NEATH II: N2_2H+^+ as a tracer of imminent star formation in quiescent high-density gas

Star formation activity in molecular clouds is often found to be correlated with the amount of material above a column density threshold of $\sim 10^{22} \, {\rm cm^{-2}}$. Attempts to connect this column density threshold to a ${\it volume}$ density above which star formation can occur are limited by the fact that the volume density of gas is difficult to reliably measure from observations. We post-process hydrodynamical simulations of molecular clouds with a time-dependent chemical network, and investigate the connection between commonly-observed molecular species and star formation activity. We find that many molecules widely assumed to specifically trace the dense, star-forming component of molecular clouds (e.g. HCN, HCO$^+$, CS) actually also exist in substantial quantities in material only transiently enhanced in density, which will eventually return to a more diffuse state without forming any stars. By contrast, N$_2$H$^+$ only exists in detectable quantities above a volume density of $10^4 \, {\rm cm^{-3}}$, the point at which CO, which reacts destructively with N$_2$H$^+$, begins to deplete out of the gas phase onto grain surfaces. This density threshold for detectable quantities of N$_2$H$^+$ corresponds very closely to the volume density at which gas becomes irreversibly gravitationally bound in the simulations: the material traced by N$_2$H$^+$ never reverts to lower densities, and quiescent regions of molecular clouds with visible N$_2$H$^+$ emission are destined to eventually form stars. The N$_2$H$^+$ line intensity is likely to directly correlate with the star formation rate averaged over timescales of around a Myr.Comment: 10 pages, 10 figures. MNRAS accepte

Non-Equilibrium Abundances Treated Holistically (NEATH): the molecular composition of star-forming clouds

Much of what we know about molecular clouds, and by extension star formation, comes from molecular line observations. Interpreting these correctly requires knowledge of the underlying molecular abundances. Simulations of molecular clouds typically only model species that are important for the gas thermodynamics, which tend to be poor tracers of the denser material where stars form. We construct a framework for post-processing these simulations with a full time-dependent chemical network, allowing us to model the behaviour of observationally-important species not present in the reduced network used for the thermodynamics. We use this to investigate the chemical evolution of molecular gas under realistic physical conditions. We find that molecules can be divided into those which reach peak abundances at moderate densities ($10^3 \, {\rm cm^{-3}}$) and decline sharply thereafter (such as CO and HCN), and those which peak at higher densities and then remain roughly constant (e.g. NH$_3$, N$_2$H$^+$). Evolving the chemistry with physical properties held constant at their final values results in a significant overestimation of gas-phase abundances for all molecules, and does not capture the drastic variations in abundance caused by different evolutionary histories. The dynamical evolution of molecular gas cannot be neglected when modelling its chemistry.Comment: 14 pages, 13 figures. MNRAS accepte

NEATH – II. N2H+ as a tracer of imminent star formation in quiescent high-density gas

Star formation activity in molecular clouds is often found to be correlated with the amount of material above a column density threshold of ∼1022cm−2 ⁠. Attempts to connect this column density threshold to a volume density above which star formation can occur are limited by the fact that the volume density of gas is difficult to reliably measure from observations. We post-process hydrodynamical simulations of molecular clouds with a time-dependent chemical network, and investigate the connection between commonly observed molecular species and star formation activity. We find that many molecules widely assumed to specifically trace the dense, star-forming component of molecular clouds (e.g. HCN, HCO+, CS) actually also exist in substantial quantities in material only transiently enhanced in density, which will eventually return to a more diffuse state without forming any stars. By contrast, N2H+ only exists in detectable quantities above a volume density of 104cm−3 ⁠, the point at which CO, which reacts destructively with N2H+, begins to deplete out of the gas phase on to grain surfaces. This density threshold for detectable quantities of N2H+ corresponds very closely to the volume density at which gas becomes irreversibly gravitationally bound in the simulations: the material traced by N2H+ never reverts to lower densities, and quiescent regions of molecular clouds with visible N2H+ emission are destined to eventually form stars. The N2H+ line intensity is likely to directly correlate with the star formation rate averaged over time-scales of around a Myr

NEATH III: A molecular line survey of a simulated star-forming cloud

We present synthetic line observations of a simulated molecular cloud, utilizing a self-consistent treatment of the dynamics and time-dependent chemical evolution. We investigate line emission from the three most common CO isotopologues (12CO, 13CO, C18O) and six supposed tracers of dense gas (NH3, HCN, N2H+, HCO+, CS, HNC). Our simulation produces a range of line intensities consistent with that observed in real molecular clouds. The HCN-to-CO intensity ratio is relatively invariant with column density, making HCN (and chemically similar species such as CS) a poor tracer of high-density material in the cloud. The ratio of N2H+ to HCN or CO, on the other hand, is highly selective of regions with densities above ⁠, and the N2H+ line is a very good tracer of the dynamics of high volume density (⁠ ⁠) material. Focusing on cores formed within the simulated cloud, we find good agreement with the line intensities of an observational sample of prestellar cores, including reproducing observed CS line intensities with an undepleted elemental abundance of sulphur. However, agreement between cores formed in the simulation, and models of isolated cores which have otherwise-comparable properties, is poor. The formation from and interaction with the large-scale environment has a significant impact on the line emission properties of the cores, making isolated models unsuitable for interpreting observational data

The selectivity, voltage-dependence and acid sensitivity of the tandem pore potassium channel TASK-1 : contributions of the pore domains

We have investigated the contribution to ionic selectivity of residues in the selectivity filter and pore helices of the P1 and P2 domains in the acid sensitive potassium channel TASK-1. We used site directed mutagenesis and electrophysiological studies, assisted by structural models built through computational methods. We have measured selectivity in channels expressed in Xenopus oocytes, using voltage clamp to measure shifts in reversal potential and current amplitudes when Rb+ or Na+ replaced extracellular K+. Both P1 and P2 contribute to selectivity, and most mutations, including mutation of residues in the triplets GYG and GFG in P1 and P2, made channels nonselective. We interpret the effects of these—and of other mutations—in terms of the way the pore is likely to be stabilised structurally. We show also that residues in the outer pore mouth contribute to selectivity in TASK-1. Mutations resulting in loss of selectivity (e.g. I94S, G95A) were associated with slowing of the response of channels to depolarisation. More important physiologically, pH sensitivity is also lost or altered by such mutations. Mutations that retained selectivity (e.g. I94L, I94V) also retained their response to acidification. It is likely that responses both to voltage and pH changes involve gating at the selectivity filter

MscS-like mechanosensitive channels in plants and microbes

The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. The latter of these two families, the MscS family, consists of members from bacteria, archaea, fungi, and plants. Genetic and electrophysiological analysis of these family members has provided insight into how organisms use mechanosensitive channels for osmotic regulation in response to changing environmental and developmental circumstances. Furthermore, determining the crystal structure of E. coli MscS and several homologues in several conformational states has contributed to our understanding of the gating mechanisms of these channels. Here we summarize our current knowledge of MscS homologues from all three domains of life and address their structure, proposed physiological functions, electrophysiological behaviors, and topological diversity

Identification of Intracellular and Plasma Membrane Calcium Channel Homologues in Pathogenic Parasites

Ca2+ channels regulate many crucial processes within cells and their abnormal activity can be damaging to cell survival, suggesting that they might represent attractive therapeutic targets in pathogenic organisms. Parasitic diseases such as malaria, leishmaniasis, trypanosomiasis and schistosomiasis are responsible for millions of deaths each year worldwide. The genomes of many pathogenic parasites have recently been sequenced, opening the way for rational design of targeted therapies. We analyzed genomes of pathogenic protozoan parasites as well as the genome of Schistosoma mansoni, and show the existence within them of genes encoding homologues of mammalian intracellular Ca2+ release channels: inositol 1,4,5-trisphosphate receptors (IP3Rs), ryanodine receptors (RyRs), two-pore Ca2+ channels (TPCs) and intracellular transient receptor potential (Trp) channels. The genomes of Trypanosoma, Leishmania and S. mansoni parasites encode IP3R/RyR and Trp channel homologues, and that of S. mansoni additionally encodes a TPC homologue. In contrast, apicomplexan parasites lack genes encoding IP3R/RyR homologues and possess only genes encoding TPC and Trp channel homologues (Toxoplasma gondii) or Trp channel homologues alone. The genomes of parasites also encode homologues of mammalian Ca2+ influx channels, including voltage-gated Ca2+ channels and plasma membrane Trp channels. The genome of S. mansoni also encodes Orai Ca2+ channel and STIM Ca2+ sensor homologues, suggesting that store-operated Ca2+ entry may occur in this parasite. Many anti-parasitic agents alter parasite Ca2+ homeostasis and some are known modulators of mammalian Ca2+ channels, suggesting that parasite Ca2+ channel homologues might be the targets of some current anti-parasitic drugs. Differences between human and parasite Ca2+ channels suggest that pathogen-specific targeting of these channels may be an attractive therapeutic prospect

Preparing for low surface brightness science with the Vera C. Rubin Observatory:Characterization of tidal features from mock images

Tidal features in the outskirts of galaxies yield unique information about their past interactions and are a key prediction of the hierarchical structure formation paradigm. The Vera C. Rubin Observatory is poised to deliver deep observations for potentially millions of objects with visible tidal features, but the inference of galaxy interaction histories from such features is not straightforward. Utilizing automated techniques and human visual classification in conjunction with realistic mock images produced using the NewHorizon cosmological simulation, we investigate the nature, frequency, and visibility of tidal features and debris across a range of environments and stellar masses. In our simulated sample, around 80 per cent of the flux in the tidal features around Milky Way or greater mass galaxies is detected at the 10-yr depth of the Legacy Survey of Space and Time (30-31 mag arcsec-2), falling to 60 per cent assuming a shallower final depth of 29.5 mag arcsec-2. The fraction of total flux found in tidal features increases towards higher masses, rising to 10 per cent for the most massive objects in our sample (M* ∼1011.5 M⊙). When observed at sufficient depth, such objects frequently exhibit many distinct tidal features with complex shapes. The interpretation and characterization of such features varies significantly with image depth and object orientation, introducing significant biases in their classification. Assuming the data reduction pipeline is properly optimized, we expect the Rubin Observatory to be capable of recovering much of the flux found in the outskirts of Milky Way mass galaxies, even at intermediate redshifts (z < 0.2)

Preparing for low surface brightness science with the Vera C. Rubin Observatory: characterisation of tidal features from mock images

Tidal features in the outskirts of galaxies yield unique information about their past interactions and are a key prediction of the hierarchical structure formation paradigm. The Vera C. Rubin Observatory is poised to deliver deep observations for potentially of millions of objects with visible tidal features, but the inference of galaxy interaction histories from such features is not straightforward. Utilising automated techniques and human visual classification in conjunction with realistic mock images produced using the NEWHORIZON cosmological simulation, we investigate the nature, frequency and visibility of tidal features and debris across a range of environments and stellar masses. In our simulated sample, around 80 per cent of the flux in the tidal features around Milky Way or greater mass galaxies is detected at the 10-year depth of the Legacy Survey of Space and Time (30-31 mag / sq. arcsec), falling to 60 per cent assuming a shallower final depth of 29.5 mag / sq. arcsec. The fraction of total flux found in tidal features increases towards higher masses, rising to 10 per cent for the most massive objects in our sample (M*~10^{11.5} Msun). When observed at sufficient depth, such objects frequently exhibit many distinct tidal features with complex shapes. The interpretation and characterisation of such features varies significantly with image depth and object orientation, introducing significant biases in their classification. Assuming the data reduction pipeline is properly optimised, we expect the Rubin Observatory to be capable of recovering much of the flux found in the outskirts of Milky Way mass galaxies, even at intermediate redshifts (z<0.2)

Clustering of InsP3 receptors by InsP3 retunes their regulation by InsP3 and Ca2+.

The versatility of Ca2+ signals derives from their spatio-temporal organization. For Ca2+ signals initiated by inositol-1,4,5-trisphosphate (InsP3), this requires local interactions between InsP3 receptors (InsP3Rs) mediated by their rapid stimulation and slower inhibition\ by cytosolic Ca2+. This allows hierarchical recruitment of Ca2+ release events as the InsP3 concentration increases. Single InsP3Rs respond first, then clustered InsP3Rs open together giving a local 'Ca2+ puff', and as puffs become more frequent they ignite regenerative Ca2+ waves. Using nuclear patch-clamp recording, here we demonstrate that InsP3Rs are initially randomly distributed with an estimated separation of 1 m. Low concentrations of InsP3 cause InsP3Rs to aggregate rapidly and reversibly into small clusters of about four closely associated InsP3Rs. At resting cytosolic [Ca2+], clustered InsP3Rs open independently, but with lower open probability, shorter open time, and less InsP3 sensitivity than lone InsP3Rs. Increasing cytosolic [Ca2+] reverses the inhibition caused by clustering, InsP3R gating becomes coupled, and the duration of multiple openings is prolonged. Clustering both exposes InsP3Rs to local Ca2+ rises and increases the effects of Ca2+. Dynamic regulation of clustering by InsP3 retunes InsP3R sensitivity to InsP3 and Ca2+, facilitating hierarchical recruitment of the elementary events that underlie all InsP3-evoked Ca2+ signals