bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus)
Authors: Noble Daniel WA , Qi Yin , Fu Jinzhong 
Published: June 2010

Abstract

Background
Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results.

Results
Assignment tests revealed two distinct nuclear DNA clusters with 95% (230/243) of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia.

Conclusions
These results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools for distinguishing closely related species and support the validity of P. putjatia. Assignment tests have the potential to play a significant role in elucidating biodiversity in the era of DNA data. Nonetheless, important limitations do exist and multiple independent datasets should be used to corroborate results from assignment programs.
Large scale interaction analysis predicts that the Gerbera hybrida floral E function is provided both by general and specialized proteins
Authors: Ruokolainen Satu , Ng Yan Peng , Albert Victor A , Elomaa Paula , Teeri Teemu H 
Published: June 2010

Abstract

Background
The ornamental plant Gerbera hybrida bears complex inflorescences with morphologically distinct floral morphs that are specific to the sunflower family Asteraceae. We have previously characterized several MADS box genes that regulate floral development in Gerbera. To study further their behavior in higher order complex formation according to the quartet model, we performed yeast two- and three-hybrid analysis with fourteen Gerbera MADS domain proteins to analyze their protein-protein interaction potential.

Results
The exhaustive pairwise interaction analysis showed significant differences in the interaction capacity of different Gerbera MADS domain proteins compared to other model plants. Of particular interest in these assays was the behavior of SEP-like proteins, known as GRCDs in Gerbera. The previously described GRCD1 and GRCD2 proteins, which are specific regulators involved in stamen and carpel development, respectively, showed very limited pairwise interactions, whereas the related GRCD4 and GRCD5 factors displayed hub-like positions in the interaction map. We propose GRCD4 and GRCD5 to provide a redundant and general E function in Gerbera, comparable to the SEP proteins in Arabidopsis. Based on the pairwise interaction data, combinations of MADS domain proteins were further subjected to yeast three-hybrid assays. Gerbera B function proteins showed active behavior in ternary complexes. All Gerbera SEP-like proteins with the exception of GRCD1 were excellent partners for B function proteins, further implicating the unique role of GRCD1 as a whorl- and flower-type specific C function partner.

Conclusions
Gerbera MADS domain proteins exhibit both conserved and derived behavior in higher order protein complex formation. This protein-protein interaction data can be used to classify and compare Gerbera MADS domain proteins to those of Arabidopsis and Petunia. Combined with our reverse genetic studies of Gerbera, these results reinforce the roles of different genes in the floral development of Gerbera. Building up the elaborate capitulum of Gerbera calls for modifications and added complexity in MADS domain protein behavior compared to the more simple flowers of, e.g., Arabidopsis.
Molecular understanding of sterically controlled compound release through an engineered channel protein (FhuA)
Authors: Güven Arcan , Fioroni Marco , Hauer Bernhard , Schwaneberg Ulrich 
Published: June 2010

Abstract

Background
Recently we reported a nanocontainer based reduction triggered release system through an engineered transmembrane channel (FhuA Δ1-160; Onaca et al., 2008). Compound fluxes within the FhuA Δ1-160 channel protein are controlled sterically through labeled lysine residues (label: 3-(2-pyridyldithio)propionic-acid-N-hydroxysuccinimide-ester). Quantifying the sterical contribution of each labeled lysine would open up an opportunity for designing compound specific drug release systems.

Results
In total, 12 FhuA Δ1-160 variants were generated to gain insights on sterically controlled compound fluxes: Subset A) six FhuA Δ1-160 variants in which one of the six lysines in the interior of FhuA Δ1-160 was substituted to alanine and Subset B) six FhuA Δ1-160 variants in which only one lysine inside the barrel was not changed to alanine. Translocation efficiencies were quantified with the colorimetric TMB (3,3',5,5'-tetramethylbenzidine) detection system employing horseradish peroxidase (HRP). Investigation of the six subset A variants identified position K556A as sterically important. The K556A substitution increases TMB diffusion from 15 to 97 [nM]/s and reaches nearly the TMB diffusion value of the unlabeled FhuA Δ1-160 (102 [nM]/s). The prominent role of position K556 is confirmed by the corresponding subset B variant which contains only the K556 lysine in the interior of the barrel. Pyridyl labeling of K556 reduces TMB translocation to 16 [nM]/s reaching nearly background levels in liposomes (13 [nM]/s). A first B-factor analysis based on MD simulations confirmed that position K556 is the least fluctuating lysine among the six in the channel interior of FhuA Δ1-160 and therefore well suited for controlling compound fluxes through steric hindrance.

Conclusions
A FhuA Δ1-160 based reduction triggered release system has been shown to control the compound flux by the presence of only one inner channel sterical hindrance based on 3-(2-pyridyldithio)propionic-acid labeling (amino acid position K556). As a consequence, the release kinetic can be modulated by introducing an opportune number of hindrances. The FhuA Δ1-160 channel embedded in liposomes can be advanced to a universal and compound independent release system which allows a size selective compound release through rationally re-engineered channels.
Association of ABO blood groups with Chikungunya virus
Authors: Kumar Naresh CVM , Nadimpalli Mahathi , Vardhan Vishnu R , Gopal Sai DVR 
Published: June 2010

Abstract
Chikungunya virus (CHIKV) an emerging arboviral infection of public health concern belongs to the genus Alphavirus, family Togaviridae. Blood group antigens are generally known to act as receptors for various etiological agents. The studies defining the relationship between blood groups and CHIKV is limited and hence it is necessary to study these parameters in detail. In the present study 1500 subjects were enrolled and demographic data (Age, Gender, Blood group, CHIKV infection status, and CHIKV infection confirmation mode) was collected from them. The risk of acquiring CHIKV disease and its association with factors such as blood group, age and gender was analyzed statistically. The data of this study showed a possible association between blood group, age and gender of the study population with CHIKV infection. It is observed that CHIKV infections were higher in individuals with Rh positive blood group when compared to their Rh negative counterparts.CHIKV infections were found to be higher in Rh positive individuals of AB and A blood groups than that of Rh negative counterparts. Results also indicated that infections were higher in adults belonging to the age group > 30 years and also higher in males as compared to females enrolled in this study. These data present further evidence for the association of the blood groups, age and gender to susceptibility to CHIKV infection. Further studies are needed to confirm these findings. This is the second study showing the possible association of blood groups with chikungunya.
Mycoplasmoses of ruminants in France: recent data from the national surveillance network
Authors: Chazel Myriam , Tardy Florence , Le Grand Dominique , Calavas Didier , Poumarat François 
Published: June 2010

Abstract

Background
Ruminant mycoplasmoses are important diseases worldwide and several are listed by the World Organization for Animal Health to be of major economic significance. In France the distribution of mycoplasmal species isolated from clinical samples collected from diseased animals upon veterinary request, is monitored by a network known as VIGIMYC (for VIGIlance to MYCoplasmoses of ruminants). The veterinary diagnostic laboratories collaborating with VIGIMYC are responsible for isolating the mycoplasmas while identification of the isolates is centralized by the French Food Safety Agency (AFSSA) in Lyon. The VIGIMYC framework can also be used for specific surveys and one example, on the prevalence of M. bovis in bovine respiratory diseases, is presented here.

Results
Between 2003 and 2008, 34 laboratories were involved in the network and 1904 mycoplasma isolates, originating from the main ruminant-breeding areas, were identified. For cattle, the high prevalence of M. bovis in bronchopneumonia, notably in young animals, was confirmed by VIGIMYC and an associated specific survey, whereas the non-emergence of species such as M. alkalescens and M. canis was also demonstrated. The etiological agent of bovine contagious pleuropneumonia was never isolated. The principal mycoplasmosis in goats was contagious agalactia with M. mycoides subsp. capri as main agent. Ovine mycoplasmoses, most of which were associated with pneumonia in lambs, were infrequently reported. One exception was ovine contagious agalactia (due to M. agalactiae) that has recently re-emerged in the Pyrénées where it had been endemic for years and was also reported in Corsica, which was previously considered free.

Conclusions
Although VIGIMYC is a passive network and somewhat biased as regards sample collection and processing, it has provided, in this study, an overview of the main mycoplasmoses of ruminants in France. The French epidemiological situation is compared to those existing elsewhere in the world.
Apremilast, a novel PDE4 inhibitor, inhibits spontaneous production of tumour necrosis factor-alpha from human rheumatoid synovial cells and ameliorates experimental arthritis
Authors: McCann Fiona E , Palfreeman Andrew C , Andrews Melanie , Perocheau Dany P , Inglis Julia J , Schafer Peter , Feldmann Marc , Williams Richard O , Brennan Fionula M 
Published: June 2010

AbstractIntroductionType 4 phosphodiesterases (PDE4) play an important role in immune cells through the hydrolysis of the second messenger, cAMP. Inhibition of PDE4 has previously been shown to suppress immune and inflammatory responses, demonstrating PDE4 to be a valid therapeutic target for immune-mediated pathologies. We assessed the anti-inflammatory effects of a novel PDE4 inhibitor, apremilast, in human synovial cells from rheumatoid arthritis (RA) patients, as well as two murine models of arthritis.MethodsCells liberated from tissue excised from arthritic joints of RA patients were cultured in the presence of increasing concentrations of apremilast for 48 hours and spontaneous tumour necrosis factor-alpha (TNFα) production was analysed in culture supernatants by ELISA. In addition, arthritis was induced in BALB/c and DBA/1 mice by passive transfer of anti-type II collagen mAb and immunisation with type II collagen, respectively. Mice with established arthritis received 5 or 25 mg/kg apremilast and disease severity was monitored relative to mice receiving vehicle alone. At the end of the study, paws were removed and processed for histopathological assessment. Behavioural effects of apremilast, relative to rolipram, were assessed in naïve DBA/1 mice using an automated activity monitor (LABORAS).ResultsApremilast dose dependently inhibited spontaneous release of TNFα from human rheumatoid synovial membrane cultures. Furthermore, apremilast significantly reduced clinical score in both murine models of arthritis over a ten day treatment period and maintained a healthy joint architecture in a dose-dependent manner. Importantly, unlike rolipram, apremilast demonstrated no adverse behavioural effects in naïve mice.ConclusionsApremilast is an orally available PDE4 inhibitor that reduces TNFα production from human synovial cells and significantly suppresses experimental arthritis. Apremilast appears to be a potential new agent for the treatment of rheumatoid arthritis.
New insights into the pathogenesis of glucocorticoid-induced avascular necrosis: microarray analysis of gene expression in a rat model
Authors: Kerachian Mohammad Amin , Cournoyer Denis , Harvey Edward J , Chow Terry Y , Bégin Louis R , Nahal Ayoub , Séguin Chantal 
Published: June 2010

Abstract
Introduction
Avascular necrosis of the femoral head (ANFH) occurs variably after exposure to corticosteroids. Microvascular thrombosis is a common pathological finding. Since systemic thrombophilia is only weakly linked with ANFH, we propose that microvascular vessel pathology may be more related to local endothelial dysfunction and femoral head apoptosis. Corticosteroid effects on the endothelium and resultant apoptosis have been reported. We hypothesize that corticosteroids contribute to a differential gene expression in the femoral head in rats with early ANFH.

Methods
Besides bone marrow necrosis, which is a common sign in ANFH and reported in the early stages, we include the presence of apoptosis in this study as a criterion for diagnosing early disease. Forty Wistar Kyoto (WKY) rats were randomized to either a corticosteroid-treated group or an age-matched control group for six months. After sacrifice, the femoral heads were examined for ANFH. Total mRNA was extracted from femoral heads. Affymetrix exon array (Santa Clara, CA, USA) was performed on 15 selected RNA samples. Validation methods included RT-PCR and immunohistochemistry (IHC).

Results
Although rat exon array demonstrated a significant upregulation of 51 genes (corticosteroid(+)/ANFH(+) VS control), alpha-2-macroglobulin (A2M) gene was particularly over-expressed. Results were validated by RT-PCR and IHC. Importantly, A2M is known to share vascular, osteogenic and cartilage functions relevant for ANFH.

Conclusions
The findings suggest that corticosteroid-induced ANFH in rats might be mediated by A2M. Investigation of A2M as a potential marker, and a treatment target, for early ANFH should be carried out.
Innate immune processes are sufficient for driving silicosis in mice
Authors: Beamer Celine A , Migliaccio Christopher T , Jessop Forrest , Trapkus Melanie , Yuan Dorothy , Holian Andrij 
Published: June 2010

Abstract
Although silica-induced fibrosis and inflammation occurs independently of T, B, NK T, and NK cells, lymphocytes regulate inflammation via modulation of the Nlrp3 inflammasome.
The lung is constantly exposed to potentially pathogenic particles and microorganisms. It has become evident recently that not only innate but also adaptive immune responses to particulates, such as SiO2 entering the respiratory tract, are complex and dynamic events. Although the cellular mechanisms and anatomical consequences involved in the development of silicosis have been studied extensively, they still remain poorly understood. Based on their capacity for immune regulation, lymphocytes may play a key role in the respiratory response to environmental challenge by SiO2. The objective of this study was to characterize the impact of SiO2 exposure on respiratory immune processes, with particular emphasis on evaluating the importance of lymphocytes in the murine silicosis model. Therefore, lymphopenic mice, including NK-deficient, Rag1−/−, or a combination (Rag1−/− NK-depleted), were used and demonstrated that SiO2-induced fibrosis and inflammation can occur independently of T, B, NK T, and NK cells. Studies in Rag1−/− mice suggest further that lymphocytes may participate in the regulation of SiO2-induced inflammation through modulation of the Nalp3 inflammasome. This observation may have clinical relevance in the treatment of inflammatory and fibrotic lung diseases that are refractory or respond suboptimally to current therapeutics.
Buccal pumping mechanics ofXenopus laevistadpoles: effects of biotic and abiotic factors
Authors: Ryerson William G. , Deban Stephen M. 
Published: June 2010

SUMMARYBiotic factors such as body size and shape have long been known to influence kinematics in vertebrates. Movement in aquatic organisms can also be strongly affected by abiotic factors such as the viscosity of the medium. We examined the effects of both biotic factors and abiotic factors on buccal pumping kinematics in Xenopus tadpoles using high-speed imaging of an ontogenetic series of tadpoles combined with experimental manipulation of the medium over a 10-fold range of viscosity. We found influences of both biotic and abiotic factors on tadpole movements; absolute velocities and excursions of the jaws and hyoid were greater in higher viscosity fluid but durations of movements were unaffected. Smaller tadpoles have relatively wider heads and more robust hyoid muscles used in buccal expansion and compression. Lever arm ratios were found to be constant at all sizes; therefore, smaller tadpoles have relatively higher resolved muscle forces and, like tadpoles in more viscous medium, displayed higher absolute velocities of jaw and hyoid movements. Nonetheless, small tadpoles drew in water at lower Reynolds numbers (Re) than predicted by kinematics, due to negative allometry of the buccal pump. Finally, tadpoles transitioned from a flow regime dominated by viscous forces (Re=2) to an intermediate regime (Re=106).
Adrenergic control of swimbladder deflation in the zebrafish (Danio rerio)
Authors: Dumbarton Tristan C. , Stoyek Matthew , Croll Roger P. , Smith Frank M. 
Published: June 2010

SUMMARYMany teleosts actively regulate buoyancy by adjusting gas volume in the swimbladder. In physostomous fishes such as the zebrafish, a connection is maintained between the swimbladder and the oesophagus via the pneumatic duct for the inflation and deflation of this organ. Here we investigated the role of adrenergic stimulation of swimbladder wall musculature in deflation of the swimbladder. Noradrenaline (NA), the sympathetic neurotransmitter (dosage 10−6 to 10−5 mol l−1), doubled the force of smooth muscle contraction in isolated tissue rings from the anterior chamber, caused a doubling of pressure in this chamber in situ, and evoked gas expulsion through the pneumatic duct, deflating the swimbladder to approximately 85% of the pre-NA volume. These effects were mediated by β-adrenergic receptors, representing a novel role for these receptors in vertebrates. No effects of adrenergic stimulation were detected in the posterior chamber. In a detailed examination of the musculature and innervation of the swimbladder to determine the anatomical substrate for these functional results, we found that the anterior chamber contained an extensive ventral band of smooth muscle with fibres organized into putative motor units, richly innervated by tyrosine hydroxylase-positive axons. Additionally, a novel arrangement of folds in the lumenal connective tissue in the wall of the anterior chamber was described that may permit small changes in muscle length to cause large changes in effective wall distensibility and hence chamber volume. Taken together, these data strongly suggest that deflation of the zebrafish swimbladder occurs primarily by β-adrenergically mediated contraction of smooth muscle in the anterior chamber and is under the control of the sympathetic limb of the autonomic nervous system.
Effects of nutritional condition on spring migration: do migrants use resource availability to keep pace with a changing world?
Authors: Bridge Eli S. , Kelly Jeffrey F. , Bjornen Paul E. , Curry Claire M. , Crawford Priscilla H. C. , Paritte Jacqueline M. 
Published: June 2010

SUMMARY
Because of their reliance on temporally predictable resources across large spatial scales, migratory birds may be especially vulnerable to anthropogenic climate and land-use changes. Although some long-distance migrants appear unable to adjust to phenological shifts on their wintering grounds, several short- and medium-distance migrants appear to have altered the timing and/or distance of their yearly movements to compensate for the environmental effects of global warming. Which environmental cues are responsible for stimulating these adjustments is an unanswered question, although most studies have focused on weather conditions. Here, we present a novel field experiment that demonstrates that an alternative cue, food availability, may be a crucial link between local conditions on the wintering grounds and the timing of spring departure. When we provided dark-eyed juncos (Junco hyemalis) with an abundant food supply in early spring, we observed an advance in migration, especially among individuals that increased their mass and fat stores in response to the treatment. This finding indicates a simple mechanism by which short-distance migrants may calibrate their migration behavior such that arrival on the breeding grounds and initiation of reproduction are in sync with resource availability.