bluuebunny/crossref_metadata_2025 huggingface dataset:
Vitamin D Status in Jordan: Dress Style and Gender Discrepancies
Authors: Batieha A. , Khader Y. , Jaddou H. , Hyassat D. , Batieha Z. , Khateeb M. , Belbisi A. , Ajlouni K.
Published: January 2011

Background/Aims: Vitamin D deficiency is highly prevalent worldwide and has been linked to many diseases. The aims of the present study were to assess the vitamin D status of Jordanians at the national level and to identify groups of the population at high risk for vitamin D deficiency. Methods: Vitamin D status was assessed in a national sample of 5,640 subjects aged ≧7 years. The study involved interviews, laboratory measurements of 25(OH)D and others, and physical measurements. The present report deals, exclusively, with subjects aged >18 years. Results: The prevalence of low vitamin D status [25(OH)D <30 ng/ml] was 37.3% in females compared to 5.1% in males. Dress style in females was independently related to low vitamin D status; women wearing ‘Hijab’ (adjusted OR = 1.7, p = 0.004) or ‘Niqab’ (adjusted OR = 1.5, p = 0.061) were at a higher risk for low vitamin D status than were western-dressed women. Conclusion: The high prevalence of low vitamin D status in females in contrast with a low prevalence in males, together with a higher prevalence in women wearing Hijab or Neqab, calls for action to increase the population’s awareness and to develop strategies to reduce this risk among women, particularly those wearing dress styles that cover most or all of their skin.
Stroke and Myocardial Infarction: A Comparative Systematic Evaluation of Gender-Specific Analysis, Funding and Authorship Patterns in Cardiovascular Research
Authors: Oertelt-Prigione Sabine , Wiedmann Silke , Endres Matthias , Nolte Christian H. , Regitz-Zagrosek Vera , Heuschmann Peter
Published: January 2011

Background: Major gender differences exist in cardiovascular diseases and lead to different outcomes in women and men. However, attention and incorporation of sex-/gender-specific research might vary among disciplines. We therefore conducted a systematic review comparing publication characteristics and trends between stroke and myocardial infarction (MI) with respect to sex- and gender-related aspects. Methods: A systematic literature search was performed in PubMed to identify gender-/sex-related articles published for stroke and MI between 1977 and 2008. A specifically designed text mining program was used, and all literature was rated by two independent investigators. Publications were classified according to type of research performed, publication year, funding, geographical location, and gender of first and last authors. Results: 962 articles were retrieved and limited to 405 (42%) gender-relevant publications; 131 on stroke and 274 on MI. Type of performed research differed, especially in disease management, which received little attention (17%) in stroke, while representing the major focus in MI (40%). In both areas, clinical presentation received little attention (3 and 5%). Although publications progressively increased in both fields, an 8- to 10-year time gap emerged for stroke compared to MI. Last authors in both areas were predominantly men, but female last authorship is increasing more significantly over time in the field of stroke. Research on sex and gender differences in MI and stroke is largely underfunded, particularly by the EU. Conclusions: The data demonstrate how sex-/gender-specific research differs between specialties, most likely due to the diverse interest, funding opportunities and authorship distributions identified.
Rescue by PF Deletion, Traces as (Non)interveners, and the That-Trace Effect
Authors: Bošković Željko
Published: January 2011

The article demonstrates that the rescue-by-PF-deletion account of the amelioration effect of island violations under ellipsis, originally noted by Ross (1969), can be extended to account for the that-trace effect, including the adverb amelioration effect, and the lack of intervention effects with certain null arguments that are otherwise found with their overt counterparts, as well as to deduce the generalizations that traces do not count as interveners for relativized minimality effects and that traces void islandhood. The fact that the rescue-by-PF-deletion analysis makes it possible to unify a number of previously unrelated phenomena should be taken as a strong argument in its favor. The current extension of the rescue-by-PF-deletion approach, on which the rescue can arise not only through the deletion process involved in ellipsis but also through regular copy deletion, also accounts for the different behavior of the Superiority Condition and the Wh-Island Condition with respect to the amelioration effect under ellipsis, a surprising difference given that both of these are generally subsumed under relativized minimality effects in current research.
Morphosemantic Mismatches, Structural Economy, and Licensing
Authors: Katzir Roni
Published: January 2011

Agreement and concord involve mismatches between the position where a syntactic or semantic contribution is made and where it is expressed morphologically. Such mismatches are often taken to involve either movement or the spreading and realization of features. I examine a number of superficially different instances of this kind of mismatch that seem to resist an account based on realization and movement alone. I argue that the patterns involved should receive a unified account in terms of licensors, elements subject to a condition of structural economy that associate indirectly with semantically contentful heads through features that those heads spread and that require a c-commanding licensor.
Acts and the Fragmentary Hellenistic Jewish Authors
Authors: Holladay Carl R.
Published: January 2011

This article reviews scholarship on the fragmentary Hellenistic Jewish authors as it relates to The Acts of the Apostles. Reviewed here are Jewish texts written in Greek during the Hellenistic-Roman period that were preserved only in the form of quotations or excerpts mostly by later Christian writers, most notably Eusebius of Caesarea in his Praeparatio Evangelica. The focus of the review is to see how these texts have been investigated, especially in Second Temple Judaism and in studies of Jewish historiography during the Graeco-Roman period, and how this scholarship informs the study of Acts.
Moral Disengagement and Support for Nonhuman Animal Farming
Authors: Mitchell Les
Published: January 2011

Nonhuman animal farming, by its fundamental nature, involves a greater or lesser degree of ill treatment and oppression. Definitions of abuse or cruelty in relation to nonhumans, however, are inconsistent and ambiguous. People support nonhuman farming by purchasing its products, but the majority of people do not themselves mistreat nonhumans. How can this incongruity be explained? Any account is likely to be complex, but work in experimental psychology has identified a number of conditions that can contribute toward individuals becoming morally disengaged from abusive acts. This paper shows that a number of these conditions are embedded in the nonhuman animal farming industry, thus providing some insight into why consumers may be disconnected from the mass abuse carried out by an industry they support. Recognizing this process can help advocates for nonhumans take steps to counter this disengagement and so allow consumers to examine their ethical choices more clearly.
Philosophical Ethology: On the Extents of What It Is to Be a Pig
Authors: Harfeld Jes
Published: January 2011

Answers to the question, “What is a farm animal?” often revolve around genetics, physical attributes, and the animals’ functions in agricultural production. The essential and defining characteristics of farm animals transcend these limited models, however, and require an answer that avoids reductionism and encompasses a de-atomizing point of view. Such an answer should promote recognition of animals as beings with extensive mental and social capabilities that outline the extent of each individual animal’s existence and—at the same time—define the animals as parts of wholes that in themselves are more than the sum of their parts and have ethological as well as ethical relevance. To accomplish this, the concepts of both anthropomorphism and sociobiology will be examined, and the article will show how the possibility of understanding animals and their characteristics deeply affects both ethology and philosophy; that is, it has an important influence on our descriptive knowledge of animals, the concept of what animal welfare is and can be, and any normative ethics that follow such knowledge.
Godliness, Self-Sufficiency, Greed, and the Enjoyment of Wealth 1 Timothy 6:3-19 Part II
Authors: Malherbe Abraham J.
Published: January 2011

In 1 Tim 5, the author turns to the church’s financial support of some of its members, and in chap. 6 discusses individual attitudes toward money and its use. The article concentrates on chap. 6, especially vv. 17-19, and argues that, while philosophical sources are of prime importance in describing the moral teaching inculcated, popular morality, represented by clichés, proverbs, gnomai, drama, satire and inscriptions, makes possible a thicker description of the moral ecology of the Pastoral Epistles. What emerges is a variety of sometimes similar teaching relating to wealth. The diversity of viewpoint on the same topics relating to wealth suggests that it is more realistic to see 1 Tim 6:17-19 as one among other viewpoints rather than as derived from one or another of them. What is striking is the prominence given to enjoyment in the proper use of wealth.
North Atlantic Tropical Storm Frequency Response to Anthropogenic Forcing: Projections and Sources of Uncertainty
Authors: Villarini Gabriele , Vecchi Gabriel A. , Knutson Thomas R. , Zhao Ming , Smith James A.
Published: January 2011

The impact of future anthropogenic forcing on the frequency of tropical storms in the North Atlantic basin has been the subject of intensive investigation. However, whether the number of North Atlantic tropical storms will increase or decrease in a warmer climate is still heavily debated and a consensus has yet to be reached. To shed light on this issue, the authors use a recently developed statistical model, in which the frequency of North Atlantic tropical storms is modeled by a conditional Poisson distribution with rate of occurrence parameter that is a function of tropical Atlantic and mean tropical sea surface temperatures (SSTs). It is shown how the disagreement among dynamical modeling projections of late-twenty-first-century tropical storm frequency can be largely explained by differences in large-scale SST patterns from the different climate model projections used in these studies. The results do not support the notion of large (~200%) increases in tropical storm frequency in the North Atlantic basin over the twenty-first century in response to increasing greenhouse gases (GHGs). Because the statistical model is computationally inexpensive, it is used to examine the impact of different climate models and climate change scenarios on the frequency of North Atlantic tropical storms. The authors estimate that the dominant drivers of uncertainty in projections of tropical storm frequency over the twenty-first century are internal climate variations and systematic intermodel differences in the response of SST patterns to increasing GHGs. Relative to them, uncertainties in total GHG emissions or other climate forcings, within the scenarios explored here, represent a minor source of uncertainty in tropical storm frequency projections. These results suggest that reducing uncertainty in future projections of North Atlantic tropical storm frequency may depend as critically on reducing the uncertainty in the sensitivity of tropical Atlantic warming relative to the tropical mean, in response to GHG increase, as on improving dynamical or statistical downscaling techniques. Moreover, the large uncertainties on century-scale trends that are due to internal climate variability are likely to remain irreducible for the foreseeable future.

As a further illustration of the statistical model’s utility, the authors model projected changes in U.S. landfalling tropical storm activity under a variety of different climate change scenarios and climate models. These results are similar to those for the overall number of North Atlantic tropical storms, and do not point to a large increase in U.S. landfalling tropical storms over the twenty-first century in response to increasing GHGs.
Influence or Convenience? Disentangling Peer Influence and Co-offending for Chronic offenders
Authors: McGloin Jean Marie , Povitsky Stickle Wendy
Published: January 2011

Both developmental and propensity theories root the etiology of chronic offending in factors other than peer influence. This does not mean that peers have no role in the expression of chronic offending, however. For instance, scholars have noted that offending with accomplices (i.e., co-offending) can reflect processes other than normative influence, such as selection and cooperation. Drawing from these notions, this investigation hypothesizes that chronic offenders will be less likely to cite peer influence as a reason for their deviance when compared to other offenders, whereas they will be equally likely to engage in group offending. The analysis uses information from the Racine cohort data and the results support the hypothesis. The discussion considers the implications of these findings for theory and research, as well as provides directions for future work.
Prayer to the Saints or the Virgin and Health Among Older Mexican Americans
Authors: Krause Neal , Bastida Elena
Published: January 2011

The purpose of this study was to evaluate a conceptual model that assesses whether praying to the saints or the Virgin is associated with the health of older Mexican Americans. A survey was conducted of 1,005 older Mexican Americans (Mean age = 73.9 years; SD = 6.6 years). Data from 795 of the Catholic respondents are presented in this study. The findings support the following relationships that are embedded in the conceptual model: (1) older Mexican Americans who attend church more often are more likely to believe in the efficacy of prayer to the saints or the Virgin; (2) stronger beliefs in the efficacy of intercessory prayer are associated with more frequent prayer to the saints or the Virgin; (3) frequent prayer is to the saints or the Virgin and is associated with greater God-mediated control beliefs; (4) stronger God-mediated control beliefs are associated with greater optimism; and (5) greater optimism is associated with better self-rated health.
Protective role of diallyl tetrasulfide on cadmium-induced testicular damage in adult rats: A biochemical and histological study
Authors: Ponnusamy Murugavel , Pari Leelavinothan
Published: January 2011

Cadmium (Cd)-induced oxidative damage is the most serious problem that leads to reproductive system failure in both human and animals. Our previous studies indicate that diallyl tetrasulfide (DTS) from garlic has the cytoprotective and antioxidant activity against Cd-induced toxicity in vivo and in vitro. The present investigation was carried out to find the influence of DTS on peroxidative damage induced by Cd in rat testes. The Cd-exposed rat testis showed a significant (p < 0.05) decrease in testes to body weight ratio, along with a significant (p < 0.05) increase in Cd accumulation, lipid peroxidation and protein carbonyl levels. In Cd-exposed rats, we also observed a significant (p < 0.05) decrease in the activities of antioxidant (superoxide dismutase, catalase and glutathione peroxidase) and glutathione metabolizing (glutathione-S-transferase, glutathione reductase and glucose-6-phosphate dehydrogenase) enzymes as well as reduced levels of non-enzymic (reduced glutathione, ascorbate and total sulphydryl groups) antioxidants. In contrast, treatment with DTS (40 mg/kg body weight orally) significantly (p < 0.05) reduced the accumulation of Cd and lipid peroxidation markers and also significantly improved the activities of antioxidant defense system in testes. Testicular protection by DTS is further substantiated by remarkable reduction of Cd-induced pathological changes. Our study has revealed that DTS renders protection against Cd-induced testicular injury by reducing Cd-mediated oxidative damage.
Family and Professional Priorities for Inclusive Early Childhood Settings
Authors: Hurley Jennifer J. , Horn Eva M.
Published: January 2011

The purpose of this study was to provide information about what characteristics from the variety of inclusive early childhood programs are most valued and least valued by families and professionals. Participants were 10 family members of young children with disabilities being served in inclusive programs and 10 early childhood professionals working in inclusive programs. A combination of Q-sort and qualitative research techniques were used. Participants generated one general factor viewpoint concerning what characteristics of inclusive early childhood programs are the most and least valuable. Interviews provided qualitative clarification concerning why participants did or did not value certain program characteristics and information about participants’ beliefs concerning inclusive early childhood programs.
β2-glycoprotein-1 autoantibodies from patients with antiphospholipid syndrome are sufficient to potentiate arterial thrombus formation in a mouse model
Authors: Arad Ariela , Proulle Valerie , Furie Richard A. , Furie Barbara C. , Furie Bruce
Published: January 2011

Antiphospholipid syndrome is characterized by thrombosis, recurrent fetal loss, and the presence of the lupus anticoagulant, anticardiolipin antibodies, or anti–β2-glycoprotein-1 (anti–β2-GP1) antibodies. Although anti–β2-GP1 antibodies have been documented as a biomarker for diagnosis of antiphospholipid syndrome, their direct role in the pathogenesis of thrombosis is unknown. We have demonstrated using intravital microscopy that anti–β2-GP1 autoantibodies purified from the sera of patients with antiphospholipid syndrome complicated by thrombosis greatly amplify thrombus size after laser-induced vessel wall injury in live mice. Anti–β2-GP1 autoantibodies from 3 patients with antiphospholipid syndrome were affinity-purified using human β2-GP1 bound to agarose. The effects of purified anti–β2-GP1 IgG autoantibodies, of anti–β2-GP1–depleted IgG, and of IgG from normal human sera on thrombus formation were measured in mice after arterial injury in the cremaster muscle. Before injury, purified anti–β2-GP1 IgG autoantibodies, anti–β2-GP1 antibody–depleted IgG, or IgG from normal human sera were infused. Increasing amounts of purified anti–β2-GP1 autoantibodies increased thrombus size in a dose-dependent manner, whereas neither anti–β2-GP1 antibody-depleted IgG nor IgG from normal serum affected thrombus size. These results indicate that anti–β2-GP1 IgG autoantibodies in antiphospholipid syndrome patient sera are not only a marker of antiphospholipid syndrome but are directly involved in the pathogenesis of thrombosis.
Fludarabine, cyclophosphamide, and rituximab chemoimmunotherapy is highly effective treatment for relapsed patients with CLL
Authors: Badoux Xavier C. , Keating Michael J. , Wang Xuemei , O'Brien Susan M. , Ferrajoli Alessandra , Faderl Stefan , Burger Jan , Koller Charles , Lerner Susan , Kantarjian Hagop , Wierda William G.
Published: January 2011

Optimal management of patients with relapsed/refractory chronic lymphocytic leukemia (CLL) is dictated by patient characteristics, prior therapy, and response to prior therapy. We report the final analysis of combined fludarabine, cyclophosphamide, and rituximab (FCR) for previously treated patients with CLL and identify patients who benefit most from this therapy. We explore efficacy of FCR in patients beyond first relapse, patients with prior exposure to fludarabine and alkylating agent combinations, and patients with prior exposure to rituximab. The FCR regimen was administered to 284 previously treated patients with CLL. Patients were assessed for response and progression by 1996 National Cancer Institute–Working Group (NCI-WG) criteria for CLL and followed for survival. The overall response rate was 74%, with 30% complete remission. The estimated median overall survival was 47 months and median progression-free survival for all patients was 21 months. Subgroup analyses indicated that the following patients were most suitable for FCR treatment: patients with up to 3 prior treatments, fludarabine-sensitive patients irrespective of prior rituximab exposure, and patients without chromosome 17 abnormalities. FCR is an active and well-tolerated therapy for patients with relapsed CLL. The addition of rituximab to FC improved quality and durability of response in this patient population.
Expression of p16INK4a prevents cancer and promotes aging in lymphocytes
Authors: Liu Yan , Johnson Soren M. , Fedoriw Yuri , Rogers Arlin B. , Yuan Hong , Krishnamurthy Janakiraman , Sharpless Norman E.
Published: January 2011

Previous authors have suggested that tumor suppressor expression promotes aging while preventing cancer, but direct experimental support for this cancer-aging hypothesis has been elusive. Here, by using somatic, tissue-specific inactivation of the p16INK4a tumor suppressor in murine T- or B-lymphoid progenitors, we report that ablation of p16INK4a can either rescue aging or promote cancer in a lineage-specific manner. Deletion of p16INK4a in the T lineage ameliorated several aging phenotypes, including thymic involution, decreased production of naive T cells, reduction in homeostatic T-cell proliferation, and attenuation of antigen-specific immune responses. Increased T-cell neoplasia was not observed with somatic p16INK4a inactivation in T cells. In contrast, B lineage–specific ablation of p16INK4a was associated with a markedly increased incidence of systemic, high-grade B-cell neoplasms, which limited studies of the effects of somatic p16INK4a ablation on B-cell aging. Together, these data show that expression of p16INK4a can promote aging and prevent cancer in related lymphoid progeny of a common stem cell.
Effector CD4+ T cells, the cytokines they generate, and GVHD: something old and something new
Authors: Coghill James M. , Sarantopoulos Stefanie , Moran Timothy P. , Murphy William J. , Blazar Bruce R. , Serody Jonathan S.
Published: January 2011

GVHD is a syndrome that results from minor and major histocompatibility complex incompatibilities between the donor and recipient. More than 50 years after its initial description, the pathophysiology of GVHD remains poorly understood. Nonetheless, donor T cells have been shown to be critical to the pathophysiology of acute and chronic GVHD, yet precisely how they function remains unclear. The effector mechanisms by which donor T cells mediate tissue inflammation is even less well understood. Identification of several new lineages of CD4+ T cells made in the past decade and their roles in the pathophysiology of T cell–mediated diseases has shed new light on these effector mechanisms. In this review, we summarize the recent descriptions of these T-cell lineages and the current data supporting their role in acute and to a lesser extent chronic GVHD. Investigations into the activity of these new T-cell lineages may provide more rationale approaches to the treatment or prevention of GVHD.
Pathogenicity of two recent Western Mediterranean West Nile virus isolates in a wild bird species indigenous to Southern Europe: the red-legged partridge
Authors: Sotelo Elena , Gutierrez-Guzmán Ana Valeria , del Amo Javier , Llorente Francisco , El-Harrak Mehdi , Pérez-Ramírez Elisa , Blanco Juan Manuel , Höfle Ursula , Jiménez-Clavero Miguel Angel
Published: January 2011

West Nile virus (WNV) is an emerging zoonotic pathogen whose geographic spread and incidence in humans, horses and birds has increased significantly in recent years. WNV has long been considered a mild pathogen causing self-limiting outbreaks. This notion has changed as WNV is causing large epidemics with a high impact on human and animal health. This has been particularly noteworthy since its introduction into North America in 1999. There, native bird species have been shown to be highly susceptible to WNV infection and disease with high mortalities. For this reason, the effect of WNV infection in North American bird species has been thoroughly studied by means of experimental inoculations in controlled trials. To a lesser extent, European wild birds have been shown to be affected clinically by WNV infection. Yet experimental studies on European wild bird species are lacking. The red-legged partridge (Alectoris rufa) is a gallinaceous bird indigenous to the Iberian Peninsula, widely distributed in South Western Europe. It plays a key role in the Mediterranean ecosystem and constitutes an economically important game species. As such it is raised intensively in outdoor facilities. In this work, red-legged partridges were experimentally infected with two recent WNV isolates from the Western Mediterranean area: Morocco/2003 and Spain/2007. All inoculated birds became viremic and showed clinical disease, with mortality rates of 70% and 30%, respectively. These results show that Western Mediterranean WNV variants can be pathogenic for some European bird species, such as the red-legged partridge.
BiologicalNetworks 2.0 - an integrative view of genome biology data
Authors: Kozhenkov Sergey , Dubinina Yulia , Sedova Mayya , Gupta Amarnath , Ponomarenko Julia , Baitaluk Michael
Published: January 2011

Background

A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems.

Results

Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other) and their relations (interactions, co-expression, co-citations, and other). The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations.

Conclusions

The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available athttp://www.biologicalnetworks.org.
GraphCrunch 2: Software tool for network modeling, alignment and clustering
Authors: Kuchaiev Oleksii , Stevanović Aleksandar , Hayes Wayne , Pržulj Nataša
Published: January 2011

Background

Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI) data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype.

Results

We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL") for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other existing tool. Finally, GraphCruch 2 implements an algorithm for clustering nodes within a network based solely on their topological similarities. Using GraphCrunch 2, we demonstrate that eukaryotic and viral PPI networks may belong to different graph model families and show that topology-based clustering can reveal important functional similarities between proteins within yeast and human PPI networks.

Conclusions

GraphCrunch 2 is a software tool that implements the latest research on biological network analysis. It parallelizes computationally intensive tasks to fully utilize the potential of modern multi-core CPUs. It is open-source and freely available for research use. It runs under the Windows and Linux platforms.
Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family
Authors: Illa Eudald , Sargent Daniel J , Girona Elena Lopez , Bushakra Jill , Cestaro Alessandro , Crowhurst Ross , Pindo Massimo , Cabrera Antonio , van der Knaap Esther , Iezzoni Amy , Gardiner Susan , Velasco Riccardo , Arús Pere , Chagné David , Troggio Michela
Published: January 2011

Background

Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence.

Results

We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae.

Conclusions

A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.
Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes
Authors: Jiang Yu , Li Yan , Lee Wenhui , Xu Xun , Zhang Yue , Zhao Ruoping , Zhang Yun , Wang Wen
Published: January 2011

Background

Kraits (genus Bungarus) and cobras (genus Naja) are two representative toxic genera of elapids in the old world. Although they are closely related genera and both of their venoms are very toxic, the compositions of their venoms are very different. To unveil their detailed venoms and their evolutionary patterns, we constructed venom gland cDNA libraries and genomic bacterial artificial chromosome (BAC) libraries for Bungarus multicinctus and Naja atra, respectively. We sequenced about 1500 cDNA clones for each of the venom cDNA libraries and screened BAC libraries of the two snakes by blot analysis using four kinds of toxin probes; i.e., three-finger toxin (3FTx), phospholipase A2 (PLA2), kunitz-type protease inhibitor (Kunitz), and natriuretic peptide (NP).

Results

In total, 1092 valid expressed sequences tags (ESTs) for B. multicinctus and 1166 ESTs for N. atra were generated. About 70% of these ESTs can be annotated as snake toxin transcripts. 3FTx (64.5%) and β bungarotoxin (25.1%) comprise the main toxin classes in B. multicinctus, while 3FTx (95.8%) is the dominant toxin in N. atra. We also observed several less abundant venom families in B. multicinctus and N. atra, such as PLA2, C-type lectins, and Kunitz. Peculiarly a cluster of NP precursors with tandem NPs was detected in B. multicinctus. A total of 71 positive toxin BAC clones in B. multicinctus and N. atra were identified using four kinds of toxin probes (3FTx, PLA2, Kunitz, and NP), among which 39 3FTx-postive BACs were sequenced to reveal gene structures of 3FTx toxin genes.

Conclusions

Based on the toxin ESTs and 3FTx gene sequences, the major components of B. multicinctus venom transcriptome are neurotoxins, including long chain alpha neurotoxins (α-ntx) and the recently originated β bungarotoxin, whereas the N. atra venom transcriptome mainly contains 3FTxs with cytotoxicity and neurotoxicity (short chain α-ntx). The data also revealed that tandem duplications contributed the most to the expansion of toxin multigene families. Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (dN/dS) indicates that not only multigene toxin families but also other less abundant toxins might have been under rapid diversifying evolution.
Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942
Authors: Delaye Luis , González-Domenech Carmen M , Garcillán-Barcia María P , Peretó Juli , de la Cruz Fernando , Moya Andrés
Published: January 2011

Background

Simpler biological systems should be easier to understand and to engineer towards pre-defined goals. One way to achieve biological simplicity is through genome minimization. Here we looked for genomic islands in the fresh water cyanobacteria Synechococcus elongatus PCC 7942 (genome size 2.7 Mb) that could be used as targets for deletion. We also looked for conserved genes that might be essential for cell survival.

Results

By using a combination of methods we identified 170 xenologs, 136 ORFans and 1401 core genes in the genome of S. elongatus PCC 7942. These represent 6.5%, 5.2% and 53.6% of the annotated genes respectively. We considered that genes in genomic islands could be found if they showed a combination of: a) unusual G+C content; b) unusual phylogenetic similarity; and/or c) a small number of the highly iterated palindrome 1 (HIP1) motif plus an unusual codon usage. The origin of the largest genomic island by horizontal gene transfer (HGT) could be corroborated by lack of coverage among metagenomic sequences from a fresh water microbialite. Evidence is also presented that xenologous genes tend to cluster in operons. Interestingly, most genes coding for proteins with a diguanylate cyclase domain are predicted to be xenologs, suggesting a role for horizontal gene transfer in the evolution of Synechococcus sensory systems.

Conclusions

Our estimates of genomic islands in PCC 7942 are larger than those predicted by other published methods like SIGI-HMM. Our results set a guide to non-essential genes in S. elongatus PCC 7942 indicating a path towards the engineering of a model photoautotrophic bacterial cell.
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related
Authors: Freitas Alex A , Vasieva Olga , de Magalhães João Pedro
Published: January 2011

Background

The ageing of the worldwide population means there is a growing need for research on the biology of ageing. DNA damage is likely a key contributor to the ageing process and elucidating the role of different DNA repair systems in ageing is of great interest. In this paper we propose a data mining approach, based on classification methods (decision trees and Naive Bayes), for analysing data about human DNA repair genes. The goal is to build classification models that allow us to discriminate between ageing-related and non-ageing-related DNA repair genes, in order to better understand their different properties.

Results

The main patterns discovered by the classification methods are as follows: (a) the number of protein-protein interactions was a predictor of DNA repair proteins being ageing-related; (b) the use of predictor attributes based on protein-protein interactions considerably increased predictive accuracy of attributes based on Gene Ontology (GO) annotations; (c) GO terms related to "response to stimulus" seem reasonably good predictors of ageing-relatedness for DNA repair genes; (d) interaction with the XRCC5 (Ku80) protein is a strong predictor of ageing-relatedness for DNA repair genes; and (e) DNA repair genes with a high expression in T lymphocytes are more likely to be ageing-related.

Conclusions

The above patterns are broadly integrated in an analysis discussing relations between Ku, the non-homologous end joining DNA repair pathway, ageing and lymphocyte development. These patterns and their analysis support non-homologous end joining double strand break repair as central to the ageing-relatedness of DNA repair genes. Our work also showcases the use of protein interaction partners to improve accuracy in data mining methods and our approach could be applied to other ageing-related pathways.
Divergent responses to peptidoglycans derived from different E. coli serotypes influence inflammatory outcome in trout, Oncorhynchus mykiss, macrophages
Authors: Boltaña Sebastian , Reyes-Lopez Felipe , Morera Davinia , Goetz Frederick , MacKenzie Simon A
Published: January 2011

Background

Pathogen-associated molecular patterns (PAMPs) are structural components of pathogens such as lipopolysaccharide (LPS) and peptidoglycan (PGN) from bacterial cell walls. PAMP-recognition by the host results in an induction of defence-related genes and often the generation of an inflammatory response. We evaluated both the transcriptomic and inflammatory response in trout (O. mykiss) macrophages in primary cell culture stimulated with DAP-PGN (DAP; meso-diaminopimelic acid, PGN; peptidoglycan) from two strains ofEscherichia coli(PGN-K12 and PGN-O111:B4) over time.

Results

Transcript profiling was assessed using function-targeted cDNA microarray hybridisation (n = 36) and results show differential responses to both PGNs that are both time and treatment dependent. Wild typeE. coli(K12) generated an increase in transcript number/diversity over time whereas PGN-O111:B4 stimulation resulted in a more specific and intense response. In line with this, Gene Ontology analysis (GO) highlights a specific transcriptomic remodelling for PGN-O111:B4 whereas results obtained for PGN-K12 show a high similarity to a generalised inflammatory priming response where multiple functional classes are related to ribosome biogenesis or cellular metabolism. Prostaglandin release was induced by both PGNs and macrophages were significantly more sensitive to PGN-O111:B4 as suggested from microarray data.

Conclusion

Responses at the level of the transcriptome and the inflammatory outcome (prostaglandin synthesis) highlight the different sensitivity of the macrophage to slight differences (serotype) in peptidoglycan structure. Such divergent responses are likely to involve differential receptor sensitivity to ligands or indeed different receptor types. Such changes in biological response will likely reflect upon pathogenicity of certain serotypes and the development of disease.
Staphylococcus aureus requires cardiolipin for survival under conditions of high salinity
Authors: Tsai Melody , Ohniwa Ryosuke L , Kato Yusuke , Takeshita Sayaka L , Ohta Toshiko , Saito Shinji , Hayashi Hideo , Morikawa Kazuya
Published: January 2011

Background

The ability of staphylococci to grow in a wide range of salt concentrations is well documented. In this study, we aimed to clarify the role of cardiolipin (CL) in the adaptation of Staphylococcus aureus to high salinity.

Results

Using an improved extraction method, the analysis of phospholipid composition suggested that CL levels increased slightly toward stationary phase, but that this was not induced by high salinity. Deletion of the two CL synthase genes, SA1155 (cls1) and SA1891 (cls2), abolished CL synthesis. The cls2 gene encoded the dominant CL synthase. In a cls2 deletion mutant, Cls1 functioned under stress conditions, including high salinity. Using these mutants, CL was shown to be unnecessary for growth in either basal or high-salt conditions, but it was critical for prolonged survival in high-salt conditions and for generation of the L-form.

Conclusions

CL is not essential for S. aureus growth under conditions of high salinity, but is necessary for survival under prolonged high-salt stress and for the generation of L-form variants.
Rasd1 interacts with Ear2 (Nr2f6) to regulate renin transcription
Authors: Tan Jen Jen , Ong Shufen Angeline , Chen Ken-Shiung
Published: January 2011

Background

The Rasd1 protein is a dexamethasone induced monomeric Ras-like G protein that oscillates in the suprachiasmatic nucleus (SCN). Previous studies have shown that Rasd1 modulates multiple signaling cascades. However, it is still unclear exactly how Rasd1 carries out its function. Studying protein-protein interactions involving Rasd1 may provide insights into its biological functions in different contexts.

Results

To further explore the molecular function of Rasd1, we performed a yeast two-hybrid screen and identified Ear2, a negative regulator of renin transcription, as an interaction partner of Rasd1. We validated the interaction in vitro and in transfected COS-7 cells. We further confirmed the interaction of endogenous Rasd1 and Ear2 from HEK293T cell and mouse brain extract. Rasd1 inhibited transcriptional repression by Ear2 on a renin promoter-luciferase reporter construct both in the presence and absence of all-trans-retinoic acid. Moreover, real-time RT-PCR showed upregulation of endogenous renin transcription in As4.1 cells over-expressing Rasd1. We demonstrated that the ligand binding domain of Ear2 is required for physical and functional interaction between the two proteins. In addition, we demonstrated that shRNA-mediated knockdown of Rasd1 results in further repression of Ear2-mediated renin transcription, whereas induction of Rasd1 by dexamethasone counteracts the effects of shRNA-mediated Rasd1 knockdown. Finally, our study showed that Rasd1 missense mutations not only attenuate their physical interaction with Ear2 but also abolish their ability to counteract repression of renin transcription mediated by Ear2.

Conclusions

Our study provides evidence for physical and functional interactions between Rasd1 and Ear2. The results suggest that their interactions are involved in renin transcriptional regulation. These findings not only reveal a novel role for Rasd1-medated signaling but also provide the basis for potential intervention of renin expression.
Harpin-induced expression and transgenic overexpression of the phloem protein gene AtPP2-A1 in Arabidopsis repress phloem feeding of the green peach aphid Myzus persicae
Authors: Zhang Chunling , Shi Haojie , Chen Lei , Wang Xiaomeng , Lü Beibei , Zhang Shuping , Liang Yuan , Liu Ruoxue , Qian Jun , Sun Weiwei , You Zhenzhen , Dong Hansong
Published: January 2011

Background

Treatment of plants with HrpNEa, a protein of harpin group produced by Gram-negative plant pathogenic bacteria, induces plant resistance to insect herbivores, including the green peach aphid Myzus persicae, a generalist phloem-feeding insect. Under attacks by phloem-feeding insects, plants defend themselves using the phloem-based defense mechanism, which is supposed to involve the phloem protein 2 (PP2), one of the most abundant proteins in the phloem sap. The purpose of this study was to obtain genetic evidence for the function of the Arabidopsis thaliana (Arabidopsis) PP2-encoding gene AtPP2-A1 in resistance to M. persicae when the plant was treated with HrpNEa and after the plant was transformed with AtPP2-A1.

Results

The electrical penetration graph technique was used to visualize the phloem-feeding activities of apterous agamic M. persicae females on leaves of Arabidopsis plants treated with HrpNEa and an inactive protein control, respectively. A repression of phloem feeding was induced by HrpNEa in wild-type (WT) Arabidopsis but not in atpp2-a1/E/142, the plant mutant that had a defect in the AtPP2-A1 gene, the most HrpNEa-responsive of 30 AtPP2 genes. In WT rather than atpp2-a1/E/142, the deterrent effect of HrpNEa treatment on the phloem-feeding activity accompanied an enhancement of AtPP2-A1 expression. In PP2OETAt (AtPP2-A1-overexpression transgenic Arabidopsis thaliana) plants, abundant amounts of the AtPP2-A1 gene transcript were detected in different organs, including leaves, stems, calyces, and petals. All these organs had a deterrent effect on the phloem-feeding activity compared with the same organs of the transgenic control plant. When a large-scale aphid population was monitored for 24 hours, there was a significant decrease in the number of aphids that colonized leaves of HrpNEa-treated WT and PP2OETAt plants, respectively, compared with control plants.

Conclusions

The repression in phloem-feeding activities of M. persicae as a result of AtPP2-A1 overexpression, and as a deterrent effect of HrpNEa treatment in WT Arabidopsis rather than the atpp2-a1/E/142 mutant suggest that AtPP2-A1 plays a role in plant resistance to the insect, particularly at the phloem-feeding stage. The accompanied change of aphid population in leaf colonies suggests that the function of AtPP2-A1 is related to colonization of the plant.
In silicocomparative analysis of SSR markers in plants
Authors: Victoria Filipe C , da Maia Luciano C , de Oliveira Antonio Costa
Published: January 2011

Background

The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.

Results

In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using theSSRLocatorsoftware in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With thisin silicostudy we confirm several microsatellite plant survey results made with available bioinformatics tools.

Conclusions

The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.