bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-level identification, gene expression, and comparative analysis of porcine β-defensin genes
Authors: Choi Min-Kyeung , Le Minh Thong , Nguyen Dinh Truong , Choi Hojun , Kim Won , Kim Jin-Hoi , Chun Jungwan , Hyeon Jiyeon , Seo Kunho , Park Chankyu 
Published: November 2012

Abstract

Background
Beta-defensins (β-defensins) are innate immune peptides with evolutionary conservation across a wide range of species and has been suggested to play important roles in innate immune reactions against pathogens. However, the complete β-defensin repertoire in the pig has not been fully addressed.

Result
A BLAST analysis was performed against the available pig genomic sequence in the NCBI database to identify β-defensin-related sequences using previously reported β-defensin sequences of pigs, humans, and cattle. The porcine β-defensin gene clusters were mapped to chromosomes 7, 14, 15 and 17. The gene expression analysis of 17 newly annotated porcine β-defensin genes across 15 tissues using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) showed differences in their tissue distribution, with the kidney and testis having the largest pBD expression repertoire. We also analyzed single nucleotide polymorphisms (SNPs) in the mature peptide region of pBD genes from 35 pigs of 7 breeds. We found 8 cSNPs in 7 pBDs.

Conclusion
We identified 29 porcine β-defensin (pBD) gene-like sequences, including 17 unreported pBDs in the porcine genome. Comparative analysis of β-defensin genes in the pig genome with those in human and cattle genomes showed structural conservation of β-defensin syntenic regions among these species.
A de novo germline mutation in MYH7 causes a progressive dominant myopathy in pigs
Authors: Murgiano Leonardo , Tammen Imke , Harlizius Barbara , Drögemüller Cord 
Published: November 2012

Abstract

Background
About 9% of the offspring of a clinically healthy Piétrain boar named ‘Campus’ showed a progressive postural tremor called Campus syndrome (CPS). Extensive backcross experiments suggested a dominant mode of inheritance, and the founder boar was believed to be a gonadal mosaic. A genome-scan mapped the disease-causing mutation to an 8 cM region of porcine chromosome 7 containing the MHY7 gene. Human distal myopathy type 1 (MPD1), a disease partially resembling CPS in pigs, has been associated with mutations in the MYH7 gene.

Results
The porcine MYH7 gene structure was predicted based on porcine reference genome sequence, porcine mRNA, and in comparison to the human ortholog. The gene structure was highly conserved with the exception of the first exon. Mutation analysis of a contiguous genomic interval of more than 22 kb spanning the complete MYH7 gene revealed an in-frame insertion within exon 30 of MYH7 (c.4320_4321insCCCGCC) which was perfectly associated with the disease phenotype and confirmed the dominant inheritance. The mutation is predicted to insert two amino acids (p.Ala1440_Ala1441insProAla) in a very highly conserved region of the myosin tail. The boar ‘Campus’ was shown to be a germline and somatic mosaic as assessed by the presence of the mutant allele in seven different organs.

Conclusion
This study illustrates the usefulness of recently established genomic resources in pigs. We have identified a spontaneous mutation in MYH7 as the causative mutation for CPS. This paper describes the first case of a disorder caused by a naturally occurring mutation in the MYH7 gene of a non-human mammalian species. Our study confirms the previous classification as a primary myopathy and provides a defined large animal model for human MPD1. We provide evidence that the CPS mutation occurred during the early development of the boar ‘Campus’. Therefore, this study provides an example of germline mosaicism with an asymptomatic founder.
Development of a genetic tool for product regulation in the diverse British pig breed market
Authors: Wilkinson Samantha , Archibald Alan L , Haley Chris S , Megens Hendrik-Jan , Crooijmans Richard PMA , Groenen Martien AM , Wiener Pamela , Ogden Rob 
Published: November 2012

Abstract

Background
The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom.

Results
The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average FST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity.

Conclusion
The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.
The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates
Authors: Irisarri Iker , Mauro Diego San , Abascal Federico , Ohler Annemarie , Vences Miguel , Zardoya Rafael 
Published: November 2012

Abstract

Background
Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians.

Results
We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia.

Conclusions
Through the analysis of the selection coefficient (ω) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.
PMRD: a curated database for genes and mutants involved in plant male reproduction
Authors: Cui Xiao , Wang Qiudao , Yin Wenzhe , Xu Huayong , Wilson Zoe A , Wei Chaochun , Pan Shenyuan , Zhang Dabing 
Published: November 2012

Abstract

Background
Male reproduction is an essential biological event in the plant life cycle separating the diploid sporophyte and haploid gametophyte generations, which involves expression of approximately 20,000 genes. The control of male reproduction is also of economic importance for plant breeding and hybrid seed production. With the advent of forward and reverse genetics and genomic technologies, a large number of male reproduction-related genes have been identified. Thus it is extremely challenging for individual researchers to systematically collect, and continually update, all the available information on genes and mutants related to plant male reproduction. The aim of this study is to manually curate such gene and mutant information and provide a web-accessible resource to facilitate the effective study of plant male reproduction.

Description
Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction. It is based upon literature and biological databases and includes 506 male sterile genes and 484 mutants with defects of male reproduction from a variety of plant species. Based on Gene Ontology (GO) annotations and literature, information relating to a further 3697 male reproduction related genes were systematically collected and included, and using in text curation, gene expression and phenotypic information were captured from the literature. PMRD provides a web interface which allows users to easily access the curated annotations and genomic information, including full names, symbols, locations, sequences, expression patterns, functions of genes, mutant phenotypes, male sterile categories, and corresponding publications. PMRD also provides mini tools to search and browse expression patterns of genes in microarray datasets, run BLAST searches, convert gene ID and generate gene networks. In addition, a Mediawiki engine and a forum have been integrated within the database, allowing users to share their knowledge, make comments and discuss topics.

Conclusion
PMRD provides an integrated link between genetic studies and the rapidly growing genomic information. As such this database provides a global view of plant male reproduction and thus aids advances in this important area.
Molecular characterization of rotavirus isolates from select Canadian pediatric hospitals
Authors: McDermid Andrew , Le Saux Nicole , Grudeski Elsie , Bettinger Julie A , Manguiat Kathy , Halperin Scott A , MacDonald Lily , Déry Pierre , Embree Joanne , Vaudry Wendy , Booth Timothy F ,   Members of the Canadian Immunization Monitoring Program, Active (IMPACT)
Published: November 2012

Abstract

Background
We report the first multi-site rotavirus genotype analysis in Canada. Prior to this study, there was a dearth of rotavirus G and P genotyping data in Canada. Publically funded universal rotavirus vaccination in Canada started in 2011 and has been introduced by four provinces to date. Uptake of rotavirus vaccines in Canada prior to 2012 has been very limited. The aim of this study was to describe the genotypes of rotavirus strains circulating in Canada prior to widespread implementation of rotavirus vaccine by genotyping samples collected from selected paediatric hospitals. Secondly we identified rotavirus strains that differed genetically from those included in the vaccines and which could affect vaccine effectiveness.

Methods
Stool specimens were collected by opportunity sampling of children with gastroenteritis who presented to emergency departments. Samples were genotyped for G (VP7) genotypes and P (VP4) genotypes by hemi-nested multiplex PCR methods. Phylogenetic analysis was carried out on Canadian G9 strains to investigate their relationship to G9 strains that have circulated in other regions of the world.

Results
348 samples were collected, of which 259 samples were rotavirus positive and genotyped. There were 34 rotavirus antigen immunoassay negative samples genotyped using PCR-based methods. Over the four rotavirus seasons, 174 samples were G1P[8], 45 were G3P[8], 22 were G2P[4], 13 were G9P[8], 3 were G4P[8] and 2 were G9P[4]. Sequence analysis showed that all Canadian G9 isolates are within lineage III.

Conclusions
Although a limited number of samples were obtained from a median of 4 centres during the 4 years of the study, it appears that currently approved rotavirus vaccines are well matched to the rotavirus genotypes identified at these hospitals. Further surveillance to monitor the emergence of rotavirus genotypes in Canada is warranted.
APOA5 Q97X Mutation Identified through homozygosity mapping causes severe hypertriglyceridemia in a Chilean consanguineous family
Authors: Dussaillant Catalina , Serrano Valentina , Maiz Alberto , Eyheramendy Susana , Cataldo Luis Rodrigo , Chavez Matías , Smalley Susan V , Fuentes Marcela , Rigotti Attilio , Rubio Lorena , Lagos Carlos F , Martinez José Alfredo , Santos José Luis 
Published: November 2012

Abstract

Background
Severe hypertriglyceridemia (HTG) has been linked to defects in LPL, APOC2, APOA5, LMF1 and GBIHBP1 genes. However, a number of severe HTG cases are probably caused by as yet unidentified mutations. Very high triglyceride plasma levels (>112 mmol/L at diagnosis) were found in two sisters of a Chilean consanguineous family, which is strongly suggestive of a recessive highly penetrant mutation. The aim of this study was to determine the genetic locus responsible for the severe HTG in this family.

Methods
We carried out a genome-wide linkage study with nearly 300,000 biallelic markers (Illumina Human CytoSNP-12 panel). Using the homozygosity mapping strategy, we searched for chromosome regions with excess of homozygous genotypes in the affected cases compared to non-affected relatives.

Results
A large homozygous segment was found in the long arm of chromosome 11, with more than 2,500 consecutive homozygous SNP shared by the proband with her affected sister, and containing the APOA5/A4/C3/A1 cluster. Direct sequencing of the APOA5 gene revealed a known homozygous nonsense Q97X mutation (p.Gln97Ter) found in both affected sisters but not in non-affected relatives nor in a sample of unrelated controls.

Conclusion
The Q97X mutation of the APOA5 gene in homozygous status is responsible for the severe hypertriglyceridemia in this family. We have shown that homozygosity mapping correctly pinpointed the genomic region containing the gene responsible for severe hypertriglyceridemia in this consanguineous Chilean family.
Percutaneous treatment of a aorto-caval fistula in a old high risk patient
Authors: Rapacciuolo Antonio , De Angelis Maria Carmen , di Pietro Elisa , Puglia Roberto , Di Tommaso Ettore , Ruggiero Danilo , Amato Bruno , Iannelli Gabriele 
Published: November 2012

Abstract

Background
To remark the feasibility of endovascular treatment of an aorto-caval fistula in a old high risk patient with “hostile” abdomen for previous surgeries.

Methods
In September 2009 a 81-years-old patient was admitted in emergency at our department because of abdominal pain and massive oedema of the lower extremities associated to dyspnoea (New York Heart Association (NYHA) functional class III). A CT scan showed an aorto-caval fistula involving the abdominal aorta below the renal arteries. This abnormal communication was likely due to the previous abdominal surgeries, was complicated by occlusion of the inferior vena cava at the diaphragm and was responsible for the massive oedema of the lower extremities. Because of unstable conditions and hostile abdomen the patient was considered unfit for conventional surgery and an endovascular approach was planned. After unsuccessful attempt by positioning of an Amplatzer vascular ring into the fistula, a Medtronic covered stent-grafts were implanted from the renal arteries to the both common iliac arteries. The patient had an impressive improvement characterized by a 18 Kg weight loss and a complete restoration of the functional capacity (from NYHA class III to NYHA class I) associated to a complete resolution of the lower extremities oedema as confirmed at the a month-CT-scan.

Conclusion
Endovascular surgery of aorto-caval fistula represents a good option in alternative to conventional surgery mostly in old high risk patient.
A novel strategy for efficient production of anti-V3 human scFvs against HIV-1 clade C
Authors: Kumar Rajesh , Andrabi Raiees , Tiwari Ashutosh , Prakash Somi Sankaran , Wig Naveet , Dutta Durgashree , Sankhyan Anurag , Khan Lubina , Sinha Subrata , Luthra Kalpana 
Published: November 2012

AbstractBackgroundProduction of human monoclonal antibodies that exhibit broadly neutralizing activity is needed for preventing HIV-1 infection, however only a few such antibodies have been generated till date. Isolation of antibodies by the hybridoma technology is a cumbersome process with fewer yields. Further, the loss of unstable or slowly growing clones which may have unique binding specificities often occurs during cloning and propagation and the strongly positive clones are often lost. This has been avoided by the process described in this paper, wherein, by combining the strategy of EBV transformation and recombinant DNA technology, we constructed human single chain variable fragments (scFvs) against the third variable region (V3) of the clade C HIV-1 envelope.ResultsAn antigen specific phage library of 7000 clones was constructed from the enriched V3- positive antibody secreting EBV transformed cells. By ligation of the digested scFv DNA into phagemid vector and bio panning against the HIV-1 consensus C and B V3 peptides followed by random selection of 40 clones, we identified 15 clones that showed V3 reactivity in phage ELISA. DNA fingerprinting analysis and sequencing showed that 13 out of the 15 clones were distinct. Expression of the positive clones was tested by SDS-PAGE and Western blot. All the 13 anti-V3 scFvs showed cross-reactivity against both the clade C and B V3 peptides and did not show any reactivity against other unrelated peptides in ELISA. Preliminary neutralization assays indicated varying degrees of neutralization of clade C and B viruses. EBV transformation, followed by antigen selection of lines to identify specific binders, enabled the selection of phage from un-cloned lines for scFv generation, thus avoiding the problems of hybridoma technology. Moreover, as the clones were pretested for antigen binding, a comparatively small library sufficed for the selection of a considerable number of unique antigen binding phage. After selection, the phage clones were propagated in a clonal manner.ConclusionsThis strategy can be efficiently used and is cost effective for the generation of diverse recombinant antibodies. This is the first study to generate anti-V3 scFvs against HIV-1 Clade C.
Piper betle shows antioxidant activities, inhibits MCF-7 cell proliferation and increases activities of catalase and superoxide dismutase
Authors: Abrahim Noor Nazirahanie , Kanthimathi M S , Abdul-Aziz Azlina 
Published: November 2012

AbstractBackgroundBreast cancer is the most common form of cancer and the focus on finding chemotherapeutic agents have recently shifted to natural products.Piper betleis a medicinal plant with various biological activities. However, not much data is available on the anti-cancer effects ofP. betleon breast cancer. Due to the current interest in the potential effects of antioxidants from natural products in breast cancer treatment, we investigated the antioxidant activities of the leaves ofP. betleand its inhibitory effect on the proliferation of the breast cancer cell line, MCF-7.MethodsThe leaves ofP. betlewere extracted with solvents of varying polarities (water, methanol, ethyl acetate and hexane) and their phenolic and flavonoid content were determined using colorimetric assays. Phenolic composition was characterized using HPLC. Antioxidant activities were measured using FRAP, DPPH, superoxide anion, nitric oxide and hyroxyl radical scavenging assays. Biological activities of the extracts were analysed using MTT assay and antioxidant enzyme (catalase, superoxide dismutase, glutathione peroxidase) assays in MCF-7 cells.ResultsOverall, the ethyl acetate extract showed the highest ferric reducing activity and radical scavenging activities against DPPH, superoxide anion and nitric oxide radicals. This extract also contained the highest phenolic content implying the potential contribution of phenolics towards the antioxidant activities. HPLC analyses revealed the presence of catechin, morin and quercetin in the leaves. The ethyl acetate extract also showed the highest inhibitory effect against the proliferation of MCF-7 cells (IC50=65 μg/ml). Treatment of MCF-7 cells with the plant extract increased activities of catalase and superoxide dismutase.ConclusionsEthyl acetate is the optimal solvent for the extraction of compounds with antioxidant and anti-proliferative activities. The increased activities of catalase and superoxide dismutase in the treated cells could alter the antioxidant defense system, potentially contributing towards the anti-proliferative effect. There is great potential for the ethyl acetate extract ofP. betleleaf as a source of natural antioxidants and to be developed as therapeutics in cancer treatment.