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Biomedical subjects

R Hull

Publications and source records attributed to R Hull.

At least 37 records · Page 2Linked to original sources
PubMed1998

Applications of Ion Microscopy and In Situ Electron Microscopy to the Study of Electronic Materials and Devices.

: We discuss the application of ion microscopy and in situ electron microscopy to the study of electronic and optical materials and devices. We demonstrate how the combination of in situ transmission electron microscopy and focused ion beam microscopy provides new avenues for the study for such structures, enabling extension of these techniques to the study of dopant distributions, nanoscale stresses, three-dimensional structural and chemical reconstruction, and real-time evolution of defect microstructure. We also discuss in situ applications of thermal, mechanical, electrical, and optical stresses during transmission electron microscopy imaging.

Journal Article↗
PubMed1998

Cloning and sequence analysis of banana streak virus DNA.

Banana streak virus (BSV), a member of the Badnavirus group of plant viruses, causes severe problems in banana cultivation, reducing fruit yield and restricting plant breeding and the movement of germplasm. Current detection methods are relatively insensitive. In order to develop a PCR-based diagnostic method that is both reliable and sensitive, the genome of a Nigerian isolate of BSV has been sequenced and shown to comprise 7389 bp and to be organized in a manner characteristic of badnaviruses. Comparison of this sequence with those of other badnaviruses showed that BSV is a distinct virus. PCR with primers based on sequence data indicated that BSV sequences are present in the banana genome.

Amino Acid Sequence↗
PubMed1998

Evaluation of a candidate human immunodeficiency virus type 1 (HIV-1) vaccine in macaques: effect of vaccination with HIV-1 gp120 on subsequent challenge with heterologous simian immunodeficiency virus-HIV-1 chimeric virus.

Human immunodeficiency virus type 1 (HIV-1) envelope vaccines can now be evaluated for efficacy in macaques by challenging with chimeric viruses in which the env, tat and rev genes of simian immunodeficiency virus (SIV) have been replaced by those of HIV-1. Most experiments have so far been conducted using gp120 molecules derived from T-cell-adapted LAI or MN strains of HIV-1, which predominantly use the CXCR-4 co-receptor. These vaccines protect against infection by apathogenic chimeric virus carrying the same envelope sequences. In the experiment described here, four macaques were vaccinated with W61D gp120 derived from a low passage Dutch isolate and capable of inhibiting the binding of MIP1beta to the co-receptor CCR-5. This vaccine was potent, inducing high titres of binding and neutralizing antibodies against the homologous HIV-1 and tenfold lower titres against a heterologous challenge virus (SHIV(SF33)) in which the env, tat and rev genes of SIV had been replaced by those of a San Francisco isolate, HIV-1(SF33). Despite strong immune responses to the vaccine there was no evidence that it protected against challenge with this chimeric virus. The antigenic divergence between vaccine and challenge virus or the increased virulence of the challenge virus may be responsible for the inability of this vaccine to protect against infection by SHIV(SF33).

AIDS Vaccines↗
PubMed1997

Variation in coat protein genes among five geographically different isolates of rice tungro spherical virus.

The variation in the sequence of the coat protein genes of four isolates of rice tungro spherical virus from different countries, Malaysia, Thailand, India and Bangladesh, was compared with an isolate from the Philippines. The evidence from RT-PCR, Southern blot hybridization and sequences of the coat protein genes indicated that the isolates appeared to fall into two groups. One comprised the Philippine and Malaysian isolates (about 95% sequence similarity) and the other the Bangladeshi and Indian isolates, the sequences of which differed by about 15% from that of the Philippine isolate. The Thai isolate seemed to be a mixture of these two subgroups.

Amino Acid Sequence↗
PubMed1997

Comparison of ELISA and RT-PCR for the detection of beet yellows closterovirus in plants and aphids.

A reverse-transcription polymerase chain reaction (RT-PCR) was developed to detect beet yellows closterovirus (BYV) in plants and single aphids using primers spanning the conserved regions of the published sequences of the coat protein gene and open reading frames 7 and 8. Three total RNA extraction procedures were examined and all were found to produce RNA of sufficient quality for RT-PCR, although the RNA extraction kit supplied by Flowgen was found to be the most versatile for the extraction of BYV from individual aphids. When 60 aphids, which had fed on virus infected sugar beet were tested by RT-PCR, 55% of individuals were found to contain BYV. Two groups of 36 individual aphids were tested by TAS-ELISA using a specific BYV monoclonal antibody; 53% gave positive absorbance values when a substrate amplification system was used, but none was found to contain virus when the system was replaced with the substrate p-nitrophenyl phosphate. An immunocapture RT-PCR method was shown to detect BYV regardless of whether the RNA had been extracted from the trapped particles or the reverse transcription and PCR mixtures were added to the wells containing intact particles. The RT-PCR method is now used to determine the numbers of BYV carrying aphids migrating into sugar-beet crops.

Animals↗
PubMed1997

Comparison of sequences of RNAs 3 and 4 of rice stripe virus from China with those of Japanese isolates.

The sequences were determined of RNAs 3 and 4 of a Chinese isolate (Y) of rice stripe tenuivirus (RStV) and were compared with those of two RStV isolates (M and T) from Japan. Both RNAs of the Y isolate were longer than those of the M and T isolates. There was almost complete conservation in the 5' and 3' non-coding regions for each RNA between the isolates. The analogous ambisense coding regions for each isolate were exactly the same size and the sequences were highly conserved. The major differences were in the intergenic regions, the sizes of which accounted for the differences in size of each RNA of the three isolates. There were no obvious patterns of differences in comparisons of the two RNA over the three isolates. The significance of the similarities and differences in sequences of isolates of RStV separated by more than 3500 km is discussed.

Base Sequence↗
PubMed1997

Genetic variation of rice tungro bacilliform virus in the Philippines.

Restriction fragment length polymorphisms (RFLPs) were found in 27 full genome length clones from a glasshouse isolate of rice tungro bacilliform pararetrovirus (RTBV) from the International Rice Research Institute (IRRI), the Philippines and from clones from 5 field isolates from different parts of the Philippines. There was much less variation between the IRRI clones than between the field isolate clones. The RFLPs were due to single base changes and represented about 10% of the potential sites. Sequencing across the region between nt 7772 and 7989 confirmed that the field isolates differed from the published sequence more than did the IRRI clones. The most common substitutions were G > A, A > G and T > C. Sequence heterogeneity was also noted in PCR products from RTBV DNA from the isolates. These observations are discussed in relation to the quasispecies population concept of viruses.

Badnavirus↗
PubMed1996

Sequence of rice hoja blanca tenuivirus RNA-2.

The sequence of rice hoja blanca tenuivirus RNA-2 is analysed and compared to its counter-part in rice stripe tenuivirus. The RNA encodes two proteins, in an ambisense arrangement. The 94 kD pc2, located in the complementary sense RNA, has several features typical of viral membrane (glyco)proteins, and also has regions of local homology to the glycoproteins of the Phleboviruses (Bunyaviridae). The 23 kD pv2 lies in the viral sense RNA and has two small conserved domains that are almost exclusively found in retro-viral membrane glycoproteins. Its genome location is analogous to the NSm protein of several of the Bunyaviridae species, which is thought to have a membrane-related function. The two open reading frames are separated by a large intergenic region which, in common with the other tenuivirus ambisense RNA segments, has a short region that is highly conserved between RStV and RHBV. The significance of these results with respect to the virus structure and gene expression is discussed.

Amino Acid Sequence↗
PubMed1996

Rice tungro spherical virus: nucleotide sequence of the 3' genomic half and studies on the two small 3' open reading frames.

Rice tungro spherical virus (RTSV) consists of a single-stranded RNA genome of about 12 kilobases that contains one large open reading frame, ORF 1 and two small ORFs 2 and 3 at its 3' end (Shen et al., 1993, Virology 193:621-630); it was suggested that ORF 2 was expressed via a frameshift. To study the genomic information of RTSV and the variation between different RTSV isolates, the 3' half of a Philippine isolate and parts of a Thai and an Indian isolate were cloned and sequenced. Significant sequence differences were found in ORF 2 and in the 3' non-translated region. Additional stop codons have been revealed in the previously described ORF 2 in several independent clones from the three different virus isolates, the most conserved stop codon in the middle of ORF 2 being confirmed by direct RNA sequencing. These results suggest that ORF 2 could only express a peptide of about 5 kDa instead of 12 kDa as proposed earlier. Polyclonal antisera were raised against ORF 2 and 3 proteins as fusions with glutathione-S-transferase. Using these antisera we failed to detect any virus-specific peptides in extracts from infected rice plants and in virus preparations. The nucleotide sequence of the 3' end of our RTSV isolates contains several small ORFs and does not contain a repeat of 256 nucleotides found in the published sequence. These results indicate that RTSV could contain an unusually long 3' non-coding region of 1240 nucleotides in length.

Amino Acid Sequence↗
PubMed1996

Rapid, small scale purification of rice hoja blanca and Echinochloa hoja blanca tenuivirus ribonucleoprotein.

Highly purified tenuivirus ribonucleoprotein was obtained from small amounts of leaf tissue by sedimenting the ribonucleoprotein particles from debris-free plant extract into a 30% sucrose cushion, in 1.5-mL microfuge tubes. Using this protocol, significant size differences were discovered in the double-stranded forms of the viral genomic RNAs of rice hoja blanca tenuivirus and a tenuivirus isolated from Echinochloa colonum, a common weed of rice cultivation.

Oryza↗
PubMed1996

Analysis of gram negative recolonization of the neuropathic bladder among patients with spinal cord injuries.

Over a 4 year period, 119 acute spinal cord injury (SCI) patients were enrolled in this study. The 101 males and 18 females had a mean age of 35.9 years (range 16-87). Sixty-two patients were tetraplegic and 57 were paraplegic. All patients had a urine specimen taken for culture, colony count and sensitivity once weekly while they were receiving intermittent catheterization. Of these, 22 patients (18.5%), none of whom had underlying genito-urinary (GU) pathology, developed recolonization by an organism of the same species and genus previously cultured. All 22 reached sterile-urine between colonizations after being treated with antibiotics for at least 7 days. The 16 males and six females had a mean age of 35.1 years (range 17-79). Sixteen were tetraplegic and six were paraplegic. Plasmid analysis (PA) was used to determine whether these recolonizations were from the same or from a different strain. In those instances where the bacteria harbored no plasmids or where the results of plasmid analysis were otherwise inconclusive, bacteria were also compared using restriction fragment length polymorphism (RFLP) analysis. Recolonization was caused primarily by E. coli and K. pneumoniae. While there was no significant difference between the two organisms with respect to the number of days when sterile urine occurred to the time when recolonization was observed, there were significant differences seen in both organisms with regard to the time lapse from one colonization to the next: the average number of days to recolonization with an identical organism was 10.3 days, whereas with a different strain it was 15.9 days (P < 0.04). When a different organism was cultured between the recolonizations, the mean recolonization interval was 17.9 days. When no intervening organism occurred, the interval was 9.5 days (P < 0.005). Both intervals measured the days from the first sterile urine after the first colonization to the next colonization. These data indicate the proclivity for two common Gram negative normal bowel inhabitants to recolonize the neuropathic bladder of spinal cord injured patients even after adequate treatment. PA and RFLP provide a means of discriminating between relapses by the same organism versus recurrences by a different organism of the same species and genus. Those with the same identity tend to recur sooner than those of different identities and may be suspected when relapse occurs within two weeks of cessation of 7 day course of antibiotics. While an intervening organism may delay the relapse (or recurrence), it does not prevent it and identical organisms can reappear even after adequate therapeutic regimens. Since none of the patients in this study had GU pathology, recolonization by an identical strain (relapse) does not necessarily warrant an extensive investigation for disease within the GU tract.

Adolescent↗