Biomedical subjects

Anita Saraf

Publications and source records attributed to Anita Saraf.

7 recordsLinked to original sources

PubMed2007

Fatty acid amide hydrolase inhibitors display broad selectivity and inhibit multiple carboxylesterases as off-targets.

Fatty acid amide hydrolase (FAAH) is the primary regulator of several bioactive lipid amides including anandamide. Inhibitors of FAAH are potentially useful for the treatment of pain, anxiety, depression, and other nervous system disorders. However, FAAH inhibitors must display selectivity for this enzyme relative to the numerous other serine hydrolases present in the human proteome in order to be therapeutically acceptable. Here we employed activity-based protein profiling (ABPP) to assess the selectivity of FAAH inhibitors in multiple rat and human tissues. We discovered that some inhibitors, including carbamate compounds SA-47 and SA-72, and AM404 are exceptionally selective while others, like URB597, BMS-1, OL-135, and LY2077855 are less selective, displaying multiple off-targets. Since proteins around 60kDa constitute the major off-targets for URB597 and several other FAAH inhibitors with different chemical structures, we employed the multi-dimensional protein identification technology (MudPIT) approach to analyze their identities. We identified multiple carboxylesterase isozymes as bona fide off-targets of FAAH inhibitors. Consistently, enzymatic assay confirmed inhibition of carboxylesterase activities in rat liver by FAAH inhibitors. Since carboxylesterases hydrolyze a variety of ester-containing drugs and prodrugs, we speculate that certain FAAH inhibitors, by inhibiting carboxylesterases, might have drug-drug interactions with other medicines if developed as therapeutic agents.

Amidohydrolases↗

PubMed2006

Gene delivery strategies for cartilage tissue engineering.

Tissue engineering is a multifaceted technology developed with a purpose of regenerating complex tissues and organs. Cartilage regeneration continues to challenge engineers and a new wave of efforts focus on developing strategies that provide sustained stimulation to cells by growth factors and other biological molecules to promote their differentiation into chondrocytes. Though significant research is dedicated to developing controlled release systems that deliver growth factors directly, a simpler approach to resolving this dilemma involves converting cells into protein producing factories. This is done through gene delivery. Gene Therapy studies published for articular diseases such as rheumatoid and osteoarthritis provide valuable information regarding different types of cells, gene delivery vectors and genes that can potentially be used to regenerate cartilage. Tissue engineering approaches provide the opportunity to combine two or more strategies used for Gene Therapy thus far and create a cohesive system that addresses both cartilage degeneration and synthesis simultaneously. Adopting gene transfer techniques for tissue engineering is a relatively novel approach, as non-viral gene delivery vectors are continually optimized for therapeutic purposes, and reservations about viral vectors have increasingly dampened their appeal. However, every element involved in gene transfection (i.e., the cell, vector and gene) is a variable which decides the physiological and biomechanical properties of the cartilage produced, and significant work still needs to be done in understanding the contribution of each of these factors to cartilage regeneration.

Animals↗

PubMed2006

Association of Catsper1 or -2 with Ca(v)3.3 leads to suppression of T-type calcium channel activity.

Sperm-specific CatSper1 and CatSper2 proteins are critical to sperm-hyperactivated motility and male fertility. Although architecturally resembling voltage-gated ion channels, neither CatSper1 nor CatSper2 alone forms functional ion channels in heterologous expression systems, which may be related to the absence of yet unidentified accessory subunits. Here we isolated CatSper1- and CatSper2-associated protein(s) from human sperm and analyzed their identities by a multidimensional protein identification technology approach. We identified the T-type voltage-gated calcium channel Ca(v)3.3 as binding to both CatSper1 and CatSper2. The specificity of their interactions was verified by co-immunoprecipitation in transfected mammalian cells. Electrophysiological studies revealed that the co-expression of CatSper1 or CatSper2 specifically inhibited the amplitude of Ca(v)3.3-evoked T-type calcium current without altering other biophysical properties of Ca(v)3.3. Immunostaining studies revealed co-localization of CatSper1 and Ca(v)3.3 on the principal piece of human sperm tail. Furthermore, fluorescence resonance energy transfer analysis revealed close proximity and physical association of these two proteins on the sperm tail. These studies demonstrate that CatSper1 and CatSper2 can associate with and modulate the function of the Ca(v)3.3 channel, which might be important in the regulation of sperm function.

Calcium Channels↗

PubMed2005

Interlaboratory evaluation of endotoxin analyses in agricultural dusts--comparison of LAL assay and mass spectrometry.

Endotoxin exposure is associated with wheeze and asthma morbidity, while early life exposure may reduce risk of allergy and asthma. Unfortunately, it is difficult to compare endotoxin results from different laboratories and environments. We undertook this study to determine if lipopolysaccharide (LPS) extraction efficiency could account for differences among laboratories. We generated and collected aerosols from chicken and swine barns, and corn processing. We randomly allocated side-by-side filter samples to five laboratories for Limulus assay of endotoxin. Lyophilized aliquots of filter extracts were analyzed for 3-hydroxy fatty acids (3-OHFAs) as a marker of LPS using gas chromatography-mass spectrometry. There were significant differences in endotoxin assay and GC-MS (LPS) results between laboratories for all dust types (p < 0.01). Patterns of differences between labs varied by dust type. Relationships between assay and GC/MS results also depended on dust type. The percentages of individual 3-OHFA chain lengths varied across labs (p < 0.0001) suggesting that each lab recovered a different fraction of the LPS available. The presence of large amounts of particle associated LPS and absence of a freezing thawing cycle were associated with lower correlations between LPS and bioactivity, consistent with an absence of Limulus response to cell-bound endotoxin. These data suggest that extraction methods affect endotoxin measurements. The LAL methods may be most suitable when comparing exposures within similar environments; GC-MS offers additional information helpful in optimizing sample treatment and extraction. GC-MS may be of use when comparing across heterogeneous environments and should be considered for inclusion in future studies of human health outcomes.

Aerosols↗

PubMed2003

GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model.

Shotgun proteomics is a powerful tool for identifying the protein content of complex mixtures via liquid chromatography and tandem mass spectrometry. The most widely used class of algorithms for analyzing mass spectra of peptides has been database search software such as SEQUEST. A new sequence tag database search algorithm, called GutenTag, makes it possible to identify peptides with unknown posttranslational modifications or sequence variations. This software automates the process of inferring partial sequence "tags" directly from the spectrum and efficiently examines a sequence database for peptides that match these tags. When multiple candidate sequences result from the database search, the software evaluates which is the best match by a rapid examination of spectral fragment ions. We compare GutenTag's accuracy to that of SEQUEST on a defined protein mixture, showing that both modified and unmodified peptides can be successfully identified by this approach. GutenTag analyzed 33,000 spectra from a human lens sample, identifying peptides that were missed in prior SEQUEST analysis due to sequence polymorphisms and posttranslational modifications. The software is available under license; visit http://fields.scripps.edu for information.

Algorithms↗

PubMed2002

Shotgun identification of protein modifications from protein complexes and lens tissue.

Large-scale genomics has enabled proteomics by creating sequence infrastructures that can be used with mass spectrometry data to identify proteins. Although protein sequences can be deduced from nucleotide sequences, posttranslational modifications to proteins, in general, cannot. We describe a process for the analysis of posttranslational modifications that is simple, robust, general, and can be applied to complicated protein mixtures. A protein or protein mixture is digested by using three different enzymes: one that cleaves in a site-specific manner and two others that cleave nonspecifically. The mixture of peptides is separated by multidimensional liquid chromatography and analyzed by a tandem mass spectrometer. This approach has been applied to modification analyses of proteins in a simple protein mixture, Cdc2p protein complexes isolated through the use of an affinity tag, and lens tissue from a patient with congenital cataracts. Phosphorylation sites have been detected with known stoichiometry of as low as 10%. Eighteen sites of four different types of modification have been detected on three of the five proteins in a simple mixture, three of which were previously unreported. Three proteins from Cdc2p isolated complexes yielded eight sites containing three different types of modifications. In the lens tissue, 270 proteins were identified, and 11 different crystallins were found to contain a total of 73 sites of modification. Modifications identified in the crystallin proteins included Ser, Thr, and Tyr phosphorylation, Arg and Lys methylation, Lys acetylation, and Met, Tyr, and Trp oxidations. The method presented will be useful in discovering co- and posttranslational modifications of proteins.

Acetylation↗

PubMedDate not supplied

Code developments to improve the efficiency of automated MS/MS spectra interpretation.

We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a computational approach to narrow charge states of precursor ions from nominal resolution ion-trap tandem mass spectra. The preprocessing code, 2to3, determines the charge state of the precursor ion using its mass-to-charge ratio (m/z) and fragment ions contained in the tandem mass spectrum. For each possible charge state the program calculates the expected fragment ions that account for precursor ion m/z values. If any one of the numbers is less than an empirically determined threshold value then the spectrum corresponding to that charge state is removed. If both numbers are higher than the threshold value then +2 and +3 copies of the spectrum are kept. We present the comparison of results from protein identification experiments with and without using 2 to 3. It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results. The decrease reduces computer requirements and researcher efforts for analysis of the results.

Crystallins↗