Biomedical subjects

S D Jayasena

Publications and source records attributed to S D Jayasena.

At least 19 recordsLinked to original sources

PubMed2001

Outcome in patients with end-stage renal disease following heart or heart--lung transplantation receiving peritoneal dialysis.

BACKGROUND: End-stage renal disease (ESRD) complicates 5--10% of heart and heart--lung transplant patients. We report our experience of peritoneal dialysis (PD) in 17 such patients. METHODS: Between March 1995 and February 1999, 13 heart transplant and four heart--lung transplant patients (11 male, 6 female) joined our PD programme (10 continuous ambulatory PD, seven automated PD). Median time from heart or heart--lung transplantation to ESRD was 9 years (range 1--13 years), and median age at introduction of renal replacement therapy was 51 years (range 23--66 years). The frequency of exit-site infections, peritonitis, and PD survival (including technique failure and death) in the transplant group (TxP) was calculated retrospectively. These were compared with two contemporary control groups: PD patients immunosuppressed for other indications (ISP, n=19) and, all other patients recruited onto the PD programme (NISP, n=132). RESULTS: Median follow-up was 10 months (range 2--27 months) for TxP, 7 months (range 2--29 months) for ISP, and 14 months (range 1--48 months) for NISP groups. The frequency of exit-site infections was similar in each group: 1 in 26 months for TxP; 1 in 30 months for ISP, and 1 in 27 months for NISP (P=NS). The frequency of peritonitis was greater in the TxP group at 1 in 15 months, compared with 1 in 20 months for ISP and 1 in 29 months for NISP (TxP vs NISP, P<0.05). PD failure following infection was 23.5% for TxP, 10.5% for ISP, and 12.9% for NISP. Actuarial PD survival at 24 months was only 25.2% in the TxP group compared with 79% in the NISP group. There were no deaths related to immediate complications of PD. CONCLUSIONS: Increased risk of PD peritonitis and reduced PD survival is reported in this cohort of 17 heart and heart--lung recipients with ESRD. Nevertheless, for patients with severely impaired cardiac function, PD may still offer therapeutic advantage.

Adolescent↗

PubMed2000

Signal amplification through nucleotide extension and excision on a dendritic DNA platform.

Techniques that provide strong signal amplification are useful in diagnostic applications, especially in detecting low concentrations of non-amplifiable target molecules. A versatile and strong signal amplification method based on activities of a DNA polymerase to generate high concentrations of pyrophosphate (PPi) is described. The generation of PPi is catalyzed by nucleotide extension and excision activities of a DNA polymerase on an oligonucleotide cassette. The signal is generated upon enzymatic conversion of PPi to ATP and ATP levels subsequently detected with firefly luciferase. Bioluminescence produced by an oligonucleotide cassette consisting of just two polymerase reaction sites is sufficient to detect them at low attomole levels. The attachment of a large number of these oligonucleotide cassettes to DNA dendrimers enabled the detection of such poly-valent substrate molecules at low zeptomole (10(-21)mol) concentrations. The extent of signal amplification obtained with dendrimer substrates is comparable to exponential target amplifications provided by nucleic acid amplification methods. The attachment of such PPi-generating dendritic DNA platforms to ligands that mediate target recognition would potentially permit detection of extremely low concentrations of analytes in diagnostic assays.

Adenosine Triphosphate↗

PubMed1999

Aptamers: an emerging class of molecules that rival antibodies in diagnostics.

Antibodies, the most popular class of molecules providing molecular recognition needs for a wide range of applications, have been around for more than three decades. As a result, antibodies have made substantial contributions toward the advancement of diagnostic assays and have become indispensable in most diagnostic tests that are used routinely in clinics today. The development of the systematic evolution of ligands by exponential enrichment (SELEX) process, however, made possible the isolation of oligonucleotide sequences with the capacity to recognize virtually any class of target molecules with high affinity and specificity. These oligonucleotide sequences, referred to as "aptamers", are beginning to emerge as a class of molecules that rival antibodies in both therapeutic and diagnostic applications. Aptamers are different from antibodies, yet they mimic properties of antibodies in a variety of diagnostic formats. The demand for diagnostic assays to assist in the management of existing and emerging diseases is increasing, and aptamers could potentially fulfill molecular recognition needs in those assays. Compared with the bellwether antibody technology, aptamer research is still in its infancy, but it is progressing at a fast pace. The potential of aptamers may be realized in the near future in the form of aptamer-based diagnostic products in the market. In such products, aptamers may play a key role either in conjunction with, or in place of, antibodies. It is also likely that existing diagnostic formats may change according to the need to better harness the unique properties of aptamers.

Antibodies↗

PubMed1998

Staining of cell surface human CD4 with 2'-F-pyrimidine-containing RNA aptamers for flow cytometry.

We have used recombinant human CD4 presented on beads as an affinity matrix to screen a 2'-F-pyrimidine-containing RNA library with a complexity of approximately 10(14) molecules. Affinity-selected aptamers bind recombinant CD4 with low nanomolar equilibrium dissociation constants. These high-affinity aptamers conjugated to different fluorophores such as fluorescein and phycoerythrin were used to stain cells, expressing human CD4 on cell surface, for analysis by flow cytometry. Aptamers, conjugated to fluorophores, stained mouse T cells that express human CD4 on the surface, but not the control mouse T cells lacking human CD4. The control cells, however, do express mouse CD4 whose extracellular domain has 55% sequence identity to the human form. These human CD4-specific aptamers selectively stained CD4(+) T cells in a preparation of human peripheral blood mononuclear cells. These results and others suggest that aptamers are emerging as a versatile class of molecules that can be used for various diagnostic applications performed under different formats or platforms.

Amino Acid Sequence↗

PubMed1998

Nature and biological significance of free radicals generated during bicarbonate hemodialysis.

This study investigates evidence of oxidative stress during bicarbonate hemodialysis by measuring total glutathione and lipid peroxidation products in plasma, and characterizes the free radicals produced by neutrophils from healthy volunteers when incubated in vitro with increasing concentrations of bicarbonate. Blood samples were taken from nine hemodialysis patients before and after two hemodialysis sessions. Plasma hydroperoxides and total glutathione were measured. A significant increase was found in total glutathione (1.04 +/- 0.4 versus 2.11 +/- 0.9 microM, P < 0.001) and hydroperoxides by ferrous oxidation in xylenol orange version 2 method (4.6 +/- 0.53 versus 6.4 +/- 0.63 microM, P < 0.001) after hemodialysis, which indicated increased oxidative injury during hemodialysis. Normal neutrophils, activated by contact adhesion, produced a dose-dependent increase in free radical production (measured by luminol-enhanced chemiluminescence) when incubated with increasing concentrations of bicarbonate (up to 35 mM). Bicarbonate had the same effect on the chemiluminescence of a cell-free hypoxanthine/acetaldehyde system generating superoxide, but not on a glucose oxidase/myeloperoxidase system generating hydrogen peroxide and hypochlorous acid. These findings are consistent with (1) the hypothesis that superoxide generated during hemodialysis reacts with bicarbonate to form the toxic carbonate and formate radicals and (2) our previous observation that some patients undergoing bicarbonate (but not lactate) dialysis have increased plasma concentrations of formate after hemodialysis. It is suggested that the increased plasma total glutathione and hydroperoxide concentrations are a result of lipid peroxidation by these species. These reactive radicals can initiate lipid peroxidation and contribute to the cardiovascular complications of hemodialysis patients.

Aged↗

PubMed1997

Inhibition of multiple thermostable DNA polymerases by a heterodimeric aptamer.

Single-stranded DNA aptamers that recognize DNA polymerase from Thermus acquaticus (Taq pol) with high affinity have been described recently. These aptamers have been shown to efficiently inhibit the polymerase activity of Taq pol and are useful in enhancing the amplification efficiency of low copy number targets by the polymerase chain reaction (PCR). Aptamers selected to bind to Taq pol fell into two different sequence families and inhibited several DNA polymerases isolated from the Thermus species, including that from Thermus thermophilus (Tth pol). Aptamers from one sequence family inhibited the Stoffel fragment of Taq pol efficiently, whereas those from the other family did not. Truncated aptamers derived from two parent ligands from both families were combined to form a heterodimeric aptamer that effectively inhibited all three polymerases and were shown to be useful in detecting a low copy number target by PCR amplification. These data demonstrate that the combination of aptamers with different properties into a single molecule broadens their spectrum of utility.

Base Sequence↗

PubMed1996

Oligonucleotide inhibitors of Taq DNA polymerase facilitate detection of low copy number targets by PCR.

A random sequence library of single stranded DNA was screened to isolate sequences with high affinity for Thermus aquaticus DNA polymerase (Taq pol), a thermostable enzyme commonly used in the polymerase chain reaction (PCR). Selected oligonucleotide sequences bound Taq pol with dissociation constants in the low picomolar range, and efficiently inhibited polymerase activity at room temperature (20 to 25 degrees C), but did not inhibit at temperatures above 40 degrees C. Moreover, inhibition was thermally reversible. A process called "hot start" PCR is commonly used to prevent non-specific PCR products in amplification of low copy number targets. We show that the addition of oligonucleotide inhibitors eliminated the need for "hot start" conditions and improved the efficiency of detection of a low copy number target in PCR.

DNA, Viral↗

PubMed1996

High-affinity and specific recognition of human thyroid stimulating hormone (hTSH) by in vitro-selected 2'-amino-modified RNA.

RNA sequences containing 2'-amino pyrimidines that bind with high-affinity to human thyroid stimulating hormone (hTSH) were isolated from a random sequence library by an in vitro selection-amplification procedure. A representative RNA ligand (T-15) has an equilibrium dissociation constant (Kd) of 2.5 nM for its interaction with hTSH and can discriminate between other members of the glycohormone family; no detectable binding was observed at low micromolar concentrations of hCG (human chorionic gonadotropin), while measured Kd values for the interactions with hLH (human leutinizing hormone) and hFSH (human follicle stimulating hormone) were > 1 microM and approximately 0.2 microM, respectively. The detection of hTSH in a dot blot assay with radiolabeled T-15 RNA was demonstrated.

Humans↗

PubMed1996

Use of a high affinity DNA ligand in flow cytometry.

To investigate the feasibility of using oligonucleotides in flow cytometry we describe a model system consisting of human neutrophil elastase (HNE) coated on 3.3 micro beads and a high affinity DNA ligand for HNE isolated by in vitro selection (SELEX). In this system the fluoresceinated DNA ligand was equally effective as an anti- HNE antibody in detecting HNE on beads. The location on and the chemistry of attachment of fluorescein to the DNA ligand is critical for the sensitivity of detection. DNA constructs in which fluorescein was conjugated via an ethylene glycol tether to either the 5'-end or near the 3'-end gave much higher signals than did probes with fluorescein directly conjugated to either end. Second-step staining with strepavidin-conjugated phycoerythrin was accomplished using a biotinylated DNA ligand in the initial staining of HNE beads. These data suggest that instead of, or in addition to, antibodies high affinity oligonucleotide probes can be useful in diagnostic applications based on flow cytometry.

Animals↗

PubMed1995

Peptide conjugation to an in vitro-selected DNA ligand improves enzyme inhibition.

An in vitro selection technique was used to identify a specific high-affinity DNA ligand targeted to human neutrophil elastase (HNE). 1H NMR data and a comparative analysis of the selected sequences suggest that the DNA folds into a G-quartet structure with duplexed ends. The high-affinity binding DNA alone did not inhibit the enzymatic activity of HNE. The DNA was covalently attached to a tetrapeptide, N-methoxysuccinyl-Ala-Ala-Pro-Val, that is a weak competitive inhibitor of HNE. HNE was inhibited by this DNA-peptide conjugate nearly five orders of magnitude more effectively than by the peptide alone. These results demonstrate that in vitro-selected nucleic acids can be used as a vehicle for molecular delivery.

Amino Acid Sequence↗

PubMed1995

Restriction fragment length polymorphism analysis rules out cross-infection among renal patients with tuberculosis.

A cluster of five cases of tuberculosis occurred on a renal unit in 1993. The initial impression was that this was an outbreak, and cross-infection was suspected. Restriction fragment length polymorphism analysis was carried out on the strains of Mycobacterium tuberculosis isolated from these cases, using a DNA probe directed against the insertion sequence IS6110. DNA fingerprints obtained by this method differed for all the strains tested, ruling out cross-infection as a cause of the outbreak. This technique is a useful adjunct to standard epidemiological investigations in outbreaks of tuberculosis.

Adult↗

PubMed1995

Nephrotic syndrome, malignant thymoma, and myasthenia gravis. Case report and review of the literature.

We describe a patient with nephrotic syndrome due to focal-segmental glomerulosclerosis, occurring 3 years after thymectomy and myasthenia gravis. Nine other cases of nephrotic syndrome associated with thymoma and myasthenia gravis reported in the literature are reviewed. The nephrotic syndrome may be due to T cell dysfunction associated with thymoma; however, animal models suggest that genetic factors may also be involved.

Female↗

PubMed1994

Modified RNA sequence pools for in vitro selection.

We report the use of modified RNA, in which the 2'-OH group of pyrimidines is replaced by a 2'-amino (2'-NH2) group to identify high affinity ligands specific for human neutrophil elastase (HNE) by in vitro selection. Compared to unmodified RNA the 2'-NH2-modified RNA ligands show enhanced stability in human serum and urine. Use of RNase T1 cleavage data in the presence of K+ and Li+ ions suggests that the modified RNA ligands selected for HNE form an intermolecular G-quartet structure.

Amino Acid Sequence↗

PubMed1993

Sequence limitations of triple helix formation by alternate-strand recognition.

Until recently, oligonucleotide-directed triplex formation has been limited to oligopurine tracts of target DNA. Triplex formation by alternate-strand recognition relaxes this limitation by allowing triplexes to form at 5'-(Pu)m(Py)n-3' and 5'-(Py)m(Pu)n-3' sequences, with the third strand pairing first with purines on one strand and then switching to pair with purines on the other strand. In this study, the interaction of several oligonucleotides with the potential to form triplexes by alternate-strand recognition at the sequence 5'-A8C8A8-3' was studied by chemical probing and affinity cleaving. The results show that triplex formation can be readily accomplished at the 5'-A8C8-3' part of the sequence; however, base triplet formation is disrupted on either side of the strand switch and the Watson-Crick helix is distorted in such a way as to expose the N7 positions of purines adjoining the strand switch. Triplex formation is weak or nonexistent at the 3'-most A8 block, despite the opportunity for recruiting a spacer sequence for the second (C8-A8) strand switch by "slippage". This finding indicates that the C8-A8 strand switch is energetically unfavorable, although pairing at other 5'-(Py)n(Pu)n-3' sequences has been observed, with or without a spacer [Beal, P. A., & Dervan, P. B. (1992) J. Am. Chem. Soc. 114, 1470-1478; Jayasena, S. D., & Johnston, B. H. (1992) Nucleic Acids Res. 20, 5279-5288]. Thus, alternate-strand recognition may not be feasible for certain sequences of 5'-(Py)m(Pu)n-3', at least under the conditions examined.

Base Sequence↗

PubMed1992

Oligonucleotide-directed triple helix formation at adjacent oligopurine and oligopyrimidine DNA tracts by alternate strand recognition.

A significant limitation to the practical application of triplex DNA is its requirement for oligopurine tracts in target DNA sequences. The repertoire of triplex-forming sequences can potentially be expanded to adjacent blocks of purines and pyrimidines by allowing the third strand to pair with purines on alternate strands, while maintaining the required strand polarities by combining the two major classes of base triplets, Py.PuPy and Pu.PuPy. The formation of triplex DNA in this fashion requires no unusual bases or backbone linkages on the third strand. This approach has previously been demonstrated for target sequences of the type 5'-(Pu)n(Py)n-3' in intramolecular complexes. Using affinity cleaving and DNase I footprinting, we show here that intermolecular triplexes can also be formed at both 5'-(Pu)n(Py)n-3' and 5'-(Py)n(Pu)n-3' target sequences. However, triplex formation at a 5'-(Py)n(Pu)n-3' sequence occurs with lower yield. Triplex formation is disfavored, even at acid pH, when a number of contiguous C+.GC base triplets are required. These results suggest that triplex formation via alternate strand recognition at sequences made up of blocks of purines and pyrimidines may be generally feasible.

Base Sequence↗

PubMed1992

Site-specific cleavage of the transactivation response site of human immunodeficiency virus RNA with a tat-based chemical nuclease.

tat, an essential transactivator of gene transcription in the human immunodeficiency virus (HIV), is believed to activate viral gene expression by binding to the transactivation response (TAR) site located at the 5' end of all viral mRNAs. The TAR element forms a stem-loop structure containing a 3-nucleotide bulge that is the site for tat binding and is required for transactivation. Here we report the synthesis of a site-specific chemical ribonuclease based on the TAR binding domain of the HIV type 1 (HIV-1) tat. A peptide consisting of this 24-amino acid domain plus an additional C-terminal cysteine residue was chemically synthesized and covalently linked to 1,10-phenanthroline at the cysteine residue. The modified peptide binds to TAR sequences of both HIV-1 and HIV-2 and, in the presence of cupric ions and a reducing agent, cleaves these RNAs at specific sites. Cleavage sites on TAR sequences are consistent with peptide binding to the 3-nucleotide bulge, and the relative displacement of cleavage sites on the two strands suggests peptide binding to the major groove of the RNA. These results and existing evidence of the rapid cellular uptake of tat-derived peptides suggest that chemical nucleases based on tat may be useful for inactivating HIV mRNA in vivo.

Amino Acid Sequence↗

PubMed1992

Intramolecular triple-helix formation at (PunPyn).(PunPyn) tracts: recognition of alternate strands via Pu.PuPy and Py.PuPy base triplets.

Triple-helical DNA shows increasing potential for applications in the control of gene expression (including therapeutics) and the development of sequence-specific DNA-cleaving agents. The major limitation in this technology has been the requirement of homopurine sequences for triplex formation. We describe a simple approach that relaxes this requirement, by utilizing both Pu.PuPy and Py.PuPy base triplets to form a continuous DNA triple helix at tandem oligopurine and oligopyrimidine tracts. [Triplex formation at such a sequence has been previously demonstrated only with the use of a special 3'-3' linkage in the third strand [Horne, D. A., & Dervan, P. B. (1990) J. Am. Chem. Soc. 112, 2435-2437].] Supporting evidence is from chemical probing experiments performed on several oligonucleotides designed to form 3-stranded fold-back structures. The third strand, consisting of both purine and pyrimidine blocks, pairs with purines in the Watson-Crick duplex, switching strands at the junction between the oligopurine and oligopyrimidine blocks but maintaining the required strand polarity without any special linkage. Although Mg2+ ions are not required for the formation of Pu.PuPy base triplets, they show enhanced stability in the presence of Mg2+. In the sequences observed. A.AT triplets appear to be more stable than G.GC triplets. As expected, triplex formation is largely independent of pH unless C+.GC base triplets are required.

Base Composition↗

PubMed1989

Competitive nucleosome reconstitution of polydeoxynucleotides containing oligoguanosine tracts.

The ability of synthetic polydeoxynucleotides composed of oligoguanosine tracts of increasing length to form nucleosomes has been determined by several reconstitution procedures. When the presence of nucleosomes is determined by resistance to nuclease digestion, a protected band of approximately 150 base-pairs is detected only with difficulty for polymers containing long tracts of contiguous guanosines. However, when assayed by a shift in the electrophoretic mobility of radiolabeled polymers exchanged at 0.7 M-NaCl with authentic nucleosomes, all polymers tested are seen to form nucleosomes. Quantitative competitive reconstitution shows that the length of the tracts per se does not adversely affect their propensity to form nucleosomes, since even 150 base-pair poly(dG).poly(dC) forms nucleosomes as well as heterogeneous-sequence DNA. However, the ability to form nucleosomes does depend on the length of the polymer repeating unit.

Animals↗