Natural development of stand structure in peatland Scots pine following drainage : results based on long-term monitoring of permanent sample plots

Abstract

Tissue-based immune monitoring I: tumor core needle biopsies allow in-depth interrogation of the tumor microenvironment.

We sought to assess the feasibility and reproducibility of performing tissue-based immune characterization of the tumor microenvironment using CT-compatible needle biopsy material. Three independent biopsies were obtained intraoperatively from one metastatic epithelial ovarian cancer lesion of 7 consecutive patients undergoing surgical cytoreduction using a 16-gauge core biopsy needle. Core specimens were snap-frozen and subjected to immunohistochemistry (IHC) against human CD3, CD4, CD8, and FoxP3. A portion of the cores was used to isolate RNA for 1) real-time quantitative (q)PCR for CD3, CD4, CD8, FoxP3, IL-10 and TGF-beta, 2) multiplexed PCR-based T cell receptor (TCR) CDR3 Vβ region spectratyping, and 3) gene expression profiling. Pearson's correlations were examined for immunohistochemistry and PCR gene expression, as well as for gene expression array data obtained from different tumor biopsies. Needle biopsy yielded sufficient tissue for all assays in all patients. IHC was highly reproducible and informative. Significant correlations were seen between the frequency of CD3+, CD8+ and FoxP3+ T cells by IHC with CD3ε, CD8A, and FoxP3 gene expression, respectively, by qPCR (r=0.61, 0.86, and 0.89; all p< 0.05). CDR3 spectratyping was feasible and highly reproducible in each tumor, and indicated a restricted repertoire for specific TCR Vβ chains in tumor-infiltrating T cells. Microarray gene expression revealed strong correlation between different biopsies collected from the same tumor. Our results demonstrate a feasible and reproducible method of immune monitoring using CT-compatible needle biopsies from tumor tissue, thereby paving the way for sophisticated translational studies during tumor biological therapy.

Height distributions of Scots pine sapling stands affected by retained tree and edge stand competition

Abstract

Natural regeneration of Scots pine and Norway spruce close to the timberline in northern Finland

Abstract

Calcitic nanofibers in soils and caves : a putative fungal contribution to carbonatogenesis

The origin of soil mineralized nanofibres remains controversial. It is attributed to either biogenic factors or physicochemical processes. Scanning electron microscope and transmission electron microscope observations show that nanofibres could originate from the breakdown of fungal hyphae, especially its cell wall. It is hypothesized that during the decay of organic matter, cell wall microfibrils are released in the soil where they are exposed to mineralizing pore fluids, leading to their calcitic pseudomorphosis and/or are used as a template for calcite precipitation. When associated with needle fibre calcite bundles, nanofibres could indicate the relict of an organic sheath in which calcite has precipitated. This paper emphasizes the important roles of both organic matter and fungi in carbonatogenesis, and consequently in the soil carbon cycle.

Outcomes of optic nerve sheath decompression for nonarteritic ischemic optic neuropathy.

Efficacy of optic nerve sheath decompression (ONSD) in treating non-arteritic ischemic optic neuropathy (NAION) is not clear. We retrospectively analyzed the records of 91 patients with NAION, who were examined during a two-year period, and compared the final Snellen visual acuities of eyes treated with ONSD with those of eyes that did not have surgery. Seven of 18 eyes with ONSD (39%) demonstrated increased visual acuity of two or more lines; whereas 23 of 71 eyes without surgery (32%) had increased acuity. The ONSD group and no surgery group were further subdivided into eyes with progressive visual loss and nonprogressive visual loss. No statistically significant differences in visual outcome between groups were found. We did not find the high frequency of visual improvement that has been reported in some studies of ONSD for NAION.

Origin of needle fibre calcite (NFC) : a geochemical approach

ABSTRACTNeedle fibre calcite (NFC) is one of the most widespread habits of pedogenic calcite. It is a monocrystal of calcite, in the shape of a needle, with a diameter of one micron and a length between 4 and 103 times its width. NFC occurs in soils with different macroscopic and microscopic morphologies. Macroscopically, two main habits of NFC exist: "cotton ball'Mike clusters and as "powder" coating on pebbles inside the soil. It can also act as nucleation sites for precipitation of calcite cements of purely physicochemical origin (LCC - Late Calcitic Cement). Although many studies have been conducted on needle fibre calcite, its origin remains a subject of debate. The NFC having never been reproduced in the laboratory whatever the considered approach, the processes responsible for its precipitation as a so particular morphology remain unexplained. The shift between the length orientation of the needle crystal and the normal axis of calcite growth (c-axis) is also unresolved.Samples taken in two soils observed in quarries (Villiers and Savagnier) in the Swiss Jura Mountains are used to investigate the processes involved in the formation of these calcite crystals in pedogenic environments. Three groups of microscopic morphologies are distinguished: (i) simple needles (SN), (ii) simple needles with overgrowths (SNO), and (iii) simple needles with nanofibres (SNN), nanofibres being either organic or mineral in nature. These groups correspond to different stages in the formation and evolution of NFC.Comparison of carbon and oxygen isotope compositions of NFC with LCC, in relationship with the composition of the carbonate host rock (CHR), and the carbon isotope signature of dissolved inorganic carbon (DIC) from the soil waters, indicates that both NFC and LCC are precipitated in isotopic equilibrium with the soil solution. Similar Ô13C and Ô180 values of the elongated NFC and the rhombohedral calcite crystals of the LCC suggest that the precipitation of these different calcite habits is not due to changes in physicochemical conditions. The growth of NFC crystals inside an organic mould formed by the fungal hyphae could explain the formation of calcite ciystals in the shape of a needle in isotopic equilibrium with the local environment.Strontium and calcium isotope compositions of the three microscopic groups of NFC and LCC were also studied, in order to determine the origin of calcium (Ca2+) entrapped in the calcite lattice and to elucidate the processes responsible for the precipitation of NFC. The 87Sr/86Sr ratio of the SN is closer to the 87Sr/86Sr ratio of the carbonate host rock than the LCC, SNO, and SNN. This could be another clue for the formation of SN inside fungal hyphae, because fungi are known to dissolve the rocks to release and translocate through their hyphae nutrients necessary for their growth. SN and SNN are depleted in Sr and enriched in ^Ca compared to the LCC. In the context of Villiers quarry, where the two ciystal shapes precipitate at similar temperature (in a range of 0,6°C), such variations are the result of a slower precipitation rate of NFC, which is inconsistent with a purely physicochemically precipitated elongate crystal.Finally, NFC is enriched in major and trace elements (i.e. Fe, Zn, Cu, and Mo) compared to the LCC. This enrichment is ascribed to modification in precipitation processes between the NFC and LCC. Right now, it is not possible to preclude the influence of the particular shape of NFC or the biological influence. REEs are not fractionated in NFC, contrary to LCC. Thus, NFC does not precipitate from a percolation solution circulating downward the soil, which should lead to the fractionation of the REEs. As explained above, fungi, are able to dissolve and translocate nutrients. This kind of processes allows releasing elements in the soil solution without fractionation and could explain the particular chemical signature of NFC regarding the REEs.The geochemical approach to investigate the origin of NFC presented in this study does not allow providing direct clues to the fungal origin of NFC, but brings several new insights in the understanding of the formation of such a particular mineral, calcite needles, by precluding definitively their physicochemical origin.RESUMELa calcite en aiguilles (NFC) est l'une des formes les plus ubiquiste de calcite pédogénique. Il s'agit d'un monocrystal de calcite d'un diamètre d'un micron et d'une longueur 4 à 102 fois supérieure à sa largeur. A l'échelle macroscopique, la NFC a été observée sous deux principaux aspects : l'une « cotonneuse » et l'autre formant un mince croûte autour des graviers du sol. La NFC peut également servir de support à la nucléation de ciments secondaires précipités de manière purement physico-chimique (LCC). Malgré les nombreuses études menées sur la NFC, son origine demeure encore inconnue. A ce jour, aucune expérience en laboratoire n'a permis de créer de la calcite en aiguilles, et ce, quelque soit l'approche abordée. Par conséquent, les processus précis responsables de la précipitation calcite avec une telle morphologie restent inconnus. Le décalage existant entre l'axe d'allongement des aiguilles de calcite et l'axe normal de croissance de la calcite (axe c) reste inexpliqué.Des échantillons de NFC, LCC, roche mère, eau de pluie des différents horizons du sol ont été prélevés principalement au front de deux carrières de graviers, ainsi que dans un profil de sol adjacent à ces carrières, dans le but de mieux comprendre les processus à l'origine de la précipitation de calcite en forme d'aiguille. Trois micro-morphologies ont été distinguées: les aiguilles simples (SN), les aiguilles simples avec surcroissances calcitiques (SNO) et enfin les aiguilles simples avec nanofibres (SNN), celles-ci pouvant être de minérales ou organiques. Ces groupes, d'après nos résultats et les études antérieures pourraient correspondre à différentes étapes de formation de la calcite en aiguilles.Dans un premier temps, la comparaison des signatures isotopiques de la calcite en aiguilles, du LCC, de la roche mère et du carbone inorganique dissout dans la solution du sol (CID) indique que la NFC, tout comme le LCC, précipite en équilibre avec la solution du sol. Les valeurs similaires en Ô13C et δ180 de cristaux de calcite allongés (NFC) et rhombohédriques (LCC) formés dans un même milieu suggère que ces différences morphologiques ne peuvent pas être attribuées à des modifications purement physico-chimiques. La croissance de NFC à l'intérieur d'un moule organique comme les hyphes de champignons semble être la seule hypothèse plausible permettant d'expliquer la formation de monocrystaux allongés de calcite en équilibre avec leur environnement.La composition isotopique en strontium (Sr) et calcium (Ca) des LCC et des trois micro¬morphologies de la NFC ont été étudiées également, afin de déterminer l'origine du Ca2+ présent dans le réseau cristallin de la calcite en aiguilles, ainsi que les processus responsables de la formation de NFC. Les valeurs du rapport 87Sr/86$r de la forme SN sont les plus proches de celles de la roche mère par rapport aux formes SNN et SNO et du LCC. Ceci pourrait être un nouvel indice de l'implication des champignons dans la précipitation de calcite en aiguilles, puisqu'ils sont connus pour avoir la capacité de dissoudre les roches afin de libérer les nutriments nécessaires à leur croissance, ainsi que de les transloquer par leurs hyphes. De plus, les formes SN et SNN sont appauvries en Sr et enrichies en "Ca, comparativement au LCC. Dans le sol étudié, tous les carbonates de calcium précipitent à la même température, par conséquent, de telles variations sont dues à un taux de précipitation plus lent de SN et SNN, ce qui est contradictoire avec l'hypothèse physico-chimique. Pour finir, la NFC est enrichie en certains éléments majeurs et traces (i.e. Fe, Zn, Cu et Mo) par rapport au LCC. Ceci peut être attribué à différents processus de formation entre la NFC et le LCC. Pour le moment il est impossible d'exclure l'influence de la forme particulière de la NFC ou celle du champignon. Les terres rares (REEs) ne sont pas fractionnées dans la NFC, contrairement au LCC. Ceci peut être expliqué par le fait que la NFC précipite à partir d'une solution qui n'a pas percolé à travers le sol. Les champignons en dissolvant les roches mettent en solution éléments sans les fractionner. L'approche géochimique de l'étude de la calcite en aiguilles ne permets pas de produire des preuves directes sur sa potentielle origine fongique, mais permet de mieux comprendre comment un minéral aussi singulier que la NFC peut se former. D'autre pare cette étude permets d'exclure définitivement l'hypothèse physico-chimique de l'origine de la calcite en aiguilles

Recruitment models for Norway spruce, Scots pine, birch and other broadleaves in young growth forests in Norway

Abstract

Defoliation by the common pine sawfly (Diprion pini) and subsequent growth reduction in Scots pine : a retrospective approach

Abstract

Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

The objective of this work was to analyze coffee (Coffea arabica) genotypes resistant to the coffee leaf miner (Leucoptera coffeella) using microsatellite markers. Sixty-six loci were evaluated, of which 63 were obtained from the Brazilian Coffee Expressed Sequence Tag (EST) database. These loci were amplified in bulks of individuals from F5 progenies of 'Siriema' (C. arabica x C. racemosa) resistant and susceptible to the insect, in eight samples of C. racemosa, and in a F6 population of 'Siriema' with 91 individuals segregating for resistance to the leaf miner. Polymorphisms were verified for two simple sequence repeat (SSR) loci in bulks of the susceptible progenies. The two polymorphic alleles were present in around 70% of the susceptible genotypes in F5 and in approximately 90% of the susceptible individuals in F6. However, the polymorphic EST-SSR markers among populations contrasting for resistance to leaf miner were not correlated to the evaluated characteristics. SSR markers show inter- and intraspecific polymorphism in C. arabica and C. racemosa.

Leaf miner incidence in coffee plants under different drip irrigation regimes and planting densities

The objective of this work was to evaluate the effect of different drip irrigation regimes and planting densities on the incidence of the leaf miner, Leucoptera coffeella, in arabica coffee plants for one year. The experiment was carried out in 2008, in a complete randomized block design, in a split-plot in time arrangement, with four replicates. The treatments consisted of four drip irrigation regimes - soil water balance, irrigations at 20 and 60 kPa soil tensions, and a nonirrigated treatment -, which were distributed at three plant densities: 2, 500, 5, 000, and 10, 000 plants per hectare. The evaluations were made on a monthly basis between January and December 2008. The highest pest occurrence period was from August to November, a season with low-air relative humidity preceded by a drought period. Irrigated coffee plants showed an incidence of intact mines 2.2 times lower than that of nonirrigated plants. Irrigation and increasing of plant density contribute to the reduction of coffee leaf miner occurrence.