bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of the microbial diversity and antimicrobial properties of Irish edible brown seaweeds
Authors: Gupta Shilpi , Rajauria Gaurav , Abu‐Ghannam Nissreen 
Published: February 2010

SummaryBrown Irish edible seaweeds, Himanthalia elongata, Laminaria sachharina and Laminaria digitata, were evaluated for the microbiota in raw and heat processed form. Raw seaweeds showed complete absence of aerobic mesophiles, halophiles, yeasts and molds. However, heating at 85 °C for 15 min resulted in spore germination. Bacterial counts as high as 107 were observed for aerobic mesophiles and halophiles. Heating above 95 °C for 15 min resulted in complete inactivation of surface microflora. Bacteria belonging to Bacillaceae, Paenibacillaceae, Moraxellaceae and Enterobacteriaceae family were identified by 16S rRNA sequencing. In vitro antimicrobial activity of the methanolic extracts of the seaweed on food pathogenic and food spoilage bacteria were also evaluated. The seaweeds in their raw state had almost 100% inhibition against Listeria monocytogenes; 98% and 93% inhibition was achieved against Pseudomonas aeruginosa by H. elongata and L. saccharina extracts, respectively. Heating the seaweeds resulted in the reduction of antimicrobial activity as compared to raw. The effect was more pronounced against Gram negative bacteria.
n‐3 Omega fatty acids: a review of current knowledge
Authors: Gogus Ugur , Smith Chris 
Published: February 2010

SummaryThe very long chain polyunsaturated fatty acids (PUFAs) (C18–C22) and n‐3 Omega PUFAs are apparently widely accepted as a part of modern nutrition because of their beneficial effects on metabolism. Most significantly, the reported protective effect of the n‐3 omega fatty acids in relation to cardiovascular inflammatory diseases and cancer has led people to consider these fatty acids more beneficial than other dietary supplements. Unfortunately, there is a lack of studies relating to the physical performance increasing effect in sports diets, cholesterol‐reducing effect in meat technology, effects on human serum profile, the application dose and the side effects with/without omega‐6 PUFAs, which has left us with several crucial unanswered questions. We still do not know the correct dose of n‐3 omega and the correct ratio of n‐3 omega to n‐6 omega or their possible contraindications when combined with drugs, other foods and herbal supplements. Another reported aspect of n‐3 omega PUFAs is that they protect and even enhance the effect in medical treatment of important diseases such as Alzheimer’s, multiple sclerosis and cancer. These reports led to PUFAs becoming one of the most accepted and consumed food supplements. Despite this weight of evidence and the considerable current use, there is still a need for studies, which will determine whether the n‐3 omega fatty acids are in fact important functional supplements with no adverse effects. This review will attempt to outline the current position of n‐3 omega fatty acids in the field of clinical nutrition and healthcare and outline the studies needed to determine whether there are significant advantages in taking them as food supplement without any adverse effects.
Industrial processing effects on chestnut fruits (Castanea sativa Mill.) 3. Minerals, free sugars, carotenoids and antioxidant vitamins
Authors: De Vasconcelos Maria do Carmo B. M. , Nunes Fernando , Viguera Cristina García , Bennett Richard N. , Rosa Eduardo A.S. , Ferreira‐Cardoso Jorge V. 
Published: February 2010

SummaryThe major aim of this study was to evaluate the effects of industrial processing on the composition of minerals, free sugars, vitamins and pigments in fruits of chestnut cultivars at four stages of industrial processing (A–fresh; B–after 3 months storage at ± 0 °C and relative humidity = 90%; C–after flame peeling at 800 °–1000 °C for 1–2 s; D–after freezing in a tunnel with a CO2 flow at −65 °C for 15–20 min) from two harvest years. Potassium and phosphorous were predominant in the fruits of all cultivars for both harvest years. Calcium, magnesium, iron, zinc and manganese were also present in the fruits. Fruits from both harvest years had a significant content of free sugars, with sucrose predominating, and these sugars were more affected by the processing stage. Significant levels of lutein, lutein esters, γ‐tocopherol and vitamin C were also found in the chestnut fruits. Fruit carotenoids and vitamin C significantly decreased during the industrial processing.
Optimising microwave vacuum puffing for blue honeysuckle snacks
Authors: Liu Chenghai , Zheng Xianzhe , Shi John , Xue Jun , Lan Yubin , Jia Shuhua 
Published: February 2010

AbstractFresh blue honeysuckle fruit slices were puffed in a microwave vacuum dryer up to a final moisture content about 5% (w.b.). The effect of initial moisture content (IMC) (25–45%), vacuum pressure (VP) (70–90 kPa) and microwave intensity (MI) (10–30 W g−1) on quality attributes, in terms of expansion ratio (ER), hardness (HD), crispness (CR) and colour of the products, were analysed by response surface methodology. Besides the effect of MI on chroma (CH), the high IMC and low VP had a significantly positive impact on the quality attributes of blue honeysuckle snacks. The optimum product qualities, which were ER (1.62 times), HD (5836.31 g), CR (4.48), and CH (28.7) were obtained at an IMC of 38.42%, VP of 82.02 kPa, and MI of 22.42 W g−1. The microwave vacuum method has obvious advantages when puffing the blue honeysuckle snacks.
Dough and crumb grain changes during mixing and fermentation and their relation with extension properties and bread quality of yeasted sweet dough
Authors: Tlapale‐Valdivia Alma D. , Chanona‐Pérez Jorge , Mora‐Escobedo Rosalva , Farrera‐Rebollo Reynold R. , Gutiérrez‐López Gustavo F. , Calderón‐Domínguez Georgina 
Published: February 2010

SummaryDough and crumb grain evolution of yeasted sweet dough, as affected by the combined effect of mixing (dough development) and fermentation times, and their relation to rheological properties and bread quality was studied. Structural changes of under or optimum developed dough, without fermentation, were related mainly to increments in extensibility (P > 95%), without a noticeable change in pH. At all mixing stages, fermentation duration increased Rm, whereas extensibility and pH decreased. When plotting Rm with bread specific volume, cell area, total cell area fraction or yellow crumb colour parameter (b*) simple mathematical models, with determination coefficients larger than 0.85 were obtained. Bread crumb image analysis showed that crumb cell size was not affected by mixing time, while fermentation duration had a direct influence on this parameter, increasing the proportion of the smallest and the largest crumb cells, without changing cell density, possibly as a result of Ostwald ripening, coalescence and separation‐redistribution mechanisms.
Insight into an island radiation: the Tarentola geckos of the Cape Verde archipelago
Authors: Vasconcelos Raquel , Carranza Salvador , James Harris D. 
Published: February 2010

AbstractAim  To reassess the relationships between Tarentola geckos from the Cape Verde Islands by including specimens from all islands in the range. To determine the variation within forms by sequencing over 400 specimens, thereby allowing the discovery of cryptic forms and resolving some of the issues raised previously. This extensive sampling was also used to shed light on distributions and to explain genetic diversity by comparing the ages and ecological and geological features of the islands (size, elevation and habitat diversity).Location  The Cape Verde Islands: an oceanic archipelago belonging to the Macaronesian biogeographic region, located around 500 km off Senegal.Methods  A total of 405 new specimens of Tarentola geckos were collected from nine islands with very different geological histories, topography, climate and habitats. Mitochondrial cytochrome b (cyt b) gene and 12S rRNA partial sequences were obtained and analysed using phylogenetic methods and networks to determine molecular diversity, demographic features and phylogeographic patterns.Results  The phylogenetic relationships between all known forms of Cape Verdean Tarentola specimens were estimated for the first time, the relationships between new forms were assessed and previously hypothesized relationships were re‐examined. Despite the large sample size, low intraspecific diversity was found using a 303‐bp cyt b fragment. Star‐like haplotype networks and statistical tests suggest the past occurrence of a rapid demographic and geographical expansion over most of the islands. Genetic variability is positively correlated with size, elevation and habitat diversity of the islands, but is not linearly related to the age of the islands. Biogeographical patterns have, in general, high concordance with phylogenetic breaks and with the three eco‐geographical island groups. Volcanism and habitat diversity, both tightly linked with island ontogeny, as postulated by the general dynamic model of oceanic island biogeography, as well as present and historical size of the islands appear to be the main factors explaining the genetic diversity of this group.Main conclusions  The Tarentola radiation was clarified and is clearly associated with the geological and ecological features of the islands. Two factors may account for the low intraspecific variation: (1) recent volcanic activity and high ecological stress, and (2) poor habitat diversity within some islands. More studies are needed to align taxonomy with phylogenetic relationships, whereas GIS modelling may help to predict precise species distributions.
Climatic water deficit, tree species ranges, and climate change in Yosemite National Park
Authors: Lutz James A. , van Wagtendonk Jan W. , Franklin Jerry F. 
Published: February 2010

AbstractAim  (1) To calculate annual potential evapotranspiration (PET), actual evapotranspiration (AET) and climatic water deficit (Deficit) with high spatial resolution; (2) to describe distributions for 17 tree species over a 2300‐m elevation gradient in a 3000‐km2 landscape relative to AET and Deficit; (3) to examine changes in AET and Deficit between past (c. 1700), present (1971–2000) and future (2020–49) climatological means derived from proxies, observations and projections; and (4) to infer how the magnitude of changing Deficit may contribute to changes in forest structure and composition.Location  Yosemite National Park, California, USA.Methods  We calculated the water balance within Yosemite National Park using a modified Thornthwaite‐type method and correlated AET and Deficit with tree species distribution. We used input data sets with different spatial resolutions parameterized for variation in latitude, precipitation, temperature, soil water‐holding capacity, slope and aspect. We used climate proxies and climate projections to model AET and Deficit for past and future climate. We compared the modelled future water balance in Yosemite with current species water‐balance ranges in North America.Results  We calculated species climatic envelopes over broad ranges of environmental gradients – a range of 310 mm for soil water‐holding capacity, 48.3°C for mean monthly temperature (January minima to July maxima), and 918 mm yr−1 for annual precipitation. Tree species means were differentiated by AET and Deficit, and at higher levels of Deficit, species means were increasingly differentiated. Modelled Deficit for all species increased by a mean of 5% between past (c. 1700) and present (1971–2000). Projected increases in Deficit between present and future (2020–49) were 23% across all plots.Main conclusions  Modelled changes in Deficit between past, present and future climate scenarios suggest that recent past changes in forest structure and composition may accelerate in the future, with species responding individualistically to further declines in water availability. Declining water availability may disproportionately affect Pinus monticola and Tsuga mertensiana. Fine‐scale heterogeneity in soil water‐holding capacity, aspect and slope implies that plant water balance may vary considerably within the grid cells of kilometre‐scale climate models. Sub‐grid‐cell soil and topographical data can partially compensate for the lack of spatial heterogeneity in gridded climate data, potentially improving vegetation‐change projections in mountainous landscapes with heterogeneous topography.
Chronic pain in people with an intellectual disability: under‐recognised and under‐treated?
Authors: McGuire B. E. , Daly P. , Smyth F. 
Published: February 2010

AbstractAim  To examine the nature, prevalence and impact of chronic pain in adults with an intellectual disability (ID) based on carer report.Methods  Postal questionnaires were sent to 250 care‐givers and 157 responses were received (63%).Results  Chronic pain was reported in 13% of the sample (n = 21), 6.3% had pain in two sites and 2% had pain in three or more sites. Of those with chronic pain, 19 experienced mild chronic pain, while severe pain was reported for two service users. Pain problems were more prevalent in those with a Mild ID than in those with more severe disability, perhaps reflecting the ability of the Mild group to communicate about their pain. Non‐prescription medication was the most common form of treatment and there was a notable absence of involvement of specialist pain services.Conclusions  Given their increased risk for chronic pain, we concluded that pain in the ID population may be under‐recognised and under‐treated, especially in those with impaired capacity to communicate about their pain.
Effects of an MHC‐DRB genotype and allele number on the load of gut parasites in the bank vole Myodes glareolus
Authors: KLOCH AGNIESZKA , BABIK WIESŁAW , BAJER ANNA , SIŃSKI EDWARD , RADWAN JACEK 
Published: February 2010

AbstractThe major histocompatibility complex (MHC) genes code for the proteins responsible for pathogen recognition. The MHC class II DRB gene is multiplicated in the bank vole, Myodes glareolus, with different numbers of loci found in different individuals. Possessing large numbers of loci should increase the probability of pathogen recognition, but according to the optimality hypothesis, there is a cost of possessing too many MHC alleles. Using 454 technology, we determined the individual DRB allelic diversity and related it to the load of intestinal parasites in voles collected from three sites separated by a distance of 12 to 27 km. The analysis of six microsatellite loci revealed significant population structure (FST = 0.07). The sites differed significantly in the prevalence and abundance of nematode species as well. We found two significant associations between MHC alleles and the intensity of the infection with the most prevalent nematode, Aspiculuris tetraptera. One of these associations was population‐specific. This result suggests that the directions of selection can differ between populations connected by a low level of gene flow, which may contribute to the maintenance of high DRB allele diversity. In accordance with the optimality hypothesis, individuals with an intermediate number of alleles carried the lowest number of nematode species and had the lowest prevalence of A. tetraptera. However, the intensity of infection with A. tetraptera was linearly and negatively associated with the number of alleles.
Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
Authors: RENAUT SÉBASTIEN , NOLTE ARNE W. , BERNATCHEZ LOUIS 
Published: February 2010

AbstractNext‐generation sequencing allows the discovery of large numbers of single nucleotide polymorphisms (SNPs) in species where little genomic information was previously available. Here, we assembled, de novo, over 130 mb of non‐normalized cDNA using 454 pyrosequencing data from dwarf and normal lake whitefish and backcross hybrids. Our main goals were to gather a large data set of SNP markers, document their distribution within coding regions, evaluate the effect of species divergence on allele frequencies and combine results with previous genomic studies to identify candidate genes underlying the adaptive divergence of lake whitefish. We identified 6094 putative SNPs in 2674 contigs (mean size: 576 bp, range: 101–6116) and 1540 synonymous and 1734 non‐synonymous mutations for a genome‐wide non‐synonymous to synonymous substitution rate ratio (pN/pS) of 0.37. As expected based on the young age (<15 000 years) of whitefish species pair, the overall level of divergence between them was relatively weak. Yet, 89 SNPs showed pronounced allele frequency differences between sympatric normal and dwarf whitefish. Among these, SNPs in genes annotated to energy metabolic functions were the most abundant and this, in addition to previous experimental data at the gene expression and phenotypic level, brings compelling evidence that genes involved in energy metabolism are prime candidates explaining the adaptive divergence of lake whitefish species pairs. Finally, we unexpectedly identified 44 contigs annotated to transposable elements and these were predominantly composed of backcross hybrids sequences. This indicates an elevated activity of transposable elements, which could potentially contribute to the reduced fitness of hybrids previously documented.
Diversity in a hidden world: potential and limitation of next‐generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
Authors: MEDINGER RALPH , NOLTE VIOLA , PANDEY RAM VINAY , JOST STEFFEN , OTTENWÄLDER BIRGIT , SCHLÖTTERER CHRISTIAN , BOENIGK JENS 
Published: February 2010

AbstractWith the delivery of millions of sequence reads in a single experiment, next‐generation sequencing (NGS) is currently revolutionizing surveys of microorganism diversity. In particular, when applied to Eukaryotes, we are still lacking a rigorous comparison of morphological and NGS‐based diversity estimates. In this report, we studied the diversity and the seasonal community turnover of alveolates (Ciliophora and Dinophyceae) in an oligotrophic freshwater lake by SSU amplicon sequencing with NGS as well as by classical morphological analysis. We complemented the morphological analysis by single‐cell PCR followed by Sanger sequencing to provide an unambiguous link to the NGS data. We show that NGS and morphological analyses generally capture frequency shifts of abundant taxa over our seasonal samples. The observed incongruencies are probably largely due to rDNA copy number variation among taxa and heterogeneity in the efficiency of cell lysis. Overall, NGS‐based amplicon sequencing was superior in detecting rare species. We propose that in the absence of other nuclear markers less susceptible to copy number variation, rDNA‐based diversity studies need to be adjusted for confounding effects of copy number variation.
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
Authors: STOECK THORSTEN , BASS DAVID , NEBEL MARKUS , CHRISTEN RICHARD , JONES MEREDITH D. M. , BREINER HANS‐WERNER , RICHARDS THOMAS A. 
Published: February 2010

AbstractSequencing of ribosomal DNA clone libraries amplified from environmental DNA has revolutionized our understanding of microbial eukaryote diversity and ecology. The results of these analyses have shown that protist groups are far more genetically heterogeneous than their morphological diversity suggests. However, the clone library approach is labour‐intensive, relatively expensive, and methodologically biased. Therefore, even the most intensive rDNA library analyses have recovered only small samples of much larger assemblages, indicating that global environments harbour a vast array of unexplored biodiversity. High‐throughput parallel tag 454 sequencing offers an unprecedented scale of sampling for molecular detection of microbial diversity. Here, we report a 454 protocol for sampling and characterizing assemblages of eukaryote microbes. We use this approach to sequence two SSU rDNA diversity markers—the variable V4 and V9 regions—from 10 L of anoxic Norwegian fjord water. We identified 38 116 V4 and 15 156 V9 unique sequences. Both markers detect a wide range of taxonomic groups but in both cases the diversity detected was dominated by dinoflagellates and close relatives. Long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes. Most tags detected represent genotypes not currently in GenBank, although many are similar to database sequences. We suggest that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and we discuss the biological significance of this high amplicon diversity.
mlRho – a program for estimating the population mutation and recombination rates from shotgun‐sequenced diploid genomes
Authors: HAUBOLD BERNHARD , PFAFFELHUBER PETER , LYNCH MICHAEL 
Published: February 2010

AbstractImprovements in sequencing technology over the past 5 years are leading to routine application of shotgun sequencing in the fields of ecology and evolution. However, the theory to estimate evolutionary parameters from these data is still being worked out. Here we present an extension and implementation of part of this theory, mlRho. This program can efficiently compute the following three maximum likelihood estimators based on shotgun sequence data obtained from single diploid individuals: the population mutation rate (4Neμ), the sequencing error rate, and the population recombination rate (4Nec). We demonstrate the accuracy of mlRho by applying it to simulated data sets. In addition, we analyse the genomes of the sea squirt Ciona intestinalis and the water flea Daphnia pulex. Ciona intestinalis is an obligate outcrosser, while D. pulex is a cyclic parthenogen, and we discuss how these contrasting life histories are reflected in our parameter estimates. The program mlRho is freely available from http://guanine.evolbio.mpg.de/mlRho.
Assembly free comparative genomics of short‐read sequence data discovers the needles in the haystack
Authors: CANNON CHARLES H. , KUA CHAI‐SHIAN , ZHANG D. , HARTING J.R. 
Published: February 2010

AbstractMost comparative genomic analyses of short‐read sequence (SRS) data rely upon the prior assembly of a reference sequence. Here, we present an assembly free analysis of SRS data that discovers sequence variants among focal genomes by tabulating the presence and frequency of ‘complex’ fragments in the data. Using data from nine tree species, we compare genomic diversity from populations to families. As a control, we simulated SRS data for three known plant genomes. The results provide insight into the quality and distributional bias of the sequencing reaction. Three main types of informative complexmers were identified, each possessing unique statistical properties. Type I complexmers are unique to a genome but suffer from a high false positive rate, being highly dependent on read coverage and distribution. Type II complexmers are shared between two genomes and can highlight potential copy‐number differences. Type III complexmers are exclusive to a subset of genomes and can be useful for associating genetic differences with phenotypic or geographic variation. At the population level in an endangered timber species, numerous markers were identified that could potentially determine geographic origin of individuals and regulate international trade. We observed that the genomic data for the four fig species were more divergent than for stone oak species, possibly due to their complex pollination syndrome and high rates of gene flow. Our approach greatly enhances the application of SRS technology to the study of non‐model organisms and directly identifies the most informative genetic elements for more detailed study and assembly.