Identification and Validation of EST-Derived Molecular Markers, TRAP and VNTRs, for Banana Research

The advent of high-throughput sequencing technology has generated abundant information on DNA sequences for the genomes of many plant species. Expressed Sequence Tags (ESTs), which are unique DNA sequences derived from a cDNA library and therefore representing genes transcribed in specific tissues or at some stage of development, are one type of DNA sequences highly available today for many important crop species. Molecular markers are used for bridging DNA sequence information with particular phenotypes and are useful tools for genotyping germplasm collections and also for tagging genes involved in desirable agronomic traits. In this sense, there is always a strong demand for suitable marker techniques to better utilise existing sequence information. A transcriptome database from banana (Musa spp.), DATAMusa, containing 42,724 ESTs from 11 different cDNA libraries and encompassing approximately 24 Mb of DNA sequence, was used in this study for the design of primers to PCR-amplify two types of EST-derived molecular markers, Variable Nucleotide Tandem Repeat (VNTR) and Target Region Amplification Polymorphism (TRAP). These primers were then validated against a panel of 14 diploid Musa genotypes and produced 32 (VNTR) and 119 (TRAP) alleles. Used separately or together, both types of markers were able to discriminate Musa genotypes from different genome background (A or B genomes). The TRAP alleles identified were derived from only one EST, while the VNTR alleles were derived from 12 unigenes. Based on the results of this study, EST-derived markers can be an important source of polymorphism to be used in genetic diversity and gene discovery studies in banan

Variable number of tandem repeat markers in the genome sequence of Mycosphaerella fijiensis, the causal agent of black leaf streak disease of banana (Musa spp)

ABSTRACT. We searched the genome of Mycosphaerella fijiensis for molecular markers that would allow population genetics analysis of this plant pathogen. M. fijiensis, the causal agent of banana leaf streak disease, also known as black Sigatoka, is the most devastating pathogen attacking bananas (Musa spp). Recently, the entire genome sequence of M. fijiensis became available. We screened this database for VNTR markers. Forty-two primer pairs were selected for validation, based on repeat type and length and the number of repeat units. Five VNTR markers showing multiple alleles were validated with a reference set of isolates from different parts of the world and a population from a banana plantation in Costa Rica. Polymorphism information content values varied from 0.6414 to 0.7544 for the reference set and from 0.0400 and 0.7373 for the population set. Eighty percent of the polymorphism information content values were above 0.60, indicating that the markers are highly informative. These markers allowed robust scoring of agarose gels and proved to be useful for variability and population genetics studies. In conclusion, the strategy we developed to identify and validate VNTR markers is an efficient means to incorporate markers that can be used for fungicide resistance management and to develop breeding strategies to control banana black leaf streak disease. This is the first report of VNTR-minisatellites from the M. fijiensis genome sequence. Key words: Molecular markers; VNTRs; Genetic diversity; Population genetics; Black Sigatok

Statistical physics and stromatolite growth: new perspectives on an ancient dilemma

This paper outlines our recent attempts to model the growth and form of microbialites from the perspective of the statistical physics of evolving surfaces. Microbialites arise from the environmental interactions of microbial communities (microbial mats). The mats evolve over time to form internally laminated organosedimentary structures (stromatolites). Modern day stromatolites exist in only a few locations, whereas ancient stromatolitic microbialites were the only form of life for much of the Earth's history. They existed in a wide variety of growth forms, ranging from almost perfect cones to branched columnar structures. The coniform structures are central to the heated debate on the oldest evidence of life. We proposed a biotic model which considers the relationship between upward growth of a phototropic or phototactic biofilm and mineral accretion normal to the surface. These processes are sufficient to account for the growth and form of many ancient stromatolities. These include domical stromatolites and coniform structures with thickened apical zones typical of Conophyton. More angular coniform structures, similar to the stromatolites claimed as the oldest macroscopic evidence of life, form when the photic effects dominate over mineral accretion.Comment: 8 pages, 3 figures. To be published in Proceedings of StatPhys-Taiwan 2004: Biologically Motivated Statistical Physics and Related Problems, 22-26 June 200

LandTrendr smoothed spectral profiles enhance woody encroachment monitoring

Secondary succession (SS) is one of the main consequences of the abandonment of agricultural and forestry practices in rural areas, causing -among other processes- woody encroachment on former pastures and croplands. In this study we model and monitor the spatial evolution of SS over semi-natural grassland communities in the mountain range of the Pyrenees in Spain, during the last 36 years (1984-2019). Independent variables for ‘annual-based’ and ‘period-based’ modeling were drawn from a suite of Surface Reflectance Landsat images, LandTrendr (LT)-algorithm-adjusted images and LT outputs. Support vector machine (SVM) classifiers were trained and tested using all possible variable combinations of all the aforementioned datasets. The best modeling strategy involved yearly time series of LT-adjusted Tasseled Cap Brightness (TCB) and Wetness (TCW) axes as predictors, attaining a F1-score of 0.85, a Matthew Correlation Coefficient (MCC) of 0.67 and an AUC 0.83. Woodlands encroached above 480, 000 ha of grasslands and crops during the study period. A model using LT outputs for the whole period also denoted good performance (F1-score = 0.85, MCC = 0.75) and estimated a similar area of woodland expansion (~509, 000 ha), but this ‘period’ approach was unable to provide temporal information on the year or the encroachment dynamics. Our results suggest an overall proportion of 66% for the Pyrenees being affected by SS, with higher intensity in the west-central part, decreasing towards the eastern end. © 2021 The Author

ZnO/ZnS heterostructures for hydrogen production by photoelectrochemical water splitting

This work studies the photoelectrochemical behavior of novel ZnO/ZnS heterostructures obtained by means of anodization in water and glycerol/water/NH4F electrolytes with different Na2S additions under controlled hydrodynamic conditions. For this purpose different techniques such as Field Emission Scanning Electronic Microscopy (FE-SEM) with EDX, Raman spectroscopy and photoelectrochemical water splitting tests under standard AM 1.5 conditions have been carried out. The obtained results showed that the hydrodynamic conditions promoted an ordered nanotubular morphology which facilitates electron-hole separation and consequently, the photoelectrochemical activity for water splitting is enhanced. Additionally, the effect of glycerol in the anodization solutions seems to be beneficial for increasing the dark current photostability

Further Studies on the Physical and Biogeochemical Causes for Large Interannual Changes in the Patagonian Shelf Spring-Summer Phytoplankton Bloom Biomass

A very strong and persistent phytoplankton bloom was observed by ocean color satellites during September - December 2003 along the northern Patagonian shelf. The 2003 bloom had the highest extent and chlorophyll a (Chl-a) concentrations of the entire Sea-viewing Wide Field-of-view Sensor (SeaWiFS) period (1997 to present). SeaWiFS-derived Chl-a exceeded 20 mg/cu m in November at the bloom center. The bloom was most extensive in December when it spanned more than 300 km across the shelf and nearly 900 km north-south (35degS to 43degS). The northward reach and the deep penetration on the shelf of the 2003 bloom were quite anomalous when compared with other years, which showed the bloom more confined to the Patagonian shelf break (PSB). The PSB bloom is a conspicuous austral spring-summer feature detected by ocean color satellites and its timing can be explained using the Sverdrup critical depth theory. Based on high-resolution numerical simulations, in situ and remote sensing data, we provide some suggestions for the probable mechanisms responsible for that large interannual change of biomass as seen by ocean color satellites. Potential sources of macro and micro (e.g., Fe) nutrients that sustain the high phytoplankton productivity of the Patagonian shelf waters are identified, and the most likely physical processes that maintain the nutrient balance in the region are discussed

A case for biotic morphogenesis of coniform stromatolites

Mathematical models have recently been used to cast doubt on the biotic origin of stromatolites. Here by contrast we propose a biotic model for stromatolite morphogenesis which considers the relationship between upward growth of a phototropic or phototactic biofilm ($v$) and mineral accretion normal to the surface ($\lambda$). These processes are sufficient to account for the growth and form of many ancient stromatolities. Domical stromatolites form when $v$ is less than or comparable to $\lambda$. Coniform structures with thickened apical zones, typical of Conophyton, form when $v >> \lambda$. More angular coniform structures, similar to the stromatolites claimed as the oldest macroscopic evidence of life, form when $v >>> \lambda$.Comment: 10 pages, 3 figures, to appear in Physica

Small-scale distributions in an indoor environment at 94GHz

[EN] In this paper, an extensive multiple-input multiple-output measurement campaign in a lab environment has been conducted at the 94GHz band. Using a vector network analyzer, updown converters, and omnidirectional antennas displaced in virtual arrays, we have obtained an estimation of the distribution parameters for the most usual distributions employed in the small-scale fading modeling, i.e., Rayleigh, Rice, Nakagami-m and -, by using statistical inference techniques. Moreover, in this scenario the best fit distribution to the experimental data is the Weibull distribution, using the Kolmogorov-Smirnov test. However, the - distribution provides the best fitting to the experimental results in terms of the lower tails of the distributions.This work was supported by the Ministerio de Economia y Competitividad MINECO, Spain (TEC2016-78028-C3-2-P) and by the European FEDER funds. Further information regarding the data obtained and included in this paper can be attained by contacting the author, Jose M. Molina ([email protected]).Reig, J.; Martinez-Ingles, M.; Molina-Garcia-Pardo, J.; Rubio Arjona, L.; Rodrigo Peñarrocha, VM. (2017). Small-scale distributions in an indoor environment at 94GHz. Radio Science. 52(7):852-861. https://doi.org/10.1002/2017RS006335S852861527Cudak, M., Ghosh, A., Kovarik, T., Ratasuk, R., Thomas, T. A., Vook, F. W., & Moorut, P. (2013). Moving Towards Mmwave-Based Beyond-4G (B-4G) Technology. 2013 IEEE 77th Vehicular Technology Conference (VTC Spring). doi:10.1109/vtcspring.2013.6692638Everitt, B. S., & Skrondal, A. (2010). The Cambridge Dictionary of Statistics. doi:10.1017/cbo9780511779633Helminger, J., Detlefsen, J., & Groll, H. (s. f.). Propagation properties of an indoor-channel at 94 GHz. ICMMT’98. 1998 International Conference on Microwave and Millimeter Wave Technology. Proceedings (Cat. No.98EX106). doi:10.1109/icmmt.1998.768215Moon-Soon Choi, Grosskopf, G., & Rohde, D. (s. f.). Statistical Characteristics of 60 GHz Wideband Indoor Propagation Channel. 2005 IEEE 16th International Symposium on Personal, Indoor and Mobile Radio Communications. doi:10.1109/pimrc.2005.1651506Kajiwara, A. (s. f.). Indoor propagation measurements at 94 GHz. Proceedings of 6th International Symposium on Personal, Indoor and Mobile Radio Communications. doi:10.1109/pimrc.1995.477099Maccartney, G. R., Rappaport, T. S., Sun, S., & Deng, S. (2015). Indoor Office Wideband Millimeter-Wave Propagation Measurements and Channel Models at 28 and 73 GHz for Ultra-Dense 5G Wireless Networks. IEEE Access, 3, 2388-2424. doi:10.1109/access.2015.2486778Marcum J. I. 1950 Table of Q functionsMartinez-Ingles, M.-T., Gaillot, D. P., Pascual-Garcia, J., Molina-Garcia-Pardo, J.-M., Rodríguez, J.-V., Rubio, L., & Juan-Llácer, L. (2016). Channel sounding and indoor radio channel characteristics in the W-band. EURASIP Journal on Wireless Communications and Networking, 2016(1). doi:10.1186/s13638-016-0530-7Rangan, S., Rappaport, T. S., & Erkip, E. (2014). Millimeter-Wave Cellular Wireless Networks: Potentials and Challenges. Proceedings of the IEEE, 102(3), 366-385. doi:10.1109/jproc.2014.2299397Reig, J., Martínez-Inglés, M.-T., Rubio, L., Rodrigo-Peñarrocha, V.-M., & Molina-García-Pardo, J.-M. (2014). Fading Evaluation in the 60 GHz Band in Line-of-Sight Conditions. International Journal of Antennas and Propagation, 2014, 1-12. doi:10.1155/2014/984102Thomas, H. J., Cole, R. S., & Siqueira, G. L. (1994). An experimental study of the propagation of 55 GHz millimeter waves in an urban mobile radio environment. IEEE Transactions on Vehicular Technology, 43(1), 140-146. doi:10.1109/25.282274Thomas, T. A., Vook, F. W., & Sun, S. (2015). Investigation into the effects of polarization in the indoor mmWave environment. 2015 IEEE International Conference on Communications (ICC). doi:10.1109/icc.2015.724851

Assessment of metals bound to marine plankton proteins and to dissolved proteins in seawater

Studies based on laser ablation–inductively coupled plasma-mass spectrometry (LA–ICP-MS) have been performed to assess metal bound to dissolved proteins and proteins from marine plankton after two-dimensional polyacrylamide gel electrophoresis (2D PAGE). Dissolved proteins were pre-concentrated from surface seawater (60 L) by tangential ultrafiltration with 10 kDa molecular weight cut-off (MWCO) membranes and further centrifugal ultrafiltration (10 kDa) before proteins isolation by methanol/chloroform/water precipitation. Proteins isolation from plankton was assessed after different trichloroacetic acid (TCA)/acetone and methanol washing stages, and further proteins extraction with a phenol solution. LA–ICP-MS analysis of the electrophoretic profiles obtained for dissolved proteins shows the presence of Cd, Cr, Cu, and Zn in five spots analyzed. These proteins exhibit quite similar molecular weights (within the 10–14 kDa range) and pIs (from 5.8 to 7.3). Cd, Cr, Cu, and Zn have also been found to be associated to proteins isolated from plankton samples. In this case, Cd has been found to be bound to proteins of quite different molecular weight (9, 13 and 22 kDa) and pIs (4.5, 5.2, 5.5, and 10). However, trace elements such as Cr, Cu and Zn appear to be mainly bound to plankton proteins of low molecular weight and variable pI