Fire impact on forest soils evaluated using near-infrared spectroscopy and multivariate calibration

L'évaluation des propriétés physicochimiques des sols forestiers affectés par des feux a été réalisée en utilisant la spectroscopie proche infra-rouge (SPIR) couplée avec des méthodes chimiométriques. Pour décrire les propriétés du sol, les mesures prises comprennent le carbone organique total sur phase solide, le contenu d'azote total, le carbone organique et l'absorbance spécifique à 254 et 280nm des substances humiques, le carbone organique dans des acides humiques et fulviques, des concentrations de NH4+, Ca2+, Mg2+, K+ et le phosphore en plus des spectres de PIR. Un indice de répétition d'incendies a été défini et calculé selon les régimes de feux affectant des sols. Ce calcul inclut l'occurrence des incendies et le temps écoulé depuis le dernier feu. Cette étude montre que la spectroscopie PIR pourrait être utilisée pour le contrôle de qualité des sols, particulièrement pour la prédiction quantitative du carbone organique total, l'azote total, le carbone organique dans les substances humiques, les concentrations de phosphore, Mg2 +, Ca2 + et NH4 + et des substances humiques UVSA254. Une nouvelle validation dans ce domaine est nécessaire cependant pour une bonne prédictions de K+, du carbone organique dans des acides humiques et fulviques et les substances humiques UVSA280. De plus, la SPIR couplée avec la régression PLS peut aussi être utile pour prévoir l'indice de répétition de feu et pour déterminer sa variabilité spatiale. Aussi cette méthode peut être utilisée pour dresser la carte de secteurs plus ou moins brûlés et pour adapter les techniques de réhabilitation, comme la reconstitution de l'humus avec des enrichissements organiques (composts) ou le reboisement. Finalement, on peut considérer que notre indice de répétition est représentatif de l'état des sols. / The assessment of physico-chemical properties in forest soils affected by fires was evaluated using near infrared reflectance (NIR) spectroscopy coupled with chemometric methods. In order to describe the soil properties, measurements were taken of the total organic carbon on solid phase, the total nitrogen content, the organic carbon and the specific absorbences at 254 and 280nm of humic substances, organic carbon in humic and fulvic acids, concentrations of NH4+, Ca2+,Mg2+, K+ and phosphorus in addition to NIR spectra. Then, a fire recurrence index was defined and calculated according to the different fires extents affecting soils. This calculation includes the occurrence of fires as well as the time elapsed since the last fire. This study shows that NIR spectroscopy could be considered as a tool for soil monitoring, particularly for the quantitative prediction of the total organic carbon, total nitrogen content, organic carbon in humic substances, concentrations of phosphorus, Mg2+, Ca2+ and NH4+ and humic substances UVSA254. Further validation in this field is necessary however, to try and make successful predictions of K+, organic carbon in humic and fulvic acids and the humic substances UVSA280. Moreover, NIR coupled with PLS can also be useful to predict the fire recurrence index in order to determine the spatial variability. Also this method can be used to map more or less burned areas and possibly to apply adequate rehabilitation techniques, like soil litter reconstitution with organic enrichments (industrial composts) or reforestation. Finally, the proposed recurrence index can be considered representative of the state of the soils

Vaccination with novel low-molecular weight proteins secreted from Trichinella spiralis inhibits establishment of infection

Trichinella spiralis muscle stage larvae (mL1) produce excretory-secreted products (ESPs), a complex mixture of protein, which are believed to be important for establishing or maintaining an infection niche within skeletal muscle and the intestine. Studies of both whole ESPs and individual cloned proteins have shown that some ESPs are potent immunogens capable of eliciting protective immune responses. Here we describe two novel proteins, Secreted from Muscle stage Larvae SML-4 and SML-5 which are 15 kDa and 12 kDa respectively. The genes encoding these proteins are highly conserved within the Trichinellids, are constituents of mL1 ESP and localized in the parasite stichosome. While SML-5 is only expressed in mL1 and early stages of adult nematode development, SML-4 is a tyvosylated glycoprotein also produced by adult nematodes, indicating it may have a function in the enteral phase of the infection. Vaccination with these proteins resulted in an impaired establishment of adult stages and consequently a reduction in the burden of mL1 in BALB/c mice. This suggests that both proteins may be important for establishment of parasite infection of the intestine and are prophylactic vaccine candidates

Characterization of a Novel Filarial Serine Protease Inhibitor, Ov-SPI-1, from Onchocerca volvulus, with Potential Multifunctional Roles During Development of the Parasite

A novel filarial serine protease inhibitor (SPI) from the human parasitic nematode Onchocerca volvulus, Ov-SPI-1, was identified through the analysis of a molting third-stage larvae expressed sequence tag dataset. Subsequent analysis of the expressed sequence tag datasets of O. volvulus and other filariae identified four other members of this family. These proteins are related to the low molecular weight SPIs originally isolated from Ascaris suumwhere they are believed to protect the parasite from host intestinal proteases. The two Ov-spi transcripts are up-regulated in the molt- ing larvae and adult stages of the development of the parasite. Recombinant Ov-SPI-1 is an active inhibitor of serine proteases, specifically elastase, chymotrypsin, and cathepsin G. Immunolocal- ization of the Ov-SPI proteins demonstrates that the endogenous proteins are localized to the basal layer of the cuticle of third-stage, molting third-stage, and fourth-stage larvae, the body channels and multivesicular bodies of third-stage larvae and the processed mate- rial found between the two cuticles during molting. In O. volvulusadult worms the Ov-SPI proteins are localized to the sperm and to eggshells surrounding the developing embryos. RNA interference targeting the Ov-spi genes resulted in the specific knockdown of the transcript levels of both Ov-spi-1 and Ov-spi-2, a loss of native pro- teins, and a significant reduction in both molting and viability of third-stage larvae. We suggest the Ov-SPI proteins play a vital role in nematode molting by controlling the activity of an endogenous serine protease(s). The localization data in adults also indicate that these inhibitors may be involved in other processes such as embryogenesis and spermatogenesis

Identificación y análisis de la variabilidad morfológica de 59 cultivares de papa criolla (solanum phureja juz. et buk.)

La identificación de la diversidad morfológica de 59 cultivaresde Solanum phureja Juz. el Buk. Se realizó mediante los descriptores estandarizados por el CIP (Centro Internacional de la Papa) en 1994. Los datos se tomaron a partir de los cultivares establecidos en los centros de investigación Tibaitatá y San Jorge, ubicados en los municipios de Mosquera y Soacha respectivamente; los datos fueronsometidos a análisis simples y multivariados tales como: correlación, componentes principales, análisis cluster y análisis de escalamiento multidimensional. Los primeros 10 componentes principales expresaron el 76% de la variabilidad total, mientras el análisis cluster y de escalamiento multidimensional discriminaron los cultivares en ocho grupos Los análisis multivariados mostraron que las variables más importantes para la caracterización e identificación de los grupos son: V25 forma general del tubérculo, V26 formas raras del tubérculo, V18 color primario de la piel del tubérculo, V20 color secundario de la piel del tubérculo, V34 grado de floración y V9 pigmentación del pistilo.The goal of this research was to identify the morphologicaldiversity of 59 genotypes of Solanum phureja Juz. el Buk.According to the descriptors of the CIP (lnternational PotatoCenter) the data were evaluated in two research centers of Corpoica (Mosquera) and ICA (Soacha) villages. The data was analyzed through simple and multivariate statistics such as: correlation, principal components, cluster, and multidimensional analyses. The first ten principal components give 76% of the total variability. The cluster analysis and multidimensional scaling refereed eight genotypes groups. The multivariate analysis showed the most important variables for the characterization and identification, whichwere (V25 tuber's general shapes), V26 (tuber's races shapes), V18 (tuber's skin primary color), V20 (tuber's skin secondary color), V34 (flowering level) and V9 (pistil pigmentation)

Crystal structure and metal binding properties of the periplasmic iron component EfeM from Pseudomonas syringae EfeUOB/M iron-transport system

EfeUOB/M has been characterised in Pseudomonas syringae pathovar. syringae as a novel type of ferrous-iron transporter, consisting of an inner-membrane protein (EfeUPsy) and three periplasmic proteins (EfeOPsy, EfeMPsy and EfeBPsy). The role of an iron permease and peroxidase function has been identified for the EfeU and EfeB proteins, respectively, but the role of EfeO/M remains unclear. EfeMPsy is an ‘M75-only’ EfeO-like protein with a C-terminal peptidase-M75 domain (EfeOII/EfeM family). Herein, we report the 1.6Å resolution crystal structure of EfeMPsy, the first structural report for an EfeM component of P. syringae pv. syringae. The structure possesses the bi-lobate architecture found in other bacterial periplasmic substrate/solute binding proteins. Metal binding studies, using SRCD and ICP-OES, reveal a preference of EfeMPsy for copper, iron and zinc. This work provides detailed knowledge of the structural scaffold, the metal site geometry, and the divalent metal binding potential of EfeM. This work provides crucial underpinning for a more detailed understanding of the role of EfeM/EfeO proteins and the peptidase-M75 domains in EfeUOB/M iron uptake systems in bacteria

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Kondo effect in systems with dynamical symmetries

This paper is devoted to a systematic exposure of the Kondo physics in quantum dots for which the low energy spin excitations consist of a few different spin multiplets $|S_{i}M_{i}>$. Under certain conditions (to be explained below) some of the lowest energy levels $E_{S_{i}}$ are nearly degenerate. The dot in its ground state cannot then be regarded as a simple quantum top in the sense that beside its spin operator other dot (vector) operators ${\bf R}_{n}$ are needed (in order to fully determine its quantum states), which have non-zero matrix elements between states of different spin multiplets $\ne 0$. These "Runge-Lenz" operators do not appear in the isolated dot-Hamiltonian (so in some sense they are "hidden"). Yet, they are exposed when tunneling between dot and leads is switched on. The effective spin Hamiltonian which couples the metallic electron spin ${\bf s}$ with the operators of the dot then contains new exchange terms, $J_{n} {\bf s} \cdot {\bf R}_{n}$ beside the ubiquitous ones $J_{i} {\bf s}\cdot {\bf S}_{i}$. The operators ${\bf S}_{i}$ and ${\bf R}_{n}$ generate a dynamical group (usually SO(n)). Remarkably, the value of $n$ can be controlled by gate voltages, indicating that abstract concepts such as dynamical symmetry groups are experimentally realizable. Moreover, when an external magnetic field is applied then, under favorable circumstances, the exchange interaction involves solely the Runge-Lenz operators ${\bf R}_{n}$ and the corresponding dynamical symmetry group is SU(n). For example, the celebrated group SU(3) is realized in triple quantum dot with four electrons.Comment: 24 two-column page

Comparison of C. elegans and C. briggsae Genome Sequences Reveals Extensive Conservation of Chromosome Organization and Synteny

To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80–110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently