Turing pattern or system heterogeneity? A numerical continuation approach to assessing the role of Turing instabilities in heterogeneous reaction-diffusion systems

Turing patterns in reaction-diffusion (RD) systems have classically been studied only in RD systems which do not explicitly depend on independent variables such as space. In practise, many systems for which Turing patterning is important are not homogeneous with ideal boundary conditions. In heterogeneous systems with stable steady states, the steady states are also necessarily heterogeneous which is problematic for applying the classical analysis. Whilst there has been some work done to extend Turing analysis to some heterogeneous systems, for many systems it is still difficult to determine if a stable patterned state is driven purely by system heterogeneity or if a Turing instability is playing a role. In this work, we try to define a framework which uses numerical continuation to map heterogeneous RD systems onto a sensible nearby homogeneous system. This framework may be used for discussing the role of Turing instabilities in establishing patterns in heterogeneous RD systems. We study the Schnakenberg and Gierer-Meinhardt models with spatially heterogeneous production as test problems. It is shown that for sufficiently large system heterogeneity (large amplitude spatial variations in morphogen production) it is possible that Turing-patterned and base states become coincident and therefore impossible to distinguish. Other exotic behaviour is also shown to be possible. We also study a novel scenario in which morphogen is produced locally at levels that could support Turing patterning but on intervals/patches which are on the scale of classical critical domain lengths. Without classical domain boundaries, Turing patterns are allowed to bleed through; an effect noted by other authors. In this case, this phenomena effectively changes the critical domain length. Indeed, we even note that this phenomena may also effectively couple local patches together and drive instability in this way.Comment: 10 figure

Analyzing and mapping fish assemblages off central California, USA

This study describes fish assemblages and their spatial patterns off the coast of California from Point Arena to Point Sal, by combining the results of the multivariate analyses of several fisheries datasets with a geographic information system. In order to provide comprehensive spatial coverage for the areas of inshore, continental shelf, and continental slope, three fisheries datasets were analyzed: 1) Inshore: the California Department of Fish and Game dataset of fishery-dependent commercial passenger fishing vessel trips that targeted rockfish; 2) Continental Shelf: the National Marine Fisheries Service (NMFS) fishery-independent bottom trawls; and 3) Continental Slope: the NMFS fishery-independent bottom trawls on the continental slope. One-hundred seven species were analyzed. These species represented those captured in at least 5% of the fishing trips or trawls in at least one of the three data sets. We analyzed each of the three datasets separately, and the three sets of results were combined to define 28 species assemblages and 23 site groups. A species assemblage consisted of species caught together, whereas a site group consisted of fishing trips or trawl locations that tended to have the same species assemblages. At the scale of these datasets, 97% of all site groups were significantly segregated by depth

Testing stellar population synthesis models with Sloan Digital Sky Survey colors of M31's globular clusters

Accurate stellar population synthesis models are vital in understanding the properties and formation histories of galaxies. In order to calibrate and test the reliability of these models, they are often compared with observations of star clusters. However, relatively little work has compared these models in the ugriz filters, despite the recent widespread use of this filter set. In this paper, we compare the integrated colors of globular clusters in the Sloan Digital Sky Survey (SDSS) with those predicted from commonly used simple stellar population (SSP) models. The colors are based on SDSS observations of M31's clusters and provide the largest population of star clusters with accurate photometry available from the survey. As such, it is a unique sample with which to compare SSP models with SDSS observations. From this work, we identify a significant offset between the SSP models and the clusters' g-r colors, with the models predicting colors which are too red by g-r\sim0.1. This finding is consistent with previous observations of luminous red galaxies in the SDSS, which show a similar discrepancy. The identification of this offset in globular clusters suggests that it is very unlikely to be due to a minority population of young stars. The recently updated SSP model of Maraston & Stromback better represents the observed g-r colors. This model is based on the empirical MILES stellar library, rather than theoretical libraries, suggesting an explanation for the g-r discrepancy.Comment: 8 pages, 4 figures, accepted for publication in Ap

Evaluation of an epigenetic assay for predicting repeat prostate biopsy outcome in African American men

OBJECTIVE: To evaluate an epigenetic assay performed on tissue from negative prostate biopsies in a group of African American (AA) men undergoing repeat biopsy, and to compare accuracy for predicting repeat biopsy outcome to prior studies conducted in predominantly Caucasian populations. MATERIALS AND METHODS: The study population consisted of 211 AA men from 7 urology centers across the United States; all of whom were undergoing 12-core transrectal ultrasound-guided repeat biopsy within 30 months from a negative index biopsy. All biopsy cores from the negative index biopsy were profiled for the epigenetic biomarkers GSTP1, APC, and RASSF1 using ConfirmMDx for Prostate Cancer (MDxHealth, Irvine, CA). RESULTS: Upon repeat biopsy, 130 of 211 subjects (62%) had no prostate cancer (PCa) detected and 81 of 211 (38%) were diagnosed with PCa. Of the subjects with PCa, 54 (67%) were diagnosed with Gleason score (GS) = 7 disease. For detection of PCa at repeat biopsy, ConfirmMDx sensitivity was 74.1% and specificity was 60.0%, equivalent to prior studies (P = .235 and .697, respectively). For detection of GS >= 7 PCa, sensitivity was 78% and specificity was 53%. The negative predictive values for detection of all PCa and GS >= 7 PCa were 78.8% and 94.2%, respectively. CONCLUSION: In this group of AA men, we successfully validated an epigenetic assay to assess the need for repeat biopsy. Results were consistent with previous studies from predominantly Caucasian populations. Therefore, the ConfirmMDx assay is a useful tool for risk stratification of AA men who had an initial negative biopsy

Prevention of wound complications following salvage laryngectomy using free vascularized tissue

Background. Total laryngectomy following radiation therapy or concurrent chemoradiation therapy is associated with unacceptably high complication rates because of wound healing difficulties. With an ever increasing reliance on organ preservation protocols as primary treatment for advanced laryngeal cancer, the surgeon must develop techniques to minimize postoperative complications in salvage laryngectomy surgery. We have developed an approach using free tissue transfer in an effort to improve tissue vascularity, reinforce the pharyngeal suture line, and minimize complications in this difficult patient population. The purpose of this study was to outline our technique and determine the effectiveness of this new approach. Methods. We conducted a retrospective review of a prospective cohort and compared it with a historical group (surgical patients of Radiation Therapy Oncology Group (RTOG)-91-11 trial). Eligibility criteria for this study included patients undergoing salvage total laryngectomy following failed attempts at organ preservation with either high-dose radiotherapy or concurrent chemo/radiation therapy regimen. Patients were excluded if the surgical defect required a skin paddle for pharyngeal closure. The prospective cohort consisted of 14 consecutive patients (10 males, 4 females; mean age, 58 years) who underwent free tissue reinforcement of the pharyngeal suture line following total laryngectomy. The historical comparison group consisted of 27 patients in the concomitant chemoradiotherapy arm of the RTOG-91-11 trial who met the same eligibility criteria (26 males, 1 female; mean age, 57 years) but did not undergo free tissue transfer or other form of suture line reinforcement. Minimum follow-up in both groups was 12 months. Results. The overall pharyngocutaneous fistula rate was similar between groups—4/14 (29%) in the flap group, compared with 8/27 (30%) in the RTOG-91-11 group. There were no major wound complications in the flap group, compared with 4 (4/27, 14.8%) in the RTOG-91-11 group. There were no major fistulas in the flap group, compared with 3/27 (11.1%) in the RTOG-91-11 group. The rate of pharyngeal stricture requiring dilation was 6/14 (42%) in the flap group, compared with 7/27 (25.9%) in the RTOG-91-11 group. In our patients, the rate of tracheoesophageal speech was 14/14 (100%), and complete oral intake was achieved in 13/14 (93%) patients. Voice-Related Quality of Life Measure (V-RQOL) and Performance Status Scale for Head and Neck Cancer Patients (PSS-HN) scores suggest that speech and swallowing functions are reasonable following free flap reinforcement. Conclusions. Free vascularized tissue reinforcement of primary pharyngeal closure in salvage laryngectomy following failed organ preservation is effective in preventing major wound complications but did not reduce the overall fistula rate. Fistulas that developed following this technique were relatively small, did not result in exposed major vessels, and were effectively treated with outpatient wound care rather than readmission to the hospital or return to operating room. Speech and swallowing results following this technique were comparable to those following total laryngectomy alone. © 2007 Wiley Periodicals, Inc. Head Neck 2007Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/56020/1/20492_ftp.pd

Potassium dependent structural changes in the selectivity filter of HERG potassium channels

The fine tuning of biological electrical signaling is mediated by variations in the rates of opening and closing of gates that control ion flux through different ion channels. Human ether-a-go-go related gene (HERG) potassium channels have uniquely rapid inactivation kinetics which are critical to the role they play in regulating cardiac electrical activity. Here, we exploit the K+ sensitivity of HERG inactivation to determine structures of both a conductive and non-conductive selectivity filter structure of HERG. The conductive state has a canonical cylindrical shaped selectivity filter. The non-conductive state is characterized by flipping of the selectivity filter valine backbone carbonyls to point away from the central axis. The side chain of S620 on the pore helix plays a central role in this process, by coordinating distinct sets of interactions in the conductive, non-conductive, and transition states. Our model represents a distinct mechanism by which ion channels fine tune their activity and could explain the uniquely rapid inactivation kinetics of HERG

The N–Terminal Tail of hERG Contains an Amphipathic α–Helix That Regulates Channel Deactivation

The cytoplasmic N–terminal domain of the human ether–a–go–go related gene (hERG) K+ channel is critical for the slow deactivation kinetics of the channel. However, the mechanism(s) by which the N–terminal domain regulates deactivation remains to be determined. Here we show that the solution NMR structure of the N–terminal 135 residues of hERG contains a previously described Per–Arnt–Sim (PAS) domain (residues 26–135) as well as an amphipathic α–helix (residues 13–23) and an initial unstructured segment (residues 2–9). Deletion of residues 2–25, only the unstructured segment (residues 2–9) or replacement of the α–helix with a flexible linker all result in enhanced rates of deactivation. Thus, both the initial flexible segment and the α–helix are required but neither is sufficient to confer slow deactivation kinetics. Alanine scanning mutagenesis identified R5 and G6 in the initial flexible segment as critical for slow deactivation. Alanine mutants in the helical region had less dramatic phenotypes. We propose that the PAS domain is bound close to the central core of the channel and that the N–terminal α–helix ensures that the flexible tail is correctly orientated for interaction with the activation gating machinery to stabilize the open state of the channel

Palaeontology, the biogeohistory of Victoria

The broad-scale distribution of fossils within Victoria is controlled by general global patterns in the biological evolution of life on Earth, the local development and environmental evolution of habitats, and the occurrence of geological processes conducive to the preservation of fossil floras and faunas. Early Palaeozoic fossils are mostly marine in origin because of the predominance of marine sedimentary rocks in Victoria and because life on land was not significant during most of this time interval. Middle Palaeozoic sequences have both terrestrial and marine fossil records. Within Victoria, marine rocks are only very minor components of strata deposited during the late Palaeozoic, so that few marine fossils are known from this time period. A similar situation existed during most of the Mesozoic except towards the end of this era when marine conditions began to prevail in the Bass Strait region. During long intervals in the Cainozoic, large areas of Victoria were flooded by shallow-marine seas, particularly in the southern basins of Bass Strait, as well as in the northwest of the State (Murray Basin). Cainozoic sediments contain an extraordinary range of animal and plant fossils. During the Quaternary, the landscape of Victoria became, and continues to be, dominated by continental environments including, at times, extensive freshwater lake systems. Fossil floras and faunas from sediments deposited in these lake systems and from other continental sediments, as well as from Quaternary sediments deposited in marginal marine environments, collectively record a history of rapid fluctuations in climate and sea level.<br /

Innate immunodeficiency following genetic ablation of Mcl1 in natural killer cells

The cytokine IL-15 is required for natural killer (NK) cell homeostasis; however, the intrinsic mechanism governing this requirement remains unexplored. Here we identify the absolute requirement for myeloid cell leukaemia sequence-1 (Mcl1) in the sustained survival of NK cells in vivo. Mcl1 is highly expressed in NK cells and regulated by IL-15 in a dose-dependent manner via STAT5 phosphorylation and subsequent binding to the 3'-UTR of Mcl1. Specific deletion of Mcl1 in NK cells results in the absolute loss of NK cells from all tissues owing to a failure to antagonize pro-apoptotic proteins in the outer mitochondrial membrane. This NK lymphopenia results in mice succumbing to multiorgan melanoma metastases, being permissive to allogeneic transplantation and being resistant to toxic shock following polymicrobial sepsis challenge. These results clearly demonstrate a non-redundant pathway linking IL-15 to Mcl1 in the maintenance of NK cells and innate immune responses in vivo

Near-infrared pyramid wavefront sensor for Keck adaptive optics: opto-mechanical design

A near-infrared, high order pyramid wavefront sensor will be implemented on the Keck telescope, with the aim of providing high resolution adaptive optics correction for the study of exoplanets around M-type stars and planet formation in obscured star forming regions. The pyramid wavefront sensor is designed to support adaptive optics correction of the light to an imaging vortex coronagraph and to a fiber injection unit that will feed a spectrograph. We present the opto-mechanical design of the near-infrared pyramid wavefront sensor, the optical performance, and the alignment strategy. The challenges of designing the assembly, as well as a fiber injection unit, to fit into the limited available space on the Keck adaptive optics bench, will also be discussed