bluuebunny/crossref_metadata_2025 huggingface dataset:
Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens
Authors: Doores Katie J. , Bonomelli Camille , Harvey David J. , Vasiljevic Snezana , Dwek Raymond A. , Burton Dennis R. , Crispin Max , Scanlan Christopher N.
Published: July 2010

The envelope spike of HIV is one of the most highly N-glycosylated structures found in nature. However, despite extensive research revealing essential functional roles in infection and immune evasion, the chemical structures of the glycans on the native viral envelope glycoprotein gp120—as opposed to recombinantly generated gp120—have not been described. Here, we report on the identity of the N-linked glycans from primary isolates of HIV-1 (clades A, B, and C) and from the simian immunodeficiency virus. MS analysis reveals a remarkably simple and highly conserved virus-specific glycan profile almost entirely devoid of medial Golgi-mediated processing. In stark contrast to recombinant gp120, which shows extensive exposure to cellular glycosylation enzymes (>70% complex type glycans), the native envelope shows barely detectable processing beyond the biosynthetic intermediate Man
5
GlcNAc
2
(<2% complex type glycans). This oligomannose (Man
5–9
GlcNAc
2
) profile is conserved across primary isolates and geographically divergent clades but is not reflected in the current generation of gp120 antigens used for vaccine trials. In the context of vaccine design, we also note that Manα1→2Man-terminating glycans (Man
6–9
GlcNAc
2
) of the type recognized by the broadly neutralizing anti-HIV antibody 2G12 are 3-fold more abundant on the native envelope than on the recombinant monomer and are also found on isolates not neutralized by 2G12. The Manα1→2Man residues of gp120 therefore provide a vaccine target that is physically larger and antigenically more conserved than the 2G12 epitope itself. This study revises and extends our understanding of the glycan shield of HIV with implications for AIDS vaccine design.
Length control of the injectisome needle requires only one molecule of Yop secretion protein P (YscP)
Authors: Wagner Stefanie , Stenta Marco , Metzger Lisa C. , Dal Peraro Matteo , Cornelis Guy R.
Published: July 2010

The needle length of the
Yersinia
spp. injectisome is determined by Yop secretion protein P (YscP), an early substrate of the injectisome itself. There is a linear correlation between the length of YscP and the length of the needle, suggesting that YscP acts as a molecular ruler. However, it is not known whether one single molecule of YscP suffices to control the length of one needle or whether several molecules of YscP are exported in alternation with the needle subunit YscF until the needle length matches the ruler length, which would stop needle growth. To address this question, three different strains expressing simultaneously a short and a long version of YscP were engineered. The experimentally obtained needle length distribution was compared with the distributions predicted by stochastic modeling of the various possible scenarios. The experimental data are compatible with the single ruler model and not with the scenarios involving more than one ruler per needle.
Dendritic processes of osteocytes are mechanotransducers that induce the opening of hemichannels
Authors: Burra Sirisha , Nicolella Daniel P. , Francis W. Loren , Freitas Christopher J. , Mueschke Nicholas J. , Poole Kristin , Jiang Jean X.
Published: July 2010

Osteocytes with long dendritic processes are known to sense mechanical loading, which is essential for bone remodeling. There has been a long-standing debate with regard to which part(s) of osteocyte, the cell body versus the dendritic process, acts as a mechanical sensor. To address this question experimentally, we used a transwell filter system that differentiates the cell body from the dendritic processes. Mechanical loading was applied to either the cell body or the dendrites, and the osteocyte’s response was observed through connexin 43 hemichannel opening. The hemichannels located on the cell body were induced to open when mechanical loading was applied to either the dendritic processes or the cell body. However, no significant hemichannel activity in the dendrites was detected when either part of the cell was mechanically stimulated. Disruption of the glycocalyx by hyaluronidase on the dendrite side alone is sufficient to diminish a dendrite’s ability to induce the opening of hemichannels on the cell body, while hyaluronidase has no such effect when applied to the cell body. Importantly, hyaluronidase treatment to the dendrite side resulted in formation of poor integrin attachments with the reduced ability of the dendrites to form integrin attachments on the underside of the transwell filter. Together, our study suggests that the glycocalyx of the osteocyte dendritic process is required for forming strong integrin attachments. These integrin attachments probably serve as the mechanotransducers that transmit the mechanical signals to the cell body leading to the opening of hemichannels, which permits rapid exchange of factors important for bone remodeling.
Ras-related protein Rab10 facilitates TLR4 signaling by promoting replenishment of TLR4 onto the plasma membrane
Authors: Wang Di , Lou Jun , Ouyang Chuan , Chen Weilin , Liu Yiqi , Liu Xinyuan , Cao Xuetao , Wang Jianli , Lu Linrong
Published: July 2010

The Toll-like receptor (TLR)4 receptor complex, TLR4/MD-2, plays an important role in the inflammatory response against lipopolysaccharide, a ubiquitous membrane component in Gram-negative bacteria. Ligand recognition by TLR4 initiates multiple intracellular signaling pathways, leading to production of proinflammatory mediators and type I IFN. Ligand interaction also leads to internalization of the surface receptor complex into lysosomes, leading to the degradation of TLR4 and the termination of LPS response. However, surface level of TLR4 receptor complex is maintained via continuous replenishment of TLR4 from intracellular compartments like Golgi and endosomes. Here we show that continuous replenishment of TLR4 from Golgi to plasma membrane is regulated by the small GTPase Rab10, which is essential for optimal macrophage activation following LPS stimulation. Expression of Rab10 is inducible by LPS. Blockade of Rab10 function leads to decreased membrane TLR4 expression and diminished production of inflammatory cytokines and interferons upon LPS stimulation. These findings suggest that Rab10 expression provides a mechanism to refine TLR4 signaling by regulating the trafficking rate of TLR4 onto the plasma membrane. In addition, we show that altered Rab10 expression in macrophages influences disease severity in an in vivo model of LPS-induced acute lung injury, suggesting Rab10 as a possible therapeutic target for human acute respiratory distress syndrome (ARDS).
In vivo evidence for the fibrillar structures of Sup35 prions in yeast cells
Authors: Kawai-Noma Shigeko , Pack Chan-Gi , Kojidani Tomoko , Asakawa Haruhiko , Hiraoka Yasushi , Kinjo Masataka , Haraguchi Tokuko , Taguchi Hideki , Hirata Aiko
Published: July 2010

Yeast prion [PSI+] is caused by aggregated structures of the Sup35 protein. Although Sup35 forms typical amyloid fibrils in vitro, there is no direct evidence for the fibrillar structures of Sup35 in vivo. We analyzed [PSI+] cells in which Sup35 fused with green fluorescent protein (GFP) formed aggregates visible by fluorescence microscopy using thin-section electron microscopy (EM). Rapid-freeze EM combined with an immunogold-labeling technique as well as correlative light EM, which allows high-resolution imaging by EM of the same structure observed by light (fluorescence) microscopy, shows that the aggregates contain bundled fibrillar structures of Sup35-GFP. Additional biochemical and fluorescent correlation spectroscopy results suggest that the Sup35 oligomers diffused in the [PSI+] lysates adopt fibril-like shapes. Our findings demonstrate that [PSI+] cells contain Sup35 fibrillar structures closely related to those formed in vitro and provide insight into the molecular mechanism by which Sup35 aggregates are assembled and remodeled in [PSI+] cells.
Sulfatase modifying factor 1–mediated fibroblast growth factor signaling primes hematopoietic multilineage development
Authors: Buono Mario , Visigalli Ilaria , Bergamasco Roberta , Biffi Alessandra , Cosma Maria Pia
Published: July 2010

Self-renewal and differentiation of hematopoietic stem cells (HSCs) are balanced by the concerted activities of the fibroblast growth factor (FGF), Wnt, and Notch pathways, which are tuned by enzyme-mediated remodeling of heparan sulfate proteoglycans (HSPGs). Sulfatase modifying factor 1 (SUMF1) activates the Sulf1 and Sulf2 sulfatases that remodel the HSPGs, and is mutated in patients with multiple sulfatase deficiency. Here, we show that the FGF signaling pathway is constitutively activated in Sumf1−/− HSCs and hematopoietic stem progenitor cells (HSPCs). These cells show increased p-extracellular signal-regulated kinase levels, which in turn promote β-catenin accumulation. Constitutive activation of FGF signaling results in a block in erythroid differentiation at the chromatophilic erythroblast stage, and of B lymphocyte differentiation at the pro–B cell stage. A reduction in mature myeloid cells and an aberrant development of T lymphocytes are also seen. These defects are rescued in vivo by blocking the FGF pathway in Sumf1−/− mice. Transplantation of Sumf1−/− HSPCs into wild-type mice reconstituted the phenotype of the donors, suggesting a cell autonomous defect. These data indicate that Sumf1 controls HSPC differentiation and hematopoietic lineage development through FGF and Wnt signaling.
miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis
Authors: Liu Gang , Friggeri Arnaud , Yang Yanping , Milosevic Jadranka , Ding Qiang , Thannickal Victor J. , Kaminski Naftali , Abraham Edward
Published: July 2010

Uncontrolled extracellular matrix production by fibroblasts in response to tissue injury contributes to fibrotic diseases, such as idiopathic pulmonary fibrosis (IPF), a progressive and ultimately fatal process that currently has no cure. Although dysregulation of miRNAs is known to be involved in a variety of pathophysiologic processes, the role of miRNAs in fibrotic lung diseases is unclear. In this study, we found up-regulation of miR-21 in the lungs of mice with bleomycin-induced fibrosis and also in the lungs of patients with IPF. Increased miR-21 expression was primarily localized to myofibroblasts. Administration of miR-21 antisense probes diminished the severity of experimental lung fibrosis in mice, even when treatment was started 5–7 d after initiation of pulmonary injury. TGF-β1, a central pathological mediator of fibrotic diseases, enhanced miR-21 expression in primary pulmonary fibroblasts. Increasing miR-21 levels promoted, whereas knocking down miR-21 attenuated, the pro-fibrogenic activity of TGF-β1 in fibroblasts. A potential mechanism for the role of miR-21 in fibrosis is through regulating the expression of an inhibitory Smad, Smad7. These experiments demonstrate an important role for miR-21 in fibrotic lung diseases and also suggest a novel approach using miRNA therapeutics in treating clinically refractory fibrotic diseases, such as IPF.
Determinants of Nosocomial Infection in 6 Neonatal Intensive Care Units: An Italian Multicenter Prospective Cohort Study
Authors: Auriti Cinzia , Ronchetti Maria Paola , Pezzotti Patrizio , Marrocco Gabriella , Quondamcarlo Anna , Seganti Giulio , Bagnoli Francesco , De Felice Claudio , Buonocore Giuseppe , Arioni Cesare , Serra Giovanni , Bacolla Gianfranco , Corso Giovanna , Mastropasqua Savino , Mari Annibale , Corchia Carlo , Di Lallo Domenico , Ravà Lucilla , Orzalesi Marcello , Di Ciommo Vincenzo
Published: July 2010

Background.

Nosocomial infections are still a major cause of morbidity and mortality among neonates admitted to neonatal intensive care units (NICUs).

Objective.

To describe the epidemiology of nosocomial infections in NICUs and to assess the risk of nosocomial infection related to the therapeutic procedures performed and to the clinical characteristics of the neonates at birth and at admission to the NICU, taking into account the time between the exposure and the onset of infection.

Design.

A multicenter, prospective cohort study.

Patients and Setting.

A total of 1,692 neonates admitted to 6 NICUs in Italy were observed and monitored for the development of nosocomial infection during their hospital stay.

Methods.

Data were collected on the clinical characteristics of the neonates admitted to the NICUs, their therapeutic interventions and treatments, their infections, and their mortality rate. The cumulative probability of having at least 1 infection and the cumulative probability of having at least 1 infection or dying were estimated. The hazard ratio (HR) for the first infection and the HR for the first infection or death were also estimated.

Results.

A total of 255 episodes of nosocomial infection were diagnosed in 217 neonates, yielding an incidence density of 6.9 episodes per 1,000 patient-days. The risk factors related to nosocomial infection in very-low-birth-weight neonates were receipt of continuous positive airway pressure (HR, 3.8 [95% confidence interval {CI}, 1.7-8.1]), a Clinical Risk Index for Babies score of 4 or greater (HR, 2.2 [95% CI, 1.4-3.4]), and a gestational age of less than 28 weeks (HR, 2.1 [95% CI, 1.2-3.8]). Among heavier neonates, the risk factors for nosocomial infection were receipt of parenteral nutrition (HR, 8.1 [95% CI, 3.2-20.5]) and presence of malformations (HR, 2.3 [95% CI, 1.5-3.5]).

Conclusions.

Patterns of risk factors for nosocomial infection differ between very-low-birth-weight neonates and heavier neonates. Therapeutic procedures appear to be strong determinants of nosocomial infection in both groups of neonates, after controlling for clinical characteristics.
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Authors: McKenna Aaron , Hanna Matthew , Banks Eric , Sivachenko Andrey , Cibulskis Kristian , Kernytsky Andrew , Garimella Kiran , Altshuler David , Gabriel Stacey , Daly Mark , DePristo Mark A.
Published: July 2010

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
The microRNA pathway and cancer
Authors: Kwak Pieter Bas , Iwasaki Shintaro , Tomari Yukihide
Published: July 2010

MicroRNAs (miRNAs) are ∼22 nt long, non‐coding RNAs that guide post‐transcriptional gene silencing of their target genes and regulate diverse biological processes including cancer. miRNAs do not act alone, but require assembly into RNA‐induced silencing complex (RISC). In this review, we summarize how miRNAs are produced, assembled into RISC, and regulate target mRNAs, and discuss how the miRNA pathway is involved in cancer. (Cancer Sci 2010; 101: 2309–2315)
Systematic review: persistent reflux symptoms on proton pump inhibitor therapy in primary care and community studies
Authors: El‐Serag H. , Becher A. , Jones R.
Published: July 2010

Background  Persistent gastro‐oesophageal reflux disease (GERD) symptoms can occur despite proton pump inhibitor (PPI) therapy.

Aim  To assess the prevalence and potential determinants of persistent GERD symptoms in primary care and community‐based studies.

Methods  Studies were identified by systematic PubMed and Embase searches; pooled prevalence data are shown as sample‐size weighted means and 95% confidence intervals.

Results  Nineteen studies in individuals with GERD taking a PPI were included. In interventional, nonrandomized primary care trials, the prevalence of persistent troublesome heartburn and regurgitation was 17% (6–28%) and 28% (26–30%) respectively; in randomized trials, it was 32% (25–39%) and 28% (26–30%), respectively. In observational primary care and community‐based studies, 45% (30–60%) of participants reported persistent GERD symptoms. Overall, persistent GERD symptoms despite PPI treatment were more likely in studies with a higher proportion of female participants [>60% vs. <50%, risk ratio (RR): 3.66; P < 0.001], but less likely in studies from Europe than in those from the USA (RR: 0.71; P < 0.001), and were associated with decreased psychological and physical well‐being.

Conclusions  Persistent GERD symptoms despite PPI treatment are common in the primary care and community setting. Alternative approaches to management are required.
Tumour lysis syndrome: an unusual presentation
Authors: Chubb E. A. , Maloney D. , Farley‐Hills E.
Published: July 2010

We report a case of spontaneous tumour lysis syndrome that developed postoperatively in a patient with undiagnosed Burkitt’s lymphoma. The former diagnosis was made, unusually, following the development of white emulsion‐like urine in the catheter bag whilst the patient was being managed in the intensive care unit. After laboratory analysis, the urine was found to contain large quantities of uric acid crystals which were the key to the prompt diagnosis. Spontaneous tumour lysis syndrome is rare and this case highlights the difficulties in making an early diagnosis when the presence of a predisposing tumour has not yet been identified. Untreated tumour lysis syndrome can be fatal due to severe biochemical disturbances causing cardiac dysfunction and multi‐organ failure. Early recognition and treatment are crucial to prevent morbidity and mortality. The unusual presentation of this case in association with an undiagnosed Burkitt’s lymphoma emphasises how vigilant anaesthetists and intensivists must be in recognising this potentially life‐threatening condition. We believe that the triggering factor in this case was laparotomy and handling of the tumour.
Shelf life extension of durum semolina‐based fresh pasta
Authors: Costa Cristina , Lucera Annalisa , Mastromatteo Marcella , Conte Amalia , Del Nobile Matteo Alessandro
Published: July 2010

In this work, the combined effects of chitosan, modified atmosphere packaging (MAP) and packaging barrier properties on shelf life of fresh pasta is presented. In particular, all pasta samples were packaged under active and passive MAP in two different polymeric films with high and low barrier properties. In order to assess the influence of the variables described beforehand on the shelf life of pasta, the sensorial and microbiological quality has been monitored during storage. Results confirmed the antimicrobial properties of chitosan. Moreover, the findings recorded in this study suggest that the shelf life of fresh pasta is limited by the sensorial characteristics. Statistically significant differences between the shelf life of pasta packaged in low barrier and high barrier films were found. The best result was obtained for samples packaged in high barrier film, due to the ability of the packaging to maintain the gas headspace conditions during the storage.
Supercritical CO2 and N2O pasteurisation of peach and kiwi juice
Authors: Spilimbergo Sara , Ciola Lara
Published: July 2010

The microbial inactivation and qualitative parameters (pH, sugar content, titratable acidity, absorbance at 420 nm and turbidity) of peach and kiwi juices treated at 35 °C with supercritical carbon dioxide (SC‐CO2) and nitrous oxide (SC‐N2O) were determined as a function of pressure and treatment time. Total inactivation of both naturally occurring microorganisms and Saccharomyces cerevisiae strain (105 cfu mL−1) was obtained after 15 min of SC‐CO2/N2O treatment, 10 MPa and 35 °C, for both juices. No significant changes in chemical‐physical or in sensorial characteristics between untreated and treated juice were detected. The results obtained demonstrate the feasibility and the potential of SC‐CO2/N2O treatment as an alternative low temperature pasteurisation process for peach and kiwi juices.
Determination of biochemical properties of foam‐mat dried mango powder
Authors: Kadam Dattatreya M. , Wilson Robin A. , Kaur Sumandeep
Published: July 2010

Investigations were carried out to see the impact of drying air temperature (65, 75 and 85 °C) and milk as foaming agent in different concentration levels (0%, 10%, 15%, 20% and 25%) on the chemical properties of foam‐mat dried mango juice powder. Chemical properties such as total sugars, ascorbic acid, total carotenes, minerals, total acid, pH, total soluble solids (TSS) and microbial load (fungal and bacterial) of foam‐mat dried mango powder were determined. Data were analysed as per two‐way anova, Duncan’s multiple range test and l.s.d. of AgRes Software statistical package. Almost all chemical properties show decreasing trend with increase in drying air temperature. Microbial load was not detected in foam‐mat dried mango powder. It was found that addition of 10% milk as foaming agent and drying at 65 °C temperature gave better results.
Comparison of the texture of fresh and preserved Agaricus bisporus and Boletus edulis mushrooms
Authors: Jaworska Grażyna , Bernaś Emilia , Biernacka Adriana , Maciejaszek Ireneusz
Published: July 2010

This work compares changes during the production process and storage period in the texture of canned Agaricus bisporus and Boletus edulis mushrooms previously blanched in water, blanched or soaked and blanched in solutions containing citric, l‐ascorbic and lactic acids. The texture was examined using instruments [textural profile analysis (TPA), Kramer shear cell (KSC)] and sensory analysis [five‐point, profiling (P)]. Canning B. edulis mushrooms reduced their hardness, chewiness and gumminess (TPA), the values for force and work (KC), and brittleness and crispiness (P), although increasing their cohesiveness (TPA). Canning A. bisporus mushrooms reduced their hardness (TPA) and the expenditure of work, but increased their cohesiveness, hardness, crispiness and firmness (P). Twelve‐month storage of both species of canned mushrooms led to a reduction in brittleness and crispiness (P). The type of pre‐treatment applied affected the texture only when determined using profile analysis, and significant differences in hardness, crispiness and firmness between blanched‐only and soaked and blanched products were mainly found in B. edulis.
Chemical stability of yellow pigment extracted from the flower bud of Sophora japonica L. (Huaimi)
Authors: Chen Wanping , Li Ping , Wang Xiaohong
Published: July 2010

The dry flower bud of Sophora japonica L., generally called Huaimi in China, has been used as traditional Chinese medicinal materials and folk edible yellow pigment material for a long time. In this paper, the yellow pigment was extracted from Huaimi, and its chemical stability related with pH value, temperature and metallic ions was studied systemically. When pH values changed from 2.0 to 9.0, the yellow pigment revealed structural transformation and colour variations. According to its mathematic model of thermal stability, the yellow pigment had good thermal stability, with a half‐life of 918.9 h at room temperature. Effect of metallic ions on the yellow pigment displayed a co‐pigmentation influence. HPLC analysis indicated that the content of rutin in it was about 42.56%. These results may be helpful for the further application investigations into its commercial prospects in food pigment industry.
Effects of cellulosic fibre on physical and rheological properties of starch, gluten and wheat flour
Authors: Goldstein Avi , Ashrafi Lida , Seetharaman Koushik
Published: July 2010

In this study, we report on the effects of cellulose fibres of different particle size on changes to dough water absorption and rheology; and on effects of fibre on starch and gluten, separately, at different levels of fibre incorporation (0.1–10%). Water absorption and dough‐mixing properties were affected with fibre incorporation, with 40‐μm fibre incorporation resulting in greater absorption values. Dough stickiness and extensibility were affected by cellulose fibre particle size, and decreased with increasing fibre addition. Flour or starch and fibre mixtures were evaluated using a Micro ViscoAmlyoGraph (MVAG), and the resulting gel firmness was measured using a texture analyzer. MVAG peak and final viscosities of flour samples decreased with increasing fibre content. Starch–fibre interactions followed a similar trend as flour–fibre treatments. Gluten–fibre interactions were also measured using a Gluten Peak Tester on flour–fibre and gluten–fibre mixtures. Cellulose fibre enhanced the kinetics of gluten aggregation.
Optimisation of processing variables affecting the osmotic dehydration of pomegranate arils
Authors: Mundada Manoj , Singh Bahadur , Maske Swati
Published: July 2010

For the optimisation of osmotic dehydration by response surface methodology, the experiments were conducted according to Central Composite Rotatable Design (CCRD) with three variables at five levels. The low and high levels of the variables were 40 and 50 °C for osmotic solution temperature, 45 and 55°Bx for sucrose solution concentration, 60 and 100 min for duration of dipping in osmotic solution, respectively. The fruit to solution ratio was kept 1:4 (w/w) during all the experiments. Before dipping the arils in sucrose solution, the freezing of the whole pomegranate at −18 °C was carried out to increase the permeability of the outer cellular layer of the arils. The arils were further convectively dehydrated at 60 °C air temperature up to final moisture content of 10% (wb) to make it a shelf stable product. The optimum conditions for osmotic solution concentration, temperature and process duration were 55°Bx, 40 °C and 100 min, respectively.
Original article: Influence of flour mill streams on cake quality
Authors: Gómez Manuel , Ruiz‐París Elena , Oliete Bonastre
Published: July 2010

Wheat‐milling process generates different flour streams that differ in particle size, composition and functional and cake‐making properties. Particle size, composition and pasting properties of flour fractions (two from break and three from reduction system) obtained during milling of three wheats varying in protein content were determined. Shape, textural, colour and sensory analyses were performed on cakes prepared with the different mill streams. The final break and reduction streams had the highest protein and ash contents, pasting temperatures and the lowest starch percentage. Cakes prepared with the last streams showed higher batter density and lower volume. These results could indicate good air incorporation but deficient air distribution. Last streams cakes showed a darker, more reddish and yellowish crumb that was significantly related to flour colour characteristics. Because of these differences, such cakes obtained the lowest sensory scores. In this study, it has been verified that, to adapt flours to cake preparation, the final streams should be eliminated. The particle size of each stream is the most determinant parameter to obtain cakes with better volume and texture, being the flours with small particle size the most adequate.
Original article: Anthocyanin profile in Monastrell grapes in six different areas from Denomination of Origen Jumilla during ripening stage
Authors: Gil‐Muñoz Rocío , Fernández‐Fernández José I. , Vila‐López Rosario , Martinez‐Cutillas Adrián
Published: July 2010

The aim of our research has been to investigate the pattern of accumulation of anthocyanins in the skin of Monastrell variety and to establish if the fingerprint of this cultivar changed in six different areas from Denomination of Origen Jumilla during ripening stage in two consecutive seasons (2007 and 2008). The results show that the anthocyanin profile for Monastrell variety is maintained: it could be observed a higher proportion of non‐acylated anthocyanins, a higher proportion of coumarylated than acetyl derivatives and a higher proportion of trihydroxylated than dihydroxylated anthocyanins. During ripening period, in all zones studied, we observed the same trends: increasing of cyanidin, peonidin and malvidin‐3‐glucoside and decreasing of the other two monoglucosides (delphinidin and petunidin). Slightly quantitative differences were observed for the different zones in the 2 years studied, leading to the conclusion that edaphoclimatic factors also influence the accumulation of anthocyanin compounds.
Short communication: A new mathematical model for thin layer drying of fruits
Authors: Diamante Lemuel M. , Ihns Reiner , Savage Geoffrey P. , Vanhanen Leo
Published: July 2010

The aim of this study was to fit a new mathematical model on the thin layer drying curves of fruits. Thin layer drying studies at different temperatures (60, 80 and 100 °C) were carried out on two varieties each of kiwifruit and apricot. The new model was compared statistically with three other drying models (Henderson and Pabis, Page and logarithmic) published in the literature. The proposed equation gave the highest coefficient of determination for both varieties of kiwifruit and apricot and closely followed by the Page equation. Statistical evaluation of the experimental and predicted moisture ratio showed that the proposed equation consistently gave the lowest reduced Chi‐square, root mean square error and mean relative percentage error. The results indicate that the proposed equation has the best curve fitting ability for both fruits. However, there is no theoretical basis offered for the good curve fitting ability of the equation.
Host diversity and environmental variables as determinants of the species richness of the parasitoids of leaf‐cutting ants
Authors: Elizalde Luciana , Folgarait Patricia Julia
Published: July 2010

Aim Because of the obligatory relationship between endoparasitoids and their hosts, we presume that hosts exert strong selection pressure on parasitoids. One prediction is a positive relationship between host diversity and parasitoid richness. This relationship could be the product of resource availability which could lead to more opportunities for speciation, or could represent shared responses to the environment by both groups.

Location Argentina and Paraguay.

Methods We sampled a 1800‐km transect to test for a correlation between the richness of leaf‐cutting ant hosts and their phorid parasitoids. Regression models were used to assess if host and environmental variables could explain phorid species richness at nest, hectare and locality spatial scales. We used canonical correspondence analysis (CCA) to explore if there were similar responses of phorid species to particular host and environmental variables at different spatial scales, and partial CCA to separate the relative importance of both groups of variables.

Results Phorid richness was positively correlated with host richness. Host richness/abundance accounted for 20–53% of the variation in parasitoid richness at the hectare and locality scales of analysis, with most of the variation accounted for by ant abundance. We were not able to assess the prediction at the nest scale as only one phorid species was found at most nests. Climatic variables did not explain phorid species richness once host variables were in the models. Partial CCA showed that host‐related variables accounted for most of the variance associated with phorid species ordination at the nest and hectare scales, but not at the largest grain, the locality, where climatic variables were more important. However, most phorid species did not show particular positions along the climatic gradient.

Main conclusions The association between parasitoid richness and host richness and abundance, and the overall weak associations with environmental variables, suggest that these host variables are key factors influencing parasitoid speciation.
Divergence time uncertainty and historical biogeography reconstruction – an example from Urophylleae (Rubiaceae)
Authors: Smedmark Jenny E. E. , Eriksson Torsten , Bremer Birgitta
Published: July 2010

Aim  When hypotheses of historical biogeography are evaluated, age estimates of individual nodes in a phylogeny often have a direct impact on what explanation is concluded to be most likely. Confidence intervals of estimated divergence times obtained in molecular dating analyses are usually very large, but the uncertainty is rarely incorporated in biogeographical analyses. The aim of this study is to use the group Urophylleae, which has a disjunct pantropical distribution, to explore how the uncertainty in estimated divergence times affects conclusions in biogeographical analysis. Two hypotheses are evaluated: (1) long‐distance dispersal from Africa to Asia and the Neotropics, and (2) a continuous distribution in the boreotropics, probably involving migration across the North Atlantic Land Bridge, followed by isolation in equatorial refugia.

Location  Tropical and subtropical Asia, tropical Africa, and central and southern tropical America.

Methods  This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA and nuclear ribosomal DNA data from 56 ingroup species, beast molecular dating and a Bayesian approach to dispersal–vicariance analysis (Bayes‐DIVA) to reconstruct the ancestral area of the group, and the dispersal–extinction–cladogenesis method to test biogeographical hypotheses.

Results  When the two models of geographic range evolution were compared using the maximum likelihood (ML) tree with mean estimates of divergence times, boreotropical migration was indicated to be much more likely than long‐distance dispersal. Analyses of a large sample of dated phylogenies did, however, show that this result was not consistent. The age estimate of one specific node had a major impact on likelihood values and on which model performed best. The results show that boreotropical migration provides a slightly better explanation of the geographical distribution patterns of extant Urophylleae than long‐distance dispersal.

Main conclusions  This study shows that results from biogeographical analyses based on single phylogenetic trees, such as a ML or consensus tree, can be misleading, and that it may be very important to take the uncertainty in age estimates into account. Methods that account for the uncertainty in topology, branch lengths and estimated divergence times are not commonly used in biogeographical inference today but should definitely be preferred in order to avoid unwarranted conclusions.
A framework for delineating biogeographical regions based on species distributions
Authors: Kreft Holger , Jetz Walter
Published: July 2010

Aim Biogeographical regionalizations, such as zoogeographical regions, floristic kingdoms or ecoregions, represent categorizations central to many basic and applied questions in biogeography, ecology, evolution and conservation. Traditionally established by experts based on qualitative evidence, the lack of transparency and quantitative support has set constraints on their utility. The recent availability of global species range maps, novel multivariate techniques and enhanced computational power now enable a quantitative scrutiny and extension of biogeographical regionalizations that will facilitate new and more rigorous uses. In this paper we develop and illustrate a methodological roadmap for species‐level biogeographical regionalizations at the global scale and apply it to mammals.

Location Global.

Methods We explore the relative usefulness of ordination and clustering methods and validation techniques. The performance of nine different clustering algorithms is tested at different taxonomic levels. The grain of regionalization (i.e. the number of clusters) will usually be driven by the purpose of the study, but we present several approaches that provide guidance.

Results Non‐metric multidimensional scaling offers a valuable first step in identifying and illustrating biogeographical transition zones. For the clustering of regions, the nine different hierarchical clustering methods varied greatly in utility, with UPGMA (unweighted pair‐group method using arithmetic averages) agglomerative hierarchical clustering having consistently the best performance. The UPGMA approach allows a tree‐like phenetic representation of the relative distances of regions and can be applied at different levels of taxonomic resolution. We find that the new quantitative biogeographical regions exhibit both striking similarities to and differences from the classic primary geographical divisions of the world’s biota. Specifically, our results provide evidence that the Sahara, northern Africa, the Arabian Peninsula and parts of the Middle East should be regarded as part of the Afrotropics. Further, the position of the New Guinean continental shelf, Lydekker’s Line, is supported as an appropriate border to separate the Oriental and Australian regions.

Main conclusions We propose that this sort of new, quantitative delineation and relationship assessment across taxonomic and geographical grains is likely to offer opportunities for more rigorous inference in historical and ecological biogeography and conservation.
Single‐dose pharmacokinetics of oxytetracycline and penicillin G in tammar wallabies (Macropus eugenii)
Authors: McLELLAND D. J. , BARKER I. K. , CRAWSHAW G. , HINDS L. A. , SPILSBURY L. , JOHNSON R.
Published: July 2010

McLelland, D.J., Barker, I.K., Crawshaw, G., Hinds, L.A., Spilsbury, L., Johnson, R. Single‐dose pharmacokinetics of oxytetracycline and penicillin G in tammar wallabies (Macropus eugenii).J. vet. Pharmacol. Therap.34, 160–167.

The pharmacokinetics of oxytetracycline and penicillin G was investigated in tammar wallabies (Macropus eugenii). Groups of eight healthy tammar wallabies were administered i.v. oxytetracycline hydrochloride (40 mg/kg), i.m. long‐acting‐oxytetracycline (20 mg/kg), i.v. sodium penicillin G (30 mg/kg), or i.m. procaine/benzathine penicillin G (30 mg/kg). Plasma concentrations of oxytetracycline were determined using high‐performance liquid chromatography. Pharmacokinetic parameters were comparable to those reported for eutherians of equivalent size and suggest that the practice of adjusting allometrically scaled doses to account for the lower metabolic rate of marsupials may not be valid. Long‐acting oxytetracycline and penicillin G both demonstrated depot effects. However, the plasma concentrations achieved question the therapeutic efficacy of the long‐acting preparations.
Oxygen levels rapidly modulate Pseudomonas aeruginosa social behaviours via substrate limitation of PqsH
Authors: Schertzer Jeffrey W. , Brown Stacie A. , Whiteley Marvin
Published: July 2010

Many bacteria use extracellular signals to coordinate group behaviours, a process referred to as quorum sensing (QS). The bacterium Pseudomonas aeruginosa utilizes a complex QS system to control expression of over 300 genes, including many involved in host colonization and disease. The Pseudomonas quinolone signal (PQS) is a component of P. aeruginosa QS, and although it contributes to virulence in some models of infection, the PQS biosynthetic pathway is not fully elucidated. Here, we show that PqsH catalyses the terminal step in PQS production, synthesizing PQS in vitro using the substrates 2‐heptyl‐4‐quinolone (HHQ), NADH and oxygen. Structure function studies reveal that the alkyl side‐chain of HHQ is critical for PqsH activity with the highest activity observed for alkyl chain lengths of 7 and 9 carbons. Due to the PqsH requirement for oxygen, PQS and PQS‐controlled virulence factors are not produced by anaerobic P. aeruginosa. Interestingly, anaerobic P. aeruginosa produced PQS in the absence of de novo protein synthesis upon introduction of oxygen, indicating that oxygen is the sole limiting substrate during anaerobic growth. We propose a model in which PqsH poises anaerobic P. aeruginosa to activate PQS‐controlled factors immediately upon exposure to molecular oxygen.
Innervation of the Pelvic Limb of the Adult Ostrich (Struthio camelus)
Authors: El‐Mahdy T. , El‐Nahla S. M. , Abbott L. C. , Hassan S. A. M.
Published: July 2010

With 24 figures

The pelvic limb of the ostrich is innervated by the lumbar and sacral plexuses. The lumbar plexus gave rise to several nerves (N.s) including, N. coxalis cranialis, lateral and cranial femoral cutaneous N.s, N. femoralis, cranial, caudal and medial crural cutaneous N.s, and N. obturatorius. The remaining nerves emanated from the sacral plexus. The N. iliotibial, N. ischiofemoralis, N. iliofibularis, and N. coxae caudalis were distributed in the thigh, while the N. ischiadica, which terminated as the tibial and fibular N.s that innervated the leg and foot. The tibial N. gave rise to the parafibular N. then divided to form the Nn. suralis medialis and lateralis. The N. suralis medialis continued as the N. metatarsalis plantaris medialis. The parafibular N. continued as the N. plantaris lateralis, which terminated as the R. digitalis of the fourth digit. The fibular N. terminated as the superficial and deep fibular N.s. The superficial fibular N. continued as the N. metatarsalis dorsalis lateralis and divided into two digital N.s to the third and fourth digits. The deep fibular N. crossed the ankle joint and continued as the N. metatarsalis dorsalis medialis that continued as the R. digitalis of the third digit. In general, the innervation of the pelvic limb of the ostrich was similar to the pelvic limbs of several different species of domesticated birds, including the chicken. We discuss the few differences as well as appropriate sites to perform nerve blocks for the lateral and medial dorsal and the lateral plantar N.s.
Study of Epidermis Development in Sturgeon (Acipenser persicus) Larvae
Authors: Saadatfar Z. , Shahsavani D. , Fatemi F. S.
Published: July 2010

With 10 figures

Fish skin is essential for survival, maintenance of body shape, and protection against the shock and infection. During week 1 of sturgeon larval development, the epidermis is thin and not differentiated in various layers yet, but by week 4–6 the thickness increases and various layers appear, depending upon the region of the body. Mucous cells differentiate early in development on the surface of epithelium and contain acid and neutral mucopolysaccharides. Primordial sensory buds are visible within the epithelia of the skin of the head in week 1 larvae, and become numerous during later larval development. Club cells are specialized epidermal cells that have an immune function and appear in the middle layer of the head and trunk epidermis on week 4.
Frequency of photoperiod‐insensitive Ppd‐A1a alleles in tetraploid, hexaploid and synthetic hexaploid wheat germplasm
Authors: Bentley A. R. , Turner A. S. , Gosman N. , Leigh F. J. , Maccaferri M. , Dreisigacker S. , Greenland A. , Laurie D. A.
Published: July 2010

With 2 tables

Differences in photoperiod sensitivity are widely used in wheat breeding to provide adaptation to diverse agronomic environments. Two photoperiod insensitive (PI) mutations in the A genome (Ppd‐A1a alleles) were previously identified using near‐isogenic lines of tetraploid durum wheat. We show that these Ppd‐A1a alleles predominate in modern durum wheat but are absent from wild tetraploid wheat and from conventional hexaploid wheat, suggesting they were selected for improved adaptation during durum cultivation. To increase genetic diversity in hexaploid wheat, synthetic hexaploid wheat lines were developed at CIMMYT by hybridizing elite durum lines with Aegilops tauschii accessions. Ppd‐A1a alleles from durum wheat were found in 71.4% of 447 synthetic hexaploids and 9.6% of 115 advanced selections. Backcrosses to hexaploid wheat showed that the durum Ppd‐A1a alleles conferred a PI phenotype and that one allele was intermediate between known B and D genome mutations, providing a new source of flowering time variation in hexaploid wheat and the potential for novel combinations of PI alleles.
Have advanced research technologies made real impact on respiratory medicine?
Authors: ASK Kjetil , EICKELBERG Oliver , GAULDIE Jack , KAMINSKI Naftali , KOLB Martin
Published: July 2010

Tremendous sophistication in our ability to detect, measure and manipulate the genes and proteins involved in lung disease has provided unique insights to the pathobiology of a number of lung disorders affecting humans today. Gene array analysis and genetic manipulation of animals have helped to identify novel pathways and their potential role in disease initiation and progression. Proteomics is a relatively novel tool in molecular research in respiratory medicine. Silencing gene expression by using small interfering RNA may, sooner than later, become part of novel therapies. Despite the excitement, to date, there has been little direct impact on therapeutic interventions available to clinicians. However, the rapidity with which these early data have accumulated, and the expected advances in bioinformatics and systems biology, should bring forward tangible therapeutic benefits for many acute and chronic lung diseases within the next ten years.
Pleural space elastance and changes in oxygenation after therapeutic thoracentesis in ventilated patients with heart failure and transudative pleural effusions
Authors: CHEN Wei‐Lin , CHUNG Chi‐Li , HSIAO Shih‐Hsin , CHANG Shi‐Chuan
Published: July 2010

Background and objective:  Therapeutic thoracentesis (TT) is required in patients with refractory pleural effusions and impaired oxygenation. In this study, the relationship between pleural space elastance (PE) and changes in oxygenation after TT was investigated in ventilated patients with heart failure and transudative pleural effusions.

Methods:  Twenty‐six mechanically ventilated patients with heart failure and significant transudative effusions, who were undergoing TT, were studied. The effusion was drained as completely as possible, with monitoring of pleural liquid pressure (Pliq) and chest symptoms. The volume of effusion removed, the changes in Pliq during TT, PE and arterial blood gases before and after TT were recorded.

Results:  The mean volume of effusion removed was 1011.9 ± 58.2 mL. The mean Pliq decreased from 14.5 ± 1.0 to 0.1 ± 1.5 cm H2O after TT, and the mean PE was 15.3 ± 1.8 cm H2O/L. TT significantly increased the mean ratio of PaO2/fraction of inspired oxygen (FiO2) from 243.2 ± 19.9 to 336.0 ± 17.8 mm Hg (P < 0.0001). The changes in PaO2/FiO2 ratio after TT were inversely correlated with PE (r = −0.803, P < 0.0001). The 14 patients (54%) with normal PE (≤14.5 cm H2O/L) had significantly greater increases in PaO2/FiO2 ratio after TT than did the 12 patients with abnormal PE (>14.5 cm H2O/L).

Conclusions:  Measurement of PE during TT may be valuable for predicting improvement in oxygenation in ventilated patients with heart failure and pleural effusions. Patients with lower PE showed greater improvement in oxygenation after TT.