Chemostratigraphy (CaCO3, TOC, d13Corg) of Sinemurian black shales

The Shales-with-'Beef' and Black Ven Marls of the Charmouth Mudstone Formation (Sinemurian) exposed on the Dorset Coast in southern England (Wessex Basin) show stratigraphic variation in carbonate, organic carbon and organic-carbon isotopes. Little environmental significance is attached to the variation of carbonate except in the case of the tabular and nodular limestones interrupting the sequence that probably record stratigraphic condensation and/or sedimentary stillstands that, in an extreme case, were accompanied by sea-floor erosion to produce the bored and encrusted 'Coinstone'. Relatively high total organiccarbon (TOC) contents are present in the laminated mudstones of the lower turneri Zone (upper brooki and lower birch Subzones) and the obtusum Zone (obtusum and stellare Subzones). Basin stratification related to fresh-water influx was the most likely aid to deoxygenation and enhanced preservation of organic matter. The organic-carbon isotope curve (d13Corg), which shows positive excursions in the upper turneri Zone (upper birchi Subzone) and highest obtusum - raricostatum Zones (highest stellare Subzone, densinodulum and lower raricostatoides Subzones), does not correlate with the TOC stratigraphy and was clearly not controlled by local patterns of organic-matter burial. Long-term (hundreds-of-thousands of years) variations in the carbon-isotope (d13Corg) curve are interpreted as reflecting changing seawater isotopic composition and, in the case of the stratigraphically higher interval, may be related to marine organic-carbon burial on the margins of the proto-Atlantic, as exemplified by the Lusitanian Basin in Portugal. Correlation of the carbon-isotope profile with putative sea-level curves is problematic in detail, although significant local transgressive pulses in the turneri and late raricostatum Zones are approximately coincident with positive d13Corg excursions.

Contents and stable carbon isotope compositions of biomarkers indicative for AOM-communities dominated by different ANME groups in two carbonate samples from Hydrate Hole pockmark

Different types of seep carbonates were recovered from the 'Kouilou pockmarks' on the Congo deep-sea fan in approximately 3100 m water depth. The carbonate aggregates are represented by pyritiferous nodules, crusts and slabs, tubes, and filled molds. The latter are interpreted to represent casts of former burrows of bivalves and holothurians. The nodules consisting of high-Mg-calcite apparently formed deeper within the sediments than the predominantly aragonitic crusts and slabs. Nodule formation was caused by anaerobic oxidation of methane dominantly involving archaea of the phylogenetic ANME-1 group, whereas aragonitic crusts resulted from the activity of archaea of the ANME-2 cluster. Evidence for this correlation is based on the distribution of specific biomarkers in the two types of carbonate aggregates, showing higher hydroxyarchaeol to archaeol ratios in the crusts as opposed to nodules. Formation of crusts closer to the seafloor than nodules is indicated by higher carbonate contents of crusts, probably reflecting higher porosities of the host sediment during carbonate formation. This finding is supported by lower d18O values of crusts, agreeing with precipitation from pore waters similar in composition to seawater. The aragonitic mineralogy of the crusts is also in accord with precipitation from sulfate-rich pore waters similar to seawater. Moreover, the interpretation regarding the relative depth of formation of crusts and nodules agrees with the commonly observed pattern that ANME-1 archaea tend to occur deeper in the sediment than members of the ANME-2 group. Methane represents the predominant carbon source of all carbonates (d13C values as low as -58.9 per mil V-PDB) and the encrusted archaeal biomarkers (d13C values as low as -140 per mil V-PDB). Oxygen isotope values of some nodular carbonates, ranging from + 3.9 to + 5.1per mil V-PDB, are too high for precipitation in equilibrium with seawater, probably reflecting the destabilization of gas hydrates, which are particularly abundant at the Kouilou pockmarks.

Geochemistry of some manganese nodules

The manganese nodules occur in greater or less quantity all over the ocean-bed, and most abundantly in the Pacific. They occur in all sizes, from minute grains to masses of a pound weight, and even greater, and form nodular concretions of concentric shells, round a nucleus, which is very frequently a piece of pumice or a shark's tooth. Their outside has a peculiar and very characteristic mammillated surface, which enables them to be identified at a glance. When freshly brought up they are very soft, being easily scraped to powder with a knife. They gradually get harder on exposure to the air. The powder, heated in a closed tube, gives out water which re-acts alkaline, and has an empyreumatic odour. Heated with strong hydrochloric acid, it liberates abundance of chlorine, and the residue which remains is white, consisting of silica, clay, and sand, the sand being the same as is found in the bottom mud from the same locality. Their composition varies greatly, different nodules containing different quantities of mechanically admixed mud, and the number of different elements found in them is very large. Copper, iron, cobalt, nickel, manganese, alumina, lime, magnesia, silica, and phosphoric acid have been detected in a large number; but I have not as yet been able to make a complete analysis of any of them. I have, however, made a few determinations of the most important component substances. For this purpose the outside and densest layers of the nodules were selected, and portions of them were pulverised and dried for ten or twelve hours at 140° C. The amount of chlorine liberated on treatment with hydrochloric acid was determined by Bunsen's method, and the iron was determined by titration with stannous chloride. The samples analysed were from four different localities.

Chemical composition of DSDP and ODP cherts

Rare earth element (REE), major, and trace element abundances and relative fractionations in forty nodular cherts sampled by the Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) indicate that the REE composition of chert records the interplay between terrigenous sources and scavenging from the local seawater. Major and (non-REE) trace element ratios indicate that the aluminosilicate fraction within the chert is similar to NASC (North American Shale Composite), with average Pacific chert including ~7% NASC-like particles, Indian chert ~11% NASC, Atlantic chert ~17% NASC, and southern high latitude (SHL) chert 53% NASC. Using La as a proxy for sum REE, approximations of excessive La (the amount of La in excess of that supplied by the detrital aluminosilicate fraction) indicate that Pacific chert contains the greatest excessive La (85% of total La) and SHL chert the least (38% of total La). As shown by interelement associations, this excessive La is most likely an adsorbed component onto aluminosilicate and phosphatic phases. Accordingly, chert from the large Pacific Ocean, where deposition occurs relatively removed from significant terrigenous input, records a depositional REE signal dominated by adsorption of dissolved REEs from seawater. Pacific chert Ce/Ce* <<1 and normative La/Yb ~ 0.8-1, resulting from adsorption of local Ce-depleted seawater and preferential adsorption of LREEs from seawater (e.g., normative La/Yb ~0.4), which increases the normative La/Yb ratio recorded in chert. Chert from the Atlantic basin, a moderately sized ocean basin lined by passive margins and with more terrigenous input than the Pacific, records a mix of adsorptive and terrigenous REE signals, with moderately negative Ce anomalies and normative La/Yb ratios intermediate to those of the Pacific and those of terrigenous input. Chert from the SHL region is dominated by the large terrigenous input on the Antarctic passive margin, with inherited Ce/Ce* ~1 and inherited normative La/Yb values of ~1.2-1.4. Ce/Ce* does not vary with age, either throughout the entire data base or within a particular basin. Overall, Ce/Ce* does not correlate with P2O5 concentrations, even though phosphatic phases may be an important REE carrier.

Oxygen isotopes and hydrocarbon composition of gas hydrate and hydrate water from ODP Leg 165 sites

Ocean Drilling Program (ODP) Leg 164 recovered a number of large solid gas hydrate from Sites 994, 996, and 997 on the Blake Ridge. Sites 994 and 997 samples, either nodular or thick massive pieces, were subjected to laboratory analysis and measurements to determine the structure, molecular and isotopic composition, thermal conductivity, and equilibrium dissociation conditions. X-ray computed tomography (CT) imagery, X-ray diffraction, nuclear magnetic resonance (NMR), and Raman spectroscopy have revealed that the gas hydrates recovered from the Blake Ridge are nearly 100% methane gas hydrate of Structure I, cubic with a lattice constant of a = 11.95 ± 0.05 angström, and a molar ratio of water to gas (hydration number) of 6.2. The d18O of water is 2.67 per mil to 3.51 per mil SMOW, which is 3.5-4.0 heavier than the ambient interstitial waters. The d13C and dD of methane are -66 per mil to -70 per mil and -201 per mil to -206 per mil, respectively, suggesting that the methane was generated through bacterial CO2 reduction. Thermal conductivity values of the Blake Ridge hydrates range from 0.3 to 0.5 W/(m K). Equilibrium dissociation experiments indicate that the three-phase equilibrium for the specimen is 3.27 MPa at 274.7 K. This is almost identical to that of synthetic pure methane hydrate in freshwater.

Native bradyrhizobial symbionts of Lupinus mariae-josephae, a unique endemism thriving in alkaline soils in Eastern Spain

Lupinus mariae-josephae (Lmj) es una especie de lupino endémica de una pequeña y específica área de Comunidad Valenciana (Este de España), donde prospera en suelos alcalinoscalcáreos, un hábitat singular para los altramuces, que crecen preferentemente en suelos ácidos o neutros. Esto hace de Lmj una especie de lupino única. Cuando se inició este trabajo, la extensión conocida de este endemismo abarcaba unos 700 kilómetros cuadrados, confinados en la provincia de Valencia. En esta área, Lmj prospera en pequeñas poblaciones aisladas que contienen un número reducido de plantas por lo que se la consideró una especie en peligro de extinción. Todos los esfuerzos, utilizando estrategias clásicas dirigidas a ampliar el área de crecimiento de Lmj y garantizar su conservación, han tenido un éxito limitado. El trabajo que se presenta está dirigido a mejorar el conocimiento de la ecología de Lmj, en particular la interacción simbiótica que establece con bacterias del suelo denominadas rizobios y se centra en la caracterización fenotípica, filogenética y genómica de esos rizobios. También se investiga la posible contribución de la simbiosis en mejorar la conservación de Lmj. Para este fin, se han estudiado diferentes aspectos que se describen a continuación. El primero objetivo se centró en aislar y estudiar de la diversidad genética de las bacterias endosimbióticas de Lmj. . Se realizó un análisis filogenético de genes esenciales que mostró que las cepas de Lmj pertenecen al género Bradyrhizobium y que presentan una gran diversidad con características fenotípicas y simbióticas diferentes de cepas de Bradyrhizobium que nodulan otras especies de lupinos nativos de España (cepas ISLU). Las cepas estudiadas se dividieron en dos grupos (Clado I y Clado II). El Clado I, incluye a las cepas Lmj, definiendo un nuevo linaje, filogenéticamente relacionado con otras especies de Bradyrhizobium, como B. jicamae y B. elkanii. El Clado II contiene cepas ISLU relacionadas con cepas de B. canariense y B. japonicum que establecen simbiosis con lupinos de suelos ácidos. Otro análisis filogenético basado en genes simbióticos, distribuyó las cepas de Lmj en sólo dos grupos diferentes. La singularidad y gran diversidad de estas cepas en una pequeña área geográfica, hacen de este, un atractivo sistema para el estudio de la evolución y adaptación de las bacterias simbióticas a su respectiva planta huésped. Adicionalmente, se estudio la presencia de bacterias capaces de nodular Lmj en suelos básicos de Chiapas, México. Sorprendentemente, estos suelos contienen bacterias capaces establecer interacciones simbióticas eficientes con Lmj en ensayos de invernadero. A continuación se investigó la taxonomía de los endosimbiontes de Lmj analizando la secuencia de cuatro genes esenciales (16S rRNA, recA, glnII y atpD) y el promedio de identidad de nucleótidos de genomas completos de algunas cepas representativas de la diversidad (ANIm). Se identificaron nuevas especies de Bradyrhizobium dentro del Clado I y se definió una de ellas: 'Bradyrhizobium valentinum' sp. nov (cepa tipo LmjM3T = CECT 8364T, LMG 2761T). También se abordó cómo conservar Lmj en su hábitat natural mediante inoculación con alguna de las cepas aisladas. Se demostró la ausencia de bacterias capaces de nodular Lmj en suelos rojos alcalinos o ‘‘terra rossa’’ de la Península Ibérica y Baleares. Dos cepas, altamente eficientes en cuanto a la fijación de nitrógeno, LmjC y LmjM3T, fueron seleccionadas para ser empleadas como inoculantes. Dos experimentos de campo llevados a cabo en años consecutivos en áreas con características edafoclimáticas similares a las que presentan las poblaciones de Lmj, lograron la reproducción exitosa de la planta. Se concluyó que un ciclo reproductivo exitoso de Lmj es absolutamente dependiente de la inoculación con sus simbiontes naturales y que la simbiosis debe ser considerada un factor esencial en estrategias de conservación de leguminosas en peligro. La obtención de varias secuencias genómicas de cepas aisladas de Lmj y de otras cepas de Bradyrhizobium reveló una alta similitud entre los genomas de las cepas del Clado I, y permitió la identificación de cinco posibles nuevas especies. Además, se estudiaron tres agrupaciones de genes relacionados con la simbiosis (nod, nif y fix) definiendo un nuevo linaje para las cepas de Lmj, diferente del symbiovar “genistearum” de B. canariense y B. japonicum. La baja diversidad encontrada en el análisis filogenético de los genes simbióticos contrasta con la gran diversidad asociada a genes esenciales. La presencia de plásmidos en cepas del género Bradyrhizobium ha sido descrita en muy pocas ocasiones, sin embargo el análisis de la secuencia genómica de la cepa ISLU101, aislada de Lupinus angustifolius, reveló la presencia de un origen de replicación extracromosómico homólogo al operón repABC, presente en el plásmido de Bradyrhizobium sp BTAi1. Gracias a esta secuencia se identificaron genes homólogos en 19 de 72 cepas ISLU. Filogenéticamente, las secuencias de repABC se agruparon en un grupo monofilético con las de pBTAi1 y separadas de los rizobios de crecimiento rápido. Finalmente, se identificaron sistemas de secreción de proteínas de tipo III (T3SS) en nueve genomas de cepas de Lmj. Los T3SS pueden inyectar proteínas efectoras al interior de células vegetales. Su presencia en rizobios se ha relacionado con la gama de hospedador que pueden nodular y puede tener un efecto beneficioso, neutro o perjudicial en la simbiosis. Los T3SS de las cepas de Lmj codifican para una proteína efectora similar a NopE, un efector dependiente de T3SS descrito en B. diazoefficiens USDA 110T. La proteína NopE de la cepa LmjC se ha caracterizado bioquímicamente. ABSTRACT Lupinus mariae-josephae (Lmj) is a lupine species endemic of a unique small area in Valencia region (Eastern Spain) where the lupine plants thrive in alkaline-limed soils, which preferentially grow in acid or neutral soils. This is the type of soils native lupines of Spain. When this work was initiated, the extension of the endemic area of Lmj was of about 700 squared kilometers confined to the Valencia province. In this area, Lmj thrives in small, isolated patches containing a reduced number of plants, and points to an endemism that can easily became endangered or extinct. Consequently, the Valencia Community authorities gave a ‘‘microreserve” status for conservation of the species. All efforts, using classical strategies directed to extend the area of Lmj growth and ensure its conservation have been so far unsuccessful. The work presented here is directed to improve our knowledge of Lmj ecology and it is centered in the characterization of the rhizobial symbiosis by phenotypic, phylogenetic and genomic analysis as well as in investigate the potential contribution of the symbiosis to improve its conservation. To this end, five different topics have been studied, and results are briefly described here. Extensive details can be followed en the attached, published articles. The first topic deals with the indigenous rhizobial symbionts of the Lmj endemism, and its genetic diversity was investigated. The Lmj root symbionts belong to the Bradyrhizobium genus, and phylogenetic analysis based on core genes identified a large diversity of Bradyrhizobium strains with phenotypic and symbiotic characteristics different from rhizobia nodulating other Lupinus spp. native of Spain. The strains were split in two clades. Clade II contained strains close to classical B. canariense and B. japonicum lineages that establish symbioses with lupines in acid soils of the Mediterranean area. Clade I included Lmj strains that define a new lineage, close to other Bradyrhizobium species as B. jicamae and B. elkanii. The phylogenetic analysis based on symbiotic genes identified only two distinct clusters. The singularity and large diversity of these strains in such a small geographical area makes this an attractive system for studying the evolution and adaptation of the rhizobial symbiont to the plant host. Additionally, the presence of bacteria able to nodulate Lmj in basic soils from Chiapas, Mexico was investigated. Surprisingly, these soils contain bacteria able to effectively nodulate and fix nitrogen with Lmj plants in greenhouse assays. In the second topic, the taxonomic status of the endosymbiotic bacteria of Lmj from Valencia endemism and Chiapas was investigated. Results from phylogenetic analysis of core genes and Average Nucleotide Identity (ANIm) using draft genomic sequences identified new Bradyrhizobium species within strains of Clade I of Lmj endosymbiotic bacteria. Only one of these potentially new species has been defined, meanwhile the others are under process of characterization. The name ‘Bradyrhizobium valentinum’ sp. nov. was proposed for the defined species (type strain LmjM3T= CECT 8364T, LMG 2761T). The third topic was directed to conservation of endangered Lmj in its natural habitat. The relevant conclusion of this experimentation is that the symbiosis should be considered as a relevant factor in the conservation strategies for endangered legumes. First, we showed absence of bacteria able to nodulate Lmj in all the inspected ‘‘terra rossa’’ or alkaline red soils of the Iberian Peninsula and Balearic Islands. Then, two efficient nitrogen fixing strains with Lmj plants, LmjC and LmjM3T, were selected as inoculum for seed coating. Two planting experiments were carried out in consecutive years under natural conditions in areas with edapho-climatic characteristics identical to those sustaining natural Lmj populations, and successful reproduction of the plant was achieved. The relevant conclusion from these assays was that the successful reproductive cycle was absolutely dependent on seedling inoculation with effective bradyrhizobia The forth topic deep into the analysis of the genomic of Lmj representative strains. To this end, draft genomic sequences of selected Lmj strains and type strains of Bradyrhizobium spp. were assembled. The comparison analysis of the draft genomic sequences of Lmj strains and related Bradyrhizobium species grouped in Clade I, revealed a high genomic homology among them, and allowed the definition of five potentially new species of Lmj nodulating bacteria. Also, based on the available draft genomic sequences, only three clusters of nod, fix and nif genes from Lmj strains were identified and showed to define a new symbiotic lineage, distant from that of B. canariense and B. japonicum bv. genistearum. The low diversity exhibited by the phylogenetic analysis of symbiotic genes contrast with the large diversity of strains as regards the housekeeping genes analyzed. Besides, the genomic analysis of a Lupinus angustifolius strain ISLU101, revealed the presence of an extrachromosomal replication origin homologous to repABC cluster from plasmid present in Bradyrhizobium spp BTAi1. This repABC cluster gene sequence allowed the identification of extrachromosomic replication origin in 19 out of 72 Bradyrhizobium strains from Lupinus spp., a highly significant result since the absence of plasmids in the Bradyrhizobium genus was traditionally assumed. The repABC gene sequences of these strains grouped them in a unique monophyletic group, related to B. sp. BTAi1 plasmid, but differentiated from the repABC gene cluster of plasmids in fast growing rhizobium strains. The last topic was focused on characterization of type III secreted effectors present in Lmj endosymbiotic bacteria. Type III secretion systems (T3SS) are specialized protein export machineries which can deliver effector proteins into plant cells. The presence of T3SS in rhizobia has frequently been related to the symbiotic nodulation host-range and may have a beneficial or detrimental effect on the symbiosis with legumes. In this context, the presence of T3SS in genomes of nine Lmj strains was investigated, and it was shown the presence of clusters encoding NopE type III-secreted protein similar to the NopE1 and NopE2 of B. diazoefficiens USDA 110T. The putative NopE protein of LmjC strain is at present being characterized regarding its structure and function.

Anatomía comparada de la madera de Cupressaceae y su correspondencia con los estudios de filogenia

La familia Cupressaceae incluye un total de 133 especies agrupadas en 30 géneros, 17 de los cuales son monospecíficos. Esta familia se encuentra representada en todos los continentes salvo en la Antártida. Sus especies se distribuyen en distintas regiones climáticas, y en altitudes que varían desde el nivel del mar hasta los 5.000 m. La falta de descripción anatómica de muchos de los géneros y especies de Cupressaceae es notable, así como la contradicción que aparece entre distintas investigaciones sobre las características anatómicas de la madera descritas para cada especie. Este estudio describe la anatomía de la madera de Cupressaceae y analiza las características que podrían representar sinapomorfías de los clados delimitados en los estudios filogenéticos. Siguiendo los métodos tradicionales de preparación y descripción de la madera a nivel microscópico, se ha estudiado la madera de 113 especies de los 30 géneros de Cupressaceae. Para ello se han empleado muestras de madera de origen trazable, procedentes de colecciones de madera de distintas instituciones internacionales. Se ha empleado una robusta filogenia molecular para la reconstrucción de los caracteres ancestrales. La anatomía de la madera de los 30 géneros de Cupressaceae, pone de manifiesto la gran homogeneidad de la familia, caracterizada por la presencia de traqueidas axiales sin engrosamientos helicoidales, parénquima radial con paredes horizontales lisas, punteaduras del campo de cruce de tipo cupresoide y la carencia de canales resiníferos fisiológicos. Además, todos presentan parénquima axial (salvo Neocallitropsis, Thuja y Xanthocyparis), punteaduras radiales areoladas con toro definido (salvo Thuja y Thujopsis), siendo habitual la presencia de punteaduras areoladas en las paredes tangenciales de la madera tardía, y verrugosidades en la cara interna de las traqueidas (salvo Ca. macleayana, Libocedrus, Papuacedrus y Neocallitropsis). Los radios leñosos son homogéneos y están compuestos de parénquima radial (con la presencia de traqueidas radiales en algunas especies de Cupressus, Sequoia, Thujopsis y X. nootkatensis) con paredes finales lisas o lisas y noduladas (exclusivamente noduladas en Cal. macrolepis, C. bakeri y en la mayoría de especies de Juniperus), y el rango de altura de los radios leñosos se encuentra entre 5 y 15 células. Se consideran posibles sinapomorfismos de Cupressaceae la presencia de verrugosidades en la cara interna de las traqueidas, la presencia de traqueidas axiales sin engrosamientos helicoidales, la presencia de parénquima axial, la presencia de radios leñosos homogéneos (compuestos únicamente de parénquima radial), la tipología de las paredes horizontales del parénquima radial, las punteaduras del campo de cruce de tipo cupresoide y la ausencia de canales resiníferos fisiológicos, pero lo que realmente diferencia a este grupo de coníferas es la simultaneidad de todos estos caracteres en sus maderas. Como sinapomorfías específicas por clados se proponen: la ausencia de toro definido y muescas en el borde de las punteaduras en Thuja-Thujopsis, la existencia de extensiones de toro en Diselma-Fitzroya-Widdringtonia; la presencia de engrosamientos callitroides en Callitris-Actinostrobus; la presencia de espacios intercelulares y las muescas en el borde de las punteaduras en el clado formado por el género Juniperus y las especies de Cupressus en la región oriental; la presencia de paredes finales del parénquima radial tanto lisas como noduladas en los clados formados por el género Xanthocyparis y las especies de Cupressus en la región occidental y en Fitzroya-Diselma; y por último, la presencia de punteaduras del campo de cruce de tipo taxodioide en los clados taxodioid y sequoioid. ABSTRACT The Cupressaceae family comprises 133 species grouped into 30 genera, 17 of which are monotypic. The family is represented in all continents except Antarctica. Its species are distributed in various climate zones and at altitudes from sea level to 5,000 m. There is a considerable lack of anatomical descriptions for many genera and species of Cupressaceae and much contradiction between studies about the wood anatomical features described for each species. This study describes the wood anatomy of Cupressaceae and analyses the features that could represent synapomorphies of the clades recovered in phylogenetic studies. Following the traditional methods of preparation and description of wood at microscopic level, a study was made of the wood of 113 species of the 30 Cupressaceae genera. The study samples had traceable origins and came from wood collections held at various international institutions. A robust molecular phylogeny was used for ancestral state reconstruction. The wood anatomy of the 30 genera of the Cupressaceae shows the high homogeneity of the family, which is characterised by the presence of axial tracheids without helical thickenings, smooth horizontal walls of ray parenchyma cells, cupressoid cross-field pits, and the absence of physiological resin canals. In addition, they all have axial parenchyma (except Neocallitropsis, Thuja and Xanthocyparis), a warty layer on the inner wall of the tracheids (except Ca. macleayana, Libocedrus, Papuacedrus and Neocallitropsis) and tracheid pitting in radial walls with a well defined torus (except Thuja and Thujopsis); tracheid pitting in the tangential walls of the latewood is common. Rays are homogeneous and are composed of ray parenchyma (with the presence of ray tracheids in some species of Cupressus, Sequoia, Thujopsis and X. nootkatensis), with smooth end walls or both smooth and nodular end walls (exclusively nodular in Cal. macrolepis, C. bakeri and most Juniperus species), and ray height range is 5 to 15 cells. Possible synapomorphies of Cupressaceae are the presence of a warty layer on the inner layer of the tracheids, axial tracheids without helical thickenings, the presence of axial parenchyma, homogeneous rays (composed exclusively of ray parenchyma), the typology of the horizontal walls of ray parenchyma cells, cupressoid cross-field pits and the absence of physiological resin canals, but what truly differentiates this group of softwoods is the co-occurrence of all these features in their wood. The following are proposed as clade-specific synapomorphies: absence of a well-defined torus and presence of pits with notched borders in Thuja-Thujopsis, torus extensions in Diselma-Fitzroya-Widdringtonia; callitroid thickenings in Callitris-Actinostrobus; intercellular spaces and pits with notched borders in the clade formed by the genus Juniperus and the species of Cupressus in the eastern region; smooth and nodular ray parenchyma end walls in the clades formed by the genus Xanthocyparis and the species of Cupressus in the western region and in Fitzroya-Diselma, and taxodioid cross-field pits in the taxodioid and sequoioid clades.

Arrest of neuronal migration by excitatory amino acids in hamster developing brain

The influence of the excitotoxic cascade on the developing brain was investigated using ibotenate, a glutamatergic agonist of both N-methyl-d-aspartate (NMDA) ionotropic receptors and metabotropic receptors. Injected in the neopallium of the golden hamster at the time of production of neurons normally destined for layers IV, III, and II, ibotenate induces arrests of migrating neurons at different distances from the germinative zone within the radial migratory corridors. The resulting cytoarchitectonic patterns include periventricular nodular heterotopias, subcortical band heterotopias, and intracortical arrests of migrating neurons. The radial glial cells and the extracellular matrix are free of detectable damage that could suggest a defect in their guiding role. The migration disorders are prevented by coinjection of dl-2-amino-7-phosphoheptanoic acid, an NMDA ionotropic antagonist, but are not prevented by coinjection of l(+)-2-amino-3-phosphonopropionic acid, a metabotropic antagonist. This implies that an excess of ionic influx through the NMDA channels of neurons alters the metabolic pathways supporting neuronal migration. Ibotenate, a unique molecular trigger of the excitotoxic cascade, produces a wide spectrum of abnormal neuronal migration patterns recognized in mammals, including the neocortical deviations encountered in the human brain.

Glycolytic Flux Is Adjusted to Nitrogenase Activity in Nodules of Detopped and Argon-Treated Alfalfa Plants1

To investigate the short-term (30–240 min) interactions among nitrogenase activity, NH4+ assimilation, and plant glycolysis, we measured the concentrations of selected C and N metabolites in alfalfa (Medicago sativa L.) root nodules after detopping and during continuous exposure of the nodulated roots to Ar:O2 (80:20, v/v). Both treatments caused an increase in the ratios of glucose-6-phosphate to fructose-1,6-bisphosphate, fructose-6-phosphate to fructose-1,6-bisphosphate, phosphoenolpyruvate (PEP) to pyruvate, and PEP to malate. This suggested that glycolytic flux was inhibited at the steps catalyzed by phosphofructokinase, pyruvate kinase, and PEP carboxylase. In the Ar:O2-treated plants the apparent inhibition of glycolytic flux was reversible, whereas in the detopped plants it was not. In both groups of plants the apparent inhibition of glycolytic flux was delayed relative to the decline in nitrogenase activity. The decline in nitrogenase activity was followed by a dramatic increase in the nodular glutamate to glutamine ratio. In the detopped plants this was coincident with the apparent inhibition of glycolytic flux, whereas in the Ar:O2-treated plants it preceded the apparent inhibition of glycolytic flux. We propose that the increase in the nodular glutamate to glutamine ratio, which occurs as a result of the decline in nitrogenase activity, may act as a signal to decrease plant glycolytic flux in legume root nodules.

Studying Early Nodulin Gene ENOD40 Expression and Induction by Nodulation Factor and Cytokinin in Transgenic Alfalfa1

ENOD40, an early nodulin gene, is expressed following inoculation with Rhizobium meliloti or by adding R. meliloti-produced nodulation (Nod) factors or the plant hormone cytokinin to uninoculated roots. We isolated two MsENOD40 clones, designated MsENOD40–1 and MsENOD40–2, with distinct promoters from an alfalfa (Medicago sativa cv Chief) genomic library. The promoters were fused to the reporter gene uidA (gus), and the constructs were introduced into alfalfa. We observed that the MsENOD40–1 construct was expressed almost exclusively under symbiotic conditions. The MsENOD40–2 construct was transcribed under both symbiotic and nonsymbiotic conditions and in nonnodular and nodular tissues. Both MsENOD40 promoter-gus constructs were similarly expressed as nodules developed, and both were expressed in roots treated with 6-benzylaminopurine or purified Nod factor. However, no blue color was detected in nodule-like structures induced by the auxin transport inhibitor N-1-(naphthyl)phthalamic acid on roots of plants containing the MsENOD40–1 promoter construct, whereas pseudonodules from plants containing the MsENOD40–2 promoter construct stained blue. A 616-bp region at the distal 5′ end of the promoter is important for proper spatial expression of MsENOD40 in nodules and also for Nod-factor and cytokinin-induced expression.

A growth-constrained environment drives tumor progression in vivo

We recently have shown that selective growth of transplanted normal hepatocytes can be achieved in a setting of cell cycle block of endogenous parenchymal cells. Thus, massive proliferation of donor-derived normal hepatocytes was observed in the liver of rats previously given retrorsine (RS), a naturally occurring alkaloid that blocks proliferation of resident liver cells. In the present study, the fate of nodular hepatocytes transplanted into RS-treated or normal syngeneic recipients was followed. The dipeptidyl peptidase type IV-deficient (DPPIV−) rat model for hepatocyte transplantation was used to distinguish donor-derived cells from recipient cells. Hepatocyte nodules were chemically induced in Fischer 344, DPPIV+ rats; livers were then perfused and larger (>5 mm) nodules were separated from surrounding tissue. Cells isolated from either tissue were then injected into normal or RS-treated DPPIV− recipients. One month after transplantation, grossly visible nodules (2–3 mm) were seen in RS-treated recipients transplanted with nodular cells. They grew rapidly, occupying 80–90% of the host liver at 2 months, and progressed to hepatocellular carcinoma within 4 months. By contrast, no liver nodules developed within 6 months when nodular hepatocytes were injected into the liver of recipients not exposed to RS, although small clusters of donor-derived cells were present in these animals. Taken together, these results directly point to a fundamental role played by the host environment in modulating the growth and the progression rate of altered cells during carcinogenesis. In particular, they indicate that conditions associated with growth constraint of the host tissue can drive tumor progression in vivo.

Avaliação de fatores virológicos associados ao desenvolvimento de carcinoma hepatocelular (CHC) em pacientes com hepatite B crônica

O objetivo principal deste estudo foi avaliar fatores virais associados com a evolução para o carcinoma hepatocelular (CHC) em pacientes com hepatite B crônica. Para tanto caracterizamos os subgenótipos do HBV, investigamos a ocorrência de mutações nos genes pré-core/core do HBV associadas à presença de CHC avaliamos por análise filogenética a associação de linhagens virais com a ocorrência de CHC e por fim a associação de outros fatores de risco com o desenvolvimento de CHC. Foram incluídos 119 amostras de soro de pacientes com infecção crônica pelo HBV, destas amostras 60 pertencem ao grupo 1 (CHC), que são pacientes com diagnóstico confirmado de carcinoma hepatocelular e 59 amostras pertencem ao grupo 2 (sem CHC) que são pacientes com hepatite crônica sem detecção prévia de nódulos hepáticos. Foram obtidas informações acerca da idade, sexo e naturalidade. Além disso, os pacientes responderam a um questionário sobre fatores de riscos associados ao desenvolvimento de CHC. Foram realizados exames bioquímicos, sorológicos, determinação da carga viral, e amplificação por nested PCR e sequenciamento das regiões S/polimerase e pré-core/core do genoma viral para posterior caracterização dos genótipos/subgenótipos do HBV e pesquisa de mutações associadas com evolução da doença hepática. Em relação à idade e sexo não houve grande variação entre os grupos. Quanto à naturalidade a maioria era procedente da região sudeste, seguido pela região nordeste; e por fim seis pacientes eram procedentes de outros países. Com base no sobrenome dos pacientes avaliou-se também a frequência de etnia oriental na casuística estudada, que foi similar nos 2 grupos. O perfil sorológico HBeAg negativo foi o mais frequente nos dois grupos de pacientes, assim como níveis de carga viral abaixo de 2.000 UI/mL. Em relação aos exames bioquímicos foram observadas diferenças estatisticamente significantes nos níveis séricos de AFP (p= 0,0013), FA (p= 0,0003) e GGT (p= 0,005). Dentre os fatores de risco analisados neste estudo, o consumo de amendoim foi o único que apresentou significância estatística (p= 0,003). A região S/pol foi amplificada e sequenciada com sucesso em 58 amostras (28 do grupo 1 e 30 do grupo 2). Entre as 58 amostras analisadas 4 genótipos e 8 subgenótipos do HBV foram identificados, sendo o subgenótipo A1 o mais frequente nos dois grupos. Não se observou diferença estatisticamente significante na distribuição dos subgenótipos entre os dois grupos de pacientes. Na topologia da árvore filogenética construída com sequências do HBV isoladas dos pacientes incluídos neste estudo e sequências disponíveis no GenBank não se observou padrões de agrupamento associados com o perfil clinico do paciente (com e sem CHC). Foram obtidas sequências de boa qualidade da região précore/ core em 44 amostras, sendo 20 amostras do grupo 1 e 24 do grupo 2. Diversas das mutações investigadas foram identificadas na região précore/ core, as quais foram avaliadas estatisticamente para verificar a existência de diferença na frequência das mesmas entre os grupos de pacientes estudados. Entre as mutações identificadas se destacaram com significância estatística as seguintes mutações: T1768A (p= 0,006), a combinação das mutações C1766T + T1768A (p= 0,043) e G1888H (p= 0,05). Na análise de regressão logística simples foi possível identificar que a chance de um paciente do grupo 2 desenvolver CHC aumenta 14,7 vezes na presença de infecção por cepas do HBV com a mutação T1768A, enquanto que a infecção com cepas do HBV que albergam a mutação G1888H reduz tal chance 2,5 vezes

Seasonality of thyroid function

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