Efectos y respuestas de la costra biológica del suelo en ecosistemas áridos: avances recientes a nivel de especie

La costra biológica del suelo (CBS) es un componente complejo del ecosistema que engloba diferentes organismos (líquenes, musgos, hepáticas, cianobacterias, hongos, algas) presentes en las primeras capas de suelo. La CBS se encuentra en una amplia variedad de ecosistemas, aunque generalmente es más abundante en ecosistemas donde la cobertura de plantas vasculares es escasa, como los ecosistemas áridos. En estos ecosistemas, la CBS contribuye considerablemente a su biodiversidad y funcionamiento. Debido a la gran dificultad para la identificación de especies de estas comunidades, la mayoría de la investigación sobre la CBS se ha desarrollado a escala de comunidad y grupo morfológico. A este nivel, se ha podido observar el gran potencial de estas comunidades de contribuir a la estructura y dinámica del ecosistema: interaccionan con las primeras capas del suelo y con otros organismos, participan en la fijación de carbono y nitrógeno, así como en procesos hidrológicos y en el ciclo de nutrientes. Sin embargo, avances recientes en el conocimiento de la CBS arrojan interesantes y marcadas diferencias en la ecología y el papel funcional de las distintas especies que la componen, con las consecuentes implicaciones en la gestión y conservación de estas comunidades y de los ecosistemas que habitan. En particular, se han observado respuestas específicas en términos de presencia, abundancia y frecuencia ante diversos factores ambientales (variables climáticas, tipo de sustrato, presencia de plantas vasculares y perturbación por pastoreo – recuperación natural), así como un efecto a nivel de especie sobre las propiedades del suelo.

Phosphorylated α-synuclein-immunoreactive retinal neuronal elements in Parkinson's disease subjects

Visual symptoms are relatively common in Parkinson's disease (PD) and optical coherence tomography has indicated possible retinal thinning. Accumulation of aggregated α-synuclein is thought to be a central pathogenic event in the PD brain but there have not as yet been reports of retinal synucleinopathy. Retinal wholemounts were prepared from subjects with a primary clinicopathological diagnosis of PD (N = 9), dementia with Lewy bodies (DLB; N = 3), Alzheimer's disease (N = 3), progressive supranuclear palsy (N = 2) as well as elderly normal control subjects (N = 4). These were immunohistochemically stained with an antibody against α-synuclein phosphorylated at serine 129, which is a specific molecular marker of synucleinopathy. Phosphorylated α-synuclein-immunoreactive (p-syn IR) nerve fibers were present in 7/9 PD subjects and in 1/3 DLB subjects; these were sparsely distributed and superficially located near or at the inner retinal surface. The fibers were either long and straight or branching, often with multiple en-passant varicosities along their length. The straight fibers most often had an orientation that was radial with respect to the optic disk. Together, these features are suggestive of either retinopetal/centrifugal fibers or of ganglion cell axons. In one PD subject there were sparse p-syn IR neuronal cell bodies with dendritic morphology suggestive of G19 retinal ganglion cells or intrinsically photosensitive ganglion cells. There were no stained nerve fibers or other specific staining in any of the non-PD or non-DLB subjects. It is possible that at least some of the observed visual function impairments in PD subjects might be due to α-synucleinopathy.

Correlation between SD-OCT, immunocytochemistry and functional findings in an animal model of retinal degeneration

Purpose: The P23H rhodopsin mutation is an autosomal dominant cause of retinitis pigmentosa (RP). The degeneration can be tracked using different anatomical and functional methods. In our case, we evaluated the anatomical changes using Spectral-Domain Optical Coherence Tomography (SD-OCT) and correlated the findings with retinal thickness values determined by immunocytochemistry.Methods: Pigmented rats heterozygous for the P23H mutation, with ages between P18 and P180 were studied. Function was assessed by means of optomotor testing and ERGs. Retinal thicknesses measurements, autofluorescence and fluorescein angiography were performed using Spectralis OCT. Retinas were studied by means of immunohistochemistry. Results: Between P30 and P180, visual acuity decreased from 0.500 to 0.182 cycles per degree (cyc/deg) and contrast sensitivity decreased from 54.56 to 2.98 for a spatial frequency of 0.089 cyc/deg. Only cone-driven b-wave responses reached developmental maturity. Flicker fusions were also comparable at P29 (42 Hz). Double flash-isolated rod-driven responses were already affected at P29. Photopic responses revealed deterioration after P29.A reduction in retinal thicknesses and morphological modifications were seen in OCT sections. Statistically significant differences were found in all evaluated thicknesses. Autofluorescence was seen in P23H rats as sparse dots. Immunocytochemistry showed a progressive decrease in the outer nuclear layer (ONL), and morphological changes. Although anatomical thickness measures were significantly lower than OCT values, there was a very strong correlation between the values measured by both techniques.Conclusions: In pigmented P23H rats, a progressive deterioration occurs in both retinal function and anatomy. Anatomical changes can be effectively evaluated using SD-OCT and immunocytochemistry, with a good correlation between their values, thus making SD-OCT an important tool for research in retinal degeneration.

Biologic therapies and non-melanoma skin cancer rates in three chronic immune-mediated diseases

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

OvisOme: atualização da base de dados de Ovis aries

Introduction: The Omics sciences are part of the research and diagnostic routines in human health. However, their application in veterinary sciences is still sparse, albeit the increasing number of proteomics studies published, especially regarding farm animals. The amount of information accumulated by these high throughput techniques, makes the existence of specialized databases fundamental. These databases are essential to store, annotate and make available to the scientific community, all the information gathered by the different omics studies, so that researchers can use it to understand the physio pathological mechanisms underlying sheep diseases, as well as to develop new and improved diagnostic, prognostic and therapeutic strategies. Objetive: The aim of this work is to present the OvisOme database and to demosntrate how it can be used to understand the molecular mechanisms urderlying sheep disease. Methodologies: OvisOme compiles all proteins identified by proteomics studies of Ovis aries. The proteins are annotated as to the sample characterization, the proteomics techniques used and all the data the authors refer regarding the donor sheep’s health. Results: The database currently has 1451 proteins, associated to 8 diseases and 10 breeds. When compared to other proteomics databases, the OvisOme stores and displays more information than other databases not specific for sheep, such as UniProt. Conclusion: OvisOme is a valuable tool for the study of the molecular mechanisms underlying sheep health and disease.

(Table 3) Pollen analytical and carpological record of the outcrop Hölle below Dwadieden Park, Rügen Island

Pollen analyses and 14C-datings were carried out on two late glacial profiles from Ruegen Island, Mecklenburg-Vorpommern at the southwestern Baltic coast. The palaeoclimatic and palaeoecologic interpretations were supported by carpological investigations. The organogenic deposits of the 'Hoelle' outcrop near Dwasieden Park were chosen because of their unique stratigraphic position, which according to PANZIG (1989), lay under a m3m-Glacial Till of the Mecklenburg Advance (W3). The results indicated that the initial phase of the late glacial sedimentation in a relatively small and asymmetrical lake basin (in comparison with the larger Nieder- and Credner lake to the southwest), probably had its origin in the older Alleroed (II a) after FIRBAS (1949). The basal clastic sediments were rapidly followed by peat deposits and later, due to a rising water table, by muds rich in organic matter. The area was covered with sparse Betula-(Pinus) forests having heliophilous late-glacial elements typical of the surrounding areas during the younger Alleroed (II b). With the climatic change to colder and drier conditions at the beginning of the Younger Dryas (III), the vegetation decreased and enhanced erosional processes led to the fill up of the depression with fine clastic sediments. The intense relief differences of the surroundings coupled with high water saturation in the sediments led to solifluction in the m3m-Glacial Till and its placement discordantly over the organogenic sequence.

(Table 3) Foraminiferal 87Sr/86Sr ratios and ages of ODP Hole 162-986D sediments

Site 986 was drilled to 965 meters below seafloor (mbsf) on the western Svalbard margin to record the onset of glaciations and to date and document the glacial evolution in the Svalbard-Barents Sea region during the Pliocene-Pleistocene. In this paper, results of sedimentological analyses are discussed in light of seismic stratigraphy and new age determinations. The latter were difficult to obtain in the glacial deposits, and datums are sparse. Through combined paleomagnetic data, biostratigraphy, and Sr isotopes, however, an overall chronology for the main evolutionary steps is suggested. The cored sequence at Site 986 is younger than 2.6 Ma, and the lower 60 m of the section contains no evidence of a major glacial influence. An initial glaciation is interpreted to have occurred at ~2.3 Ma, resulting in increased sand deposition from debris flows at Site 986 and forming a prominent seismic reflector, R7. However, glaciers probably did not reach the shelf break until ~1.6-1.7 Ma (Reflector R6), after which the depositional environment was dominated by diamictic debris flows. A gradual change in source area from the Barents Sea to Svalbard is recorded primarily by changes in carbonate and smectite content, ~355 mbsf (Reflector R5), at an interpolated age of 1.4-1.5 Ma. During the last ~1 m.y., Site 986 has undergone more distal deposition as the main depocenters have shifted laterally. This has resulted in less frequent debris flows and more turbidites and hemipelagic deposits, with a slight fining upward of the cored sediments.

Mineral and chemical composition of hydrothermally altered rocks and sediments from the Middle Valley, ODP Leg 139 data

The Middle Valley segment at the northern end of the Juan de Fuca Ridge is a deep extensional rift blanketed with 200-500 m of Pleistocene turbiditic sediment. Sites 857 and 858 were drilled during Ocean Drilling Program Leg 139 to determine whether these two sites were hydrologically linked end members of an active hydrothermal circulation system. Site 858 was placed in an area of active hydrothermal discharge with fluids up to 270°C venting through anhydrite-bearing mounds on top of altered sediment. The shallow basement of fine-grained basalt that underlies the vents at Site 858 is interpreted as a seamount that was subsequently buried by turbidites. Site 857 was placed 1.6 km south of the Site 858 vents in a zone of high heat flow and numerous seismically imaged ridge-parallel faults. Drilling at Site 857 encountered sediments that are increasingly altered with depth and that overlie a series of mafic sills at depths of 460-940 m below sea floor. Sill margins and adjacent baked sediment are highly altered to magnesian chlorite and crosscut with veins filled with quartz, chlorite, sulfides, epidote, and wairakite. The sill interiors vary from slightly altered, with unaltered plagioclase and clinopyroxene in a mesostasis replaced by chlorite, to local zones of intense alteration and brecciation. In these latter zones, the sill interiors are pervasively replaced by chlorite, epidote, quartz, pyrite, titanite, and rare actinolite. The most complete replacement is associated with brecciated horizons with low recovery and slickensides on fracture surfaces, which we interpret as intersections between faults and the sills. Geochemically, the alteration of the sill complex is reflected in significant whole-rock depletions in Ca, Sr, and Na with corresponding enrichments in Mg, Al, and most metals. The latter results from the formation of conspicuous sulfide poikiloblasts. In contrast, metamorphism of the Site 858 seamount includes incomplete albitization of plagioclase phenocrysts and replacement of sparse mafic phenocrysts. Much of the basement alteration at Site 858 is confined to crosscutting veins except for a highly altered and veined horizon at the contact between basaltic basement and the overlying sediment. The sill complex at Site 857 is more highly depleted in 18O (d18O = 2.4 per mil - 4.7 per mil) and more pervasively replaced by secondary minerals relative to the extrusives at Site 858 (d18O = 4.5 per mil - 5.5 per mil). There is no evidence of significant albitization of the plagioclase at Site 857, suggesting high Ca/Na in the pore fluids. Fluid-inclusion data from hydrothermal minerals in altered mafic rocks and veins at Sites 857 and 858 show a consistency of homogenization temperatures, varying from 245 to 270°C, which is within the range of temperatures observed for the fluids venting at Site 858. The consistency of the fluid inclusion temperatures, the lack of albitization within the Site 857 sills, and the apparently low water/rock ratio collectively suggest that the sill complex at Site 857 is in thermal equilibrium and being altered by a highly evolved Ca-rich fluid similar to the fluids now venting at Site 858. The alteration evident in these two deep crustal drillsites is a result of the ongoing hydrothermal circulation and is consistent with downhole logging results, instrumented borehole results, and hydrothermal fluid chemistry. The pervasive alteration of the laterally extensive sill-sediment complex at Site 857 determines the chemistry of the fluids that are venting at Site 858. The limited alteration of the Site 858 lavas suggests that this basement edifice acts as a penetrator or ventilator for the regional hydrothermal reservoir with much of the flow focussed at the highly altered and veined sediment-basalt contact.

Abundance of ostracoda in sediment cores CRP-1 and CRP-2

Sparse, poorly preserved late Oligocene (3 species) and early Miocene (4 species) ostracod faunas have been recovered from CRP-2A, while relatively more abundant Quaternary faunas occur in CRP-1 (24 species). All taxa are marine. No definitive age assignments can be made on the two older faunas, which are not considered to be in situ, although the taxa identified are not at variance with sediment ages determined on other grounds. The Oligocene ostracods (Lithostratigraphical Unit, LSU 9.4) suggest deposition in cold, relatively shallow, shelf waters with faunal connections to the Antarctic Peninsula and South America, while the Miocene fauna (LSU 5.1) is considered to be a cool-cold, deeper water (?outer shelf) association with faunal connections to both New Zealand and the Antarctic Peninsula. The Quaternary faunas are primarily from LSU 3.1 (carbonate-rich layer), and suggest deposition in very cold, relatively quiet water that was at least 100 m, and possibly 130-200 m deep. None of the taxa are known from pre-Pleistocene sediments, and all occur in modern Antarctic/sub-Antarctic regimes, predominantly from south of 60° S. Specimens in the "carbonate-rich layer" probably have suffered minor penecontemporaneous fractionation, while the fauna in LSU 2.2 has suffered more extensive post-mortem transportation and possible reworking (though not necessarily from pre-Quaternary sources).

Radiolarian assemblages of ODP Leg 117 sites

Significant numbers of radiolarians ranging in age from late middle Miocene to Recent were recovered from six sites drilled on the Oman margin and Owen Ridge. Sparse faunas were recovered from five additional sites on the Oman margin and one site on the Indus Fan. Detailed range charts and biozonations are presented for most sites. The radiolarian assemblages are peculiar in that numerous common tropical forms, some of which are biomarkers, are absent or very rare. In addition, some species not usually found in tropical assemblages are present. These forms, indicative of up welling conditions, fall into three categories: (1) endemic upwelling: species endemic to upwelling and not previously described from the Indian Ocean; (2) displaced temperate: temperate forms not usually found in tropical waters; and (3) enhanced tropical: tropical forms which are more abundant and/or robust in areas of upwelling. Comparison of the Oman margin/Owen Ridge fauna with that recovered from the Peru margin upwelling area (ODP Leg 112) suggests that the assemblage may be globally diagnostic of upwelling conditions. The onset of upwelling is marked by the appearance of siliceous biota at about 11.9 Ma, and there is some indication of a decrease in the strength of the upwelling signal at about 9.6 Ma. A strong pulse in, or strengthening of, the upwelling mechanism is indicated by a marked fauna change at 4.7 Ma. There is a weaker signal, implying a change in upwelling conditions, at about 1.5 Ma.

Lithology, mineralogy and geochemistry of ODP Hole 118-735B and 176-735B respectively

Ocean Drilling Program (ODP) Hole 735B, located on Atlantis Bank on the Southwest Indian Ridge, penetrated 1508 meters below seafloor with an average recovery of 87%, providing a nearly continuous sample of a significant part of oceanic Layer 3. Based on variations in texture and mineralogy, 12 major lithologic units are recognized in the section, ranging from 39.5 to 354 m thick. The principal lithologies include troctolite, troctolitic gabbro, olivine gabbro and microgabbro, gabbro, gabbronorite and Fe-Ti oxide gabbro, gabbronorite, and microgabbro. Highly deformed mylonites, cataclasites, and amphibole gneisses are locally present, as are small quantities of pyroxenite, anorthositic gabbro, and trondhjemite. Downhole variations in mineral composition, particularly for olivine and clinopyroxene, show a number of cyclic variations. Plagioclase compositions show the widest variations and correspond to different degrees of deformation and alteration as well as primary processes. Downhole chemical variations correspond reasonably well with variations in mineral compositions. Iron and titanium mainly reflect the presence of Fe-Ti oxide gabbros but show some cyclical variations in the lower part of the core where oxide gabbros are sparse. CaO is highly variable but shows a small but consistent increase downhole. MgO is more uniform than CaO and shows a very small downward increase. Sulfur and CO2 contents are generally low, but S shows significant enrichment in lithologic Unit IV, which consists of Fe-Ti oxide gabbro, reflecting the presence of sulfide minerals in the sequence. The lithologic, mineralogical, and geochemical data provided here will allow detailed comparisons with ophiolite sections as well as sections of in situ ocean crust drilled in the future.

Depth profiles of dissolved sulfide and sulfate in the pore water of hydrocarbon seep sediments offshore Pakistan

The interaction between fluid seepage, bottom water redox, and chemosynthetic communities was studied at cold seeps across one of the world's largest oxygen minimum zones (OMZ) located at the Makran convergent continental margin. Push cores were obtained from seeps within and below the core-OMZ with a remotely operated vehicle. Extracted sediment pore water was analyzed for sulfide and sulfate concentrations. Depending on oxygen availability in the bottom water, seeps were either colonized by microbial mats or by mats and macrofauna. The latter, including ampharetid polychaetes and vesicomyid clams, occurred in distinct benthic habitats, which were arranged in a concentric fashion around gas orifices. At most sites colonized by microbial mats, hydrogen sulfide was exported into the bottom water. Where macrofauna was widely abundant, hydrogen sulfide was retained within the sediment. Numerical modeling of pore water profiles was performed in order to assess rates of fluid advection and bioirrigation. While the magnitude of upward fluid flow decreased from 11 cm yr**-1 to <1 cm yr**-1 and the sulfate/methane transition (SMT) deepened with increasing distance from the central gas orifice, the fluxes of sulfate into the SMT did not significantly differ (6.6-9.3 mol m**-2 yr**-1). Depth-integrated rates of bioirrigation increased from 120 cm yr**-1 in the central habitat, characterized by microbial mats and sparse macrofauna, to 297 cm yr**-1 in the habitat of large and few small vesicomyid clams. These results reveal that chemosynthetic macrofauna inhabiting the outer seep habitats below the core-OMZ efficiently bioirrigate and thus transport sulfate down into the upper 10 to 15 cm of the sediment. In this way the animals deal with the lower upward flux of methane in outer habitats by stimulating rates of anaerobic oxidation of methane (AOM) with sulfate high enough to provide hydrogen sulfide for chemosynthesis. Through bioirrigation, macrofauna engineer their geochemical environment and fuel upward sulfide flux via AOM. Furthermore, due to the introduction of oxygenated bottom water into the sediment via bioirrigation, the depth of the sulfide sink gradually deepens towards outer habitats. We therefore suggest that - in addition to the oxygen levels in the water column, which determine whether macrofaunal communities can develop or not - it is the depth of the SMT and thus of sulfide production that determines which chemosynthetic communities are able to exploit the sulfide at depth. We hypothesize that large vesicomyid clams, by efficiently expanding the sulfate zone down into the sediment, could cut off smaller or less mobile organisms, as e.g. small clams and sulfur bacteria, from the sulfide source.

Marine palynomorph abundance estimates of sediment core CRP-2A (Fig. 2)

A diverse assemblage of marine palynomorphs was recovered from the Oligocene - Miocene section of CRP-2/2A. Most of the assemblage is composed of previously unrecognised species. Three distinct groups of marine palynomorph were recognised: (1) prasinophytes, mainly Cymatiosphaera, (2) acritarchs, mainly Leiosphaeridia and Sigmopollis although Leiofusa is an important component of the bottom half of the hole, and (3) dinoflagellate cysts. About 27 species of in situ dinoflagellate cysts were recorded, of which seven apparently undescribed species of Lejeunecysta form a prominent component. Reworked specimens of several species of the Paleogene Transantarctic Flora occur in CRP-2/2A sediments. Several abundance peaks of reworked taxa from the Transantarctic Flora are recorded. Three marine palynomorph zones were recognised (MP3, MP2, MP1), considered to be early Oligocene, late Oligocene, and late Oligocene/early Miocene in age respectively. Samples from the Quaternary and Pliocene part of CRP-2/2A were also examined. These proved either barren or yielded very sparse low diversity floras.

Clay mineralogy and shear strength of subglacial and glaciomarine sediments in the southern Bellingshausen Sea

The Belgica Trough and the adjacent Belgica Trough Mouth Fan in the southern Bellingshausen Sea (Pacific sector of the Southern Ocean) mark the location of a major outlet for the West Antarctic Ice Sheet during the Late Quaternary. The drainage basin of an ice stream that advanced through Belgica Trough across the shelf during the last glacial period comprised an area exceeding 200,000 km**2 in the West Antarctic hinterland. Previous studies, mainly based on marine-geophysical data from the continental shelf and slope, focused on the bathymetry and seafloor bedforms, and the reconstruction of associated depositional processes and ice- drainage patterns. In contrast, there was only sparse information from seabed sediments recovered by coring. In this paper, we present lithological and clay mineralogical data of 21 sediment cores collected from the shelf and slope of the southern Bellingshausen Sea. Most cores recovered three lithological units, which can be attributed to facies types deposited under glacial, transitional and seasonally open-marine conditions. The clay mineral assemblages document coinciding changes in provenance. The relationship between the clay mineral assemblages in the subglacial and proglacial sediments on the shelf and the glacial diamictons on the slope confirms that a grounded ice stream advanced through Belgica Trough to the shelf break during the past, thereby depositing detritus eroded in the West Antarctic hinterland as soft till on the shelf and as glaciogenic debris flows on the slope. The thinness of the transitional and seasonally open-marine sediments in the cores suggests that this ice advance occurred during the last glacial period. Clay mineralogical, acoustic sub-bottom and seismic data furthermore demonstrate that the palaeo-ice stream probably reworked old sedimentary strata, including older tills, on the shelf and incorporated this debris into its till bed. The geographical heterogeneity of the clay mineral assemblages in the sub- and proglacial diamictons and gravelly deposits indicates that they were eroded from underlying sedimentary strata of different ages. These strata may have been deposited during either different phases of the last glacial period or different glacial and interglacial periods. Additionally, the clay mineralogical heterogeneity of the soft tills recovered on the shelf suggests that the drainage area of the palaeo-ice stream flowing through Belgica Trough changed through time.

(Table 1) Abundance of selected diatom taxa in the mid-Pliocene of ODP Hole 167-1022A

Diatom assemblages from the middle part of the Pliocene (3.2-2.5 Ma) were investigated from Ocean Drilling Program Sites 1016, 1021, and 1022 in an effort to infer paleotemperature fluctuations off California. Diatoms are very sparse in virtually all of the samples that were examined from Sites 1016 and 1021. This is presumably because these sites were seaward (west) of the coastal zone of diatom productivity during the middle part of the Pliocene. Diatoms are relatively common in the vast majority of samples that were examined from Hole 1022A. Diatom assemblages are dominated by Chaetoceros spores (a coastal upwelling component), the cold-water (subarctic) taxa Neodenticula kamtschatica and its descendant Neodenticula koizumii, and Thalassionema nitzschioides, a temperate taxon that is typically found at the seaward edge of coastal upwelling zones. Paleotemperature interpretations, however, are not possible at this time because of the scarcity of comparative modern core-top data.