bluuebunny/crossref_metadata_2025_split huggingface dataset:
siRNA against the G gene of human metapneumovirus
Authors: Preston Faith Maxine , Straub Claire P , Ramirez Ruben , Mahalingam Suresh , Spann Kirsten M 
Published: June 2012

AbstractBackgroundHuman metapneumovirus (hMPV) is a significant viral respiratory pathogen of infants and children, the elderly and immunocompromised individuals. Disease associated with hMPV infection resembles that of human respiratory syncytial virus (RSV) and includes bronchiolitis and pneumonia. The glycosylated G attachment protein of hMPV is required for viral entryin vivoand has also been identified as an inhibitor of innate immune responses.FindingsWe designed and validated two siRNA molecules against the G gene using A549 cells and demonstrated consistent 88-92% knock-down for one siRNA molecule, which was used in subsequent experiments. Significant reduction of G mRNA in A549 cells infected with hMPV did not result in a reduction in viral growth, nor did it significantly increase the production of type I interferon (α/β) in response to infection. However, there was a moderate increase in IFN-β mRNA expression in response to infection in siG-transfected cells compared to untransfected and si-mismatch-transfected cells. Expression of G by recombinant adenovirus did not affect type I IFN expression.ConclusionG has been previously described as a type I interferon antagonist, although our findings suggest it may not be a significant antagonist.
Traditional food and herbal uses of wild plants in the ancient South-Slavic diaspora of Mundimitar/Montemitro (Southern Italy)
Authors: di Tizio Alessandro , Łuczaj Łukasz Jakub , Quave Cassandra L , Redžić Sulejman , Pieroni Andrea 
Published: June 2012

Abstract

Background
In Europe, only a limited number of cross-cultural comparative field studies or meta-analyses have been focused on the dynamics through which folk plant knowledge changes over space and time, while a few studies have contributed to the understanding of how plant uses change among newcomers. Nevertheless, ethnic minority groups and/or linguistic “isles” in Southern and Eastern Europe may provide wonderful arenas for understanding the various factors that influence changes in plant uses.

Methods
A field ethnobotanical study was carried out in Mundimitar (Montemitro in Italian), a village of approx. 450 inhabitants, located in the Molise region of South-Eastern Italy. Mundimitar is a South-Slavic community, composed of the descendants of people who migrated to the area during the first half of the 14th century, probably from the lower Neretva valley (Dalmatia and Herzegovina regions). Eighteen key informants (average age: 63.7) were selected using the snowball sampling technique and participated in in-depth interviews regarding their Traditional Knowledge (TK) of the local flora.

Results
Although TK on wild plants is eroded in Montemitro among the youngest generations, fifty-seven taxa (including two cultivated species, which were included due to their unusual uses) were quoted by the study participants. Half of the taxa have correspondence in the Croatian and Herzegovinian folk botanical nomenclature, and the other half with South-Italian folk plant names. A remarkable link to the wild vegetable uses recorded in Dalmatia is evident. A comparison of the collected data with the previous ethnobotanical data of the Molise region and of the entire Italian Peninsula pointed out a few uses that have not been recorded in Italy thus far: the culinary use of boiled black bryony (Tamus communis) shoots in sauces and also on pasta; the use of squirting cucumber ( Ecballium elaterium) juice for treating malaria in humans; the aerial parts of the elderberry tree ( Sambucus nigra) for treating erysipelas in pigs; the aerial parts of pellitory ( Parietaria judaica) in decoctions for treating haemorrhoids.

Conclusions
The fact that half of the most salient species documented in our case study – widely available both in Molise and in Dalmatia and Herzegovina – retain a Slavic name could indicate that they may have also been used in Dalmatia and Herzegovina before the migration took place. However, given the occurrence of several South-Italian plant names and uses, also a remarkable acculturation process affected the Slavic community of Montemitro during these last centuries. Future directions of research should try to simultaneously compare current ethnobotanical knowledge of both migrated communities and their counterparts in the areas of origin.
Primary traumatic patellar dislocation
Authors: Tsai Chun-Hao , Hsu Chin-Jung , Hung Chih-Hung , Hsu Horng-Chaung 
Published: June 2012

AbstractAcute traumatic patellar dislocation is a common injury in the active and young adult populations. MRI of the knee is recommended in all patients who present with acute patellar dislocation. Numerous operative and non-operative methods have been described to treat the injuries; however, the ideal management of the acute traumatic patellar dislocation in young adults is still in debate. This article is intended to review the studies to the subjects of epidemiology, initial examination and management.
Novel genetic linkage of rat Sp6 mutation to Amelogenesis imperfecta
Authors: Muto Taro , Miyoshi Keiko , Horiguchi Taigo , Hagita Hiroko , Noma Takafumi 
Published: June 2012

Abstract

Background
Amelogenesis imperfecta (AI) is an inherited disorder characterized by abnormal formation of tooth enamel. Although several genes responsible for AI have been reported, not all causative genes for human AI have been identified to date. AMI rat has been reported as an autosomal recessive mutant with hypoplastic AI isolated from a colony of stroke-prone spontaneously hypertensive rat strain, but the causative gene has not yet been clarified. Through a genetic screen, we identified the causative gene of autosomal recessive AI in AMI and analyzed its role in amelogenesis.

Methods
cDNA sequencing of possible AI-candidate genes so far identified using total RNA of day 6 AMI rat molars identified a novel responsible mutation in specificity protein 6 (Sp6). Genetic linkage analysis was performed between Sp6 and AI phenotype in AMI. To understand a role of SP6 in AI, we generated the transgenic rats harboring Sp6 transgene in AMI (Ami/Ami + Tg). Histological analyses were performed using the thin sections of control rats, AMI, and Ami/Ami + Tg incisors in maxillae, respectively.

Results
We found the novel genetic linkage between a 2-bp insertional mutation of Sp6 gene and the AI phenotype in AMI rats. The position of mutation was located in the coding region of Sp6, which caused frameshift mutation and disruption of the third zinc finger domain of SP6 with 11 cryptic amino acid residues and a stop codon. Transfection studies showed that the mutant protein can be translated and localized in the nucleus in the same manner as the wild-type SP6 protein. When we introduced the CMV promoter-driven wild-type Sp6 transgene into AMI rats, the SP6 protein was ectopically expressed in the maturation stage of ameloblasts associated with the extended maturation stage and the shortened reduced stage without any other phenotypical changes.

Conclusion
We propose the addition of Sp6 mutation as a new molecular diagnostic criterion for the autosomal recessive AI patients. Our findings expand the spectrum of genetic causes of autosomal recessive AI and sheds light on the molecular diagnosis for the classification of AI. Furthermore, tight regulation of the temporospatial expression of SP6 may have critical roles in completing amelogenesis.
Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Authors: Gu Zuguang , Liu Jialin , Cao Kunming , Zhang Junfeng , Wang Jin 
Published: June 2012

AbstractBackgroundBiological pathways are important for understanding biological mechanisms. Thus, finding important pathways that underlie biological problems helps researchers to focus on the most relevant sets of genes. Pathways resemble networks with complicated structures, but most of the existing pathway enrichment tools ignore topological information embedded within pathways, which limits their applicability.ResultsA systematic and extensible pathway enrichment method in which nodes are weighted by network centrality was proposed. We demonstrate how choice of pathway structure and centrality measurement, as well as the presence of key genes, affects pathway significance. We emphasize two improvements of our method over current methods. First, allowing for the diversity of genes’ characters and the difficulty of covering gene importance from all aspects, we set centrality as an optional parameter in the model. Second, nodes rather than genes form the basic unit of pathways, such that one node can be composed of several genes and one gene may reside in different nodes. By comparing our methodology to the original enrichment method using both simulation data and real-world data, we demonstrate the efficacy of our method in finding new pathways from biological perspective.ConclusionsOur method can benefit the systematic analysis of biological pathways and help to extract more meaningful information from gene expression data. The algorithm has been implemented as an R package CePa, and also a web-based version of CePa is provided.
Stochastic simulations of a synthetic bacteria-yeast ecosystem
Authors: Biliouris Konstantinos , Babson David , Schmidt-Dannert Claudia , Kaznessis Yiannis N 
Published: June 2012

Abstract

Background
The field of synthetic biology has greatly evolved and numerous functions can now be implemented by artificially engineered cells carrying the appropriate genetic information. However, in order for the cells to robustly perform complex or multiple tasks, co-operation between them may be necessary. Therefore, various synthetic biological systems whose functionality requires cell-cell communication are being designed. These systems, microbial consortia, are composed of engineered cells and exhibit a wide range of behaviors. These include yeast cells whose growth is dependent on one another, or bacteria that kill or rescue each other, synchronize, behave as predator-prey ecosystems or invade cancer cells.

Results
In this paper, we study a synthetic ecosystem comprising of bacteria and yeast that communicate with and benefit from each other using small diffusible molecules. We explore the behavior of this heterogeneous microbial consortium, composed of Saccharomyces cerevisiae and Escherichia coli cells, using stochastic modeling. The stochastic model captures the relevant intra-cellular and inter-cellular interactions taking place in and between the eukaryotic and prokaryotic cells. Integration of well-characterized molecular regulatory elements into these two microbes allows for communication through quorum sensing. A gene controlling growth in yeast is induced by bacteria via chemical signals and vice versa. Interesting dynamics that are common in natural ecosystems, such as obligatory and facultative mutualism, extinction, commensalism and predator-prey like dynamics are observed. We investigate and report on the conditions under which the two species can successfully communicate and rescue each other.

Conclusions
This study explores the various behaviors exhibited by the cohabitation of engineered yeast and bacterial cells. The way that the model is built allows for studying the dynamics of any system consisting of two species communicating with one another via chemical signals. Therefore, key information acquired by our model may potentially drive the experimental design of various synthetic heterogeneous ecosystems.
Structural characterization of alkaline hydrogen peroxide pretreated grasses exhibiting diverse lignin phenotypes
Authors: Li Muyang , Foster Cliff , Kelkar Shantanu , Pu Yunqiao , Holmes Daniel , Ragauskas Arthur , Saffron Christopher M , Hodge David B 
Published: June 2012

Abstract

Background
For cellulosic biofuels processes, suitable characterization of the lignin remaining within the cell wall and correlation of quantified properties of lignin to cell wall polysaccharide enzymatic deconstruction is underrepresented in the literature. This is particularly true for grasses which represent a number of promising bioenergy feedstocks where quantification of grass lignins is particularly problematic due to the high fraction of p- hydroxycinnamates. The main focus of this work is to use grasses with a diverse range of lignin properties, and applying multiple lignin characterization platforms, attempt to correlate the differences in these lignin properties to the susceptibility to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic deconstruction.

Results
We were able to determine that the enzymatic hydrolysis of cellulose to to glucose (i.e. digestibility) of four grasses with relatively diverse lignin phenotypes could be correlated to total lignin content and the content of p-hydroxycinnamates, while S/G ratios did not appear to contribute to the enzymatic digestibility or delignification. The lignins of the brown midrib corn stovers tested were significantly more condensed than a typical commercial corn stover and a significant finding was that pretreatment with alkaline hydrogen peroxide increases the fraction of lignins involved in condensed linkages from 88–95% to ~99% for all the corn stovers tested, which is much more than has been reported in the literature for other pretreatments. This indicates significant scission of β-O-4 bonds by pretreatment and/or induction of lignin condensation reactions. The S/G ratios in grasses determined by analytical pyrolysis are significantly lower than values obtained using either thioacidolysis or 2DHSQC NMR due to presumed interference by ferulates.

Conclusions
It was found that grass cell wall polysaccharide hydrolysis by cellulolytic enzymes for grasses exhibiting a diversity of lignin structures and compositions could be linked to quantifiable changes in the composition of the cell wall and properties of the lignin including apparent content of the p-hydroxycinnamates while the limitations of S/G estimation in grasses is highlighted.
Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum
Authors: Valenzuela Jacob , Mazurie Aurelien , Carlson Ross P , Gerlach Robin , Cooksey Keith E , Peyton Brent M , Fields Matthew W 
Published: June 2012

AbstractBackgroundPhaeodactylum tricornutumis a unicellular diatom in the classBacillariophyceae.The full genome has been sequenced (<30 Mb), and approximately 20 to 30% triacylglyceride (TAG) accumulation on a dry cell basis has been reported under different growth conditions. To elucidateP. tricornutumgene expression profiles during nutrient-deprivation and lipid-accumulation, cell cultures were grown with a nitrate to phosphate ratio of 20:1 (N:P) and whole-genome transcripts were monitored over time via RNA-sequence determination.ResultsThe specific Nile Red (NR) fluorescence (NR fluorescence per cell) increased over time; however, the increase in NR fluorescence was initiated before external nitrate was completely exhausted. Exogenous phosphate was depleted before nitrate, and these results indicated that the depletion of exogenous phosphate might be an early trigger for lipid accumulation that is magnified upon nitrate depletion. As expected, many of the genes associated with nitrate and phosphate utilization were up-expressed. The diatom-specific cyclinscyc7 andcyc10 were down-expressed during the nutrient-deplete state, and cyclin B1 was up-expressed during lipid-accumulation after growth cessation. While many of the genes associated with the C3 pathway for photosynthetic carbon reduction were not significantly altered, genes involved in a putative C4 pathway for photosynthetic carbon assimilation were up-expressed as the cells depleted nitrate, phosphate, and exogenous dissolved inorganic carbon (DIC) levels.P. tricornutumhas multiple, putative carbonic anhydrases, but only two were significantly up-expressed (2-fold and 4-fold) at the last time point when exogenous DIC levels had increased after the cessation of growth. Alternative pathways that could utilize HCO3-were also suggested by the gene expression profiles (e.g., putative propionyl-CoA and methylmalonyl-CoA decarboxylases).ConclusionsThe results indicate thatP. tricornutumcontinued carbon dioxide reduction when population growth was arrested and different carbon-concentrating mechanisms were used dependent upon exogenous DIC levels. Based upon overall low gene expression levels for fatty acid synthesis, the results also suggest that the build-up of precursors to the acetyl-CoA carboxylases may play a more significant role in TAG synthesis rather than the actual enzyme levels of acetyl-CoA carboxylasesper se. The presented insights into the types and timing of cellular responses to inorganic carbon will help maximize photoautotrophic carbon flow to lipid accumulation.
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing
Authors: Wirth Roland , Kovács Etelka , Maróti Gergely , Bagi Zoltán , Rákhely Gábor , Kovács Kornél L 
Published: June 2012

Abstract

Background
Renewable energy production is currently a major issue worldwide. Biogas is a promising renewable energy carrier as the technology of its production combines the elimination of organic waste with the formation of a versatile energy carrier, methane. In consequence of the complexity of the microbial communities and metabolic pathways involved the biotechnology of the microbiological process leading to biogas production is poorly understood. Metagenomic approaches are suitable means of addressing related questions. In the present work a novel high-throughput technique was tested for its benefits in resolving the functional and taxonomical complexity of such microbial consortia.

Results
It was demonstrated that the extremely parallel SOLiD™ short-read DNA sequencing platform is capable of providing sufficient useful information to decipher the systematic and functional contexts within a biogas-producing community. Although this technology has not been employed to address such problems previously, the data obtained compare well with those from similar high-throughput approaches such as 454-pyrosequencing GS FLX or Titanium. The predominant microbes contributing to the decomposition of organic matter include members of the Eubacteria, class Clostridia, order Clostridiales, family Clostridiaceae. Bacteria belonging in other systematic groups contribute to the diversity of the microbial consortium. Archaea comprise a remarkably small minority in this community, given their crucial role in biogas production. Among the Archaea, the predominant order is the Methanomicrobiales and the most abundant species is Methanoculleus marisnigri. The Methanomicrobiales are hydrogenotrophic methanogens. Besides corroborating earlier findings on the significance of the contribution of the Clostridia to organic substrate decomposition, the results demonstrate the importance of the metabolism of hydrogen within the biogas producing microbial community.

Conclusions
Both microbiological diversity and the regulatory role of the hydrogen metabolism appear to be the driving forces optimizing biogas-producing microbial communities. The findings may allow a rational design of these communities to promote greater efficacy in large-scale practical systems. The composition of an optimal biogas-producing consortium can be determined through the use of this approach, and this systematic methodology allows the design of the optimal microbial community structure for any biogas plant. In this way, metagenomic studies can contribute to significant progress in the efficacy and economic improvement of biogas production.
Schistosoma haematobium infections among schoolchildren in central Sudan one year after treatment with praziquantel
Authors: Ahmed Abedaziz M , Abbas Hana , Mansour Fathi A , Gasim Gasim I , Adam Ishag 
Published: June 2012

Abstract

Background
Chemotherapy with praziquantel (PZQ) is the mainstay of schistosomiasis control. However, there are recent concerns about tolerance or resistance to PZQ, so that monitoring its efficacy in different settings is required.

Methods
A longitudinal study was conducted to evaluate the impact of PZQ for the treatment of Schistosoma haematobium infection among schoolchildren at Al Salamania, Central Sudan. Parasitological examinations for S. haematobium were performed in a cohort of schoolchildren (6–15 years of age) before and 1 year after treatment with a single dose of PZQ 40 mg/kg.

Results
Out of 562 (309 boys and 253 girls) schoolchildren recruited from three elementary schools, 420 completed one longitudinal dataset that comprised of data from two time points; baseline, and follow-up 1 year after treatment with a single dose of PZQ 40 mg/kg for S. haematobium infection. A single dose of PZQ significantly reduced the prevalence of S. haematobium infection by 83.3% (from 51.4% to 8.6%) and the geometric mean intensity of infection of positive individuals by 17.0% (from 87.7 to 72.8 eggs/10 ml of urine) 1 year after treatment. While there was no significant difference in the reduction of the prevalence of S. haematobium infection between the gender or age groups, there was a significantly higher reduction of intensity of S. haematobium infection among girls in comparison with boys.

Conclusion
There was a significant reduction of S. haematobium infection 1 year after PZQ treatment in this setting.
Meta-analysis of human lung cancer microRNA expression profiling studies comparing cancer tissues with normal tissues
Authors: Guan Peng , Yin Zhihua , Li Xuelian , Wu Wei , Zhou Baosen 
Published: June 2012

Abstract

Background
Lung cancer is the major cause of cancer death globally, it is often diagnosed at an advanced stage and has one of the lowest survival rates of any type of cancer. The common interest in the field of lung cancer research is the identification of biomarkers for early diagnosis and accurate prognosis. There is increasing evidence to suggest that microRNAs play important and complex roles in lung cancer.

Methods
A meta-analysis was conducted to review the published microRNA expression profiling studies that compared the microRNAs expression profiles in lung cancer tissues with those in normal lung tissues. A vote-counting strategy that considers the total number of studies reporting its differential expression, the total number of tissue samples used in the studies and the average fold change was employed.

Results
A total of 184 differentially expressed microRNAs were reported in the fourteen microRNA expression profiling studies that compared lung cancer tissues with normal tissues, with 61 microRNAs were reported in at least two studies. In the panel of consistently reported up-regulated microRNAs, miR-210 was reported in nine studies and miR-21 was reported in seven studies. In the consistently reported down-regulated microRNAs, miR-126 was reported in ten studies and miR-30a was reported in eight studies. Four up-regulated microRNAs (miR-210, miR-21, miR-31 and miR-182) and two down-regulated mcroiRNAs (miR-126 and miR-145) were consistently reported both in squamous carcinoma and adenocarcinoma-based subgroup analysis, with the other 14 microRNAs solely reported in one or the other subset.

Conclusions
In conclusion, the top two most consistently reported up-regulated microRNAs were miR-210 and miR-21. The results of this meta-analysis of human lung cancer microRNA expression profiling studies might provide some clues of the potential biomarkers in lung cancer. Further mechanistic and external validation studies are needed for their clinical significance and role in the development of lung cancer.