fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, allowing us to build on recent advances in optimization theory to develop fast inference tools. In addition, we propose useful heuristic scores to identify the number of populations represented in a data set and a new hierarchical prior to detect weak population structure in the data. We test the variational algorithms on simulated data and illustrate using genotype data from the CEPH–Human Genome Diversity Panel. The variational algorithms are almost two orders of magnitude faster than STRUCTURE and achieve accuracies comparable to those of ADMIXTURE. Furthermore, our results show that the heuristic scores for choosing model complexity provide a reasonable range of values for the number of populations represented in the data, with minimal bias toward detecting structure when it is very weak. Our algorithm, fastSTRUCTURE, is freely available online at http://pritchardlab.stanford.edu/structure.html.     

Extremely high alkaline protease from a deep-subsurface bacterium, Alkaliphilus transvaalensis

A new high-alkaline protease (ALTP) was purified to homogeneity from a culture of the strictly anaerobic and extremely alkaliphilic Alkaliphilus transvaalensis. The molecular mass was 30 kDa on sodium dodecyl sulfate–polyacrylamide gel electrophoresis. The enzyme showed the maximal caseinolytic activity higher than pH 12.6 in KCl–NaOH buffer at 40°C. Hydrolysis of the oxidized insulin B-chain followed by mass spectrometric analysis of the cleaved products revealed that as many as 24 of the total 29 peptide bonds are hydrolyzed in a block-cutting manner, suggesting that ALTP has a widespread proteolytic functions. Calcium ion had no effect on the activity and stability of ALTP, unlike known subtilisins. The deduced amino acid sequence of the enzyme comprised 279 amino acids plus 97 prepropeptide amino acids. The amino acid sequence of mature ALTP was confirmed by capillary liquid chromatography coupled to tandem mass spectrometry, which was the 93% coverage of the deduced amino acid sequence. The mature enzyme showed moderate homology to subtilisin LD1 from the alkaliphilic Bacillus sp. strain KSM-LD1 with 64% identity, and both enzymes formed a new subcluster at an intermediate position among true subtilisins and high-alkaline proteases in a phylogenetic tree of subtilase family A. ALTP is the first high-alkaline protease reported from a strict anaerobe in this family.     

On the ecology of <Emphasis Type="Italic">Caecidotea williamsi</Emphasis> Escobar-Briones &; Alcocer (Crustacea: Isopoda: Asellidae) from Alchichica saline lake,Central Mexico

Caecidotea williamsi Escobar-Briones & Alcocer (2002) is the first asellid described from a saline aquatic habitat in America, Alchichica crater-lake, Puebla, Central Mexico. No previous reports exist for asellid isopods from inland saline waters in America in spite of the extensive research undertaken so far on the continent. Differing from other asellids, C. williamsi inhabits saline waters (i.e. 8.5 g l⁻¹) dominated by sodium, magnesium, chloride, and bicarbonate ions and markedly alkaline (pH 9.0 ± 0.1). Water temperature ranges from 14.5°C throughout the water column in winter and in the deep waters for the rest of the year, up to 20°C in the surface waters in summer. C. williamsi occurs in a depth range of surface to 30 m (lake’s maximum depth is 64 m), below which an anoxic layer is found during 9 months of the year. Generally it lives cryptically in tufa crevices and at shallower depths many inhabit empty trichopteran cases embedded within the tufa crevices. Some specimens are heavily covered by epizooic ciliates on the thoracic and abdominal segments of the exoskeleton and the pleopods. Data are presented on the diet, possible predators, saprobity and trophism, and regional distribution of C. williamsi. The continued survival of this unique isopod is threatened by anthropogenic desiccation of its habitat. Guest Editor: John M. Melack Saline Water and their Biota     

Seasonal nutrient and plankton dynamics in a physical-biological model of Crater Lake

A coupled 1D physical-biological model of Crater Lake is presented. The model simulates the seasonal evolution of two functional phytoplankton groups, total chlorophyll, and zooplankton in good quantitative agreement with observations from a 10-year monitoring study. During the stratified period in summer and early fall the model displays a marked vertical structure: the phytoplankton biomass of the functional group 1, which represents diatoms and dinoflagellates, has its highest concentration in the upper 40 m; the phytoplankton biomass of group 2, which represents chlorophyta, chrysophyta, cryptomonads and cyanobacteria, has its highest concentrations between 50 and 80 m, and phytoplankton chlorophyll has its maximum at 120 m depth. A similar vertical structure is a reoccurring feature in the available data. In the model the key process allowing a vertical separation between biomass and chlorophyll is photoacclimation. Vertical light attenuation (i.e., water clarity) and the physiological ability of phytoplankton to increase their cellular chlorophyll-to-biomass ratio are ultimately determining the location of the chlorophyll maximum. The location of the particle maxima on the other hand is determined by the balance between growth and losses and occurs where growth and losses equal. The vertical particle flux simulated by our model agrees well with flux measurements from a sediment trap. This motivated us to revisit a previously published study by Dymond et al. (1996). Dymond et al. used a box model to estimate the vertical particle flux and found a discrepancy by a factor 2.5–10 between their model-derived flux and measured fluxes from a sediment trap. Their box model neglected the exchange flux of dissolved and suspended organic matter, which, as our model and available data suggests is significant for the vertical exchange of nitrogen. Adjustment of Dymond et al.’s assumptions to account for dissolved and suspended nitrogen yields a flux estimate that is consistent with sediment trap measurements and our model.     

Optimal deep brain stimulation of the subthalamic nucleus—a computational study

Deep brain stimulation (DBS) of the subthalamic nucleus, typically with periodic, high frequency pulse trains, has proven to be an effective treatment for the motor symptoms of Parkinson’s disease (PD). Here, we use a biophysically-based model of spiking cells in the basal ganglia (Terman et al., Journal of Neuroscience, 22, 2963–2976, 2002; Rubin and Terman, Journal of Computational Neuroscience, 16, 211–235, 2004) to provide computational evidence that alternative temporal patterns of DBS inputs might be equally effective as the standard high-frequency waveforms, but require lower amplitudes. Within this model, DBS performance is assessed in two ways. First, we determine the extent to which DBS causes Gpi (globus pallidus pars interna) synaptic outputs, which are burstlike and synchronized in the unstimulated Parkinsonian state, to cease their pathological modulation of simulated thalamocortical cells. Second, we evaluate how DBS affects the GPi cells’ auto- and cross-correlograms. In both cases, a nonlinear closed-loop learning algorithm identifies effective DBS inputs that are optimized to have minimal strength. The network dynamics that result differ from the regular, entrained firing which some previous studies have associated with conventional high-frequency DBS. This type of optimized solution is also found with heterogeneity in both the intrinsic network dynamics and the strength of DBS inputs received at various cells. Such alternative DBS inputs could potentially be identified, guided by the model-free learning algorithm, in experimental or eventual clinical settings. Action Editor: Steven J. Schiff Xiao-Jiang Feng and Eric Shea-Brown contributed equally to this work.     

A new phylogenetic test for comparing multiple high‐dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae)

The interplay between evolutionary rates and modularity influences the evolution of organismal body plans by both promoting and constraining the magnitude and direction of trait response to ecological conditions. However, few studies have examined whether the best‐fit hypothesis of modularity is the same as the shape subset with the greatest difference in evolutionary rate. Here, we develop a new phylogenetic comparative method for comparing evolutionary rates among high‐dimensional traits, and apply this method to analyze body shape evolution in bioluminescent lanternfishes. We frame the study of evolutionary rates and modularity through analysis of three hypotheses derived from the literature on fish development, biomechanics, and bioluminescent communication. We show that a development‐informed partitioning of shape exhibits the greatest evolutionary rate differences among modules, but that a hydrodynamically informed partitioning is the best‐fit modularity hypothesis. Furthermore, we show that bioluminescent lateral photophores evolve at a similar rate as, and are strongly integrated with, body shape in lanternfishes. These results suggest that overlapping life‐history constraints on development and movement define axes of body shape evolution in lanternfishes, and that the positions of their lateral photophore complexes are likely a passive outcome of the interaction of these ecological pressures.     

Anesthetic management in atrial fibrillation ablation procedure: Adding non-invasive ventilation to deep sedation

Anesthetic management of patients undergoing pulmonary vein isolation for atrial fibrillation has specific requirements. The feasibility of non-invasive ventilation (NIV) added to deep sedation procedure was evaluated.Seventy-two patients who underwent ablation procedure were retrospectively revised, performed with (57%) or without (43%) application of NIV (Respironic^® latex-free total face mask connected to Garbin ventilator-Linde Inc.) during deep sedation (Midazolam 0.01–0.02 mg/kg, fentanyl 2.5–5 μg/kg and propofol: bolus dose 1–1.5 mg/kg, maintenance 2–4 mg/kg/h).In the two groups (NIV vs deep sedation), differences were detected in intraprocedural (pH 7.37 ± 0.05 vs 7.32 ± 0.05, p = 0.001; PaO₂ 117.10 ± 27.25 vs 148.17 ± 45.29, p = 0.004; PaCO₂ 43.37 ± 6.91 vs 49.33 ± 7.34, p = 0.002) and in percentage variation with respect to basal values (pH −0.52 ± 0.83 vs −1.44 ± 0.87, p = 0.002; PaCO₂ 7.21 ± 15.55 vs 34.91 ± 25.76, p = 0.001) of arterial blood gas parameters. Two episodes of respiratory complications, treated with application of NIV, were reported in deep sedation procedure. Endotracheal intubation was not necessary in any case. Adverse events related to electrophysiological procedures and recurrence of atrial fibrillation were recorded, respectively, in 36% and 29% of cases.NIV proved to be feasible in this context and maintained better respiratory homeostasis and better arterial blood gas balance when added to deep sedation.     

Leaching potential and forms of phosphorus in deep row applied biosolids underlying hybrid poplar

Biosolids deep row incorporation (DRI) offers an alternative recycling approach for bioenergy crop production, but phosphorus additions in excess of the vegetation requirements can potentially impair water quality. The effects of DRI of anaerobically digested (AD) and lime-stabilized (LS) biosolids at four rates (213, 426 Mg ha⁻¹ for AD and 328, 656 Mg ha⁻¹ for LS) and a single rate of conventional P fertilizer on leaching of PO₄-P, and TKP were investigated in a hybrid poplar plantation in a coastal plain heavy mineral mine reclamation site. The effects of AD and LS biosolids aging on the transformations and losses of P applied with the biosolids were also studied. Zero tension lysimeters were installed at the site to collect leachate. Samples were collected at least monthly for 30 months between July 2006 and December 2008. We also analyzed biosolids P (labile P, Al-, Fe-bound-P, Ca-bound-P, total P, Mehlich 1 P) fractions. The loss of P was determined and P binding constituents were described via regression analysis. Orthophosphate and TKP from the DRI biosolids leached in negligible amounts, and were similar to leaching from conventional P fertilization. Most of the P was Al- and Fe-bound in the AD biosolids and Ca-bound in the LS biosolids. Labile P decreased with decrease in organic C, which indicated that P leaching potential from the DRI biosolids decreased with aging. Our results indicated that P mobility from biosolids of the type used should not pose a water quality risk.