Comparison of fermentation characteristics and bacterial diversity in the rumen of sheep and batch cultures of rumen microorganisms

The objective of the current study was to assess how closely batch cultures (BC) of rumen microorganisms can mimic the dietary differences in fermentation characteristics found in the rumen, and to analyse changes in bacterial diversity over the in vitro incubation period. Four ruminally and duodenally cannulated sheep were fed four diets having forage : concentrate ratios (FCR) of 70 : 30 or 30 : 70, with either alfalfa hay or grass hay as forage. Rumen fluid from each sheep was used to inoculate BC containing the same diet fed to the donor sheep, and the main rumen fermentation parameters were determined after 24 h of incubation. There were differences between BC and sheep in the magnitude of most measured parameters, but BC detected differences among diets due to forage type similar to those found in sheep. In contrast, BC did not reproduce the dietary differences due to FCR found in sheep for pH, degradability of neutral detergent fibre and total volatile fatty acid (VFA) concentrations. There were differences between systems in the magnitude of most determined parameters and BC showed higher pH values and NH3–N concentrations, but lower fibre degradability and VFA and lactate concentrations compared with sheep. There were significant relationships between in vivo and in vitro values for molar proportions of acetate, propionate and butyrate, and the acetate : propionate ratio. The automated ribosomal intergenic spacer analysis (ARISA) of 16S ribosomal deoxyribonucleic acid showed that FCR had no effect on bacterial diversity either in the sheep rumen fluid used as inoculum (IN) or in BC samples. In contrast, bacterial diversity was greater with alfalfa hay diets than those with grass hay in the IN, but was unaffected by forage type in the BC. Similarity index between the bacterial communities in the inocula and those in the BC ranged from 67·2 to 74·7%, and was unaffected by diet characteristics. Bacterial diversity was lower in BC than in the inocula with 14 peaks out of a total of 181 detected in the ARISA electropherograms never appearing in BC samples, which suggests that incubation conditions in the BC may have caused a selection of some bacterial strains. However, each BC sample showed the highest similarity index with its corresponding rumen IN, which highlights the importance of using rumen fluid from donors fed a diet similar to that being incubated in BC when conducting in vitro experiments.

Explaining the saproxylic beetle diversity of a protected Mediterranean area

Saproxylic beetle diversity is high at the Cabañeros National Park (central Spain), where woodland habitats exhibit remarkable heterogeneity. Our aim was to explain the diversity of saproxylic beetles, focusing on species turnover among mature woodland types. We surveyed five woodland types that represented the heterogeneity of the park’s woodland habitats. Beetles were collected using window traps over a period of 20 months. The Jaccard Similarity Index was used as indirect value of beta diversity among woodlands and to test the relation between species turnover and geographical distance. We also identified the contribution of species turnover to landscape diversity by using a partitioning model. Moreover, the presence of mixed woodlands (more than one tree species) allowed us to attempt to valorise the effect of tree species (coupled with their historical management) on species turnover among woodlands. Finally, we looked for different saproxylic beetle preferences for habitat and tree species using an indicator value method. We found that saproxylic beetle species composition varied significantly among the studied woodlands. The variation in species turnover was independent from the distance among woodlands, which suggested that beetle dispersal abilities could not explain this high turnover. Tree species within woodlands were a key factor that increased diversity turnover in woodlands and, consequently, the diversity of the park. Moreover, we found saproxylic beetle species that had different habitat and tree species preferences. We conclude that woodland heterogeneity (highly affected by woodland composition) seems to be the driving force for saproxylic beetle diversity in this protected area.

Sea-surface temperature reconstruction for sediment core GIK18287-3 in the tropical South China Sea

The timing and magnitude of sea-surface temperature (SST) changes in the tropical southern South China Sea (SCS) during the last 16,500 years have been reconstructed on a high-resolution, 14C-dated sediment core using three different foraminiferal transfer functions (SIMMAX28, RAM, FP-12E) and geochemical (Uk'37) SST estimates. In agreement with CLIMAP reconstructions, both the FP-12E and the Uk'37 SST estimates show an average late glacial-interglacial SST difference of 2.0°C, whereas the RAM and SIMMAX28 foraminiferal transfer functions show only a minor (0.6°C) or no consistent late glacial-interglacial SST change, respectively. Both the Uk'37 and the FP-12E SST estimates, as well as the planktonic foraminiferal delta18O values, indicate an abrupt warming (ca. 1°C in <200 yr) at the end of the last glaciation, synchronous (within dating uncertainties) with the Bølling transition as recorded in the Greenland Ice Sheet Project 2 (GISP2) ice core, whereas the RAM-derived deglacial SST increase appears to lag during this event by ca. 500 yr. The similarity in abruptness and timing of the warming associated with the Bølling transition in Greenland and the southern SCS suggest a true synchrony of the Northern Hemisphere warming at the end of the last glaciation. In contrast to the foraminiferal transfer function estimates that do not indicate any consistent cooling associated with the Younger Dryas (YD) climate event in the tropical SCS, the Uk'37 SST estimates show a cooling of ca. 0.2-0.6°C compared to the Bølling-Allerød period. These Uk'37 SST estimates from the southern SCS argue in favor of a Northern Hemisphere-wide, synchronous cooling during the YD period.

Sea-surface temperature reconstructions for the Quaternary western Atlantic

Paleotemperature estimates calculated by the SIMMAX Modern Analog Technique are presented for two gravity cores from the Rio Grande Rise, one from the Brazil Slope, and one from the Ceara Rise. The estimates are based on comparisons between modern and fossil planktonic foraminiferal assemblages and were carried out on samples from Quaternary sediments. Estimated warm-season temperatures from the Rio Grande Rise (at approx. 30° S) range from around 19°C to 24°C, with some coincidence of warm peaks with interglacial stages. The temperature estimates (also warm-season) from the more tropical Brazil Slope (at approx. 8° S) and Ceara Rise (at approx. 4° N) cores are more stable, remaining between 26°C and 28°C throughout most of their lengths. This fairly stable situation in the tropical western Atlantic is interrupted in oxygen isotope stage 6 by a significant drop of 2-3°C in both of these cores. Temperature estimates from the uppermost samples in all cores compare very well to the modern-day measured values. Affinities of some foraminiferal species for warmer or cooler surface temperatures are identified within the temperature range of the examined samples based on their abundance values. Especially notable among the warmer species are, Globorotalia menardii, Globigerinita glutinata, Globigerinoides ruber, and Globigerinoides sacculifer. Species indicative of cooler surface temperatures include Globorotalia inflata, Globigerina bulloides, Neogloboquadrina pachyderma, and Globigerina falconensis. A cluster analysis was carried out to assist in understanding the degree of variation which occurs in the foraminiferal assemblages, and how temperature differences influence the faunal compositions of the samples. It is demonstrated that fairly similar samples may have unexpectedly different estimated temperatures due to small differences in key species and, conversely, quite different assemblages can result in similar or identical temperature estimates which confirms that other parameters than just temperature affect faunal content.

Fertilization of branching Acropora

Acropora is one of the largest taxonomic groups of scleractinian corals in the Indo-Pacific and contributes towards the establishment of coral communities in the Ryukyu Islands. Branching Acropora populations have a component of asexual reproduction; however, this may lead to a decline in genetic diversity, leaving populations vulnerable to environmental changes. Therefore, a sufficient supply of larvae produced via sexual reproduction is necessary to maintain genetic diversity in the branching Acropora communities. Fertilization success in branching Acropora depends on a variety of factors, including genetic and environmental conditions. How genotype and/or genetic compatibility drives fertilization rates in Acropora communities under natural conditions has not been investigated. To investigate how genotype and/or genetic compatibility determine fertilization rates in Acropora communities over the long-term, cross-mating experiments with branching Acropora using the same colonies were conducted from 2006 to 2011 in an aquarium. Acropora from cultured and natural colonies collected from a reef (26° 40' 19.2'' N, 127° 52' 40.8'' E) were used. Fertilization rates showed less variation within the same crossing combinations, but large variation across years for the same genotypes of focal colonies. Results indicated that fertilization rate was highly variable depending on genotype compatibility with different mating partners. Additionally, simulations of fertilization rates with increasing population size revealed that small populations that had low genetic diversity (fewer than 10 genotypes) failed to fertilize. These results support the establishment or maintenance of source populations that facilitate sufficient genetic diversity of branching Acropora to enhance coral community restoration.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

A comparison of denoising methods for X-ray fluoroscopic images

Fluoroscopic images exhibit severe signal-dependent quantum noise, due to the reduced X-ray dose involved in image formation, that is generally modelled as Poisson-distributed. However, image gray-level transformations, commonly applied by fluoroscopic device to enhance contrast, modify the noise statistics and the relationship between image noise variance and expected pixel intensity. Image denoising is essential to improve quality of fluoroscopic images and their clinical information content. Simple average filters are commonly employed in real-time processing, but they tend to blur edges and details. An extensive comparison of advanced denoising algorithms specifically designed for both signal-dependent noise (AAS, BM3Dc, HHM, TLS) and independent additive noise (AV, BM3D, K-SVD) was presented. Simulated test images degraded by various levels of Poisson quantum noise and real clinical fluoroscopic images were considered. Typical gray-level transformations (e.g. white compression) were also applied in order to evaluate their effect on the denoising algorithms. Performances of the algorithms were evaluated in terms of peak-signal-to-noise ratio (PSNR), signal-to-noise ratio (SNR), mean square error (MSE), structural similarity index (SSIM) and computational time. On average, the filters designed for signal-dependent noise provided better image restorations than those assuming additive white Gaussian noise (AWGN). Collaborative denoising strategy was found to be the most effective in denoising of both simulated and real data, also in the presence of image gray-level transformations. White compression, by inherently reducing the greater noise variance of brighter pixels, appeared to support denoising algorithms in performing more effectively. © 2012 Elsevier Ltd. All rights reserved.

Glacial North Atlantic: Sea surface conditions reconstructed by GLAMAP 2000

The response of the tropical ocean to global climate change and the extent of sea ice in the glacial nordic seas belong to the great controversies in paleoclimatology. Our new reconstruction of peak glacial sea surface temperatures (SSTs) in the Atlantic is based on census counts of planktic foraminifera, using the Maximum Similarity Technique Version 28 (SIMMAX-28) modern analog technique with 947 modern analog samples and 119 well-dated sediment cores. Our study compares two slightly different scenarios of the Last Glacial Maximum (LGM), the Environmental Processes of the Ice Age: Land, Oceans, Glaciers (EPILOG), and Glacial Atlantic Ocean Mapping (GLAMAP 2000) time slices. The comparison shows that the maximum LGM cooling in the Southern Hemisphere slightly preceeded that in the north. In both time slices sea ice was restricted to the north western margin of the nordic seas during glacial northern summer, while the central and eastern parts were ice-free. During northern glacial winter, sea ice advanced to the south of Iceland and Faeroe. In the central northern North Atlantic an anticyclonic gyre formed between 45° and 60°N, with a cool water mass centered west of Ireland, where glacial cooling reached a maximum of >12°C. In the subtropical ocean gyres the new reconstruction supports the glacial-to-interglacial stability of SST as shown by CLIMAP Project Members (CLIMAP) [1981]. The zonal belt of minimum SST seasonality between 2° and 6°N suggests that the LGM caloric equator occupied the same latitude as today. In contrast to the CLIMAP reconstruction, the glacial cooling of the tropical east Atlantic upwelling belt reached up to 6°-8°C during Northern Hemisphere summer. Differences between these SIMMAX-based and published U37[k]- and Mg/Ca-based equatorial SST records are ascribed to strong SST seasonalities and SST signals that were produced by different planktic species groups during different seasons.

Distribution of planktic foraminifera in surface sediments of the Atlantic Ocean

We present a data set of 738 planktonic foraminiferal species counts from sediment surface samples of the eastern North Atlantic and the South Atlantic between 87°N and 40°S, 35°E and 60°W including published Climate: Long-Range Investigation, Mapping, and Prediction (CLIMAP) data. These species counts are linked to Levitus's [1982] modern water temperature data for the four caloric seasons, four depth ranges (0, 30, 50, and 75 m), and the combined means of those depth ranges. The relation between planktonic foraminiferal assemblages and sea surface temperature (SST) data is estimated using the newly developed SIMMAX technique, which is an acronym for a modern analog technique (MAT) with a similarity index, based on (1) the scalar product of the normalized faunal percentages and (2) a weighting procedure of the modern analog's SSTs according to the inverse geographical distances of the most similar samples. Compared to the classical CLIMAP transfer technique and conventional MAT techniques, SIMMAX provides a more confident reconstruction of paleo-SSTs (correlation coefficient is 0.994 for the caloric winter and 0.993 for caloric summer). The standard deviation of the residuals is 0.90°C for caloric winter and 0.96°C for caloric summer at 0-m water depth. The SST estimates reach optimum stability (standard deviation of the residuals is 0.88°C) at the average 0- to 75-m water depth. Our extensive database provides SST estimates over a range of -1.4 to 27.2°C for caloric winter and 0.4 to 28.6°C for caloric summer, allowing SST estimates which are especially valuable for the high-latitude Atlantic during glacial times.

Paleotemperature and productivity reconstruction of sediment core D11957P on the Iberian Margin

Foraminifera counts and climatic assemblages from the Tore Seamount are used to approach the glacial and interglacial changes in temperature and productivity on the Iberian Margin over the last 225 kyr. Chronostratigraphy is based on Globigerinoides ruber and Globigerina bulloides oxygen isotopes and supported by foraminifera and carbonate stadial fluctuations. Foraminifera indicate cooling from late interglacial stage 5 to the beginning of Termination I (TI). Neogloboquadnna pachyderma-s reflects cold conditions during glacial stages 4-2. In contrast, glacial stage 6 is dominated by warmer N. pachyderma-d and dutertrei and a restricted arctic assemblage. Past sea surface temperatures confirm the general cooling, reaching 4.3°C (SIMMAX.28) during stage 2. Multiple productivity proxies such as organic carbon, productivity-related foraminifera, and delta13C constrain the changes observed. A productivity increase occurs after interglacial stage 5, enhanced from late glacial stage 3 to TI Present-day satellite-detected phytoplankton plumes off Portugal would have accounted in the past glacial stages for the general productivity increase over the Tore. On top of this, welldefined peaks of organic carbon and productivity-related foraminifera correspond with Heinrich events 1-4.

Sea surface temperature reconstruction based on planktonic foraminifera of surface sediments and sediment cores off Iberia

Quantitative and qualitative analyses of planktonic foraminiferal assemblages from 134 core-top sediment samples collected along the western Iberian margin were used to assess the latitudinal and longitudinal changes in surface water conditions and to calibrate a Sea Surface Temperature (SST) transfer function for this seasonal coastal upwelling region. Q-mode factor analysis performed on relative abundances yielded three factors that explain 96% of the total variance: factor 1 (50%) is exclusively defined by Globigerina bulloides, the most abundant and widespread species, and reflects the modern seasonal (May to September) coastal upwelling areas; factor 2 (32%) is dominated by Neogloboquadrina pachyderma (dextral) and Globorotalia inflata and seems to be associated with the Portugal Current, the descending branch of the North Atlantic Drift; factor 3 (14%) is defined by the tropical-sub-tropical species Globigerinoides ruber (white), Globigerinoides trilobus trilobus, and G. inflata and mirrors the influence of the winter-time eastern branch of the Azores Current. In conjunction with satellite-derived SST for summer and winter seasons integrated over an 18 year period the regional foraminiferal data set is used to calibrate a SST transfer function using Imbrie & Kipp, MAT and SIMMAX(ndw) techniques. Similar predicted errors (RMSEP), correlation coefficients, and residuals' deviation from SST estimated for both techniques were observed for both seasons. All techniques appear to underestimate SST off the southern Iberia margin, an area mainly occupied by warm waters where upwelling occurs only occasionally, and overestimate SST on the northern part of the west coast of the Iberia margin, where cold waters are present nearly all year round. The comparison of these regional calibrations with former Atlantic and North Atlantic calibrations for two cores, one of which is influenced by upwelling, reveals that the regional one attests more robust paleo-SSTs than for the other approaches.