http://www.hindawi.com The latest articles from Hindawi Publishing Corporation © 2013 , Hindawi Publishing Corporation . All rights reserved. Thu, 23 May 2013 08:27:23 +0000 http://www.hindawi.com/journals/ijg/2013/376454/ Insulin resistance has a central role in the pathogenesis of several metabolic diseases, including type 2 diabetes, obesity, glucose intolerance, metabolic syndrome, atherosclerosis, and cardiovascular diseases. Insulin resistance and related traits are likely to be caused by abnormalities in the genes encoding for proteins involved in the composite network of insulin-signaling; in this review we have focused our attention on genetic variants of insulin-signaling inhibitor molecules. These proteins interfere with different steps in insulin-signaling: ENPP1/PC-1 and the phosphatases PTP1B and PTPRF/LAR inhibit the insulin receptor activation; INPPL1/SHIP-2 hydrolyzes PI3-kinase products, hampering the phosphoinositide-mediated downstream signaling; and TRIB3 binds the serine-threonine kinase Akt, reducing its phosphorylation levels. While several variants have been described over the years for all these genes, solid evidence of an association with type 2 diabetes and related diseases seems to exist only for rs1044498 of the ENPP1 gene and for rs2295490 of the TRIB3 gene. However, overall the data recapitulated in this Review article may supply useful elements to interpret the results of novel, more technically advanced genetic studies; indeed it is becoming increasingly evident that genetic information on metabolic diseases should be interpreted taking into account the complex biological pathways underlying their pathogenesis. Carlo de Lorenzo, Annalisa Greco, Teresa Vanessa Fiorentino, Gaia Chiara Mannino, and Marta Letizia Hribal Copyright © 2013 Carlo de Lorenzo et al. All rights reserved. Mon, 20 May 2013 11:53:25 +0000 http://www.hindawi.com/journals/ijg/2013/269191/ Despite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, we de novo assembled 130 million mRNA-Seq reads into a total of 49,115 contigs. Searching public databases revealed that about 45% of the total contigs can be annotated as known proteins, indicating that some of the assembled contigs may have previously uncharacterized functions. Functional classification by KOG and GO showed that activities associated with metabolism are predominant in goat skin during anagen phase. Many signaling pathways was also created based on the mapping of assembled contigs to the KEGG pathway database, some of which have been previously demonstrated to have diverse roles in hair follicle and hair shaft formation. Furthermore, gene expression profiling of three skin types identified ~6,300 transcript-derived contigs that are differentially expressed. These genes mainly enriched in the functional cluster associated with cell cycle and cell division. The large contig catalogue as well as the genes which were differentially expressed in different skin types provide valuable candidates for further characterization of gene functions. Teng Xu, Xudong Guo, Hui Wang, Xiaoyuan Du, Xiaoyu Gao, and Dongjun Liu Copyright © 2013 Teng Xu et al. All rights reserved. Sun, 19 May 2013 11:35:34 +0000 http://www.hindawi.com/journals/ijg/2013/972852/ Salinity is one of the major abiotic stresses that affect crop productivity. Identification of the potential novel genes responsible for salt tolerance in barley will contribute to understanding the molecular mechanism of barley responses to salt stress. We compared changes in transcriptome between Hua 11 (a salt-tolerant genotype) and Hua 30 (a salt sensitive genotype) in response to salt stress at the seedling stage using barley cDNA microarrays. In total, 557 and 247 salt-responsive genes were expressed exclusively in the shoot and root tissue of the salt-tolerant genotype, respectively. Among these genes, a number of signal-related genes, transcription factors and compatible solutes were identified and some of these genes were carefully discussed. Notably, a LysM RLK was firstly found involved in salt stress response. Moreover, key enzymes in the pathways of jasmonic acid biosynthesis, lipid metabolism and indole-3-acetic acid homeostasis were specifically affected by salt stress in salt tolerance genotype. These salt-responsive genes and biochemical pathways identified in this study could provide further information for understanding the mechanisms of salt tolerance in barley. Runhong Gao, Ke Duan, Guimei Guo, Zhizhao Du, Zhiwei Chen, Liang Li, Ting He, Ruiju Lu, and Jianhua Huang Copyright © 2013 Runhong Gao et al. All rights reserved. Thu, 09 May 2013 14:14:29 +0000 http://www.hindawi.com/journals/ijg/2013/361327/ Bioinformatics is advanced from in-house computing infrastructure to cloud computing for tackling the vast quantity of biological data. This advance enables large number of collaborative researches to share their works around the world. In view of that, retrieving biological data over the internet becomes more and more difficult because of the explosive growth and frequent changes. Various efforts have been made to address the problems of data discovery and delivery in the cloud framework, but most of them suffer the hindrance by a MapReduce master server to track all available data. In this paper, we propose an alternative approach, called PRKad, which exploits a Peer-to-Peer (P2P) model to achieve efficient data discovery and delivery. PRKad is a Kademlia-based implementation with Round-Trip-Time (RTT) as the associated key, and it locates data according to Distributed Hash Table (DHT) and XOR metric. The simulation results exhibit that our PRKad has the low link latency to retrieve data. As an interdisciplinary application of P2P computing for bioinformatics, PRKad also provides good scalability for servicing a greater number of users in dynamic cloud environments. Chun-Hung Richard Lin, Chun-Hao Wen, Ying-Chih Lin, Kuang-Yuan Tung, Rung-Wei Lin, and Chun-Yuan Lin Copyright © 2013 Chun-Hung Richard Lin et al. All rights reserved. Wed, 08 May 2013 15:05:42 +0000 http://www.hindawi.com/journals/ijg/2013/257218/ Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches. Alessandra Traini, Massimo Iorizzo, Harpartap Mann, James M. Bradeen, Domenico Carputo, Luigi Frusciante, and Maria Luisa Chiusano Copyright © 2013 Alessandra Traini et al. All rights reserved. Wed, 08 May 2013 11:34:56 +0000 http://www.hindawi.com/journals/ijg/2013/305971/ Craniosynostosis is the premature fusion of the cranial vault sutures. We have previously described a colony of rabbits with a heritable pattern of nonsyndromic, coronal suture synostosis; however, the underlying genetic defect remains unknown. We now report a molecular analysis to determine if four genes implicated in human craniosynostosis, TWIST1 and fibroblast growth factor receptors 1–3 (FGFR1–3), could be the loci of the causative mutation in this unique rabbit model. Single nucleotide polymorphisms (SNPs) were identified within the Twist1, FGFR1, and FGFR2 genes, and the allelic patterns of these silent mutations were examined in 22 craniosynostotic rabbits. SNP analysis of the Twist1, FGFR1, and FGFR2 genes indicated that none were the locus of origin of the craniosynostotic phenotype. In addition, no structural mutations were identified by direct sequence analysis of Twist1 and FGFR3 cDNAs. These data indicate that the causative locus for heritable craniosynostosis in this rabbit model is not within the Twist1, FGFR1, and FGFR2 genes. Although a locus in intronic or flanking sequences of FGFR3 remains possible, no direct structural mutation was identified for FGFR3. Phillip H. Gallo, James J. Cray Jr., Emily L. Durham, Mark P. Mooney, Gregory M. Cooper, and Sandeep Kathju Copyright © 2013 Phillip H. Gallo et al. All rights reserved. Thu, 02 May 2013 15:35:32 +0000 http://www.hindawi.com/journals/ijg/2013/456356/ Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their variable genome sequences. This study investigates the infection processes in protein-protein interactions between hosts and NoVs. Protein-protein interactions were collected from related Pfam NoV domains. The related Pfam domains were accumulated incrementally from the protein domain interaction database. To examine the influence of domain intimacy, the 7 NoV domains were grouped by depth. The number of domain-domain interactions increased exponentially as the depth increased. Many protein-protein interactions were relevant; therefore, cloud techniques were used to analyze data because of their computational capacity. The infection relationship between hosts and NoVs should be used in clinical applications and drug design. Chuan-Ching Huang and Chuan Yi Tang Copyright © 2013 Chuan-Ching Huang and Chuan Yi Tang. All rights reserved. Thu, 02 May 2013 14:08:47 +0000 http://www.hindawi.com/journals/ijg/2013/832756/ Until recently, the apicomplexan parasites, Cryptosporidium hominis and C. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic and other pathways, and the local sequence identity between the genes of these two Cryptosporidium species. Our observations show that the phenotypic differences between C. hominis and C. parvum are not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host. Aurélien J. Mazurie, João M. Alves, Luiz S. Ozaki, Shiguo Zhou, David C. Schwartz, and Gregory A. Buck Copyright © 2013 Aurélien J. Mazurie et al. All rights reserved. Thu, 18 Apr 2013 13:40:56 +0000 http://www.hindawi.com/journals/ijg/2013/105108/ In order to be inherited in progeny generations, novel genes should originate in germ cells. Here, we suggest that the testes may play a special “catalyst” role in the birth and evolution of new genes. Cancer/testis antigen encoding genes (CT genes) are predominantly expressed both in testes and in a variety of tumors. By the criteria of evolutionary novelty, the CT genes are, indeed, novel genes. We performed homology searches for sequences similar to human CT in various animals and established that most of the CT genes are either found in humans only or are relatively recent in their origin. A majority of all human CT genes originated during or after the origin of Eutheria. These results suggest relatively recent origin of human CT genes and align with the hypothesis of the special role of the testes in the evolution of the gene families. Pavel Dobrynin, Ekaterina Matyunina, S. V. Malov, and A. P. Kozlov Copyright © 2013 Pavel Dobrynin et al. All rights reserved. Sun, 31 Mar 2013 09:03:18 +0000 http://www.hindawi.com/journals/ijg/2013/614923/ Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. Che-Lun Hung and Chun-Yuan Lin Copyright © 2013 Che-Lun Hung and Chun-Yuan Lin. All rights reserved. Wed, 27 Mar 2013 13:11:08 +0000 http://www.hindawi.com/journals/ijg/2013/670623/ A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based on a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium, E. coli K12 and C. crescenttus, we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily. Wenhong Tian and Nagiza F. Samatova Copyright © 2013 Wenhong Tian and Nagiza F. Samatova. All rights reserved. Tue, 26 Mar 2013 17:19:40 +0000 http://www.hindawi.com/journals/ijg/2013/145450/ Storage protein 2 (SP2) not only is an important source of energy for the growth and development of silkworm but also has inhibitory effects on cell apoptosis. Endothelial cell (EC) apoptosis is an important contributing factor in the development of atherosclerosis; therefore, study of the antiapoptotic activity of SP2 on ECs provides information related to the treatment of atherosclerosis and other cardiovascular diseases. In this study, the sp2 gene was cloned and expressed in Escherichia coli to produce a 6xHis-tagged fusion protein, which was then used to generate a polyclonal antibody. Western blot results revealed that SP2 levels were higher in the pupal stage and hemolymph of fifth-instar larvae but low in the egg and adult stages. Subcellular localization results showed that SP2 is located mainly on the cell membrane. In addition, a Bac-to-Bac system was used to construct a recombinant baculovirus for SP2 expression. The purified SP2 was then added to a culture medium for human umbilical vein ECs (HUVECs), which were exposed to staurosporine. A cell viability assay demonstrated that SP2 could significantly enhance the viability of HUVEC. Furthermore, both ELISA and flow cytometry results indicated that SP2 has anti-apoptotic effects on staurosporine-induced HUVEC apoptosis. Wei Yu, Meihui Wang, Hanming Zhang, Yanping Quan, and Yaozhou Zhang Copyright © 2013 Wei Yu et al. All rights reserved. Mon, 25 Mar 2013 08:23:37 +0000 http://www.hindawi.com/journals/ijg/2013/439681/ Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. Che-Lun Hung and Yaw-Ling Lin Copyright © 2013 Che-Lun Hung and Yaw-Ling Lin. All rights reserved. Tue, 12 Mar 2013 15:00:09 +0000 http://www.hindawi.com/journals/ijg/2013/910321/ Heritable and nonheritable factors play a role in multiple sclerosis, but their effect size appears too small, explaining relatively little about disease etiology. Assuming that the factors that trigger the onset of the disease are, to some extent, also those that generate its remissions and relapses, we attempted to model the erratic behaviour of the disease course as observed on a dataset containing the time series of relapses and remissions of 70 patients free of disease-modifying therapies. We show that relapses and remissions follow exponential decaying distributions, excluding periodic recurrences and confirming that relapses manifest randomly in time. It is found that a mechanistic model with a random forcing describes in a satisfactory manner the occurrence of relapses and remissions, and the differences in the length of time spent in each one of the two states. This model may describe how interactions between “soft” etiologic factors occasionally reach the disease threshold thanks to comparably small external random perturbations. The model offers a new context to rethink key problems such as “missing heritability” and “hidden environmental structure” in the etiology of complex traits. Isabella Bordi, Renato Umeton, Vito A. G. Ricigliano, Viviana Annibali, Rosella Mechelli, Giovanni Ristori, Francesca Grassi, Marco Salvetti, and Alfonso Sutera Copyright © 2013 Isabella Bordi et al. All rights reserved. Mon, 11 Mar 2013 10:17:22 +0000 http://www.hindawi.com/journals/ijg/2013/261730/ We characterized the male-specific region on the Y chromosome of rainbow trout, which contains both sdY (the sex-determining gene) and the male-specific genetic marker, OmyY1. Several clones containing the OmyY1 marker were screened from a BAC library from a YY clonal line and found to be part of an 800 kb BAC contig. Using fluorescence in situ hybridization (FISH), these clones were localized to the end of the short arm of the Y chromosome in rainbow trout, with an additional signal on the end of the X chromosome in many cells. We sequenced a minimum tiling path of these clones using Illumina and 454 pyrosequencing. The region is rich in transposons and rDNA, but also appears to contain several single-copy protein-coding genes. Most of these genes are also found on the X chromosome; and in several cases sex-specific SNPs in these genes were identified between the male (YY) and female (XX) homozygous clonal lines. Additional genes were identified by hybridization of the BACs to the cGRASP salmonid 4x44K oligo microarray. By BLASTn evaluations using hypothetical transcripts of OmyY1-linked candidate genes as query against several EST databases, we conclude at least 12 of these candidate genes are likely functional, and expressed. Ruth B. Phillips, Jenefer J. DeKoning, Joseph P. Brunelli, Joshua J. Faber-Hammond, John D. Hansen, Kris A. Christensen, Suzy C. P. Renn, and Gary H. Thorgaard Copyright © 2013 Ruth B. Phillips et al. All rights reserved. Sun, 10 Mar 2013 13:18:49 +0000 http://www.hindawi.com/journals/ijg/2013/678969/ Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future. H. C. Rawal, N. K. Singh, and T. R. Sharma Copyright © 2013 H. C. Rawal et al. All rights reserved. Sun, 10 Mar 2013 09:54:21 +0000 http://www.hindawi.com/journals/ijg/2013/387594/ The SUPT16H gene known as FACTP140 is required for the transcription of other genes. For transcription, genes need to be complexed with accessory factors, including transcription factors and RNA polymerase II. One such factor, FACT, interacts with histones H2A/H2B for nucleosome disassembly and transcription elongation. The SUPT16H gene has a transcript and many expressed sequence tags (ESTs). We were especially interested in an MaLR-derived transcript (EST, BX333035) that included a new exon introduced by a transposable element, a mammalian apparent LTR retrotransposon (MaLR). The MaLR was detected ranging from humans to galagos, indicating the MaLR in the SUPT16H gene is integrated into the primate ancestor genome. A new exon was created by alternative donor site provided by the MaLR. The original transcript and the MaLR-derived transcript were expressed in various human, rhesus monkey, and other primate tissues. Additionally, we identified a new alternative transcript that included the MaLR, but there was no significant difference in the expression of the original transcript and the MaLR-derived transcript. Interestingly, the new alternative transcript and the MaLR-derived transcript had the MaLR sequence in the new exon, but they had different structures by adopting different splice sites. From this study, we verified transposable elements that contributed to transcriptome diversity. Min-In Bae, Yun-Ji Kim, Ja-Rang Lee, Yi-Deun Jung, and Heui-Soo Kim Copyright © 2013 Min-In Bae et al. All rights reserved. Sun, 03 Mar 2013 13:42:00 +0000 http://www.hindawi.com/journals/ijg/2013/671316/ Introns comprise a considerable portion of eukaryotic genomes; however, their evolution is understudied. Numerous works of the last years largely disagree on many aspects of intron evolution. Interpretation of these differences is hindered because different algorithms and taxon sampling strategies were used. Here, we present the first attempt of a systematic evaluation of the effects of taxon sampling on popular intron evolution estimation algorithms. Using the “taxon jackknife” method, we compared the effect of taxon sampling on the behavior of intron evolution inferring algorithms. We show that taxon sampling can dramatically affect the inferences and identify conditions where algorithms are prone to systematic errors. Presence or absence of some key species is often more important than the taxon sampling size alone. Criteria of representativeness of the taxonomic sampling for reliable reconstructions are outlined. Presence of the deep-branching species with relatively high intron density is more important than sheer number of species. According to these criteria, currently available genomic databases are representative enough to provide reliable inferences of the intron evolution in animals, land plants, and fungi, but they underrepresent many groups of unicellular eukaryotes, including the well-studied Alveolata. Mikhail A. Nikitin and Vladimir V. Aleoshin Copyright © 2013 Mikhail A. Nikitin and Vladimir V. Aleoshin. All rights reserved. Thu, 27 Dec 2012 12:51:55 +0000 http://www.hindawi.com/journals/ijg/2012/628204/ Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon. Anti Vasemägi, Jan Nilsson, Philip McGinnity, Tom Cross, Patrick O’Reilly, Brian Glebe, Bo Peng, Paul Ragnar Berg, and Craig Robert Primmer Copyright © 2012 Anti Vasemägi et al. All rights reserved. Wed, 19 Dec 2012 13:08:23 +0000 http://www.hindawi.com/journals/ijg/2012/783138/ Designing primers and probes for polymerase chain reaction (PCR) is a preliminary and critical step that requires the identification of highly conserved regions in a given set of sequences. This task can be challenging if the targeted sequences display a high level of diversity, as frequently encountered in microbiologic studies. We developed Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes based on multiple aligned sequences. This tool can be used for the purpose of real-time and conventional PCR and can deal efficiently with large sets of sequences of a large size. Haitham Sobhy and Philippe Colson Copyright © 2012 Haitham Sobhy and Philippe Colson. All rights reserved. Wed, 21 Nov 2012 10:50:47 +0000 http://www.hindawi.com/journals/ijg/2012/968267/ Asthma has been an inflammatory disorder accompanied by tissue remodeling and protease-antiprotease imbalance in lungs. The SNPs of alpha-1 antitrypsin (α1AT) and tissue inhibitor of metalloproteinase-1 (TIMP-1) genes were studied for their association with asthma. Genotyping of α1AT and TIMP-1 genes was performed in 202 asthmatics and 204 controls. Serum levels of α1AT, TIMP-1 and cytokines were estimated to find if the interplay between genotypes and cellular biomarkers determines the pathogenesis of asthma. The analysis of results showed significantly low level of α1AT in the serum of asthmatics as compared to controls (), whereas cytokines were elevated in patients. No significant difference was observed in the concentration of TIMP-1 in patients and controls. Genotyping led to the identification of 3 SNPs (Val213Ala, Glu363Lys, and Glu376Asp) in α1AT gene. The novel SNP Glu363Lys of α1AT was found to be associated with asthma (). The analysis of TIMP-1 gene showed the occurrence of seven SNPs, including a novel intronic SNP at base G3774A. The allele frequency of G3774A and Phe124Phe was significantly higher in asthmatics as compared to controls. Thus, the SNP Glu363Lys of α1AT and G3774A and Phe124Phe of TIMP-1 could be important genetic markers for use in better management of the disease. Manish Kumar, D. P. Bhadoria, Koushik Dutta, Mitesh Kumar F., Bharat Singh, Seema Singh, Anil K. Chhillar, D. Behera, and G. L. Sharma Copyright © 2012 Manish Kumar et al. All rights reserved. Sun, 18 Nov 2012 16:01:38 +0000 http://www.hindawi.com/journals/ijg/2012/678761/ Transposases (Tnps) are enzymes that participate in the movement of insertion sequences (ISs) within and between genomes. Genes that encode Tnps are amongst the most abundant and widely distributed genes in nature. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of ISs. This need prompted us to develop a web service, termed TnpPred for Tnp discovery. It provides better sensitivity and specificity for Tnp predictions than given by currently available programs as determined by ROC analysis. TnpPred should be useful for improving genome annotation. The TnpPred web service is freely available for noncommercial use. Gonzalo Riadi, Cristobal Medina-Moenne, and David S. Holmes Copyright © 2012 Gonzalo Riadi et al. All rights reserved. Wed, 26 Sep 2012 15:35:49 +0000 http://www.hindawi.com/journals/ijg/2012/912843/ Porphyra yezoensis Ueda is an intertidal marine red algae that has received increasing attention as a model organism owing to its important role in biological research and the agronomic industry. The two generations of Porphyra yezoensis, the sporophyte and the gametophyte, have the same genome but show great differences in many aspects, including structural features, habitat, and gene expression. To identify miRNAs and their probable roles in P. yezoensis development, we constructed and sequenced libraries of small RNA from P. yezoensis sporophytes and gametophytes. The sequencing data were analyzed, and 14 miRNAs were identified, with only one common to these two samples. Our results show that P. yezoensis has a complex small RNA processing system containing novel miRNAs that have no identifiable homolog in other organisms. These miRNAs might have important regulatory roles in development of the different generations of P. yezoensis. Linwen He, Aiyou Huang, Songdong Shen, Jianfeng Niu, and Guangce Wang Copyright © 2012 Linwen He et al. All rights reserved. Wed, 26 Sep 2012 11:17:15 +0000 http://www.hindawi.com/journals/ijg/2012/546930/ Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins. Xun Yue, XiangYu Zhao, YuKui Fei, and Xiansheng Zhang Copyright © 2012 Xun Yue et al. All rights reserved. Mon, 17 Sep 2012 11:11:26 +0000 http://www.hindawi.com/journals/ijg/2012/538639/ Lucia Latella, Daniela Palacios, Sonia Forcales, and Pier Lorenzo Puri Copyright © 2012 Lucia Latella et al. All rights reserved. Thu, 06 Sep 2012 09:54:29 +0000 http://www.hindawi.com/journals/ijg/2012/752867/ Members of the Burkholderia family occupy diverse ecological niches. In pathogenic family members, glycan-associated proteins are often linked to functions that include virulence, protein conformation maintenance, surface recognition, cell adhesion, and immune system evasion. Comparative analysis of available Burkholderia genomes has revealed a core set of 178 glycan-associated proteins shared by all Burkholderia of which 68 are homologous to known essential genes. The genome sequence comparisons revealed insights into species-specific gene acquisitions through gene transfers, identified an S-layer protein, and proposed that significantly reactive surface proteins are associated to sugar moieties as a potential means to circumvent host defense mechanisms. The comparative analysis using a curated database of search queries enabled us to gain insights into the extent of conservation and diversity, as well as the possible virulence-associated roles of glycan-associated proteins in members of the Burkholderia spp. The curated list of glycan-associated proteins used can also be directed to screen other genomes for glycan-associated homologs. Hui San Ong, Rahmah Mohamed, and Mohd Firdaus-Raih Copyright © 2012 Hui San Ong et al. All rights reserved. Thu, 06 Sep 2012 08:27:47 +0000 http://www.hindawi.com/journals/ijg/2012/759407/ Skeletal myogenesis depends on the strict regulation of the expression of various gene subsets. Therefore, the understanding of genome wide gene regulation is imperative for elucidation of skeletal myogenesis. In recent years, systems approach has contributed to the understanding of various biological processes. Our group recently revealed the critical genome network of skeletal myogenesis by using a novel systems approach combined with whole-mount in situ hybridization (WISH) database, high-throughput screening, and microarray analysis. In this paper, we introduce our systems approach for understanding the myogenesis regulatory network and describe the advantages of systems approach. Yoshiaki Ito, Tomohiro Kayama, and Hiroshi Asahara Copyright © 2012 Yoshiaki Ito et al. All rights reserved. Sun, 26 Aug 2012 13:34:03 +0000 http://www.hindawi.com/journals/ijg/2012/564381/ B cell development is a multistep process that is tightly regulated at the transcriptional level. In recent years, investigators have shed light on the transcription factor networks involved in all the differentiation steps comprising B lymphopoiesis. The interplay between transcription factors and the epigenetic machinery involved in establishing the correct genomic landscape characteristic of each cellular state is beginning to be dissected. The participation of “epigenetic regulator-transcription factor” complexes is also crucial for directing cells during reprogramming into pluripotency or lineage conversion. In this context, greater knowledge of epigenetic regulation during B cell development, transdifferentiation, and reprogramming will enable us to understand better how epigenetics can control cell lineage commitment and identity. Herein, we review the current knowledge about the epigenetic events that contribute to B cell development and reprogramming. Bruna Barneda-Zahonero, Lidia Roman-Gonzalez, Olga Collazo, Tokameh Mahmoudi, and Maribel Parra Copyright © 2012 Bruna Barneda-Zahonero et al. All rights reserved. Wed, 22 Aug 2012 13:37:37 +0000 http://www.hindawi.com/journals/ijg/2012/376706/ A number of empirical Bayes models (each with different statistical distribution assumptions) have now been developed to analyze differential DNA methylation using high-density oligonucleotide tiling arrays. However, it remains unclear which model performs best. For example, for analysis of differentially methylated regions for conservative and functional sequence characteristics (e.g., enrichment of transcription factor-binding sites (TFBSs)), the sensitivity of such analyses, using various empirical Bayes models, remains unclear. In this paper, five empirical Bayes models were constructed, based on either a gamma distribution or a log-normal distribution, for the identification of differential methylated loci and their cell division—(1, 3, and 5) and drug-treatment-(cisplatin) dependent methylation patterns. While differential methylation patterns generated by log-normal models were enriched with numerous TFBSs, we observed almost no TFBS-enriched sequences using gamma assumption models. Statistical and biological results suggest log-normal, rather than gamma, empirical Bayes model distribution to be a highly accurate and precise method for differential methylation microarray analysis. In addition, we presented one of the log-normal models for differential methylation analysis and tested its reproducibility by simulation study. We believe this research to be the first extensive comparison of statistical modeling for the analysis of differential DNA methylation, an important biological phenomenon that precisely regulates gene transcription. Mingxiang Teng, Yadong Wang, Seongho Kim, Lang Li, Changyu Shen, Guohua Wang, Yunlong Liu, Tim H. M. Huang, Kenneth P. Nephew, and Curt Balch Copyright © 2012 Mingxiang Teng et al. All rights reserved. Thu, 16 Aug 2012 11:10:37 +0000 http://www.hindawi.com/journals/ijg/2012/653174/ Genetic robustness refers to a compensatory mechanism for buffering deleterious mutations or environmental variations. Gene duplication has been shown to provide such functional backups. However, the overall contribution of duplication-based buffering for genetic robustness is rather small. In this study, we investigated whether transcriptional compensation also exists among genes that share similar functions without sequence homology. A set of nonhomologous synthetic-lethal gene pairs was assessed by using a coexpression network, protein-protein interactions, and other types of genetic interactions in yeast. Our results are notably different from those of previous studies on buffering paralogs. The low expression similarity and the conditional coexpression alone do not play roles in identifying the functionally compensatory genes. Additional properties such as synthetic-lethal interaction, the ratio of shared common interacting partners, and the degree of coregulation were, at least in part, necessary to extract functional compensatory genes. Our network-based approach is applicable to select several well-documented cases of compensatory gene pairs and a set of new pairs. The results suggest that transcriptional reprogramming plays a limited role in functional compensation among nonhomologous genes. Our study aids in understanding the mechanism and features of functional compensation more in detail. Chien-Hua Peng, Shu-Hsi Lin, Shih-Chi Peng, Ping-Chiang Lyu, Masanori Arita, and Chuan-Yi Tang Copyright © 2012 Chien-Hua Peng et al. All rights reserved.