DETECTION OF PHYTOPLASMAS ASSOCIATED WITH KALIMANTAN WILT DISEASE OF COCONUT BY THE POLYMERASE CHAIN REACTION

ABSTRACTCoconut is the second Indonesia’s most important social commodityafter rice. There are more than 3.6 million hectares of coconut plantationsin Indonesia equivalent to one third of the total world coconut area.However, the production and productivity of the coconut are very low andunstable for various reasons, including pests and diseases. Kalimantan wilt(KW) disease causes extensive damage to coconut plantation. In previousinvestigations, bacteria, fungi, viruses, viroids and soil-borne pathogenssuch as nematodes were tested, but none of them were consistentlyassociated with the disease. The objective of this research was to detectand diagnose the phytoplasma associating with KW. Two DNA extractionmethods, namely a modification of CTAB method involving grindingcoconut trunk tissue in pre-warmed CTAB instead of liquid nitrogen, and asmall scale DNA extraction method, were used to prepare DNA fromcoconut trunk tissues. Research results showed that both methods werefound equally suitable for preparing DNA from coconut trunk tissues forPCR analysis. The phytoplasmas aetiology of KW has been proved by thenested PCR approach using P1/P7 and R16F2n/R16R2 primercombinations. The study has further demonstrated that the nested PCRapproach can be employed to effectively detect the presence ofphytoplasma both in infected and in symptomless coconut trunk tissues.Phytoplasma DNA was amplified from 95 out of 116 samples (81.9%).Based on source of samples, phytoplasma DNA was amplified from KWinfected and symptomless samples, 95.1% and 67.3% respectively. Thisstudy confirmed that KW is caused by phytoplasma.Key words : Coconut, Cocos nucifera L., plant disease, Kalimantan wiltdisease, phytoplasma, polymerase chain reaction, CentralKalimantanABSTRAKDeteksi phytoplasma yang berasosiasi dengan penyakitlayu Kalimantan pada kelapa dengan reaksi rantaipolymeraseKelapa merupakan komoditi sosial kedua setelah padi di Indonesiadengan luasan areal lebih dari 3.6 juta ha pertanaman, ekuivalen dengansepertiga luas kelapa dunia, hal ini menjadikan Indonesia sebagai negaraprodusen kelapa terluas di dunia. Sekarang ini produksi dan produktivitaskelapa sangat rendah dan tidak stabil yang disebabkan oleh berbagai alasantermasuk serangan hama dan penyakit. Penyakit layu Kalimantan telahmengakibatkan kerugian yang besar pada pertanaman kelapa. Penelitiansebelumnya untuk mengetahui penyebab penyakit dilakukan denganmenguji bakteri, cendawan, virus, viroid dan patogen tanah sepertinematoda tetapi tidak ada yang secara konsisten berasosiasi denganpenyakit layu Kalimantan. Penelitian ini bertujuan untuk mendeteksi danmendiagnosa phytoplasma sebagai penyebab penyakit yang berasosiasidengan layu Kalimantan. Penelitian ini menggunakan dua metode untukmengekstraksi DNA yaitu metode CTAB yang biasanya menggunakannitrogen cair dimodifikasi dengan menghancurkan sampel tanaman padaCTAB yang dipanaskan, dan metode skala kecil. Hasil penelitianmenunjukkan bahwa kedua metode yang digunakan menghasilkan DNAyang sama baiknya untuk analisis PCR. Teknik nested PCR menggunakankombinasi primer P1/P7 dan R16F2n/R16R2 dapat membuktikan bahwapenyebab penyakit layu Kalimantan adalah phytoplasma. Teknik ini jugasecara efektif dapat mendeteksi phytoplasma dalam jaringan tanamankelapa yang sudah terinfeksi maupun yang belum menunjukkan gejalapenyakit. DNA phytoplasma dapat dideteksi pada 95 sampel dari 116sampel (81.9%) yang dianalisis. Berdasarkan jenis sample yang diperiksaternyata phytoplasma dapat dideteksi pada sample yang terinfeksi maupunyang belum menunjukkan gejala penyakit masing-masing 95.1% dan67.3%. Hasil penelitian ini mengkonfirmasi bahwa penyakit layuKalimantan disebabkan oleh phytoplasma.Kata kunci: Kelapa, Cocos nucifera L., penyakit tanaman, penyakit layuKalimantan,  phytoplasma,  reaksi  rantai  polymerase,Kalimantan Tenga

The brainstem reticular formation is a small-world, not scale-free, network

Recently, it has been demonstrated that several complex systems may have simple graph-theoretic characterizations as so-called ‘small-world’ and ‘scale-free’ networks. These networks have also been applied to the gross neural connectivity between primate cortical areas and the nervous system of Caenorhabditis elegans. Here, we extend this work to a specific neural circuit of the vertebrate brain—the medial reticular formation (RF) of the brainstem—and, in doing so, we have made three key contributions. First, this work constitutes the first model (and quantitative review) of this important brain structure for over three decades. Second, we have developed the first graph-theoretic analysis of vertebrate brain connectivity at the neural network level. Third, we propose simple metrics to quantitatively assess the extent to which the networks studied are small-world or scale-free. We conclude that the medial RF is configured to create small-world (implying coherent rapid-processing capabilities), but not scale-free, type networks under assumptions which are amenable to quantitative measurement

Petrography and Geochemistry of Metals in Almahata Sitta Ureilites

Ureilites are ultramafic achondrites, predominantly composed of olivine and pyroxenes with accessory carbon, metal and sulfide. The majority of ureilites are believed to represent the mantle of the ureilite parent body (UPB) [1]. Although ureilites have lost much of their original metal [2], the metal that remains retains a record of the formative processes. Almahata Sitta is predominantly composed of unbrecciated ureilites with a wide range of silicate compositions [3,4]. As a fall it presents a rare opportunity to examine fresh ureilite metal in-situ, and analyzing their highly siderophile element (HSE) ratios gives clues to their formation. Bulk siderophile element analyses of Almahata Sitta fall within the range observed in other ureilites [5]. We have examined the metals in seven ureilitic samples of Almahata Sitta (AS) and one associated chondrite fragment (AS#25)

In Situ Measurements of Micro-Scale Surface Roughness of Sea Ice

Surface roughness at the centimetre and millimetre scale is an important factor governing radar backscatter, especially in the case of warm (>-5 degrees C) or highly saline sea ice types. Quantitative measurements of surface roughness are required as input to backscatter models. Several field techniques have been used to quantitatively measure the surface roughness of sea ice. These techniques usually posses at least one of the following obstacles: difficult field operation, expense, poor accuracies or arduous data processing. A prototype portable field instrument called the Surface Roughness Meter has been designed to measure micro-scale surface roughness. The instrument provides measurements of two surface roughness parameters, root mean square height and correlation length. The instrument consists of a 35 mm camera and a flash mounted on a platform. The system illuminates and photographs a rectangle of known size on the surface from a fixed height. The negatives are digitized and the root mean square height and correlation length are calculated and recorded using a PC-based image analysis system in the laboratory. The first sea ice application for the instrument was the Labrador Ice Margin Experiment (LIMEX) 1989. The instrument was used to measure surface roughness of first-year deformed pack ice. The resulting data from LIMEX '89 were digitized and surface roughness statistics were computed using a PC image analysis system. LIMEX '89 Surface Roughness Meter data compared favourably to roughness statistics obtained from LIMEX '87.Key words: surface roughness, radar backscatter, sea ice, Surface Roughness Meter, root mean square height, correlation length, LIMEX ’89Mots clés: rugosité de la surface, rétrodiffusion radar, glace de mer, profilographe, hauteur quadratique moyenne, longueur de corrélation, LIMEX ’8

Incorporating Distributed Debris Thickness in a Glacio-Hydrological Model: Khumbu Himalaya, Nepal

Understanding the future evolution of Himalayan glaciers is important in terms of runoff that provides an essential water source to local populations and has far-reaching downstream impacts. However, the climatic response of glaciers in High-Mountain Asia is complicated by ice stagnation and considerable supraglacial debris coverage, which insulates the ice from warming. Typical runoff modelling only crudely incorporates debris cover and there is currently no consensus on how significantly this may impact future glacier and runoff evolution. Here, a glacio-hydrological model is modified to incorporate fully distributed debris cover, using melt reduction factors that vary depending on debris thickness, and to redistribute mass losses according to observed surface elevation changes. A range of debris thickness data are implemented, including a remote-sensing survey and a modelled debris surface, to analyse the sensitivity of glacier evolution and runoff to possible future debris-cover changes in a series of experiments in the upper Khumbu catchment, Nepal. Simulations are undertaken using climate input data from Regional Climate Model simulations from CORDEX (Coordinated Regional Downscaling Experiment) which are further statistically downscaled using data from the Pyramid meteorological station. Results suggest that the accurate calibration of the model to volume change compensates for the inclusion of distributed debris cover but only if the climatic sensitivity of the calibration period (1999–2010) and the nature of the debris-covered surface remain constant during future simulations. Altering the nature of the debris surface has a significant impact on simulated ice volume, with melt rates under debris suppressed by up to 85 %. The sensitivity of runoff ranges from 60 to 140 million m3 yr-1, although there are considerable uncertainties relating to non-glacial snow melt. Moreover, incorporating locally enhanced melt at ice cliffs into the model also impacts upon volume loss and discharge, with a greater proportion of ice cliffs leading to enhanced volume losses compared to a homogeneous debris surface. Finally, using the most representative model configuration, the future evolution of Khumbu Glacier under various climate scenarios shows continued mass losses with a reduction in volume ranging from 60 % to 97 % by 2100. Runoff trends show an initial increase followed by an eventual decrease, with runoff in 2100 predicted to be 8 % lower than current levels

Superfluid Spin-down, with Random Unpinning of the Vortices

The so-called ``creeping'' motion of the pinned vortices in a rotating superfluid involves ``random unpinning'' and ``vortex motion'' as two physically separate processes. We argue that such a creeping motion of the vortices need not be (biased) in the direction of an existing radial Magnus force, nor should a constant microscopic radial velocity be assigned to the vortex motion, in contradiction with the basic assumptions of the ``vortex creep'' model. We point out internal inconsistencies in the predictions of this model which arise due to this unjustified foundation that ignores the role of the actual torque on the superfluid. The proper spin-down rate of a pinned superfluid is then calculated and turns out to be much less than that suggested in the vortex creep model, hence being of even less observational significance for its possible application in explaining the post-glitch relaxations of the radio pulsars.Comment: To be published in J. Low Temp. Phys., Vol. 139, May 2005 [Eqs 11, 15-17 here, have been revised and, may be substituted for the corresponding ones in that paper

Combinatorial expression for universal Vassiliev link invariant

The most general R-matrix type state sum model for link invariants is constructed. It contains in itself all R-matrix invariants and is a generating function for "universal" Vassiliev link invariants. This expression is more simple than Kontsevich's expression for the same quantity, because it is defined combinatorially and does not contain any integrals, except for an expression for "the universal Drinfeld's associator".Comment: 20 page

Benchmark low-mass objects in Moving Groups

This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.In order to compile a sample of ultracool dwarfs that will serve as benchmarks for testing theoretical formation and evolutionary models, we selected low-mass cool (>M7) objects that are potentially members of five known young Moving Groups in the solar neighbourhood. We have studied the kinematics of the sample, finding that 49 targets belong to the young disk area, from which 36 are kinematic member of one of the five moving groups under study. Some of the identified low-mass members have been spectroscopically characterised (T-eff, log g) and confirmed as young members through a detailed study of age indicators

Optimisation and validation of a PCR to detect viable Tenacibaculum maritimum in salmon skin tissue samples

A PCR protocol was optimised and validated for the detection of viable Tenacibaculum maritimum cells in salmon skin tissue. Viability conventional (vPCR) and quantitative PCR (v-qPCR) assays both had a limit of detection of 103 CFU mL−1 viable cells. The v-qPCR assay showed a linear quantification over 4 log units. Conventional vPCR showed complete signal suppression when only dead cells were present at concentrations lower than 106 CFU mL−1. While the v-qPCR did not result in complete suppression when only dead cells were present, a method was developed to determine if viable cells were present based on the % Δ in cycle threshold (Ct) value. The procedure was validated for high-throughput processing and an enrichment protocol was validated to reliably detect low concentrations of viable cells both with and without a high background of dead cells. Performing this protocol on naturally infected tissues showed that vPCR and v-qPCR reduced the potential for false positives compared to using conventional PCR and qPCR. The optimised protocol developed for this study provides an efficient, reliable and robust alternative for the detection of viable T. maritimum in skin tissue

Orbital evolution of P\v{r}\'{i}bram and Neuschwanstein

The orbital evolution of the two meteorites P\v{r}\'{i}bram and Neuschwanstein on almost identical orbits and also several thousand clones were studied in the framework of the N-body problem for 5000 years into the past. The meteorites moved on very similar orbits during the whole investigated interval. We have also searched for photographic meteors and asteroids moving on similar orbits. There were 5 meteors found in the IAU MDC database and 6 NEAs with currently similar orbits to P\v{r}\'{i}bram and Neuschwanstein. However, only one meteor 161E1 and one asteroid 2002 QG46 had a similar orbital evolution over the last 2000 years.Comment: 7 pages, 2 figures, 3 table