Biomedical subjects

Trushar Patel

Publications and source records attributed to Trushar Patel.

5 recordsLinked to original sources

PubMed2025

Discovery of functional factorless internal ribosome entry site-like structures through virome mining.

All viruses must co-opt the host translational machinery for viral protein synthesis. The dicistrovirus intergenic region internal ribosome entry site (IGR-IRES) utilizes the most streamlined translation mechanism by adopting a triple pseudoknot structure that directly recruits and binds within the intersubunit space of the ribosome and initiates translation from a non-AUG codon. The origin of this unprecedented mechanism is not known. Using a bioinformatics pipeline to examine the diversity and function of IRESs across RNA viromes, we searched for IRES-like RNA structures using RNA covariance models for multiple IRES sub-types, and tested functional IRES by using a dual-fluorescent lentiviral library reporter screen. We identified over >4,700 dicistro-like genomes with ~32% containing putative IRES structures, including novel viral genome arrangements with multiple IRESs and IRESs embedded within open-reading frames (ORFs). Predicted IRESs bound directly to purified ribosomes and supported internal ribosome entry activity in vitro and in vivo. Moreover, internal IRESs embedded within an ORF of monocistronic genomes were functional and operated simultaneously to produce the downstream ORF. We also identified IRES-like structures within non-dicistrovirus viral genomes, including in the families Tombusviridae and Narnaviridae that bound to ribosomes directly and a subset can direct internal ribosome entry. This study provides a framework to map the origin of factorless IRES mechanisms and study the diverse viral strategies utilizing RNA-based mechanisms.

Internal Ribosome Entry Sites↗

PubMed2006

The effect of intracellular ascorbate on the susceptibility of HL60 and Jurkat cells to chemotherapy agents.

Chemotherapy agents initiate tumour cell apoptosis and this is thought to involve oxidative stress. In this study we have investigated the effect of the important antioxidant Vitamin C (ascorbate) on the response of HL60 and Jurkat cells to three chemotherapy drugs, namely etoposide, melphalan and arsenic trioxide (As(2)O(3)). Cells grown in routine culture media are deficient in ascorbate and to determine its effect on chemotherapy drug-induced apoptosis we supplemented the cells prior to drug exposure. We found that ascorbate had a varied effect on apoptosis and cell cycle progression. Etoposide-induced apoptosis in HL60 cells was significantly increased in ascorbate-loaded cells as measured by caspase-3 activation and DNA degradation, and this appeared to reflect a decrease in the number of necrotic cells rather than increased cytotoxicity. In contrast, ascorbate had no effect on etoposide-induced apoptosis in Jurkat cells. In both cell types melphalan-induced apoptosis was unaffected by intracellular ascorbate, whereas both apoptosis and growth arrest with low concentrations of As(2)O(3) were diminished. These results indicate that intracellular ascorbate can affect cell responses to chemotherapy drugs in a complex and somewhat unpredictable manner and that it may play an important role in the responsiveness of tumour cells to chemotherapy regimes.

Antineoplastic Agents↗

PubMed2006

Structures and structure-activity relationships of three mitogenic and complement fixing pectic arabinogalactans from the malian antiulcer plants Cochlospermum tinctorium A. Rich and Vernonia kotschyana Sch. Bip. ex Walp.

Structures of three pectic arabinogalactans, one from Vernonia kotschyana (Vk2a) and two from Cochlospermum tinctorium (Ct50A1 and Ct50A2), and their complement fixation and induction of B cell proliferation in vitro were compared. The polysaccharide Vk2a expressed potent biological activity in both assays compared with Ct50A1 and Ct50A2. Vk2a possessed a very high molecular weight (1150 +/- 20 kDa) compared with Ct50A1 and Ct50A2 which both showed a polydisperse nature with the highest molecular weight polymers in each fraction estimated at approximately 105 kDa (Ct1a) and 640 +/- 100 kDa (Ct2a), respectively. The HMW polymers showed complement fixation in the same range as the native fractions. The arabinogalactan II content was low in Vk2a (2%) compared with that in Ct50A1 (23%) and Ct50A2 (12%). The high molecular weight polymers were subjected to digestion with a beta-d-(1, 3)-galactanase-rich fraction from Driselase, oligomers were isolated by HPAEC, and their finer structures were determined by MALDI- and ES-qoToF-MS, linkage, and monosaccharide composition analyses. Vk2a consists of both a galacturonan core and a rhamnogalacturonan core rich in neutral side chains. The backbones of both Ct-polysaccharides consist mainly of RG-I regions with numerous neutral side chains dominated by galactosyl residues, whereas the homogalacturonan regions seem to be small. Differences in the chain lengths of the 6-linked galacto-oligosaccharides attached to the 3-linked galactan core could not be related to the differences in the potencies of the biological activities observed.

Amino Acids↗

PubMed2005

Damaged starch characterisation by ultracentrifugation.

The relative molecular size distributions of a selection of starches (waxy maize, pea and maize) that had received differing amounts of damage from ball milling (as quantified by susceptibility to alpha-amylase) were compared using analytical ultracentrifugation. Starch samples were solubilised in 90% dimethyl sulfoxide, and relative size distributions were determined in terms of the apparent distribution of sedimentation coefficients g*(s) versus s(20,w). For comparison purposes, the sedimentation coefficients were normalised to standard conditions of density and viscosity of water at 20 degrees C, and measurements were made with a standard starch loading concentration of 8 mg/mL. The modal molecular size of the native unmilled alpha-glucans were found to be approximately 50S, 51S and 79S for the waxy maize, pea and maize amylopectin molecules, respectively, whilst the pea and maize amylose modal molecular sizes were approximately 14S and approximately 12S, respectively. As the amount of damaged starch increased, the amylopectin molecules were eventually fragmented, and several components appeared, with the smallest fractions approaching the sedimentation coefficient values of amylose. For the waxy maize starch, the 50S material (amylopectin) was gradually converted to 14S, and the degradation process included the appearance of 24S material. For the pea starch, the situation was more complicated than the waxy maize due to the presence of amylose. As the amylopectin molecules (51S) were depolymerised by damage within this starch, low-molecular-weight fragments added to the proportion of the amylose fraction (14S)--although tending towards the high-molecular-weight region of this fraction. As normal maize starch was progressively damaged, a greater number of fragments appeared to be generated compared to the other two starches. Here, the 79S amylopectin peak (native starch) was gradually converted into 61 and 46S material and eventually to 11S material with a molecular size comparable to amylose. Amylose did not appear to be degraded, implying that all the damage was focused on the amylopectin fraction in all three cases. Specific differences in the damage profiles for the pea and maize starches may reflect the effect of lipid-complexed amylose in the maize starch.

Amylopectin↗

PubMed2002

Blockade of HIV-1 infection of New World monkey cells occurs primarily at the stage of virus entry.

HIV-1 naturally infects chimpanzees and humans, but does not infect Old World monkeys because of replication blocks that occur after virus entry into the cell. To understand the species-specific restrictions operating on HIV-1 infection, the ability of HIV-1 to infect the cells of New World monkeys was examined. Primary cells derived from common marmosets and squirrel monkeys support every phase of HIV-1 replication with the exception of virus entry. Efficient HIV-1 entry typically requires binding of the viral envelope glycoproteins and host cell receptors, CD4 and either CCR5 or CXCR4 chemokine receptors. HIV-1 did not detectably bind or utilize squirrel monkey CD4 for entry, and marmoset CD4 was also very inefficient compared with human CD4. A marmoset CD4 variant, in which residues 48 and 59 were altered to the amino acids found in human CD4, supported HIV-1 entry efficiently. The CXCR4 molecules of both marmosets and squirrel monkeys supported HIV-1 infection, but the CCR5 proteins of both species were only marginally functional. These results demonstrate that the CD4 and CCR5 proteins of New World monkeys represent the major restriction against HIV-1 replication in these primates. Directed adaptation of the HIV-1 envelope glycoproteins to common marmoset receptors might allow the development of New World monkey models of HIV-1 infection.

Amino Acid Sequence↗