In this study, we tested the NuGEN Ovation RNA-Seq System for library preparation followed by nex... more In this study, we tested the NuGEN Ovation RNA-Seq System for library preparation followed by next-generation sequencing on an Illumina GAIIx. The cDNA product of the NuGEN kit may have significant amounts of ssDNA with hairpin structures that are generated during the amplification process. These structures interfere with efficient downstream end repair, A-tailing, and adapter ligation, all standard steps in post-amplification sequencing library construction. We were able to increase the efficiency of sequencing library yields 4- to 6-fold or greater by treatment of NuGEN-amplified cDNA product with the single-strand endonuclease S1. These results suggest that this treatment effectively cleaves hairpin structures generated during amplification that are resistant to the standard enzyme cocktails used for the end-repair step.
Proteins Structure Function and Bioinformatics, Nov 1, 1998
We present a computational approach for predicting structures of ligand-protein complexes and ana... more We present a computational approach for predicting structures of ligand-protein complexes and analyzing binding energy landscapes that combines Monte Carlo simulated annealing technique to determine the ligand bound conformation with the dead-end elimination algorithm for side-chain optimization of the protein active site residues. Flexible ligand docking and optimization of mobile protein side-chains have been performed to predict structural effects in the V32I/I47V/V82I HIV-1 protease mutant bound with the SB203386 ligand and in the V82A HIV-1 protease mutant bound with the A77003 ligand. The computational structure predictions are consistent with the crystal structures of these ligand-protein complexes. The emerging relationships between ligand docking and side-chain optimization of the active site residues are rationalized based on the analysis of the ligand-protein binding energy landscape.
Using a focused glycan-gene microarray, we compared the glycosyltransferase (GT) and sulfotransfe... more Using a focused glycan-gene microarray, we compared the glycosyltransferase (GT) and sulfotransferase gene expression profiles of human monocytes, dendritic cells (DCs) and macrophages (Mphis), isolated or differentiated from the same donors. Microarray analysis indicated that monocytes express transcripts for a full set of enzymes involved in the biosynthesis of multi-multiantennary branched N-glycans, potentially elongated by poly-N-acetyl-lactosamine chains, and of mucin-type Core 1 and Core 2 sialylated O-glycans. Monocytes also express genes involved in the biosynthesis and modification of glycosaminoglycans, but display a limited expression of GTs implicated in glycolipid synthesis. Among genes expressed in monocytes (90 out of 175), one third is significantly modulated in DCs and Mphi respectively, most of them being increased in both cell types relative to monocytes. These changes might potentially enforce the capacity of differentiated cells to synthesize branched N-glycans...
The number of circulating B-cells in peripheral blood plateaus between 2 and 24 months of age, an... more The number of circulating B-cells in peripheral blood plateaus between 2 and 24 months of age, and thereafter declines gradually. How this reflects the kinetics of the precursor B-cell pool in the bone marrow is of clinical interest, but has not been studied thoroughly in humans. The authors analyzed bone marrow (n = 37) from healthy children and adults (flow cytometry) searching for age-related changes in the total precursor B-cell compartment. In an age-matched cohort (n = 25) they examined age-related global gene expression changes (Affymetrix) in unsorted bone marrow with special reference to the recombination activating gene 1, RAG1. Subsequently, they searched the entire gene set for transcripts correlating to the RAG1 profile to discover other known and possibly new precursor B-cell related transcripts. Both methods disclosed a marked, transient increase of total precursor B-cells at 6-20 months, followed by a rapid decrease confined to the first 2 years. The decline thereafter was considerably slower, but continued until adulthood. The relative composition of total precursor B-cells, however, did not change significantly with age. The authors identified 54 genes that were highly correlated to the RAG1 profile (r >or= .9, p < 1 x 10(-8)). Of these 54 genes, 15 were characteristically B-lineage associated like CD19, CD79, VPREB, EBF1, and PAX5; the remaining 39 previously not described as distinctively B-lineage related. The marked, transient increase in precursor B-cells and RAG1 transcriptional activity is not reflected by a similar peak in B-cells in peripheral blood, whereas the sustained plateau concurs in time.
In this study, we tested the NuGEN Ovation RNA-Seq System for library preparation followed by nex... more In this study, we tested the NuGEN Ovation RNA-Seq System for library preparation followed by next-generation sequencing on an Illumina GAIIx. The cDNA product of the NuGEN kit may have significant amounts of ssDNA with hairpin structures that are generated during the amplification process. These structures interfere with efficient downstream end repair, A-tailing, and adapter ligation, all standard steps in post-amplification sequencing library construction. We were able to increase the efficiency of sequencing library yields 4- to 6-fold or greater by treatment of NuGEN-amplified cDNA product with the single-strand endonuclease S1. These results suggest that this treatment effectively cleaves hairpin structures generated during amplification that are resistant to the standard enzyme cocktails used for the end-repair step.
Proteins Structure Function and Bioinformatics, Nov 1, 1998
We present a computational approach for predicting structures of ligand-protein complexes and ana... more We present a computational approach for predicting structures of ligand-protein complexes and analyzing binding energy landscapes that combines Monte Carlo simulated annealing technique to determine the ligand bound conformation with the dead-end elimination algorithm for side-chain optimization of the protein active site residues. Flexible ligand docking and optimization of mobile protein side-chains have been performed to predict structural effects in the V32I/I47V/V82I HIV-1 protease mutant bound with the SB203386 ligand and in the V82A HIV-1 protease mutant bound with the A77003 ligand. The computational structure predictions are consistent with the crystal structures of these ligand-protein complexes. The emerging relationships between ligand docking and side-chain optimization of the active site residues are rationalized based on the analysis of the ligand-protein binding energy landscape.
Using a focused glycan-gene microarray, we compared the glycosyltransferase (GT) and sulfotransfe... more Using a focused glycan-gene microarray, we compared the glycosyltransferase (GT) and sulfotransferase gene expression profiles of human monocytes, dendritic cells (DCs) and macrophages (Mphis), isolated or differentiated from the same donors. Microarray analysis indicated that monocytes express transcripts for a full set of enzymes involved in the biosynthesis of multi-multiantennary branched N-glycans, potentially elongated by poly-N-acetyl-lactosamine chains, and of mucin-type Core 1 and Core 2 sialylated O-glycans. Monocytes also express genes involved in the biosynthesis and modification of glycosaminoglycans, but display a limited expression of GTs implicated in glycolipid synthesis. Among genes expressed in monocytes (90 out of 175), one third is significantly modulated in DCs and Mphi respectively, most of them being increased in both cell types relative to monocytes. These changes might potentially enforce the capacity of differentiated cells to synthesize branched N-glycans...
The number of circulating B-cells in peripheral blood plateaus between 2 and 24 months of age, an... more The number of circulating B-cells in peripheral blood plateaus between 2 and 24 months of age, and thereafter declines gradually. How this reflects the kinetics of the precursor B-cell pool in the bone marrow is of clinical interest, but has not been studied thoroughly in humans. The authors analyzed bone marrow (n = 37) from healthy children and adults (flow cytometry) searching for age-related changes in the total precursor B-cell compartment. In an age-matched cohort (n = 25) they examined age-related global gene expression changes (Affymetrix) in unsorted bone marrow with special reference to the recombination activating gene 1, RAG1. Subsequently, they searched the entire gene set for transcripts correlating to the RAG1 profile to discover other known and possibly new precursor B-cell related transcripts. Both methods disclosed a marked, transient increase of total precursor B-cells at 6-20 months, followed by a rapid decrease confined to the first 2 years. The decline thereafter was considerably slower, but continued until adulthood. The relative composition of total precursor B-cells, however, did not change significantly with age. The authors identified 54 genes that were highly correlated to the RAG1 profile (r >or= .9, p < 1 x 10(-8)). Of these 54 genes, 15 were characteristically B-lineage associated like CD19, CD79, VPREB, EBF1, and PAX5; the remaining 39 previously not described as distinctively B-lineage related. The marked, transient increase in precursor B-cells and RAG1 transcriptional activity is not reflected by a similar peak in B-cells in peripheral blood, whereas the sustained plateau concurs in time.
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Papers by Lana Schaffer