Biomedical subjects

R Sears

Publications and source records attributed to R Sears.

At least 19 recordsLinked to original sources

PubMed2001

A draft annotation and overview of the human genome.

BACKGROUND: The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. RESULTS: We report here a functionally annotated human gene index placed directly on the genome. The index is based on the integration of public transcript, protein, and mapping information, supplemented with computational prediction. We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. In addition, initial sequence analysis reveals highly ordered chromosomal landscapes associated with paralogous gene clusters and distinct functional compartments. Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. Such a global approach had previously been described only for chromosomes 21 and 22, which together account for 2.2% of the genome. CONCLUSIONS: We estimate that the genome contains 65,000-75,000 transcriptional units, with exon sequences comprising 4%. The creation of a comprehensive gene index requires the synthesis of all available computational and experimental evidence.

Chromosome Mapping↗

PubMed2001

Field cooling induced changes in the antiferromagnetic structure of NiO films.

The magnetic anisotropy in antiferromagnetic 500 A thick NiO films, before and after the establishment of an exchange bias field with Co84Fe16 ferromagnetic layers, was measured using magnetic linear dichroism in soft x-ray absorption. Both <111> textured NiO and untextured NiO films show exchange-bias induced in-plane magnetic anisotropy of nearly equal magnitude and with the Ni moment axis being nearly parallel to the exchange bias field direction. These results represent the first observation of the key step in the exchange biasing process, namely, repopulation of the antiferromagnetic domains whose magnetization axis is closest to the exchange bias field direction.

Journal Article↗

PubMed2001

Myc requires distinct E2F activities to induce S phase and apoptosis.

Previous work has shown that the Myc transcription factor induces transcription of the E2F1, E2F2, and E2F3 genes. Using primary mouse embryo fibroblasts deleted for individual E2F genes, we now show that Myc-induced S phase and apoptosis requires distinct E2F activities. The ability of Myc to induce S phase is impaired in the absence of either E2F2 or E2F3 but not E2F1 or E2F4. In contrast, the ability of Myc to induce apoptosis is markedly reduced in cells deleted for E2F1 but not E2F2 or E2F3. From this data, we propose that the induction of specific E2F activities is an essential component in the Myc pathways that control cell proliferation and cell fate decisions.

Adenoviridae↗

PubMed2001

Assembly, annotation, and integration of UNIGENE clusters into the human genome draft.

The recent release of the first draft of the human genome provides an unprecedented opportunity to integrate human genes and their functions in a complete positional context. However, at least three significant technical hurdles remain: first, to assemble a complete and nonredundant human transcript index; second, to accurately place the individual transcript indices on the human genome; and third, to functionally annotate all human genes. Here, we report the extension of the UNIGENE database through the assembly of its sequence clusters into nonredundant sequence contigs. Each resulting consensus was aligned to the human genome draft. A unique location for each transcript within the human genome was determined by the integration of the restriction fingerprint, assembled genomic contig, and radiation hybrid (RH) maps. A total of 59,500 UNIGENE clusters were mapped on the basis of at least three independent criteria as compared with the 30,000 human genes/ESTs currently mapped in Genemap'99. Finally, the extension of the human transcript consensus in this study enabled a greater number of putative functional assignments than the 11,000 annotated entries in UNIGENE. This study reports a draft physical map with annotations for a majority of the human transcripts, called the Human Index of Nonredundant Transcripts (HINT). Such information can be immediately applied to the discovery of new genes and the identification of candidate genes for positional cloning.

Alleles↗

PubMed2000

Multiple Ras-dependent phosphorylation pathways regulate Myc protein stability.

Our recent work has shown that activation of the Ras/Raf/ERK pathway extends the half-life of the Myc protein and thus enhances the accumulation of Myc activity. We have extended these observations by investigating two N-terminal phosphorylation sites in Myc, Thr 58 and Ser 62, which are known to be regulated by mitogen stimulation. We now show that the phosphorylation of these two residues is critical for determining the stability of Myc. Phosphorylation of Ser 62 is required for Ras-induced stabilization of Myc, likely mediated through the action of ERK. Conversely, phosphorylation of Thr 58, likely mediated by GSK-3 but dependent on the prior phosphorylation of Ser 62, is associated with degradation of Myc. Further analysis demonstrates that the Ras-dependent PI-3K pathway is also critical for controlling Myc protein accumulation, likely through the control of GSK-3 activity. These observations thus define a synergistic role for multiple Ras-mediated phosphorylation pathways in the control of Myc protein accumulation during the initial stage of cell proliferation.

Amino Acid Sequence↗

PubMed2000

Identification of a novel E2F3 product suggests a mechanism for determining specificity of repression by Rb proteins.

The tumor suppressor function of Rb is intimately related to its ability to interact with E2F and repress the transcription of E2F target genes. Here we describe a novel E2F product that specifically interacts with Rb in quiescent cells. This novel E2F, which we term E2F3b, is encoded by a unique mRNA transcribed from an intronic promoter within the E2F3 locus. The E2F3b RNA differs from the previously characterized E2F3 RNA, which we now term E2F3a, by the utilization of a unique coding exon. In contrast to the E2F3a product that is tightly regulated by cell growth, the E2F3b product is expressed equivalently in quiescent and proliferating cells. But, unlike the E2F4 and E2F5 proteins, which are also expressed in quiescent cells and form complexes with the p130 protein, the E2F3b protein associates with Rb and represents the predominant E2F-Rb complex in quiescent cells. Thus, the previously described specificity of Rb function as a transcriptional repressor in quiescent cells coincides with the association of Rb with this novel E2F product.

Base Sequence↗

PubMed2000

Complex transcriptional regulatory mechanisms control expression of the E2F3 locus.

E2F transcription activity has been shown to play a critical role in cell growth control, regulating the expression of a variety of genes that encode proteins important for the initiation of DNA replication and cell cycle regulation. We have shown that the E2F3 locus encodes two protein products: the E2F3a product, which is tightly regulated by cell growth, and the E2F3b product, which is constitutively expressed throughout the cell cycle. To further explore the mechanism controlling the expression of the two E2F3 gene products, we analyzed the genomic sequences flanking the 5' region of E2F3a and E2F3b. We find that a series of E2F binding sites confer negative control on the E2F3a promoter in quiescent cells, similar to the control of the E2F1 and E2F2 promoters. In addition, a group of E-box elements, which are Myc binding sites, confer responsiveness to Myc and are necessary for full activation of the E2F3a promoter in response to growth stimulation. Based on these results and past experiments, it appears that the E2F1, E2F2, and E2F3a genes are similarly regulated by growth stimulation, involving a combination of E2F-dependent negative control and Myc-mediated positive control. In contrast, the constitutive expression of the E2F3b gene more closely reflects the control of expression of the E2F4 and E2F5 genes.

Base Sequence↗

PubMed1999

Ras enhances Myc protein stability.

Various experiments have demonstrated a collaborative action of Myc and Ras, both in normal cell growth control as well as during oncogenesis. We now show that Ras enhances the accumulation of Myc activity by stabilizing the Myc protein. Whereas Myc has a very short half-life when produced in the absence of mitogenic signals, due to degradation by the 26S proteasome, the half-life of Myc increases markedly in growth-stimulated cells. This stabilization is dependent on the Ras/Raf/MAPK pathway and is not augmented by proteasome inhibition, suggesting that Ras inhibits the proteasome-dependent degradation of Myc. We propose that one aspect of Myc-Ras collaboration is an ability of Ras to enhance the accumulation of transcriptionally active Myc protein.

Animals↗

PubMed1998

Population genetic structure of North Atlantic, Mediterranean Sea and Sea of Cortez fin whales, Balaenoptera physalus (Linnaeus 1758): analysis of mitochondrial and nuclear loci.

Samples were collected from 407 fin whales, Balaenoptera physalus, at four North Atlantic and one Mediterranean Sea summer feeding area as well as the Sea of Cortez in the Pacific Ocean. For each sample, the sex, the sequence of the first 288 nucleotides of the mitochondrial (mt) control region and the genotype at six microsatellite loci were determined. A significant degree of divergence was detected at all nuclear and mt loci between North Atlantic/Mediterranean Sea and the Sea of Cortez. However, the divergence time estimated from the mt sequences was substantially lower than the time elapsed since the rise of the Panama Isthmus, suggesting occasional gene flow between the North Pacific and North Atlantic ocean after the separation of the two oceans. Within the North Atlantic and Mediterranean Sea, significant levels of heterogeneity were observed in the mtDNA between the Mediterranean Sea, the eastern (Spain) and the western (the Gulf of Maine and the Gulf of St Lawrence) North Atlantic. Samples collected off West Greenland and Iceland could not be unequivocally assigned to either of the two areas. The homogeneity tests performed using the nuclear data revealed significant levels of divergence only between the Mediterranean Sea and the Gulf of St Lawrence or West Greenland. In conclusion, our results suggest the existence of several recently diverged populations in the North Atlantic and Mediterranean Sea, possibly with some limited gene flow between adjacent populations, a population structure which is consistent with earlier population models proposed by Kellogg, Ingebrigtsen, and Sergeant.

Animals↗

PubMed1997

Genetic tagging of humpback whales.

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa. However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers ('tags') represents a viable alternative to traditional methods of individual recognition, as they are permanent and exist in all individuals. We tested the use of genetic markers as the primary means of identifying individuals in a study of humpback whales in the North Atlantic Ocean. Analysis of six microsatellite loci among 3,060 skin samples collected throughout this ocean allowed the unequivocal identification of individuals. Analysis of 692 'recaptures', identified by their genotype, revealed individual local and migratory movements of up to 10,000 km, limited exchange among summer feeding grounds, and mixing in winter breeding areas, and also allowed the first estimates of animal abundance based solely on genotypic data. Our study demonstrates that genetic tagging is not only feasible, but generates data (for example, on sex) that can be valuable when interpreting the results of tagging experiments.

Animals↗

PubMed1997

Myc and Ras collaborate in inducing accumulation of active cyclin E/Cdk2 and E2F.

Considerable evidence points to a role for G1 cyclin-dependent kinase (CDK) in allowing the accumulation of E2F transcription factor activity and induction of the S phase of the cell cycle. Numerous experiments have also demonstrated a critical role for both Myc and Ras activities in allowing cell-cycle progression. Here we show that inhibition of Ras activity blocks the normal growth-dependent activation of G1 CDK, prevents activation of the target genes of E2F, and results in cell-cycle arrest in G1. We also show that Ras is essential for entry into the S phase in Rb+/+ fibroblasts but not in Rb-/- fibroblasts, establishing a link between Ras and the G1 CDK/Rb/E2F pathway. However, although expression of Ras alone will not induce G1 CDK activity or S phase, coexpression of Ras with Myc allows the generation of cyclin E-dependent kinase activity and the induction of S phase, coincident with the loss of the p27 cyclin-dependent kinase inhibitor (CKI). These results suggest that Ras, along with the activation of additional pathways, is required for the generation of G1 CDK activity, and that activation of cyclin E-dependent kinase in particular depends on the cooperative action of Ras and Myc.

Animals↗

PubMed1997

Microsatellite genetic distances between oceanic populations of the humpback whale (Megaptera novaeangliae).

Mitochondrial DNA haplotypes of humpback whales show strong segregation between oceanic populations and between feeding grounds within oceans, but this highly structured pattern does not exclude the possibility of extensive nuclear gene flow. Here we present allele frequency data for four microsatellite loci typed across samples from four major oceanic regions: the North Atlantic (two mitochondrially distinct populations), the North Pacific, and two widely separated Antarctic regions, East Australia and the Antarctic Peninsula. Allelic diversity is a little greater in the two Antarctic samples, probably indicating historically greater population sizes. Population subdivision was examined using a wide range of measures, including Fst, various alternative forms of Slatkin's Rst, Goldstein and colleagues' delta mu, and a Monte Carlo approximation to Fisher's exact test. The exact test revealed significant heterogeneity in all but one of the pairwise comparisons between geographically adjacent populations, including the comparison between the two North Atlantic populations, suggesting that gene flow between oceans is minimal and that dispersal patterns may sometimes be restricted even in the absence of obvious barriers, such as land masses, warm water belts, and antitropical migration behavior. The only comparison where heterogeneity was not detected was the one between the two Antarctic population samples. It is unclear whether failure to find a difference here reflects gene flow between the regions or merely lack of statistical power arising from the small size of the Antarctic Peninsula sample. Our comparison between measures of population subdivision revealed major discrepancies between methods, with little agreement about which populations were most and least separated. We suggest that unbiased Rst (URst, see Goodman 1995) is currently the most reliable statistic, probably because, unlike the other methods, it allows for unequal sample sizes. However, in view of the fact that these alternative measures often contradict one another, we urge caution in the use of microsatellite data to quantify genetic distance.

Alleles↗

PubMed1997

Identification of positively and negatively acting elements regulating expression of the E2F2 gene in response to cell growth signals.

Mammalian cell growth is governed by regulatory activities that include the products of genes such as c-myc and ras that act early in G1, as well as the E2F family of transcription factors that accumulate later in G1 to regulate the expression of genes involved in DNA replication. Previous work has shown that the expression of the E2F1, E2F2, and E2F3 gene products is tightly regulated by cell growth. To further explore the mechanisms controlling accumulation of E2F activity, we have isolated genomic sequences flanking the 5' region of the E2F2 coding sequence. Various assays demonstrate promoter activity in this sequence that reproduces the normal control of E2F2 expression during a growth stimulation. Sequence comparison reveals the presence of a variety of known transcription factor binding sites, including E-box elements that are consensus Myc binding sites, as well as E2F binding sites. We demonstrate that the E-box elements, which we show can function as Myc-responsive sites, contribute in a positive fashion to promoter function. We also find that E2F-dependent negative regulation in quiescent cells plays a significant role in the cell growth-dependent control of the promoter, similar to the regulation of the E2F1 gene promoter.

Base Sequence↗

PubMed1996

Placebo-controlled trial of cisapride in postgastrectomy patients with duodenogastroesophageal reflux.

Medical treatment of duodenogastroesophageal reflux in postgastrectomy patients has been disappointing. Using ambulatory esophageal bilirubin monitoring, we evaluated the efficacy of cisapride in this disorder. Ten chronically symptomatic partial gastrectomy patients (5 Billroth I, 5 Billroth II; 8 men; average age 57) with duodenogastroesophageal reflux were randomized to four weeks of either placebo or cisapride (20 mg four times a day) in a double-blind crossover study. Significantly improved patients continued to take cisapride for an additional four months. Duodenogastroesophageal reflux was assessed at baseline and after four weeks on each therapy. Daily diary recorded symptoms and mean monthly scores were determined. Global symptom improvements were assessed at the end of each treatment period. Compared to placebo, cisapride significantly (P < 0.05) decreased duodenogastroesophageal reflux. Overall symptom improvements were assessed at the end of each treatment period. Compared to placebo, cisapride significantly (P < 0.05) decreased duodenogastroesophageal reflux. Overall symptoms improved in 70% of patients on cisapride compared to 10% on placebo (P < 0.01). Mean monthly scores significantly (P < 0.05) improved for abdominal pain, regurgitation, and belching. These symptoms remained improved after four months of chronic therapy. We conclude that cisapride significantly reduces duodenogastroesophageal reflux and results in short- and long-term symptom improvements in postgastrectomy patients and that cisapride offers the first successful medical therapy for duodenogastroesophageal reflux in postgastrectomy patients.

Anti-Ulcer Agents↗

PubMed1990

Surgeons' knowledge, attitude, and use of preoperative autologous blood donation.

Before a comprehensive educational program on preoperative autologous blood donation was begun, 118 surgeons from three different areas of the country were tested to assess their baseline knowledge and attitude about this practice. Test results were correlated with the percentage of eligible patients that the surgeons actually referred for preoperative donation during a period of observation. The purpose of this preliminary effort was to identify areas in the educational program that required emphasis. Overall, the surgeons' attitude toward preoperative donation was quite favorable, but their depth of knowledge varied. Misunderstandings may have led to diminished use of this service (eg, about 50% didn't realize that many patients with medical conditions or low hematocrits are permitted to donate). However, it is not clear that simply bolstering surgeons' knowledge will increase their appropriate use of preoperative donation. When all 118 surgeons were studied, their knowledge and attitude were unrelated to the percentage of eligible patients referred. However, when 44 surgeons who managed the largest number of eligible patients were analyzed separately, their use of preoperative donation was directly correlated with their knowledge and attitude. The local awareness of AIDS also significantly influenced the use of this service. It is proposed that knowledge of preoperative donation may be important for inducing surgeons to begin referring patients for this service. Once a pattern of successful participation is established, referral seems to increase with the acquisition of working knowledge.

Blood Transfusion, Autologous↗

PubMed1988

Changes in the migratory properties of neural crest and early crest-derived cells in vivo following treatment with a phorbol ester drug.

In previous work, we found that the phorbol ester drug 12-O-tetradecanoyl phorbol acetate (TPA) reversed the developmental restriction of melanogenesis that normally occurs in neural crest-derived Schwann cell precursors around embryonic Day 5 of quail development. That is, TPA treatment of dorsal root ganglia (DRG) from 7-day quail embryos caused Schwann cell precursors to regain the ability to give rise to melanocytes. In this paper, we examine other long-term effects of TPA on the differentiative and migratory properties of neural crest and crest-derived DRG cells, using heterospecific grafting methods. We report that TPA treatment in culture increased the extent of cell migration following grafting into host embryos, including some ectopic migration into the central nervous system and other locations. TPA did not, however, seem to change the fate of these crest-derived cells, except that some DRG cells underwent pigmentation, as had been observed previously. Interestingly, graft cells associated with peripheral nerves were found to be exclusively unpigmented, whereas graft cells found in all other locations, including the central nervous system, were both pigmented and unpigmented. This suggests that peripheral nerves may act in a fashion antagonistic to the effects of TPA. These findings are consistent with the notion that TPA treatment causes early crest-derived cells to regain developmental properties lost with developmental age.

Age Factors↗

PubMed1987

Predeposited autologous blood for elective surgery. A national multicenter study.

To determine the extent to which autologous blood that has been donated in advance ("predeposited") is used in patients undergoing elective surgery and to assess whether predonation decreases the use of homologous blood and the demand on the blood supply, we studied 4996 patients undergoing elective surgery at 18 tertiary care hospitals. Cross-matched blood was ordered for 1287 patients (26 percent), and of these, 590 (46 percent) were considered eligible for predepositing blood. Only 5 percent (32) of the eligible patients actually predeposited blood, indicating that predonation is not widely used. Of those who predeposited, only 13 percent (4 of 32) subsequently received homologous blood, as compared with 36 percent (199 of 558) of those who did not predeposit (P less than 0.01). Among the 199 patients who did not predeposit but required transfusion, we estimate that predonation could have avoided homologous transfusion in as many as 68 percent. If all eligible patients had predeposited autologous blood, they could have supplied as much as 72 percent of their own transfused red cells. The blood for as much as 10 percent of all red-cell transfusions could have been predonated by and transfused into the patients undergoing elective surgery. Greater use of predonation would not only reduce the demand on the blood supply by decreasing the need for homologous transfusion, but would probably also reduce the risk of hepatitis and other transfusion-associated illnesses.

Blood Banks↗

PubMed1986

Underutilization of autologous blood donation among eligible elective surgical patients.

In January 1983, blood banks encouraged the use of autologous blood for transfusion in elective surgical patients due to the advent of transfusion-associated AIDS. Since autologous blood does not transmit hepatitis and other viruses and does not cause alloimmunization, it should be utilized whenever possible. To determine whether patients eligible to predeposit autologous blood before elective operation were actually doing so, we studied patients at three hospitals between January 1 and June 30, 1985. Patients considered eligible for autologous predeposit blood donation were adults with preoperative hemoglobin levels of 11 g/dl or more who underwent elective surgical procedures for which blood transfusion was anticipated. Excluded were patients undergoing cardiovascular, intracranial, or renal transplant procedures. Of eligible patients, only 11 percent (32 of 278) predeposited blood; of these, 81 percent (26 of 32) were transfused with only autologous blood. Among eligible patients who did not predeposit blood, all could have benefited from predepositing because transfusion was likely for the procedure. Of those who did not predeposit, 33 percent (83 of 246) received homologous blood and therefore would have benefited from autologous donation. We conclude that autologous donations are underutilized for medically eligible patients undergoing elective operation.

Acquired Immunodeficiency Syndrome↗