bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low costs, high output: reproduction in an insular pit‐viper (Gloydius shedaoensis, Viperidae) from north‐eastern China
Authors: Li‐xin Sun , Shine Richard , Debi Zhao , Zhengren Tang 
Published: September 2010

AbstractCurrent life‐history paradigms predict that an organism's total reproductive output is determined by its intrinsic level of ‘reproductive effort’ (RE), interacting with local resource availability. In turn, RE is driven by ‘costs of reproduction’. Within the total allocation, selective forces on offspring size ultimately determine both the number and size of offspring (because of a trade‐off between these two traits). Although patterns of life‐history variation are broadly consistent with this scenario, the evidence is weak: it is generally difficult to measure ‘costs’ or selective forces on offspring size. To test this paradigm, we need a study organism which differs in these respects from related taxa, so that we can unequivocally generate predictions about life‐history traits. A remarkable island population of Asian pit‐vipers Gloydius shedaoensis was studied for which (unlike mainland conspecifics) ‘costs of reproduction’ are low, food availability is high, and there is intense selection for large offspring size. Maternal body sizes and condition, and offspring numbers and sizes were quantified for 79 litters over 2 years. As predicted, the snakes display high reproductive output per female (relative to maternal body mass, litter mass is about twice as high as in related taxa), large offspring size (about three times the mass of related taxa) and a strong trade‐off between offspring size and litter size. Reproductive output was only weakly correlated with maternal body size, and output was adjusted mostly by manipulating litter size rather than offspring size. Reproductive output varied between years, but maternal body condition after parturition did not. Measures of reproductive output (such as the mass or energy content of the litter) bear little relationship to ‘costs of reproduction’ in this system.
Inter‐specific variation inMacropuscrania: form, function and phylogeny
Authors: Milne Nicholas , O'Higgins Paul 
Published: September 2010

AbstractMorphological variation was studied in the crania of seven species of kangaroos and wallabies (Macropus). How function and phylogeny interact to influence cranial form amongst adults of diverse species was considered. Thirty‐six, three‐dimensional landmarks were acquired on each of 65 adultMacropusspecimens from Western Australia. The different species occupy a wide range of habitats and latitudes and there are well‐known differences in diet among the species. Size and shape variability was examined using the methods of geometric morphometrics. Aspects of inter‐specific variation explained by principal components were visualized and examined for correlations with size, latitude, and diet. The first principal component correlates strongly with inter‐specific differences in latitude and it primarily contrasts species on the basis of the relative length of the snout anterior to the molar teeth, this being greater in species that live in cooler climates. Species scores on the second principal component correlate strongly with centroid size such that smaller crania have more flexed muzzles. Principal component three separates the short grass‐eating, red kangarooM. rufus, from all other species (most of which eat tough herbage from trees and shrubs). This principal component represents differences in the masticatory apparatus. Variation on the fourth principal component also seems to be functionally interpretable in terms of further differences in the masticatory apparatus ofM. agilis. The relationship between phylogeny and cranial form was investigated by comparing a phenogram based on the shape distances between taxa with a consensus phylogeny drawn from the literature onMacropusgenetics, ecology and morphology. The phenogram shows considerable similarity to current taxonomic views, but, our results also indicate differences that are related to function. Thus, this study serves to unravel the interaction of functional and phylogenetic influences on cranial form amongstMacropusspecies and raises further issues relating to ontogeny and phylogeny.
The western pond turtle (Clemmys marmorata) in the Mojave River, California, USA: highly adapted survivor or tenuous relict?
Authors: Lovich Jeff , Meyer Kathie 
Published: September 2010

AbstractAspects of the ecology of populations of the western pond turtle Clemmys marmorata were investigated in the Mojave River of the central Mojave Desert, California, U.S.A. One population occupied man‐made ponds and the other occurred in natural ponds in the flood plain of the Mojave River. Both habitats are severely degraded as a result of ground water depletion from human activities along the river and one is infested with the exotic shrub saltcedar Tamarix ramosissima. Mean female carapace length (CL) was significantly greater (14.4 cm) than that of males (13.7 cm). Live juveniles were not detected during the period of study. Shelled eggs were visible in X‐radiographs from 26 May to 14 July. Mean clutch size was 4.46 and ranged from 3 to 6 eggs. Clutch size did not vary between 1998 and 1999 but was significantly correlated with CL for both years combined, increasing at the rate of 0.548 eggs/cm CL. Gravid female CL ranged from 13.3–16.0 cm. Some females nested in both years. Mean X‐ray egg width (21.8 mm) was not significantly correlated with CL or clutch size. X‐ray egg width differed more among clutches than within, whether including CL as a co‐variate or not. Nesting migrations occurred from 6 June to 8 July with minimum round trip distances ranging from 17.5–585 m with a mean of 195 m. Mean estimated time of departure as measured at the drift fence was 18:13. Most females returned to the ponds in the early morning. Nesting migrations required females to be out of the water for estimated periods of 0.83 to 86 h. The destination of nesting females was typically fluvial sand bars in the channel of the dry riverbed. Overall, the ecology of C. marmorata in the Mojave River is very similar to that reported for populations in less severe habitats along the west coast of the United States. Notable exceptions include long nesting migrations to sandbars in the dry river channel, a possible result of human modifications to the environment, and an apparent lack of terrestrial overwintering behaviour in Mojave River populations. The general similarity of desert and coastal populations is possibly a reflection of their recent geographic separation. Overall, populations in the Mojave River exhibit few obvious adaptations to living in the desert and are considered to be tenuous relicts of the Pleistocene. The small size and tenuous status of these populations suggests that immediate conservation action is needed, including establishment of satellite populations as a hedge against extirpation.
A new high-resolution bathymetry model for the Terre Adélie and George V continental margin, East Antarctica
Authors: Beaman Robin J. , O’Brien Philip E. , Post Alexandra L. , De Santis Laura 
Published: September 2010

AbstractThe Collaborative East Antarctic Marine Census (CEAMARC) surveys to the Terre Adélie and George V continental margin highlight the requirement for a revised high-resolution bathymetry model that can be used as a spatial tool for improving information on the physical environment of the region. We have combined shiptrack singlebeam and multibeam bathymetry, coastline data, and land and ice sheet topographic data to develop a new regional-scale bathymetry grid, called GVdem (short for George V digital elevation model). The GVdem grid spans an area between 138–148°E and 63–69°S, with a cell pixel size of 0.001-arcdegree (c. 100 m). The revised digital elevation model is a large improvement over previously available regional-scale grids from the area, and highlights seabed physiographic detail not formerly observed in this part of East Antarctica. In particular, the extent and complexity of the rugged inner-shelf valleys are revealed, and their spatial relationship with large shelf basins and adjacent flat-topped banks. The new grid also reveals further insight into the spatial distribution of the submarine canyons found on the continental slope.
The Calabi–Yau equation on the Kodaira–Thurston manifold
Authors: Tosatti Valentino , Weinkove Ben 
Published: September 2010

AbstractWe prove that the Calabi–Yau equation can be solved on the Kodaira–Thurston manifold for all given T2-invariant volume forms. This provides support for Donaldson's conjecture that Yau's theorem has an extension to symplectic 4-manifolds with compatible but non-integrable almost complex structures.
Unfolded protein response (UPR) gene expression during antibody-dependent enhanced infection of cultured monocytes correlates with dengue disease severity
Authors: Paradkar Prasad N. , Ooi Eng Eong , Hanson Brendon J. , Gubler Duane J. , Vasudevan Subhash G. 
Published: September 2010

DENV (dengue virus) induces UPR (unfolded protein response) in the host cell, which strikes a balance between pro-survival and pro-apoptotic signals. We previously showed that Salubrinal, a drug that targets the UPR, inhibits DENV replication. Here, we examine the impact on UPR after direct or ADE (antibody-dependent enhanced) infection of cells with DENV clinical isolates. THP-1 cells in the presence of subneutralizing concentration of humanized antibody 4G2 (cross-reactive with flavivirus envelope protein) or HEK-293 cells (human embryonic kidney 293 cells) were infected with DENV-1–4 serotypes. UPR gene expression was monitored under these infection conditions using real-time RT–PCR (reverse transcription–PCR) and Western blots to analyse serotype-dependent variations. Subsequently, in a blinded study, strain-specific differences were compared between DENV-2 clinical isolates obtained from a single epidemic. Results showed that THP-1 cells were infected efficiently and equally by DENV-1–4 in the ADE mode. At 48 hpi (h post infection), DENV-1 and -3 showed a higher replication rate and induced higher expression of several UPR genes such as BiP (immunoglobulin heavy-chain-binding protein), GADD34 (growth arrest DNA damage-inducible protein 34) and CHOP [C/EBP (CCAAT/enhancer-binding protein)-homologous protein]. The ADE infection of THP-1 cells with epidemic DENV-2 high-UPR-gene-expressing strains appears to correlate with severe disease; however, no such correlation could be made when the same viruses were used to infect HEK-293 cells. Our finding that UPR gene expression in THP-1 cells during ADE infection correlates with dengue disease severity is consistent with a previous study [Morens, Marchette, Chu and Halstead (1991) Am. J. Trop. Med. Hyg. 45, 644–651] that showed that the growth of DENV 2 isolates in human peripheral blood leucocytes correlated with severe and mild dengue diseases.
Why does yeast ferment? A flux balance analysis study
Authors: Simeonidis Evangelos , Murabito Ettore , Smallbone Kieran , Westerhoff Hans V. 
Published: September 2010

Advances in biological techniques have led to the availability of genome-scale metabolic reconstructions for yeast. The size and complexity of such networks impose limits on what types of analyses one can perform. Constraint-based modelling overcomes some of these restrictions by using physicochemical constraints to describe the potential behaviour of an organism. FBA (flux balance analysis) highlights flux patterns through a network that serves to achieve a particular objective and requires a minimal amount of data to make quantitative inferences about network behaviour. Even though FBA is a powerful tool for system predictions, its general formulation sometimes results in unrealistic flux patterns. A typical example is fermentation in yeast: ethanol is produced during aerobic growth in excess glucose, but this pattern is not present in a typical FBA solution. In the present paper, we examine the issue of yeast fermentation against respiration during growth. We have studied a number of hypotheses from the modelling perspective, and novel formulations of the FBA approach have been tested. By making the observation that more respiration requires the synthesis of more mitochondria, an energy cost related to mitochondrial synthesis is added to the FBA formulation. Results, although still approximate, are closer to experimental observations than earlier FBA analyses, at least on the issue of fermentation.
Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models
Authors: Bakker Barbara M. , van Eunen Karen , Jeneson Jeroen A.L. , van Riel Natal A.W. , Bruggeman Frank J. , Teusink Bas 
Published: September 2010

Human metabolic diseases are typically network diseases. This holds not only for multifactorial diseases, such as metabolic syndrome or Type 2 diabetes, but even when a single gene defect is the primary cause, where the adaptive response of the entire network determines the severity of disease. The latter may differ between individuals carrying the same mutation. Understanding the adaptive responses of human metabolism naturally requires a systems biology approach. Modelling of metabolic pathways in micro-organisms and some mammalian tissues has yielded many insights, qualitative as well as quantitative, into their control and regulation. Yet, even for a well-known pathway such as glycolysis, precise predictions of metabolite dynamics from experimentally determined enzyme kinetics have been only moderately successful. In the present review, we compare kinetic models of glycolysis in three cell types (African trypanosomes, yeast and skeletal muscle), evaluate their predictive power and identify limitations in our understanding. Although each of these models has its own merits and shortcomings, they also share common features. For example, in each case independently measured enzyme kinetic parameters were used as input. Based on these ‘lessons from glycolysis’, we will discuss how to make best use of kinetic computer models to advance our understanding of human metabolic diseases.
Two Coordinately Regulated Homologs of FLOWERING LOCUS T Are Involved in the Control of Photoperiodic Flowering in Soybean
Authors: Kong Fanjiang , Liu Baohui , Xia Zhengjun , Sato Shusei , Kim Bo Min , Watanabe Satoshi , Yamada Tetsuya , Tabata Satoshi , Kanazawa Akira , Harada Kyuya , Abe Jun 
Published: September 2010

Abstract
FLOWERING LOCUS T (FT) is a key flowering integrator in Arabidopsis (Arabidopsis thaliana), with homologs that encode florigens in many plant species regardless of the type of photoperiodic response. We identified 10 FT homologs, which were arranged as five pairs of linked genes in different homoeologous chromosomal regions, in soybean (Glycine max), a paleopolyploid species. Two of the FT homologs, GmFT2a and GmFT5a, were highly up-regulated under short-day (SD) conditions (inductive for flowering in soybean) and had diurnal expression patterns with the highest expression 4 h after dawn. Under long-day (LD) conditions, expression of GmFT2a and GmFT5a was down-regulated and did not follow a diurnal pattern. Flowering took much longer to initiate under LD than under SD, and only the GmFT5a transcript accumulated late in development under LD. Ectopic expression analysis in Arabidopsis confirmed that both GmFT2a and GmFT5a had the same function as Arabidopsis FT, but the effect of GmFT5a was more prominent. A double-mutant soybean line for two PHYTOCHROME A (PHYA) genes expressed high levels of GmFT2a and GmFT5a under LD, and it flowered slightly earlier under LD than the wild type grown under SD. The expression levels of GmFT2a and GmFT5a were regulated by the PHYA-mediated photoperiodic regulation system, and the GmFT5a expression was also regulated by a photoperiod-independent system in LD. Taken together, our results suggest that GmFT2a and GmFT5a coordinately control flowering and enable the adaptation of soybean to a wide range of photoperiodic environments.
A High-Throughput Data Mining of Single Nucleotide Polymorphisms inCoffeaSpecies Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the AllotetraploidCoffea arabica
Authors: Vidal Ramon Oliveira , Mondego Jorge Maurício Costa , Pot David , Ambrósio Alinne Batista , Andrade Alan Carvalho , Pereira Luiz Filipe Protasio , Colombo Carlos Augusto , Vieira Luiz Gonzaga Esteves , Carazzolle Marcelo Falsarella , Pereira Gonçalo Amarante Guimarães 
Published: September 2010

AbstractPolyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
The 20S proteasome α5subunit ofArabidopsis thalianacarries an RNase activity and interactsin plantawith theLettuce mosaic potyvirusHcPro protein
Authors: DIELEN ANNE‐SOPHIE , SASSAKI FLAVIO TETSUO , WALTER JOCELYNE , MICHON THIERRY , MÉNARD GUILLAUME , PAGNY GAËLLE , KRAUSE‐SAKATE RENATE , MAIA IVAN DE GODOY , BADAOUI SALOUA , LE GALL OLIVIER , CANDRESSE THIERRY , GERMAN‐RETANA SYLVIE 
Published: September 2010

SUMMARYIn plants, the ubiquitin/26S proteasome system (UPS) plays a central role in protein degradation and is involved in many steps of defence mechanisms, regardless of the types of pathogen targeted. In addition to its proteolytic activities, the UPS ribonuclease (RNase) activity, previously detected in 20S proteasome preparations from cauliflower and sunflower (Helianthus annuus), has been shown to specifically target plant viral RNAsin vitro. In this study, we show that recombinantArabidopsis thalianaproteasomal α5subunit expressed inEscherichia coliharbours an RNase activity that degradesTobacco mosaic virus(TMV, Tobamovirus)‐ andLettuce mosaic virus(LMV, Potyvirus)‐derived RNAsin vitro. The analysis of mutated forms of the α5subunit demonstrated that mutation of a glutamic acid at position 110 affects RNase activity. Furthermore, it was demonstrated, using a bimolecular fluorescence complement assay, that the multifunctional helper component proteinase (HcPro) of LMV, already known to interfere with the 20S proteasome RNase activityin vitro, can interactin vivowith the recombinant α5subunit. Further experiments demonstrated that, in LMV‐infected lettuce cells, α5is partially relocalized to HcPro‐containing infection‐specific inclusions. Susceptibility analyses ofArabidopsismutants, knocked out for eachAt‐PAEgene encoding α5, showed that one (KO‐pae1) of the two mutants exhibited a significantly increased susceptibility to LMV infection. Taken together, these results extend toA. thalianaα5the range of HcPro‐interacting proteasomal subunits, and suggest that HcPro may modulate its associated RNase activity which may contribute to an antiviral response.
Erythropoietin enhances endogenous haem oxygenase-1 and represses immune responses to ameliorate experimental autoimmune encephalomyelitis
Authors: Chen Shyi-Jou , Wang Yen-Ling , Lo Wen-Tsung , Wu Chia-Cho , Hsieh Chia-Wen , Huang Ching-Feng , Lan Yu-Hsin , Wang Chih-Chien , Chang Deh-Ming , Sytwu Huey-Kang 
Published: September 2010

SummaryBoth erythropoietin (EPO) and haem oxygenase-1 (HO-1), an anti-oxidative stress protein, have proven protective roles in experimental autoimmune encephalomyelitis (EAE), a reliable animal model of multiple sclerosis. In this study, EPO delivered intraperitoneally could reduce disease severity in myelin oligodendrocyte glycoprotein (MOG)–EAE mice. To assess the effect of EPO on endogenous HO-1 in EAE, we investigated expression of HO-1 mRNA by real-time polymerase chain reaction (RT–PCR), protein expression centrally and peripherally by Western blot and immunohistochemistry and mean fluorescence intensity of splenic HO-1 by flow cytometry. A significantly higher expression of HO-1 in both the central nervous system (CNS) and spleen was shown in EPO-treated MOG–EAE mice than in controls. We further examined the immunomodulatory effect of EPO in EAE, and via RT–PCR demonstrated significantly lower expression of interferon-γ, interleukin (IL)-23, IL-6 and IL-17 mRNA, and significantly higher expression of IL-4 and IL-10 mRNA in CNS of EPO-treated MOG–EAE mice than in controls. Using flow cytometry, we also observed a significantly decreased ratio of both T helper type 1 (Th1) and Th17 lymphocyte subsets isolated from CNS and a significantly increased ratio of splenic regulatory CD4 T cells in EPO-treated MOG–EAE mice. In addition, we demonstrated that MOG-specific T cell proliferation was lower in the EPO-treated group than in controls and showed amelioration of EAE by adoptive transfer of splenocytes from EPO-treated MOG–EAE mice. Together, our data show that in EAE, EPO induction of endogenous HO-1 and modulation of adaptive immunity both centrally and peripherally may involve the repression of inflammatory responses.
Hiatus concretions
Authors: Zatoń Michał 
Published: September 2010

The term ‘hiatus concretions’ was introduced for the first time by the late Ehrhard Voigt, a well‐known German bryozoan specialist, in 1968 (originally as Hiatus‐Konkretionen). Hiatus concretions are early diagenetic bodies that formed within the host sediment. In this respect, they are similar in composition to other concretions that are very common in siliciclastic deposits of different ages, some of which are known to contain fossils or minerals. Hiatus concretions, however, differ from conventional concretions in their complex post‐diagenetic history, including exhumation on the sea‐floor, colonization by various encrusting and/or boring organisms during a break in sedimentation, and final burial. Thus, the name ‘hiatus concretions’ refers to the fact that they indicate hiatal surfaces in sedimentary sequences (Fig. 1). It is known that hiatus concretions may have developed during very different time‐spans: for example, within a part of one ammonite subzone (i.e. tens of thousands to a few hundreds of thousands of years) or much longer, during a time embracing more than a stage (i.e. several millions of years). The majority of the hiatus concretions known from the fossil record have carbonate cements, usually calcite, and these are the main focus of this article. Some hiatus concretions, however, are cemented by phosphate minerals.Hiatus concretions in the field. A. A horizon of hiatus concretions weathered out from the Middle Jurassic (Bathonian) clay sediments at Krzyworzeka, Polish Jura, Poland. B. Close‐up of the hiatus concretions.image