Sedimentology of cores from the Iberian margin

Bioturbation in marine sediments has basically two aspects of interest for palaeo-environmental studies. First, the traces left by the burrowing organisms reflect the prevailing environmental conditions at the seafloor and thus can be used to reconstruct the ecologic and palaeoceanographic situation. Traces have the advantage over other proxies of practically always being preserved in situ. Secondly, for high- resolution stratigraphy, bioturbation is a nuisance due to the stirring and mixing processes that destroy the stratigraphic record. In order to evaluate the applicability of biogenic traces as palaeoenvironmental indicators, a number of gravity cores from the Portuguese continental slope, covering the period from the last glacial to the present were investigated through X-ray radiographs. In addition, physical and chemical parameters were determined to define the environmental niche in each core interval. A number of traces could be recognized, the most important being: Thalassinoides, Planolites, Zoophycos, Chondrites, Scolicia, Palaeophycus, Phycosiphon and the generally pyritized traces Trichichnus and Mycellia. The shifts between the different ichnofabrics agree strikingly well with the variations in ocean circulation caused by the changing climate. On the upper and middle slope, variations in current intensity and oxygenation of the Mediterranean Outflow Water were responsible for shifts in the ichnofabric. Larger traces such as Planolites and Thalassinoides dominated in coarse, well oxygenated intervals, while small traces such as Chondrites and Trichichnus dominated in fine grained, poorly oxygenated intervals. In contrast, on the lower slope where calm steady sedimentation conditions prevail, changes in sedimentation rate and nutrient flux have controlled variations in the distribution of larger traces such as Planolites, Thalassinoides, and Palaeophycus. Additionally, distinct layers of abundant Chondrites correspond to Heinrich events 1, 2, and 4, and are interpreted as a response to incursions of nutrient rich, oxygen depleted Antarctic waters during phases of reduced thermohaline circulation. The results clearly show that not one single factor but a combination of several factors is necessary to explain the changes in ichnofabric. Furthermore, large variations in the extent and type of bioturbation and tiering between different settings clearly show that a more detailed knowledge of the factors governing bioturbation is necessary if we shall fully comprehend how proxy records are disturbed. A first attempt to automatize a part of the recognition and quantification of the ichnofabric was performed using the DIAna image analysis program on digitized X-ray radiographs. The results show that enhanced abundance of pyritized microburrows appears to be coupled to organic rich sediments deposited under dysoxic conditions. Coarse grained sediments inhibit the formation of pyritized burrows. However, the smallest changes in program settings controlling the grey scale threshold and the sensitivity resulted in large shifts in the number of detected burrows. Therefore, this method can only be considered to be semi-quantitative. Through AMS-^C dating of sample pairs from the Zoophycos spreiten and the surrounding host sediment, age reversals of up to 3,320 years could be demonstrated for the first time. The spreiten material is always several thousands of years younger than the surrounding host sediment. Together with detailed X-ray radiograph studies this shows that the trace maker collects the material on the seafloor, and then transports it downwards up to more than one meter in to the underlying sediment where it is deposited in distinct structures termed spreiten. This clearly shows that age reversals of several thousands of years can be expected whenever Zoophycos is unknowingly sampled. These results also render the hitherto proposed ethological models proposed for Zoophycos as largely implausible. Therefore, a combination of detritus feeding, short time caching, and hibernation possibly combined also with gardening, is suggested here as an explanation for this complicated burrow.

Romano-British wall-painting fragments: a spectroscopic analysis

Raman spectroscopic analyses of fragmented wall-painting specimens from a Romano-British villa dating from ca. 200 AD are reported. The predominant pigment is red haematite, to which carbon, chalk and sand have been added to produce colour variations, applied to a typical Roman limewash putty composition. Other pigment colours are identified as white chalk, yellow (goethite), grey (soot/chalk mixture) and violet. The latter pigment is ascribed to caput mortuum, a rare form of haematite, to which kaolinite (possibly from Cornwall) has been added, presumably in an effort to increase the adhesive properties of the pigment to the substratum. This is the first time that kaolinite has been reported in this context and could indicate the successful application of an ancient technology discovered by the Romano-British artists. Supporting evidence for the Raman data is provided by X-ray diffraction and SEM-EDAX analyses of the purple pigment.

Wrapped fragments : Drapery, the eighteenth century portrait bust and the male subject

The depiction of drapery (generalised cloth as opposed to clothing) is a well-established convention of Neo-Classical sculpture and is often downplayed by art historians as of purely rhetorical value. It can be argued however that sculpted drapery has served a spectrum of expressive ends, the variety and complexity of which are well illustrated by a study of its use in portrait sculpture. For the Neo-Classical portrait bust, drapery had substantial iconographic and political meaning, signifying the new Enlightenment notions of masculine authority. Within the portrait bust, drapery also served highly strategic aesthetic purposes, alleviating the abruptness of the truncated format and the compromising visual consequences of the “cropped” body. With reference to Joseph Nollekens’ portraits of English statesman Charles James Fox and the author’s own sculptural practice, this paper analyses the Neo-Classical use of drapery to propose that rendered fabric, far from mere stylistic flourish, is a highly charged visual signifier with much scope for exploration in contemporary sculptural practice.

Fusion or non fusion of coral fragments in Acropora

Corals inhabit high energy environments where frequent disturbances result in physical damage to coralla, including fragmentation, as well as generating and mobilizing large sediment clasts. The branching growth form common in the Acropora genus makes it particularly susceptible to such disturbances and therefore useful for study of the fate of large sediment clasts. Living Acropora samples with natural, extraneous, broken coral branches incorporated on their living surface and dead Acropora skeletons containing embedded clasts of isolated branch sections of Acropora were observed and/or collected from the reef flat of Heron Reef, southern Great Barrier Reef and Bargara, Australia respectively. Here we report three different outcomes when pebble-sized coral branches became lodged on living coral colonies during sedimentation events in natural settings in Acropora: 1) Where live coral branches produced during a disturbance event come to rest on probable genetic clone-mate colonies they become rapidly stabilised leading to complete soft tissue and skeletal fusion; 2) Where the branch and underlying colony are not clone-mates, but may still be the same or similar species, the branches still may be stabilised rapidly by soft tissue, but then one species will overgrow the other; and 3) Where branches represent dead skeletal debris, they are treated like any foreign clast and are surrounded by clypeotheca and incorporated into the corallum by overgrowth. The retention of branch fragments on colonies in high energy reef flat settings may suggest an active role of coral polyps to recognise and fuse with each other. Also, in all cases the healing of disturbed tissue and subsequent skeletal growth is an adaptation important for protecting colonies from invasion by parasites and other benthos following disturbance events and may also serve to increase corallum strength. Knowledge of such adaptations is important in studies of coral behaviour during periods of environmental stress.

Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants. © 2013 Loss-Morais et al.; licensee BioMed Central Ltd.

Circulating fragments of N-Terminal Pro-B-Type Natriuretic Peptides in plasma of heart failure patients

BACKGROUND: The use of nonstandardized N-terminal pro-B-type natriuretic peptide (NT-proBNP) assays can contribute to the misdiagnosis of heart failure (HF). Moreover, there is yet to be established a common consensus regarding the circulating forms of NT-proBNP being used in current assays. We aimed to characterize and quantify the various forms of NT-proBNP in the circulation of HF patients. METHODS: Plasma samples were collected from HF patients (n = 20) at rest and stored at -80 degrees C. NT-proBNP was enriched from HF patient plasma by use of immunoprecipitation followed by mass spectrometric analysis. Customized homogeneous sandwich AlphaLISA (R) immunoassays were developed and validated to quantify 6 fragments of NT-proBNP. RESULTS: Mass spectrometry identified the presence of several N- and C-terminally processed forms of circulating NT-proBNP, with physiological proteolysis between Pro2-Leu3, Leu3-Gly4, Pro6-Gly7, and Pro75-Arg76. Consistent with this result, AlphaLISA immunoassays demonstrated that antibodies targeting the extreme N or C termini measured a low apparent concentration of circulating NT-proBNP. The apparent circulating NT-proBNP concentration was increased with antibodies targeting nonglycosylated and nonterminal epitopes (P < 0.05). CONCLUSIONS: In plasma collected from HF patients, immunoreactive NT-proBNP was present as multiple N- and C-terminally truncated fragments of the full length NT-proBNP molecule. Immunodetection of NT-proBNP was significantly improved with the use of antibodies that did not target these terminal regions. These findings support the development of a next generation NT-proBNP assay targeting nonterminal epitopes as well as avoiding the central glycosylated region of this molecule. (c) 2013 American Association for Clinical Chemistry

Extinction risk in cloud forest fragments under climate change and habitat loss

Aim: To quantify the consequences of major threats to biodiversity, such as climate and land-use change, it is important to use explicit measures of species persistence, such as extinction risk. The extinction risk of metapopulations can be approximated through simple models, providing a regional snapshot of the extinction probability of a species. We evaluated the extinction risk of three species under different climate change scenarios in three different regions of the Mexican cloud forest, a highly fragmented habitat that is particularly vulnerable to climate change. Location: Cloud forests in Mexico. Methods: Using Maxent, we estimated the potential distribution of cloud forest for three different time horizons (2030, 2050 and 2080) and their overlap with protected areas. Then, we calculated the extinction risk of three contrasting vertebrate species for two scenarios: (1) climate change only (all suitable areas of cloud forest through time) and (2) climate and land-use change (only suitable areas within a currently protected area), using an explicit patch-occupancy approximation model and calculating the joint probability of all populations becoming extinct when the number of remaining patches was less than five. Results: Our results show that the extent of environmentally suitable areas for cloud forest in Mexico will sharply decline in the next 70 years. We discovered that if all habitat outside protected areas is transformed, then only species with small area requirements are likely to persist. With habitat loss through climate change only, high dispersal rates are sufficient for persistence, but this requires protection of all remaining cloud forest areas. Main conclusions: Even if high dispersal rates mitigate the extinction risk of species due to climate change, the synergistic impacts of changing climate and land use further threaten the persistence of species with higher area requirements. Our approach for assessing the impacts of threats on biodiversity is particularly useful when there is little time or data for detailed population viability analyses. © 2013 John Wiley & Sons Ltd.

Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia

The native Asian oyster, Crassostrea ariakensis is one of the most common and important Crassostrea species that occur naturally along the coast of East Asia. Molecular species diagnosis is a prerequisite for population genetic analysis of wild oyster populations because oyster species cannot be discriminated reliably using external morphological characters alone due to character ambiguity. To date there have been few phylogeographic studies of natural edible oyster populations in East Asia, in particular this is true of the common species in Korea C. ariakensis. We therefore assessed the levels and patterns of molecular genetic variation in East Asian wild populations of C. ariakensis from Korea, Japan, and China using DNA sequence analysis of five concatenated mtDNA regions namely; 16S rRNA, cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, and cytochrome b. Two divergent C. ariakensis clades were identified between southern China and remaining sites from the northern region. In addition, hierarchical AMOVA and pairwise UST analyses showed that genetic diversity was discontinuous among wild populations of C. ariakensis in East Asia. Biogeographical and historical sea level changes are discussed as potential factors that may have influenced the genetic heterogeneity of wild C. ariakensis stocks across this region.

The helical conformations of 14- and 16-residue fragments of suzukacillin, a membrane channel-forming polypeptide

The suzukacillin fragments, Boc-Ala-Aib-Aib-Gln-Aib-Leu-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-OMe (14), Boc-Ala-Aib-Ala-Aib-Aib-Gln-Aib-Leu-Aib-Gly-Leu-Aib-Pro-Val-Aib-Aib-OMe (16G) and the completely apolar 16-residue peptide in which the glutamine residue has been replaced by alanine (16A) have been studied by 270 MHz 1H-HMR, in C2HCl3 and (C2H3)2SO solution. Intramolecularly hydrogen-bonded NH groups have been identified by temperature and solvent dependence of chemical shifts. Peptides 14 and 16A adopt folded 310 helical conformations stabilized by 11 and 13 hydrogen bonds, respectively. In peptide 16G there are 12 intramolecular hydrogen bonds, with the glycine NH being solvent-exposed, in contrast to 14 and 16A.

A sensitive immunochemical method for detecting 5mC in DNA fragments

Abstract is not available.