster Ovary cells stably expressing protein-based biosensors for glucose and glutamine. Herein, we demonstrate that these can accurately reflect changing intracellular metabolite concentrations in vivo during batch and fed-batch culture of CHO cells. The ability to monitor intracellular depletion of essential nutrients in high throughput will allow rapid development of improved bioprocesses

Regulation of Inflammatory Gene Expression in PBMCs by Immunostimulatory Botanicals

Many hundreds of botanicals are used in complementary and alternative medicine for therapeutic use as antimicrobials and immune stimulators. While there exists many centuries of anecdotal evidence and few clinical studies on the activity and efficacy of these botanicals, limited scientific evidence exists on the ability of these botanicals to modulate the immune and inflammatory responses. Using botanogenomics (or herbogenomics), this study provides novel insight into inflammatory genes which are induced in peripheral blood mononuclear cells following treatment with immunomodulatory botanical extracts. These results may suggest putative genes involved in the physiological responses thought to occur following administration of these botanical extracts. Using extracts from immunostimulatory herbs (Astragalus membranaceus, Sambucus cerulea, Andrographis paniculata) and an immunosuppressive herb (Urtica dioica), the data presented supports previous cytokine studies on these herbs as well as identifying additional genes which may be involved in immune cell activation and migration and various inflammatory responses, including wound healing, angiogenesis, and blood pressure modulation. Additionally, we report the presence of lipopolysaccharide in medicinally prepared extracts of these herbs which is theorized to be a natural and active component of the immunostimulatory herbal extracts. The data presented provides a more extensive picture on how these herbs may be mediating their biological effects on the immune and inflammatory responses

HOW AGN JETS HEAT the INTRACLUSTER MEDIUM - INSIGHTS from HYDRODYNAMIC SIMULATIONS

© 2016. The American Astronomical Society. All rights reserved. Feedback from active galactic nuclei (AGNs) is believed to prevent catastrophic cooling in galaxy clusters. However, how the feedback energy is transformed into heat, and how the AGN jets heat the intracluster medium (ICM) isotropically, still remain elusive. In this work, we gain insights into the relative importance of different heating mechanisms using three-dimensional hydrodynamic simulations including cold gas accretion and momentum-driven jet feedback, which are the most successful models to date in terms of reproducing the properties of cool cores. We find that there is net heating within two "jet cones" (within ∼30° from the axis of jet precession) where the ICM gains entropy by shock heating and mixing with the hot thermal gas within bubbles. Outside the jet cones, the ambient gas is heated by weak shocks, but not enough to overcome radiative cooling, therefore, forming a "reduced" cooling flow. Consequently, the cluster core is in a process of "gentle circulation" over billions of years. Within the jet cones, there is significant adiabatic cooling as the gas is uplifted by buoyantly rising bubbles; outside the cones, energy is supplied by the inflow of already-heated gas from the jet cones as well as adiabatic compression as the gas moves toward the center. In other words, the fluid dynamics self-adjusts such that it compensates and transports the heat provided by the AGN, and hence no fine-tuning of the heating profile of any process is necessary. Throughout the cluster evolution, turbulent energy is only at the percent level compared to gas thermal energy, and thus turbulent heating is not the main source of heating in our simulation

The spindle assembly function of Caenorhabditis elegans katanin does not require microtubule-severing activity

We show that katanin protein, but not katanin's microtubule-severing activity, is required for assembly of acentriolar meiotic spindle poles

Towards a reference genome that captures global genetic diversity.

The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity

Towards a reference genome that captures global genetic diversity.

The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity

Dynactin-dependent cortical dynein and spherical spindle shape correlate temporally with meiotic spindle rotation in Caenorhabditis elegans

Oocyte meiotic spindles orient with one pole juxtaposed to the cortex to facilitate extrusion of chromosomes into polar bodies. In Caenorhabditis elegans, these acentriolar spindles initially orient parallel to the cortex and then rotate to the perpendicular orientation. To understand the mechanism of spindle rotation, we characterized events that correlated temporally with rotation, including shortening of the spindle in the pole-to pole axis, which resulted in a nearly spherical spindle at rotation. By analyzing large spindles of polyploid C. elegans and a related nematode species, we found that spindle rotation initiated at a defined spherical shape rather than at a defined spindle length. In addition, dynein accumulated on the cortex just before rotation, and microtubules grew from the spindle with plus ends outward during rotation. Dynactin depletion prevented accumulation of dynein on the cortex and prevented spindle rotation independently of effects on spindle shape. These results support a cortical pulling model in which spindle shape might facilitate rotation because a sphere can rotate without deforming the adjacent elastic cytoplasm. We also present evidence that activation of spindle rotation is promoted by dephosphorylation of the basic domain of p150 dynactin

A novel chromosome segregation mechanism during female meiosis

In a wide range of eukaryotes, chromosome segregation occurs through anaphase A, in which chromosomes move toward stationary spindle poles, anaphase B, in which chromosomes move at the same velocity as outwardly moving spindle poles, or both. In contrast, Caenorhabditis elegans female meiotic spindles initially shorten in the pole-to-pole axis such that spindle poles contact the outer kinetochore before the start of anaphase chromosome separation. Once the spindle pole-to-kinetochore contact has been made, the homologues of a 4-μm-long bivalent begin to separate. The spindle shortens an additional 0.5 μm until the chromosomes are embedded in the spindle poles. Chromosomes then separate at the same velocity as the spindle poles in an anaphase B–like movement. We conclude that the majority of meiotic chromosome movement is caused by shortening of the spindle to bring poles in contact with the chromosomes, followed by separation of chromosome-bound poles by outward sliding