Search results for: de novo

Authors: Z. Babic, I. Veza, A. Balic, M. Crnjac

Abstract:

The linear programming model is sometimes difficult to apply in real business situations due to its assumption of proportionality. This paper shows an example of how to use De Novo programming approach instead of linear programming. In the De Novo programming, resources are not fixed like in linear programming but resource quantities depend only on available budget. Budget is a new, important element of the De Novo approach. Two different production situations are presented: increasing costs and quantity discounts of raw materials. The focus of this paper is on advantages of the De Novo approach in the optimization of production plan for production company which produces souvenirs made from famous stone from the island of Brac, one of the greatest islands from Croatia.

Keywords: De Novo Programming, production plan, stone souvenirs, variable prices.

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Authors: Mohamed Hafez, Georg Hausner

Abstract:

The full length mitochondrial small subunit ribosomal (mt-rns) gene has been characterized for Ophiostoma novo-ulmi subspecies americana. The gene was also characterized for Ophiostoma ulmi and a group II intron was noted in the mt-rns gene of O. ulmi. The insertion in the mt-rns gene is at position S952 and it is a group IIB1 intron that encodes a double motif LAGLIDADG homing endonuclease from an open reading frame located within a loop of domain III. Secondary structure models for the mt-rns RNA of O. novo-ulmi subsp. americana and O. ulmi were generated to place the intron within the context of the ribosomal RNA. The in vivo splicing of the O.ul-mS952 group II intron was confirmed with reverse transcription-PCR. A survey of 182 strains of Dutch Elm Diseases causing agents showed that the mS952 intron was absent in what is considered to be the more aggressive species O. novo-ulmi but present in strains of the less aggressive O. ulmi. This observation suggests that the O.ul-mS952 intron can be used as a PCR-based molecular marker to discriminate between O. ulmi and O. novo-ulmi subsp. americana.

Keywords: Dutch Elm Disease, group II introns, mtDNA, species identification

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

Abstract:

Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy

Abstract:

Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.

Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

Abstract:

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.

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Authors: Kuniyasu Soda

Abstract:

Surgical trauma seems to facilitate metastatic spread, although the underlying mechanisms are not known. Increased concentrations of polyamines (spermine and spermidine) in the blood seem to have associated with the enhanced malignant potential of cancer cells and decrease in anti-tumor immunity of cancer patients. In addition to de novo synthesis in rapidly growing cells such as normal regenerating cells and cancer cells, cells can take up polyamines from extra-cellular sources. We have shown that increased polyamine concentration results in decreases in cytokine production and expression of adhesion molecules involved in anti-tumor immunity, such as CD11a. And, immune cells in an environment with increased polyamine levels lose anti-tumor immune functions, such as lymphokine activated killer cell (LAK) activities. Because blood polyamine levels are increased in post-surgical patients, polyamine seems to have roles on post-traumatic tumor spread.

Keywords: Immune function, LAK, Polyamine, Surgical trauma.

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