Assessing the Phylogenetic Utility of DNA Barcoding Using the New Zealand Cicada Genus Kikihia

DNA Barcoding (Hebert et al. 2003) has the potential to revolutionize the process of identifying and cataloguing biodiversity; however, significant controversy surrounds some of the proposed applications. In the seven years since DNA barcoding was introduced, the Web of Science records more than 600 studies that have weighed the pros and cons of this procedure. Unfortunately, the scientific community has been unable to come to any consensus on what threshold to use to differentiate species or even whether the barcoding region provides enough information to serve as an accurate species identification tool. The purpose of my thesis is to analyze mitochondrial DNA (mtDNA) barcoding’s potential to identify known species and provide a well-resolved phylogeny for the New Zealand cicada genus Kikihia. In order to do this, I created a phylogenetic tree for species in the genus Kikihia based solely on the barcoding region and compared it to a phylogeny previously created by Marshall et al. (2008) that benefits from information from other mtDNA and nuclear genes as well as species-specific song data. I determined how well the barcoding region delimits species that have been recognized based on morphology and song. In addition, I looked at the effect of sampling on the success of barcoding studies. I analyzed subsets of a larger, more densely sampled dataset for the Kikihia Muta Group to determine which aspects of my sampling strategy led to the most accurate identifications. Since DNA barcoding would by definition have problems in diagnosing hybrid individuals, I studied two species (K. “murihikua” and K. angusta) that are known to hybridize. Individuals that were not obvious hybrids (determined by morphology) were selected for the case study. Phylogenetic analysis of the barcoding region revealed insights into the reasons these two species could not be successfully differentiated using barcoding alone.

The role of AKT-mediated phosphorylation in suppression of MAD1 and the development of new approach in protein complex detection

MAX dimerization protein 1 (MAD1) is a basic-helix-loop-helix transcription factors that recruits transcription repressor such as HDAC to suppress target genes transcription. It antagonizes to MYC because the promoter binding sites for MYC are usually also serve as the binding sites for MAD1 so they compete for it. However, the mechanism of the switch between MYC and MAD1 in turning on and off of genes' transcription is obscure. In this study, we demonstrated that AKT-mediated MAD1 phosphorylation inhibits MAD1 transcription repression function. The association between MAD1 and its target genes' promoter is reduced after been phosphorylated by AKT; therefore, consequently, allows MYC to occupy the binding site and activates transcription. Mutation of such phosphorylation site abrogates the inhibition from AKT. In addition, functional assays demonstrated that AKT suppressed MAD1-mediated transcription repression of its target genes hTERT and ODC. Cell cycle and cell growth were also been released from inhibition by MAD1 in the presents of AKT. Taken together, our study suggests that MAD1 is a novel substrate of AKT and AKT-mediated MAD1 phosphorylation inhibits MAD1function; therefore, activates MAD1 target genes expression. ^ Furthermore, analysis of protein-protein interaction is indispensable for current molecular biology research, but multiplex protein dynamics in cells is too complicated to be analyzed by using existing biochemical methods. To overcome the disadvantage, we have developed a single molecule level detection system with nanofluidic chip. Single molecule was analyzed based on their fluorescent profile and their profiles were plotted into 2 dimensional time co-incident photon burst diagram (2DTP). From this 2DTP, protein complexes were characterized. These results demonstrate that the nanochannel protein detection system is a promising tool for future molecular biology. ^

Homology Cloning, Heterologous Expression and Characterization of a New Channelrhodopsin

Channelrhodopsins are phototaxis receptors in the plasma membranes of motile unicellular algae. They function as light-gated cation channels and this channel activity has been exploited to trigger action potentials in neurons with light to control neural circuits (“optogenetics"). Four channelrhodopsins were identified in two algal species, Chlamydomonas reinhardtii and Volvox carteri, with known genome sequences; each species contains 2 channelrhodopsins, one absorbing at longer wavelengths and one at shorter wavelengths, named CrChR1 and CrChR2, respectively. Our goals are to expand knowledge of channelrhodopsin mechanisms and also to identify new channelrhodopsins from various algal species with improved properties for optogenetic use. For these aims we are targeting algae from extreme environments to establish the natural diversity of their properties. We cloned a new channelrhodopsin from the psychrophilic (cold-loving) alga, Chlamydomonas augustae, with degenerate primers based on the 4 known homologs. The new protein is 48% and 52% identical to CrChR1 and CrChR2, respectively. We expressed the channelrhodopsin in HEK293 cells and measured light-induced currents to assess their kinetics and action spectrum. Based on the primary structure, kinetics of light-induced photocurrents in HEK293 cells, and action spectrum maximum of 520 nm near that of the two previously found CrChR1, we named the new channelrhodopsin CaChR1. The properties of robust channel activity at physiological pH, fast on-and-off kinetics, and greatly red-shifted action spectrum maximum from that of CrChR2, make CaChR1 advantageous as an optogenetic tool. To know this new channelrhodopsin better, we expressed His-tagged CaChR1 in Pichia pastoris and the yield is about 6 mg/L. The purified His-tagged CaChR1 exhibited an absorption spectrum identical to the action spectrum of CaChR1-generated photocurrents. The future work will be measurement of the photocycles of CaChR1 by flash photolysis, crystallization of CaChR1 for the structure and mutagenesis of CaChR1 to find the critical amino acids accounting for red-shifted spectra, slow inactivation and rapid on-and-off kinetics. Seven new channelrhodopsins including CaChR1 from different algal species have been cloned in our lab at this time, bringing the total known to 13. The work of cloning of these new channelrhodopsins along with the expression of CaChR1 was published in Photochemistry and Photobiology in January 2012

A new modern analogue reference dataset and its application to the 430-kyr pollen record from Lake Biwa

This study presents a newly compiled dataset of modern pollen and climate data from 798 sites across Japan and the Russian Far East. This comprehensive reference dataset combined with the modern analogue technique (MAT) provides a powerful tool for pollen-based reconstruction of the Quaternary Northwest Pacific climate. Pollen-derived reconstruction of the modern climate at the reference pollen-sampling sites matches well with the estimated modern climate values (R2 values vary between 0.79 and 0.95, and RMSEP values vary between 5.8 and 9.7% of the modern climatic range for all nine tested variables). The successful testing of the method encourages its application to the fossil pollen records. We used a coarse-resolution pollen record from Lake Biwa to reconstruct glacial-interglacial climate dynamics in central Japan since ~438 kyr and compared it to the earlier reconstruction based on a less representative reference dataset. The current and earlier results consistently demonstrate that the coldest glacial intervals experienced pronounced cooling in winter and moderate cooling in summer, supporting the growth of cool mixed forest (COMX) where warm mixed forest (WAMX) predominates today. During the last glacial, maximum (~24 kyr BP) mean temperatures of the coldest (MTCO) and warmest (MTWA) month were about -13 °C (RMSEP = 2.34 °C) and 21 °C (RMSEP = 1.66 °C) respectively, and annual precipitation (PANN) was about 800 mm (RMSEP = 158.06 mm). During the thermal optimums of the interglacial intervals, the temperatures of the coldest and warmest month were above 0 °C and 25 °C respectively, leading to the reconstruction of WAMX and temperate conifer forest (TECO). Although both these vegetation types grow in the southern part of Japan today, WAMX requires warmer space. The presence of WAMX during marine isotope stages (MIS) 11 and 1, and its absence during MIS 9 and MIS 5 contradict the marine isotope and Antarctic ice records, suggesting that the latter two interglacials were the warmest of the last 800 kyr. The apparent contradiction allows at least three different explanations including low temporal resolution of the pollen record; different trends in CO2 concentrations during 'short' and 'long' interglacials; and regional climate variability and non-linear response of different regions to the global forcing. More definitive conclusions will be possible on the basis of forthcoming high-resolution pollen records from central Japan.

Neogene and Paleocene-Maestrichtian calcareous nannofossils in sediments of the upper continental rise off New Jersey

Maestrichtian to Holocene calcareous nannofossils from two closely spaced sites on the upper continental rise some 100 miles (161 km) southeast of Atlantic City, New Jersey, were zoned in order to help date a major canyon-cutting event in the late Miocene and to delineate and correlate other hiatuses with seismic stratigraphy. Mid-middle Eocene through middle Miocene sediments (Zones CP14 to CN6) were not recovered in these holes, but nearly all other zones are accounted for. The Eocene section is described in a companion chapter (Applegate and Wise, 1987, doi:10.2973/dsdp.proc.93.118.1987). Nannofossils are generally sparse and moderately preserved in the clastic sediments of Site 604. Sedimentation rates are extremely high for the upper Pleistocene (201 m/m.y. minimum) above a hiatus calculated to span 0.44 to 1.1 Ma. The associated disconformity is correlated with local seismic reflection Horizon Pr . Sedimentation rates continue to be high (93 m/m.y.) down to a second hiatus in the upper Pliocene dated from about 2.4 to 2.9 (or possibly 3.3) Ma. The disconformity associated with this hiatus is correlated with local seismic reflection Horizon P2 and regional Reflector Blue, which can be interpreted to mark either the onset of Northern Hemisphere continental glaciation or circulation changes associated with the closure of the Central American Seaway. Sedimentation rates in the pre-glacial lower Pliocene are only about a third those in the glacial upper Pliocene. A prominent disconformity in the upper Miocene marks a major lithologic boundary that separates Messinian(?) glauconitic claystones above from lower Tortonian conglomeratic debris flows and turbidites below. The debris flows recovered are assigned to nannofossil Zones CN8a and CN7, but drilling difficulties prevented penetration of the bottom of this sequence some 100 m below the terminal depth of the hole. Correlation of the lower bounding seismic reflector (M2/Merlin?) to a drift sequence drilled on the lower rise at DSDP Site 603, however, predicts that the debris flows began close to the beginning of the late Miocene (upper Zone CN6 time) at about 10.5 Ma. The debris flows represent a major canyon-cutting event that we correlate with the beginning of the particularly severe late Miocene glaciations believed to be associated with the formation of the West Antarctic Ice Sheet. The existence of these spectacular debris flows strongly suggest that the late Miocene glacio-eustatic low stand occurred during Vail Cycle TM3.1 (lower Tortonian) rather than during Vail Cycle TM3.2 (Messinian) as originally published. Beneath a set of coalesced regional disconformities centered upon seismic reflection Horizon Au, coccoliths are abundant and in general are moderately preserved at Site 605 in a 619-m carbonate section extending from the middle Eocene Zone CP13b to the upper Maestrichtian Lithraphidites quadratus Zone. Sedimentation rates are 37 m/m.y. in the Eocene down to a condensed interval near the base (Zone CP9). A disconformity is suspected near the Eocene/Paleocene boundary. Sedimentation rates for the upper Paleocene Zone CP8 are similar to those of the Eocene, but Zones CP7 and CP6 lie within another condensed interval. The highest Paleocene rates are 67 m/m.y. down through Zones CP5 and CP4 to a major disconformity that separates the upper Paleocene from the Danian. This hiatus spans about 2.6 m.y. (upper Zone CP3 to lower Zone CP2) and corresponds to the major sea-level drop at the base of Vail Cycle TE2.1. As the most prominent break in this Paleogene section, it may correspond to seismic reflection Horizon A* of the North American Basin. Sedimentation rates from this point to the Cretaceous/Tertiary boundary drop to 11 m/m.y., still high for a Paleocene DSDP section. No major break in deposition could be detected at the Cretaceous/Tertiary boundary.

Large-Area Photo-Mosaicking tool (LAPM tool)

This paper presents a new tool for large-area photo-mosaicking (LAPM tool). This tool was developed specifically for the purpose of underwater mosaicking, and it is aimed at providing end-user scientists with an easy and robust way to construct large photo-mosaics from any set of images. It is notably capable of constructing mosaics with an unlimited number of images on any modern computer (minimum 1.30 GHz, 2 GB RAM). The mosaicking process can rely on both feature matching and navigation data. This is complemented by an intuitive graphical user interface, which gives the user the ability to select feature matches between any pair of overlapping images. Finally, mosaic files are given geographic attributes that permit direct import into ArcGIS. So far, the LAPM tool has been successfully used to construct geo-referenced photo-mosaics with photo and video material from several scientific cruises. The largest photo-mosaic contained more than 5000 images for a total area of about 105,000 m**2. This is the first article to present and to provide a finished and functional program to construct large geo-referenced photo-mosaics of the seafloor using feature detection and matching techniques. It also presents concrete examples of photo-mosaics produced with the LAPM tool.

Adolists: A new concept for Stata

A new package called adolist is presented. adolist is a tool to create, install, and uninstall lists of user ado-packages (“adolists”). For example, adolist can create a list of all user packages installed on a system and then install the same packages on another system. Moreover, ado-list can be used to put together thematic lists of packages such as, say, a list on income inequality analysis or time-series add-ons, or the list of “41 user ados everyone should know”. Such lists can then be shared with others, who can easily install and uninstall the listed packages using the adolist command.

Ado-lists: A new concept for Stata

A new command called adolist is presented. adolist is a tool to create, install, and uninstall lists of user ado-packages (“adolists”). For example, adolist can create a list of all user packages installed on a system and then install the same packages on another system. Moreover, ado-list can be used to put together thematic lists of packages such as, say, a list on income inequality analysis or time-series add-ons, or the list of “41 user ados everyone should know”. Such lists can then be shared with others, who can easily install and uninstall the listed packages using the adolist command.

On Understanding How Developers Use the Spotter Search Tool

Analyzing how software engineers use the Integrated Development Environment (IDE) is essential to better understanding how engineers carry out their daily tasks. Spotter is a code search engine for the Pharo programming language. Since its inception, Spotter has been rapidly and broadly adopted within the Pharo community. However, little is known about how practitioners employ Spotter to search and navigate within the Pharo code base. This paper evaluates how software engineers use Spotter in practice. To achieve this, we remotely gather user actions called events. These events are then visually rendered using an adequate navigation tool chain. Sequences of events are represented using a visual alphabet. We found a number of usage patterns and identified underused Spotter features. Such findings are essential for improving Spotter.

A new OCT finding in tuberculous serpiginous-like choroidopathy.

PURPOSE To present a case of tubercular serpiginous-like choroiditis (SLC) with previously unreported choroidal findings on enhanced depth imaging OCT (EDI-OCT). DESIGN Case report. METHODS A 60-year-old female presented with decreased vision. Serpiginous choroidopathy was diagnosed. Laboratory workup revealed an infectious etiology. EDI-OCT revealed previously unreported choroidal findings. RESULTS Laboratory workup revealed nonreactive Treponema pallidum antibodies and positive QuantiFERON Gold. CT chest showed scars of prior granulomatous disease. OCT with EDI of active lesions demonstrated infiltration of the choroid, elevation of the RPE-Bruch's membrane complex and focal increase of choroidal thickness. CONCLUSIONS Choroidal infiltration with elevation of the RPE was demonstrated on EDI-OCT in active areas of tuberculous serpiginous-like choroiditis in this patient. This finding has not been described in imaging of patients with noninfectious serpiginous choroidopathy and may be a useful tool to differentiate serpiginous choroidopathy (SC) from serpiginous-like choroiditis (SLC). EDI-OCT may provide characterization of choroidal involvement.

Blogs: On the Cutting Edge of the Next-generation Web

This article analyses a number of social and cultural aspects of the blog phenomenon with the methodological aid of a complexity model, the New Techno-social Environment (hereinafter also referred to by its Spanish acronym, NET, or Nuevo Entorno Tecnosocial) together with the socio-technical approach of the two blogologist authors. Both authors are researchers interested in the new reality of the Digital Universal Network (DUN). After a review of some basic definitions, the article moves on to highlight some key characteristics of an emerging blog culture and relates them to the properties of the NET. Then, after a brief practical parenthesis for people entering the blogosphere for the first time, we present some reflections on blogs as an evolution of virtual communities and on the changes experienced by the inhabitants of the infocity emerging from within the NET. The article concludes with a somewhat disturbing question; whether among these changes there might not be a gradual transformation of the structure and form of human intelligence.

Foresight as an innovative tool for designing tourist destinations

Foresight is a relatively new field of study which initially arose to make provisions for the future in science and technology, but nowadays it is increasingly being used in territorial issues. Although the use of foresight tools in the tourism realm has been limited, there is a growing need to manage the increasing uncertainty that surrounds tourism development. Based on these premises, this paper tries to prove the capability of foresight tools to anticipate the impacts of complex global challenges on the tourism field. This assumption is tested through a future vision exercise which explores the evolution of tourism demand segments and its implications in planning tourism destinations. Two major demand segments are visualised for the year 2020 horizon: “Niche and Innovative Demand” and “Massive and Predictable Demand”. For both segments, the tourism consumption chain value is displayed and spatial design guidelines are recommended for sun and beach destinations

New methods for the estimation of Takagi-Sugeno model based extended Kalman filter and its applications to optimal control for nonlinear systems

This paper describes new approaches to improve the local and global approximation (matching) and modeling capability of Takagi–Sugeno (T-S) fuzzy model. The main aim is obtaining high function approximation accuracy and fast convergence. The main problem encountered is that T-S identification method cannot be applied when the membership functions are overlapped by pairs. This restricts the application of the T-S method because this type of membership function has been widely used during the last 2 decades in the stability, controller design of fuzzy systems and is popular in industrial control applications. The approach developed here can be considered as a generalized version of T-S identification method with optimized performance in approximating nonlinear functions. We propose a noniterative method through weighting of parameters approach and an iterative algorithm by applying the extended Kalman filter, based on the same idea of parameters’ weighting. We show that the Kalman filter is an effective tool in the identification of T-S fuzzy model. A fuzzy controller based linear quadratic regulator is proposed in order to show the effectiveness of the estimation method developed here in control applications. An illustrative example of an inverted pendulum is chosen to evaluate the robustness and remarkable performance of the proposed method locally and globally in comparison with the original T-S model. Simulation results indicate the potential, simplicity, and generality of the algorithm. An illustrative example is chosen to evaluate the robustness. In this paper, we prove that these algorithms converge very fast, thereby making them very practical to use.

A New Multidisciplinary Home Care Telemedicine System to Monitor Stable Chronic Human Immunodeficiency Virus-Infected Patients: A Randomized Study

BACKGROUND: Antiretroviral therapy has changed the natural history of human immunodeficiency virus (HIV) infection in developed countries, where it has become a chronic disease. This clinical scenario requires a new approach to simplify follow-up appointments and facilitate access to healthcare professionals. METHODOLOGY: We developed a new internet-based home care model covering the entire management of chronic HIV-infected patients. This was called Virtual Hospital. We report the results of a prospective randomised study performed over two years, comparing standard care received by HIV-infected patients with Virtual Hospital care. HIV-infected patients with access to a computer and broadband were randomised to be monitored either through Virtual Hospital (Arm I) or through standard care at the day hospital (Arm II). After one year of follow up, patients switched their care to the other arm. Virtual Hospital offered four main services: Virtual Consultations, Telepharmacy, Virtual Library and Virtual Community. A technical and clinical evaluation of Virtual Hospital was carried out. FINDINGS: Of the 83 randomised patients, 42 were monitored during the first year through Virtual Hospital (Arm I) and 41 through standard care (Arm II). Baseline characteristics of patients were similar in the two arms. The level of technical satisfaction with the virtual system was high: 85% of patients considered that Virtual Hospital improved their access to clinical data and they felt comfortable with the videoconference system. Neither clinical parameters [level of CD4+ T lymphocytes, proportion of patients with an undetectable level of viral load (p = 0.21) and compliance levels >90% (p = 0.58)] nor the evaluation of quality of life or psychological questionnaires changed significantly between the two types of care. CONCLUSIONS: Virtual Hospital is a feasible and safe tool for the multidisciplinary home care of chronic HIV patients. Telemedicine should be considered as an appropriate support service for the management of chronic HIV infection. TRIAL REGISTRATION: Clinical-Trials.gov: NCT01117675.

Tools for constraint visualization: The VIFID/TRIFID tool

Visualization of program executions has been used in applications which include education and debugging. However, traditional visualization techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding the behavior of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this chapter we discuss techniques for visualizing data evolution in CLP. We briefly review some previously proposed visualization paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyze the behavior and characteristics of an execution. In particular, we concéntrate on the representation of the run-time valúes of the variables, and the constraints among them. Given our interest in visualizing large executions, we also pay attention to abstraction techniques, i.e., techniques which are intended to help in reducing the complexity of the visual information.