Molecular cloning of the Na,K-ATPase α-subunit in developing brine shrimp and sequence comparison with higher organisms

AbstractWe report here the molecular cloning, nucleotide sequence, and predicted amino acid sequence of an α-subunit of the developmentally useful model, Artemia. The animo acid sequence shows divergence from that of mammals, birds, Torpedo, and Drosophila. However, regions in the putative ATP binding and transmembrane domains show absolute or high levels of conservation. Major differences occur in the amino-terminal domain and several other hypervariable regions. These differences are consistent with the suggestion that the brine shrimp is a ‘fast clock’ organism which diverged from the precursors of vertebrates 0.5–1 billion years ago.Na,K-ATPase; Molecular cloning; DNA, complementary; Amino acid sequence; (Artemia

MSI-CIEC: MSI Cyberinfrastructure Empowerment Coalition and the TeraGrid

Paper written as a collaboration of the following institutions and presented at the 2006 TeraGrid Conference, Indianapolis, IN June 12-16: 1. University of Houston Downtown 2. NAFEO: National Association for Equal Opportunity in Higher Education 3. SDSC: San Diego Supercomputer Center 4. Indiana University, Computer Science Department 5. AIHEC: The American Indiana Highter Education Consortium 6. HACU: Hispanic Association of Colleges and Universitie

Successful unrelated marrow transplantation for patients over the age of 40 with chronic myelogenous leukemia

AbstractSome older patients (> or =40 years) with chronic myelogenous leukemia (CML) who lack human leukocyte antigen (HLA)-identical sibling donors are not offered unrelated marrow transplantation because of concerns over excessive regimen-related toxicity, in particular due to graft-vs.-host disease (GVHD). The purpose of this study was to determine the efficacy and toxicity of unrelated marrow transplantation in older CML patients using a regimen designed to minimize the severity of GVHD. Thirty-one consecutive patients over the age of 40 with CML received unrelated marrow transplants between January 1988 and June 1997. Twenty-one patients were transplanted in chronic phase while ten were transplanted in the accelerated phase of their disease. Fifteen patients received transplants from phenotypically matched donors while 16 received marrow grafts from donors who were mismatched at one HLA locus. GVHD prophylaxis consisted of ex vivo T cell depletion of the donor marrow graft plus posttransplant cyclosporine administration. Durable engraftment was achieved in 29 of 31 patients (94%). The probability of developing grades II-IV or severe grades III-IV acute GVHD was 39.2 and 7.1%, respectively. There was no difference in the incidence of grades II-IV acute GVHD between patients transplanted with marrow grafts from phenotypically matched (38.1%) vs. those transplanted from mismatched unrelated donors (40%, p = 0.99). The 2-year probability of relapse for the entire population was 29.4%. Relapse was significantly higher for patients transplanted in accelerated phase (60%) than for those in chronic phase (13.8%, p = 0.027). The 2-year probability of overall survival and disease-free survival for the entire cohort was 56 and 45%, respectively. There was no significant difference in survival or disease-free survival for patients receiving phenotypically matched vs. mismatched marrow grafts. Immunological reconstitution for this cohort was compared with a younger (<40 years) patient population that had been similarly transplanted over the same time period. Immune function as assessed by total T cell, B cell, NK cell, and T cell subset reconstitution posttransplant was quantitatively equivalent in the two groups with most parameters normalizing within 18 months of transplant. We conclude that CML patients over the age of 40 who have either phenotypically matched or one antigen-mismatched unrelated donors can successfully undergo allogeneic marrow transplantation. T cell depletion of the marrow graft may be advantageous in these older patients by reducing GVHD severity, particularly in those patients transplanted with HLA-disparate marrow grafts.Biol Blood Marrow Transplant 1998;4(1):3-12

Next generation multiplexing for digital PCR using a novel melt-based hairpin probe design

Digital PCR (dPCR) is a powerful tool for research and diagnostic applications that require absolute quantification of target molecules or detection of rare events, but the number of nucleic acid targets that can be distinguished within an assay has limited its usefulness. For most dPCR systems, one target is detected per optical channel and the total number of targets is limited by the number of optical channels on the platform. Higher-order multiplexing has the potential to dramatically increase the usefulness of dPCR, especially in scenarios with limited sample. Other potential benefits of multiplexing include lower cost, additional information generated by more probes, and higher throughput. To address this unmet need, we developed a novel melt-based hairpin probe design to provide a robust option for multiplexing digital PCR. A prototype multiplex digital PCR (mdPCR) assay using three melt-based hairpin probes per optical channel in a 16-well microfluidic digital PCR platform accurately distinguished and quantified 12 nucleic acid targets per well. For samples with 10,000 human genome equivalents, the probe-specific ranges for limit of blank were 0.00%–0.13%, and those for analytical limit of detection were 0.00%–0.20%. Inter-laboratory reproducibility was excellent (r2 = 0.997). Importantly, this novel melt-based hairpin probe design has potential to achieve multiplexing beyond the 12 targets/well of this prototype assay. This easy-to-use mdPCR technology with excellent performance characteristics has the potential to revolutionize the use of digital PCR in research and diagnostic settings

HLA diversity in ethnic populations can affect detection of donor-specific antibodies by single antigen beads

IntroductionIn solid-organ transplantation, human leukocyte antigen (HLA) donor-specific antibodies (DSA) are strongly associated with graft rejection, graft loss, and patient death. The predominant tests used for detecting HLA DSA before and after solid-organ transplantation are HLA single antigen bead (SAB) assays. However, SAB assays may not detect antibodies directed against HLA epitopes that are not represented in the SAB. The prevalence and potential impact of unrepresented HLA epitopes are expected to vary by ethnicity, but have not been thoroughly investigated. To address this knowledge gap, HLA allele frequencies from seven ethnic populations were compared with HLA proteins present in SAB products from two manufacturers to determine unrepresented HLA proteins.MaterialsAllele frequencies were obtained from the Common, Intermediate, and Well Documented HLA catalog v3.0, and frequencies of unrepresented HLA types were calculated. Next-generation sequencing was used to determine HLA types of 60 deceased solid-organ donors, and results were used to determine if their HLA-A, -B, -C, and -DRB1 proteins were not present in SAB reagents from two vendors. Unrepresented HLA proteins were compared with the most similar protein in SAB assays from either vendor and then visualized using modeling software to assess potential HLA epitopes.ResultsFor the seven ethnic populations, 0.5% to 11.8% of each population had HLA proteins not included in SAB assays from one vendor. Non-European populations had greater numbers of unrepresented alleles. Among the deceased donors, 26.7% (16/60) had at least one unrepresented HLA-A, -B, -C, or -DRB1 protein. Structural modeling demonstrated that a subset of these had potential HLA epitopes that are solvent accessible amino acid mismatches and are likely to be accessible to B cell receptors.DiscussionIn conclusion, SAB assays cannot completely rule out the presence of HLA DSA. HLA epitopes not represented in those assays vary by ethnicity and should not be overlooked, especially in non-European populations. Allele-level HLA typing can help determine the potential for HLA antibodies that could evade detection

Antibiotic-refractory Lyme arthritis is associated with HLA-DR molecules that bind a Borrelia burgdorferi peptide

An association has previously been shown between antibiotic-refractory Lyme arthritis, the human histocompatibility leukocyte antigen (HLA)–DR4 molecule, and T cell recognition of an epitope of Borrelia burgdorferi outer-surface protein A (OspA163–175). We studied the frequencies of HLA-DRB1-DQA1-DQB1 haplotypes in 121 patients with antibiotic-refractory or antibiotic-responsive Lyme arthritis and correlated these frequencies with in vitro binding of the OspA163–175 peptide to 14 DRB molecules. Among the 121 patients, the frequencies of HLA-DRB1-DQA1-DQB1 haplotypes were similar to those in control subjects. However, when stratified by antibiotic response, the frequencies of DRB1 alleles in the 71 patients with antibiotic-refractory arthritis differed significantly from those in the 50 antibiotic-responsive patients (log likelihood test, P = 0.006; exact test, P = 0.008; effect size, Wn = 0.38). 7 of the 14 DRB molecules (DRB1*0401, 0101, 0404, 0405, DRB5*0101, DRB1*0402, and 0102) showed strong to weak binding of OspA163–175, whereas the other seven showed negligible or no binding of the peptide. Altogether, 79% of the antibiotic-refractory patients had at least one of the seven known OspA peptide–binding DR molecules compared with 46% of the antibiotic-responsive patients (odds ratio = 4.4; P < 0.001). We conclude that binding of a single spirochetal peptide to certain DRB molecules is a marker for antibiotic-refractory Lyme arthritis and might play a role in the pathogenesis of the disease

Development of a sensitive, highly controlled assay for molecular detection of the Philadelphia chromosome in patients with chronic myelogenous leukemia

The Philadelphia chromosome (Ph1), present in [ges]95% of chronic myelogenous leukemia (CML) patients, is a well-characterized translocation that results in a unique chimeric gene product (BCR/ABL) with transforming capability. Molecular methods utilizing the polymerase chain reaction (PCR) to detect BCR/ABL mRNA transcripts has been useful for detecting minimal residual disease (MRD) after treatment, as well as for establishing the diagnosis of CML. Amplification-based assays for the BCR/ABL transcript, however, have shown variable reproducibility and sensitivity. This variability may be largely due to technical differences and insufficient controls. In this report, we describe the development of a highly controlled, reproducible, and sensitive PCR assay to detect Ph1 that is well suited to clinical and research applications. A validation study of 82 samples was performed consisting of 25 dilutions of K562 cells (Ph1+) into normal cultured B cells, 26 pre- and post-transplant peripheral blood samples from CML patients, 16 peripheral blood samples for diagnosis of CML, and 15 peripheral blood samples from healthy individuals. RNA isolated from 3 to 5 million leukocytes was reverse transcribed (RT) and amplified by nested primer PCR. The products were characterized using agarose gel electrophoresis. Approximately 1000 Ph1-positive cells admixed with 106 normal cells were detectable after one round of amplification. In 60% of assays where one Ph1-positive cell was admixed with 106 normal cells, a BCR/ABL product was detectable after nested primer PCR. Specific measures to ensure accurate results in routine testing included (a) assessing RNA integrity and adequate cDNA preparation by detection of the constitutively expressed ABL mRNA, (b) monitoring sensitivity with the addition and detection of K562 RNA mixed with RNA from unknown samples (failure to detect the "spiked" K562 RNA indicates the presence of inhibitors or ribonucleases within the unknown RNA sample), (c) detection of nucleic acid contaminants by using negative controls in every assay, and (d) duplicate analysis of all samples and controls. Internally, this assay was 100% reproducible. Our results verify that nested primer RT-PCR is a fast, sensitive alternative to cytogenetic or Southern blot analysis for monitoring MRD after treatment and for diagnosis of CML. In addition, the highly controlled detection scheme presented here can be used as a general model for the development of other amplification-based detection assays.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31883/1/0000835.pd

Domain Structures in Fourth-Order Phase and Ginzburg-Landau Equations

In pattern-forming systems, competition between patterns with different wave numbers can lead to domain structures, which consist of regions with differing wave numbers separated by domain walls. For domain structures well above threshold we employ the appropriate phase equation and obtain detailed qualitative agreement with recent experiments. Close to threshold a fourth-order Ginzburg-Landau equation is used which describes a steady bifurcation in systems with two competing critical wave numbers. The existence and stability regime of domain structures is found to be very intricate due to interactions with other modes. In contrast to the phase equation the Ginzburg-Landau equation allows a spatially oscillatory interaction of the domain walls. Thus, close to threshold domain structures need not undergo the coarsening dynamics found in the phase equation far above threshold, and can be stable even without phase conservation. We study their regime of stability as a function of their (quantized) length. Domain structures are related to zig-zags in two-dimensional systems. The latter are therefore expected to be stable only when quenched far enough beyond the zig-zag instability.Comment: Submitted to Physica D, 11 pages (RevTeX 3), 12 postscript figure

Nonlinear dynamics of waves and modulated waves in 1D thermocapillary flows. I: General presentation and periodic solutions

We present experimental results on hydrothermal traveling-waves dynamics in long and narrow 1D channels. The onset of primary traveling-wave patterns is briefly presented for different fluid heights and for annular or bounded channels, i.e., within periodic or non-periodic boundary conditions. For periodic boundary conditions, by increasing the control parameter or changing the discrete mean-wavenumber of the waves, we produce modulated waves patterns. These patterns range from stable periodic phase-solutions, due to supercritical Eckhaus instability, to spatio-temporal defect-chaos involving traveling holes and/or counter-propagating-waves competition, i.e., traveling sources and sinks. The transition from non-linearly saturated Eckhaus modulations to transient pattern-breaks by traveling holes and spatio-temporal defects is documented. Our observations are presented in the framework of coupled complex Ginzburg-Landau equations with additional fourth and fifth order terms which account for the reflection symmetry breaking at high wave-amplitude far from onset. The second part of this paper (nlin.PS/0208030) extends this study to spatially non-periodic patterns observed in both annular and bounded channel.Comment: 45 pages, 21 figures (elsart.cls + AMS extensions). Accepted in Physica D. See also companion paper "Nonlinear dynamics of waves and modulated waves in 1D thermocapillary flows. II: Convective/absolute transitions" (nlin.PS/0208030). A version with high resolution figures is available on N.G. web pag