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R A Greene

Publications and source records attributed to R A Greene.

At least 19 recordsLinked to original sources
PubMed2004

Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map.

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.

Blotting, Southern↗
PubMed2004

Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis.

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E < or = e(-10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses.

Arabidopsis↗
PubMed2004

A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice.

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.

Chromosome Mapping↗
PubMed2004

Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1.

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes approximately 21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.

Chromosome Mapping↗
PubMed2004

Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags.

To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.

Chromosome Mapping↗
PubMed2004

A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

Chromosome Mapping↗
PubMed2004

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat.

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

Chromosome Mapping↗
PubMed2001

Current perspectives on benefits and risks of hormone replacement therapy.

Hormone replacement therapy with estrogen alone or with added progestin relieves menopausal symptoms and physical changes associated with depleted endogenous estrogen levels. Estrogen replacement has also demonstrated a clear benefit in the prevention of osteoporosis. Hormone replacement therapy with added progestin maintains spinal bone density, protects against postmenopausal hip fractures, and provides these benefits even when therapy is started after age 60. More recently, additional benefits have emerged. Current estrogen and hormone replacement therapy users have a 34% reduction in the risk of colorectal cancer and a 20% to 60% reduction in the risk of Alzheimer's disease. Until recently, the body of evidence indicated that hormone replacement therapy with estrogen only reduced cardiovascular disease risk by 40% to 50% in healthy patients; whether the findings of 3 ongoing trials will change this conclusion is pending availability of the final results. The many benefits of estrogen and hormone replacement therapy must be weighed against a slight increase in the risk of breast cancer diagnosis with use for 5 or more years, but which disappears following cessation of therapy. Overall, estrogen and hormone replacement therapy improves the quality of life and increases life expectancy for most menopausal women.

Alzheimer Disease↗
PubMed2000

Cerebrovascular changes in the basal ganglia with HIV dementia.

BACKGROUND: HIV dementia is a form of subcortical dementia. Clinical, radiologic, pathologic, and biochemical studies suggest a major contribution of basal ganglia dysfunction to the pathogenesis of this disorder. Many investigators have proposed a contribution of a disrupted blood-brain barrier (BBB) to the pathogenesis of HIV dementia. OBJECTIVE: To identify microvascular abnormalities in vivo in basal ganglia or white matter of persons with HIV dementia. METHODS: Time course of MRI postcontrast enhancement was determined in basal ganglia and white matter of HIV-infected persons without dementia (Memorial Sloan Kettering [MSK] score of 0; n = 4); HIV-infected persons with mild dementia (MSK score of 0.5; n = 2); and HIV-infected persons with moderate-to-severe dementia (MSK > or = 1.0; n = 6). RESULTS: Increased basal ganglia enhancement was observed in individuals with moderate-to-severe dementia relative to nondemented individuals, both immediately and 30 minutes after contrast administration. Decline of basal ganglia enhancement was slower in the moderately to severely demented patients and, when normalized to intravascular enhancement of sagittal sinus, suggested leakage of contrast agent, consistent with increased permeability of BBB. A significant correlation between the postcontrast fractional enhancement at 30 minutes (FE30) and the MSK score was noted. White matter showed no significant differences in postcontrast enhancement among the three groups. CONCLUSION: Increased early enhancement in basal ganglia of the HIV dementia group is consistent with increased regional cerebral blood volume (rCBV). Increased late enhancement is strongly suggestive of BBB disruption. Similar abnormalities were absent in the white matter adjacent to the caudate nucleus.

AIDS Dementia Complex↗
PubMed2000

Obstetric and neonatal outcome of babies weighing more than 4.5 kg: an analysis by parity.

OBJECTIVES: To analyse by parity the obstetric and neonatal outcome of babies delivered weighing more than 4.5 kg. METHODS: All deliveries resulting in a baby weighing more than 4.5 kg, in the 5 years from 1991 to 1995, were identified using a computerised database. The following variables confined to singleton, cephalic pregnancies were recorded: mode of delivery, duration of labour, incidence of shoulder dystocia and admission to the neonatal centre. Outcome measures in primigravidae and multigravidae were compared using the Epi Info package (WHO, Version 6.0b January 1997). RESULTS: There were 32,834 deliveries over the study period and 828 (2.5%) weighed more than 4.5 kg. Birthweight more than 4.5 kg occurred in 1.6% (n=198) of primigravidae and 3.1% (n=630) of multigravidae (P<0.05). Primigravidae had a higher risk of prolonged labour (27.7% vs. 4.9%), operative vaginal delivery (32% vs.9%) and emergency caesarean section (24.2% vs. 5.7%) compared to multigravidae. When delivering a macrosomic baby, primigravidae had a higher incidence of prolonged labour (27% vs. 7.9%), operative vaginal delivery (32% vs.25%) and emergency caesarean section (24.2% vs. 5.7%) compared to normal weight babies. The incidence of shoulder dystocia and elective caesarean section were similar in both primigravidae and multigravidae. CONCLUSIONS: Macrosomic infants have an increased incidence of prolonged labour, operative vaginal delivery and emergency caesarean section compared with normal weight babies and these complications are more pronounced in primigravidae compared to multigravidae. Shoulder dystocia occurs with equal frequency in primigravidae and multigravidae. The poor antenatal predictability of macrosomia, the high rate of vaginal delivery and the low incidence of shoulder dystocia would not support the use of elective caesarean section for delivery of the macrosomic infant either in primigravidae or multigravidae.

Birth Weight↗
PubMed1998

Does increased resistance on umbilical artery Doppler preclude a trial of labour?

OBJECTIVE: To determine whether patients with increased resistance on umbilical artery Doppler velocimetry could be safely allowed a trial of labour. DESIGN: The Coombe Womens' Hospital is a university teaching hospital which takes tertiary referrals. All singleton pregnancies found to have increased resistance (>2 SD above the mean for gestational age) on umbilical artery Doppler ultrasound between 1993 and 1995 inclusively were identified from the ultrasound database and reviewed, retrospectively. Cases where the umbilical artery waveform reverted to normal or deteriorated to absent end diastolic flow on a subsequent scan were excluded. The 118 cases identified were divided into two groups, those that were delivered by elective caesarean section and those that laboured. RESULTS: Forty-five patients were delivered by elective caesarean section and 73 were allowed to labour. In the group that laboured over 90% delivered vaginally and 9.8% were delivered by emergency caesarean section. Three babies had a cord pH less than 7.20 in the group that laboured. Two babies had an Apgar score of less than 7 at 5 min in the group that were delivered electively. There were no neonatal seizures or perinatal deaths in either of the two groups. CONCLUSIONS: This study shows that patients with increased resistance on umbilical artery Doppler can be allowed a trial of labour without compromising the fetal outcome. We would suggest that consideration be given to induction of labour in selected patients as an alternative to elective section.

Adult↗
PubMed1998

What are the maternal implications of a classical caesarean section?

Sixty-two caesarean sections involving a vertical upper uterine segment incision were performed at the Coombe Women's Hospital between January 1983 and December 1995. A detailed chart review was performed. There were no maternal deaths. The maternal outcome was complicated by infection in 49% of cases, and haemorrhage in 19% requiring hysterectomy in two cases. In 15 subsequent pregnancies scar rupture occurred in one case and scar separation in two cases. The perinatal mortality was 200/ 1000; no perinatal death was directly related to the surgery. The operation is associated with a high incidence of maternal morbidity. It also has implications for subsequent deliveries. We recommend that every effort should be made to evaluate critically the need for a caesarean section in the first place and where possible to use a lower uterine segment transverse incision. The patient should be informed of the additional morbidity and long-term risks associated with a vertical incision.

Journal Article↗
PubMed1996

Determination of HIV-1 susceptibility to reverse transcriptase (RT) inhibitors by a quantitative cell-free RT assay.

BACKGROUND: Mutations in the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) gene confer resistance to antiviral drugs acting on RT. Current methods employed to detect such resistance require time-consuming culture techniques during which selective pressures may affect the outcome of the test. OBJECTIVES: We sought to determine whether drug-susceptible and drug-resistant HIV-1 derived from clinical specimens could be distinguished by the effects of the active form of the drug on the enzyme activity in a quantitative, cell-free RT assay. STUDY DESIGN: Polyethylene glycol (PEG)-precipitated virus was obtained from 7-day culture supernatants. RT activity in the lysed viral extracts was measured in the presence of increasing concentrations of the active form of the drug being tested. IC50 (50% inhibitory concentration) values were determined by application of the median effect equation. RESULTS: Assays from nine post-nevirapine therapy isolates gave IC50 values at least 2 logs greater than pre-nevirapine isolates. The method also correctly distinguished between isolates sensitive and resistant to 2',3'-dideoxyinosine (ddI), but not between the ZDV-sensitive and ZDV-resistant isolates tested. The results agreed with data obtained by sequencing and by culture-based susceptibility assays.

Cell-Free System↗
PubMed1987

Nail changes associated with diabetes mellitus.

The varied systemic pathologic alterations that occur in patients with diabetes mellitus may result in profound changes that affect the nail unit. These findings vary from simple onycholysis to a spectrum of infectious processes, as well as extensive, irreversible destruction. The influence of the vascular and neurologic systems in producing these clinical findings is presented. The purpose of this review is to alert the physician to another aspect of diabetes mellitus, namely, its effect on the various components of the nail unit.

Diabetes Complications↗