Stretchable receive coil for 7T small animal MRI.

Receive coils used in small animal MRI are rigid, inflexible surface loops that do not conform to the anatomy being imaged. The recent trend toward design of stretchable coils that are tailored to fit any anatomical curvature has been focused on human imaging. This work demonstrates the application of stretchable coils for small animal imaging at 7T. A stretchable coil measuring 3.5 × 3.5 cm was developed for acquisition of rat brain and spine images. The SNR maps of the stretchable coil were compared with those of a traditional flexible PCB coil and a commercial surface coil. Stretch and conformance testing of the coil was performed. Ex vivo images of rat brain and spine from the stretchable a coil was acquired using T1 FLASH and T2 Turbo RARE sequences. The axial phantom SNR maps showed that the stretchable coil provided 48.5% and 42.8% higher SNR than the commercial coil for T1-w and T2-w images within the defined ROI. A 33% increase in average penetration depth was observed within the ROI using the stretchable coil when compared to the commercial coil. The ex-vivo rat brain and spine images showed distinguishable anatomical details. Stretching the coil reduced the resonant frequency with reduction in SNR, while the conformance to varying sample volumes increased the resonant frequency with decreased SNR. This study also features an open-source plug-and-play system with preamplifiers that can be used to interface surface coils with the 7T Bruker scanner.

Parametric Design of a 3D-Printed Removable Common-Mode Trap for Magnetic Resonance Imaging.

Radiofrequency coils are utilized during transmit and receive of MRI signals. Cable traps remove common-mode current from the coaxial cable shield, which helps improve the image quality and reduces risks of burns to the patient. Traditional cable traps use wounded coaxial cables that limit the flexibility in the design process. Floating cable traps were introduced which eliminated any physical connection between the trap and coaxial cable, allowing complete flexibility in design and placement. However, the design process of floating cable traps is iterative and may take several rounds of 3D modeling. This work seeks to optimize the design process through the use of parametric design methodologies. The proposed methodology allows for 3D printing the floating cable trap after inputting the design parameters. The cable trap was able to attenuate currents in the coaxial shields to -48 dB, highlighting its performance and design robustness.

Restriction fragment mass polymorphism (RFMP) analysis based on MALDI-TOF mass spectrometry for detecting antiretroviral resistance in HIV-1 infected patients.

Viral genotype assessment is important for effective clinical management of HIV-1 infected patients, especially when access and/or adherence to antiretroviral treatment is reduced. In this study, we describe development of a matrix-assisted laser desorption/ionization-time of flight mass spectrometry-based viral genotyping assay, termed restriction fragment mass polymorphism (RFMP). This assay is suitable for sensitive, specific and high-throughput detection of multiple drug-resistant HIV-1 variants. One hundred serum samples from 60 HIV-1-infected patients previously exposed to nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) were analysed for the presence of drug-resistant viruses using the RFMP and direct sequencing assays. Probit analysis predicted a detection limit of 223.02 copies/mL for the RFMP assay and 1268.11 copies/mL for the direct sequencing assays using HIV-1 RNA Positive Quality Control Series. The concordance rates between the RFMP and direct sequencing assays for the examined codons were 97% (K65R), 97% (T69Ins/D), 97% (L74VI), 97% (K103N), 96% (V106AM), 97% (Q151M), 97% (Y181C), 97% (M184VI) and 94% (T215YF) in the reverse transcriptase coding region, and 100% (D30N), 100% (M46I), 100% (G48V), 100% (I50V), 100% (I54LS), 99% (V82A), 99% (I84V) and 100% (L90M) in the protease coding region. Defined mixtures were consistently and accurately identified by RFMP at 5% relative concentration of mutant to wild-type virus while at 20% or greater by direct sequencing. The RFMP assay based on mass spectrometry proved to be sensitive, accurate and reliable for monitoring the emergence and early detection of HIV-1 genotypic variants that lead to drug resistance.

Prevalence and predictors of traditional medicine utilization among persons living with AIDS (PLWA) on antiretroviral (ARV) and prophylaxis treatment in both rural and urban areas in South Africa.

Previous studies have reported that majority of antiretroviral (ARV) treatment-naïve patients use traditional medicine (TM). Given that TM use is ubiquitous in South Africa especially for chronic conditions, there is a potential for ARV non-adherence and serious drug interactions among patients with HIV/AIDs who use TM. The motivating factors for TM use in HIV/AIDS patients on ARV and prophylaxis treatment have not been well defined in South Africa. This study aimed to investigate the prevalence, facilitators, predictors, and types of TM used among persons living with HIV/AIDS on antiretroviral treatment. The study was a cross-sectional survey which involved 100 participants enrolled at ARV clinics in two South African provinces. Univariate and bivariate analyses were performed to assess the relationships between variables and potential predictors of TM. Sixteen percent of participants on ARV reported TM use. Seventy-nine percent used TM prior to a diagnosis of HIV. Participants were more likely to use TM if they were from a rural province, female, older, unmarried, employed, had limited education, or were HIV-positive for less than five years. TM users reported utilizing herbal or medicinal mixtures that were claimed to heal all conditions. This study provides insights into the treatment modalities selected by patients with HIV/AIDS in South Africa who are receiving ARV. This study revealed that less than 20% of participants co-used TM and ARV. However, close to 80% of participants utilize TM before contracting HIV, which is in keeping with approximate estimates by the WHO.

Why HIV positive patients on antiretroviral treatment and/or cotrimoxazole prophylaxis use traditional medicine: perceptions of health workers, traditional healers and patients: a study in two provinces of South Africa.

The study explored the perceptions, knowledge and attitudes of patients, health workers and traditional healers about the use of traditional medicine and Anti Retroviral Therapy (ART). The study explored the perceptions, knowledge and attitudes of patients, health workers and traditional healers about the use of traditional medicine and Anti Retroviral Therapy (ART), using an exploratory qualitative design in two provinces of South Africa: an urban township health facility in the Western Cape, and a rural district hospital in KwaZulu-Natal (KZN) with antennal HIV rate of 32% and 28%'respectively. In-depth interviews were conducted with 14 participants: six HIV patients on ART and using Traditional Medicine(TM), two doctors, two nurses and four traditional healers. Two focus group discussions -one at each site - were held with community health workers who work with HIV-positive patients (Western Cape [5] and in KZN [4]). Patient said to have used Traditional Healing Practices (THP) before they were diagnosed with HIV, and some who have been diagnosed with HIV continue using TM in conjunction with ART and/or Cotrimoxazole prophylaxis. Patients preferred not to disclose THP to health professionals because of lack of support and understanding. Patients utilize THP because of family expectations, privacy and confidentiality, especially when they have not disclosed their HIV status. Healthcare professionals had strong negative opinions about THP, especially for HIV-positive patients. Traditional healers supported the patient's rationale for THP use. This study revealed a need to better understand factors involved in patients' choosing to use THP concurrently with ART.

Tulbaghia alliacea phytotherapy: a potential anti-infective remedy for candidiasis.

The reproductive health of individuals is severely compromised by HIV infection, with candidiasis being the most prevalent oral complication in patients. Although not usually associated with severe morbidity, oropharyngeal candidiasis can be clinically significant, as it can interfere with the administration of medications and adequate nutritional intake, and may spread to the esophagus. Azole antifungal agents are commonly prescribed for the treatment and prophylaxis of candidal infections, however, the emergence of drug resistant strains and dose limiting toxic effects has complicated the treatment of candidiasis. Consequently, safe and effective and affordable medicine is required to combat this fungus. Commercial garlic (Allium sativum) has been used since time immemorial as a natural antibiotic, however, very little is known about the antifungal properties of two indigenous South African species of garlic, namely Tulbaghia alliacea and Tulbaghia violacea, used as folk medicines for a variety of infections. This study compares the in vitro anticandidal activity of Tulbaghia alliacea, Tulbaghia violacea and Allium sativum extracts. It was found that the greatest concentrations of inhibitory components were extracted by chloroform or water. The IC50 concentrations of Tulbaghia alliacea were 0.007-0.038% (w/v). Assays using S. cerevisiae revealed that the T. alliacea extract was fungicidal, with a killing half-life of approximately 2 h. This inhibitory effect of the T. alliacea extracts was observed via TLC, and may be due to an active compound called marasmicin, that was identified using NMR. This investigation confirms that extracts of T. alliacea exhibit anti-infective activity against candida species in vitro.

Expression of urokinase plasminogen activator and receptor in conjunction with the ets family and AP-1 complex transcription factors in high grade prostate cancers.

Expression of the urokinase plasminogen activator (uPA) and its receptor (uPAR) correlates with tumour cell invasiveness and helps to determine the prognosis of prostate and other cancers. The purpose of this study was to establish in prostate cancer, the ets family and AP-1 complex transcription factors that might activate the inducible AP-1 and AP-1/PEA3 elements of the uPA enhancer. uPA and uPAR were expressed preferentially in adenocarcinoma cells, but not the stroma of high grade prostate cancers. The ets family paralogues Fli-1 and Elf-1 were also highly expressed in adenocarcinoma cells of the majority of cancers, while Erg 1,2 and Ets-2 were expressed in a minority of cancers and Elk-1, PEA3 and PU.1 were minimally expressed. A minority of cancers expressed high levels of cytoplasmic and/or nuclear c-Jun and c-Fos transcription factors. We speculate as to the molecular basis for such expression.

RNA polymerase I holoenzymes.

In eukaryotes, holoenzymes are large preassembled complexes containing RNA polymerases and variable sets of general transcription initiation factors and cofactors that are important for the regulation of gene expression. Recent advances in purification and characterization of RNA polymerase I holoenzyme from plants provide experimental data suggesting that it plays a key role in transcriptional regulation. These findings have a significant implication on our understanding of the mechanisms of promoter recognition, assembly of transcription initiation complexes, RNA chain elongation and transcription termination.

NMR structure of the N-terminal J domain of murine polyomavirus T antigens. Implications for DnaJ-like domains and for mutations of T antigens.

The NMR structure of the N-terminal, DnaJ-like domain of murine polyomavirus tumor antigens (PyJ) has been determined to high precision, with root mean square deviations to the mean structure of 0.38 A for backbone atoms and 0.94 A for all heavy atoms of ordered residues 5-41 and 50-69. PyJ possesses a three-helix fold, in which anti-parallel helices II and III are bridged by helix I, similar to the four-helix fold of the J domains of DnaJ and human DnaJ-1. PyJ differs significantly in the lengths of N terminus, helix I, and helix III. The universally conserved HPD motif appears to form a His-Pro C-cap of helix II. Helix I features a stabilizing Schellman C-cap that is probably conserved universally among J domains. On the helix II surface where positive charges of other J domains have been implicated in binding of hsp70s, PyJ contains glutamine residues. Nonetheless, chimeras that replace the J domain of DnaJ with PyJ function like wild-type DnaJ in promoting growth of Escherichia coli. This activity can be modulated by mutations of at least one of these glutamines. T antigen mutations reported to impair cellular transformation by the virus, presumably via interactions with PP2A, cluster in the hydrophobic folding core and at the extreme N terminus, remote from the HPD loop.

Identity elements and aminoacylation of plant tRNATrp.

Mutation of the Arabidopsis thaliana tRNA (Trp)(CCA) anticodon or of the A73 discriminator base greatly diminishes in vitro aminoacylation with tryptophan, indicating the importance of these nucleotides for recognition by the plant tryptophanyl-tRNA synthetase. Mutation of the tRNA (Trp)(CCA) anticodon to CUA so as to translate amber nonsense codons permits tRNA (Trp)(CCA) to be aminoacylated by A.thaliana lysyl-tRNA synthetase. Thus, translational suppression by tRNA (TRP)(CCA) observed in plant cells includes significant incorporation of lysine into protein.

Nonsense and missense translational suppression in plant cells mediated by tRNA(Lys).

A nuclear tRNA(Lys) gene from Arabidopsis thaliana was cloned and mutated so as to express tRNAs with altered anticodons which bind to a UAG nonsense (amber) codon and to the Arg (AGG), Asn (AAC,AAT), Gln (CAG) or Glu (GAG) codons. Concomitantly, a codon in the firefly luciferase gene for a functionally important Lys was altered to an amber codon, or to Arg, Asn, Gln, Glu, Thr and Trp codons, so as to construct reporter genes reliant upon incorporation of Lys. The altered tRNA(Lys) and luciferase genes were introduced into Nicotiana benthamiana protoplasts and expression of the mutated tRNAs was verified by translational suppression of the mutant firefly luciferase genes. Expression of the amber suppressor tRNA(LysCUA) from non-replicative vectors promoted 10-40% suppression of the luciferase nonsense reporters while expression of the amber and missense tRNA(Lys) suppressor genes from a geminivirus vector capable of replication promoted 30-80% suppression of the luciferase nonsense reporter and up to 10% suppression of the luciferase missense reporters with Arg, Asn, Gln and Glu codons.

AtMSI4 and RbAp48 WD-40 repeat proteins bind metal ions.

The mammalian RbAp48 protein is the most extensively studied member of the conserved family of Msi1-like WD-40 repeat proteins, which are components of complexes involved in the assembly and modification of chromatin. We have isolated a plant homolog of RbAp48, AtMSI4. By metal affinity chromatography, zinc blotting and atomic absorption analysis, we demonstrate that purified recombinant RbAp48 and AtMSI4 proteins bind 3-4 metal ions per molecule of protein. Metal competition assays indicate a preference for zinc. Both N- and C-terminal halves of RbAp48 and AtMSI4 display zinc binding activity, suggesting it is an intrinsic property of the propeller structures likely to be formed by these proteins. Metal binding might mediate and/or regulate protein-protein interactions which are functionally important in chromatin metabolism.

Tiny T antigen: an autonomous polyomavirus T antigen amino-terminal domain.

Three mRNAs from the murine polyomavirus early region encode the three well-characterized tumor antigens. We report the existence of a fourth alternatively spliced mRNA which encodes a fourth tumor antigen, tiny T antigen, which comprises the amino-terminal domain common to all of the T antigens but is extended by six unique amino acid residues. The amount of tiny T antigen in infected cells is small because of its short half-life. Tiny T antigen stimulates the ATPase activity of Hsc70, most likely because of its DnaJ-like motif. The common amino-terminal domain may interface with chaperone complexes to assist the T antigens in carrying out their diverse functions of replication, transcription, and transformation in the appropriate cellular compartments.

Regulated expression of plant tRNA genes by the prokaryotic tet and lac repressors.

The prokaryotic tet operator (tetO) sequence was inserted at positions upstream and downstream of sequences encoding the Arabidopsis thaliana tRNA(Lys)AUC or tRNA(Trp)AUC suppressor tRNAs, and tRNA expression in carrot protoplasts was measured by translational suppression of a nonsense codon in a luciferase reporter gene. Regulation of tRNA expression by the tetracycline repressor (tetR) occurred from genes with the tetO inserted at position -1 (for the tRNA(Trp)AUC gene), or at positions -2, -6 and -10 (for the tRNA(Lys)AUC gene), and repression reached 90%. The inducer tetracycline (Tc) restored tRNA expression. Similarly, carrot protoplasts transfected with human tRNA(Ser)AUC genes containing the lac operator (lacO) in their 5'-flanking sequence with or without the lac repressor (lacI) gene, conditionally expressed tRNAs which suppressed the luciferase reporter. Up to 30-fold repression occurred by the lactose repressor when lacO was located at position -1 of the tRNA(Ser)AUC coding sequence. In the presence of the inducer isopropyl-beta-thiogalactoside (IPTG), repression was relieved. These results demonstrate that sequences flanking tRNA genes can strongly influence tRNA expression in plants, and in a conditional fashion when bound by inducible proteins.

AP1 enhances polyomavirus DNA replication by promoting T-antigen-mediated unwinding of DNA.

An early step in the initiation of polyomavirus DNA replication is viral large-T-antigen-mediated unwinding of the origin. We report that components of the AP1 transcription factor, Fos and Jun, interact with T antigen in vitro to enhance unwinding of the viral origin. This provides a biochemical basis for the capacity of AP1 to activate viral DNA replication in vivo.

Sequences flanking the pentanucleotide T-antigen binding sites in the polyomavirus core origin help determine selectivity of DNA replication.

Replication of the genomes of the polyomaviruses requires two virus-specified elements, the cis-acting origin of DNA replication, with its auxiliary DNA elements, and the trans-acting viral large tumor antigen (T antigen). Appropriate interactions between them initiate the assembly of a replication complex which, together with cellular proteins, is responsible for primer synthesis and DNA chain elongation. The organization of cis-acting elements within the origins of the polyomaviruses which replicate in mammalian cells is conserved; however, these origins are sufficiently distinct that the T antigen of one virus may function inefficiently or not at all to initiate replication at the origin of another virus. We have studied the basis for such replication selectivity between the murine polyomavirus T antigen and the primate lymphotropic polyomavirus origin. The murine polyomavirus T antigen is capable of carrying out the early steps of the assembly of an initiation complex at the lymphotropic papovavirus origin, including binding to and deformation of origin sequences in vitro. However, the T antigen inefficiently unwinds the origin, and unwinding is influenced by sequences flanking the T antigen pentanucleotide binding sites on the late side of the viral core origin. These same sequences contribute to the replication selectivity observed in vivo and in vitro, suggesting that the inefficient unwinding is the cause of the replication defect. These observations suggest a mechanism by which origins of DNA replication can evolve replication selectivity and by which the function of diverse cellular origins might be temporally activated during the S phase of the eukaryotic cell cycle.

Analysis of the role of 5' and 3' flanking sequence elements upon in vivo expression of the plant tRNATrp genes.

We have isolated the majority (seven) of the tRNA(Trp) genes of Arabidopsis and have studied the 5' and 3' flanking sequence requirements for their efficient expression in vivo by using an assay requiring translational suppression of the luciferase reporter gene. The expressed tRNA(Trp) genes contain no highly conserved 5' flanking sequences; however, these sequences are distinctly AT rich, contain several possible TATA elements, and are bound in vitro by recombinant plant TATA binding protein. Replacement of the natural 5' flanking sequences with three different sequences lacking TATA elements reduced expression in vivo up to 10-fold; the same effect was observed when the TATA elements of the natural 5' sequences were inactivated by point mutations. Introduction of a single TATA element from the adenovirus major late promoter into an artificial 5' flanking region of the tRNA(Trp) gene enhanced expression in vivo when the TATA element was placed at position -32 relative to the first nucleotide of the mature tRNA sequence, but not when it was placed at position -24. Primer extension analyses of in vitro transcripts revealed that the position of the TATA element helps dictate the start site of transcription. Efficient expression of the tRNA genes in vivo also required 3' flanking sequences capable of terminating transcription.

Hsp70 heat shock protein cognate is expressed and stored in developing tomato pollen.

Pollen of angiosperms lacks the ability to respond to heat stress by synthesizing heat shock proteins (hsps). In tomato developing microspores were found to have 70 kDa heat shock proteins (hsp70s) present throughout development, even in the absence of heat stress. Heat shock protein family members expressed in the absence of heat stress are called cognate (hsc70) genes. Antisense RNA and antibody probes were used for in situ hybridizations which detected hsc70 expression in developing pollen of immature buds. Hsc70 mRNA transcripts and proteins were detected in nonstressed sporogenous tissues, microspores and in pre-tapetal layers during early pollen development. While immunoblot analysis detected hsc70 proteins stored in mature pollen, heat stress could not induce the synthesis of new hsp70 protein as measured by 35S-methionine labeling followed by immunoprecipitation.