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Biomedical subjects

Matthew Levy

Publications and source records attributed to Matthew Levy.

At least 19 recordsLinked to original sources
PubMed2007

Molecular optical imaging of therapeutic targets of cancer.

Recent progress in discerning the molecular events that accompany carcinogenesis has led to development of new cancer therapies directly targeted against the molecular changes of neoplasia. Molecular-targeted therapeutics have shown significant improvements in response rates and decreased toxicity as compared to conventional cytotoxic therapies which lack specificity for tumor cells. In order to fully explore the potential of molecular-targeted therapy, a new set of tools is required to dynamically and quantitatively image and monitor the heterogeneous molecular profiles of tumors in vivo. Currently, molecular markers can only be visualized in vitro using complex immunohistochemical staining protocols. In this chapter, we discuss emerging optical tools to image in vivo a molecular profile of risk-based hallmarks of cancer for selecting and monitoring therapy. We present the combination of optically active, targeted nanoparticles for molecular imaging with advances in minimally invasive optical imaging systems, which can be used to dynamically image both a molecular and phenotypic profile of risk and to monitor changes in this profile during therapy.

Animals↗
PubMed2006

Aptamer:toxin conjugates that specifically target prostate tumor cells.

We have used RNA aptamer:gelonin conjugates to target and specifically destroy cells overexpressing the known cancer biomarker prostate-specific membrane antigen (PSMA). Aptamer:toxin conjugates have an IC50 of 27 nmol/L and display an increased potency of at least 600-fold relative to cells that do not express PSMA. The aptamer not only promotes uptake into target cells but also decreases the toxicity of gelonin in non-target cells. These results validate the notion that "escort aptamers" may be useful for the treatment of specific tumors expressing unique antigen targets.

Antineoplastic Agents, Phytogenic↗
PubMed2006

Aptamer mediated siRNA delivery.

Nucleic acids that bind to cells and are subsequently internalized could prove to be novel delivery reagents. An anti-prostate specific membrane antigen aptamer that has previously been shown to bind to prostate tumor cells was coupled to siRNAs via a modular streptavidin bridge. The resulting conjugates could be simply added onto cells without any further preparation, and were taken up within 30 min. The siRNA-mediated inhibition of gene expression was as efficient as observed with conventional lipid-based reagents, and was dependent upon conjugation to the aptamer. These results suggest new venues for the therapeutic delivery of siRNAs and for the development of reagents that can be used to probe cellular physiology.

Aptamers, Nucleotide↗
PubMed2006

Deoxyribozymes that recode sequence information.

Allosteric nucleic acid ligases have been used previously to transform analyte-binding into the formation of oligonucleotide templates that can be amplified and detected. We have engineered binary deoxyribozyme ligases whose two components are brought together by bridging oligonucleotide effectors. The engineered ligases can 'read' one sequence and then 'write' (by ligation) a separate, distinct sequence, which can in turn be uniquely amplified. The binary deoxyribozymes show great specificity, can discriminate against a small number of mutations in the effector, and can read and recode DNA information with high fidelity even in the presence of excess obscuring genomic DNA. In addition, the binary deoxyribozymes can read non-natural nucleotides and write natural sequence information. The binary deoxyribozyme ligases could potentially be used in a variety of applications, including the detection of single nucleotide polymorphisms in genomic DNA or the identification of short nucleic acids such as microRNAs.

Allosteric Regulation↗
PubMed2006

Labeling tumor cells with fluorescent nanocrystal-aptamer bioconjugates.

Aptamers that bind to prostate specific membrane antigen (PSMA) were conjugated to luminescent CdSe and CdTe nanocrystals for cell-labeling studies. The aptamer-nanocrystal conjugates showed specific targeting of both fixed and live cells that overexpressed PSMA. More importantly, aptamers were able to label cells dispersed in a collagen gel matrix simulating tissue. The specific binding abilities and synthetic accessibility of aptamers combined with the photostability and small size of semiconductor nanocrystals offers a powerful and general tool for cellular imaging.

Aptamers, Peptide↗
PubMed2005

Synthetic biology: engineering Escherichia coli to see light.

We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.

Agar↗
PubMed2005

Proximity ligation assays with peptide conjugate 'burrs' for the sensitive detection of spores.

The proximity ligation assay (PLA) has previously been used for the sensitive and specific detection of single proteins. In order to adapt PLA methods for the detection of cell surfaces, we have generated multivalent peptide-oligonucleotide-phycoerythrin conjugates ('burrs') that can bind adjacent to one another on a cell surface and be ligated together to form unique amplicons. Real-time PCR detection of burr ligation events specifically identified as few as 100 Bacillus anthracis, 10 Bacillus subtilis and 1 Bacillus cereus spore. Burrs should prove to be generally useful for detecting and mapping interactions and distances between cell surface proteins.

Bacillus anthracis↗
PubMed2005

Direct selection of trans-acting ligase ribozymes by in vitro compartmentalization.

We have used a compartmentalized in vitro selection method to directly select for ligase ribozymes that are capable of acting on and turning over separable oligonucleotide substrates. Starting from a degenerate pool, we selected a trans-acting variant of the Bartel class I ligase which statistically may have been the only active variant in the starting pool. The isolation of this sequence from the population suggests that this selection method is extremely robust at selecting optimal ribozymes and should, therefore, prove useful for the selection and optimization of other trans-acting nucleic acid catalysts capable of multiple turnover catalysis.

Base Pairing↗
PubMed2005

Functional RNA microarrays for high-throughput screening of antiprotein aptamers.

High-throughput methods for generating aptamer microarrays are described. As a proof-of-principle, the microarrays were used to screen the affinity and specificity of a pool of robotically selected antilysozyme RNA aptamers. Aptamers were transcribed in vitro in reactions supplemented with biotinyl-guanosine 5'-monophosphate, which led to the specific addition of a 5' biotin moiety, and then spotted on streptavidin-coated microarray slides. The aptamers captured target protein in a dose-dependent manner, with linear signal response ranges that covered seven orders of magnitude and a lower limit of detection of 1 pg/mL (70 fM). Aptamers on the microarray retained their specificity for target protein in the presence of a 10,000-fold (w/w) excess of T-4 cell lysate protein. The RNA aptamer microarrays performed comparably to current antibody microarrays and within the clinically relevant ranges of many disease biomarkers. These methods should also prove useful for generating other functional RNA microarrays, including arrays for genomic noncoding RNAs that bind proteins. Integrating RNA aptamer microarray production with the maturing technology for automated in vitro selection of antiprotein aptamers should result in the high-throughput production of proteome chips.

Base Sequence↗
PubMed2005

Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP.

An allosteric ribozyme (aptazyme) has been used to transduce the binding of a small organic analyte (ATP) into the ligation of a circular template for rolling circle amplification (RCA). An ATP-activated deoxyribozyme ligase was immobilized on a glass slide and, upon addition of ATP, catalyzed the ligation of a circular padlock probe. The ligated products could be directly amplified and visualized via RCA. The coupled reaction exhibited could detect as little as 1 muM of ATP and could discriminate against structurally similar nucleotides such as GTP, CTP, and UTP. Cooperative ATP activation of the deoxyribozyme was faithfully mimicked by RCA, yielding an amplified "switch" that was responsive to ATP concentration.

Adenosine Triphosphate↗
PubMed2005

Treatment of agitation following traumatic brain injury: a review of the literature.

Agitation, restlessness, and aggression are frequent neurobehavioural sequelae in the early stages of recovery from traumatic brain injury (TBI). These behavioural symptoms disrupt patient care and impede rehabilitation efforts. We review the current literature (1985 onwards) examining the pharmacological management of post-TBI agitation in both acute and post-acute conditions. This article will assess the evidence for the use of selected alkylphenols, benzodiazepines, estrogens, antiandrogens, neuroleptics/antipsychotics, antidepressants, anti-Parkinsonian agents, antipsychotics, anticonvulsants, lithium carbonate, buspirone, beta-blockers, and psychostimulants in agitated TBI survivors. Review of the literature suggests that there is limited evidence to accurately guide clinicians in the management of this patient population.

Adrenergic beta-Antagonists↗
PubMed2004

Utilization of low-volume hospitals for total hip replacement.

OBJECTIVE: To identify factors associated with utilization of low-volume hospitals for total hip replacement (THR) and to estimate differences in the distances that Medicare beneficiaries had to travel to reach low- or high-volume hospitals. METHODS: We studied a population-based sample of 1,146 Medicare beneficiaries who underwent elective THR in 1995. Using multiple data sources including medical record review, Medicare claims data, 1990 Census data, and a patient survey, we examined factors independently associated with utilization of low-volume hospitals for elective THR. We estimated the magnitude of difference in distances for patients undergoing THR in low- and high-volume hospitals. We determined the distance between each patient's residence and the treating hospital using MapQuest. RESULTS: Rural residency, low income, and low educational attainment, as well as belief in the importance of convenient location in the choice of hospital, were associated with higher utilization of low-volume hospitals. Rural and suburban patients who went to low-volume hospitals traveled much less than patients operated upon in high-volume centers. CONCLUSION: Policies aimed at restricting THR to high-volume centers would differentially affect poor, less educated, and rural patients. Voluntary efforts to shift THR to high-volume centers should involve educating these patients and their referring physicians about differences in both short-term and longer-term outcomes between high- and low-volume centers.

Aged↗
PubMed2004

The importance of prebiotic chemistry in the RNA world.

In vitro selection experiments have clearly demonstrated that RNA can perform many of the functions necessary to support an RNA world. Moreover, it appears that novel functions could have readily evolved from existing functional RNA molecules. Therefore, diverse molecular ecosystems could potentially have arisen from an initial, small population of functional replicators. These findings suggest that the sequences of living systems may have been determined in part by chance occurrences at origins. Any extrapolations linking sequences (as opposed to functions) obtained in the laboratory to what may have occurred ca. 4 billion years ago are tenuous at best. Thus, perhaps the best way to understand origins is not by examining relatively unconstrained sequence information, but by examining the inherent constraints imposed by prebiotic chemistry.

Biological Evolution↗
PubMed2003

Exponential growth by cross-catalytic cleavage of deoxyribozymogens.

We have designed an autocatalytic cycle based on the highly efficient 10-23 RNA-cleaving deoxyribozyme that is capable of exponential amplification of catalysis. In this system, complementary 10-23 variants were inactivated by circularization, creating deoxyribozymogens. Upon linearization, the enzymes can act on their complements, creating a cascade in which linearized species accumulate exponentially. Seeding the system with a pool of linear catalysts resulted not only in amplification of function but in sequence selection and represents an in vitro selection experiment conducted in the absence of any protein enzymes.

Base Sequence↗
PubMed2003

Peptide-templated nucleic acid ligation.

Short oligonucleotide and peptide replicators have been described. To determine whether cross-replication could have occurred between such systems, we have attempted to show that peptides can specifically template the ligation of nucleic acids. A complex between a 35-mer anti-Rev RNA aptamer and a 17-mer arginine-rich motif (ARM) peptide from the HIV-1 Rev protein served as a model system. Aptamer half-molecules were activated for ligation via two activation chemistries, representing two distinct kinetic possibilities for early replicators. Cyanogen bromide activation was transient relative to oligonucleotides that terminated with a 5'-iodine and a 3'phosphorothioate, respectively. The Rev ARM specifically enhanced the degree or rate of ligation by both methods: there was a 10-fold increase in the production of full-length aptamer in the presence of cyanogen bromide and a 5.9- to 7.6-fold enhancement in the rate of ligation for stably activated aptamer half-molecules. These results support the possibility that life could have originated with peptide replicators and transitioned to nucleic acid replicators or that peptide and nucleic acid replicators could have been interdependent.

Amino Acid Sequence↗
PubMed2002

In vitro selection of a deoxyribozyme that can utilize multiple substrates.

Deoxyribozymes that could catalyze the formation of an internucleotide phosphorothioester linkage were selected from a random sequence pool. During the course of the selection, the pool was successively challenged with five oligonucleotide substrates, each of which terminated in the same hexanucleotide sequence. Selected deoxyribozyme ligases could use all five substrates, albeit to different degrees, and appeared to form secondary structures that allow differential pairing between the deoxyribozyme and each substrate. These results suggest that early replicases may have been able to bind a variety of oligonucleotide substrates while catalyzing ligation via a common junction.

Animals↗
PubMed2002

ATP-dependent allosteric DNA enzymes.

Effector-activated ribozymes that respond to small organic molecules have previously been generated by appending binding species (aptamers) to ribozymes. In order to determine if deoxyribozymes can similarly be activated by effector molecules, we have appended an anti-adenosine aptamer to a selected deoxyribozyme ligase. The resultant constructs are specifically activated by ATP. Optimization of the joining region resulted in ligases that are activated up to 460-fold by ATP. The selected deoxyribozyme catalyzes ligation largely via a templating mechanism. Effector activation is surprisingly achieved by suppression of the rate of the background, templated ligation reaction in the absence of the effector molecule, probably by misalignment of the oligonucleotide substrates. This novel allosteric mechanism has not previously been observed for nucleic-acid catalysts and is rare even in protein catalysts.

Adenosine Triphosphate↗